View source for Deep Divergences of Human Gene Trees andModels of Human Origins

<p>Deep Divergences of Human Gene Trees andModels of Human<br />
Origins<br />
Michael G. B. Blum*,1 and Mattias Jakobsson2<br />
1Laboratoire des Techniques de l&rsquo;Ing&acute;enierie M&acute;edicale et de la Complexit&acute;e (TIMC-IMAG), Equipe Biologie Computationnelle et<br />
Math&acute;ematique (BCM), Centre National de la Recherche Scientifique (CNRS), Universit&acute;e Joseph Fourier (UJF), Grenoble, France<br />
2Department of Evolutionary Biology, Uppsala University, Sweden<br />
*Corresponding author: E-mail: <a href="mailto:michael.blum@imag.fr">michael.blum@imag.fr</a>.<br />
Associate editor: Sarah Tishkoff<br />
Abstract<br />
Two competing hypotheses are at the forefront of the debate on modern human origins. In the first scenario, known as the<br />
recent Out-of-Africa hypothesis, modern humans arose in Africa about 100,000&ndash;200,000 years ago and spread throughout<br />
the world by replacing the local archaic human populations. By contrast, the second hypothesis posits substantial gene flow<br />
between archaic and emerging modern humans. In the last two decades, the young time estimates&mdash;between 100,000 and<br />
200,000 years&mdash;of the most recent common ancestors for the mitochondrion and the Y chromosome provided evidence in<br />
favor of a recent African origin of modern humans. However, the presence of very old lineages for autosomal and X-linked<br />
genes has often been claimed to be incompatible with a simple, single origin of modern humans. Through the analysis of a<br />
public DNA sequence database, we find, similar to previous estimates, that the common ancestors of autosomal and X-linked<br />
genes are indeed very old, living, on average, respectively, 1,500,000 and 1,000,000 years ago. However, contrary to previous<br />
conclusions, we find that these deep gene genealogies are consistent with the Out-of-Africa scenario provided that the ancestral<br />
effective population size was approximately 14,000 individuals. We show that an ancient bottleneck in the Middle<br />
Pleistocene, possibly arising from an ancestral structured population, can reconcile the contradictory findings fromthemitochondrion<br />
on the one hand, with the autosomes and the X chromosome on the other hand.<br />
Key words: human origins, time to the most recent common ancestor, TMRCA, archaic admixture, African bottleneck,<br />
coalescent.</p>
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<p><a href="http://mbe.oxfordjournals.org/content/28/2/889.full.pdf+html">http://mbe.oxfordjournals.org/content/28/2/889.full.pdf+html</a></p>
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