From 05bacc5b5a19c44199b0ef0c0338a25b7a0af768 Mon Sep 17 00:00:00 2001 From: nicholascarey Date: Sat, 2 Sep 2023 10:12:24 +0100 Subject: [PATCH 01/13] minor readme update --- README.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 03b95b96..26272102 100644 --- a/README.md +++ b/README.md @@ -44,6 +44,12 @@ A highlight of the package is the `auto_rate()` function. This uses machine lear install.packages("respR") ``` +You can also install the latest version direct from [**Github**](https://github.com/januarharianto/respr/): + +```r +devtools::install_github("januarharianto/respR") +``` + ## Getting started Visit the `respR` [**website**](https://januarharianto.github.io/respR/) to get started. The site has a range of vignettes detailing the functionality, plus example workflows, documentation, and more. @@ -70,7 +76,7 @@ For the latest news and regular updates from the world of respirometry follow `r ## Support package development -If you would like to help support the package development or just buy us a beer to say thanks see [here](https://januarharianto.github.io/respR/articles/contact.html#support-future-development) +If you would like to help support the package development or just buy us a beer to say thanks see [**here**](https://januarharianto.github.io/respR/articles/contact.html#support-future-development) ## Developers From f2a1b0296934c223dce0831f65e707094344b5cf Mon Sep 17 00:00:00 2001 From: nicholascarey Date: Wed, 15 Nov 2023 17:18:33 +0000 Subject: [PATCH 02/13] vig updates --- NEWS.md | 5 + pkgdown/pkgdown_script.R | 5 +- tests/testthat/test-oxy_crit.R | 4 +- vignettes/citations.Rmd | 50 ++++++- vignettes/intermittent_long.Rmd | 2 +- vignettes/references_citations.bib | 201 +++++++++++++++++++++++++++-- 6 files changed, 252 insertions(+), 15 deletions(-) diff --git a/NEWS.md b/NEWS.md index d5dd3b39..19b794dd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -13,6 +13,11 @@ Security: to invite users to upgrade in case of vulnerabilities. All version changes go in here now when you make a commit! ---> +## Version 2.3.2 -- 2023-11-15 + +Minor changes to unit tests and documentation. + + ## Version 2.3.1 -- 2023-06-05 Ever been reading a paper and wanted to compare metabolic rates to your own results but they were in a different unit? New in this release is `convert_MR()`, a function for converting between different units of oxygen uptake or production rate. These can be absolute, mass-specific, or area-specific rates. See `help("convert_MR")` for examples. It also works on `convert_rate` or `convert_rate.ft` objects so you can change the output units of a `respR` analysis without having to re-run the whole thing. diff --git a/pkgdown/pkgdown_script.R b/pkgdown/pkgdown_script.R index 3e12b22d..49e2a8f1 100644 --- a/pkgdown/pkgdown_script.R +++ b/pkgdown/pkgdown_script.R @@ -15,17 +15,20 @@ pkgdown::build_site(lazy = TRUE, devel = TRUE, preview = TRUE) # ? not sure what this does #pkgdown::preview_site(pkg = ".", path = ".", preview = NA) +# builds top page pkgdown::build_home(preview = TRUE) +# build a single article pkgdown::build_article("closed") pkgdown::build_article("flowthrough") pkgdown::preview_page('articles/flowthrough.html') +# add a new vignetter usethis::use_vignette("intermittent_old", "Intermittent-flow respirometry: Alternative approaches") -# sets up GH Actions workflow. Which isn't working. +# sets up GH Actions workflow. Needs tested. #usethis::use_pkgdown_github_pages() diff --git a/tests/testthat/test-oxy_crit.R b/tests/testthat/test-oxy_crit.R index b08ebfb7..88755294 100644 --- a/tests/testthat/test-oxy_crit.R +++ b/tests/testthat/test-oxy_crit.R @@ -149,8 +149,8 @@ capture.output({ ## stops printing of outputs on assigning 2.6003) expect_equal(round(oxy_crit(squid, plot=F)$crit$crit.midpoint, 4), 2.5944) - expect_equal(round(oxy_crit(squid, method = "segmented", plot=F)$crit, 4), - 2.6003) + expect_equal(round(oxy_crit(squid, method = "segmented", plot=F)$crit, 2), + 2.60) }) test_that("oxy_crit - works with oxygen~rate data", { diff --git a/vignettes/citations.Rmd b/vignettes/citations.Rmd index 449df6d9..17d31a58 100644 --- a/vignettes/citations.Rmd +++ b/vignettes/citations.Rmd @@ -40,6 +40,54 @@ If you use the package please [**cite**](https://januarharianto.github.io/respR/ The following publications (most recent first) have used and cited `respR`. If we have missed any [**let us know**](https://januarharianto.github.io/respR/articles/contact.html). +#### @rubinFeedingFrequencyDoes2023 + +This study examined if BPA exposure affects metabolic rates and behaviour in zebrafish. Turns out lots of disruption to regular behaviour, less so to physiological functioning. + +#### @espinel-velascoInteractiveEffectsOcean2023 + +Another study showing that `respR` can help anaylyse respirometry data from really tiny organisms, in this case not just a copepod, but its larvae. Here, they found metabolic rates increase in response to ocean warming and acidification combined, but not separately. Interesting! + +#### @schusterRoleKelpAvailability2023 + +Another nice urchin study, with some bonus gastropods thrown in. This study shows the links between food availability and heat resistance, and the role of metabolic depression. + +#### @dimosLocalThermalAdaptation2023 + +The preprint on [bioRxiv](https://www.biorxiv.org/content/10.1101/2023.09.28.560008v1) examines how Chinook salmon thermal adaptation occurs, and the role of mitochondrial function. The authors used `respR` to analyses intermittent-flow respirometry experiments. Looking forward to seeing it officially in print. + +#### @hawkeExposurePetroleumderivedBiopolymer2024 + +Having done a lot of both, I love seeing studies that combine metabolism and escape responses! This looked at how exposure to petroleum products affects these parameters in a marine fish. Great example of how `auto_rate` can be used to extract a rolling rate, which can then be filtered to identify a maximum rate for a fixed period. Great study that ticks all our boxes. + +#### @stellUsingElectronTransport2023 + +This study used intermittent-flow respirometry to examine thermal tolerance in largemouth bass. They show that enzyme activity associated with the electron transport system could be another tool to determine thermal tolerances in a way that is a non-lethal, rapid, and efficient alternative to traditional techniques. Nice! + +#### @jourdain-bonneauMetabolicTranscriptomicResponse2023 + +This study looks at the responses of brook charr to thermal stress, with negative effects to aerobic scope and MMR. Nice example of using the package to extract metabolic rates using specific criteria (high r2, 10th percentile etc) to arrive at a final SMR. + +#### @pettersenIntergenerationalPlasticityAligns2023 + +The preprint on [EcoEvoRxiv](https://ecoevorxiv.org/repository/view/5705/) examines how metabolic rates (or 'pace of life') may be passed on to zebrafish by their parents. Looking forward to seeing it officially in print. + +#### @evensenRolesHeatingRate2023 + +This follows up on Nicolas Evensen's [2021 study](https://januarharianto.github.io/respR/articles/citations.html#evensenremarkablyhighconsistent2021) paper looking at physiological responses of Red Sea corals to thermal stress. Once again, it's gratifying to see the package being used to extract not just respiration rates, but also photosynthesis rates. + +#### @marquezborrasEffectsOceanChange2023 + +Francisco Márquez Borrás's PhD project used long-term mesocosm experiments to examine how a New Zealand brittlestar species adapts or acclimates to ocean warming and acidification. He examined a wide range of responses, including physiological and behavioural, and used `respR` for analysing respirometry data. Hope to see these as papers soon and congrats on the PhD! 🥳 + +#### @duncanOxygenAvailabilityBody2023 + +A timely and prominent paper examining how oxygen and body size modulate responses to warming in marine invertebrates. Very nicely done study. + +#### @lowesImpactsCombinedNatural2023 + +Hannah Lowes has already published a chapter of her MSc thesis (see below) on sea cucumber responses to copper exposure, so massive congrats on the MSC! 🥳 Hopefully we see the rest published soon. + #### @connellyAntibioticsReducePocillopora2023 This study used `respR` to get metabolic rates of microfragments of corals to examine the effects of antibiotics on the holobiont community. Great to see the package being used to analyse micro-respirometry data like this. @@ -50,7 +98,7 @@ This MSc project looked at thermal microclimates amongst kelp holdfasts, and use #### @gomesImpactsAcuteHypoxia2023 -This pre-print study looks at the effects of extreme hypoxia on metabolic rate and behaviour in a seahorse. Perhaps unsurprisingly, extreme hypoxia led to a signicant reduction in metabolic rate and also signs of movement lethargy. Looking forward to seeing this officially published. +This study used `respR` to anaylse data from experiments looking at the effects of extreme hypoxia on metabolic rate and behaviour in a seahorse. Perhaps unsurprisingly, extreme hypoxia led to a signicant reduction in metabolic rate and also signs of movement lethargy. #### @zhangLossBehavioralStress2023 diff --git a/vignettes/intermittent_long.Rmd b/vignettes/intermittent_long.Rmd index 0813a6e3..b647d298 100644 --- a/vignettes/intermittent_long.Rmd +++ b/vignettes/intermittent_long.Rmd @@ -41,7 +41,7 @@ From this experiment dataset we want to extract several metrics: 2. *Maximum metabolic rate (MMR)*. Before this experiment the fish had been exercised to exhaustion, then immediately placed in the respirometer. The first replicate during which it is recovering from the accrued oxygen debt will represent MMR. -3. *Routine metabolic rate (RMR)*. This will be calculated using the later replicates once the animal has recovered from the exercise. This is generally defined as the routine use of oxygen, which fuels basal metabolism and minor, spontaneous movements to maintain station or posture. +3. *Routine metabolic rate (RMR)*. This will be calculated using the later replicates once the animal has recovered from the exercise. This is generally defined as the routine use of oxygen to fuel basal metabolism and minor spontaneous movements for maintaining station or posture. 4. *Standard metabolic rate (SMR)*. Sometimes also known as basal or minimum metabolic rate. This is also calculated using the later replicates once the animal has recovered. This is generally defined as the lowest oxygen use rates observed, which are representative of the requirements of basal metabolism only. diff --git a/vignettes/references_citations.bib b/vignettes/references_citations.bib index c18c975c..c8be4c58 100644 --- a/vignettes/references_citations.bib +++ b/vignettes/references_citations.bib @@ -101,6 +101,44 @@ @article{connellyAntibioticsReducePocillopora2023 file = {/Users/nicholascarey/Documents/Zotero/storage/RTNLVABI/Connelly et al. - 2023 - Antibiotics reduce Pocillopora coral‐associ.pdf} } +@misc{dimosLocalThermalAdaptation2023, + title = {Local {{Thermal Adaptation}} Occurs via {{Modulation}} of {{Mitochondrial Activity}} in {{Chinook Salmon}}}, + author = {Dimos, Bradford A. and Lopez, Alex C. and Schulte, Patricia M. and Phelps, Michael P.}, + year = {2023}, + month = oct, + primaryclass = {New Results}, + pages = {2023.09.28.560008}, + publisher = {{bioRxiv}}, + doi = {10.1101/2023.09.28.560008}, + urldate = {2023-10-03}, + abstract = {Freshwater and anadromous fish have been identified as one of the most at-risk groups threatened by climate induced warming given their metabolic dependence on environmental temperature and limited ability to track favorable environmental conditions. The future of these fish will depend on their ability to adapt to new thermal regimes over biologically relevant timescales. However, the mechanistic understanding of temperature responses required to predict if adaption can keep pace with climate change is limited. To address this question, we investigated the mechanistic basis of thermal adaptation across multiple levels of biological organization in the iconic and endangered Chinook Salmon (Oncorhynchus tshawytscha). We uncovered a mechanistic basis of thermal adaptation centered on the thermal responsiveness of mitochondrial function which modulates the extent to which rising temperatures increase metabolic demand on the cardio-respiratory system. These insights demonstrate that the populations studied here are able to maintain high levels of physiological performance at temperatures several degrees above historic averages, indicating that the decline Chinook Salmon and failure to recover despite conservation efforts is unlikely to be due to increased temperatures as a consequence of climate change.}, + archiveprefix = {bioRxiv}, + chapter = {New Results}, + copyright = {\textcopyright{} 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}, + langid = {english}, + file = {/Users/nicholascarey/Documents/Zotero/storage/MW6ENL4R/Dimos et al. - 2023 - Local Thermal Adaptation occurs via Modulation of .pdf} +} + +@article{duncanOxygenAvailabilityBody2023, + title = {Oxygen Availability and Body Mass Modulate Ectotherm Responses to Ocean Warming}, + author = {Duncan, Murray I. and Micheli, Fiorenza and Boag, Thomas H. and Marquez, J. Andres and Deres, Hailey and Deutsch, Curtis A. and Sperling, Erik A.}, + year = {2023}, + month = jun, + journal = {Nature Communications}, + volume = {14}, + number = {1}, + pages = {3811}, + publisher = {{Nature Publishing Group}}, + issn = {2041-1723}, + doi = {10.1038/s41467-023-39438-w}, + urldate = {2023-06-30}, + abstract = {In an ocean that is rapidly warming and losing oxygen, accurate forecasting of species' responses must consider how this environmental change affects fundamental aspects of their physiology. Here, we develop an absolute metabolic index ({$\Phi$}A) that quantifies how ocean temperature, dissolved oxygen and organismal mass interact to constrain the total oxygen budget an organism can use to fuel sustainable levels of aerobic metabolism. We calibrate species-specific parameters of {$\Phi$}A with physiological measurements for red abalone (Haliotis rufescens) and purple urchin (Strongylocentrotus purpuratus). {$\Phi$}A models highlight that the temperature where oxygen supply is greatest shifts cooler when water loses oxygen or organisms grow larger, providing a mechanistic explanation for observed thermal preference patterns. Viable habitat forecasts are disproportionally deleterious for red abalone, revealing how species-specific physiologies modulate the intensity of a common climate signal, captured in the newly developed {$\Phi$}A framework.}, + copyright = {2023 The Author(s)}, + langid = {english}, + keywords = {Climate-change ecology,Ecophysiology,Marine biology}, + file = {/Users/nicholascarey/Documents/Zotero/storage/7GG4SP65/Duncan et al. - 2023 - Oxygen availability and body mass modulate ectothe.pdf;/Users/nicholascarey/Documents/Zotero/storage/8Y4QJSTC/Duncan et al. - 2023 - Oxygen availability and body mass modulate ectothe.pdf} +} + @article{durtscheThermalConditionsEmbryogenesis2021, title = {Thermal Conditions during Embryogenesis Influence Metabolic Rates of Juvenile Brown Trout {{{\emph{Salmo}}}}{\emph{ Trutta}}}, author = {Durtsche, Richard D. and Jonsson, Bror and Greenberg, Larry A.}, @@ -117,6 +155,18 @@ @article{durtscheThermalConditionsEmbryogenesis2021 file = {/Users/nicholascarey/Documents/Zotero/storage/8F2A5Y48/Durtsche et al. - 2021 - Thermal conditions during embryogenesis influence .pdf} } +@article{espinel-velascoInteractiveEffectsOcean2023, + title = {Interactive Effects of Ocean Acidification and Temperature on Oxygen Uptake Rates in {{Calanus}} Hyperboreus Nauplii}, + author = {{Espinel-Velasco}, Nadjejda and Gawinski, Christine and Kohlbach, Doreen and Pitusi, Vanessa and Graeve, Martin and Hop, Haakon}, + year = {2023}, + journal = {Frontiers in Marine Science}, + volume = {10}, + issn = {2296-7745}, + urldate = {2023-11-02}, + abstract = {The Arctic region is undergoing rapid and significant changes, characterized by high rates of acidification and warming. These transformations prompt critical questions about the resilience of marine communities in the face of environmental change. In the Arctic, marine zooplankton and in particular calanoid copepods play a vital role in the food web. Changes in environmental conditions could disrupt zooplankton communities, posing detrimental consequences for the entire ecosystem. Copepod early-life stages have been shown to be particularly sensitive to environmental stressors since they represent a bottleneck in the life cycle. Here, we investigated the responses of 4-day old Calanus hyperboreus nauplii when exposed to acidification (pH 7.5 and 8.1) and warming (0 and 3\textdegree C), both independently and in combination. Naupliar respiration rates increased when exposed to a combination of acidification and warming, but not when exposed to the stressors individually. Moreover, we found no discernible differences in lipid content and fatty acid (FA) composition of the nauplii across the different experimental treatments. Wax esters accounted for approximately 75\% of the lipid reserves, and high amounts of long chain fatty acids 20:1 and 22:1, crucial for the reproduction cycle in copepods, were also detected. Our results indicate a sensitivity of these nauplii to a combination of acidification and warming, but not to the individual stressors, aligning with a growing body of evidence from related studies. This study sheds light on the potential implications of global change for Arctic copepod populations by elucidating the responses of early-life stages to these environmental stressors.}, + file = {/Users/nicholascarey/Documents/Zotero/storage/7YIM2YGU/Espinel-Velasco et al. - 2023 - Interactive effects of ocean acidification and tem.pdf} +} + @article{evensenRemarkablyHighConsistent2021, title = {Remarkably High and Consistent Tolerance of a {{Red Sea}} Coral to Acute and Chronic Thermal Stress Exposures}, author = {Evensen, Nicolas R. and Fine, Maoz and Perna, Gabriela and Voolstra, Christian R. and Barshis, Daniel J.}, @@ -134,6 +184,23 @@ @article{evensenRemarkablyHighConsistent2021 file = {/Users/nicholascarey/Documents/Zotero/storage/DAT8L6P8/Evensen et al. - 2021 - Remarkably high and consistent tolerance of a Red .pdf} } +@article{evensenRolesHeatingRate2023, + title = {The Roles of Heating Rate, Intensity, and Duration on the Response of Corals and Their Endosymbiotic Algae to Thermal Stress}, + author = {Evensen, Nicolas R. and Bateman, Timothy G. and Klepac, Courtney N. and {Schmidt-Roach}, Sebastian and Barreto, Marcelle and Aranda, Manuel and Warner, Mark E. and Barshis, Daniel J.}, + year = {2023}, + month = oct, + journal = {Journal of Experimental Marine Biology and Ecology}, + volume = {567}, + pages = {151930}, + issn = {0022-0981}, + doi = {10.1016/j.jembe.2023.151930}, + urldate = {2023-07-29}, + abstract = {Anthropogenic ocean warming is one of the biggest threats to marine organisms worldwide. However, it remains unclear how the duration and intensity of thermal anomalies affect organismal stress responses and thermal thresholds. We used detailed tracking of coral endosymbiont and host physiology and dose-response analyses to compare the effects of multiple heating rates, intensities, and exposure durations on two reef-building corals, Acropora hemprichii and Porites lobata, from adjacent sides of a reef (protected vs. exposed) in the Central Red Sea known to differ in high-frequency ({$<$} 24~h) temperature variability. Corals were exposed to acute heat exposures (18~h) with four target temperatures (32~\textdegree C, 35~\textdegree C, 36.5~\textdegree C, and 38~\textdegree C), versus prolonged heat exposures lasting 7\textendash 15~days where temperatures were raised 0.5 and 1.5~\textdegree C~day-1 to four target temperatures (32~\textdegree C, 33.5~\textdegree C, 35~\textdegree C, and 36.5~\textdegree C). In the prolonged experiment, dose-response curves assessing algal endosymbiont Fv/Fm revealed little initial effect of temperature, before an exponential decline above 34~\textdegree C for both species. Temperature at time of measurement and degree heating hours above 34~\textdegree C (DHH34) were the variables most strongly associated with declines in Fv/Fm. The Fv/Fm thermal thresholds for P. lobata from the high-variability protected site were higher than the exposed site in the faster heating, prolonged heat stress experiment despite minimal differences in endosymbiont density, chlorophyll-a, and host protein between sites. Together, our dose-response analysis revealed complex effects of DHH34, heating rate, and species-specific differences in the influence of local thermal histories shaping thermotolerance limits for these corals.}, + langid = {english}, + keywords = {Acute heat stress,Coral bleaching,Marine heatwaves,Ramping rate,Stress exposure,Upper thermal limits}, + file = {/Users/nicholascarey/Documents/Zotero/storage/M2QJ674E/Evensen et al. - 2023 - The roles of heating rate, intensity, and duration.pdf;/Users/nicholascarey/Documents/Zotero/storage/38KU4P2B/S002209812300062X.html} +} + @article{garnerCanSeagrassModify2022, title = {Can Seagrass Modify the Effects of Ocean Acidification on Oysters?}, author = {Garner, Natasha and Ross, Pauline M. and Falkenberg, Laura J. and Seymour, Justin R. and Siboni, Nachshon and Scanes, Elliot}, @@ -166,14 +233,16 @@ @article{gomesImpactsAcuteHypoxia2023 title = {Impacts of Acute Hypoxia on the Short-Snouted Seahorse Metabolism and Behaviour}, author = {Gomes, Matilde and Lopes, Vanessa M. and Mai, Monica G. and Paula, Jos{\'e} R. and Bispo, Regina and Batista, Hugo and Barraca, Catarina and Baylina, N{\'u}ria and Rosa, Rui and Pimentel, Marta S.}, year = {2023}, - month = may, - journal = {Research Square}, - number = {Preprint}, - doi = {10.21203/rs.3.rs-2899092/v1}, - urldate = {2023-05-10}, - abstract = {Seahorses are one of the most unique and enigmatic animals, recognized as flagship species for several conservation issues. Unfortunately, seahorses\’ populations have been declining worldwide and their unique lifestyle may constrain the ability of these animals to evolve in the future cl...}, - langid = {english}, - file = {/Users/nicholascarey/Documents/Zotero/storage/GT7ZV3RI/2023 - Impacts of acute hypoxia on the short-snouted seah.pdf} + month = dec, + journal = {Science of The Total Environment}, + volume = {904}, + pages = {166893}, + issn = {0048-9697}, + doi = {10.1016/j.scitotenv.2023.166893}, + urldate = {2023-09-17}, + abstract = {Seahorses are one of the most unique and enigmatic animals, recognized as flagship species for several conservation issues. Unfortunately, seahorses' populations have been declining and their unique lifestyle may constrain the ability of these animals to evolve in the future climate scenarios. They inhabit shallow coastal waters that display daily or seasonal environmental fluctuations. Yet, few studies have scrutinized the impacts of climate changes on these iconic species. Within this context, the objective of this work was to test the effects of an extreme hypoxia exposure (\textasciitilde 27~\% dissolved oxygen for approximately 7~h) on the metabolism, behaviour and food intake of the temperate seahorse Hippocampus hippocampus. Regarding metabolism, hypoxia exposure led to a significant reduction in metabolic rates and an increase in ventilation rates. Seahorses showed signs of movement lethargy under oxygen depletion. The results show that a small but extreme exposure to hypoxia is tolerable by seahorses despite inducing metabolic and behavioural changes, that may jeopardize the future development and survival of these iconic organisms.}, + keywords = {Behaviour,Hypoxia,Metabolism,Seahorse}, + file = {/Users/nicholascarey/Documents/Zotero/storage/Y94RD8QN/Gomes et al. - 2023 - Impacts of acute hypoxia on the short-snouted seah.pdf;/Users/nicholascarey/Documents/Zotero/storage/WDXC96HJ/S0048969723055183.html} } @phdthesis{gomezisazaAnthropogenicDisturbancesFreshwater2020, @@ -279,6 +348,22 @@ @phdthesis{hawadleEffectsMultipleEnvironmental2023 file = {/Users/nicholascarey/Documents/Zotero/storage/D33JK9XJ/Hawadle - 2022 - The Effects of Multiple Environmental Stressors on.pdf} } +@article{hawkeExposurePetroleumderivedBiopolymer2024, + title = {Exposure to Petroleum-Derived and Biopolymer Microplastics Affect Fast Start Escape Performance and Aerobic Metabolism in a Marine Fish}, + author = {Hawke, Ashleigh M. and Trujillo, Jos{\'e} E. and Oey, Indrawati and Giteru, Stephen G. and Allan, Bridie J. M.}, + year = {2024}, + month = jan, + journal = {Science of The Total Environment}, + volume = {906}, + pages = {167423}, + issn = {0048-9697}, + doi = {10.1016/j.scitotenv.2023.167423}, + urldate = {2023-10-01}, + abstract = {Evidence suggests that petroleum-derived polymers can impact marine organisms however, little is understood about whether biopolymers affect the behaviour and physiology of marine teleost fish. The aim of this research was to examine the potential effects of microplastics from a petroleum-derived polymer, (polyethylene, PE), and a biopolymer, (edible food coating EFC) on the escape performance, routine swimming, and aerobic metabolism of Forsterygion capito (the mottled triplefin). PE exposure negatively affected fish through longer latencies ({$\sim$}25~\% slower to respond), slower maximum speeds and higher responsiveness in escape performance compared to control fish. Furthermore, fish exposed to PE displayed slower mean speeds and reduced the distance travelled by {$\sim$}25~\%. After an exhaustive challenge, PE-exposed fish showed higher excess post-exercise oxygen consumption during recovery, compared to control fish. By contrast, EFC exposure only negatively affected maximum speed during an escape. Directionality and mean speed in escape performance, metabolic rate and recovery time were unaffected by biopolymer exposure. With the ever-increasing number of microplastics in the ocean, a shift to biodegradable polymers may be beneficial to marine organisms due to the smaller effect found when compared to petroleum-derived polymers in this study. As a central tool for conservation, this study represents a significant advance to predict the impact of microplastics on wild fish populations.}, + keywords = {Anti-predator behaviour,Bioplastics,EPOC,Metabolic rate,Microplastics,Pollution,Routine swimming}, + file = {/Users/nicholascarey/Documents/Zotero/storage/A666FYWW/S0048969723060503.html} +} + @phdthesis{hawkePetroleumderivedBiopolymerMicroplastic2022, title = {Petroleum-Derived and Biopolymer Microplastic Affects Fast Start Escape Performance and Aerobic Metabolism in a {{New Zealand Triplefin}} ({{{\emph{Forsterygion}}}}{\emph{ Capito}}).}, author = {Hawke, Ashleigh}, @@ -317,6 +402,20 @@ @mastersthesis{internicolaMicroplasticsDelawareBay2020 file = {/Users/nicholascarey/Documents/Zotero/storage/W7EREKRE/Internicola_udel_0060M_14348.pdf} } +@article{jourdain-bonneauMetabolicTranscriptomicResponse2023, + title = {Metabolic and Transcriptomic Response of Two Juvenile Anadromous Brook Charr ({{Salvelinus}} Fontinalis) Genetic Lines towards a Chronic Thermal Stress}, + author = {{Jourdain-Bonneau}, Christophe and Deslauriers, David and Gourtay, Cl{\'e}mence and Jeffries, Kenneth M. and Audet, C.}, + year = {2023}, + month = jun, + journal = {Canadian Journal of Zoology}, + publisher = {{NRC Research Press}}, + issn = {0008-4301}, + doi = {10.1139/cjz-2023-0049}, + urldate = {2023-07-29}, + abstract = {Many salmonid species are particularly susceptible to chronic and acute temperature changes caused by global warming. We aimed to study the differences in metabolic and transcriptomic responses of a chronic heat stress on a control and selected (absence of early sexual maturation and growth) line of brook charr Salvelinus fontinalis (Mitchill, 1814). We exposed individuals to different temperatures for 35\,days (15, 17, and 19\,\textdegree C). High temperature reduced the growth rate (in length) and the Fulton condition factor. Both maximal metabolic rate and the aerobic scope were higher in fish reared at 17\,\textdegree C, while they decreased in fish maintained at 19\,\textdegree C. The relative gene expression of cytochrome c oxidase was lower at 19\,\textdegree C than at 15\,\textdegree C. The relative gene expressions of both liver and gill hsp90 was higher at the highest temperature. The standard metabolic rate, while not affected by temperature, was higher for the control line over the selected line. Only in the control line, the relative expression of catalase and of receptor of insulin-like growth factor-1 increased at 19\,\textdegree C. Our results showed that the selected line was able to cope more effectively with the oxidative stress caused by the rise in temperature.}, + file = {/Users/nicholascarey/Documents/Zotero/storage/63C6V7E9/Jourdain-Bonneau et al. - 2023 - Metabolic and transcriptomic response of two juven.pdf} +} + @article{joyceRegulationHeartRate2022, title = {The Regulation of Heart Rate Following Genetic Deletion of the SS1 Adrenergic Receptor in Larval Zebrafis}, author = {Joyce, William and Pan, Yihang K and Garvey, Kayla and Saxena, Vishal and Perry, Steve F}, @@ -444,6 +543,19 @@ @article{lowesCopperExposureDoes2023 file = {/Users/nicholascarey/Documents/Zotero/storage/B4FT2UBY/Lowes et al. - 2023 - Copper exposure does not alter the ability of inte.pdf;/Users/nicholascarey/Documents/Zotero/storage/VCPBDLG4/S0048969723007015.html} } +@mastersthesis{lowesImpactsCombinedNatural2023, + title = {Impacts of {{Combined Natural}} and {{Anthropogenic Stressors}} on {{Pacific Intertidal Invertebrates}}}, + author = {Lowes, Hannah M.}, + year = {2023}, + address = {{Edmonton}}, + doi = {10.7939/r3-vhcd-6f09}, + urldate = {2023-06-28}, + abstract = {The intertidal zone provides extensive habitat around the world for countless species, but there are many challenges associated with life...}, + langid = {english}, + school = {University of Alberta}, + file = {/Users/nicholascarey/Documents/Zotero/storage/6R8522YE/Lowes - 2023 - Impacts of Combined Natural and Anthropogenic Stre.pdf} +} + @article{luceyClimateWarmingErodes2023, title = {Climate Warming Erodes Tropical Reef Habitat through Frequency and Intensity of Episodic Hypoxia}, author = {Lucey, Noelle M. and Deutsch, Curtis A. and Carignan, Marie-H{\'e}l{\`e}ne and Vermandele, Fanny and Collins, Mary and Johnson, Maggie D. and Collin, Rachel and Calosi, Piero}, @@ -495,6 +607,18 @@ @article{mallonLightDrivenDynamics2022 file = {/Users/nicholascarey/Documents/Zotero/storage/6W58FE2K/Mallon et al. - 2022 - Light‐driven dynamics between calcification and pr.pdf} } +@phdthesis{marquezborrasEffectsOceanChange2023, + title = {The Effects of Ocean Change Drivers on the Ecophysiology of the Mottled Brittle Star {{{\emph{Ophionereis}}}}{\emph{ Fasciata}}}, + author = {M{\'a}rquez Borr{\'a}s, Francisco}, + year = {2023}, + address = {{New Zealand}}, + urldate = {2023-07-29}, + copyright = {Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated.