African admixture in Southern Europeans
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Europeans are mainly the descendants of Neolithic farmers from the Near East and native European Mesolithic hunter-gatherers, with the Mesolithic component peaking in Northeastern Europe. Moreover, all Europeans have prehistoric East Asian admixture, but Northern Europeans have more of it than Southern Europeans. However, Southern Europeans have recent Sub-Saharan African ancestry that Northern Europeans lack.
Source
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Inference of human demographic parameters using haplotype patterns from genome-wide SNP data. K. E. Lohmueller1,2, A. Auton2, C. D. Bustamante2, A. G. Clark1 1) Dept Mol Biol and Genetics, Cornell Univ, Ithaca, NY; 2) Dept Biol Stats and Comp Biol, Cornell Univ, Ithaca, NY.
Accurate inference of human demographic history from genetic data is essential for identification of single nucleotide polymorphism (SNP) association with disease and for inference of natural selection. Haplotype diversity and haplotype sharing carry additional demographic information to that obtainable from SNP frequency spectra, and so we propose a novel method using haplotype summary statistics to fit demographic models to genome-wide SNP data. We divide the genome into 0.25 cM windows and for each we tabulate the number of distinct haplotypes and the frequency of the most common haplotype. We summarize the data by the genome-wide joint distribution of these two statistics. Coalescent simulations are then used to evaluate whether different demographic models are compatible with the observed data. Application of our method to simulated data shows that our method can reliably infer parameters from complex demographic models (such as bottlenecks) and is relatively robust to the levels of SNP ascertainment bias found in many genome-wide datasets. We have applied our method to data collected by the International HapMap Consortium and find that a bottleneck model best fits the CEU population. We have also analyzed a large dataset consisting of Affymetrix 500k data from ~2,900 individuals with ancestry from Taiwan, Japan, India, Mexico and many European countries. Since this dataset includes ~2,300 European individuals, we are able to study haplotype patterns at a fine scale within Europe. Interestingly, we find that within Europe there is a south-to-north gradient with decreasing levels of haplotype diversity moving north, consistent with south to north migrations. We also find that the southwestern European sample has higher haplotype diversity than the southeastern European sample. Additionally, a higher proportion of haplotypes are shared between the southwestern European sample and the Yoruba sample than between southeastern European sample and the Yoruba sample. These two patterns are consistent with recent admixture across the Mediterranean from Northern Africa.
Pure Southern Europeans=RIP
