Neandertal admixture in Eurasia confirmed by maximum-likelihood analysis of three genomes.

Bibliographic Collection: 
Publication Type: Journal Article
Authors: Lohse, Konrad; Frantz, Laurent A F
Year of Publication: 2014
Journal: Genetics
Volume: 196
Issue: 4
Pagination: 1241-51
Date Published: 2014 Apr
Publication Language: eng
ISSN: 1943-2631
Keywords: Animals, Asian Continental Ancestry Group, Computer Simulation, European Continental Ancestry Group, Evolution, Molecular, Genome, Humans, Likelihood Functions, Neanderthals, Phylogeography

Although there has been much interest in estimating histories of divergence and admixture from genomic data, it has proved difficult to distinguish recent admixture from long-term structure in the ancestral population. Thus, recent genome-wide analyses based on summary statistics have sparked controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. Here we derive the probability of full mutational configurations in nonrecombining sequence blocks under both admixture and ancestral structure scenarios. Dividing the genome into short blocks gives an efficient way to compute maximum-likelihood estimates of parameters. We apply this likelihood scheme to triplets of human and Neandertal genomes and compare the relative support for a model of admixture from Neandertals into Eurasian populations after their expansion out of Africa against a history of persistent structure in their common ancestral population in Africa. Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neandertal admixture in Eurasia at a higher rate (3.4-7.3%) than suggested previously. Using analysis and simulations we show that our inference is more powerful than previous summary statistics and robust to realistic levels of recombination.

DOI: 10.1534/genetics.114.162396
Alternate Journal: Genetics