}, + school = {University of Auckland}, + annotation = {Accepted: 2023-07-11T02:50:39Z}, + file = {/Users/nicholascarey/Documents/Zotero/storage/WW8FVPAZ/Márquez Borrás - 2023 - The effects of ocean change drivers on the ecophys.pdf} +} + @article{morganReducedPhysiologicalPlasticity2022, title = {Reduced Physiological Plasticity in a Fish Adapted to Stable Temperatures}, author = {Morgan, Rachael and Andreassen, Anna H. and {\AA}sheim, Eirik R. and Finn{\o}en, Mette H. and Dresler, Gunnar and Brembu, Tore and Loh, Adrian and Miest, Joanna J. and Jutfelt, Fredrik}, @@ -556,8 +680,7 @@ @article{paulaAccessCleaningServices2022 file = {/Users/nicholascarey/Documents/Zotero/storage/TLL35WV7/Paula et al. - 2022 - Access to Cleaning Services Alters Fish Physiology.pdf} } -@phdthesis{perryMicroclimatesHoldfastsBull2023, - type = {{{MSc Thesis}}}, +@mastersthesis{perryMicroclimatesHoldfastsBull2023, title = {Microclimates in the Holdfasts of Bull Kelp ({{Durvillaea}} Spp.) and the Thermal Physiology of the Associated Invertebrates}, author = {Perry, Frances}, year = {2023}, @@ -580,6 +703,19 @@ @mastersthesis{petreikyteEfficiencyNileTilapia2021 file = {/Users/nicholascarey/Documents/Zotero/storage/AGE4FGFP/Tilapijų and Akvakultūros - KLAIPĖDOS UNIVERSITETAS JŪROS TYRIMŲ INSTITUTAS.pdf} } +@article{pettersenIntergenerationalPlasticityAligns2023, + title = {Intergenerational Plasticity Aligns with Temperature-Dependent Selection on Offspring Metabolic Rates}, + author = {Pettersen, Amanda Kate and Metcalfe, Neil B. and Seebacher, Frank}, + year = {2023}, + month = jul, + publisher = {{EcoEvoRxiv}}, + urldate = {2023-10-11}, + abstract = {Metabolic rates are linked to key life history traits that are thought to set the pace of life and affect fitness, yet the role that parents may have in shaping the metabolism of their offspring to enhance survival remains unclear. Here, we investigated the effect of temperature (24 C or 30 C) and feeding frequency experienced by parent zebrafish (Danio rerio) on offspring phenotypes and early survival at different developmental temperatures (24 C or 30 C). We found that embryo size was larger, but survival lower, in offspring from the parental low food treatment. Parents exposed to the warmer temperature and lower food treatment also produced offspring with lower standard metabolic rates \textendash{} aligning with selection on embryo metabolic rates. Lower metabolic rates were correlated with reduced developmental and growth rates, suggesting selection for a slow pace of life. Our results show that intergenerational effects on offspring size and metabolic rate can be adaptive when parent and offspring temperatures are matched: the direction of selection on embryo size and metabolism aligned with intergenerational plasticity towards lower metabolism at higher temperatures, particularly in offspring from low condition parents. These findings highlight the importance of anticipatory parental effects, but only when parental and offspring environments match.}, + copyright = {No Creative Commons license}, + langid = {english}, + file = {/Users/nicholascarey/Documents/Zotero/storage/V29JND9B/Pettersen et al. - 2023 - Intergenerational plasticity aligns with temperatu.pdf} +} + @article{pilletPhysiologicalPerformanceCommon2021, title = {Physiological Performance of Common Carp ({{Cyprinus}} Carpio, {{L}}., 1758) Exposed to a Sublethal Copper/Zinc/Cadmium Mixture}, author = {Pillet, M. and Castaldo, G. and Rodgers, E. M. and Poleksi{\'c}, V. and Ra{\v s}kovi{\'c}, B. and Bervoets, L. and Blust, R. and De Boeck, G.}, @@ -707,6 +843,21 @@ @article{rosEnvironmentalStressResponses2021 file = {/Users/nicholascarey/Documents/Zotero/storage/4LATJP5A/Ros et al. - 2021 - Environmental stress responses in sympatric congen.pdf} } +@article{rubinFeedingFrequencyDoes2023, + title = {Feeding Frequency Does Not Interact with {{BPA}} Exposure to Influence Metabolism or Behaviour in Zebrafish ({{Danio}} Rerio)}, + author = {Rubin, Alexander M and Seebacher, Frank}, + year = {2023}, + month = nov, + journal = {Physiology \& Behavior}, + pages = {114403}, + issn = {0031-9384}, + doi = {10.1016/j.physbeh.2023.114403}, + urldate = {2023-11-08}, + abstract = {Resource limitation can constrain energy (ATP) production, and thereby affect locomotion and behaviour such as exploration of novel environments and boldness. Consequently, ecological processes such as dispersal and interactions within and between species may be influenced by food availability. Energy metabolism, and behaviour are regulated by endocrine signaling, and may therefore be impacted by endocrine disrupting compounds (EDCs) such as bisphenol A (BPA) derived from plastic manufacture and pollution. It is important to determine the impacts of these novel environmental contexts to understand how human activity alters individual physiology and behaviour and thereby populations. Our aim was to determine whether BPA exposure interacts with feeding frequency to alter metabolism and behaviour. In a fully factorial experiment, we show that low feeding frequency reduced zebrafish (Danio rerio) mass, condition, resting metabolic rates, total distance moved and speed in a novel arena, as well as anxiety indicated by the number of times fish returned to a dark shelter. However, feeding frequency did not significantly affect maximal metabolic rates, aerobic scope, swimming performance, latency to leave a shelter, or metabolic enzyme activities (citrate synthase and lactate dehydrogenase). Natural or anthropogenic fluctuation in food resources can therefore impact energetics and movement of animals with repercussions for ecological processes such as dispersal. BPA exposure reduced LDH activity and body mass, but did not interact with feeding frequency. Hence, behaviour of adult fish is relatively insensitive to disruption by BPA. However, alteration of LDH activity by BPA could disrupt lactate metabolism and signalling and together with reduction in body mass could affect size-dependent reproductive output. BPA released by plastic manufacture and pollution can thereby impact conservation and management of natural resources.}, + keywords = {aerobic scope,anxiety,boldness,energy limitation,Exploration,locomotor performance}, + file = {/Users/nicholascarey/Documents/Zotero/storage/LLW8MB24/Rubin and Seebacher - 2023 - Feeding frequency does not interact with BPA expos.pdf;/Users/nicholascarey/Documents/Zotero/storage/WRYA4MH2/S0031938423003281.html} +} + @article{schusterDistinctRealizedPhysiologies2022, title = {Distinct Realized Physiologies in Green Sea Urchin ({{Strongylocentrotus}} Droebachiensis) Populations from Barren and Kelp Habitats}, author = {Schuster, Jasmin M. and Kurt Gamperl, A. and Gagnon, Patrick and Bates, Amanda E.}, @@ -721,6 +872,22 @@ @article{schusterDistinctRealizedPhysiologies2022 file = {/Users/nicholascarey/Documents/Zotero/storage/EHL4LK39/Schuster et al. - 2022 - Distinct realized physiologies in green sea urchin.pdf} } +@article{schusterRoleKelpAvailability2023, + title = {The Role of Kelp Availability and Quality on the Energetic State and Thermal Tolerance of Sea Urchin and Gastropod Grazers}, + author = {Schuster, Jasmin M. and Bates, Amanda E.}, + year = {2023}, + month = dec, + journal = {Journal of Experimental Marine Biology and Ecology}, + volume = {569}, + pages = {151947}, + issn = {0022-0981}, + doi = {10.1016/j.jembe.2023.151947}, + urldate = {2023-10-03}, + abstract = {Widespread decline in underwater forests, formed by kelps and other macroalgae, is occurring in all oceans. Loss of the vulnerable surface canopy typically leads to alternate rocky reef states dominated by substrate-near, understory vegetation, or reefs without any large fleshy macroalgae such as sea urchin barrens. Such alternate reef states represent a major shift in food availability and quality, and may impact kelp-preferring grazers forced to rely on less nutritious foods. Here we investigate the physiological responses of grazers to changes in food quality and quantity. We quantify the mass-independent oxygen consumption (\.MO2), as a proxy of whole-organism physiology, of four grazing invertebrate species (two sea urchins: Mesocentrotus franciscanus and Strongylocentrotus purpuratus; and two gastropods: Pomaulax gibberosus and Tegula pulligo) provisioned with one of three diet treatments over seven weeks: 1) higher quality, canopy kelp, 2) lower quality, substrate-near kelp, or 3) restricted: no kelp. We further test for differences in the heat resistance of four grazers using an acute, near-lethal heat exposure after completion of the provisioning period. Food restrictions had the strongest influence on oxygen consumption in the two urchins (mass-independent \.MO2 was reduced by 26\textendash 78\%). By contrast, the two gastropod grazers did not display metabolic depression under food restrictions. Although kelp restrictions had clear physiological consequences in sea urchins, overall, the type of kelp provisioned (Macrocystis and Saccharina) did not relate to oxygen consumption after seven weeks. While heat resistance was also similar across food treatments, unfed individuals showed a slight tendency for lower heat tolerance compared to fed individuals. These results suggest a weak coupling between heat resistance and food quality and quantity, at least for these species and at short time spans. Our work highlights the importance of diet diversity and metabolic depression as strategies to cope with the energetic costs of warming.}, + keywords = {Heat stress,Herbivore,Metabolism,Resource limitation,Starvation,Underwater forest}, + file = {/Users/nicholascarey/Documents/Zotero/storage/ZXBK3KTQ/Schuster and Bates - 2023 - The role of kelp availability and quality on the e.pdf;/Users/nicholascarey/Documents/Zotero/storage/8URRNN4X/S0022098123000795.html} +} + @phdthesis{somoIntegrativeAnalysisRespiratory2022, title = {An Integrative Analysis of Respiratory Capacity, Osmoregulatory Function, Body Size, and Metabolism in Intertidal Fishes}, author = {Somo, Derek Anthony}, @@ -750,6 +917,20 @@ @article{spindelZombiesNearshoreMetabolic2020 file = {/Users/nicholascarey/Documents/Zotero/storage/M3FDTHQS/Spindel et al. - 2020 - Zombies of the nearshore Metabolic depression in .pdf;/Users/nicholascarey/Documents/Zotero/storage/UIE8KUA6/2020.11.28.html} } +@article{stellUsingElectronTransport2023, + title = {Using the Electron Transport System as an Indicator of Organismal Thermal Tolerance and Respiratory Exploitation.}, + author = {Stell, Ehlana G and Brewer, Shannon K and Horne, Lindsay and Wright, Russell A and DeVries, Dennis R}, + year = {2023}, + month = aug, + journal = {Canadian Journal of Zoology}, + publisher = {{NRC Research Press}}, + issn = {0008-4301}, + doi = {10.1139/cjz-2023-0027}, + urldate = {2023-08-27}, + abstract = {Freshwater ecosystems are undergoing rapid thermal shifts, making it increasingly important to understand species-specific responses to these changes. Traditional techniques for determining a species' thermal tolerance are often lethal and time consuming. Using the enzyme activity associated with the electron transport system (ETS; hereafter referred to as enzyme assay) may provide a non-lethal, rapid, and efficient alternative to traditional techniques for some species. We used largemouth bass Micropterus salmoides Lacepede, 1802 to test the efficacy of using an enzyme assay to determine thermal tolerance and respiratory exploitation in response to variable acclimation temperatures. Three tissue types were dissected from fish acclimated to 20, 25, or 30\textdegree C and used in ETS assays at temperatures ranging from 7.5-40\textdegree C. While there were significant differences among tissue types and acclimation temperatures, maximal enzyme activity occurred from 25.23-31.91\textdegree C. Fish lost equilibrium at 39-42\textdegree C in traditional CTmax trials, significantly higher than the upper optimum range determined via enzyme assays. The ratio of enzyme activity to measured whole organism respiration rate decreased with increasing water temperature, with the largest changes occurring at the upper optimum thermal range determined by enzyme assays. Our results indicate ETS analysis may prove useful for obtaining biologically relevant thermal tolerances.}, + file = {/Users/nicholascarey/Documents/Zotero/storage/CE2LPY8Z/Stell et al. - 2023 - Using the electron transport system as an indicato.pdf} +} + @article{thambithuraiFishVulnerabilityCapture2022, title = {Fish Vulnerability to Capture by Trapping Is Modulated by Individual Parasite Density}, author = {Thambithurai, Davide and Lanthier, Isabel and Contant, Eloi and Killen, Shaun S. and Binning, Sandra A.}, From 416d637d8cea630adafa5612ed5eb280e8f875c9 Mon Sep 17 00:00:00 2001 From: nicholascarey Date: Wed, 15 Nov 2023 17:20:19 +0000 Subject: [PATCH 03/13] news update --- NEWS.md | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/NEWS.md b/NEWS.md index 19b794dd..5598e863 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,18 +1,4 @@ - - ## Version 2.3.2 -- 2023-11-15 Minor changes to unit tests and documentation. From 66aded72ed471363b27df30196ad825c19f220e8 Mon Sep 17 00:00:00 2001 From: nicholascarey Date: Wed, 15 Nov 2023 17:21:13 +0000 Subject: [PATCH 04/13] version 2.3.2 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index b5b58f6c..147a0acf 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: respR Type: Package Title: Import, Process, Analyse, and Calculate Rates from Respirometry Data Date: 2023-06-04 -Version: 2.3.1 +Version: 2.3.2 Maintainer: Nicholas Carey Authors@R: c( person(given = "Nicholas", From 6feb957b3c4e926b74b18ea846efb2fdc291b0ca Mon Sep 17 00:00:00 2001 From: nicholascarey Date: Thu, 16 Nov 2023 09:47:49 +0000 Subject: [PATCH 05/13] Minor updates --- .Rbuildignore | 2 +- DESCRIPTION | 2 +- cran-comments.md | 1 + 3 files changed, 3 insertions(+), 2 deletions(-) create mode 100644 cran-comments.md diff --git a/.Rbuildignore b/.Rbuildignore index 855b0fef..db6428b4 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -3,7 +3,6 @@ ^\.Rproj\.user$ # used for temporary files. ^README\.Rmd$ # An Rmarkdown file used to generate README.md ^cran-comments\.md$ # Comments for CRAN submission -^NEWS\.md$ # A news file written in Markdown ^manuscript$ # Folder that contains the files for the manuscript ^docs$ # Folder that stores HTML vignettes ^doc$ # Folder that stores HTML vignettes @@ -13,6 +12,7 @@ ^data-raw$ ^.DS_Store$ ^t5.rda$ +cran-comments.md # Insurance vignettes diff --git a/DESCRIPTION b/DESCRIPTION index 147a0acf..f66b2010 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: respR Type: Package Title: Import, Process, Analyse, and Calculate Rates from Respirometry Data -Date: 2023-06-04 +Date: 2023-11-16 Version: 2.3.2 Maintainer: Nicholas Carey Authors@R: c( diff --git a/cran-comments.md b/cran-comments.md new file mode 100644 index 00000000..55a38b93 --- /dev/null +++ b/cran-comments.md @@ -0,0 +1 @@ +No code changes, so should be no issues. Literally the only change is slight alteration to a value in one unit test. This is done in response to a package author contacting me because a pending dependency update was rejected by CRAN due to this test failing in my package. From 226aa1123bbae736d52aa8a8010702e091d244e3 Mon Sep 17 00:00:00 2001 From: nicholascarey Date: Thu, 16 Nov 2023 09:48:36 +0000 Subject: [PATCH 06/13] cran comments update --- cran-comments.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cran-comments.md b/cran-comments.md index 55a38b93..d019fa81 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1 +1 @@ -No code changes, so should be no issues. Literally the only change is slight alteration to a value in one unit test. This is done in response to a package author contacting me because a pending dependency update was rejected by CRAN due to this test failing in my package. +No code changes, so should be no issues. Literally the only change is slight alteration to a value in one unit test. This is done in response to a package author contacting me because a pending update was rejected by CRAN due to this test failing in my package, which is a reverse dependency. From 4fd7664709e0b332dd12e1553963a1d8baec7de0 Mon Sep 17 00:00:00 2001 From: nicholascarey Date: Thu, 16 Nov 2023 10:45:32 +0000 Subject: [PATCH 07/13] Vig update, cran stuff --- .Rbuildignore | 1 + CRAN-SUBMISSION | 3 +++ pkgdown/pkgdown_script.R | 3 +++ vignettes/citations.Rmd | 8 ++++---- 4 files changed, 11 insertions(+), 4 deletions(-) create mode 100644 CRAN-SUBMISSION diff --git a/.Rbuildignore b/.Rbuildignore index db6428b4..6a4371ee 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -24,3 +24,4 @@ vignettes Changelog ^CITATION\.cff$ ^codecov\.yml$ +^CRAN-SUBMISSION$ diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 00000000..d668ceb3 --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 2.3.2 +Date: 2023-11-16 10:15:59 UTC +SHA: 226aa1123bbae736d52aa8a8010702e091d244e3 diff --git a/pkgdown/pkgdown_script.R b/pkgdown/pkgdown_script.R index 49e2a8f1..de8a52c4 100644 --- a/pkgdown/pkgdown_script.R +++ b/pkgdown/pkgdown_script.R @@ -38,4 +38,7 @@ usethis::use_vignette("intermittent_old", "Intermittent-flow respirometry: Alter ## Sometimes gets stuck on git command. ## Stopping and building site then trying again seems to work. ## Although last time took MANY attempts +## +## BUT - even if it seems to freeze check GHub and site - it might have successfully +## triggered the 'pages build and deployment' GH action anyway... pkgdown::deploy_to_branch() diff --git a/vignettes/citations.Rmd b/vignettes/citations.Rmd index 17d31a58..3f8ab0e5 100644 --- a/vignettes/citations.Rmd +++ b/vignettes/citations.Rmd @@ -40,6 +40,10 @@ If you use the package please [**cite**](https://januarharianto.github.io/respR/ The following publications (most recent first) have used and cited `respR`. If we have missed any [**let us know**](https://januarharianto.github.io/respR/articles/contact.html). +#### @hawkeExposurePetroleumderivedBiopolymer2024 + +Having done a lot of both, I love seeing studies that combine metabolism and escape responses! This looked at how exposure to petroleum products affects these parameters in a marine fish. Great example of how `auto_rate` can be used to extract a rolling rate, which can then be filtered to identify a maximum rate for a fixed period. Great study that ticks all our boxes. + #### @rubinFeedingFrequencyDoes2023 This study examined if BPA exposure affects metabolic rates and behaviour in zebrafish. Turns out lots of disruption to regular behaviour, less so to physiological functioning. @@ -56,10 +60,6 @@ Another nice urchin study, with some bonus gastropods thrown in. This study show The preprint on [bioRxiv](https://www.biorxiv.org/content/10.1101/2023.09.28.560008v1) examines how Chinook salmon thermal adaptation occurs, and the role of mitochondrial function. The authors used `respR` to analyses intermittent-flow respirometry experiments. Looking forward to seeing it officially in print. -#### @hawkeExposurePetroleumderivedBiopolymer2024 - -Having done a lot of both, I love seeing studies that combine metabolism and escape responses! This looked at how exposure to petroleum products affects these parameters in a marine fish. Great example of how `auto_rate` can be used to extract a rolling rate, which can then be filtered to identify a maximum rate for a fixed period. Great study that ticks all our boxes. - #### @stellUsingElectronTransport2023 This study used intermittent-flow respirometry to examine thermal tolerance in largemouth bass. They show that enzyme activity associated with the electron transport system could be another tool to determine thermal tolerances in a way that is a non-lethal, rapid, and efficient alternative to traditional techniques. Nice! From 2cdfcb90c240c379300bf0f55abbb8df2b6a2e5d Mon Sep 17 00:00:00 2001 From: nicholascarey Date: Thu, 16 Nov 2023 15:32:06 +0000 Subject: [PATCH 08/13] Cran 2nd sub 2.3.2 --- CRAN-SUBMISSION | 4 ++-- R/auto_rate_funs.R | 28 ++++++++++++++-------------- man/time_roll.Rd | 6 +++--- man/validate_auto_rate.Rd | 4 ++-- 4 files changed, 21 insertions(+), 21 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index d668ceb3..601d1c23 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ Version: 2.3.2 -Date: 2023-11-16 10:15:59 UTC -SHA: 226aa1123bbae736d52aa8a8010702e091d244e3 +Date: 2023-11-16 14:26:12 UTC +SHA: 4fd7664709e0b332dd12e1553963a1d8baec7de0 diff --git a/R/auto_rate_funs.R b/R/auto_rate_funs.R index 8b9804ec..93544910 100644 --- a/R/auto_rate_funs.R +++ b/R/auto_rate_funs.R @@ -2,7 +2,7 @@ #' #' This is an internal function for `auto_rate()`. Used to validate inputs #' -#' @param df data.frame object. +#' @param x data.frame object. #' @param by string. #' @param method string. #' @@ -424,14 +424,14 @@ static_roll <- function(df, win) { #' @return a data.table object #' @keywords internal #' @import parallel -time_roll <- function(dt, width, parallel = FALSE) { +time_roll <- function(df, width, parallel = FALSE) { future_lapply <- plan <- NULL # global variables hack (unfortunate) - dt <- data.table::data.table(dt) - data.table::setnames(dt, 1:2, c("V1", "V2")) + df <- data.table::data.table(df) + data.table::setnames(df, 1:2, c("V1", "V2")) # The cutoff specifies where to stop the rolling regression, based on width - time_cutoff <- max(dt[,1]) - width - row_cutoff <- max(dt[, which(V1 <= time_cutoff)]) + time_cutoff <- max(df[,1]) - width + row_cutoff <- max(df[, which(V1 <= time_cutoff)]) # if(parallel) { # oplan <- plan() @@ -439,11 +439,11 @@ time_roll <- function(dt, width, parallel = FALSE) { # if (os() == 'win') { # plan(multicore) # } else plan(multisession) - # out <- future_lapply(1:row_cutoff, function(x) time_lm(dt, - # dt[[1]][x], dt[[1]][x] + width)) + # out <- future_lapply(1:row_cutoff, function(x) time_lm(df, + # df[[1]][x], df[[1]][x] + width)) # } else { - # out <- lapply(1:row_cutoff, function(x) time_lm(dt, - # dt[[1]][x], dt[[1]][x] + width)) + # out <- lapply(1:row_cutoff, function(x) time_lm(df, + # df[[1]][x], df[[1]][x] + width)) # } # parallelisation @@ -453,11 +453,11 @@ time_roll <- function(dt, width, parallel = FALSE) { cl <- parallel::makeCluster(no_cores) } else cl <- parallel::makeCluster(no_cores, type = "FORK") parallel::clusterExport(cl, "time_lm") - out <- parallel::parLapply(cl, 1:row_cutoff, function(x) time_lm(dt, - dt[[1]][x], dt[[1]][x] + width)) + out <- parallel::parLapply(cl, 1:row_cutoff, function(x) time_lm(df, + df[[1]][x], df[[1]][x] + width)) parallel::stopCluster(cl) # stop cluster (release cores) - } else out <- lapply(1:row_cutoff, function(x) time_lm(dt, - dt[[1]][x], dt[[1]][x] + width)) + } else out <- lapply(1:row_cutoff, function(x) time_lm(df, + df[[1]][x], df[[1]][x] + width)) out <- data.table::rbindlist(out) return(out) diff --git a/man/time_roll.Rd b/man/time_roll.Rd index a691ba2f..8c062f02 100644 --- a/man/time_roll.Rd +++ b/man/time_roll.Rd @@ -4,12 +4,12 @@ \alias{time_roll} \title{Perform time-width rolling regression} \usage{ -time_roll(dt, width, parallel = FALSE) +time_roll(df, width, parallel = FALSE) } \arguments{ -\item{width}{numeric. width in time} - \item{df}{data.frame object.} + +\item{width}{numeric. width in time} } \value{ a data.table object diff --git a/man/validate_auto_rate.Rd b/man/validate_auto_rate.Rd index 943ec30e..33d53ca8 100644 --- a/man/validate_auto_rate.Rd +++ b/man/validate_auto_rate.Rd @@ -7,11 +7,11 @@ validate_auto_rate(x, by, method) } \arguments{ +\item{x}{data.frame object.} + \item{by}{string.} \item{method}{string.} - -\item{df}{data.frame object.} } \value{ a data.frame object of the original data From cf7817610c4fd279d64531104390e966a6be7a58 Mon Sep 17 00:00:00 2001 From: nicholascarey Date: Thu, 16 Nov 2023 17:08:51 +0000 Subject: [PATCH 09/13] Last CRAN nonsense --- CRAN-SUBMISSION | 4 ++-- R/inspect.R | 2 ++ man/inspect.Rd | 2 ++ 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 601d1c23..4b311e97 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ Version: 2.3.2 -Date: 2023-11-16 14:26:12 UTC -SHA: 4fd7664709e0b332dd12e1553963a1d8baec7de0 +Date: 2023-11-16 15:53:23 UTC +SHA: 2cdfcb90c240c379300bf0f55abbb8df2b6a2e5d diff --git a/R/inspect.R b/R/inspect.R index dc8d2c47..1a356430 100644 --- a/R/inspect.R +++ b/R/inspect.R @@ -191,6 +191,7 @@ #' @export #' #' @examples +#' \donttest{ #' ## By default, assumes time is col 1 and oxygen col2: #' inspect(sardine.rd) #' @@ -222,6 +223,7 @@ #' ## allow better y-axis label visibility #' inspect(sardine.rd, time = 1, oxygen = 2, #' las = 1, mai = c(0.3, 0.35, 0.35, 0.15)) +#' } inspect <- function(x, time = NULL, oxygen = NULL, width = 0.1, plot = TRUE, add.data = NULL, ...) { diff --git a/man/inspect.Rd b/man/inspect.Rd index d75df13f..6b917b59 100644 --- a/man/inspect.Rd +++ b/man/inspect.Rd @@ -218,6 +218,7 @@ website at \url{https://januarharianto.github.io/respR/} } } \examples{ +\donttest{ ## By default, assumes time is col 1 and oxygen col2: inspect(sardine.rd) @@ -250,3 +251,4 @@ inspect(algae.rd, time = 1, oxygen = 2, width = 0.4, inspect(sardine.rd, time = 1, oxygen = 2, las = 1, mai = c(0.3, 0.35, 0.35, 0.15)) } +} From b5ca28bd4b5efa7446c967e3fa314ef6fadc6aac Mon Sep 17 00:00:00 2001 From: nicholascarey Date: Fri, 29 Mar 2024 11:42:33 +0000 Subject: [PATCH 10/13] website update --- R/startup.R | 4 - README.md | 1 - vignettes/citations.Rmd | 72 +++++- vignettes/references_citations.bib | 386 ++++++++++++++++++++++------- 4 files changed, 358 insertions(+), 105 deletions(-) diff --git a/R/startup.R b/R/startup.R index 12ed2d4c..b053d212 100644 --- a/R/startup.R +++ b/R/startup.R @@ -19,10 +19,6 @@ Visit this site for help documentation and vignettes: http://bit.ly/respr_pkg -And follow respR on Twitter for latest news: - - http://twitter.com/respr_pkg - ======================================================================") packageStartupMessage(start_msg) diff --git a/README.md b/README.md index 26272102..870016f0 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,6 @@ [![Github watchers](https://img.shields.io/github/watchers/januarharianto/respR?label=Watch&style=social)](https://img.shields.io/github/watchers/januarharianto/respR?style=social) [![Github sponsor](https://img.shields.io/static/v1?label=Sponsor&message=%E2%9D%A4&logo=GitHub&style=social)](https://github.com/sponsors/nicholascarey) [![Mastodon](https://img.shields.io/badge/dynamic/json?label=Mastodon&query=totalItems&url=https%3A%2F%2Fmas.to%2Fusers%2FrespR%2Ffollowers.json&logo=mastodon&style=social)](https://mas.to/@respR) -[![Twitter](https://img.shields.io/twitter/follow/respR_pkg.svg?label=Follow&style=social)](https://twitter.com/respR_pkg?ref_src=twsrc%5Etfw) diff --git a/vignettes/citations.Rmd b/vignettes/citations.Rmd index 3f8ab0e5..6aa262d9 100644 --- a/vignettes/citations.Rmd +++ b/vignettes/citations.Rmd @@ -40,11 +40,47 @@ If you use the package please [**cite**](https://januarharianto.github.io/respR/ The following publications (most recent first) have used and cited `respR`. If we have missed any [**let us know**](https://januarharianto.github.io/respR/articles/contact.html). +#### @kellyInvestigatingMetabolicOxidative2024 + +This preprint examines how biofouling on microplastics effects on fish physiology using intermittent-flow respirometry. The authors used `auto_rate` to obstain MMR and SMR from a kingfish. Looking forward to seeing it officially in print. + +#### @scharfensteinPushingLimitsExpanding2024 + +This preprint on [bioRxiv](https://www.biorxiv.org/content/10.1101/2024.02.11.579409v1) examines the thermal tolerances of a coral symbiont. Yet another study which used `respR` to get both respiration rates and net photosynthesis. Great to see and looking forward to seeing it officially in print. + +#### @sheffeyMicroplasticsVibrioBacteria2023 + +Heather Leigh Sheffey's MSc thesis done at the Old Dominion University looks at the effects on a coral of warming, bacterial disease, *and* microplastics. Ambitious! Congrats on the MSc! 🥳 + +#### @maskreyDifferentialMetabolicResponses2024 + +Personality is not something you think of when you think of sea anemones, but they do come in types which might be described as 'bold' or 'shy'. This study looked at the metabolic rates of these two types under a simulated heatwave event. Very different responses: shy anemones had highest metabolic rates at low temperatures, but bold anemones higher rates at high temperatures. Interesting stuff. + +#### @taorminaEffectsSeaLice2024 + +This study looked at how a chemical treatment for sea lice in Norwegian fish farming affects the physiology of sea pens. The contaminant did not have an apparent effect on mortality, behaviour or metabolism, though was present in tissues. Nice to see 'null' results being published by prominent journals. These are just as important as positive results! + #### @hawkeExposurePetroleumderivedBiopolymer2024 Having done a lot of both, I love seeing studies that combine metabolism and escape responses! This looked at how exposure to petroleum products affects these parameters in a marine fish. Great example of how `auto_rate` can be used to extract a rolling rate, which can then be filtered to identify a maximum rate for a fixed period. Great study that ticks all our boxes. -#### @rubinFeedingFrequencyDoes2023 +#### @pettersenIntergenerationalPlasticityAligns2024 + +This study examines how metabolic rates (or 'pace of life') traits may be passed on to zebrafish by their parents. `respR` was used to extract rates from closed respirometry experiments. + +#### @gonzalez-ferrerasChronicExposureEnvironmental2023 + +This study used in-situ respirometry to examine the metabolic rates of stream salmonids transferred between naturally variable thermal regimes. They used `auto_rate` to identify the metabolic rates from their respirometry data. + +#### @rocknerOctopusCrawlingLand2024 + +Who doesn't like octopuses? This study examined the unusual behaviour of octopuses crawling on land, and the physiological consequences of that behaviour. They did respirometry experiments on specimens which had been exposed to air and also a chase protocol, showing the octopuses' metabolic rate did not differ between exposure and having been chased. So it seems it is something they can handle quite well. Very cool study! + +#### @plazaSublethalEffectsMethylmercury2023 + +Maria Auxiliadora Sabando Plaza's MSc thesis done at the University of Delaware looks at the sublethal effects of methylmercury on spiny dogfish, which include lower growth rates and food consumption. She used `respR` to analyse the respirometry data which showed increased SMR in response to doses. Congrats on the MSc! 