Identifying model violations under the multispecies coalescent model using P2C2M.SNAPP
| Autor: | Bryan C. Carstens, Drew Duckett, Tara A. Pelletier |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
Empirical data Bioinformatics Computer science Posterior probability lcsh:Medicine computer.software_genre 010603 evolutionary biology 01 natural sciences General Biochemistry Genetics and Molecular Biology Coalescent theory 03 medical and health sciences Genetics Multispecies coalescent model 030304 developmental biology Simulation testing 0303 health sciences General Neuroscience lcsh:R General Medicine Software package Posterior predictive simulation Evolutionary Studies Predictive simulation R package Posterior predictive distribution Species trees Coalescent Data mining General Agricultural and Biological Sciences computer |
| Zdroj: | PeerJ, Vol 8, p e8271 (2020) PeerJ |
| ISSN: | 2167-8359 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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