Gene-wide identification of episodic selection.

TitleGene-wide identification of episodic selection.
Publication TypeJournal Article
Year of Publication2015
AuthorsMurrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, Scheffler K, Kosakovsky Pond SL
JournalMol Biol Evol
Volume32
Issue5
Pagination1365-71
Date Published2015 May
ISSN1537-1719
Abstract

We present BUSTED, a new approach to identifying gene-wide evidence of episodic positive selection, where the non-synonymous substitution rate is transiently greater than the synonymous rate. BUSTED can be used either on an entire phylogeny (without requiring an a priori hypothesis regarding which branches are under positive selection) or on a pre-specified subset of foreground lineages (if a suitable a priori hypothesis is available). Selection is modeled as varying stochastically over branches and sites, and we propose a computationally inexpensive evidence metric for identifying sites subject to episodic positive selection on any foreground branches. We compare BUSTED with existing models on simulated and empirical data. An implementation is available on www.datamonkey.org/busted, with a widget allowing the interactive specification of foreground branches.

DOI10.1093/molbev/msv035
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/25701167?dopt=Abstract
Alternate JournalMol. Biol. Evol.
PubMed ID25701167
Grant ListU01 GM110749 / GM / NIGMS NIH HHS / United States
Track(s): 
Biomedical Informatics