🥳 + +#### @rubinFeedingFrequencyDoes2024 This study examined if BPA exposure affects metabolic rates and behaviour in zebrafish. Turns out lots of disruption to regular behaviour, less so to physiological functioning. @@ -58,7 +94,7 @@ Another nice urchin study, with some bonus gastropods thrown in. This study show #### @dimosLocalThermalAdaptation2023 -The preprint on [bioRxiv](https://www.biorxiv.org/content/10.1101/2023.09.28.560008v1) examines how Chinook salmon thermal adaptation occurs, and the role of mitochondrial function. The authors used `respR` to analyses intermittent-flow respirometry experiments. Looking forward to seeing it officially in print. +This preprint on [bioRxiv](https://www.biorxiv.org/content/10.1101/2023.09.28.560008v1) examines how Chinook salmon thermal adaptation occurs, and the role of mitochondrial function. The authors used `respR` to analyses intermittent-flow respirometry experiments. Looking forward to seeing it officially in print. #### @stellUsingElectronTransport2023 @@ -68,10 +104,6 @@ This study used intermittent-flow respirometry to examine thermal tolerance in l This study looks at the responses of brook charr to thermal stress, with negative effects to aerobic scope and MMR. Nice example of using the package to extract metabolic rates using specific criteria (high r2, 10th percentile etc) to arrive at a final SMR. -#### @pettersenIntergenerationalPlasticityAligns2023 - -The preprint on [EcoEvoRxiv](https://ecoevorxiv.org/repository/view/5705/) examines how metabolic rates (or 'pace of life') may be passed on to zebrafish by their parents. Looking forward to seeing it officially in print. - #### @evensenRolesHeatingRate2023 This follows up on Nicolas Evensen's [2021 study](https://januarharianto.github.io/respR/articles/citations.html#evensenremarkablyhighconsistent2021) paper looking at physiological responses of Red Sea corals to thermal stress. Once again, it's gratifying to see the package being used to extract not just respiration rates, but also photosynthesis rates. @@ -86,7 +118,7 @@ A timely and prominent paper examining how oxygen and body size modulate respons #### @lowesImpactsCombinedNatural2023 -Hannah Lowes has already published a chapter of her MSc thesis (see below) on sea cucumber responses to copper exposure, so massive congrats on the MSC! 🥳 Hopefully we see the rest published soon. +Hannah Lowes has already published a chapter of her MSc thesis (see below) on sea cucumber responses to copper exposure, so massive congrats on the MSc! 🥳 Hopefully we see the rest published soon. #### @connellyAntibioticsReducePocillopora2023 @@ -206,6 +238,26 @@ In this study Jenni Prokkola *et al*. examine the genetic basis of how energy me Jennifer Mallon is another researcher who took advantage of our open offer to help get users started with `respR` by sending us a data file. Great to see the work published! They looked at both oxygen uptake and production in corals and coralline algae to calculate net photosynthesis. Really great to again see oxygen production being calculated using the package, not just consumption. +#### @jourdainbonneauEffetStressThermique2022 + +Lewis Jone's MSc thesis, in which he used `respR` to get the Pcrit from a flounder acclimated to different temperatures. Congrats on the Masters! 🥳 + +#### @andersenEffectAqueousAluminium2022 + +Ivar Optun Andersen's MSc thesis, in which he used `respR` to get the metabolic rate and Pcrit of a isopod exposed to aqueous aluminium. Congrats on the Masters! 🥳 + +#### @jonesThermalPhysiologyYellowbelly2021 + +Christophe Jourdain Bonneau's MSc thesis, which he later went on to publish in CJZ - see above. Congrats on the Masters! 🥳 + +#### @mullerEcophysiologicalInvestigationFisheriesinduced2021 + +Cuen Muller's PhD thesis, which examined fisheries-induced evolution under ocean acidification. Congrats on the PhD! 🥳 + +#### @zhangInterpretingSpeciesIntraspecific2021 + +Yangfan Zhang's PhD thesis. He has gone on to publish much of it. Congrats on the PhD! + #### @burnsMetabolicRateCritical2021 Alexandra Burns used `respR` in this MSc project, looking at oxygen supply capacity under different temperatures in a species of shrimp. Congrats on the Masters! 🥳 @@ -258,6 +310,10 @@ This study used `respR` to calculate the aerobic scope of juvenile brown trout t This study looked at thermal tolerance and oxygen supply capacity in newborn sharks. This shows a great use for `respR` outside of the lab, in that it was used to determine oxygen decline from field recordings of oxygen off the coast of Moorea. We were especially pleased to see the `auto_rate()` function get a mention in the manuscript for calculating maximum metabolic rates. +#### @guitardEffetsPhysiologiquesInfection2020 + +Joëlle Guitard's MSc thesis, which she later published in JEB. Congrats on the Masters! 🥳 + #### @zhangMeasuringMaximumOxygen2020 This study compared the results of different methods of determining maximum metabolic rates. The authors point out minimum sampling window is a very important factor in determining MMR. We always thought this was pretty obvious, which is why `respR` has always allowed rolling regressions of different window sizes to be performed, with visualisations to see the results of how this affects rate calculations. 🤔 @@ -266,7 +322,7 @@ This study compared the results of different methods of determining maximum meta This is a really cool study looking at how warming may affect brain size and cognition in minnows, as well as metabolic rate. Warm fish had bigger brains, but weren't as good at finding their way through a maze! Awesome stuff. It used `respR` to determine SMR, MMR and aerobic scope. -#### @spindelZombiesNearshoreMetabolic2020 +#### @spindelMetabolicDepressionSea2021 We have a special fondness for studies doing respirometry on sea urchins (we feel your pain, especially the spines under the fingernails). This study compared the physiology of urchins from kelp barrens and kelp forests, and found those in barrens have dramatically reduced resting metabolic rates, by up to 40%. Cool stuff! diff --git a/vignettes/references_citations.bib b/vignettes/references_citations.bib index c8be4c58..86cb21f2 100644 --- a/vignettes/references_citations.bib +++ b/vignettes/references_citations.bib @@ -1,9 +1,22 @@ +@mastersthesis{andersenEffectAqueousAluminium2022, + title = {The Effect of Aqueous Aluminium on Mortality and Respiration of the Isopoda {{{\emph{Asellus}}}}{\emph{ Aquaticus}}}, + author = {Andersen, Ivar Optun}, + year = {2022}, + address = {Evenstad, Norwat}, + urldate = {2024-03-29}, + abstract = {The present study investigates the effect of aqueous aluminium (Al) and acidic water on mortality and respiration in the isopoda Asellus aquaticus. I conducted one mortality experiment lasting 22 days exposing A. aquaticus to an acidic Al-rich medium (pH 5.8), an acidic Al-poor medium (pH 5.8) and untreated natural water (control) (pH 7.0). Followed by three respirometry experiments exposing A. aquaticus to an acidic Al-rich medium, an acidic Al-poor and untreated natural water each for five days and then transferring the animals into closed-respirometry chambers for 48 hours. In the mortality experiment A. aquaticus was more sensitive to the acidic Al-rich medium than the acidic Al-poor- and the control media. In the respirometry experiment Al-exposed A. aquaticus displayed a lower normoxic O2 consumption than in the acidic Al-poor- and control media. Similarly, the critical O2 tension was lower in Al-exposed A. aquaticus than acidic Al-poor- and control media. The critical O2 tension was inconsistent with the mortality A. aquaticus experienced in the mortality experiment. I draw the conclusion that A. aquaticus is more sensitive to aqueous aluminium than to an acidic Al poor medium.}, + langid = {english}, + school = {H{\o}gskolen i Innlandet}, + annotation = {Accepted: 2023-03-16T09:12:03Z}, + file = {/Users/nicholascarey/Documents/Zotero/storage/793S65ZL/Andersen - 2022 - The effect of aqueous aluminium on mortality and r.pdf} +} + @mastersthesis{bergerRegionalVulnerabilityAssessment2022, title = {A {{Regional Vulnerability Assessment}} for the {{Dungeness Crab}} ({{{\emph{Metacarcinus}}}}{\emph{ Magister}}) to {{Changing Ocean Conditions}}: {{Insights From Model Projections}} and {{Empirical Experiments}}}, shorttitle = {A {{Regional Vulnerability Assessment}} for the {{Dungeness Crab}} ({{Metacarcinus}} Magister) to {{Changing Ocean Conditions}}}, author = {Berger, Halle}, year = {2022}, - address = {{Storrs, USA}}, + address = {Storrs, USA}, langid = {english}, school = {University of Connecticut}, file = {/Users/nicholascarey/Documents/Zotero/storage/XLXUKZVN/1543.html} @@ -49,11 +62,11 @@ @article{burfordRapidRangeExpansion2022a journal = {The American Naturalist}, volume = {199}, number = {4}, - publisher = {{The University of Chicago Press}}, + publisher = {The University of Chicago Press}, issn = {0003-0147}, doi = {10.1086/718575}, urldate = {2022-03-04}, - abstract = {The distributions of marine ectotherms are governed by physiological sensitivities to long-term trends in seawater temperature and dissolved oxygen. Short-term variability in these parameters has the potential to facilitate rapid range expansions, and the resulting ecological and socioeconomic consequences may portend those of future marine communities. Here, we combine physiological experiments with ecological and demographic surveys to assess the causes and consequences of sudden but temporary poleward range expansions of a marine ectotherm with considerable life history plasticity (California market squid, Doryteuthis opalescens). We show that sequential factors related to resource accessibility in the core range\textemdash the buildup of large populations as a result of competitive release and climate-associated temperature increase and oxygen loss that constrain aerobic activity\textemdash may drive these expansions. We also reveal that poleward range expansion alters the body size\textemdash and therefore trophic role\textemdash of invading populations, with potential negative implications for socioeconomically valuable resident species. To help forecast rapid range expansions of marine ectotherms, we advocate that research efforts focus on factors impacting resource accessibility in core ranges. Determining how environmental conditions in receiving ecosystems affect body size and how body size is related to trophic role will help refine estimates of the impacts of future marine communities.}, + abstract = {The distributions of marine ectotherms are governed by physiological sensitivities to long-term trends in seawater temperature and dissolved oxygen. Short-term variability in these parameters has the potential to facilitate rapid range expansions, and the resulting ecological and socioeconomic consequences may portend those of future marine communities. Here, we combine physiological experiments with ecological and demographic surveys to assess the causes and consequences of sudden but temporary poleward range expansions of a marine ectotherm with considerable life history plasticity (California market squid, Doryteuthis opalescens). We show that sequential factors related to resource accessibility in the core range---the buildup of large populations as a result of competitive release and climate-associated temperature increase and oxygen loss that constrain aerobic activity---may drive these expansions. We also reveal that poleward range expansion alters the body size---and therefore trophic role---of invading populations, with potential negative implications for socioeconomically valuable resident species. To help forecast rapid range expansions of marine ectotherms, we advocate that research efforts focus on factors impacting resource accessibility in core ranges. Determining how environmental conditions in receiving ecosystems affect body size and how body size is related to trophic role will help refine estimates of the impacts of future marine communities.}, keywords = {body size,California Current System,environmental variability,Gulf of Alaska,rapid range expansion,trophic ecology}, file = {/Users/nicholascarey/Documents/Zotero/storage/7KHQ25M2/Burford et al. - 2022 - Rapid Range Expansion of a Marine Ectotherm Reveal.pdf} } @@ -62,7 +75,7 @@ @mastersthesis{burnsMetabolicRateCritical2021 title = {Metabolic Rate, Critical Oxygen Partial Pressure, and Oxygen Supply Capacity of {{{\emph{Farfantepenaeus}}}}{\emph{ Duorarum}} at Their Lower Thermal Limit}, author = {Burns, L., Alexandra}, year = {2021}, - address = {{Tampa, USA}}, + address = {Tampa, USA}, urldate = {2021-09-09}, langid = {english}, school = {University of South Florida}, @@ -77,11 +90,11 @@ @article{castrillon-cifuentesSpatiotemporalVariabilityOxygen2023 journal = {PeerJ}, volume = {11}, pages = {e14586}, - publisher = {{PeerJ Inc.}}, + publisher = {PeerJ Inc.}, issn = {2167-8359}, doi = {10.7717/peerj.14586}, urldate = {2023-01-28}, - abstract = {Dissolved oxygen concentration (DO) is one of the main factors limiting benthic species distribution. Due to ocean warming and eutrophication, the ocean is deoxygenating. In the Eastern Tropical Pacific (ETP), deep waters with low DO ({$<$}1 mg L-1) may reach coral reefs, because upwelling will likely intensify due to climate change. To understand oxygen variability and its effects on corals, we characterize the Spatio-temporal changes of DO in coral reefs of Gorgona Island and calculate the critical oxygen tension (Pcrit) to identify the DO concentration that could represent a hypoxic condition for Pocillopora capitata, one of the main reef-building species in the ETP. The mean ({$\pm$}SD) DO concentration in the coral reefs of Gorgona Island was 4.6 {$\pm$} 0.89 mg L-1. Low DO conditions were due to upwelling, but hypoxia ({$<$}3.71 mg L-1, defined as a DO value 1 SD lower than the Mean) down to 3.0 mg O2 L-1 sporadically occurred at 10 m depth. The Pcrit of P. capitata was 3.7 mg L-1 and lies close to the hypoxic condition recorded on coral reefs during the upwelling season at 10 m depth. At Gorgona Island oxygen conditions lower than 2.3 mg L-1 occur at {$>$}20 m depth and coincide with the deepest bathymetric distribution of scattered colonies of Pocillopora. Because DO concentrations in coral reefs of Gorgona Island were comparably low to other coral reefs in the Eastern Tropical Pacific, and the hypoxic threshold of P. capitata was close to the minimum DO record on reefs, hypoxic events could represent a threat if conditions that promote eutrophication (and consequently hypoxia) increase.}, + abstract = {Dissolved oxygen concentration (DO) is one of the main factors limiting benthic species distribution. Due to ocean warming and eutrophication, the ocean is deoxygenating. In the Eastern Tropical Pacific (ETP), deep waters with low DO ({$<$}1 mg L-1) may reach coral reefs, because upwelling will likely intensify due to climate change. To understand oxygen variability and its effects on corals, we characterize the Spatio-temporal changes of DO in coral reefs of Gorgona Island and calculate the critical oxygen tension (Pcrit) to identify the DO concentration that could represent a hypoxic condition for Pocillopora capitata, one of the main reef-building species in the ETP. The mean ({\textpm}SD) DO concentration in the coral reefs of Gorgona Island was 4.6 {\textpm} 0.89 mg L-1. Low DO conditions were due to upwelling, but hypoxia ({$<$}3.71 mg L-1, defined as a DO value 1 SD lower than the Mean) down to 3.0 mg O2 L-1 sporadically occurred at 10 m depth. The Pcrit of P. capitata was 3.7 mg L-1 and lies close to the hypoxic condition recorded on coral reefs during the upwelling season at 10 m depth. At Gorgona Island oxygen conditions lower than 2.3 mg L-1 occur at {$>$}20 m depth and coincide with the deepest bathymetric distribution of scattered colonies of Pocillopora. Because DO concentrations in coral reefs of Gorgona Island were comparably low to other coral reefs in the Eastern Tropical Pacific, and the hypoxic threshold of P. capitata was close to the minimum DO record on reefs, hypoxic events could represent a threat if conditions that promote eutrophication (and consequently hypoxia) increase.}, langid = {english}, file = {/Users/nicholascarey/Documents/Zotero/storage/73Y2CUZ5/Castrillón-Cifuentes et al. - 2023 - Spatiotemporal variability of oxygen concentration.pdf} } @@ -96,7 +109,7 @@ @article{connellyAntibioticsReducePocillopora2023 issn = {0962-1083, 1365-294X}, doi = {10.1111/mec.17049}, urldate = {2023-06-18}, - abstract = {Corals are important models for understanding invertebrate host\textendash\-microbe interactions; however, to fully discern mechanisms involved in these relationships, experimental approaches for manipulating coral\textendash\-bacteria associations are needed. Coral-\-associated bacteria affect holobiont health via nutrient cycling, metabolic exchanges and pathogen exclusion, yet it is not fully understood how bacterial community shifts affect holobiont health and physiology. In this study, a combination of antibiotics (ampicillin, streptomycin and ciprofloxacin) was used to disrupt the bacterial communities of 14 colonies of the reef framework-\-building corals Pocillopora meandrina and P.\,verrucosa, originally collected from Panama and hosting diverse algal symbionts (family Symbiodiniaceae). Symbiodiniaceae photochemical efficiencies and holobiont oxygen consumption (as proxies for coral health) were measured throughout a 5-\-day exposure. Antibiotics altered bacterial community composition and reduced alpha and beta diversity, however, several bacteria persisted, leading to the hypothesis that these bacteria are either antibiotics resistant or occupy internal niches that are shielded from antibiotics. While antibiotics did not affect Symbiodiniaceae photochemical efficiency, antibiotics-\-treated corals had lower oxygen consumption rates. RNAseq revealed that antibiotics increased expression of Pocillopora immunity and stress response genes at the expense of cellular maintenance and metabolism functions. Together, these results reveal that antibiotic disruption of corals' native bacteria negatively impacts holobiont health by decreasing oxygen consumption and activating host immunity without directly impairing Symbiodiniaceae photosynthesis, underscoring the critical role of coral-\-associated bacteria in holobiont health. They also provide a baseline for future experiments that manipulate Pocillopora corals' symbioses by first reducing the diversity and complexity of coral-\-associated bacteria.}, + abstract = {Corals are important models for understanding invertebrate host--\-microbe interactions; however, to fully discern mechanisms involved in these relationships, experimental approaches for manipulating coral--\-bacteria associations are needed. Coral-\-associated bacteria affect holobiont health via nutrient cycling, metabolic exchanges and pathogen exclusion, yet it is not fully understood how bacterial community shifts affect holobiont health and physiology. In this study, a combination of antibiotics (ampicillin, streptomycin and ciprofloxacin) was used to disrupt the bacterial communities of 14 colonies of the reef framework-\-building corals Pocillopora meandrina and P.\,verrucosa, originally collected from Panama and hosting diverse algal symbionts (family Symbiodiniaceae). Symbiodiniaceae photochemical efficiencies and holobiont oxygen consumption (as proxies for coral health) were measured throughout a 5-\-day exposure. Antibiotics altered bacterial community composition and reduced alpha and beta diversity, however, several bacteria persisted, leading to the hypothesis that these bacteria are either antibiotics resistant or occupy internal niches that are shielded from antibiotics. While antibiotics did not affect Symbiodiniaceae photochemical efficiency, antibiotics-\-treated corals had lower oxygen consumption rates. RNAseq revealed that antibiotics increased expression of Pocillopora immunity and stress response genes at the expense of cellular maintenance and metabolism functions. Together, these results reveal that antibiotic disruption of corals' native bacteria negatively impacts holobiont health by decreasing oxygen consumption and activating host immunity without directly impairing Symbiodiniaceae photosynthesis, underscoring the critical role of coral-\-associated bacteria in holobiont health. They also provide a baseline for future experiments that manipulate Pocillopora corals' symbioses by first reducing the diversity and complexity of coral-\-associated bacteria.}, langid = {english}, file = {/Users/nicholascarey/Documents/Zotero/storage/RTNLVABI/Connelly et al. - 2023 - Antibiotics reduce Pocillopora coral‐associ.pdf} } @@ -108,13 +121,13 @@ @misc{dimosLocalThermalAdaptation2023 month = oct, primaryclass = {New Results}, pages = {2023.09.28.560008}, - publisher = {{bioRxiv}}, + publisher = {bioRxiv}, doi = {10.1101/2023.09.28.560008}, urldate = {2023-10-03}, abstract = {Freshwater and anadromous fish have been identified as one of the most at-risk groups threatened by climate induced warming given their metabolic dependence on environmental temperature and limited ability to track favorable environmental conditions. The future of these fish will depend on their ability to adapt to new thermal regimes over biologically relevant timescales. However, the mechanistic understanding of temperature responses required to predict if adaption can keep pace with climate change is limited. To address this question, we investigated the mechanistic basis of thermal adaptation across multiple levels of biological organization in the iconic and endangered Chinook Salmon (Oncorhynchus tshawytscha). We uncovered a mechanistic basis of thermal adaptation centered on the thermal responsiveness of mitochondrial function which modulates the extent to which rising temperatures increase metabolic demand on the cardio-respiratory system. These insights demonstrate that the populations studied here are able to maintain high levels of physiological performance at temperatures several degrees above historic averages, indicating that the decline Chinook Salmon and failure to recover despite conservation efforts is unlikely to be due to increased temperatures as a consequence of climate change.}, archiveprefix = {bioRxiv}, chapter = {New Results}, - copyright = {\textcopyright{} 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}, + copyright = {{\copyright} 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}, langid = {english}, file = {/Users/nicholascarey/Documents/Zotero/storage/MW6ENL4R/Dimos et al. - 2023 - Local Thermal Adaptation occurs via Modulation of .pdf} } @@ -128,7 +141,7 @@ @article{duncanOxygenAvailabilityBody2023 volume = {14}, number = {1}, pages = {3811}, - publisher = {{Nature Publishing Group}}, + publisher = {Nature Publishing Group}, issn = {2041-1723}, doi = {10.1038/s41467-023-39438-w}, urldate = {2023-06-30}, @@ -150,7 +163,7 @@ @article{durtscheThermalConditionsEmbryogenesis2021 issn = {2150-8925, 2150-8925}, doi = {10.1002/ecs2.3374}, urldate = {2021-06-14}, - abstract = {The projected climate change and increase in thermal conditions in northern latitudes over the next 60 yr has the potential to alter the metabolic scope and potential fitness of aquatic ectotherms. Here, we experimentally tested if elevated egg incubation temperature affected metabolic scope in juvenile brown trout (Salmo trutta) as a phenotypically plastic response. Cohorts of brown trout from anadromous and resident crosses were raised through embryogenesis in either natural river temperatures (cold) or elevated (+3\textdegree C, warm) temperatures until they could feed exogenously. The standard metabolic rate (SMR), maximum metabolic rate (MMR), and aerobic scope (AS = MMR - SMR) of juveniles from four anadromous-resident crosses and from both incubation temperatures were tested at 13\textdegree C. We found that metabolic measures (SMR, MMR, AS) were lower in warm than cold-incubated fish. There was no difference in the metabolic rates of fish from different anadromous-resident crosses. The results of this experiment are consistent with the countergradient variation hypothesis (CGV) in which phenotypic variation, in this case variation in metabolic rates, is inversely related to thermal conditions, originally proposed in relation to altitudinal or latitudinal gradients. While previous studies have related CGV to genetic differences between populations, our study shows that thermal differences encountered at the embryonic stage can produce a phenotypic pattern consistent with CGV. It is difficult to predict the consequences of these metabolic changes in a future warmer climate, as lower metabolic rates indicate that brown trout will probably expend less energy, but a reduced aerobic scope may counteract this affect, limiting their ability as a top predator and in escaping predators. Our results suggest that there are mechanisms used to adjust to elevated water temperature that can be initiated during embryogenesis. Given that there were no differences among crosses, it is likely that temperature-induced differences are the result of plastic responses.}, + abstract = {The projected climate change and increase in thermal conditions in northern latitudes over the next 60 yr has the potential to alter the metabolic scope and potential fitness of aquatic ectotherms. Here, we experimentally tested if elevated egg incubation temperature affected metabolic scope in juvenile brown trout (Salmo trutta) as a phenotypically plastic response. Cohorts of brown trout from anadromous and resident crosses were raised through embryogenesis in either natural river temperatures (cold) or elevated (+3{$^\circ$}C, warm) temperatures until they could feed exogenously. The standard metabolic rate (SMR), maximum metabolic rate (MMR), and aerobic scope (AS = MMR - SMR) of juveniles from four anadromous-resident crosses and from both incubation temperatures were tested at 13{$^\circ$}C. We found that metabolic measures (SMR, MMR, AS) were lower in warm than cold-incubated fish. There was no difference in the metabolic rates of fish from different anadromous-resident crosses. The results of this experiment are consistent with the countergradient variation hypothesis (CGV) in which phenotypic variation, in this case variation in metabolic rates, is inversely related to thermal conditions, originally proposed in relation to altitudinal or latitudinal gradients. While previous studies have related CGV to genetic differences between populations, our study shows that thermal differences encountered at the embryonic stage can produce a phenotypic pattern consistent with CGV. It is difficult to predict the consequences of these metabolic changes in a future warmer climate, as lower metabolic rates indicate that brown trout will probably expend less energy, but a reduced aerobic scope may counteract this affect, limiting their ability as a top predator and in escaping predators. Our results suggest that there are mechanisms used to adjust to elevated water temperature that can be initiated during embryogenesis. Given that there were no differences among crosses, it is likely that temperature-induced differences are the result of plastic responses.}, langid = {english}, file = {/Users/nicholascarey/Documents/Zotero/storage/8F2A5Y48/Durtsche et al. - 2021 - Thermal conditions during embryogenesis influence .pdf} } @@ -163,7 +176,7 @@ @article{espinel-velascoInteractiveEffectsOcean2023 volume = {10}, issn = {2296-7745}, urldate = {2023-11-02}, - abstract = {The Arctic region is undergoing rapid and significant changes, characterized by high rates of acidification and warming. These transformations prompt critical questions about the resilience of marine communities in the face of environmental change. In the Arctic, marine zooplankton and in particular calanoid copepods play a vital role in the food web. Changes in environmental conditions could disrupt zooplankton communities, posing detrimental consequences for the entire ecosystem. Copepod early-life stages have been shown to be particularly sensitive to environmental stressors since they represent a bottleneck in the life cycle. Here, we investigated the responses of 4-day old Calanus hyperboreus nauplii when exposed to acidification (pH 7.5 and 8.1) and warming (0 and 3\textdegree C), both independently and in combination. Naupliar respiration rates increased when exposed to a combination of acidification and warming, but not when exposed to the stressors individually. Moreover, we found no discernible differences in lipid content and fatty acid (FA) composition of the nauplii across the different experimental treatments. Wax esters accounted for approximately 75\% of the lipid reserves, and high amounts of long chain fatty acids 20:1 and 22:1, crucial for the reproduction cycle in copepods, were also detected. Our results indicate a sensitivity of these nauplii to a combination of acidification and warming, but not to the individual stressors, aligning with a growing body of evidence from related studies. This study sheds light on the potential implications of global change for Arctic copepod populations by elucidating the responses of early-life stages to these environmental stressors.}, + abstract = {The Arctic region is undergoing rapid and significant changes, characterized by high rates of acidification and warming. These transformations prompt critical questions about the resilience of marine communities in the face of environmental change. In the Arctic, marine zooplankton and in particular calanoid copepods play a vital role in the food web. Changes in environmental conditions could disrupt zooplankton communities, posing detrimental consequences for the entire ecosystem. Copepod early-life stages have been shown to be particularly sensitive to environmental stressors since they represent a bottleneck in the life cycle. Here, we investigated the responses of 4-day old Calanus hyperboreus nauplii when exposed to acidification (pH 7.5 and 8.1) and warming (0 and 3{$^\circ$}C), both independently and in combination. Naupliar respiration rates increased when exposed to a combination of acidification and warming, but not when exposed to the stressors individually. Moreover, we found no discernible differences in lipid content and fatty acid (FA) composition of the nauplii across the different experimental treatments. Wax esters accounted for approximately 75\% of the lipid reserves, and high amounts of long chain fatty acids 20:1 and 22:1, crucial for the reproduction cycle in copepods, were also detected. Our results indicate a sensitivity of these nauplii to a combination of acidification and warming, but not to the individual stressors, aligning with a growing body of evidence from related studies. This study sheds light on the potential implications of global change for Arctic copepod populations by elucidating the responses of early-life stages to these environmental stressors.}, file = {/Users/nicholascarey/Documents/Zotero/storage/7YIM2YGU/Espinel-Velasco et al. - 2023 - Interactive effects of ocean acidification and tem.pdf} } @@ -179,7 +192,7 @@ @article{evensenRemarkablyHighConsistent2021 issn = {0024-3590, 1939-5590}, doi = {10.1002/lno.11715}, urldate = {2021-06-14}, - abstract = {Global warming is resulting in unprecedented levels of coral mortality due to mass bleaching events and, more recently, marine heatwaves, where rapid increases in seawater temperature cause mortality within days. Here, we compare the response of a ubiquitous scleractinian coral, Stylophora pistillata, from the northern Red Sea to acute (7 h) and chronic (7\textendash 11 d) thermal stress events that include temperature treatments of 27 C (i.e., the local maximum monthly mean), 29.5 C, 32 C, and 34.5 C, and assess recovery of the corals following exposure. Overall, S. pistillata exhibited remarkably similar responses to acute and chronic thermal stress, responding primarily to the temperature treatment rather than duration or heating rate. Additionally, corals displayed an exceptionally high thermal tolerance, maintaining their physiological performance and suffering little to no loss of algal symbionts or chlorophyll a up to 32 C, before the host suffered from rapid tissue necrosis and mortality at 34.5 C. While there was some variability in physiological response metrics, photosynthetic efficiency measurements (i.e., maximum quantum yield Fv/Fm) accurately reflected the overall physiological response patterns, with these measurements used to produce the Fv/Fm effective dose (ED50) metric as a proxy for the thermal tolerance of corals. This approach produced similar ED50 values for the acute and chronic experiments (34.47 C vs. 33.81 C), highlighting the potential for acute thermal assays with measurements of Fv/Fm as a systematic and standardized approach to quantitively compare the upper thermal limits of reef-building corals using a portable experimental system.