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MBE Advance Access originally published online on December 28, 2006
Molecular Biology and Evolution 2007 24(3):757-768; doi:10.1093/molbev/msl209
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© The Author 2006. 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 Articles

Whole-mtDNA Genome Sequence Analysis of Ancient African Lineages

Mary Katherine Gonder*, Holly M. Mortensen*, Floyd A. Reed*, Alexandra de Sousa{dagger},{ddagger} and Sarah A. Tishkoff*

* Department of Biology, University of Maryland
{dagger} Center for the Advanced Study of Hominid Paleobiology
{ddagger} Department of Anthropology, George Washington University

E-mail: tishkoff{at}umd.edu.

Accepted for publication December 12, 2006.

Studies of human mitochondrial (mt) DNA genomes demonstrate that the root of the human phylogenetic tree occurs in Africa. Although 2 mtDNA lineages with an African origin (haplogroups M and N) were the progenitors of all non-African haplogroups, macrohaplogroup L (including haplogroups L0–L6) is limited to sub-Saharan Africa. Several L haplogroup lineages occur most frequently in eastern Africa (e.g., L0a, L0f, L5, and L3g), but some are specific to certain ethnic groups, such as haplogroup lineages L0d and L0k that previously have been found nearly exclusively among southern African "click" speakers. Few studies have included multiple mtDNA genome samples belonging to haplogroups that occur in eastern and southern Africa but are rare or absent elsewhere. This lack of sampling in eastern Africa makes it difficult to infer relationships among mtDNA haplogroups or to examine events that occurred early in human history. We sequenced 62 complete mtDNA genomes of ethnically diverse Tanzanians, southern African Khoisan speakers, and Bakola Pygmies and compared them with a global pool of 226 mtDNA genomes. From these, we infer phylogenetic relationships amongst mtDNA haplogroups and estimate the time to most recent common ancestor (TMRCA) for haplogroup lineages. These data suggest that Tanzanians have high genetic diversity and possess ancient mtDNA haplogroups, some of which are either rare (L0d and L5) or absent (L0f) in other regions of Africa. We propose that a large and diverse human population has persisted in eastern Africa and that eastern Africa may have been an ancient source of dispersion of modern humans both within and outside of Africa.

Key Words: genetics • mtDNA genomes • Africa • mtDNA haplogroups • Homo sapiens • Tanzania • Khoisan speakers

Lisa Matisoo-Smith, Associate Editor


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