Inference of sex‐specific expansion patterns in human populations from Y‐chromosome polymorphism

Abstract

Studying the current distribution of genetic diversity in humans has important implications for our understanding of the history of our species. We analyzed a set of linked STR and SNP loci from the paternally inherited Y chromosome to infer the past demography of 55 African and Eurasian populations, using both the parametric and nonparametric coalescent-based methods implemented in the BEAST application. We inferred expansion events in most sedentary farmer populations, while we found constant effective population sizes for both nomadic hunter-gatherers and seminomadic herders. Our results differed, on several aspects, from previous results on mtDNA and autosomal markers. First, we found more recent expansion patterns in Eurasia than in Africa. This discrepancy, substantially stronger than the ones found with the other kind of markers, may result from a lower effective population size for men, which might have made male-transmitted markers more sensitive to the out-of-Africa bottleneck. Second, we found expansion signals only for sedentary farmers but not for nomadic herders in Central Asia, while these signals were found for both kind of populations in this area when using mtDNA or autosomal markers. Expansion signals in this area may result from spatial expansion processes and may have been erased for the Y chromosome among the herders because of restricted male gene flow.

Different kinds of genetic markers permit inference of Paleolithic and Neolithic expansions in humans

“…[21][22][23][24] However, in a study on microsatellite data, 25 we did not find signals of Palaeolithic expansions, either in Eurasia or Africa: the observed signals of expansion events were indeed consistent with the Neolithic transition. Finally, in Aimé et al, 4 we also found signals of expansion events that were consistent with the Neolithic transition for Eurasia using Y-chromosome microsatellite data.…”

“…In Aimé et al, 4,25 we suggested that these contrasted findings may result from the specificities of each type of genetic markers and indicate two successive expansion events in the studied populations. Indeed, as explained above, the higher mutation rate of microsatellites as compared to DNA sequences may increase their sensitivity to recent events.…”

“…The simulated data were analysed using the parametric approach implemented in BEAST v1.8, following the same procedure as in Aimé et al 4,20,25 Four demographic models are implemented in BEAST: constant effective population size (N 0 ; constant model), population expansion with an increasing growth rate (g) (exponential model), population expansion with a decreasing growth rate (logistic model) and the expansion model, in which N 0 is the present day population size, N 1 the population size that the model asymptotes to going into the distant past and g the exponential growth rate that determines how fast the transition is from near the N 1 population size to N 0 population size. As in Aimé et al, 20 we selected the best-fitting demographic model by estimating marginal likelihoods using two methods: path sampling and stepping-stone sampling.…”

“…Using Simcoal version 2.1.2, 26 we simulated here both DNA sequences (mitochondrial or autosomal) and microsatellite (autosomal or from the Y chromosome) data sets under several scenarios involving either one or two successive expansion events, starting at different points in time, consistent with either a Paleolithic or a Neolithic expansion. These data sets were similar to those used in Aimé et al 4,20,25 in terms of numbers of loci.…”

“…For instance, as they are uni-parentally transmitted, mitochondrial sequences are informative only about maternal lineages, whereas the Y-chromosome provides information about paternal lineages. In Aimé et al, 4 it has been shown that these two types of markers sometimes provide different inferences on the demographic history of human populations, especially as females generally exhibit higher effective population sizes and higher migration rates than males. 5,6 Conversely, autosomal markers provide synthetic information about both maternal and paternal lineages.…”