}, + abstract = {Global warming is resulting in unprecedented levels of coral mortality due to mass bleaching events and, more recently, marine heatwaves, where rapid increases in seawater temperature cause mortality within days. Here, we compare the response of a ubiquitous scleractinian coral, Stylophora pistillata, from the northern Red Sea to acute (7 h) and chronic (7--11 d) thermal stress events that include temperature treatments of 27 C (i.e., the local maximum monthly mean), 29.5 C, 32 C, and 34.5 C, and assess recovery of the corals following exposure. Overall, S. pistillata exhibited remarkably similar responses to acute and chronic thermal stress, responding primarily to the temperature treatment rather than duration or heating rate. Additionally, corals displayed an exceptionally high thermal tolerance, maintaining their physiological performance and suffering little to no loss of algal symbionts or chlorophyll a up to 32 C, before the host suffered from rapid tissue necrosis and mortality at 34.5 C. While there was some variability in physiological response metrics, photosynthetic efficiency measurements (i.e., maximum quantum yield Fv/Fm) accurately reflected the overall physiological response patterns, with these measurements used to produce the Fv/Fm effective dose (ED50) metric as a proxy for the thermal tolerance of corals. This approach produced similar ED50 values for the acute and chronic experiments (34.47 C vs. 33.81 C), highlighting the potential for acute thermal assays with measurements of Fv/Fm as a systematic and standardized approach to quantitively compare the upper thermal limits of reef-building corals using a portable experimental system.}, langid = {english}, file = {/Users/nicholascarey/Documents/Zotero/storage/DAT8L6P8/Evensen et al. - 2021 - Remarkably high and consistent tolerance of a Red .pdf} } @@ -195,7 +208,7 @@ @article{evensenRolesHeatingRate2023 issn = {0022-0981}, doi = {10.1016/j.jembe.2023.151930}, urldate = {2023-07-29}, - abstract = {Anthropogenic ocean warming is one of the biggest threats to marine organisms worldwide. However, it remains unclear how the duration and intensity of thermal anomalies affect organismal stress responses and thermal thresholds. We used detailed tracking of coral endosymbiont and host physiology and dose-response analyses to compare the effects of multiple heating rates, intensities, and exposure durations on two reef-building corals, Acropora hemprichii and Porites lobata, from adjacent sides of a reef (protected vs. exposed) in the Central Red Sea known to differ in high-frequency ({$<$} 24~h) temperature variability. Corals were exposed to acute heat exposures (18~h) with four target temperatures (32~\textdegree C, 35~\textdegree C, 36.5~\textdegree C, and 38~\textdegree C), versus prolonged heat exposures lasting 7\textendash 15~days where temperatures were raised 0.5 and 1.5~\textdegree C~day-1 to four target temperatures (32~\textdegree C, 33.5~\textdegree C, 35~\textdegree C, and 36.5~\textdegree C). In the prolonged experiment, dose-response curves assessing algal endosymbiont Fv/Fm revealed little initial effect of temperature, before an exponential decline above 34~\textdegree C for both species. Temperature at time of measurement and degree heating hours above 34~\textdegree C (DHH34) were the variables most strongly associated with declines in Fv/Fm. The Fv/Fm thermal thresholds for P. lobata from the high-variability protected site were higher than the exposed site in the faster heating, prolonged heat stress experiment despite minimal differences in endosymbiont density, chlorophyll-a, and host protein between sites. Together, our dose-response analysis revealed complex effects of DHH34, heating rate, and species-specific differences in the influence of local thermal histories shaping thermotolerance limits for these corals.}, + abstract = {Anthropogenic ocean warming is one of the biggest threats to marine organisms worldwide. However, it remains unclear how the duration and intensity of thermal anomalies affect organismal stress responses and thermal thresholds. We used detailed tracking of coral endosymbiont and host physiology and dose-response analyses to compare the effects of multiple heating rates, intensities, and exposure durations on two reef-building corals, Acropora hemprichii and Porites lobata, from adjacent sides of a reef (protected vs. exposed) in the Central Red Sea known to differ in high-frequency ({$<$} 24~h) temperature variability. Corals were exposed to acute heat exposures (18~h) with four target temperatures (32~{$^\circ$}C, 35~{$^\circ$}C, 36.5~{$^\circ$}C, and 38~{$^\circ$}C), versus prolonged heat exposures lasting 7--15~days where temperatures were raised 0.5 and 1.5~{$^\circ$}C~day-1 to four target temperatures (32~{$^\circ$}C, 33.5~{$^\circ$}C, 35~{$^\circ$}C, and 36.5~{$^\circ$}C). In the prolonged experiment, dose-response curves assessing algal endosymbiont Fv/Fm revealed little initial effect of temperature, before an exponential decline above 34~{$^\circ$}C for both species. Temperature at time of measurement and degree heating hours above 34~{$^\circ$}C (DHH34) were the variables most strongly associated with declines in Fv/Fm. The Fv/Fm thermal thresholds for P. lobata from the high-variability protected site were higher than the exposed site in the faster heating, prolonged heat stress experiment despite minimal differences in endosymbiont density, chlorophyll-a, and host protein between sites. Together, our dose-response analysis revealed complex effects of DHH34, heating rate, and species-specific differences in the influence of local thermal histories shaping thermotolerance limits for these corals.}, langid = {english}, keywords = {Acute heat stress,Coral bleaching,Marine heatwaves,Ramping rate,Stress exposure,Upper thermal limits}, file = {/Users/nicholascarey/Documents/Zotero/storage/M2QJ674E/Evensen et al. - 2023 - The roles of heating rate, intensity, and duration.pdf;/Users/nicholascarey/Documents/Zotero/storage/38KU4P2B/S002209812300062X.html} @@ -222,7 +235,7 @@ @phdthesis{gilbertThermalLimitsCardiorespiratory2020 title = {Thermal Limits to the Cardiorespiratory Performance of Arctic Char ({{{\emph{Salvelinus}}}}{\emph{ Alpinus}}) in a Rapidly Warming {{North}}}, author = {Gilbert, Matthew James Henry}, year = {2020}, - address = {{Vancouver, Canada}}, + address = {Vancouver, Canada}, urldate = {2021-06-24}, langid = {english}, school = {University of British Columbia}, @@ -240,7 +253,7 @@ @article{gomesImpactsAcuteHypoxia2023 issn = {0048-9697}, doi = {10.1016/j.scitotenv.2023.166893}, urldate = {2023-09-17}, - abstract = {Seahorses are one of the most unique and enigmatic animals, recognized as flagship species for several conservation issues. Unfortunately, seahorses' populations have been declining and their unique lifestyle may constrain the ability of these animals to evolve in the future climate scenarios. They inhabit shallow coastal waters that display daily or seasonal environmental fluctuations. Yet, few studies have scrutinized the impacts of climate changes on these iconic species. Within this context, the objective of this work was to test the effects of an extreme hypoxia exposure (\textasciitilde 27~\% dissolved oxygen for approximately 7~h) on the metabolism, behaviour and food intake of the temperate seahorse Hippocampus hippocampus. Regarding metabolism, hypoxia exposure led to a significant reduction in metabolic rates and an increase in ventilation rates. Seahorses showed signs of movement lethargy under oxygen depletion. The results show that a small but extreme exposure to hypoxia is tolerable by seahorses despite inducing metabolic and behavioural changes, that may jeopardize the future development and survival of these iconic organisms.}, + abstract = {Seahorses are one of the most unique and enigmatic animals, recognized as flagship species for several conservation issues. Unfortunately, seahorses' populations have been declining and their unique lifestyle may constrain the ability of these animals to evolve in the future climate scenarios. They inhabit shallow coastal waters that display daily or seasonal environmental fluctuations. Yet, few studies have scrutinized the impacts of climate changes on these iconic species. Within this context, the objective of this work was to test the effects of an extreme hypoxia exposure ({\textasciitilde}27~\% dissolved oxygen for approximately 7~h) on the metabolism, behaviour and food intake of the temperate seahorse Hippocampus hippocampus. Regarding metabolism, hypoxia exposure led to a significant reduction in metabolic rates and an increase in ventilation rates. Seahorses showed signs of movement lethargy under oxygen depletion. The results show that a small but extreme exposure to hypoxia is tolerable by seahorses despite inducing metabolic and behavioural changes, that may jeopardize the future development and survival of these iconic organisms.}, keywords = {Behaviour,Hypoxia,Metabolism,Seahorse}, file = {/Users/nicholascarey/Documents/Zotero/storage/Y94RD8QN/Gomes et al. - 2023 - Impacts of acute hypoxia on the short-snouted seah.pdf;/Users/nicholascarey/Documents/Zotero/storage/WDXC96HJ/S0048969723055183.html} } @@ -249,7 +262,7 @@ @phdthesis{gomezisazaAnthropogenicDisturbancesFreshwater2020 title = {Anthropogenic Disturbances to Freshwater Taxa: Interactions between Nitrate and Additional Stressors on Various Physiological Traits}, author = {Gomez Isaza, Daniel F.}, year = {2020}, - address = {{Brisband, Australia}}, + address = {Brisband, Australia}, urldate = {2021-06-24}, langid = {english}, school = {University of Queensland}, @@ -266,11 +279,31 @@ @article{gomezisazaThermalAcclimationOffsets2020 issn = {1477-9145, 0022-0949}, doi = {10.1242/jeb.224444}, urldate = {2021-06-14}, - abstract = {Rising temperatures are set to imperil freshwater fishes as climate change ensues unless compensatory strategies are employed. However, the presence of additional stressors, such as elevated nitrate concentrations, may affect the efficacy of compensatory responses. Here, juvenile silver perch (Bidyanus bidyanus) were exposed to current-day summer temperatures (28oC) or a future climate-warming scenario (32oC) and simultaneously exposed to one of three ecologically relevant nitrate concentrations (0, 50 or 100 mg L-1). We measured indicators of fish performance (growth, swimming), aerobic scope (AS) and upper thermal tolerance (CTMAX) to test the hypothesis that nitrate exposure would increase susceptibility to elevated temperatures and limit thermal compensatory responses. After 8 weeks of acclimation, the thermal sensitivity and plasticity of AS and swimming performance were tested at three test temperatures (28, 32, 36oC). The AS of 28oC-acclimated fish declined with increasing temperature, and the effect was more pronounced in nitrate exposed individuals. In these fish, declines in AS corresponded with poorer swimming performance and a 0.8oC decrease in CTMAX compared to unexposed fish. In contrast, acclimation to 32oC masked the effects of nitrate; fish acclimated to 32oC displayed a thermally insensitive phenotype whereby locomotor performance remained unchanged, AS was maintained and CTMAX was increased by \textasciitilde 1oC irrespective of nitrate treatment compared to fish acclimated to 28oC. Growth was however markedly reduced in 32oC-acclimated compared to 28oC-acclimated fish. Our results indicate that nitrate exposure increases the susceptibility of fish to acute high temperatures, but thermal compensation can override some of these potential detrimental effects.}, + abstract = {Rising temperatures are set to imperil freshwater fishes as climate change ensues unless compensatory strategies are employed. However, the presence of additional stressors, such as elevated nitrate concentrations, may affect the efficacy of compensatory responses. Here, juvenile silver perch (Bidyanus bidyanus) were exposed to current-day summer temperatures (28oC) or a future climate-warming scenario (32oC) and simultaneously exposed to one of three ecologically relevant nitrate concentrations (0, 50 or 100 mg L-1). We measured indicators of fish performance (growth, swimming), aerobic scope (AS) and upper thermal tolerance (CTMAX) to test the hypothesis that nitrate exposure would increase susceptibility to elevated temperatures and limit thermal compensatory responses. After 8 weeks of acclimation, the thermal sensitivity and plasticity of AS and swimming performance were tested at three test temperatures (28, 32, 36oC). The AS of 28oC-acclimated fish declined with increasing temperature, and the effect was more pronounced in nitrate exposed individuals. In these fish, declines in AS corresponded with poorer swimming performance and a 0.8oC decrease in CTMAX compared to unexposed fish. In contrast, acclimation to 32oC masked the effects of nitrate; fish acclimated to 32oC displayed a thermally insensitive phenotype whereby locomotor performance remained unchanged, AS was maintained and CTMAX was increased by {\textasciitilde}1oC irrespective of nitrate treatment compared to fish acclimated to 28oC. Growth was however markedly reduced in 32oC-acclimated compared to 28oC-acclimated fish. Our results indicate that nitrate exposure increases the susceptibility of fish to acute high temperatures, but thermal compensation can override some of these potential detrimental effects.}, langid = {english}, file = {/Users/nicholascarey/Documents/Zotero/storage/FF4NXPV5/Gomez Isaza et al. - 2020 - Thermal acclimation offsets the negative effects o.pdf} } +@article{gonzalez-ferrerasChronicExposureEnvironmental2023, + title = {Chronic Exposure to Environmental Temperature Attenuates the Thermal Sensitivity of Salmonids}, + author = {{Gonz{\'a}lez-Ferreras}, Alexia M. and Barqu{\'i}n, Jose and Blyth, Penelope S. A. and Hawksley, Jack and Kinsella, Hugh and Lauridsen, Rasmus and Morris, Olivia F. and Pe{\~n}as, Francisco J. and Thomas, Gareth E. and Woodward, Guy and Zhao, Lei and O'Gorman, Eoin J.}, + year = {2023}, + month = dec, + journal = {Nature Communications}, + volume = {14}, + number = {1}, + pages = {8309}, + publisher = {Nature Publishing Group}, + issn = {2041-1723}, + doi = {10.1038/s41467-023-43478-7}, + urldate = {2023-12-16}, + abstract = {Metabolism, the biological processing of energy and materials, scales predictably with temperature and body size. Temperature effects on metabolism are normally studied via acute exposures, which overlooks the capacity for organisms to moderate their metabolism following chronic exposure to warming. Here, we conduct respirometry assays in situ and after transplanting salmonid fish among different streams to disentangle the effects of chronic and acute thermal exposure. We find a clear temperature dependence of metabolism for the transplants, but not the in-situ assays, indicating that chronic exposure to warming can attenuate salmonid thermal sensitivity. A bioenergetic model accurately captures the presence of fish in warmer streams when accounting for chronic exposure, whereas it incorrectly predicts their local extinction with warming when incorporating the acute temperature dependence of metabolism. This highlights the need to incorporate the potential for thermal acclimation or adaptation when forecasting the consequences of global warming on ecosystems.}, + copyright = {2023 The Author(s)}, + langid = {english}, + keywords = {Ecology,Ecophysiology,Limnology}, + file = {/Users/nicholascarey/Documents/Zotero/storage/9NY25NA6/González-Ferreras et al. - 2023 - Chronic exposure to environmental temperature atte.pdf} +} + @article{grigorSwimmingActivityIndicator2022, title = {Swimming {{Activity}} as an {{Indicator}} of {{Seasonal Diapause}} in the {{Copepod Calanus}} Finmarchicus}, author = {Grigor, Jordan J. and Freer, Jennifer J. and Tarling, Geraint A. and Cohen, Jonathan H. and Last, Kim S.}, @@ -280,10 +313,21 @@ @article{grigorSwimmingActivityIndicator2022 issn = {2296-7745}, doi = {10.3389/fmars.2022.909528}, urldate = {2022-07-01}, - abstract = {Copepods dominate zooplankton biomass of the upper ocean, especially in the highly seasonal boreal and polar regions, for which specific life-cycle traits such as the accumulation of lipid reserves, migration into deep water and diapause are key adaptations. Understanding such traits is central to determining the energetic consequences of high latitude range shifts related to climate change and ultimately, biogeochemical models of carbon flow. Using the calanoid copepod Calanus finmarchicus, we explore a new indicator of diapause, swimming activity, and assess its relationship with respiration. Stage CV copepods were sampled in late summer from shallow (epipelagic) and deep (mesopelagic) water at both slope and basin locations within the Fram Strait at a time when the animals had entered diapause. Using high-throughput quantitative behaviour screening on ex-situ swimming activity, we found that irrespective of sampling station copepods from the mesopelagic show highly reduced activity (88.5 {$\pm$} 3.4\% reduction) when compared to those from the epipelagic with a clearly defined threshold between epi- and mesopelagic animals (\textasciitilde 5 beam breaks 30 min-1). Mesopelagic individuals were also larger (12.4 {$\pm$} 8.8\%) and had more lipid reserves (19.3 {$\pm$} 2.2\%) than epipelagic individuals. On average, copepods from the basin station exhibited respiration rates similar to overwintering rates observed elsewhere (1.23 {$\pm$} 0.76 \textmu g C d-1), while respiration rates of copepods from the shelf station were more consistent with active metabolism (2.46 {$\pm$} 1.02 \textmu g C d-1). Nevertheless, active and diapausing rates were observed in individuals from both stations at both epi- and mesopelagic depths. We suggest that rapid screening of activity may provide an early indicator of diapause before it becomes fully apparent and consistent in other physiological indicators. Ultimately, swimming activity may provide a useful tool to assess the putative endogenous and exogenous factors involved in diapause onset, provide a handle on the energetics of diapause, and input to biogeochemical carbon models on C. finmarchicus.}, + abstract = {Copepods dominate zooplankton biomass of the upper ocean, especially in the highly seasonal boreal and polar regions, for which specific life-cycle traits such as the accumulation of lipid reserves, migration into deep water and diapause are key adaptations. Understanding such traits is central to determining the energetic consequences of high latitude range shifts related to climate change and ultimately, biogeochemical models of carbon flow. Using the calanoid copepod Calanus finmarchicus, we explore a new indicator of diapause, swimming activity, and assess its relationship with respiration. Stage CV copepods were sampled in late summer from shallow (epipelagic) and deep (mesopelagic) water at both slope and basin locations within the Fram Strait at a time when the animals had entered diapause. Using high-throughput quantitative behaviour screening on ex-situ swimming activity, we found that irrespective of sampling station copepods from the mesopelagic show highly reduced activity (88.5 {\textpm} 3.4\% reduction) when compared to those from the epipelagic with a clearly defined threshold between epi- and mesopelagic animals ({\textasciitilde}5 beam breaks 30 min-1). Mesopelagic individuals were also larger (12.4 {\textpm} 8.8\%) and had more lipid reserves (19.3 {\textpm} 2.2\%) than epipelagic individuals. On average, copepods from the basin station exhibited respiration rates similar to overwintering rates observed elsewhere (1.23 {\textpm} 0.76 {\textmu}g C d-1), while respiration rates of copepods from the shelf station were more consistent with active metabolism (2.46 {\textpm} 1.02 {\textmu}g C d-1). Nevertheless, active and diapausing rates were observed in individuals from both stations at both epi- and mesopelagic depths. We suggest that rapid screening of activity may provide an early indicator of diapause before it becomes fully apparent and consistent in other physiological indicators. Ultimately, swimming activity may provide a useful tool to assess the putative endogenous and exogenous factors involved in diapause onset, provide a handle on the energetics of diapause, and input to biogeochemical carbon models on C. finmarchicus.}, file = {/Users/nicholascarey/Documents/Zotero/storage/DDJJR59U/Grigor et al. - 2022 - Swimming Activity as an Indicator of Seasonal Diap.pdf} } +@mastersthesis{guitardEffetsPhysiologiquesInfection2020, + title = {{Effets physiologiques de l'infection parasitaire chez le crapet-soleil (Lepomis gibbosus)}}, + author = {Guitard, Jo{\"e}lle}, + year = {2020}, + urldate = {2024-03-29}, + langid = {fra}, + school = {Universit{\'e} de Montr{\'e}al}, + annotation = {Accepted: 2021-09-07T17:01:48Z}, + file = {/Users/nicholascarey/Documents/Zotero/storage/DM4JZQGJ/Guitard - 2021 - Effets physiologiques de l’infection parasitaire c.pdf} +} + @article{guitardIncreasedParasiteLoad2022a, title = {Increased Parasite Load Is Associated with Reduced Metabolic Rates and Escape Responsiveness in Pumpkinseed Sunfish}, author = {Guitard, Jo{\"e}lle J. and Chr{\'e}tien, Emmanuelle and De Bonville, J{\'e}r{\'e}my and Roche, Dominique G. and Boisclair, Daniel and Binning, Sandra A.}, @@ -312,7 +356,7 @@ @article{hariantoImpactsAcclimationWarmlow2021 issn = {2296-7745}, doi = {10.3389/fmars.2020.588938}, urldate = {2021-06-14}, - abstract = {Ocean warming (OW) and acidification (OA) affects nearly all aspects of marine organism physiology and it is important to consider both stressors when predicting responses to climate change. We investigated the effects of long-term exposure to OW and OA on the physiology of adults of the sea urchin, Heliocidaris erythrogramma, a species resident in the southeast Australia warming hotspot. The urchins were slowly introduced to stressor conditions in the laboratory over a 7-week adjustment period to three temperature (ambient, +2{$\smwhtcircle$}C, +3{$\smwhtcircle$}C) and two pH (ambient: pHT 8.0; -0.4 units: pHT 7.6) treatments. They were then maintained in a natural pattern of seasonal temperature and photoperiod change, and fixed pH, for 22 weeks. Survival was monitored through week 22 and metabolic rate was measured at 4 and 12 weeks of acclimation, feeding rate and ammonia excretion rate at 12 weeks and assimilation efficiency at 13 weeks. Acclimation to +3{$\smwhtcircle$}C was deleterious regardless of pH. Mortality from week 6 indicated that recent marine heatwaves are likely to have been deleterious to this species. Acclimation to +2{$\smwhtcircle$}C did not affect survival. Increased temperature decreased feeding and increased excretion rates, with no effect of acidification. While metabolic rate increased additively with temperature and low pH at week 4, there was no difference between treatments at week 12, indicating physiological acclimation in surviving urchins to stressful conditions. Regardless of treatment, H. erythrogramma had a net positive energy budget indicating that the responses were not due to energy limitation. To test for the effect of parental acclimation on offspring responses, the offspring of acclimated urchins were reared to the juvenile stage in OW and OA conditions. Parental acclimation to warming, but not acidification altered juvenile physiology with an increase in metabolic rate. Our results show that incorporation of gradual seasonal environmental change in longterm acclimation can influence outcomes, an important consideration in predicting the consequences of changing climate for marine species.}, + abstract = {Ocean warming (OW) and acidification (OA) affects nearly all aspects of marine organism physiology and it is important to consider both stressors when predicting responses to climate change. We investigated the effects of long-term exposure to OW and OA on the physiology of adults of the sea urchin, Heliocidaris erythrogramma, a species resident in the southeast Australia warming hotspot. The urchins were slowly introduced to stressor conditions in the laboratory over a 7-week adjustment period to three temperature (ambient, +2{\textopenbullet}C, +3{\textopenbullet}C) and two pH (ambient: pHT 8.0; -0.4 units: pHT 7.6) treatments. They were then maintained in a natural pattern of seasonal temperature and photoperiod change, and fixed pH, for 22 weeks. Survival was monitored through week 22 and metabolic rate was measured at 4 and 12 weeks of acclimation, feeding rate and ammonia excretion rate at 12 weeks and assimilation efficiency at 13 weeks. Acclimation to +3{\textopenbullet}C was deleterious regardless of pH. Mortality from week 6 indicated that recent marine heatwaves are likely to have been deleterious to this species. Acclimation to +2{\textopenbullet}C did not affect survival. Increased temperature decreased feeding and increased excretion rates, with no effect of acidification. While metabolic rate increased additively with temperature and low pH at week 4, there was no difference between treatments at week 12, indicating physiological acclimation in surviving urchins to stressful conditions. Regardless of treatment, H. erythrogramma had a net positive energy budget indicating that the responses were not due to energy limitation. To test for the effect of parental acclimation on offspring responses, the offspring of acclimated urchins were reared to the juvenile stage in OW and OA conditions. Parental acclimation to warming, but not acidification altered juvenile physiology with an increase in metabolic rate. Our results show that incorporation of gradual seasonal environmental change in longterm acclimation can influence outcomes, an important consideration in predicting the consequences of changing climate for marine species.}, langid = {english}, file = {/Users/nicholascarey/Documents/Zotero/storage/59VU9I75/Harianto et al. - 2021 - Impacts of Acclimation in Warm-Low pH Conditions o.pdf} } @@ -339,9 +383,9 @@ @phdthesis{hawadleEffectsMultipleEnvironmental2023 title = {The {{Effects}} of {{Multiple Environmental Stressors}} on the {{Respiration Rate}} of {{{\emph{Mytilus}}}}{\emph{ Galloprovincialis}}}, author = {Hawadle, Abdisalan}, year = {2023}, - address = {{Friday Harbor Laboratories}}, + address = {Friday Harbor Laboratories}, urldate = {2023-02-28}, - abstract = {Intertidal organisms are subject to environmental variations that may influence their physiological performance. As processes such as respiration depend on gas exchange between organisms and their environment, they are potentially affected by water temperature and velocity. In this study, we compare the effects of multiple environmental stressors (temperature and flow velocity) on the respiration rate in two mytilids, the Mediterranean mussel, Mytilus galloprovincialis and the temperate bay mussel M. trossulus. Thermal performance curves (5, 11, 17, 23, and 29 \textdegree C) for respiration rate were quantified at five different flow velocities (2, 4, 6, 10, 20 cm s-1) in a fully crossed design. Well-defined thermal performance curves were present at moderate to high water velocities, whereas, at the lowest velocity (2 cm s-1) respiration rates remained low across all temperatures. Although Mediterranean mussels displayed higher thermal optima than Bay mussels under moderate flow speeds (4-6 cm s-1), those differences were absent at higher flow velocities ({$>$}10 cm s-1). These results highlight the importance of considering hydrodynamic conditions when estimating thermal tolerance in marine mussels.}, + abstract = {Intertidal organisms are subject to environmental variations that may influence their physiological performance. As processes such as respiration depend on gas exchange between organisms and their environment, they are potentially affected by water temperature and velocity. In this study, we compare the effects of multiple environmental stressors (temperature and flow velocity) on the respiration rate in two mytilids, the Mediterranean mussel, Mytilus galloprovincialis and the temperate bay mussel M. trossulus. Thermal performance curves (5, 11, 17, 23, and 29 {$^\circ$}C) for respiration rate were quantified at five different flow velocities (2, 4, 6, 10, 20 cm s-1) in a fully crossed design. Well-defined thermal performance curves were present at moderate to high water velocities, whereas, at the lowest velocity (2 cm s-1) respiration rates remained low across all temperatures. Although Mediterranean mussels displayed higher thermal optima than Bay mussels under moderate flow speeds (4-6 cm s-1), those differences were absent at higher flow velocities ({$>$}10 cm s-1). These results highlight the importance of considering hydrodynamic conditions when estimating thermal tolerance in marine mussels.}, langid = {english}, school = {University of Washington}, annotation = {Accepted: 2023-02-24T20:20:44Z}, @@ -361,7 +405,7 @@ @article{hawkeExposurePetroleumderivedBiopolymer2024 urldate = {2023-10-01}, abstract = {Evidence suggests that petroleum-derived polymers can impact marine organisms however, little is understood about whether biopolymers affect the behaviour and physiology of marine teleost fish. The aim of this research was to examine the potential effects of microplastics from a petroleum-derived polymer, (polyethylene, PE), and a biopolymer, (edible food coating EFC) on the escape performance, routine swimming, and aerobic metabolism of Forsterygion capito (the mottled triplefin). PE exposure negatively affected fish through longer latencies ({$\sim$}25~\% slower to respond), slower maximum speeds and higher responsiveness in escape performance compared to control fish. Furthermore, fish exposed to PE displayed slower mean speeds and reduced the distance travelled by {$\sim$}25~\%. After an exhaustive challenge, PE-exposed fish showed higher excess post-exercise oxygen consumption during recovery, compared to control fish. By contrast, EFC exposure only negatively affected maximum speed during an escape. Directionality and mean speed in escape performance, metabolic rate and recovery time were unaffected by biopolymer exposure. With the ever-increasing number of microplastics in the ocean, a shift to biodegradable polymers may be beneficial to marine organisms due to the smaller effect found when compared to petroleum-derived polymers in this study. As a central tool for conservation, this study represents a significant advance to predict the impact of microplastics on wild fish populations.