Phylogeny estimation by integration over isolation with migration models
Genre
Journal ArticleDate
2018-01-01Author
Hey, JChung, Y
Sethuraman, A
Lachance, J
Tishkoff, S
Sousa, VC
Wang, Y
Permanent link to this record
http://hdl.handle.net/20.500.12613/4815
Metadata
Show full item recordDOI
10.1093/molbev/msy162Abstract
© The Author(s) 2018. Phylogeny estimation is difficult for closely related populations and species, especially if they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain Monte Carlo method with a state space that includes all possible phylogenies in a full Isolation-with-Migration model framework. The method is based on a new type of genealogy augmentation called a “hidden genealogy” that enables efficient updating of the phylogeny. This is the first likelihood-based method to fully incorporate directional gene flow and genetic drift for estimation of a species or population phylogeny. Application to human hunter-gatherer populations from Africa revealed a clear phylogenetic history, with strong support for gene exchange with an unsampled ghost population, and relatively ancient divergence between a ghost population and modern human populations, consistent with human/archaic divergence. In contrast, a study of five chimpanzee populations reveals a clear phylogeny with several pairs of populations having exchanged DNA, but does not support a history with an unsampled ghost population.Citation to related work
Oxford University Press (OUP)Has part
Molecular Biology and EvolutionADA compliance
For Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.eduae974a485f413a2113503eed53cd6c53
http://dx.doi.org/10.34944/dspace/4797