Deep Divergences of Human Gene Trees andModels of Human Origins

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Deep Divergences of Human Gene Trees andModels of Human
Michael G. B. Blum*,1 and Mattias Jakobsson2
1Laboratoire des Techniques de l’Ing´enierie M´edicale et de la Complexit´e (TIMC-IMAG), Equipe Biologie Computationnelle et
Math´ematique (BCM), Centre National de la Recherche Scientifique (CNRS), Universit´e Joseph Fourier (UJF), Grenoble, France
2Department of Evolutionary Biology, Uppsala University, Sweden

Associate editor: Sarah Tishkoff
Two competing hypotheses are at the forefront of the debate on modern human origins. In the first scenario, known as the
recent Out-of-Africa hypothesis, modern humans arose in Africa about 100,000–200,000 years ago and spread throughout
the world by replacing the local archaic human populations. By contrast, the second hypothesis posits substantial gene flow
between archaic and emerging modern humans. In the last two decades, the young time estimates—between 100,000 and
200,000 years—of the most recent common ancestors for the mitochondrion and the Y chromosome provided evidence in
favor of a recent African origin of modern humans. However, the presence of very old lineages for autosomal and X-linked
genes has often been claimed to be incompatible with a simple, single origin of modern humans. Through the analysis of a
public DNA sequence database, we find, similar to previous estimates, that the common ancestors of autosomal and X-linked
genes are indeed very old, living, on average, respectively, 1,500,000 and 1,000,000 years ago. However, contrary to previous
conclusions, we find that these deep gene genealogies are consistent with the Out-of-Africa scenario provided that the ancestral
effective population size was approximately 14,000 individuals. We show that an ancient bottleneck in the Middle
Pleistocene, possibly arising from an ancestral structured population, can reconcile the contradictory findings fromthemitochondrion
on the one hand, with the autosomes and the X chromosome on the other hand.
Key words: human origins, time to the most recent common ancestor, TMRCA, archaic admixture, African bottleneck,