Population Structure in a Comprehensive Genomic Data Set on Human Microsatellite Variation

Abstract

Over the past two decades, microsatellite genotypes have provided the data for landmark studies of human population-genetic variation. However, the various microsatellite data sets have been prepared with different procedures and sets of markers, so that it has been difficult to synthesize available data for a comprehensive analysis. Here, we combine eight human population-genetic data sets at the 645 microsatellite loci they share in common, accounting for procedural differences in the production of the different data sets, to assemble a single data set containing 5795 individuals from 267 worldwide populations. We perform a systematic analysis of genetic relatedness, detecting 240 intra-population and 92 inter-population pairs of previously unidentified close relatives and proposing standardized subsets of unrelated individuals for use in future studies. We then augment the human data with a data set of 84 chimpanzees at the 246 loci they share in common with the human samples. Multidimensional scaling and neighbor-joining analyses of these data sets offer new insights into the structure of human populations and enable a comparison of genetic variation patterns in chimpanzees with those in humans. Our combined data sets are the largest of their kind reported to date and provide a resource for use in human population-genetic studies.

Population Diversity, Division of Labor and the Emergence of Trade and State

“…8 The genetic diversity on the full set of 645 loci is almost perfectly correlated with the measure used in the paper for the 267 original ethnicities in Pemberton et al (2013). Their correlation is 0.99 (p < 0.01).…”

“…This research constructs a novel dataset on georeferenced genetic diversity at the ethnicity level using the most comprehensive genomic data set on human micro-satellite variation to date (Pemberton et al, 2013). In particular, Pemberton et al (2013) combine eight previous population-genetic data sets and analyze them following a standardized procedure, which ensures all the data is produced following a uniform procedure, ensuring comparability across populations and samples.…”

“…In particular, Pemberton et al (2013) combine eight previous population-genetic data sets and analyze them following a standardized procedure, which ensures all the data is produced following a uniform procedure, ensuring comparability across populations and samples. This data set contains information on 645 common singlenucleotide protein (SNP) loci for 5435 individuals from 267 independent ethnicities.…”

“…In particular, the "Out-of-Africa" theory of the geographic origin and early migration of anatomically modern humans posits that the process leading to the peopling of planet Earth by anatomically modern humans started with their migration out of East Africa more than sixty thousand years ago (Cann et al, 1987;Pemberton et al, 2013;Ramachandran et al, 2005). This process consisted of a series of discrete successive migrations, in which new settlements were established by smaller subgroups from an originally larger population.…”

“…In particular, according to the "Out-of-Africa" theory of the geographic origin and early migration of anatomically modern humans (Cann et al, 1987;Pemberton et al, 2013;Ramachandran et al, 2005), genetic diversity decreases with the distance from East Africa due to the serial founder effect. Thus, the analysis exploits the variations in the pre-historical migratory distance to East Africa (Addis Ababa) in order to generate the predicted genetic diversity for the full sample of ethnicities available in the EA.…”