Genetics, Vol. 177, 2195-2207, December 2007, Copyright © 2007
doi:10.1534/genetics.107.077495

Inferring Human Population Sizes, Divergence Times and Rates of Gene Flow From Mitochondrial, X and Y Chromosome Resequencing Data

Daniel Garrigan^*,, Sarah B. Kingan^*,, Maya M. Pilkington^,, Jason A. Wilder, Murray P. Cox^,**, Himla Soodyall, Beverly Strassmann, Giovanni Destro-Bisol, Peter de Knijff^***, Andrea Novelletto, Jonathan Friedlaender and Michael F. Hammer^,,,1

^* Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, ARL Division of Biotechnology, Department of Ecology and Evolutionary Biology and Department of Anthropology, University of Arizona, Tucson, Arizona 85721, Department of Biology, Williams College, Williamstown, Massachusetts 01267, ^** Santa Fe Institute, Santa Fe, New Mexico 87501, Human Genomic Diversity and Disease Research Unit, University of Witwatersand, Johannesburg 2000, South Africa, Department of Anthropology, University of Michigan, Ann Arbor, Michigan 48109, Department of Animal and Human Biology, University of Rome "La Sapienza," 00185 Rome, Italy, ^*** Forensic Laboratory for DNA Research, Leiden University, 2300 RC Leiden, The Netherlands, Department of Biology, University of Rome "Tor Vergata," 00173 Rome, Italy and Department of Anthropology, Temple University, Philadelphia, Pennsylvania 19122

¹ Corresponding author: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721.
E-mail: mfh{at}u.arizona.edu

We estimate parameters of a general isolation-with-migration model using resequence data from mitochondrial DNA (mtDNA), the Y chromosome, and two loci on the X chromosome in samples of 25–50 individuals from each of 10 human populations. Application of a coalescent-based Markov chain Monte Carlo technique allows simultaneous inference of divergence times, rates of gene flow, as well as changes in effective population size. Results from comparisons between sub-Saharan African and Eurasian populations estimate that 1500 individuals founded the ancestral Eurasian population 40 thousand years ago (KYA). Furthermore, these small Eurasian founding populations appear to have grown much more dramatically than either African or Oceanian populations. Analyses of sub-Saharan African populations provide little evidence for a history of population bottlenecks and suggest that they began diverging from one another upward of 50 KYA. We surmise that ancestral African populations had already been geographically structured prior to the founding of ancestral Eurasian populations. African populations are shown to experience low levels of mitochondrial DNA gene flow, but high levels of Y chromosome gene flow. In particular, Y chromosome gene flow appears to be asymmetric, i.e., from the Bantu-speaking population into other African populations. Conversely, mitochondrial gene flow is more extensive between non-African populations, but appears to be absent between European and Asian populations.

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