}, keywords = {Anti-predator behaviour,Bioplastics,EPOC,Metabolic rate,Microplastics,Pollution,Routine swimming}, - file = {/Users/nicholascarey/Documents/Zotero/storage/A666FYWW/S0048969723060503.html} + file = {/Users/nicholascarey/Documents/Zotero/storage/Y5KMZ5ZY/Hawke et al. - 2024 - Exposure to petroleum-derived and biopolymer micro.pdf;/Users/nicholascarey/Documents/Zotero/storage/A666FYWW/S0048969723060503.html} } @phdthesis{hawkePetroleumderivedBiopolymerMicroplastic2022, @@ -382,11 +426,11 @@ @article{holmes-hackerdNaupliarExposureAcute2023a volume = {18}, number = {4}, pages = {e0282380}, - publisher = {{Public Library of Science}}, + publisher = {Public Library of Science}, issn = {1932-6203}, doi = {10.1371/journal.pone.0282380}, urldate = {2023-04-23}, - abstract = {Short-term, acute warming events are increasing in frequency across the world's oceans. For short-lived species like most copepods, these extreme events can occur over both within- and between-generational time scales. Yet, it is unclear whether exposure to acute warming during early life stages of copepods can cause lingering effects on metabolism through development, even after the event has ended. These lingering effects would reduce the amount of energy devoted to growth and affect copepod population dynamics. We exposed nauplii of an ecologically important coastal species, Acartia tonsa, to a 24-hour warming event (control: 18\textdegree C; treatment: 28\textdegree C), and then tracked individual respiration rate, body length, and stage duration through development. As expected, we observed a decrease in mass-specific respiration rates as individuals developed. However, exposure to acute warming had no effect on the ontogenetic patterns in per-capita or mass-specific respiration rates, body length, or development time. The lack of these carryover effects through ontogeny suggests within-generational resilience to acute warming in this copepod species.}, + abstract = {Short-term, acute warming events are increasing in frequency across the world's oceans. For short-lived species like most copepods, these extreme events can occur over both within- and between-generational time scales. Yet, it is unclear whether exposure to acute warming during early life stages of copepods can cause lingering effects on metabolism through development, even after the event has ended. These lingering effects would reduce the amount of energy devoted to growth and affect copepod population dynamics. We exposed nauplii of an ecologically important coastal species, Acartia tonsa, to a 24-hour warming event (control: 18{$^\circ$}C; treatment: 28{$^\circ$}C), and then tracked individual respiration rate, body length, and stage duration through development. As expected, we observed a decrease in mass-specific respiration rates as individuals developed. However, exposure to acute warming had no effect on the ontogenetic patterns in per-capita or mass-specific respiration rates, body length, or development time. The lack of these carryover effects through ontogeny suggests within-generational resilience to acute warming in this copepod species.}, langid = {english}, keywords = {Copepods,Heat shock response,Morphogenesis,Ocean temperature,Oxygen,Physiological parameters,Protein metabolism,Respiration}, file = {/Users/nicholascarey/Documents/Zotero/storage/ALDR8EWP/Holmes-Hackerd et al. - 2023 - Naupliar exposure to acute warming does not affect.pdf} @@ -396,26 +440,48 @@ @mastersthesis{internicolaMicroplasticsDelawareBay2020 title = {Microplastics in the {{Delaware Bay}}: {{Distribution}} and Direct Effects on Major Zooplankton}, author = {Internicola, Anna M}, year = {2020}, - address = {{Delaware, USA}}, + address = {Delaware, USA}, langid = {english}, school = {University of Delaware}, file = {/Users/nicholascarey/Documents/Zotero/storage/W7EREKRE/Internicola_udel_0060M_14348.pdf} } +@mastersthesis{jonesThermalPhysiologyYellowbelly2021, + title = {The Thermal Physiology of Yellowbelly Flounder ({{{\emph{Rhombosolea}}}}{\emph{ Leporina}}) in a Coastal, {{New Zealand}} Lake}, + author = {Jones, Lewis}, + year = {2021}, + address = {Christchurch, New Zealand}, + langid = {english}, + school = {University of Canterbury}, + file = {/Users/nicholascarey/Documents/Zotero/storage/EUHH8KSR/Jones, Lewis_final Master's Thesis.pdf} +} + @article{jourdain-bonneauMetabolicTranscriptomicResponse2023, title = {Metabolic and Transcriptomic Response of Two Juvenile Anadromous Brook Charr ({{Salvelinus}} Fontinalis) Genetic Lines towards a Chronic Thermal Stress}, author = {{Jourdain-Bonneau}, Christophe and Deslauriers, David and Gourtay, Cl{\'e}mence and Jeffries, Kenneth M. and Audet, C.}, year = {2023}, month = jun, journal = {Canadian Journal of Zoology}, - publisher = {{NRC Research Press}}, + publisher = {NRC Research Press}, issn = {0008-4301}, doi = {10.1139/cjz-2023-0049}, urldate = {2023-07-29}, - abstract = {Many salmonid species are particularly susceptible to chronic and acute temperature changes caused by global warming. We aimed to study the differences in metabolic and transcriptomic responses of a chronic heat stress on a control and selected (absence of early sexual maturation and growth) line of brook charr Salvelinus fontinalis (Mitchill, 1814). We exposed individuals to different temperatures for 35\,days (15, 17, and 19\,\textdegree C). High temperature reduced the growth rate (in length) and the Fulton condition factor. Both maximal metabolic rate and the aerobic scope were higher in fish reared at 17\,\textdegree C, while they decreased in fish maintained at 19\,\textdegree C. The relative gene expression of cytochrome c oxidase was lower at 19\,\textdegree C than at 15\,\textdegree C. The relative gene expressions of both liver and gill hsp90 was higher at the highest temperature. The standard metabolic rate, while not affected by temperature, was higher for the control line over the selected line. Only in the control line, the relative expression of catalase and of receptor of insulin-like growth factor-1 increased at 19\,\textdegree C. Our results showed that the selected line was able to cope more effectively with the oxidative stress caused by the rise in temperature.}, + abstract = {Many salmonid species are particularly susceptible to chronic and acute temperature changes caused by global warming. We aimed to study the differences in metabolic and transcriptomic responses of a chronic heat stress on a control and selected (absence of early sexual maturation and growth) line of brook charr Salvelinus fontinalis (Mitchill, 1814). We exposed individuals to different temperatures for 35\,days (15, 17, and 19\,{$^\circ$}C). High temperature reduced the growth rate (in length) and the Fulton condition factor. Both maximal metabolic rate and the aerobic scope were higher in fish reared at 17\,{$^\circ$}C, while they decreased in fish maintained at 19\,{$^\circ$}C. The relative gene expression of cytochrome c oxidase was lower at 19\,{$^\circ$}C than at 15\,{$^\circ$}C. The relative gene expressions of both liver and gill hsp90 was higher at the highest temperature. The standard metabolic rate, while not affected by temperature, was higher for the control line over the selected line. Only in the control line, the relative expression of catalase and of receptor of insulin-like growth factor-1 increased at 19\,{$^\circ$}C. Our results showed that the selected line was able to cope more effectively with the oxidative stress caused by the rise in temperature.}, file = {/Users/nicholascarey/Documents/Zotero/storage/63C6V7E9/Jourdain-Bonneau et al. - 2023 - Metabolic and transcriptomic response of two juven.pdf} } +@mastersthesis{jourdainbonneauEffetStressThermique2022, + title = {{Effet d'un stress thermique chronique et de la s{\'e}lection g{\'e}n{\'e}tique sur la r{\'e}ponse m{\'e}tabolique et transcriptomique d'ombles de fontaine juv{\'e}niles (Salvelinus fontinalis)}}, + author = {Jourdain Bonneau, Christophe}, + year = {2022}, + month = jun, + address = {Rimouski}, + urldate = {2024-03-29}, + langid = {french}, + school = {Universit{\'e} du Qu{\'e}bec {\`a} Rimouski}, + file = {/Users/nicholascarey/Documents/Zotero/storage/RL25TNNH/Jourdain Bonneau - 2022 - Effet d'un stress thermique chronique et de la sél.pdf;/Users/nicholascarey/Documents/Zotero/storage/2H6RFC2A/2105.html} +} + @article{joyceRegulationHeartRate2022, title = {The Regulation of Heart Rate Following Genetic Deletion of the SS1 Adrenergic Receptor in Larval Zebrafis}, author = {Joyce, William and Pan, Yihang K and Garvey, Kayla and Saxena, Vishal and Perry, Steve F}, @@ -427,12 +493,28 @@ @article{joyceRegulationHeartRate2022 issn = {1748-1716}, doi = {10.1111/apha.13849}, urldate = {2022-06-08}, - abstract = {Aim Although zebrafish are gaining popularity as biomedical models of cardiovascular disease, our understanding of their cardiac control mechanisms is fragmentary. Our goal was to clarify the controversial role of the \ss 1-adrenergic receptor (AR) in the regulation of heart rate in zebrafish. Methods CRISPR-Cas9 was used to delete the adrb1 gene in zebrafish allowing us to generate a stable adrb1-/- line. Larval heart rates were measured during pharmacological protocols and with exposure to hypercapnia. Expression of the five zebrafish adrb genes were measured in larval zebrafish hearts using qPCR. Results Compared to genetically matched wild-types (adrb1+/+), adrb1-/- larvae exhibited 20 beats min-1 lower heart rate, measured from 2 to 21 days post-fertilisation (dpf). Nevertheless, adrb1-/- larvae exhibited preserved positive chronotropic responses to pharmacological treatment with AR agonists (adrenaline, noradrenaline, isoproterenol), which were blocked by propranolol (general \ss -AR antagonist). Regardless of genotype, larvae exhibited similar increases in heart rate in response to hypercapnia (1\% CO2) at 5 dpf but the tachycardia was blunted in adrb1-/- larvae at 6 dpf. adrb1 gene expression was abolished in the hearts of adrb1-/- larvae, confirming successful knockout. While gene expression of adrb2a and adrb3a were unchanged, adrb2b and adrb3b mRNA levels increased in adrb1-/- larval hearts. Conclusion Despite adrb1 contributing to the setting of resting heart rate in larvae, it is not strictly essential for zebrafish, as we generated a viable and breeding adrb1-/- line. The chronotropic effects of adrenergic stimulation persist in adrb1-/- zebrafish, likely due to the upregulation of other \ss -AR subtypes.}, + abstract = {Aim Although zebrafish are gaining popularity as biomedical models of cardiovascular disease, our understanding of their cardiac control mechanisms is fragmentary. Our goal was to clarify the controversial role of the {\ss}1-adrenergic receptor (AR) in the regulation of heart rate in zebrafish. Methods CRISPR-Cas9 was used to delete the adrb1 gene in zebrafish allowing us to generate a stable adrb1-/- line. Larval heart rates were measured during pharmacological protocols and with exposure to hypercapnia. Expression of the five zebrafish adrb genes were measured in larval zebrafish hearts using qPCR. Results Compared to genetically matched wild-types (adrb1+/+), adrb1-/- larvae exhibited 20 beats min-1 lower heart rate, measured from 2 to 21 days post-fertilisation (dpf). Nevertheless, adrb1-/- larvae exhibited preserved positive chronotropic responses to pharmacological treatment with AR agonists (adrenaline, noradrenaline, isoproterenol), which were blocked by propranolol (general {\ss}-AR antagonist). Regardless of genotype, larvae exhibited similar increases in heart rate in response to hypercapnia (1\% CO2) at 5 dpf but the tachycardia was blunted in adrb1-/- larvae at 6 dpf. adrb1 gene expression was abolished in the hearts of adrb1-/- larvae, confirming successful knockout. While gene expression of adrb2a and adrb3a were unchanged, adrb2b and adrb3b mRNA levels increased in adrb1-/- larval hearts. Conclusion Despite adrb1 contributing to the setting of resting heart rate in larvae, it is not strictly essential for zebrafish, as we generated a viable and breeding adrb1-/- line. The chronotropic effects of adrenergic stimulation persist in adrb1-/- zebrafish, likely due to the upregulation of other {\ss}-AR subtypes.}, langid = {english}, keywords = {adrenaline,cardiac,catecholamine,GPCR,hypercapnia}, file = {/Users/nicholascarey/Documents/Zotero/storage/G2ZC8SYK/Joyce et al. - 2022 - The regulation of heart rate following genetic del.pdf;/Users/nicholascarey/Documents/Zotero/storage/ASNFFKZT/apha.html} } +@misc{kellyInvestigatingMetabolicOxidative2024, + type = {{{SSRN Scholarly Paper}}}, + title = {Investigating the {{Metabolic}} and {{Oxidative Stress Induced}} by {{Biofouled Microplastics Exposure}} in {{Seriola Lalandi}} ({{Yellowtail Kingfish}})}, + author = {Kelly, Eleanor Rachel May and Trujillo, Jos{\'e} E. and Setiawan, Alvin and Pether, Steve and Burritt, David and Allan, Bridie JM}, + year = {2024}, + month = mar, + number = {4758309}, + address = {Rochester, NY}, + doi = {10.2139/ssrn.4758309}, + urldate = {2024-03-29}, + abstract = {When plastic debris enters the ocean, it is quickly colonised by a community of microorganisms that form a biofilm on the surface of plastic unique to that of the surrounding seawater. When microplastics are accidentally consumed by marine organisms, any microbial community is also being consumed. While some of the microbial community may be associated with a regular food source for these organisms, others may pose a risk to fish, such as certain bacteria. Here, we investigate the physiological impacts of ingesting biofouled microplastics in juvenile kingfish (Seriola lalandi). Using intermittent-flow respirometry, it was found that fish exposed to biofouled microplastic had a wider aerobic scope compared to those exposed to clean plastics. Similarly, antioxidant enzyme activity (superoxide dismutase, catalase, and glutathione peroxidase) and lipid peroxidation levels in fish exposed to biofouled plastics were higher than the control, but still lower than those exposed to clean plastics.}, + langid = {english}, + keywords = {microplasticsoxidative stressrespirometry kingfish biofilm}, + file = {/Users/nicholascarey/Documents/Zotero/storage/TKVLLPMC/Kelly et al. - 2024 - Investigating the Metabolic and Oxidative Stress I.pdf} +} + @article{killenGuidelinesReportingMethods2021, title = {Guidelines for Reporting Methods to Estimate Metabolic Rates by Aquatic Intermittent-Flow Respirometry}, author = {Killen, Shaun S. and Christensen, Emil A. F. and Cortese, Daphne and Z{\'a}vorka, Libor and Norin, Tommy and Cotgrove, Lucy and Crespel, Am{\'e}lie and Munson, Amelia and Nati, Julie J. H. and Papatheodoulou, Magdalene and McKenzie, David J.}, @@ -445,7 +527,7 @@ @article{killenGuidelinesReportingMethods2021 issn = {0022-0949}, doi = {10.1242/jeb.242522}, urldate = {2023-05-10}, - abstract = {Interest in the measurement of metabolic rates is growing rapidly, because of the importance of metabolism in advancing our understanding of organismal physiology, behaviour, evolution and responses to environmental change. The study of metabolism in aquatic animals is undergoing an especially pronounced expansion, with more researchers utilising intermittent-flow respirometry as a research tool than ever before. Aquatic respirometry measures the rate of oxygen uptake as a proxy for metabolic rate, and the intermittent-flow technique has numerous strengths for use with aquatic animals, allowing metabolic rate to be repeatedly estimated on individual animals over several hours or days and during exposure to various conditions or stimuli. There are, however, no published guidelines for the reporting of methodological details when using this method. Here, we provide the first guidelines for reporting intermittent-flow respirometry methods, in the form of a checklist of criteria that we consider to be the minimum required for the interpretation, evaluation and replication of experiments using intermittent-flow respirometry. Furthermore, using a survey of the existing literature, we show that there has been incomplete and inconsistent reporting of methods for intermittent-flow respirometry over the past few decades. Use of the provided checklist of required criteria by researchers when publishing their work should increase consistency of the reporting of methods for studies that use intermittent-flow respirometry. With the steep increase in studies using intermittent-flow respirometry, now is the ideal time to standardise reporting of methods, so that \textendash{} in the future \textendash{} data can be properly assessed by other scientists and conservationists.}, + abstract = {Interest in the measurement of metabolic rates is growing rapidly, because of the importance of metabolism in advancing our understanding of organismal physiology, behaviour, evolution and responses to environmental change. The study of metabolism in aquatic animals is undergoing an especially pronounced expansion, with more researchers utilising intermittent-flow respirometry as a research tool than ever before. Aquatic respirometry measures the rate of oxygen uptake as a proxy for metabolic rate, and the intermittent-flow technique has numerous strengths for use with aquatic animals, allowing metabolic rate to be repeatedly estimated on individual animals over several hours or days and during exposure to various conditions or stimuli. There are, however, no published guidelines for the reporting of methodological details when using this method. Here, we provide the first guidelines for reporting intermittent-flow respirometry methods, in the form of a checklist of criteria that we consider to be the minimum required for the interpretation, evaluation and replication of experiments using intermittent-flow respirometry. Furthermore, using a survey of the existing literature, we show that there has been incomplete and inconsistent reporting of methods for intermittent-flow respirometry over the past few decades. Use of the provided checklist of required criteria by researchers when publishing their work should increase consistency of the reporting of methods for studies that use intermittent-flow respirometry. With the steep increase in studies using intermittent-flow respirometry, now is the ideal time to standardise reporting of methods, so that -- in the future -- data can be properly assessed by other scientists and conservationists.}, file = {/Users/nicholascarey/Documents/Zotero/storage/PHRUQRVQ/Killen et al. - 2021 - Guidelines for reporting methods to estimate metab.pdf;/Users/nicholascarey/Documents/Zotero/storage/HI5M56CT/Guidelines-for-reporting-methods-to-estimate.html} } @@ -455,7 +537,7 @@ @article{klementievDevelopmentVersatileLowCost2022 year = {2022}, journal = {Applied and Environmental Microbiology}, pages = {e00434-22}, - publisher = {{American Society for Microbiology}}, + publisher = {American Society for Microbiology}, doi = {10.1128/aem.00434-22}, urldate = {2022-06-29}, file = {/Users/nicholascarey/Documents/Zotero/storage/ZZ45NWN6/Klementiev and Whiteley - Development of a Versatile, Low-Cost Electrochemic.pdf} @@ -547,7 +629,7 @@ @mastersthesis{lowesImpactsCombinedNatural2023 title = {Impacts of {{Combined Natural}} and {{Anthropogenic Stressors}} on {{Pacific Intertidal Invertebrates}}}, author = {Lowes, Hannah M.}, year = {2023}, - address = {{Edmonton}}, + address = {Edmonton}, doi = {10.7939/r3-vhcd-6f09}, urldate = {2023-06-28}, abstract = {The intertidal zone provides extensive habitat around the world for countless species, but there are many challenges associated with life...}, @@ -565,7 +647,7 @@ @article{luceyClimateWarmingErodes2023 volume = {2}, number = {3}, pages = {e0000095}, - publisher = {{Public Library of Science}}, + publisher = {Public Library of Science}, issn = {2767-3200}, doi = {10.1371/journal.pclm.0000095}, urldate = {2023-03-04}, @@ -611,7 +693,7 @@ @phdthesis{marquezborrasEffectsOceanChange2023 title = {The Effects of Ocean Change Drivers on the Ecophysiology of the Mottled Brittle Star {{{\emph{Ophionereis}}}}{\emph{ Fasciata}}}, author = {M{\'a}rquez Borr{\'a}s, Francisco}, year = {2023}, - address = {{New Zealand}}, + address = {New Zealand}, urldate = {2023-07-29}, copyright = {Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated.}, school = {University of Auckland}, @@ -619,6 +701,21 @@ @phdthesis{marquezborrasEffectsOceanChange2023 file = {/Users/nicholascarey/Documents/Zotero/storage/WW8FVPAZ/Márquez Borrás - 2023 - The effects of ocean change drivers on the ecophys.pdf} } +@article{maskreyDifferentialMetabolicResponses2024, + title = {Differential Metabolic Responses in Bold and Shy Sea Anemones during a Simulated Heatwave}, + author = {Maskrey, Daniel K. and Killen, Shaun S. and Sneddon, Lynne U. and Arnold, Kathryn E. and Wolfenden, David C. C. and Thomson, Jack S.}, + year = {2024}, + month = jan, + journal = {Journal of Experimental Biology}, + pages = {jeb.244662}, + issn = {0022-0949, 1477-9145}, + doi = {10.1242/jeb.244662}, + urldate = {2024-01-24}, + abstract = {Statement Plastic changes in metabolic rates are associated with boldness in beadlet anemones, such that different personalities show opposite metabolic patterns under a simulated heatwave, as compared to a non-stressful temperature.}, + langid = {english}, + file = {/Users/nicholascarey/Documents/Zotero/storage/DCW6UKM5/jeb244662-2.pdf} +} + @article{morganReducedPhysiologicalPlasticity2022, title = {Reduced Physiological Plasticity in a Fish Adapted to Stable Temperatures}, author = {Morgan, Rachael and Andreassen, Anna H. and {\AA}sheim, Eirik R. and Finn{\o}en, Mette H. and Dresler, Gunnar and Brembu, Tore and Loh, Adrian and Miest, Joanna J. and Jutfelt, Fredrik}, @@ -631,11 +728,23 @@ @article{morganReducedPhysiologicalPlasticity2022 issn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.2201919119}, urldate = {2022-05-29}, - abstract = {Significance Plastic individuals can buffer environmental changes, maintaining a stable performance across gradients. Plasticity is therefore thought to be particularly beneficial for the survival of wild populations that experience large environmental fluctuations, such as diel and seasonal temperature changes. Maintaining plasticity is widely assumed to be costly; however, empirical evidence demonstrating this cost is scarce. Here, we predict that if plasticity is costly, it would be readily lost in a stable environment, such as a laboratory. To test this, we measured a diverse range of phenotypic traits, spanning gene expression, physiology, and behavior, in wild and laboratory zebrafish acclimated to 15 temperatures. We show that laboratory fish have lost plasticity in many traits, demonstrating that maintaining plasticity carries a cost. , Plasticity can allow organisms to maintain consistent performance across a wide range of environmental conditions. However, it remains largely unknown how costly plasticity is and whether a trade-off exists between plasticity and performance under optimal conditions. Biological rates generally increase with temperature, and to counter that effect, fish use physiological plasticity to adjust their biochemical and physiological functions. Zebrafish in the wild encounter large daily and seasonal temperature fluctuations, suggesting they should display high physiological plasticity. Conversely, laboratory zebrafish have been at optimal temperatures with low thermal fluctuations for over 150 generations. We treated this domestication as an evolution experiment and asked whether this has reduced the physiological plasticity of laboratory fish compared to their wild counterparts. We measured a diverse range of phenotypic traits, from gene expression through physiology to behavior, in wild and laboratory zebrafish acclimated to 15 temperatures from 10\,\textdegree C to 38\,\textdegree C. We show that adaptation to the laboratory environment has had major effects on all levels of biology. Laboratory fish show reduced plasticity and are thus less able to counter the direct effects of temperature on key traits like metabolic rates and thermal tolerance, and this difference is detectable down to gene expression level. Rapid selection for faster growth in stable laboratory environments appears to have carried with it a trade-off against physiological plasticity in captive zebrafish compared with their wild counterparts.}, + abstract = {Significance Plastic individuals can buffer environmental changes, maintaining a stable performance across gradients. Plasticity is therefore thought to be particularly beneficial for the survival of wild populations that experience large environmental fluctuations, such as diel and seasonal temperature changes. Maintaining plasticity is widely assumed to be costly; however, empirical evidence demonstrating this cost is scarce. Here, we predict that if plasticity is costly, it would be readily lost in a stable environment, such as a laboratory. To test this, we measured a diverse range of phenotypic traits, spanning gene expression, physiology, and behavior, in wild and laboratory zebrafish acclimated to 15 temperatures. We show that laboratory fish have lost plasticity in many traits, demonstrating that maintaining plasticity carries a cost. , Plasticity can allow organisms to maintain consistent performance across a wide range of environmental conditions. However, it remains largely unknown how costly plasticity is and whether a trade-off exists between plasticity and performance under optimal conditions. Biological rates generally increase with temperature, and to counter that effect, fish use physiological plasticity to adjust their biochemical and physiological functions. Zebrafish in the wild encounter large daily and seasonal temperature fluctuations, suggesting they should display high physiological plasticity. Conversely, laboratory zebrafish have been at optimal temperatures with low thermal fluctuations for over 150 generations. We treated this domestication as an evolution experiment and asked whether this has reduced the physiological plasticity of laboratory fish compared to their wild counterparts. We measured a diverse range of phenotypic traits, from gene expression through physiology to behavior, in wild and laboratory zebrafish acclimated to 15 temperatures from 10\,{$^\circ$}C to 38\,{$^\circ$}C. We show that adaptation to the laboratory environment has had major effects on all levels of biology. Laboratory fish show reduced plasticity and are thus less able to counter the direct effects of temperature on key traits like metabolic rates and thermal tolerance, and this difference is detectable down to gene expression level. Rapid selection for faster growth in stable laboratory environments appears to have carried with it a trade-off against physiological plasticity in captive zebrafish compared with their wild counterparts.}, langid = {english}, file = {/Users/nicholascarey/Documents/Zotero/storage/Z3PGLRNU/Morgan et al. - 2022 - Reduced physiological plasticity in a fish adapted.pdf} } +@phdthesis{mullerEcophysiologicalInvestigationFisheriesinduced2021, + title = {An Eco-Physiological Investigation of Fisheries-Induced Evolution: Comparing the Resilience of Larvae from Exploited and Unexploited Commercial Reef Fish Populations to Projected Ocean Acidification}, + shorttitle = {An Eco-Physiological Investigation of Fisheries-Induced Evolution}, + author = {Muller, Cuen}, + year = {2021}, + address = {Makhanda, South Africa}, + urldate = {2024-03-29}, + langid = {english}, + school = {Rhodes University}, + file = {/Users/nicholascarey/Documents/Zotero/storage/WVFN3DKQ/Muller - 2021 - An eco-physiological investigation of fisheries-in.pdf} +} + @article{mullerEffectsExperimentalOcean2020, title = {Effects of Experimental Ocean Acidification on the Larval Morphology and Metabolism of a Temperate Sparid, {{{\emph{Chrysoblephus}}}}{\emph{ Laticeps}}}, author = {Muller, Cuen and Childs, Amber-Robyn and James, Nicola C. and Potts, Warren M.}, @@ -648,7 +757,7 @@ @article{mullerEffectsExperimentalOcean2020 issn = {2673-1924}, doi = {10.3390/oceans2010002}, urldate = {2021-06-14}, - abstract = {Ocean acidification is predicted to have widespread impacts on marine species. The early life stages of fishes, being particularly sensitive to environmental deviations, represent a critical bottleneck to recruitment. We investigated the effects of ocean acidification ({$\increment$}pH = -0.4) on the oxygen consumption and morphometry during the early ontogeny of a commercially important seabream, Chrysoblephus laticeps, up until flexion. Hatchlings appeared to be tolerant to hypercapnic conditions, exhibiting no difference in oxygen consumption or morphometry between treatments, although the yolk reserves were marginally reduced in the low-pH treatment. The preflexion stages appeared to undergo metabolic depression, exhibiting lower metabolic rates along with lower growth metrics in hypercapnic conditions. However, although the sample sizes were low, the flexion-stage larvae exhibited greater rates of metabolic and growth metric increases in hypercapnic conditions. This study shows that the effects of OA may be stage specific during early ontogeny and potentially related to the development of crucial organs, such as the gills. Future studies investigating the effects of climate change on fish larvae should endeavour to include multiple developmental stages in order to make more accurate predictions on recruitment dynamics for the coming decades.}, + abstract = {Ocean acidification is predicted to have widespread impacts on marine species. The early life stages of fishes, being particularly sensitive to environmental deviations, represent a critical bottleneck to recruitment. We investigated the effects of ocean acidification (∆pH = -0.4) on the oxygen consumption and morphometry during the early ontogeny of a commercially important seabream, Chrysoblephus laticeps, up until flexion. Hatchlings appeared to be tolerant to hypercapnic conditions, exhibiting no difference in oxygen consumption or morphometry between treatments, although the yolk reserves were marginally reduced in the low-pH treatment. The preflexion stages appeared to undergo metabolic depression, exhibiting lower metabolic rates along with lower growth metrics in hypercapnic conditions. However, although the sample sizes were low, the flexion-stage larvae exhibited greater rates of metabolic and growth metric increases in hypercapnic conditions. This study shows that the effects of OA may be stage specific during early ontogeny and potentially related to the development of crucial organs, such as the gills. Future studies investigating the effects of climate change on fish larvae should endeavour to include multiple developmental stages in order to make more accurate predictions on recruitment dynamics for the coming decades.}, langid = {english}, file = {/Users/nicholascarey/Documents/Zotero/storage/HI7JWYAX/Muller et al. - 2020 - Effects of Experimental Ocean Acidification on the.pdf} } @@ -663,7 +772,7 @@ @article{negreteMethodologicalEvaluationDetermination2019a issn = {2046-6390}, doi = {10.1242/bio.045310}, urldate = {2021-06-14}, - abstract = {One measure of hypoxia tolerance is the critical oxygen threshold, Pcrit, which is the point where standard metabolism can no longer be maintained through aerobic processes. Traditionally, Pcrit was determined using closed respirometry, whereby the fish's respiration naturally lowered O2. More recently, intermittent flow techniques have been adopted, where N2 is used to displace O2, which ostensibly reduces end-product build-up. This study used a paired design on the marine teleost, red drum. Pcrit is comparable between closed (4.6{$\pm$} 0.2 kPa; mean{$\pm$}s.e.m.) and intermittent flow (4.4{$\pm$}0.2 kPa; mean{$\pm$} s.e.m.) respirometry. pCO2, ammonia and pH changes within the chamber were measured prior to the onset of Pcrit and at the end of a typical Pcrit trial and revealed changes in water chemistry in both closed and intermittent flow. Pcrit values were similar in both methods of hypoxia induction regardless of subsequent water chemistry changes that occurred in both methods.