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FiguresTablesEtc
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ModelBuild/GlobalModel
StemBiomass
StemMeasurementError
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README.Rmd
README.md

README.md

Disentangling herbivore impacts in primary succession by refocusing the plant stress and vigor hypotheses on phenology

Che-Castaldo, C., C. M. Crisafulli J. G. Bishop, E. F. Zipkin, and W. F. Fagan. 2019. Ecological Monographs.

DOI

Please contact the first author for questions about the code or data: Christian Che-Castaldo (chrischecastaldo@icloud.com)


Abstract

The plant stress and plant vigor hypotheses are widely used to explain the distribution and abundance of insect herbivores across their host plants. These hypotheses are the subject of contentious debate within the plant herbivore research community, with several studies finding simultaneous support for both hypotheses for the same plant-herbivore interaction. We address the question of how such support is possible using dynamic site-occupancy models to quantify the attack dynamics of Cryptorynchus lapathi (poplar-willow weevil) on Salix sitchensis (Sitka willow), a dioecious shrub colonizing Mount St. Helens after the 1980 eruption, in relation to host plant stress, vigor, and sex. We also introduce several scaling criteria as a rigorous test of the plant vigor hypothesis and demonstrate why modeling insect detection is important in plant-insect studies. Weevils responded positively to water stress associated with seasonal dry-downs, and this response was phenologically compartmentalized by larval feeding mode. Weevils preferentially attacked large and/or flowering stems, imposing an ecological cost on willow reproduction via increased stem mortality and susceptibility to future attack. We propose that the dual response to host plant stress and vigor is due to the synchronization between young weevil larval feeding and willow nutrient pulses that are mediated by environmental stress. In turn, this process drives successional dynamics, causing the juvenilization of upland willow plants and possibly delaying establishment of a willow-dominated upland sere. These results highlight the common, but often overlooked, phenological basis of the plant stress and plant vigor hypotheses, which both focus on how stress changes the quality of plant resources available to immature insects.


Repository Directory

  1. Library contains the 12 datasets used in this paper. The metadata for each dataset are listed below.

  2. ModelBuild contains the R and bash scripts used to fit the willow-weevil occupancy model in JAGS on AWS, as well as all model output.

  3. FiguresTablesEtc contains the R scripts used to make all figures and tables.

  4. StemBiomass contains the R script for the model of willow stem biomass as a function of willow basal stem diameter used to estimate the scaling coefficient n1.

  5. StemMeasurementError contains the R script for the model that estimates the routine error associated with measuring willow basal stem diameters using calipers.


Library Metadata

SalixBorderWide

Metadata for the willow-weevil dataset described in the Methods and Appendices S4-S7.

field description
transect name of transect, see methods and Appendix S4
point meter mark along transect, see Methods and Appendix S4
plantid willow plant identifier used during field surveys, see Methods and Appendix S4
stemid willow 1st order stem identifier used during field surveys, see Methods and Appendix S5
habitat habitat of willow plant: 0 = riparian, 1 = upland
sex sex of willow plant: 0 = male, 1 = female
plant willow plant identifier used in occupancy model
stem willow stem identifier used in occupancy model
site09 status of willow stem in 2009: 0 = dead or did not exist, 1 = alive, see Methods and Appendix S5
site10 status of willow stem in 2010: 0 = dead or did not exist, 1 = alive, see Methods and Appendix S5
site11 status of willow stem in 2011: 0 = dead or did not exist, 1 = alive, see Methods and Appendix S5
br09 number of 2nd order branches on willow stem in 2009, see Methods and Appendix S5
br10 number of 2nd order branches on willow stem in 2010, see Methods and Appendix S5
br11 number of 2nd order branches on willow stem in 2011, see Methods and Appendix S5
tbd09 estimated total basal stem diameter in mm (tbd) in 2009, see Methods and Appendices S6-S7
tbd10 estimated total basal stem diameter in mm (tbd) in 2010, see Methods and Appendices S6-S7
tbd11 estimated total basal stem diameter in mm (tbd) in 2011, see Methods and Appendices S6-S7
gr09 relative growth rate (rgr) of tbd from 2009 to 2010, see Methods and Appendix S7
gr10 relative growth rate (rgr) of tbd from 2010 to 2011, see Methods and Appendix S7
tbd09.sd standardized 2009 tbd, see Methods
tbd10.sd standardized 2010 tbd, see Methods
tbd11.sd standardized 2011 tbd, see Methods
gr09.sd standardized 2009 to 2010 rgr, see Methods
gr10.sd standardized 2010 to 2011 rgr, see Methods
repro09 stem reproductive status in 2009: 0 = non-reproductive, 1 = reproductive, see Methods
repro10 stem reproductive status in 2010: 0 = non-reproductive, 1 = reproductive, see Methods
repro11 stem reproductive status in 2011: 0 = non-reproductive, 1 = reproductive, see Methods
borer1.09 weevil larvae visual survey by observer 1 in 2009: 0 = no, 1 = yes, see Methods and Fig. S1-S2B
borer2.09 weevil larvae visual survey by observer 2 in 2009: 0 = no, 1 = yes, see Methods and Fig. S1-S2B
borer1.10 weevil larvae visual survey by observer 1 in 2010: 0 = no, 1 = yes, see Methods and Fig. S1-S2B
borer2.10 weevil larvae visual survey by observer 2 in 2010: 0 = no, 1 = yes, see Methods and Fig. S1-S2B
borer1.11 weevil larvae visual survey by observer 1 in 2011: 0 = no, 1 = yes, see Methods and Fig. S1-S2B
borer2.11 weevil larvae visual survey by observer 2 in 2011: 0 = no, 1 = yes, see Methods and Fig. S1-S2B
tbd1.mean mean tbd of upland (habitat = 1) 2009 stems, see Methods for explanation
tbd1.sd standard deviation of tbd of upland (habitat = 1) 2009 stems, see Methods for explanation
tbd2.mean mean tbd of 2009 riparian (habitat = 0) and all stems in 2010 and 2011
tbd2.sd standard deviation of 2009 riparian (habitat = 0) and all stems in 2010 and 2011
rgr.mean mean rgr of all stems
rgr.sd standard deviation of rgr of all stems

