Resequencing data provide no evidence for a human bottleneck in Africa during the penultimate glacial period

• Published in: Molecular biology and evolution 2012-07, Vol.29 (7), p.1851-1860
• Main Authors: Sjödin, Per, E Sjöstrand, Agnès, Jakobsson, Mattias, Blum, Michael G B
• Format: Article
• Language: English
• Subjects: Africa; African bottleneck; African genetic diversity; Anthropology; approximate Bayesian computation; Bayes Theorem; Bayesian analysis; Bottlenecks; Climate; Deoxyribonucleic acid; DNA; Fossils; Founder Effect; Genetic diversity; Genetics; Genetics, Medical; human origins; Humans; Ice ages; Life Sciences; Models, Genetic; oxygen isotope 6; Paleontology; penultimate glacial age; Pleistocene; Population Density; Population number; Populations and Evolution; Primates; Sequence Analysis, DNA
• ISSN: 0737-4038; 1537-1719; 1537-1719
• DOI: 10.1093/molbev/mss061

Based on the accumulation of genetic, climatic, and fossil evidence, a central theory in paleoanthropology stipulates that a demographic bottleneck coincided with the origin of our species Homo Sapiens. This theory proposes that anatomically modern humans--which were only present in Africa at the time--experienced a drastic bottleneck during the penultimate glacial age (130-190 kya) when a cold and dry climate prevailed. Two scenarios have been proposed to describe the bottleneck, which involve either a fragmentation of the range occupied by humans or the survival of one small group of humans. Here, we analyze DNA sequence data from 61 nuclear loci sequenced in three African populations using Approximate Bayesian Computation and numerical simulations. In contrast to the bottleneck theory, we show that a simple model without any bottleneck during the penultimate ice age has the greatest statistical support compared with bottleneck models. Although the proposed bottleneck is ancient, occurring at least 130 kya, we can discard the possibility that it did not leave detectable footprints in the DNA sequence data except if the bottleneck involves a less than a 3-fold reduction in population size. Finally, we confirm that a simple model without a bottleneck is able to reproduce the main features of the observed patterns of genetic variation. We conclude that models of Pleistocene refugium for modern human origins now require substantial revision.