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      Inferring the Demographic History of African Farmers and Pygmy Hunter–Gatherers Using a Multilocus Resequencing Data Set

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The transition from hunting and gathering to farming involved a major cultural innovation that has spread rapidly over most of the globe in the last ten millennia. In sub-Saharan Africa, hunter–gatherers have begun to shift toward an agriculture-based lifestyle over the last 5,000 years. Only a few populations still base their mode of subsistence on hunting and gathering. The Pygmies are considered to be the largest group of mobile hunter–gatherers of Africa. They dwell in equatorial rainforests and are characterized by their short mean stature. However, little is known about the chronology of the demographic events—size changes, population splits, and gene flow—ultimately giving rise to contemporary Pygmy (Western and Eastern) groups and neighboring agricultural populations. We studied the branching history of Pygmy hunter–gatherers and agricultural populations from Africa and estimated separation times and gene flow between these populations. We resequenced 24 independent noncoding regions across the genome, corresponding to a total of ∼33 kb per individual, in 236 samples from seven Pygmy and five agricultural populations dispersed over the African continent. We used simulation-based inference to identify the historical model best fitting our data. The model identified included the early divergence of the ancestors of Pygmy hunter–gatherers and farming populations ∼60,000 years ago, followed by a split of the Pygmies' ancestors into the Western and Eastern Pygmy groups ∼20,000 years ago. Our findings increase knowledge of the history of the peopling of the African continent in a region lacking archaeological data. An appreciation of the demographic and adaptive history of African populations with different modes of subsistence should improve our understanding of the influence of human lifestyles on genome diversity.

          Author Summary

          The central African belt represents a key region for understanding recent changes in human history and modes of subsistence because the largest group of hunter–gatherers of Africa, the Pygmies, still inhabits this region and coexists with neighboring agricultural populations. However, the understanding of the peopling history of equatorial Africa is hampered by the rapid disintegration of fossil remains in the rainforest's acidic soils. When archaeology fails, population genetics can reconstruct the history of populations from their present-day genetic variation. We generated a large resequencing dataset in different farming, Western Pygmy, and Eastern Pygmy populations dispersed over the African continent. By means of simulation-based inferences, we show that the ancestors of Pygmy hunter–gatherers and farming populations started to diverge ∼60,000 years ago. This indicates that the transition to agriculture—occurring in Africa ∼5,000 years ago—was not responsible for the separation of the ancestors of modern-day Pygmies and farmers. We also show that Western and Eastern Pygmy groups separated roughly 20,000 years ago from a common ancestral population. This finding suggests that the shared physical and cultural features of Pygmies were inherited from a common ancestor, rather than reflecting convergent adaptation to the rainforest.

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          Most cited references58

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          DnaSP, DNA polymorphism analyses by the coalescent and other methods.

          DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (approximately 5 Mb per sequence); (2) conducting a large number of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical outputs for an easy visualization of results. The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp
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            Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation.

            Although many algorithms exist for estimating haplotypes from genotype data, none of them take full account of both the decay of linkage disequilibrium (LD) with distance and the order and spacing of genotyped markers. Here, we describe an algorithm that does take these factors into account, using a flexible model for the decay of LD with distance that can handle both "blocklike" and "nonblocklike" patterns of LD. We compare the accuracy of this approach with a range of other available algorithms in three ways: for reconstruction of randomly paired, molecularly determined male X chromosome haplotypes; for reconstruction of haplotypes obtained from trios in an autosomal region; and for estimation of missing genotypes in 50 autosomal genes that have been completely resequenced in 24 African Americans and 23 individuals of European descent. For the autosomal data sets, our new approach clearly outperforms the best available methods, whereas its accuracy in inferring the X chromosome haplotypes is only slightly superior. For estimation of missing genotypes, our method performed slightly better when the two subsamples were combined than when they were analyzed separately, which illustrates its robustness to population stratification. Our method is implemented in the software package PHASE (v2.1.1), available from the Stephens Lab Web site.
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              Stratigraphic placement and age of modern humans from Kibish, Ethiopia.

              In 1967 the Kibish Formation in southern Ethiopia yielded hominid cranial remains identified as early anatomically modern humans, assigned to Homo sapiens. However, the provenance and age of the fossils have been much debated. Here we confirm that the Omo I and Omo II hominid fossils are from similar stratigraphic levels in Member I of the Kibish Formation, despite the view that Omo I is more modern in appearance than Omo II. 40Ar/39Ar ages on feldspar crystals from pumice clasts within a tuff in Member I below the hominid levels place an older limit of 198 +/- 14 kyr (weighted mean age 196 +/- 2 kyr) on the hominids. A younger age limit of 104 +/- 7 kyr is provided by feldspars from pumice clasts in a Member III tuff. Geological evidence indicates rapid deposition of each member of the Kibish Formation. Isotopic ages on the Kibish Formation correspond to ages of Mediterranean sapropels, which reflect increased flow of the Nile River, and necessarily increased flow of the Omo River. Thus the 40Ar/39Ar age measurements, together with the sapropel correlations, indicate that the hominid fossils have an age close to the older limit. Our preferred estimate of the age of the Kibish hominids is 195 +/- 5 kyr, making them the earliest well-dated anatomically modern humans yet described.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS Genet
                plos
                plosgen
                PLoS Genetics
                Public Library of Science (San Francisco, USA )
                1553-7390
                1553-7404
                April 2009
                April 2009
                10 April 2009
                : 5
                : 4
                : e1000448
                Affiliations
                [1 ]Institut Pasteur, Human Evolutionary Genetics, CNRS, URA3012, Paris, France
                [2 ]Unité d'Eco-Anthropologie et Ethnobiologie, MNHN/P7/CNRS UMR5145, Musée de l'Homme, Paris, France
                [3 ]Unidade de Xenética, Instituto de Medicina Legal, Universidad de Santiago de Compostela, Galicia, Spain
                [4 ]Dipartimento di Genetica e Microbiologia, Universita di Pavia, Pavia, Italy
                [5 ]Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
                [6 ]Laboratoire Dynamique Du Langage, CNRS UMR5596, Université Lumière Lyon 2, Lyon, France
                [7 ]Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, Paris, France
                University of Chicago, United States of America
                Author notes

                Conceived and designed the experiments: EP LQM. Performed the experiments: EP. Analyzed the data: EP GL. Contributed reagents/materials/analysis tools: AS OS SSB KKK JRK LVdV JMH AG AF EH. Wrote the paper: EP LQM. Critically read the manuscript: GL LBB KKK JRK JMH SB EH. Obtained funding: EH LQM.

                Article
                08-PLGE-RA-1128R4
                10.1371/journal.pgen.1000448
                2661362
                19360089
                d2b5e217-be49-412d-9463-e94ef0ca8ab5
                Patin et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                : 28 August 2008
                : 10 March 2009
                Page count
                Pages: 13
                Categories
                Research Article
                Evolutionary Biology/Human Evolution
                Genetics and Genomics/Population Genetics

                Genetics
                Genetics

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