fix error in puttick ref

JOSS/paper.bib

@@ -4,5 +4,5 @@ @article{Guillerme_Puttick_Marcy_Weisbecker_2020
  @article{Keating_Sansom_Sutton_Knight_Garwood_2020, title={Morphological Phylogenetics Evaluated Using Novel Evolutionary Simulations}, volume={69}, rights={All rights reserved}, ISSN={1063-5157}, DOI={10.1093/sysbio/syaa012}, abstractNote={Abstract.  Evolutionary inferences require reliable phylogenies. Morphological data have traditionally been analyzed using maximum parsimony, but recent simulat}, number={5}, journal={Systematic Biology}, publisher={Oxford Academic}, author={Keating, Joseph N. and Sansom, Robert S. and Sutton, Mark D. and Knight, Christopher G. and Garwood, Russell J.}, year={2020}, month=sep, pages={897–912}, language={en} }
  @article{Mongiardino_Koch_Garwood_Parry_2021, title={Fossils improve phylogenetic analyses of morphological characters}, volume={288}, rights={All rights reserved}, DOI={10.1098/rspb.2021.0044}, abstractNote={Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate divergences, as well as elucidate macroevolutionary dynamics. However, the effect fossils have on phylogenetic reconstruction from morphology remains controversial. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here, we use simulations to evaluate the performance of inference methods across different levels of fossil sampling and missing data. Our results show that fossil taxa improve phylogenetic analysis of morphological datasets, even when highly fragmentary. Irrespective of inference method, fossils improve the accuracy of phylogenies and increase the number of resolved nodes. They also induce the collapse of ancient and highly uncertain relationships that tend to be incorrectly resolved when sampling only extant taxa. Furthermore, tip-dated analyses under the fossilized birth–death process outperform undated methods of inference, demonstrating that the stratigraphic ages of fossils contain vital phylogenetic information. Fossils help to extract true phylogenetic signals from morphology, an effect that is mediated by both their distinctive morphology and their temporal information, and their incorporation in total-evidence phylogenetics is necessary to faithfully reconstruct evolutionary history.}, number={1950}, journal={Proceedings of the Royal Society B: Biological Sciences}, publisher={Royal Society}, author={Mongiardino Koch, Nicolás and Garwood, Russell J. and Parry, Luke A.}, year={2021}, month=may, pages={20210044} }
  @article{Mongiardino_Koch_Garwood_Parry_2023, title={Inaccurate fossil placement does not compromise tip-dated divergence times}, volume={66}, rights={© 2023 The Authors. Palaeontology published by John Wiley & Sons Ltd on behalf of The Palaeontological Association.}, ISSN={1475-4983}, DOI={10.1111/pala.12680}, abstractNote={Time-scaled phylogenies underpin the interrogation of evolutionary processes across deep timescales, as well as attempts to link these to Earth’s history. By inferring the placement of fossils and using their ages as temporal constraints, tip dating under the fossilized birth–death (FBD) process provides a coherent prior on divergence times. At the same time, it also links topological and temporal accuracy, as incorrectly placed fossil terminals should misinform divergence times. This could pose serious issues for obtaining accurate node ages, yet the interaction between topological and temporal error has not been thoroughly explored. We simulate phylogenies and associated morphological datasets using methodologies that incorporate evolution under selection, and are benchmarked against empirical datasets. We find that datasets of 300 characters and realistic levels of missing data generally succeed in inferring the correct placement of fossils on a constrained extant backbone topology, and that true node ages are usually contained within Bayesian posterior distributions. While increased fossil sampling improves the accuracy of inferred ages, topological and temporal errors do not seem to be linked: analyses in which fossils resolve less accurately do not exhibit elevated errors in node age estimates. At the same time, inferred divergence times are biased, probably due to a mismatch between the FBD prior and the shape of our simulated trees. While these results are encouraging, suggesting that even fossils with uncertain affinities can provide useful temporal information, they also emphasize that palaeontological information cannot overturn discrepancies between model priors and the true diversification history.}, number={6}, journal={Palaeontology}, author={Mongiardino Koch, Nicolás and Garwood, Russell J. and Parry, Luke A.}, year={2023}, pages={e12680}, language={en} }
- @article{Puttick_O'Reilly_Pisani_Donoghue_2019, title={Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model}, volume={62}, ISSN={00310239}, DOI={10.1111/pala.12388}, abstractNote={Abstract: To understand patterns and processes of the diversification of life, we require an accurate understanding of taxon interrelationships. Recent studies have suggested that analyses of morphological character data using the Bayesian and maximum likelihood Mk model provide phylogenies of higher accuracy compared to parsimony methods. This has proved controversial, particularly studies simulating morphology-data under Markov models that assume shared branch lengths for characters, as it is claimed this leads to bias favouring the Bayesian or maximum likelihood Mk model over parsimony models which do not explicitly make this assumption. We avoid these potential issues by employing a simulation protocol in which character states are randomly assigned to tips, but datasets are constrained to an empirically realistic distribution of homoplasy as measured by the consistency index. Datasets were analysed with equal weights and implied weights parsimony, and the maximum likelihood and Bayesian Mk model. We find that consistent (low homoplasy) datasets render method choice largely irrelevant, as all methods perform well with high consistency (low homoplasy) datasets, but the largest discrepancies in accuracy occur with low consistency datasets (high homoplasy). In such cases, the Bayesian Mk model is significantly more accurate than alternative models and implied weights parsimony never significantly outperforms the Bayesian Mk model. When poorly supported branches are collapsed, the Bayesian Mk model recovers trees with higher resolution compared to other methods. As it is not possible to assess homoplasy independently of a tree estimate, the Bayesian Mk model emerges as the most reliable approach for categorical morphological analyses.}, number={1}, journal={Palaeontology}, author={Puttick, Mark N. and O’Reilly, Joseph E. and Pisani, Davide and Donoghue, Philip C. J.}, editor={Rahman, Imran}, year={2019}, pages={1–17}, language={en} }
+ @article{Puttick_O_Reilly_Pisani_Donoghue_2019, title={Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model}, volume={62}, ISSN={00310239}, DOI={10.1111/pala.12388}, abstractNote={Abstract: To understand patterns and processes of the diversification of life, we require an accurate understanding of taxon interrelationships. Recent studies have suggested that analyses of morphological character data using the Bayesian and maximum likelihood Mk model provide phylogenies of higher accuracy compared to parsimony methods. This has proved controversial, particularly studies simulating morphology-data under Markov models that assume shared branch lengths for characters, as it is claimed this leads to bias favouring the Bayesian or maximum likelihood Mk model over parsimony models which do not explicitly make this assumption. We avoid these potential issues by employing a simulation protocol in which character states are randomly assigned to tips, but datasets are constrained to an empirically realistic distribution of homoplasy as measured by the consistency index. Datasets were analysed with equal weights and implied weights parsimony, and the maximum likelihood and Bayesian Mk model. We find that consistent (low homoplasy) datasets render method choice largely irrelevant, as all methods perform well with high consistency (low homoplasy) datasets, but the largest discrepancies in accuracy occur with low consistency datasets (high homoplasy). In such cases, the Bayesian Mk model is significantly more accurate than alternative models and implied weights parsimony never significantly outperforms the Bayesian Mk model. When poorly supported branches are collapsed, the Bayesian Mk model recovers trees with higher resolution compared to other methods. As it is not possible to assess homoplasy independently of a tree estimate, the Bayesian Mk model emerges as the most reliable approach for categorical morphological analyses.}, number={1}, journal={Palaeontology}, author={Puttick, Mark N. and O’Reilly, Joseph E. and Pisani, Davide and Donoghue, Philip C. J.}, editor={Rahman, Imran}, year={2019}, pages={1–17}, language={en} }
  @article{Wright_Hillis_2014, title={Bayesian Analysis Using a Simple Likelihood Model Outperforms Parsimony for Estimation of Phylogeny from Discrete Morphological Data}, volume={9}, ISSN={1932-6203}, DOI={10.1371/journal.pone.0109210}, number={10}, journal={PLoS ONE}, author={Wright, April M. and Hillis, David M.}, editor={Poon, Art F. Y.}, year={2014}, month=oct, pages={e109210}, language={en} }

