Natural Science Forum / Biology / Paleontology / May 2008

Copyright © 2008 The American Society of Human Genetics. All rights reserved.
The American Journal of Human Genetics, 24 April 2008

doi:10.1016/j.ajhg.2008.04.002

The Dawn of Human Matrilineal Diversity

Doron M. Behar1, 13, Richard Villems2, 13, Himla Soodyall3, Jason Blue-Smith4, Luisa Pereira5, 6, Ene Metspalu2, Rosaria Scozzari7, Heeran Makkan3, Shay Tzur1, David Comas8, Jaume Bertranpetit8, Lluis Quintana-Murci9, Chris Tyler-Smith10, R. Spencer Wells4, Saharon Rosset11, 12, The Genographic Consortium14

1 Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel
2 Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
3 School of Pathology, Division of Human Genetics, National Health Laboratory Service and University of the Witwatersrand, Johannesburg 2000, South Africa
4 Mission Programs, National Geographic Society, Washington, D.C. 20036, USA
5 Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto 4200-465, Portugal
6 Medical Faculty, University of Porto, Porto 4200-319, Portugal
7 Dipartimento di Genetica e Biologia Molecolare, Sapienza Università di Roma, Rome 00185, Italy
8 Evolutionary Biology Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain
9 Unit of Human Evolutionary Genetics, CNRS URA3012, Institut Pasteur, Paris 75724, France
10 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
11 Data Analytics Research Group, IBM T.J. Watson Research Center, Yorktown Heights, NY 10598, USA
12 Department of Statistics and Operations Research, School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel
13 These authors contributed equally to this work.
14 See Acknowledgments.

Abstract
The quest to explain demographic history during the early part of human evolution has been limited because of the scarce paleoanthropological record from the Middle Stone Age. To shed light on the structure of the mitochondrial DNA (mtDNA) phylogeny at the dawn of Homo sapiens, we constructed a matrilineal tree composed of 624 complete mtDNA genomes from sub-Saharan Hg L lineages. We paid particular attention to the Khoi and San (Khoisan) people of South Africa because they are considered to be a unique relic of hunter-gatherer lifestyle and to carry paternal and maternal lineages belonging to the deepest clades known among modern humans. Both the tree phylogeny and coalescence calculations suggest that Khoisan matrilineal ancestry diverged from the rest of the human mtDNA pool 90,000-150,000 years before present (ybp) and that at least five additional, currently extant maternal lineages existed during this period in parallel. Furthermore, we estimate that a minimum of 40 other evolutionarily successful lineages flourished in sub-Saharan Africa during the period of modern human dispersal out of Africa approximately 60,000-70,000 ybp. Only much later, at the beginning of the Late Stone Age, about 40,000 ybp, did introgression of additional lineages occur into the Khoisan mtDNA pool. This process was further accelerated during the recent Bantu expansions. Our results suggest that the early settlement of humans in Africa was already matrilineally structured and involved small, separately evolving isolated populations.

Introduction
Current genetic data support the hypothesis of a predominantly single origin for anatomically modern humans. The phylogeny of the maternally inherited mitochondrial DNA (mtDNA) has played a pivotal role in this model by anchoring our most recent maternal common ancestor to sub-Saharan Africa and suggesting a single dispersal wave out of that continent which populated the rest of the world much later. However, despite its importance as the cradle of humanity and the main location of anatomically modern humans for most of their existence, the initial Homo sapiens population dynamics and dispersal routes remain poorly understood. The potential to use present-day genetic patterns to detect the existence, or lack thereof, of matrilineal genetic structure among early Homo sapiens populations in sub-Saharan Africa is therefore of particular interest.
The human mtDNA phylogeny can be collapsed into two daughter branches, L0 and L1'2'3'4'5'6 (L1'5), located on opposite sides of its root (Figure 1). The L1'5 branch is far more widespread and has given rise to almost every mtDNA lineage found today, with two clades on this branch, (L3)M and (L3)N, forming the bulk of worldwide non-African genetic diversity and marking the out-of-Africa dispersal 50,000-65,000 years before present (ybp) (Figure 1). Current models, predating the recognition of L0 as sister to L1'5, suggest that the contemporary sub-Saharan mtDNA gene pool is the result of an early expansion of modern humans from their homeland, often suggested to be East Africa, to most of the African continent by exclusively L1 Hg clades, before being overwhelmed by a later expansion wave of L2 and L3 clades dated to 60,000-80,000 ybp. A more recent geographically restricted enrichment of the African maternal gene pool was shown to have occurred during the early Upper Paleolithic, when populations carrying mtDNA clades M1 and U6 arrived to north and northeast Africa from Eurasia, hardly penetrating the sub-Saharan portion of the continent, except Ethiopia. Therefore, the current sub-Saharan mtDNA gene pool is overwhelmingly a rich mix of L0 and L1'5 clades, found at varying frequencies throughout the continent.

Source: The American Journal of Human Genetics (AJHG) [Open Access Paper]
http://www.ajhg.org/AJHG/fulltext/S0002-9297(08)00255-3?large_figure=true

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Robert Karl Stonjek [Thanks John Roth]