Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies Coalescent

Systematic Biology
Anthony J BarleyRobert C Thomson

Abstract

The use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown. This is concerning given the large amount of empirical data and theory that highlight the complexity of the speciation process. Here, we seek to fill this gap by using simulation to characterize the sensitivity of inference under the multispecies coalescent (MSC) to several violations of model assumptions thought to be common in empirical data. We also assess the fit of the MSC model to empirical data in the context of species delimitation. Our results show substantial variation in model fit across data sets. Posterior predictive tests find the poorest model performance in data sets that were hypothesized to be impacted by model violations. We also show that while the inferences assuming the MSC are robust to minor model violations, such inferences can be ...Continue Reading

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Citations

Oct 29, 2017·Proceedings of the National Academy of Sciences of the United States of America·Dario CopettiMichael J Sanderson
Nov 7, 2019·Systematic Biology·Luke C CampilloRobert C Thomson
May 10, 2020·Molecular Ecology Resources·Bernhard Hausdorf, Christian Hennig
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Jan 24, 2021·Journal of Fish Biology·Bruno GuinandChristelle Tougard
Feb 7, 2020·Molecular Phylogenetics and Evolution·Elyse S FreitasCameron D Siler
Dec 28, 2018·Molecular Phylogenetics and Evolution·Brendan J PintoTony Gamble
May 14, 2021·PLoS Computational Biology·Jeet SukumaranL Lacey Knowles
May 4, 2021·Molecular Phylogenetics and Evolution·Thomas L MarshallDavid M Hillis

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