}, + abstract = {One measure of hypoxia tolerance is the critical oxygen threshold, Pcrit, which is the point where standard metabolism can no longer be maintained through aerobic processes. Traditionally, Pcrit was determined using closed respirometry, whereby the fish's respiration naturally lowered O2. More recently, intermittent flow techniques have been adopted, where N2 is used to displace O2, which ostensibly reduces end-product build-up. This study used a paired design on the marine teleost, red drum. Pcrit is comparable between closed (4.6{\textpm} 0.2 kPa; mean{\textpm}s.e.m.) and intermittent flow (4.4{\textpm}0.2 kPa; mean{\textpm} s.e.m.) respirometry. pCO2, ammonia and pH changes within the chamber were measured prior to the onset of Pcrit and at the end of a typical Pcrit trial and revealed changes in water chemistry in both closed and intermittent flow. Pcrit values were similar in both methods of hypoxia induction regardless of subsequent water chemistry changes that occurred in both methods.}, langid = {english}, file = {/Users/nicholascarey/Documents/Zotero/storage/QGAX574Z/Negrete and Esbaugh - 2019 - A methodological evaluation of the determination o.pdf} } @@ -676,7 +785,7 @@ @article{paulaAccessCleaningServices2022 volume = {13}, issn = {1664-042X}, urldate = {2022-06-09}, - abstract = {Cleaning symbioses are key mutualistic interactions where cleaners remove ectoparasites and tissues from client fishes. Such interactions elicit beneficial effects on clients' ecophysiology, with cascading effects on fish diversity and abundance. Ocean acidification (OA), resulting from increasing CO2 concentrations, can affect the behavior of cleaner fishes making them less motivated to inspect their clients. This is especially important as gnathiid fish ectoparasites are tolerant to ocean acidification. Here, we investigated how access to cleaning services, performed by the cleaner wrasse Labroides dimidiatus, affect individual client's (damselfish, Pomacentrus amboinensis) aerobic metabolism in response to both experimental parasite infection and OA. Access to cleaning services was modulated using a long-term removal experiment where cleaner wrasses were consistently removed from patch reefs around Lizard Island (Australia) for 17~years or left undisturbed. Only damselfish with access to cleaning stations had a negative metabolic response to parasite infection (maximum metabolic rate\textemdash\.MO2Max; and both factorial and absolute aerobic scope). Moreover, after an acclimation period of 10~days to high CO2 ({$\sim$}1,000~\textmu atm CO2), the fish showed a decrease in factorial aerobic scope, being the lowest in fish without the access to cleaners. We propose that stronger positive selection for parasite tolerance might be present in reef fishes without the access to cleaners, but this might come at a cost, as readiness to deal with parasites can impact their response to other stressors, such as OA.}, + abstract = {Cleaning symbioses are key mutualistic interactions where cleaners remove ectoparasites and tissues from client fishes. Such interactions elicit beneficial effects on clients' ecophysiology, with cascading effects on fish diversity and abundance. Ocean acidification (OA), resulting from increasing CO2 concentrations, can affect the behavior of cleaner fishes making them less motivated to inspect their clients. This is especially important as gnathiid fish ectoparasites are tolerant to ocean acidification. Here, we investigated how access to cleaning services, performed by the cleaner wrasse Labroides dimidiatus, affect individual client's (damselfish, Pomacentrus amboinensis) aerobic metabolism in response to both experimental parasite infection and OA. Access to cleaning services was modulated using a long-term removal experiment where cleaner wrasses were consistently removed from patch reefs around Lizard Island (Australia) for 17~years or left undisturbed. Only damselfish with access to cleaning stations had a negative metabolic response to parasite infection (maximum metabolic rate---{\.M}O2Max; and both factorial and absolute aerobic scope). Moreover, after an acclimation period of 10~days to high CO2 ({$\sim$}1,000~{\textmu}atm CO2), the fish showed a decrease in factorial aerobic scope, being the lowest in fish without the access to cleaners. We propose that stronger positive selection for parasite tolerance might be present in reef fishes without the access to cleaners, but this might come at a cost, as readiness to deal with parasites can impact their response to other stressors, such as OA.}, file = {/Users/nicholascarey/Documents/Zotero/storage/TLL35WV7/Paula et al. - 2022 - Access to Cleaning Services Alters Fish Physiology.pdf} } @@ -684,7 +793,7 @@ @mastersthesis{perryMicroclimatesHoldfastsBull2023 title = {Microclimates in the Holdfasts of Bull Kelp ({{Durvillaea}} Spp.) and the Thermal Physiology of the Associated Invertebrates}, author = {Perry, Frances}, year = {2023}, - address = {{Otago, New Zealand}}, + address = {Otago, New Zealand}, urldate = {2023-06-06}, langid = {english}, school = {University of Otago}, @@ -696,24 +805,28 @@ @mastersthesis{petreikyteEfficiencyNileTilapia2021 title = {{Efficiency of Nile tilapia (Oreochromis niloticus) recirculating aquaculture technology under brackish water conditions}}, author = {Petreikyt{\.e}, Gerda}, year = {2021}, - address = {{Lithuania}}, - abstract = {There are many areas in the world where scarcity of freshwater are threatening the human population. So humans have to look for solutions to replace freshwater when use of it is not necessary. This also has an effect to aquaculture \textendash{} more and more farmers are farming freshwater fish in brackish water. Many authors have demonstrated the benefits of brackish water for fish growth and other physiological functions. Nile tilapia (Oreochromis niloticus) is valuable fish for its tolerance to high temperatures, salinity, low amount of dissolved oxygen. They are fairly easy to farm and the quality of the meat and the taste is good. But, despite all the qualities, farmers in Lithuania do not choose to farm these fish. The aim of this study was to evaluate the effect of brackish water on the efficiency of Nile tilapia aquaculture technology. To achieve the goal an experiment was conducted in the Laboratory of Fishery and Aquaculture of the Marine Research Institute of Klaipeda University on August 5 December 18, 2020. During it, three separate recirculating aquaculture systems were constructed from system B. One such system consisted of three tanks. Tank volume \textendash{} 2,83 m3. Total amount of biofilter filler \textendash{} 130 L, water inflow \textendash{} 36 L min-1. All tanks were equipped with the same bio and mechanical filters, oxygen diffusers, the room is heated by heaters. In the experiment water of three different salinities were used: fresh water (0\textperthousand ), water from the Baltic Sea (6\textperthousand ) and diluted sea water (3\textperthousand ). The remaining three basins are used as reserve tanks for storing and diluting seawater. Seawater is pumped to the laboratory from the shores of the Baltic Sea, and fresh water is obtained from a well. Nile tilapia were sorted and distributed into tanks. At the beginning of the study, the average fish weight was: 0\textperthousand{} \textendash{} 84,4 {$\pm$} 19,51 g, 3\textperthousand{} \textendash{} 81,28 {$\pm$} 22,31 g, 6\textperthousand{} \textendash{} 84,08 {$\pm$} 16.47 g, stocking density - 0\textperthousand{} \textendash{} 8,08 kg m-3, 3\textperthousand{} ir 6\textperthousand{} \textendash{} po 8,22 kg m 3. Fish were acclimatized for three weeks, their health and behavior were monitored. Water quality parameters were measured daily \textendash{} temperature (\textdegree C), dissolved oxygen content (\%), pH. Tests of water saples from each system were conducted to determine the amount of ammonium (NH4), nitrite (NO2) and nitrate (NO3) in the water. Dead fish were counted. During the experiment, approximately every three weeks, 30 fishes were randomly caught and measured from tank. Caught individuals were placed in plastic buckets filled with water. If present, juveniles were collected. Eggs and larvae were photographed, the amount was counted from the photo and fry was counted by transferring from one container to another. Counted juveniles were released into individual aquariums filled with water of appropriate salinity. Adult individuals were weighed, the total length (L) and the length to the caudal fin (l) were measured. During the last two measurements, the sex of the fish was determined according to the shape and size of the papilla and the urogenital organs. A toluidine blue solution diluted with distilled water was used for determination of gender. At the end of the experiment, the following were calculated: mean fish weight, specific growth rate (SGR), weight gain ({$\Delta$}w), feed conversion ratio (FCR), initial and final Fulton coefficients (Ki and Kf), final biomass, and survival. A respiration experiment was conducted using Nile tilapia juveniles to determine their metabolic rate (MO2). A PyroScience FireSting O2 optical oxygen meter was used for the respiration experiment. Experiment was conducted in two trials. First one: water of different salinity (0\textperthousand, 3\textperthousand, 6\textperthousand ) was added to each respirometry system, the water temperature was 22 \textdegree C. Juveniles from 0\textperthousand{} aquarium were placed in 0\textperthousand{} system, from 3\textperthousand{} to 3\textperthousand{} systems and from 6\textperthousand{} aquarium to 6\textperthousand{} system. Second trial: water of different salinity (0\textperthousand, 3\textperthousand, 6\textperthousand ) was added to each system, the water temperature was 23 \textdegree C., Juveniles from 0\textperthousand, 3\textperthousand{} and 6\textperthousand{} aquariums were placed in each system. Intermitted respirometry method were used: when the amount of oxygen dropped \textasciitilde{} 2 mg L-1 from the initial amount, the water was renewed \textendash{} the former water was poured out of the bottle and a new, well-oxygenated water was added. Fry in the bottles were not changed. After the experiment, the fry was weighed (g). A study of physico-chemical properties of fish meat was conducted. After the growth experiment, three females and three males were randomly transferred from each pool to the reservoirs of the system with water of appropriate salinity. A total of 54 tilapias were used in the study. Skinless fish fillets were used for the study, each piece was weighed. A total of 18 samples were taken, 6 from each system (3 females and 3 males). Due to the low weight of the female fillets, the samples were pooled \textendash{} one sample consisted of three fish using one half of their fillets. Samples were kept on ice until they reached the laboratory. The study of physico-chemical properties of meat was performed at the Veterinary Academy of the Lithuanian University of Health Sciences. The percentage of protein, fat, ash, dry matter, water binding and water content of the sample was determined and the pH was determined. In this study were found that water salinity had a statistically significant effect on dissolved oxygen content, pH, and nitrite content in water. Also, due failed adaptation of freshwater recirculating aquaculture system to the brackish water, the water quality deteriorated during the study, especially in the 6 \textperthousand{} system, which affected other results. Growth and feed conversion ratios did not differ statistically significantly under different salinity conditions. The worst survival was in the 6 \textperthousand{} system due to deteriorating water quality during the study, and the best in the 0 \textperthousand{} system. Gender had a statistically significant effect on fish weight, with the final weight of males being 54\% higher than females. Brackish water conditions did not significantly affect the spawning of Nile tilapia females, larval and fry amount. There were also no statistically significant differences in the measurement of pup metabolic rate. When assessing meat quality, there was a statistically significant difference in meat pH and water content between systems. Water content in fish meat also differed statistically significantly between the sexes.}, + address = {Lithuania}, + abstract = {There are many areas in the world where scarcity of freshwater are threatening the human population. So humans have to look for solutions to replace freshwater when use of it is not necessary. This also has an effect to aquaculture -- more and more farmers are farming freshwater fish in brackish water. Many authors have demonstrated the benefits of brackish water for fish growth and other physiological functions. Nile tilapia (Oreochromis niloticus) is valuable fish for its tolerance to high temperatures, salinity, low amount of dissolved oxygen. They are fairly easy to farm and the quality of the meat and the taste is good. But, despite all the qualities, farmers in Lithuania do not choose to farm these fish. The aim of this study was to evaluate the effect of brackish water on the efficiency of Nile tilapia aquaculture technology. To achieve the goal an experiment was conducted in the Laboratory of Fishery and Aquaculture of the Marine Research Institute of Klaipeda University on August 5 December 18, 2020. During it, three separate recirculating aquaculture systems were constructed from system B. One such system consisted of three tanks. Tank volume -- 2,83 m3. Total amount of biofilter filler -- 130 L, water inflow -- 36 L min-1. All tanks were equipped with the same bio and mechanical filters, oxygen diffusers, the room is heated by heaters. In the experiment water of three different salinities were used: fresh water (0‰), water from the Baltic Sea (6‰) and diluted sea water (3‰). The remaining three basins are used as reserve tanks for storing and diluting seawater. Seawater is pumped to the laboratory from the shores of the Baltic Sea, and fresh water is obtained from a well. Nile tilapia were sorted and distributed into tanks. At the beginning of the study, the average fish weight was: 0‰ -- 84,4 {\textpm} 19,51 g, 3‰ -- 81,28 {\textpm} 22,31 g, 6‰ -- 84,08 {\textpm} 16.47 g, stocking density - 0‰ -- 8,08 kg m-3, 3‰ ir 6‰ -- po 8,22 kg m 3. Fish were acclimatized for three weeks, their health and behavior were monitored. Water quality parameters were measured daily -- temperature ({$^\circ$}C), dissolved oxygen content (\%), pH. Tests of water saples from each system were conducted to determine the amount of ammonium (NH4), nitrite (NO2) and nitrate (NO3) in the water. Dead fish were counted. During the experiment, approximately every three weeks, 30 fishes were randomly caught and measured from tank. Caught individuals were placed in plastic buckets filled with water. If present, juveniles were collected. Eggs and larvae were photographed, the amount was counted from the photo and fry was counted by transferring from one container to another. Counted juveniles were released into individual aquariums filled with water of appropriate salinity. Adult individuals were weighed, the total length (L) and the length to the caudal fin (l) were measured. During the last two measurements, the sex of the fish was determined according to the shape and size of the papilla and the urogenital organs. A toluidine blue solution diluted with distilled water was used for determination of gender. At the end of the experiment, the following were calculated: mean fish weight, specific growth rate (SGR), weight gain ({$\Delta$}w), feed conversion ratio (FCR), initial and final Fulton coefficients (Ki and Kf), final biomass, and survival. A respiration experiment was conducted using Nile tilapia juveniles to determine their metabolic rate (MO2). A PyroScience FireSting O2 optical oxygen meter was used for the respiration experiment. Experiment was conducted in two trials. First one: water of different salinity (0‰, 3‰, 6‰) was added to each respirometry system, the water temperature was 22 {$^\circ$}C. Juveniles from 0‰ aquarium were placed in 0‰ system, from 3‰ to 3‰ systems and from 6‰ aquarium to 6‰ system. Second trial: water of different salinity (0‰, 3‰, 6‰) was added to each system, the water temperature was 23 {$^\circ$}C., Juveniles from 0‰, 3‰ and 6‰ aquariums were placed in each system. Intermitted respirometry method were used: when the amount of oxygen dropped {\textasciitilde} 2 mg L-1 from the initial amount, the water was renewed -- the former water was poured out of the bottle and a new, well-oxygenated water was added. Fry in the bottles were not changed. After the experiment, the fry was weighed (g). A study of physico-chemical properties of fish meat was conducted. After the growth experiment, three females and three males were randomly transferred from each pool to the reservoirs of the system with water of appropriate salinity. A total of 54 tilapias were used in the study. Skinless fish fillets were used for the study, each piece was weighed. A total of 18 samples were taken, 6 from each system (3 females and 3 males). Due to the low weight of the female fillets, the samples were pooled -- one sample consisted of three fish using one half of their fillets. Samples were kept on ice until they reached the laboratory. The study of physico-chemical properties of meat was performed at the Veterinary Academy of the Lithuanian University of Health Sciences. The percentage of protein, fat, ash, dry matter, water binding and water content of the sample was determined and the pH was determined. In this study were found that water salinity had a statistically significant effect on dissolved oxygen content, pH, and nitrite content in water. Also, due failed adaptation of freshwater recirculating aquaculture system to the brackish water, the water quality deteriorated during the study, especially in the 6 ‰ system, which affected other results. Growth and feed conversion ratios did not differ statistically significantly under different salinity conditions. The worst survival was in the 6 ‰ system due to deteriorating water quality during the study, and the best in the 0 ‰ system. Gender had a statistically significant effect on fish weight, with the final weight of males being 54\% higher than females. Brackish water conditions did not significantly affect the spawning of Nile tilapia females, larval and fry amount. There were also no statistically significant differences in the measurement of pup metabolic rate. When assessing meat quality, there was a statistically significant difference in meat pH and water content between systems. Water content in fish meat also differed statistically significantly between the sexes.}, langid = {lithuanian}, - school = {Klaip\.edos universitetas}, + school = {Klaip{\.e}dos universitetas}, file = {/Users/nicholascarey/Documents/Zotero/storage/AGE4FGFP/Tilapijų and Akvakultūros - KLAIPĖDOS UNIVERSITETAS JŪROS TYRIMŲ INSTITUTAS.pdf} } -@article{pettersenIntergenerationalPlasticityAligns2023, +@article{pettersenIntergenerationalPlasticityAligns2024, title = {Intergenerational Plasticity Aligns with Temperature-Dependent Selection on Offspring Metabolic Rates}, - author = {Pettersen, Amanda Kate and Metcalfe, Neil B. and Seebacher, Frank}, - year = {2023}, - month = jul, - publisher = {{EcoEvoRxiv}}, - urldate = {2023-10-11}, - abstract = {Metabolic rates are linked to key life history traits that are thought to set the pace of life and affect fitness, yet the role that parents may have in shaping the metabolism of their offspring to enhance survival remains unclear. Here, we investigated the effect of temperature (24 C or 30 C) and feeding frequency experienced by parent zebrafish (Danio rerio) on offspring phenotypes and early survival at different developmental temperatures (24 C or 30 C). We found that embryo size was larger, but survival lower, in offspring from the parental low food treatment. Parents exposed to the warmer temperature and lower food treatment also produced offspring with lower standard metabolic rates \textendash{} aligning with selection on embryo metabolic rates. Lower metabolic rates were correlated with reduced developmental and growth rates, suggesting selection for a slow pace of life. Our results show that intergenerational effects on offspring size and metabolic rate can be adaptive when parent and offspring temperatures are matched: the direction of selection on embryo size and metabolism aligned with intergenerational plasticity towards lower metabolism at higher temperatures, particularly in offspring from low condition parents. These findings highlight the importance of anticipatory parental effects, but only when parental and offspring environments match.}, - copyright = {No Creative Commons license}, - langid = {english}, - file = {/Users/nicholascarey/Documents/Zotero/storage/V29JND9B/Pettersen et al. - 2023 - Intergenerational plasticity aligns with temperatu.pdf} + author = {Pettersen, Amanda K. and Metcalfe, Neil B. and Seebacher, Frank}, + year = {2024}, + month = jan, + journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, + volume = {379}, + number = {1896}, + pages = {20220496}, + publisher = {Royal Society}, + doi = {10.1098/rstb.2022.0496}, + urldate = {2024-01-10}, + abstract = {Metabolic rates are linked to key life-history traits that are thought to set the pace of life and affect fitness, yet the role that parents may have in shaping the metabolism of their offspring to enhance survival remains unclear. Here, we investigated the effect of temperature (24{$^\circ$}C or 30{$^\circ$}C) and feeding frequency experienced by parent zebrafish (Danio rerio) on offspring phenotypes and early survival at different developmental temperatures (24{$^\circ$}C or 30{$^\circ$}C). We found that embryo size was larger, but survival lower, in offspring from the parental low food treatment. Parents exposed to the warmer temperature and lower food treatment also produced offspring with lower standard metabolic rates---aligning with selection on embryo metabolic rates. Lower metabolic rates were correlated with reduced developmental and growth rates, suggesting selection for a slow pace of life. Our results show that intergenerational phenotypic plasticity on offspring size and metabolic rate can be adaptive when parent and offspring temperatures are matched: the direction of selection on embryo size and metabolism aligned with intergenerational plasticity towards lower metabolism at higher temperatures, particularly in offspring from low-condition parents. These findings provide evidence for adaptive parental effects, but only when parental and offspring environments match. This article is part of the theme issue `The evolutionary significance of variation in metabolic rates'.}, + keywords = {development,energy,maternal effects,metabolism,parental investment,reproductive investment}, + file = {/Users/nicholascarey/Documents/Zotero/storage/L4EQC9M2/Pettersen et al. - 2024 - Intergenerational plasticity aligns with temperatu.pdf} } @article{pilletPhysiologicalPerformanceCommon2021, @@ -727,12 +840,24 @@ @article{pilletPhysiologicalPerformanceCommon2021 issn = {1532-0456}, doi = {10.1016/j.cbpc.2020.108954}, urldate = {2021-06-24}, - abstract = {In a natural ecosystem, fish are subjected to a multitude of variable environmental factors. It is important to analyze the impact of combined factors to obtain a realistic understanding of the mixed stress occurring in nature. In this study, the physiological performance of juvenile common carp (Cyprinus carpio) exposed for one week to an environmentally relevant metal mixture (4.8~{$\mu$}g/L of copper; 2.9~{$\mu$}g/L of cadmium and 206.8~{$\mu$}g/L of zinc) and to two temperatures (10~\textdegree C and 20~\textdegree C), were evaluated. After 1, 3 and 7~days, standard (SMR) and maximum metabolic rate (MMR) were measured and aerobic scope (AS) was calculated. In addition, hematocrit, muscle lactate, histology of the gills and metal accumulation in gills were measured. While SMR, MMR and AS were elevated at the higher temperature, the metal mixture did not have a strong effect on these parameters. At 20~\textdegree C, SMR transiently increased, but no significant changes were observed for MMR and AS. During metal exposure, hematocrit levels were elevated in the 20~\textdegree C group. The bioaccumulation of Cd in the gills reflected the increased metabolic rate at the higher temperature, with more accumulation at 20~\textdegree C than at 10~\textdegree C. Anaerobic metabolism was not increased, which corresponds with the lack of significant histopathological damage in the gill tissue. These results show that common carp handled these metal exposures well, although increased temperature led to higher Cd accumulation and necessitated increased hematocrit levels to maintain aerobic performance.}, + abstract = {In a natural ecosystem, fish are subjected to a multitude of variable environmental factors. It is important to analyze the impact of combined factors to obtain a realistic understanding of the mixed stress occurring in nature. In this study, the physiological performance of juvenile common carp (Cyprinus carpio) exposed for one week to an environmentally relevant metal mixture (4.8~{$\mu$}g/L of copper; 2.9~{$\mu$}g/L of cadmium and 206.8~{$\mu$}g/L of zinc) and to two temperatures (10~{$^\circ$}C and 20~{$^\circ$}C), were evaluated. After 1, 3 and 7~days, standard (SMR) and maximum metabolic rate (MMR) were measured and aerobic scope (AS) was calculated. In addition, hematocrit, muscle lactate, histology of the gills and metal accumulation in gills were measured. While SMR, MMR and AS were elevated at the higher temperature, the metal mixture did not have a strong effect on these parameters. At 20~{$^\circ$}C, SMR transiently increased, but no significant changes were observed for MMR and AS. During metal exposure, hematocrit levels were elevated in the 20~{$^\circ$}C group. The bioaccumulation of Cd in the gills reflected the increased metabolic rate at the higher temperature, with more accumulation at 20~{$^\circ$}C than at 10~{$^\circ$}C. Anaerobic metabolism was not increased, which corresponds with the lack of significant histopathological damage in the gill tissue. These results show that common carp handled these metal exposures well, although increased temperature led to higher Cd accumulation and necessitated increased hematocrit levels to maintain aerobic performance.}, langid = {english}, keywords = {Aerobic scope,Bioaccumulation,Gill histology,Metal,Mixture stress,Temperature}, file = {/Users/nicholascarey/Documents/Zotero/storage/LHXC3EEM/Pillet et al. - 2021 - Physiological performance of common carp (Cyprinus.pdf;/Users/nicholascarey/Documents/Zotero/storage/XWQZNWXI/S1532045620302544.html} } +@mastersthesis{plazaSublethalEffectsMethylmercury2023, + title = {Sublethal {{Effects}} of {{Methylmercury}} on the {{Physiology}} of a {{Small}}, {{Coastal Elasmobranch}}, {{Smooth Dogfish}} ({{{\emph{Mustelus}}}}{\emph{ Canis}})}, + author = {Plaza, Maria Auxiliadora Saband}, + year = {2023}, + address = {Newark, Delaware}, + urldate = {2023-11-23}, + langid = {english}, + school = {University of Delaware}, + annotation = {https://udspace.udel.edu/handle/19716/33461}, + file = {/Users/nicholascarey/Documents/Zotero/storage/G2RDEMNK/Sublethal Effects of Methylmercury on the Physiolo.pdf;/Users/nicholascarey/Documents/Zotero/storage/WKN8TYUI/1.html} +} + @article{prinzingAnalyticalMethodsMatter2021, title = {Analytical Methods Matter Too: {{Establishing}} a Framework for Estimating Maximum Metabolic Rate for Fishes}, author = {Prinzing, Tanya S and Zhang, Yangfan and Wegner, Nicholas C and Dulvy, Nicholas K}, @@ -753,10 +878,10 @@ @article{prokkolaGeneticCouplingLifehistory2022 volume = {289}, number = {1967}, pages = {20212500}, - publisher = {{Royal Society}}, + publisher = {Royal Society}, doi = {10.1098/rspb.2021.2500}, urldate = {2022-01-31}, - abstract = {A better understanding of the genetic and phenotypic architecture underlying life-history variation is a longstanding aim in biology. Theories suggest energy metabolism determines life-history variation by modulating resource acquisition and allocation trade-offs, but the genetic underpinnings of the relationship and its dependence on ecological conditions have rarely been demonstrated. The strong genetic determination of age-at-maturity by two unlinked genomic regions (vgll3 and six6) makes Atlantic salmon (Salmo salar) an ideal model to address these questions. Using more than 250 juveniles in common garden conditions, we quantified the covariation between metabolic phenotypes\textemdash standard and maximum metabolic rates (SMR and MMR), and aerobic scope (AS)\textemdash and the life-history genomic regions, and tested if food availability modulates the relationships. We found that the early maturation genotype in vgll3 was associated with higher MMR and consequently AS. Additionally, MMR exhibited physiological epistasis; it was decreased when late maturation genotypes co-occurred in both genomic regions. Contrary to our expectation, the life-history genotypes had no effects on SMR. Furthermore, food availability had no effect on the genetic covariation, suggesting a lack of genotype-by-environment interactions. Our results provide insights on the key organismal processes that link energy use at the juvenile stage to age-at-maturity, indicating potential mechanisms by which metabolism and life-history can coevolve.}, + abstract = {A better understanding of the genetic and phenotypic architecture underlying life-history variation is a longstanding aim in biology. Theories suggest energy metabolism determines life-history variation by modulating resource acquisition and allocation trade-offs, but the genetic underpinnings of the relationship and its dependence on ecological conditions have rarely been demonstrated. The strong genetic determination of age-at-maturity by two unlinked genomic regions (vgll3 and six6) makes Atlantic salmon (Salmo salar) an ideal model to address these questions. Using more than 250 juveniles in common garden conditions, we quantified the covariation between metabolic phenotypes---standard and maximum metabolic rates (SMR and MMR), and aerobic scope (AS)---and the life-history genomic regions, and tested if food availability modulates the relationships. We found that the early maturation genotype in vgll3 was associated with higher MMR and consequently AS. Additionally, MMR exhibited physiological epistasis; it was decreased when late maturation genotypes co-occurred in both genomic regions. Contrary to our expectation, the life-history genotypes had no effects on SMR. Furthermore, food availability had no effect on the genetic covariation, suggesting a lack of genotype-by-environment interactions. Our results provide insights on the key organismal processes that link energy use at the juvenile stage to age-at-maturity, indicating potential mechanisms by which metabolism and life-history can coevolve.