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

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

Konrad Lohse et al. Genetics. 2014 Apr.

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.

Keywords: D statistic; Neandertal introgression; ancestral admixture; maximum likelihood.

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Figures

Figure 1
Figure 1

Models of divergence between three populations with either (A) a recent instantaneous, unidirectional admixture event (IUA model) or (B) persistent structure in the ancestral population (AS model). Both histories lead to an excess of incongruent genealogies characterized by an internal branch tab (in green). However, the distribution of branch lengths, in particular that of the external branch ta (in red), differs between the IUA and AS models (Figure 2).

Figure 2
Figure 2

The length distribution of the internal branches tab (colored in green in Figure 1) and tac that specify genealogies that are incongruent with the order of population divergence and the shorter external branch ta (colored in red in Figure 1) under (A) the admixture (IUA) model or (B) a model of ancestral structure (AS) (Figure 1). Branch length distributions for genealogies with topologies tab (the frequency of which is increased by admixture or population structure) are shown as solid lines and those for the alternative incongruent topology tac as dashed lines. A is based on the parameters of Durand et al. (2011) with high admixture (f = 0.2); the parameters in B are chosen to give the same expected D value.

Figure 3
Figure 3

(A) The expected difference in support (E[ΔlnL]) between the IUA model and the AS model (thick solid curve) and between the IUA and a null model of strict divergence (dashed curve), when IUA is true plotted against the admixture fraction f. B shows analogous results for E[ΔlnL] against barrier strength (1/M) when the AS model is true. Plots are based on analytic results for the likelihood and assuming 10,000 sequence blocks, θ = 3, and the time parameters of Durand et al. (2011, table 6).

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