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MBE Advance Access first published online on December 18, 2007
This version published online on January 3, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msm277
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

mtDNA Variation Predicts Population Size in Humans and Reveals a Major Southern Asian Chapter in Human Prehistory

Quentin D. Atkinson1, Russell D. Gray2 and Alexei J. Drummond3

1 Institute of Cognitive and Evolutionary Anthropology, University of Oxford, 58A Banbury Rd, OX2 6QS, UNITED KINGDOM
2 Psychology Department, University of Auckland, Private Bag 92019, Auckland 1001, NEW ZEALAND
3 Bioinformatics Institute and Department of Computer Science, University of Auckland, Private Bag 92019, Auckland 1001, NEW ZEALAND

Institute of Cognitive and Evolutionary Anthropology, University of Oxford, 58A Banbury Rd, OX2 6QS, UNITED KINGDOM Telephone: - +44 (0)186 527 4680 or +44 (0)789 482 8426 E-mail: - quentin.atkinson{at}anthro.ox.ac.uk

Received for publication July 18, 2007. Revision received October 19, 2007. Accepted for publication December 11, 2007.

The relative timing and size of regional human population growth following our expansion from Africa remains unknown. Human mitochondrial DNA (mtDNA) diversity carries a legacy of our population history. Given a set of sequences, we can use coalescent theory to estimate past population size through time and draw inferences about human population history. However, recent work has challenged the validity of using mtDNA diversity to infer species population sizes. Here we use Bayesian coalescent inference methods, together with a global dataset of 357 human mtDNA coding region sequences, to infer human population sizes through time across eight major geographic regions. Our estimates of relative population sizes show remarkable concordance with the contemporary regional distribution of humans across Africa, Eurasia and the Americas, indicating that mtDNA diversity is a good predictor of population size in humans. Plots of population size through time show slow growth in sub-Saharan Africa beginning 143-193kya, followed by a rapid expansion into Eurasia after the emergence of the first non-African mtDNA lineages 50-70kya. Outside Africa, the earliest and fastest growth is inferred in Southern Asia ~52kya, followed by a succession of growth phases in Northern and Central Asia (~49kya), Australia (~48kya), Europe (~42kya), the Middle East and North Africa (~40kya), New Guinea (~39kya), the Americas (~18kya), and a second expansion in Europe (~10-15kya). Comparisons of relative regional population sizes through time suggest that between approximately 45kya and 20kya most of humanity lived in Southern Asia. These findings not only support the use of mtDNA data for estimating human population size but also provide a unique picture of human prehistory and demonstrate the importance of Southern Asia to our recent evolutionary past.

Key Words: Mitochondrial DNA • Human Evolution • Population genetics • Bayesian Skyline Plot • Anthropology


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