}, keywords = {age-at-maturity,energetics,life-history evolution,metabolic rate}, file = {/Users/nicholascarey/Documents/Zotero/storage/WQT2AE8J/Prokkola et al. - 2022 - Genetic coupling of life-history and aerobic perfo.pdf} } @@ -789,10 +914,28 @@ @article{rochePathsGreaterConsensus2022 issn = {0022-0949}, doi = {10.1242/jeb.243559}, urldate = {2022-03-11}, - abstract = {In a recent editorial, the Editors-in-Chief of Journal of Experimental Biology argued that consensus building, data sharing, and better integration across disciplines are needed to address the urgent scientific challenges posed by climate change. We agree and expand on the importance of cross-disciplinary integration and transparency to improve consensus building and advance climate change research in experimental biology. We investigated reproducible research practices in experimental biology through a review of open data and analysis code associated with empirical studies on three debated paradigms and for unrelated studies published in leading journals in comparative physiology and behavioural ecology over the last 10\hspace{0.25em}years. Nineteen per cent of studies on the three paradigms had open data, and 3.2\% had open code. Similarly, 12.1\% of studies in the journals we examined had open data, and 3.1\% had open code. Previous research indicates that only 50\% of shared datasets are complete and re-usable, suggesting that fewer than 10\% of studies in experimental biology have usable open data. Encouragingly, our results indicate that reproducible research practices are increasing over time, with data sharing rates in some journals reaching 75\% in recent years. Rigorous empirical research in experimental biology is key to understanding the mechanisms by which climate change affects organisms, and ultimately promotes evidence-based conservation policy and practice. We argue that a greater adoption of open science practices, with a particular focus on FAIR (Findable, Accessible, Interoperable, Re-usable) data and code, represents a much-needed paradigm shift towards improved transparency, cross-disciplinary integration, and consensus building to maximize the contributions of experimental biologists in addressing the impacts of environmental change on living organisms.}, + abstract = {In a recent editorial, the Editors-in-Chief of Journal of Experimental Biology argued that consensus building, data sharing, and better integration across disciplines are needed to address the urgent scientific challenges posed by climate change. We agree and expand on the importance of cross-disciplinary integration and transparency to improve consensus building and advance climate change research in experimental biology. We investigated reproducible research practices in experimental biology through a review of open data and analysis code associated with empirical studies on three debated paradigms and for unrelated studies published in leading journals in comparative physiology and behavioural ecology over the last 10\>years. Nineteen per cent of studies on the three paradigms had open data, and 3.2\% had open code. Similarly, 12.1\% of studies in the journals we examined had open data, and 3.1\% had open code. Previous research indicates that only 50\% of shared datasets are complete and re-usable, suggesting that fewer than 10\% of studies in experimental biology have usable open data. Encouragingly, our results indicate that reproducible research practices are increasing over time, with data sharing rates in some journals reaching 75\% in recent years. Rigorous empirical research in experimental biology is key to understanding the mechanisms by which climate change affects organisms, and ultimately promotes evidence-based conservation policy and practice. We argue that a greater adoption of open science practices, with a particular focus on FAIR (Findable, Accessible, Interoperable, Re-usable) data and code, represents a much-needed paradigm shift towards improved transparency, cross-disciplinary integration, and consensus building to maximize the contributions of experimental biologists in addressing the impacts of environmental change on living organisms.}, file = {/Users/nicholascarey/Documents/Zotero/storage/KDKEB6YT/Roche et al. - 2022 - Paths towards greater consensus building in experi.pdf;/Users/nicholascarey/Documents/Zotero/storage/W9QEM8BQ/Paths-towards-greater-consensus-building-in.html} } +@article{rocknerOctopusCrawlingLand2024, + title = {Octopus Crawling on Land: Physiological and Biochemical Responses of {{Octopus}} Vulgaris to Emersion}, + shorttitle = {Octopus Crawling on Land}, + author = {R{\"o}ckner, Janina Leonie and Lopes, Vanessa M. and Paula, Jos{\'e} Ricardo and Pegado, Maria Rita and Seco, Martim Costa and Diniz, M{\'a}rio and Repolho, Tiago and Rosa, Rui}, + year = {2024}, + journal = {Marine Biology}, + volume = {171}, + number = {1}, + pages = {14}, + issn = {1432-1793}, + doi = {10.1007/s00227-023-04333-x}, + urldate = {2023-11-23}, + abstract = {Cephalopods are well known for their cognitive capabilities and unique behavioural repertoires. Yet, certain life strategies and behaviours are still not fully understood. For instance, coastal octopuses have been documented (mainly through citizen science and TV documentaries) to occasionally leave the water and crawl in intertidal areas. Yet, there is a complete lack of knowledge on this behaviour's physiological and biochemical basis. Within this context, this study aimed to investigate, for the first time, physiological (routine and maximum metabolic rates and aerobic scope) and biochemical (i.e., antioxidant enzymes activities, heat shock protein and ubiquitin levels, DNA damage, lipid peroxidation) responses of the common octopus, Octopus vulgaris, to emersion. The octopuses' physiological performance was determined by measuring metabolic rates in different emersion treatments and biochemical markers. The size-adjusted maximum metabolic rates (MMRadj) of octopuses exposed to 2:30 min of air exposure followed by re-immersion did not differ significantly from the MMRadj of the chased individuals (control group). Yet, most biochemical markers revealed no significant differences among the different emersion treatments. Our findings showed that O. vulgaris could tolerate exposure to short-term emersion periods due to an efficient antioxidant machinery and cellular repair mechanisms. Alongside, we argue that the use of atmospheric air through the mucus-covered gills and/or cutaneous respiration may also help octopus withstand emersion and crawling on land.}, + langid = {english}, + keywords = {Air exposure,Metabolism,Octopus vulgaris,Oxidative stress,Tidepools}, + file = {/Users/nicholascarey/Documents/Zotero/storage/U5RY6RQ2/Röckner et al. - 2023 - Octopus crawling on land physiological and bioche.pdf} +} + @article{rodgersDoubleWhammyNitrate2021, title = {Double Whammy: {{Nitrate}} Pollution Heightens Susceptibility to Both Hypoxia and Heat in a Freshwater Salmonid}, shorttitle = {Double Whammy}, @@ -805,7 +948,7 @@ @article{rodgersDoubleWhammyNitrate2021 issn = {00489697}, doi = {10.1016/j.scitotenv.2020.142777}, urldate = {2021-06-14}, - abstract = {Species persistence in a changing world will depend on how they cope with co-occurring stressors. Stressors can interact in unanticipated ways, where exposure to one stressor may heighten or reduce resilience to another stressor. We examined how a leading threat to aquatic species, nitrate pollution, affects susceptibility to hypoxia and heat stress in a salmonid, the European grayling (Thymallus thymallus). Fish were exposed to nitrate pollution (0, 50 or 200 mg NO3- L-1) at two acclimation temperatures (18 \textdegree C or 22 \textdegree C) for eight weeks. Hypoxia- and heattolerance were subsequently assessed, and the gills of a subset of fish were sampled for histological analyses. Nitrate-exposed fish were significantly more susceptible to acute hypoxia at both acclimation temperatures. Similarly, in 18 \textdegree C- acclimated fish, exposure to 200 mg NO3- L- 1 caused a 1 \textdegree C decrease in heat tolerance (critical thermal maxima, CTMax). However, the opposite effect was observed in 22 \textdegree C-acclimated fish, where nitrate exposure increased heat tolerance by \textasciitilde 1 \textdegree C. Further, nitrate exposure induced some histopathological changes to the gills, which limit oxygen uptake. Our findings show that nitrate pollution can heighten the susceptibility of fish to additional threats in their habitat, but interactions are temperature dependent.}, + abstract = {Species persistence in a changing world will depend on how they cope with co-occurring stressors. Stressors can interact in unanticipated ways, where exposure to one stressor may heighten or reduce resilience to another stressor. We examined how a leading threat to aquatic species, nitrate pollution, affects susceptibility to hypoxia and heat stress in a salmonid, the European grayling (Thymallus thymallus). Fish were exposed to nitrate pollution (0, 50 or 200 mg NO3- L-1) at two acclimation temperatures (18 {$^\circ$}C or 22 {$^\circ$}C) for eight weeks. Hypoxia- and heattolerance were subsequently assessed, and the gills of a subset of fish were sampled for histological analyses. Nitrate-exposed fish were significantly more susceptible to acute hypoxia at both acclimation temperatures. Similarly, in 18 {$^\circ$}C- acclimated fish, exposure to 200 mg NO3- L- 1 caused a 1 {$^\circ$}C decrease in heat tolerance (critical thermal maxima, CTMax). However, the opposite effect was observed in 22 {$^\circ$}C-acclimated fish, where nitrate exposure increased heat tolerance by {\textasciitilde}1 {$^\circ$}C. Further, nitrate exposure induced some histopathological changes to the gills, which limit oxygen uptake. Our findings show that nitrate pollution can heighten the susceptibility of fish to additional threats in their habitat, but interactions are temperature dependent.}, langid = {english}, file = {/Users/nicholascarey/Documents/Zotero/storage/CWX2WW37/Rodgers et al. - 2021 - Double whammy Nitrate pollution heightens suscept.pdf} } @@ -821,7 +964,7 @@ @article{rodriguezRoleTemperatureOxygen2020 issn = {1077-8306, 1744-7410}, doi = {10.1111/ivb.12305}, urldate = {2021-06-14}, - abstract = {The invasiveness of Corbicula largillierti has been underestimated, but this bivalve is currently receiving more attention. The first study of the distribution of this species along one of the major basins of central Argentina showed that it was completely absent in the major central reservoir, but was present along its tributary and effluent rivers. Ten years later, this discontinuous distribution has not changed, despite the bivalve's high dispersion capacity. The main environmental differences between the reservoir and the rivers are that the former has finer sediment grain size, higher temperatures, and lower oxygen concentration during summer months. This study aimed to evaluate whether one of these factors could be limiting the distribution of C. largillierti. We assessed the metabolic response and burial behavior (under different grain sizes) of C. largillierti over 8 weeks at 30\textdegree C against a control condition at 20\textdegree C. We also analyzed the oxygen consumption (vO2) as a function of environmental oxygen concentration (pO2) at 25\textdegree C, estimating its metabolic regulation capacity (R). This showed the existence of an environmental oxygen concentration threshold (Pt) that could be an indicative of physiological limiting concentrations that compromise species survival and settlement. After 8 weeks at 30\textdegree C, the metabolic rate of individuals of C. largillierti increased and their burial behavior was slightly compromised but mostly for coarser sediments. Concerning environmental oxygen availability, C. largillierti is an oxyconformer with a low R (39.9\%), a clear pattern of negative regulation, and a low Pt (48.4\% air saturation). The lack of any regulation capacity of C. largillierti under environmental oxygen limitations and the extremely low pO2 at the bottom of the reservoir during summer months may explain its failure to colonize and survive there.}, + abstract = {The invasiveness of Corbicula largillierti has been underestimated, but this bivalve is currently receiving more attention. The first study of the distribution of this species along one of the major basins of central Argentina showed that it was completely absent in the major central reservoir, but was present along its tributary and effluent rivers. Ten years later, this discontinuous distribution has not changed, despite the bivalve's high dispersion capacity. The main environmental differences between the reservoir and the rivers are that the former has finer sediment grain size, higher temperatures, and lower oxygen concentration during summer months. This study aimed to evaluate whether one of these factors could be limiting the distribution of C. largillierti. We assessed the metabolic response and burial behavior (under different grain sizes) of C. largillierti over 8 weeks at 30{$^\circ$}C against a control condition at 20{$^\circ$}C. We also analyzed the oxygen consumption (vO2) as a function of environmental oxygen concentration (pO2) at 25{$^\circ$}C, estimating its metabolic regulation capacity (R). This showed the existence of an environmental oxygen concentration threshold (Pt) that could be an indicative of physiological limiting concentrations that compromise species survival and settlement. After 8 weeks at 30{$^\circ$}C, the metabolic rate of individuals of C. largillierti increased and their burial behavior was slightly compromised but mostly for coarser sediments. Concerning environmental oxygen availability, C. largillierti is an oxyconformer with a low R (39.9\%), a clear pattern of negative regulation, and a low Pt (48.4\% air saturation). The lack of any regulation capacity of C. largillierti under environmental oxygen limitations and the extremely low pO2 at the bottom of the reservoir during summer months may explain its failure to colonize and survive there.}, langid = {english}, file = {/Users/nicholascarey/Documents/Zotero/storage/GVC65NJQ/Rodriguez et al. - 2020 - The role of temperature and oxygen availability on.pdf} } @@ -843,19 +986,39 @@ @article{rosEnvironmentalStressResponses2021 file = {/Users/nicholascarey/Documents/Zotero/storage/4LATJP5A/Ros et al. - 2021 - Environmental stress responses in sympatric congen.pdf} } -@article{rubinFeedingFrequencyDoes2023, - title = {Feeding Frequency Does Not Interact with {{BPA}} Exposure to Influence Metabolism or Behaviour in Zebrafish ({{Danio}} Rerio)}, +@article{rubinFeedingFrequencyDoes2024, + title = {Feeding Frequency Does Not Interact with {{BPA}} Exposure to Influence Metabolism or Behaviour in Zebrafish ({{{\emph{Danio}}}}{\emph{ Rerio}})}, author = {Rubin, Alexander M and Seebacher, Frank}, - year = {2023}, - month = nov, + year = {2024}, + month = jan, journal = {Physiology \& Behavior}, + volume = {273}, pages = {114403}, issn = {0031-9384}, doi = {10.1016/j.physbeh.2023.114403}, - urldate = {2023-11-08}, - abstract = {Resource limitation can constrain energy (ATP) production, and thereby affect locomotion and behaviour such as exploration of novel environments and boldness. Consequently, ecological processes such as dispersal and interactions within and between species may be influenced by food availability. Energy metabolism, and behaviour are regulated by endocrine signaling, and may therefore be impacted by endocrine disrupting compounds (EDCs) such as bisphenol A (BPA) derived from plastic manufacture and pollution. It is important to determine the impacts of these novel environmental contexts to understand how human activity alters individual physiology and behaviour and thereby populations. Our aim was to determine whether BPA exposure interacts with feeding frequency to alter metabolism and behaviour. In a fully factorial experiment, we show that low feeding frequency reduced zebrafish (Danio rerio) mass, condition, resting metabolic rates, total distance moved and speed in a novel arena, as well as anxiety indicated by the number of times fish returned to a dark shelter. However, feeding frequency did not significantly affect maximal metabolic rates, aerobic scope, swimming performance, latency to leave a shelter, or metabolic enzyme activities (citrate synthase and lactate dehydrogenase). Natural or anthropogenic fluctuation in food resources can therefore impact energetics and movement of animals with repercussions for ecological processes such as dispersal. BPA exposure reduced LDH activity and body mass, but did not interact with feeding frequency. Hence, behaviour of adult fish is relatively insensitive to disruption by BPA. However, alteration of LDH activity by BPA could disrupt lactate metabolism and signalling and together with reduction in body mass could affect size-dependent reproductive output. BPA released by plastic manufacture and pollution can thereby impact conservation and management of natural resources.}, - keywords = {aerobic scope,anxiety,boldness,energy limitation,Exploration,locomotor performance}, - file = {/Users/nicholascarey/Documents/Zotero/storage/LLW8MB24/Rubin and Seebacher - 2023 - Feeding frequency does not interact with BPA expos.pdf;/Users/nicholascarey/Documents/Zotero/storage/WRYA4MH2/S0031938423003281.html} + urldate = {2024-03-29}, + abstract = {Resource limitation can constrain energy (ATP) production, and thereby affect locomotion and behaviour such as exploration of novel environments and boldness. Consequently, ecological processes such as dispersal and interactions within and between species may be influenced by food availability. Energy metabolism, and behaviour are regulated by endocrine signalling, and may therefore be impacted by endocrine disrupting compounds (EDCs) including bisphenol A (BPA) derived from plastic manufacture and pollution. It is important to determine the impacts of these novel environmental contexts to understand how human activity alters individual physiology and behaviour and thereby populations. Our aim was to determine whether BPA exposure interacts with feeding frequency to alter metabolism and behaviour. In a fully factorial experiment, we show that low feeding frequency reduced zebrafish (Danio rerio) mass, condition, resting metabolic rates, total distance moved and speed in a novel arena, as well as anxiety indicated by the number of times fish returned to a dark shelter. However, feeding frequency did not significantly affect maximal metabolic rates, aerobic scope, swimming performance, latency to leave a shelter, or metabolic enzyme activities (citrate synthase and lactate dehydrogenase). Natural or anthropogenic fluctuation in food resources can therefore impact energetics and movement of animals with repercussions for ecological processes such as dispersal. BPA exposure reduced LDH activity and body mass, but did not interact with feeding frequency. Hence, behaviour of adult fish is relatively insensitive to disruption by BPA. However, alteration of LDH activity by BPA could disrupt lactate metabolism and signalling and together with reduction in body mass could affect size-dependent reproductive output. BPA released by plastic manufacture and pollution can thereby impact conservation and management of natural resources.}, + keywords = {Aerobic scope,Anxiety,Boldness,Energy limitation,Exploration,Locomotor performance}, + file = {/Users/nicholascarey/Documents/Zotero/storage/6BB873AB/S0031938423003281.html} +} + +@misc{scharfensteinPushingLimitsExpanding2024, + title = {Pushing the Limits: Expanding the Temperature Tolerance of a Coral Photosymbiont through Differing Selection Regimes}, + shorttitle = {Pushing the Limits}, + author = {Scharfenstein, Hugo James and Peplow, Lesa M. and {Alvarez-Roa}, Carlos and Nitschke, Matthew and Buerger, Patrick and Chan, Wing Yan and van Oppen, Madeleine J. H.}, + year = {2024}, + month = feb, + primaryclass = {New Results}, + pages = {2024.02.11.579409}, + publisher = {bioRxiv}, + doi = {10.1101/2024.02.11.579409}, + urldate = {2024-02-14}, + abstract = {Coral thermal bleaching resilience can be improved by enhancing photosymbiont thermal tolerance via experimental evolution. While successful for some strains, selection under stable temperatures was ineffective at increasing the thermal threshold of an already thermo-tolerant photosymbiont (Durusdinium trenchii). Corals from environments with fluctuating temperatures tend to have comparatively high heat tolerance. Therefore, we investigated whether exposure to temperature oscillations can raise the upper thermal limit of D. trenchii. We exposed a D. trenchii strain to stable and fluctuating temperatures profiles, which varied in oscillation frequency. After 2.1 years (54-73 generations), we characterised the adaptive responses under the various experimental evolution treatments by constructing thermal performance curves of growth from 21 to 31 degrees C for the heat-evolved and wild-types lineages. Additionally, oxidative stress, photophysiology, photosynthesis and respiration rates were assessed under increasing temperatures. Of the fluctuating temperature profiles investigated, selection under the most frequent oscillations (diurnal) induced the greatest widening of D. trenchii's thermal niche. Continuous selection under elevated temperatures induced the only increase in thermal optimum and a degree of generalism. Our findings demonstrate how differing levels of thermal homogeneity during selection drive unique adaptive responses to heat in a coral photosymbiont.}, + archiveprefix = {bioRxiv}, + chapter = {New Results}, + copyright = {{\copyright} 2024, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/}, + langid = {english}, + file = {/Users/nicholascarey/Documents/Zotero/storage/KK84HBUZ/Scharfenstein et al. - 2024 - Pushing the limits expanding the temperature tole.pdf} } @article{schusterDistinctRealizedPhysiologies2022, @@ -866,7 +1029,7 @@ @article{schusterDistinctRealizedPhysiologies2022 journal = {FACETS}, volume = {7}, pages = {822--842}, - publisher = {{Canadian Science Publishing}}, + publisher = {Canadian Science Publishing}, doi = {10.1139/facets-2021-0125}, urldate = {2022-06-05}, file = {/Users/nicholascarey/Documents/Zotero/storage/EHL4LK39/Schuster et al. - 2022 - Distinct realized physiologies in green sea urchin.pdf} @@ -883,38 +1046,48 @@ @article{schusterRoleKelpAvailability2023 issn = {0022-0981}, doi = {10.1016/j.jembe.2023.151947}, urldate = {2023-10-03}, - abstract = {Widespread decline in underwater forests, formed by kelps and other macroalgae, is occurring in all oceans. Loss of the vulnerable surface canopy typically leads to alternate rocky reef states dominated by substrate-near, understory vegetation, or reefs without any large fleshy macroalgae such as sea urchin barrens. Such alternate reef states represent a major shift in food availability and quality, and may impact kelp-preferring grazers forced to rely on less nutritious foods. Here we investigate the physiological responses of grazers to changes in food quality and quantity. We quantify the mass-independent oxygen consumption (\.MO2), as a proxy of whole-organism physiology, of four grazing invertebrate species (two sea urchins: Mesocentrotus franciscanus and Strongylocentrotus purpuratus; and two gastropods: Pomaulax gibberosus and Tegula pulligo) provisioned with one of three diet treatments over seven weeks: 1) higher quality, canopy kelp, 2) lower quality, substrate-near kelp, or 3) restricted: no kelp. We further test for differences in the heat resistance of four grazers using an acute, near-lethal heat exposure after completion of the provisioning period. Food restrictions had the strongest influence on oxygen consumption in the two urchins (mass-independent \.MO2 was reduced by 26\textendash 78\%). By contrast, the two gastropod grazers did not display metabolic depression under food restrictions. Although kelp restrictions had clear physiological consequences in sea urchins, overall, the type of kelp provisioned (Macrocystis and Saccharina) did not relate to oxygen consumption after seven weeks. While heat resistance was also similar across food treatments, unfed individuals showed a slight tendency for lower heat tolerance compared to fed individuals. These results suggest a weak coupling between heat resistance and food quality and quantity, at least for these species and at short time spans. Our work highlights the importance of diet diversity and metabolic depression as strategies to cope with the energetic costs of warming.}, + abstract = {Widespread decline in underwater forests, formed by kelps and other macroalgae, is occurring in all oceans. Loss of the vulnerable surface canopy typically leads to alternate rocky reef states dominated by substrate-near, understory vegetation, or reefs without any large fleshy macroalgae such as sea urchin barrens. Such alternate reef states represent a major shift in food availability and quality, and may impact kelp-preferring grazers forced to rely on less nutritious foods. Here we investigate the physiological responses of grazers to changes in food quality and quantity. We quantify the mass-independent oxygen consumption ({\.M}O2), as a proxy of whole-organism physiology, of four grazing invertebrate species (two sea urchins: Mesocentrotus franciscanus and Strongylocentrotus purpuratus; and two gastropods: Pomaulax gibberosus and Tegula pulligo) provisioned with one of three diet treatments over seven weeks: 1) higher quality, canopy kelp, 2) lower quality, substrate-near kelp, or 3) restricted: no kelp. We further test for differences in the heat resistance of four grazers using an acute, near-lethal heat exposure after completion of the provisioning period. Food restrictions had the strongest influence on oxygen consumption in the two urchins (mass-independent {\.M}O2 was reduced by 26--78\%). By contrast, the two gastropod grazers did not display metabolic depression under food restrictions. Although kelp restrictions had clear physiological consequences in sea urchins, overall, the type of kelp provisioned (Macrocystis and Saccharina) did not relate to oxygen consumption after seven weeks. While heat resistance was also similar across food treatments, unfed individuals showed a slight tendency for lower heat tolerance compared to fed individuals. These results suggest a weak coupling between heat resistance and food quality and quantity, at least for these species and at short time spans. Our work highlights the importance of diet diversity and metabolic depression as strategies to cope with the energetic costs of warming.}, keywords = {Heat stress,Herbivore,Metabolism,Resource limitation,Starvation,Underwater forest}, file = {/Users/nicholascarey/Documents/Zotero/storage/ZXBK3KTQ/Schuster and Bates - 2023 - The role of kelp availability and quality on the e.pdf;/Users/nicholascarey/Documents/Zotero/storage/8URRNN4X/S0022098123000795.html} } +@mastersthesis{sheffeyMicroplasticsVibrioBacteria2023, + title = {Do {{Microplastics}}, {{{\emph{Vibrio}}}} {{Bacteria}}, and {{Warming Water Temperatures Cause Disease}} in the {{Northern Star Coral}}, {{{\emph{Astrangia}}}}{\emph{ Poculata}}?}, + author = {Sheffey, Heather Leigh}, + year = {2023}, + address = {Norfolk, Virginia}, + urldate = {2024-02-11}, + abstract = {As marine plastic pollution increases, it becomes imperative to study the effects of microplastics on marine fauna. Marine plastic debris is a vector for disease to marine invertebrates (Lamb et al., 2018; Rotjan et al., 2019). In this context, studies have shown Astrangia poculata will consume microplastics as they do their normal food (Allen et al, 2017; Rotjan et al., 2019). Further, with temperatures increasing worldwide, there is a concern the virulence of disease-causing bacteria will increase (Vezzulli et al., 2015). In a series of manipulative laboratory experiments, this study quantified changes in respiration rates and visual health of Astrangia poculata when exposed to microplastics alone, microplastics having a biofilm of putative disease-causing bacteria, and warming temperatures. Astrangia fragments were exposed to 4 different temperatures: 22{\textcelsius}, 25{\textcelsius}, 28{\textcelsius}, and 32{\textcelsius}. The initial experiments at 22{\textcelsius} compared visually determined effects on health exerted by two bacteria known to cause disease in coral, Vibrio alginolyticus and Vibrio coralliilyticus. A significant difference was not found between the bacterial treatments. Within each experiment at higher temperatures, coral fragments were exposed either to ``clean'' microplastics or microplastics coated with V. coralliilyticus. Although respiration rate and visual health responded significantly to warmer temperatures, significant changes were not observed in response to disease-causing bacteria or microplastics.}, + langid = {english}, + school = {Old Dominion University}, + file = {/Users/nicholascarey/Documents/Zotero/storage/KGLQ3KWF/Sheffey - 2023 - Do Microplastics, Vibrio Bacteria, and Warming Wat.pdf} +} + @phdthesis{somoIntegrativeAnalysisRespiratory2022, title = {An Integrative Analysis of Respiratory Capacity, Osmoregulatory Function, Body Size, and Metabolism in Intertidal Fishes}, author = {Somo, Derek Anthony}, year = {2022}, month = dec, - address = {{Vancouver, Canada}}, + address = {Vancouver, Canada}, langid = {english}, school = {University of British Columbia}, file = {/Users/nicholascarey/Documents/Zotero/storage/2CRYZDCM/Somo - AN INTEGRATIVE ANALYSIS OF RESPIRATORY CAPACITY, O.pdf} } -@article{spindelZombiesNearshoreMetabolic2020, - title = {Zombies of the Nearshore: {{Metabolic}} Depression in Sea Urchin Barrens Associated with Food Deprivation}, - shorttitle = {Zombies of the Nearshore}, +@article{spindelMetabolicDepressionSea2021, + title = {Metabolic Depression in Sea Urchin Barrens Associated with Food Deprivation}, author = {Spindel, Nathan B. and Lee, Lynn C. and Okamoto, Daniel K.