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Identifying model violations under the multispecies coalescent model using P2C2M.SNAPP.

Drew J Duckett1, Tara A Pelletier2, Bryan C Carstens1

  • 1Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA.

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|January 18, 2020
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Summary

Phylogenetic analyses using the multispecies coalescent model (MSCM) can be biased by gene flow. P2C2M.SNAPP, an R package, uses posterior predictive simulation to detect MSCM model violations, improving phylogenetic accuracy.

Keywords:
CoalescentMultispecies coalescent modelPosterior predictive simulationSpecies trees

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Area of Science:

  • Computational Biology
  • Phylogenetics
  • Evolutionary Biology

Background:

  • The multispecies coalescent model (MSCM) is widely used for phylogenetic inference.
  • Incongruence among gene trees and species trees can arise from incomplete lineage sorting or other processes like gene flow.
  • Violations of MSCM assumptions can lead to biased phylogenetic estimates.

Purpose of the Study:

  • To develop a method for detecting violations of the multispecies coalescent model (MSCM) in phylogenetic analyses.
  • To provide a user-friendly tool for researchers using the SNAPP software for phylogenetic estimation.

Main Methods:

  • P2C2M.SNAPP, an R package, employs posterior predictive simulation to identify MSCM model violations.
  • It simulates datasets under the MSCM using posterior distributions from SNAPP.
  • Summary statistics are used to compare empirical data or posterior distributions with simulated data to detect model violations.

Main Results:

  • P2C2M.SNAPP successfully identified MSCM model violations in simulation testing.
  • Classification accuracy reached up to 83%, depending on the summary statistic employed.
  • The package offers a practical approach for assessing phylogenetic model assumptions.

Conclusions:

  • P2C2M.SNAPP provides a valuable tool for researchers to perform posterior predictive model checks.
  • This enhances the reliability of phylogenetic estimates derived from SNAPP.
  • The R package is freely available, promoting wider adoption and methodological rigor in phylogenetics.