期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 35, 期 11, 页码 2805-2818出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msy162
关键词
isolation with migration; speciation; population genetics; coalescent; gene flow; divergence
资金
- National Institutes of Health NRSA postdoctoral fellowship [F32HG006648]
- National Institutes of Health [R01GM078204, S10OD020095, R01DK104339, R01GM113657]
- National Science Foundation [1625061]
- US Army Research Laboratory [W911NF-16-2-0189]
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.
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