}, - year = {2020}, - month = dec, - journal = {bioRxiv}, - pages = {2020.11.28.402156}, - publisher = {{Cold Spring Harbor Laboratory}}, - doi = {10.1101/2020.11.28.402156}, - urldate = {2021-06-24}, - abstract = {{$<$}h3{$>$}Abstract{$<$}/h3{$>$} {$<$}p{$>$}The proliferation of sea urchins can decimate macroalgal forests in coastal ecosystems, leading to persistent barren seascapes. While kelp forests are among the most productive ecosystems on the planet, productivity in these urchin barrens is dramatically reduced. Moreover, urchins inhabiting these food-depauperate barrens face starvation and many survive in these barrens for years or decades. Urchins in barrens can persist by eating food subsidies from drift algae, pelagic salps, tubeworms, as well as encrusting and filamentous algae, microbial mats, and slow-growing species resistant to herbivory. Despite both food from endogenous production and exogenous subsidies, many urchins in barrens likely experience prolonged food deprivation. This resource limitation may create a trade-off between reproduction and survival; for example, fecundity of purple sea urchins (\emph{Strongylocentrotus purpuratus}) is 99.9\% lower in barrens. Despite food constraints, red sea urchins (\emph{Mesocentrotus franciscanus}), the dominant urchin species at our study sites, can live in excess of 100 years and barrens in Haida Gwaii, British Columbia (BC), Canada, have persisted for at least 143 years. While these phenomena are widespread and well documented, the bioenergetic adaptations that allow urchins to persist in these food-depauperate barrens remain poorly understood. To quantify habitat-specific differences in metabolic rates and energy reserves (as measured by gonadal mass), we conducted respirometry on and measured gonadal mass in \emph{M. franciscanus} at three locations in BC inside and outside of adjacent kelp forest and barrens habitat. Here we demonstrate that \emph{M. franciscanus} in barrens versus kelp forests have substantially lower energy reserves and, importantly, also exhibit dramatic reductions in size-specific resting metabolic rates (RMR), even after standardizing by metabolically active body mass. On average, gonadal mass was 44.6\% lower and RMR scaled to metabolically active body mass was 40\% lower in barrens urchins than in kelp forest urchins. Such a shift in metabolic rate may provide a mechanism that facilitates barren state stability over long time scales as \emph{M. franciscanus} can lower energetic demands while they wait for small pulses of food, scrape by on low-productivity resources, and suppress recruitment of macroalgae for months, years, or decades.{$<$}/p{$>$}}, - chapter = {New Results}, - copyright = {\textcopyright{} 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NoDerivs 4.0 International), CC BY-ND 4.0, as described at http://creativecommons.org/licenses/by-nd/4.0/}, + year = {2021}, + month = nov, + journal = {Ecology}, + volume = {102}, + number = {11}, + pages = {e03463}, + issn = {0012-9658, 1939-9170}, + doi = {10.1002/ecy.3463}, + urldate = {2024-03-24}, langid = {english}, - file = {/Users/nicholascarey/Documents/Zotero/storage/M3FDTHQS/Spindel et al. - 2020 - Zombies of the nearshore Metabolic depression in .pdf;/Users/nicholascarey/Documents/Zotero/storage/UIE8KUA6/2020.11.28.html} + file = {/Users/nicholascarey/Documents/Zotero/storage/DGUV3TYL/Spindel et al. - 2021 - Metabolic depression in sea urchin barrens associa.pdf} } @article{stellUsingElectronTransport2023, @@ -923,14 +1096,30 @@ @article{stellUsingElectronTransport2023 year = {2023}, month = aug, journal = {Canadian Journal of Zoology}, - publisher = {{NRC Research Press}}, + publisher = {NRC Research Press}, issn = {0008-4301}, doi = {10.1139/cjz-2023-0027}, urldate = {2023-08-27}, - abstract = {Freshwater ecosystems are undergoing rapid thermal shifts, making it increasingly important to understand species-specific responses to these changes. Traditional techniques for determining a species' thermal tolerance are often lethal and time consuming. Using the enzyme activity associated with the electron transport system (ETS; hereafter referred to as enzyme assay) may provide a non-lethal, rapid, and efficient alternative to traditional techniques for some species. We used largemouth bass Micropterus salmoides Lacepede, 1802 to test the efficacy of using an enzyme assay to determine thermal tolerance and respiratory exploitation in response to variable acclimation temperatures. Three tissue types were dissected from fish acclimated to 20, 25, or 30\textdegree C and used in ETS assays at temperatures ranging from 7.5-40\textdegree C. While there were significant differences among tissue types and acclimation temperatures, maximal enzyme activity occurred from 25.23-31.91\textdegree C. Fish lost equilibrium at 39-42\textdegree C in traditional CTmax trials, significantly higher than the upper optimum range determined via enzyme assays. The ratio of enzyme activity to measured whole organism respiration rate decreased with increasing water temperature, with the largest changes occurring at the upper optimum thermal range determined by enzyme assays. Our results indicate ETS analysis may prove useful for obtaining biologically relevant thermal tolerances.}, + abstract = {Freshwater ecosystems are undergoing rapid thermal shifts, making it increasingly important to understand species-specific responses to these changes. Traditional techniques for determining a species' thermal tolerance are often lethal and time consuming. Using the enzyme activity associated with the electron transport system (ETS; hereafter referred to as enzyme assay) may provide a non-lethal, rapid, and efficient alternative to traditional techniques for some species. We used largemouth bass Micropterus salmoides Lacepede, 1802 to test the efficacy of using an enzyme assay to determine thermal tolerance and respiratory exploitation in response to variable acclimation temperatures. Three tissue types were dissected from fish acclimated to 20, 25, or 30{$^\circ$}C and used in ETS assays at temperatures ranging from 7.5-40{$^\circ$}C. While there were significant differences among tissue types and acclimation temperatures, maximal enzyme activity occurred from 25.23-31.91{$^\circ$}C. Fish lost equilibrium at 39-42{$^\circ$}C in traditional CTmax trials, significantly higher than the upper optimum range determined via enzyme assays. The ratio of enzyme activity to measured whole organism respiration rate decreased with increasing water temperature, with the largest changes occurring at the upper optimum thermal range determined by enzyme assays. Our results indicate ETS analysis may prove useful for obtaining biologically relevant thermal tolerances.}, file = {/Users/nicholascarey/Documents/Zotero/storage/CE2LPY8Z/Stell et al. - 2023 - Using the electron transport system as an indicato.pdf} } +@article{taorminaEffectsSeaLice2024, + title = {Effects of the Sea Lice Chemotherapeutant, Emamectin Benzoate, on Metabolism and Behaviour of the Sea-Pen {{Pennatula}} Phosphorea}, + author = {Taormina, Bastien and {Escobar-Lux}, Rosa Helena and Legrand, Erwann and Parsons, Aoife Elizabeth and Kutti, Tina and Husa, Vivian and Hannisdal, Rita and Samuelsen, Ole B. and Agnalt, Ann-Lisbeth}, + year = {2024}, + month = jan, + journal = {Marine Pollution Bulletin}, + volume = {198}, + pages = {115903}, + issn = {0025-326X}, + doi = {10.1016/j.marpolbul.2023.115903}, + urldate = {2023-12-14}, + abstract = {Chemotherapeutants used to control infestations by sea lice can be released into the marine environment surrounding aquaculture farms. Among these therapeutic agents, emamectin benzoate is extensively utilized even though its impact on non-target taxa has not been thoroughly examined. In this context, we explored the effects of emamectin benzoate on a common Norwegian habitat-forming species: the phosphorescent sea-pen Pennatula phosphorea. Specifically, we examined P. phosphorea metabolic and responses before, during and after exposure to emamectin benzoate. Results indicate that an 8-day emamectin benzoate exposure (0.8~mg/L) did not induce P. phosphorea mortality or significant behavioural or metabolic modifications. However, we highlighted the presence and persistence of emamectin benzoate in exposed P. phosphorea tissue. These results indicate that emamectin benzoate is unlikely to adversely impact P. phosphorea populations in the environment. However, persistence of emamectin benzoate in tissue constitutes a potential for bioaccumulation with repeated treatments and should be examined in further studies.}, + keywords = {Aquaculture,Bioluminescence,Emamectin benzoate,Sea lice,Sea pens}, + file = {/Users/nicholascarey/Documents/Zotero/storage/MNWJJDX4/Taormina et al. - 2024 - Effects of the sea lice chemotherapeutant, emamect.pdf;/Users/nicholascarey/Documents/Zotero/storage/6WGX2E6D/S0025326X23013383.html} +} + @article{thambithuraiFishVulnerabilityCapture2022, title = {Fish Vulnerability to Capture by Trapping Is Modulated by Individual Parasite Density}, author = {Thambithurai, Davide and Lanthier, Isabel and Contant, Eloi and Killen, Shaun S. and Binning, Sandra A.}, @@ -940,10 +1129,10 @@ @article{thambithuraiFishVulnerabilityCapture2022 volume = {289}, number = {1989}, pages = {20221956}, - publisher = {{Royal Society}}, + publisher = {Royal Society}, doi = {10.1098/rspb.2022.1956}, urldate = {2022-12-15}, - abstract = {Commercial fishery harvest is a powerful evolutionary agent, but we know little about whether environmental stressors affect harvest-associated selection. We test how parasite infection relates to trapping vulnerability through selective processes underlying capture. We used fish naturally infected with parasites, including trematodes causing black spots under fish skin. We first assessed how individual parasite density related to standard metabolic rate (SMR), maximum metabolic rate (MMR) and absolute aerobic scope (AAS)\textemdash then used laboratory fishing simulations to test how capture vulnerability was related to parasite density. We further explored group-trapping dynamics using experimental shoals containing varying proportions of infected fish (groups of six with either 0, 2, 4 or 6 infected individuals). At the individual level, we found a positive relationship between parasite presence and SMR, but not MMR or AAS. While we saw no relationship between individual metabolic capacity and vulnerability to trapping, we found the length of time fish spent in traps increased with increasing parasite density, a predictor of trapping-related capture probability. At the group level, the number of infected individuals in a shoal did not affect overall group trapping vulnerability. Our results suggest that parasite infection has some capacity to shift individual vulnerability patterns in fisheries, and potentially influence the evolutionary outcomes of fisheries-induced evolution.}, + abstract = {Commercial fishery harvest is a powerful evolutionary agent, but we know little about whether environmental stressors affect harvest-associated selection. We test how parasite infection relates to trapping vulnerability through selective processes underlying capture. We used fish naturally infected with parasites, including trematodes causing black spots under fish skin. We first assessed how individual parasite density related to standard metabolic rate (SMR), maximum metabolic rate (MMR) and absolute aerobic scope (AAS)---then used laboratory fishing simulations to test how capture vulnerability was related to parasite density. We further explored group-trapping dynamics using experimental shoals containing varying proportions of infected fish (groups of six with either 0, 2, 4 or 6 infected individuals). At the individual level, we found a positive relationship between parasite presence and SMR, but not MMR or AAS. While we saw no relationship between individual metabolic capacity and vulnerability to trapping, we found the length of time fish spent in traps increased with increasing parasite density, a predictor of trapping-related capture probability. At the group level, the number of infected individuals in a shoal did not affect overall group trapping vulnerability. Our results suggest that parasite infection has some capacity to shift individual vulnerability patterns in fisheries, and potentially influence the evolutionary outcomes of fisheries-induced evolution.}, keywords = {fisheries-induced evolution,freshwater fish,group behaviour,marine stressors,metabolic rate,pathogen}, file = {/Users/nicholascarey/Documents/Zotero/storage/V8MQ9MX7/Thambithurai et al. - 2022 - Fish vulnerability to capture by trapping is modul.pdf} } @@ -957,10 +1146,10 @@ @article{wuEndocrineDisruptionPlastic2022 volume = {289}, number = {1967}, pages = {20212077}, - publisher = {{Royal Society}}, + publisher = {Royal Society}, doi = {10.1098/rspb.2021.2077}, urldate = {2022-01-31}, - abstract = {Energetic cost of growth determines how much food-derived energy is needed to produce a given amount of new biomass and thereby influences energy transduction between trophic levels. Growth and development are regulated by hormones and are therefore sensitive to changes in temperature and environmental endocrine disruption. Here, we show that the endocrine disruptor bisphenol A (BPA) at an environmentally relevant concentration (10 \textmu gl-1) decreased fish (Danio rerio) size at 30\textdegree C water temperature. Under the same conditions, it significantly increased metabolic rates and the energetic cost of growth across development. By contrast, BPA decreased the cost of growth at cooler temperatures (24\textdegree C). BPA-mediated changes in cost of growth were not associated with mitochondrial efficiency (P/O ratios (i.e. adenosine diphosphate (ADP) used/oxygen consumed) and respiratory control ratios) although BPA did increase mitochondrial proton leak. In females, BPA decreased age at maturity at 24\textdegree C but increased it at 30\textdegree C, and it decreased the gonadosomatic index suggesting reduced investment into reproduction. Our data reveal a potentially serious emerging problem: increasing water temperatures resulting from climate warming together with endocrine disruption from plastic pollution can impact animal growth efficiency, and hence the dynamics and resilience of animal populations and the services these provide.}, + abstract = {Energetic cost of growth determines how much food-derived energy is needed to produce a given amount of new biomass and thereby influences energy transduction between trophic levels. Growth and development are regulated by hormones and are therefore sensitive to changes in temperature and environmental endocrine disruption. Here, we show that the endocrine disruptor bisphenol A (BPA) at an environmentally relevant concentration (10 {\textmu}gl-1) decreased fish (Danio rerio) size at 30{$^\circ$}C water temperature. Under the same conditions, it significantly increased metabolic rates and the energetic cost of growth across development. By contrast, BPA decreased the cost of growth at cooler temperatures (24{$^\circ$}C). BPA-mediated changes in cost of growth were not associated with mitochondrial efficiency (P/O ratios (i.e. adenosine diphosphate (ADP) used/oxygen consumed) and respiratory control ratios) although BPA did increase mitochondrial proton leak. In females, BPA decreased age at maturity at 24{$^\circ$}C but increased it at 30{$^\circ$}C, and it decreased the gonadosomatic index suggesting reduced investment into reproduction. Our data reveal a potentially serious emerging problem: increasing water temperatures resulting from climate warming together with endocrine disruption from plastic pollution can impact animal growth efficiency, and hence the dynamics and resilience of animal populations and the services these provide.}, keywords = {bisphenol A,climate change,metabolism,mitochondria,trophic levels,zebrafish}, file = {/Users/nicholascarey/Documents/Zotero/storage/XI3MWC4Y/Wu et al. - 2022 - Endocrine disruption from plastic pollution and wa.pdf} } @@ -975,11 +1164,24 @@ @article{zavorkaReducedExplorationCapacity2020 issn = {1477-9145, 0022-0949}, doi = {10.1242/jeb.223453}, urldate = {2021-06-14}, - abstract = {While evidence suggests that warming may impact cognition of ectotherms, the underlying mechanisms remain poorly understood. A possible, but rarely considered mechanism is that metabolic response of ectotherms to warming associate with changes in brain morphology and functioning. Here we compared aerobic metabolism, volume of brain, boldness, and accuracy of maze solving of common minnows (Phoxinus phoxinus) acclimated for eight months to either their current optimal natural (14 \textdegree C) or warm (20 \textdegree C) water temperature. Metabolic rates indicated increased energy expenditure in warm acclimated fish, but also at least partial thermal compensation as warm acclimate fish maintained high aerobic scope. Warm acclimated fish had larger brain than cool acclimated fish. Volume of dorsal medulla relative to the overall brain size was larger in warm than cool acclimated fish, but proportion of other brain regions did not differ between the temperature treatments. Warm acclimated fish did not differ in boldness but did more errors than cool acclimated fish in exploring the maze across four trials. Inter-individual differences in numbers of exploration errors were repeatable across the four trials of the maze test. Our findings suggest that in warm environments, maintaining a high aerobic scope which is important for the performance of physically demanding tasks, can come at the cost of changes in brain morphology and impairment of the capacity to explore novel environments. This trade-off could have strong fitness implications for wild ectotherms.}, + abstract = {While evidence suggests that warming may impact cognition of ectotherms, the underlying mechanisms remain poorly understood. A possible, but rarely considered mechanism is that metabolic response of ectotherms to warming associate with changes in brain morphology and functioning. Here we compared aerobic metabolism, volume of brain, boldness, and accuracy of maze solving of common minnows (Phoxinus phoxinus) acclimated for eight months to either their current optimal natural (14 {$^\circ$}C) or warm (20 {$^\circ$}C) water temperature. Metabolic rates indicated increased energy expenditure in warm acclimated fish, but also at least partial thermal compensation as warm acclimate fish maintained high aerobic scope. Warm acclimated fish had larger brain than cool acclimated fish. Volume of dorsal medulla relative to the overall brain size was larger in warm than cool acclimated fish, but proportion of other brain regions did not differ between the temperature treatments. Warm acclimated fish did not differ in boldness but did more errors than cool acclimated fish in exploring the maze across four trials. Inter-individual differences in numbers of exploration errors were repeatable across the four trials of the maze test. Our findings suggest that in warm environments, maintaining a high aerobic scope which is important for the performance of physically demanding tasks, can come at the cost of changes in brain morphology and impairment of the capacity to explore novel environments. This trade-off could have strong fitness implications for wild ectotherms.}, langid = {english}, file = {/Users/nicholascarey/Documents/Zotero/storage/AIM8HEZ8/Závorka et al. - 2020 - Reduced exploration capacity despite brain volume .pdf} } +@phdthesis{zhangInterpretingSpeciesIntraspecific2021, + title = {Interpreting Species, Intraspecific and Intra-Individual Variability by Comprehensively Characterizing a Fish's Respiratory Phenotype with Valid Measures of Oxygen Uptake}, + author = {Zhang, Yangfan}, + year = {2021}, + address = {Vancouver, Canada}, + doi = {10.14288/1.0396683}, + urldate = {2024-03-29}, + abstract = {Vertebrate life is sustained by aerobic metabolism and temporary bouts of anaerobic metabolism. Steady-state aerobic metabolism can be assessed by measuring whole-organism oxygen uptake ({\.M}O{$_2$}), the core of Fry's paradigm, which becomes a part of a respiratory phenotype that also i}, + langid = {english}, + school = {University of British Columbia}, + file = {/Users/nicholascarey/Documents/Zotero/storage/G82BMHNJ/Zhang - 2021 - Interpreting species, intraspecific and intra-indi.pdf} +} + @article{zhangLossBehavioralStress2023, title = {Loss of Behavioral Stress Response in Blind Cavefish Reduces Energy Expenditure}, author = {Zhang, Jiang-Hui and Long, Rui and Jing, Yang-Yang and Zhang, Pan and Xu, Yuan and Xiong, Wei and Zhu, Yan-Qiu and Luo, Yi-Ping}, @@ -988,7 +1190,7 @@ @article{zhangLossBehavioralStress2023 journal = {Zoological Research}, volume = {44}, pages = {1--16}, - publisher = {{Zoological Research}}, + publisher = {Zoological Research}, issn = {2095-8137}, doi = {10.24272/j.issn.2095-8137.2022.354}, urldate = {2023-05-02}, @@ -1010,7 +1212,7 @@ @article{zhangMeasuringMaximumOxygen2020 issn = {0022-1112, 1095-8649}, doi = {10.1111/jfb.14311}, urldate = {2021-06-14}, - abstract = {This study hypothesized that oxygen uptake (\.MO2) measured with a novel protocol of chasing rainbow trout Oncorhynchus mykiss to exhaustion inside a static respirometer while simultaneously monitoring \.MO2 (\.MO2chase) would generate the same and repeatable peak value as when peak active \.MO2 (\.MO2active) is measured in a critical swimming speed protocol. To reliably determine peak \.MO2chase, and compare to the peak during recovery of \.MO2 after a conventional chase protocol outside the respirometer (\.MO2rec), this study applied an iterative algorithm and a minimum sampling window duration (i.e., 1 min based on an analysis of the variance in background and exercise \.MO2) to account for \.MO2 dynamics. In support of this hypothesis, peak \.MO2active (707 {$\pm$} 33 mg O2 h-1 kg-1) and peak \.MO2chase (663 {$\pm$} 43 mg O2 h-1 kg-1) were similar (P = 0.49) and repeatable (Pearson's and Spearman's correlation test; r {$\geq$} 0.77; P {$<$} 0.05) when measured in the same fish. Therefore, estimates of \.MO2max can be independent of whether a fish is exhaustively chased inside a respirometer or swum to fatigue in a swim tunnel, provided \.MO2 is analysed with an iterative algorithm and a minimum but reliable sampling window. The importance of using this analytical approach was illustrated by peak \.MO2chase being 23\% higher (P {$<$} 0.05) when compared with a conventional sequential interval regression analysis, whereas using the conventional chase protocol (1-min window) outside the respirometer increased this difference to 31\% (P {$<$} 0.01). Moreover, because peak \.MO2chase was 18\% higher (P {$<$} 0.05) than peak \.MO2rec, chasing a fish inside a static respirometer may be a better protocol for obtaining maximum \.MO2.}, + abstract = {This study hypothesized that oxygen uptake ({\.M}O2) measured with a novel protocol of chasing rainbow trout Oncorhynchus mykiss to exhaustion inside a static respirometer while simultaneously monitoring {\.M}O2 ({\.M}O2chase) would generate the same and repeatable peak value as when peak active {\.M}O2 ({\.M}O2active) is measured in a critical swimming speed protocol. To reliably determine peak {\.M}O2chase, and compare to the peak during recovery of {\.M}O2 after a conventional chase protocol outside the respirometer ({\.M}O2rec), this study applied an iterative algorithm and a minimum sampling window duration (i.e., 1 min based on an analysis of the variance in background and exercise {\.M}O2) to account for {\.M}O2 dynamics. In support of this hypothesis, peak {\.M}O2active (707 {\textpm} 33 mg O2 h-1 kg-1) and peak {\.M}O2chase (663 {\textpm} 43 mg O2 h-1 kg-1) were similar (P = 0.49) and repeatable (Pearson's and Spearman's correlation test; r {$\geq$} 0.77; P {$<$} 0.05) when measured in the same fish. Therefore, estimates of {\.M}O2max can be independent of whether a fish is exhaustively chased inside a respirometer or swum to fatigue in a swim tunnel, provided {\.M}O2 is analysed with an iterative algorithm and a minimum but reliable sampling window. The importance of using this analytical approach was illustrated by peak {\.M}O2chase being 23\% higher (P {$<$} 0.05) when compared with a conventional sequential interval regression analysis, whereas using the conventional chase protocol (1-min window) outside the respirometer increased this difference to 31\% (P {$<$} 0.01). Moreover, because peak {\.M}O2chase was 18\% higher (P {$<$} 0.05) than peak {\.M}O2rec, chasing a fish inside a static respirometer may be a better protocol for obtaining maximum {\.M}O2.}, langid = {english}, file = {/Users/nicholascarey/Documents/Zotero/storage/HVARTLNU/Zhang et al. - 2020 - Measuring maximum oxygen uptake with an incrementa.pdf} } From e1fe296fbdd14f8c1987338537663ceefcebd422 Mon Sep 17 00:00:00 2001 From: nicholascarey Date: Fri, 29 Mar 2024 13:58:03 +0000 Subject: [PATCH 11/13] readxl not suggests not import --- DESCRIPTION | 2 +- NAMESPACE | 1 - R/import_file.R | 7 +++---- README.md | 2 +- _pkgdown.yml | 2 +- pkgdown/pkgdown_script.R | 2 +- vignettes/citations.Rmd | 4 ++-- 7 files changed, 9 insertions(+), 11 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f66b2010..574784c3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -37,7 +37,6 @@ Imports: magrittr, marelac, purrr, - readxl, roll, segmented, stats, @@ -51,4 +50,5 @@ Suggests: FishResp, respirometry, testthat, + readxl, covr diff --git a/NAMESPACE b/NAMESPACE index 09cbcd4a..7ad4e97e 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -117,7 +117,6 @@ importFrom(parallel,makeCluster) importFrom(parallel,parLapply) importFrom(parallel,stopCluster) importFrom(purrr,reduce) -importFrom(readxl,read_excel) importFrom(roll,roll_lm) importFrom(stats,quantile) importFrom(stringr,str_replace) diff --git a/R/import_file.R b/R/import_file.R index 5b736e5e..bea3a452 100644 --- a/R/import_file.R +++ b/R/import_file.R @@ -76,7 +76,6 @@ #' directory, as determined by the `path` parameter. #' #' @importFrom data.table data.table fread -#' @importFrom readxl read_excel #' @importFrom xml2 xml_text #' @importFrom xml2 read_html #' @importFrom tools file_path_sans_ext @@ -110,7 +109,7 @@ import_file <- function(path, export = FALSE) { if (grepl(".xls", path)) { message("Excel file detected. Only Loligo/Presens Multiplate Excel files currently supported. \nImport will fail for others saved as Excel format. Use raw output files only.") - raw <- suppressMessages(read_excel(path, n_max = 20)) + raw <- suppressMessages(readxl::read_excel(path, n_max = 20)) raw <- as.character(raw) } else if (grepl("gmbl", path)) { raw <- suppressWarnings(readLines(path)) @@ -213,11 +212,11 @@ import_file <- function(path, export = FALSE) { # Loligo/Presens multiplate system ---------------------------------------- parse_multiplate_excel <- function(path, dec = dec){ - raw <- suppressMessages(read_excel(path, col_names = TRUE)) + raw <- suppressMessages(readxl::read_excel(path, col_names = TRUE)) ## which row has "Date/Time" start_row <- which(grepl("^Date/Time$", raw[[1]])) ## inport from that row on - raw <- suppressMessages(read_excel(path, skip = start_row - 1)) + raw <- suppressMessages(readxl::read_excel(path, skip = start_row - 1)) ## remove column 27 - empty raw <- raw[,-27] out <- data.table(raw) diff --git a/README.md b/README.md index 870016f0..5db50fc5 100644 --- a/README.md +++ b/README.md @@ -61,7 +61,7 @@ We are also happy to help directly. If you have problems using the package or ge The package has also been [**peer reviewed and published**](https://doi.org/10.1111/2041-210X.13162) in *Methods in Ecology and Evolution*. Please cite this publication if you use `respR` in your published work. -`respR` has been used to examine metabolic rates and photosynthesis in corals, plankton, micro- and macro-algae, fish, crustaceans, echinoderms, cephalopods, bivalves and more, in both lab and field studies. Check the [**respR in use**](https://januarharianto.github.io/respR/articles/citations.html) page to see a list of published studies which have used the package to analyse their data. +`respR` has been used to examine metabolic rates and photosynthesis in corals, plankton, micro- and macro-algae, fish, crustaceans, echinoderms, cephalopods, bivalves and more, in both lab and field studies. Check the [**respR Citations**](https://januarharianto.github.io/respR/articles/citations.html) page to see a list of published studies which have used the package to analyse their data.  \  \ diff --git a/_pkgdown.yml b/_pkgdown.yml index ccc6e70b..cd36fb5e 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -140,7 +140,7 @@ navbar: href: articles/contact.html - text: "Release Notes" href: articles/release_notes.html - - text: "respR in Use" + - text: "respR Citations" href: articles/citations.html - text: "Future Features" href: articles/future.html diff --git a/pkgdown/pkgdown_script.R b/pkgdown/pkgdown_script.R index de8a52c4..93f66468 100644 --- a/pkgdown/pkgdown_script.R +++ b/pkgdown/pkgdown_script.R @@ -39,6 +39,6 @@ usethis::use_vignette("intermittent_old", "Intermittent-flow respirometry: Alter ## Stopping and building site then trying again seems to work. ## Although last time took MANY attempts ## -## BUT - even if it seems to freeze check GHub and site - it might have successfully +## BUT - even if it seems to freeze - check GHub and site - it might have successfully ## triggered the 'pages build and deployment' GH action anyway... pkgdown::deploy_to_branch() diff --git a/vignettes/citations.Rmd b/vignettes/citations.Rmd index 6aa262d9..a969a22a 100644 --- a/vignettes/citations.Rmd +++ b/vignettes/citations.Rmd @@ -1,11 +1,11 @@ --- -title: respR in use by the scientific community +title: respR Citations output: rmarkdown::html_vignette: toc: true toc_depth: 3 vignette: > - %\VignetteIndexEntry{respR in Use} + %\VignetteIndexEntry{respR Citations} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} bibliography: references_citations.bib From d4cf65d1fa46c6036d57d48a317dacac830f7c37 Mon Sep 17 00:00:00 2001 From: nicholascarey Date: Fri, 29 Mar 2024 16:09:09 +0000 Subject: [PATCH 12/13] more read_xl --- DESCRIPTION | 1 - R/import_file.R | 6 +++--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 574784c3..f161b355 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -50,5 +50,4 @@ Suggests: FishResp, respirometry, testthat, - readxl, covr diff --git a/R/import_file.R b/R/import_file.R index bea3a452..b34d5e43 100644 --- a/R/import_file.R +++ b/R/import_file.R @@ -109,7 +109,7 @@ import_file <- function(path, export = FALSE) { if (grepl(".xls", path)) { message("Excel file detected. Only Loligo/Presens Multiplate Excel files currently supported. \nImport will fail for others saved as Excel format. Use raw output files only.") - raw <- suppressMessages(readxl::read_excel(path, n_max = 20)) + raw <- suppressMessages(read_excel(path, n_max = 20)) raw <- as.character(raw) } else if (grepl("gmbl", path)) { raw <- suppressWarnings(readLines(path)) @@ -212,11 +212,11 @@ import_file <- function(path, export = FALSE) { # Loligo/Presens multiplate system ---------------------------------------- parse_multiplate_excel <- function(path, dec = dec){ - raw <- suppressMessages(readxl::read_excel(path, col_names = TRUE)) + raw <- suppressMessages(read_excel(path, col_names = TRUE)) ## which row has "Date/Time" start_row <- which(grepl("^Date/Time$", raw[[1]])) ## inport from that row on - raw <- suppressMessages(readxl::read_excel(path, skip = start_row - 1)) + raw <- suppressMessages(read_excel(path, skip = start_row - 1)) ## remove column 27 - empty raw <- raw[,-27] out <- data.table(raw) From 3f47f34d0e9e1edd8c4f9d57880c35782cc07b8d Mon Sep 17 00:00:00 2001 From: nicholascarey Date: Fri, 29 Mar 2024 16:12:04 +0000 Subject: [PATCH 13/13] rm twitter --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5db50fc5..ddae9db5 100644 --- a/README.md +++ b/README.md @@ -71,7 +71,7 @@ The package has also been [**peer reviewed and published**](https://doi.org/10.1 See [**here**](https://januarharianto.github.io/respR/articles/contact.html) for more ways of providing feedback and getting in touch if you are having issues. -For the latest news and regular updates from the world of respirometry follow `respR` on **Mastodon** or [**Twitter**](https://twitter.com/respR_pkg). +For the latest news and regular updates from the world of respirometry follow `respR` on **Mastodon**. ## Support package development