stemBiomass

Metadata for the harvested upland willow stem dataset described in the Methods and Appendix S8.

field description
stem stem identifier
soma aboveground stem biomass (g)
bd basal stem diameter (mm)

pairedStemMeasurements

Metadata for the caliper measurement error dataset described in the Methods and Appendix S6.

field description
bd_observer1 basal stem diameter (mm) measured by observer 1
bd_observer2 basal stem diameter (mm) measured by observer 2

transectPoints

Metadata for the sf dataset of upland and riparian transect point locations referenced in the willow-weevil dataset.

field description
transect name of transect, see methods and Appendix S4
point meter mark along transect, see Methods and Appendix S4
type type of transect point, riparian vs. upland
geometry transect point coordinates in WGS84 (epsg:4326)

weevilPhenology

Metadata for the willow-phenology dataset described in the Methods and Appendix S9.

field description
stem_id willow stem identifier
date date willow stem harvested
month month willow stem harvested
year year willow stem harvested
habitat habitat willow stem harvested from: riparian vs. upland
stage life stage of weevils found inside willow stem: eggs vs. early instars
count number of weevil eggs or early instars per willow stem_id

soilReleaseCurve

Metadata for the soil release curve dataset described in Appendices S2 and S3.

field description
ec5 raw sensor voltage (mV)
vwc variable water content (m3 water m-3 soil)
kpa soil water potential (-kPa)

soilProbes

Metadata for the soil moisture dataset described and/or plotted in Appendices S2 and S3.

field description
unit Decagon logger id
port Decagon EC-5 soil moisture sensor port id
treatment sensor emplaced in dry vs. irrigated soil
year year of sensor reading
date date and time of sensor reading
raw raw sensor voltage (mV)
vwc variable water content (m3 water m-3 soil)
pfc percent soil field capacity

dailyPrecipitation

Metadata for the Spirit Lake SNOTEL 777 daily precipitation dataset plotted in Appendix S2.

field description
date date and time of measurement
precip daily precipitation (cm) based on the PREC.I-1 field

monthlySnotel

Metadata for the Spirit Lake SNOTEL 777 monthly precipitation dataset plotted in Appendix S2.

field description
year year of measurement
month month of measurement
precip monthly precipitation (cm) based on the precipitation accumulation field

hoboPumicePlain

Metadata for the hobo temperature and relative humidity dataset plotted in Appendix S2.

field description
month month
habitat habitat Hobo loggers were deployed in: 0 = riparian, 1 = upland
temp.m mean daily temperature (°C)
temp.sd standard deviation of daily temperature (°C)
RH.m mean minimum daily relative humidity (percent)
RH.sd standard deviation minimum daily relative humidity (percent)

leafGasExchange

Metadata for the leaf gas exchange dataset described in Appendix S3.

field description
plant_id plant tag identifier
rill artificial stream identifier, W vs. E, see Appendix S3
block identifier for 3 m subunits of stream containing 3 male and 3 female plants, see Appendix S3
section identifier for section of stream with similar soil water content in response to experimental irrigation
pfc percent soil field capacity of each section on dates indicated below, see Appendix S3
leaf_id leaf identifier unique to each plant
year year of gas exchange measurements and leaf harvesting
date date of gas exchange measurements and leaf harvesting
time time of gas exchange measurements and leaf harvesting
chamber_area area of leaf area inside Licor 6400 portable photosynthesis system leaf chamber (mm2)
leaf_area area of entire leaf measured in imageJ (mm2)
leaf_mass mass of dried leaf (g)
lma leaf mass to area ratio (g mm-2)
transpiration instantaneous transpiration rate (mol H2O m-2 s-1) measured with Licor 6400
photosynthesis instantaneous photosynthetic rate (mol CO2 m-2 s-1) measured with Licor 6400
conductance stomatal conductance (mol H2O m-2 s-1) measured with Licor 6400
ci intercellular CO2 concentration measured with Licor 6400
wue instantaneous water use efficiency calculated as photosynthesis / conductance

leafP

Metadata for the leaf gas exchange dataset described in Appendix S3.

field description
plant_id plant tag identifier
rill artificial stream identifier, W vs. E, see Appendix S3
block identifier for 3 m subunits of stream containing 3 male and 3 female plants, see Appendix S3
section identifier for section of stream with similar soil water content in response to experimental irrigation
pfc percent soil field capacity of each section on dates indicated below, see Appendix S3
year year of gas exchange measurements and leaf harvesting
P leaf percent phosphorus
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