Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations

Murray P Cox,David A Morales,Jeffrey D Wall,Jesse Sozanski,Michael F Hammer,August E Woerner,John Hawks

doi:10.1371/journal.pone.0006366

Murray P Cox, David A Morales + Show 5 more

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https://doi.org/10.1371/journal.pone.0006366

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Abstract

BackgroundA major unanswered question in the evolution of Homo sapiens is when anatomically modern human populations began to expand: was demographic growth associated with the invention of particular technologies or behavioral innovations by hunter-gatherers in the Late Pleistocene, or with the acquisition of farming in the Neolithic?Methodology/Principal FindingsWe investigate the timing of human population expansion by performing a multilocus analysis of≥20 unlinked autosomal noncoding regions, each consisting of ∼6 kilobases, resequenced in ∼184 individuals from 7 human populations. We test the hypothesis that the autosomal polymorphism data fit a simple two-phase growth model, and when the hypothesis is not rejected, we fit parameters of this model to our data using approximate Bayesian computation.Conclusions/SignificanceThe data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories. In contrast, data from all four sub-Saharan African populations fit the two-phase growth model, and a range of onset times and growth rates is inferred for each population. Interestingly, both hunter-gatherers (San and Biaka) and food-producers (Mandenka and Yorubans) best fit models with population growth beginning in the Late Pleistocene. Moreover, our hunter-gatherer populations show a tendency towards slightly older and stronger growth (∼41 thousand years ago, ∼13-fold) than our food-producing populations (∼31 thousand years ago, ∼7-fold). These dates are concurrent with the appearance of the Late Stone Age in Africa, supporting the hypothesis that population growth played a significant role in the evolution of Late Pleistocene human cultures.

Highlights

Reconstructing the timing and magnitude of changes in human population size is important for understanding the impact of climatic fluctuation, technological innovation, natural selection, and random processes in the evolution of our species
Do the Data Fit a Two-Phase Growth Model? We tried to reject a series of two-phase growth models for each of the six populations reported in Wall et al (2008) separately using Tajima’s D, Rozas’ R2, and the variances of these two summary statistics
In contrast to the three nonAfrican populations, we find that the two-phase growth model cannot be rejected for a range of t and a when applied to the African autosomal data (Figure 1A–C)

Summary

Introduction

Reconstructing the timing and magnitude of changes in human population size is important for understanding the impact of climatic fluctuation, technological innovation, natural selection, and random processes in the evolution of our species. A major unanswered question is whether expansion began with hunter-gatherer groups, perhaps as a result of the invention of particular technologies or behavioral innovations, or much more recently with the advent of agriculture [3]. African growth to 213–12 kya, depending in part on mtDNA haplogroup [5,6] It is populations—not haplogroups— that are subject to growth, and many present-day hunter-gatherer groups, including those in Africa, do not exhibit any mtDNA signal of demographic expansion at all [7]. A major unanswered question in the evolution of Homo sapiens is when anatomically modern human populations began to expand: was demographic growth associated with the invention of particular technologies or behavioral innovations by hunter-gatherers in the Late Pleistocene, or with the acquisition of farming in the Neolithic?

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