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

PeerJ

Tara A. Pelletier¹  Bryan C. Carstens²  Drew J. Duckett² 

[1] Biology Department, Radford University, Radford, VA, USA;Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA;

关键词: Species trees;    Coalescent;    Posterior predictive simulation;    Multispecies coalescent model;   

DOI  :  10.7717/peerj.8271

来源: DOAJ

【 摘 要 】

Phylogenetic estimation under the multispecies coalescent model (MSCM) assumes all incongruence among loci is caused by incomplete lineage sorting. Therefore, applying the MSCM to datasets that contain incongruence that is caused by other processes, such as gene flow, can lead to biased phylogeny estimates. To identify possible bias when using the MSCM, we present P2C2M.SNAPP. P2C2M.SNAPP is an R package that identifies model violations using posterior predictive simulation. P2C2M.SNAPP uses the posterior distribution of species trees output by the software package SNAPP to simulate posterior predictive datasets under the MSCM, and then uses summary statistics to compare either the empirical data or the posterior distribution to the posterior predictive distribution to identify model violations. In simulation testing, P2C2M.SNAPP correctly classified up to 83% of datasets (depending on the summary statistic used) as to whether or not they violated the MSCM model. P2C2M.SNAPP represents a user-friendly way for researchers to perform posterior predictive model checks when using the popular SNAPP phylogenetic estimation program. It is freely available as an R package, along with additional program details and tutorials.

【 授权许可】

Unknown