JOSS/paper.md

@@ -138,7 +138,7 @@ TREvoSim v3.0.0 introduces a test suite covering all aspects of the simulation m
 
 # Statement of need
 
-Typically, phylogenetic simulations are conducted using deterministic or stochastic approaches [e.g. @Puttick_O'Reilly_Pisani_Donoghue_2019; Guillerme_Puttick_Marcy_Weisbecker_2020], such as birth-death models or randomly generated data. TREvoSim complements these by using a selection-driven, agent-based approach: the data generated are different in a number of ways to those created using a stochastic model (Keating et al. 2020). The data generated by the software is likely to violate the assumptions of many common models used in the process of phylogenetic inference, incorporating a level of model misspecification resembling that expected from empirical datasets. Default settings have also been validated to reflect a number of features of empirical data matrices and trees. Given that (true) phylogenetic trees and character data are an emergent property of the simulation, the software is particularly well suited to simulation studies that can be analysed through phylogenetic trees and character data matrices. These include, for example: the impact of missing data on phylogenetic inference; the impact of rates of environmental change on character evolution; and the nature of evolution under different fitness landscapes. 
+Typically, phylogenetic simulations are conducted using deterministic or stochastic approaches [e.g. @Puttick_O_Reilly_Pisani_Donoghue_2019; Guillerme_Puttick_Marcy_Weisbecker_2020], such as birth-death models or randomly generated data. TREvoSim complements these by using a selection-driven, agent-based approach: the data generated are different in a number of ways to those created using a stochastic model (Keating et al. 2020). The data generated by the software is likely to violate the assumptions of many common models used in the process of phylogenetic inference, incorporating a level of model misspecification resembling that expected from empirical datasets. Default settings have also been validated to reflect a number of features of empirical data matrices and trees. Given that (true) phylogenetic trees and character data are an emergent property of the simulation, the software is particularly well suited to simulation studies that can be analysed through phylogenetic trees and character data matrices. These include, for example: the impact of missing data on phylogenetic inference; the impact of rates of environmental change on character evolution; and the nature of evolution under different fitness landscapes. 
 
 # Current associated projects