Out of Africa again and again


The publication of a haplotype tree of human mitochondrial DNA variation in 1987 provoked a controversy about the details of recent human evolution that continues to this day. Now many haplotype trees are available, and new analytical techniques exist for testing hypotheses about recent evolutionary history using haplotype trees. Here I present formal statistical analysis of human haplotype trees for mitochondrial DNA, Y-chromosomal DNA, two X-linked regions and six autosomal regions. A coherent picture of recent human evolution emerges with two major themes. First is the dominant role that Africa has played in shaping the modern human gene pool through at least two—not one—major expansions after the original range extension of Homo erectus out of Africa. Second is the ubiquity of genetic interchange between human populations, both in terms of recurrent gene flow constrained by geographical distance and of major population expansion events resulting in interbreeding, not replacement.

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Figure 1: A new model of recent human evolution.
Figure 2: The distributions for the ages of the youngest clade contributing to a significant inference of gene flow constrained by isolation by distance at the highest nesting level for the genes MX1, PDHA1, EDN and ECP, and at intermediate nesting levels for the β-globin (β-Hb) locus and the Xq13.3 region.
Figure 3: The distributions for the ages of the youngest clade contributing to a significant inference of a population range expansion for mtDNA, Y-DNA, MC1R, MS205, and the β-globin (β-Hb) locus.


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I thank J. Brisson, J. Hess, R. Koch, M. Kramer, R. Robertson and J. Strasburg for suggestions on an earlier draft of this manuscript. I also thank E. Trinkhaus and J. Relethford for their reviews. This work was supported in part by a Burroughs Wellcome Fund Innovation Award in Functional Genomics.

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Supplementary information

Overview and content listing for all other Supplementary Information files (PDF 4 kb)

Nested clade method of phylogeographic analysis (PDF 4 kb)

GeoDis v2.0. documentation (PDF 55 kb)

Geodis inference key (PDF 6 kb)

Geodis ECP date set analysis (PDF 6 kb)

Geodis EDN data set analysis (PDF 5 kb)

Geodis MC1R data set analysis (PDF 6 kb)

Geodis mtDNA data set analysis (PDF 27 kb)

Geodis PDHA data set analysis (PDF 9 kb)

Geodis MS205a data set analysis (PDF 11 kb)

Geodis MS205b data set analysis (PDF 11 kb)

Geodis MS205c data set analysis (PDF 10 kb)

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