Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 490178
Title Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes
Author(s) Lohse, K.; Frantz, L.A.F.
Source Genetics 196 (2014)4. - ISSN 0016-6731 - p. 1241 - 1251.
DOI https://doi.org/10.1534/genetics.114.162396
Department(s) Animal Breeding and Genomics
WIAS
Publication type Refereed Article in a scientific journal
Publication year 2014
Keyword(s) ancestral population sizes - dna-sequences - divergence - speciation - history - number - recombination - coalescent - migration - inference
Abstract 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.
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