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Reversible polymorphism-aware phylogenetic models and their application to tree inference

Abstract:

We present a reversible Polymorphism-Aware Phylogenetic Model (revPoMo) for species tree estimation from genome-wide data. revPoMo enables the reconstruction of large scale species trees for many within-species samples. It expands the alphabet of DNA substitution models to include polymorphic states, thereby, naturally accounting for incomplete lineage sorting. We implemented revPoMo in the maximum likelihood software IQ-TREE. A simulation study and an application to great apes data show that...

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Publication status:
Published
Peer review status:
Peer reviewed

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Institution:
University of Oxford
Division:
MSD
Department:
NDM
Sub department:
NDM Experimental Medicine
Role:
Author
More from this funder
Name:
Vienna Graduate School of Population Genetics
Grant:
FWF-W1225
More from this funder
Name:
Austrian Science Fund
Grant:
FWF-P24551
I-2805-B29
Publisher:
Elsevier
Journal:
Journal of Theoretical Biology More from this journal
Volume:
407
Pages:
362-370
Publication date:
2016-10-01
Acceptance date:
2016-07-27
DOI:
EISSN:
1095-8541
ISSN:
0022-5193
Pmid:
27480613
Language:
English
Keywords:
Pubs id:
pubs:638879
UUID:
uuid:24c37eea-3cf3-44f5-b4ff-67288bc1964d
Local pid:
pubs:638879
Source identifiers:
638879
Deposit date:
2016-09-29

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