Possible ancestral structure in human populations

Abstract

Determining the evolutionary relationships between fossil hominid groups such as Neanderthals and modern humans has been a question of enduring interest in human evolutionary genetics. Here we present a new method for addressing whether archaic human groups contributed to the modern gene pool (called ancient admixture), using the patterns of variation in contemporary human populations. Our method improves on previous work by explicitly accounting for recent population history before performing the analyses. Using sequence data from the Environmental Genome Project, we find strong evidence for ancient admixture in both a European and a West African population (p approximately 10(-7)), with contributions to the modern gene pool of at least 5%. While Neanderthals form an obvious archaic source population candidate in Europe, there is not yet a clear source population candidate in West Africa.

Figure 1. Demographic Model for European and African Populations with the Value of Our Best-Fitting Parameters

DOI: 10.1371/journal.pgen.0020105.g001

Figure 2. Polymorphism Data Using the Visual Genotype Display Format

See [35,36] for the gene chrna4. The first 12 rows are Yoruba genotypes and the last 22 rows are CEPH genotypes. For the gene chrna4, S^* _CEPH picks 18 SNPs divided into three congruent sets. All selected SNPs, denoted by a black dot, are segregating in the European sample and fixed in the Yoruba sample. The associated p-value is 0.039. DOI: 10.1371/journal.pgen.0020105.g002

Figure 3. Quantile–Quantile Plot Comparing the Distribution of S^* (Left Graph) and the Recombination Rate ρ^_CEPH (Right Graph), When There Is No Admixture (x-Axis) and When the Level of Admixture is 5% (y-Axis)

Since for S^* _CEPH many points are far away from the diagonal, we can conclude that the two models are easily distinguishable from each other. This would not be possible based on the distribution of ρ^_CEPH. DOI: 10.1371/journal.pgen.0020105.g003

Figure 4. Quantile–Quantile Plot Comparing the Distribution of p-Values Associated with S^* _All (Left) and S^* _CEPH (Right) with the Expected Uniform Distribution between 0 and 1

The deviation from the diagonal line shows a discrepancy between the data and the null model for S^* _CEPH but not for S^* _All. DOI: 10.1371/journal.pgen.0020105.g004