contain click consonants and is spoken by hunter-gatherer populations in eastern (Hadza and Sandawe) and southern Africa [the San, referred to here as “southern African Khoesan” (“SAK”)], is the most contentious of the African language families because there is so much divergence among the Hadza, Sandawe, and SAK languages (Nurse, 1997; Sands, 1998).
The earliest emergence of anatomically modern humans in the fossil record occurred in eastern Africa 200–150 thousand years ago (kya) (McDermott et al., 1996; J.D. Clark et al., 2003; McDougall et al., 2005; Trinkaus, 2005). Although the earliest dated modern humans outside of Africa were identified in the Middle East ~90 kya (Schwarcz et al., 1988; Stringer et al., 1989; McDermott et al., 1993; Mercier et al., 1993; Trinkaus, 2005), there was no continuous occupation of regions outside of Africa until ~60–40 kya; modern human remains are documented in Papua New Guinea 60–40 kya (Groube et al., 1986), southwest Asia ~35 kya, Europe ~40 kya, and mainland Asia ~35 kya (Trinkaus, 2005). Therefore, over half of modern human history took place within Africa exclusively, and understanding patterns of variation within Africa is critical for the elucidation of modern human demographic history.
Genetic data from extant modern humans complement the fossil record in the reconstruction of modern human origins. The uniparentally inherited mitochondrial DNA (mtDNA) and nonrecombinant portion of the Y chromosome (NRY) are two loci that have been extensively studied in human populations, in part because they represent the maternal and paternal population histories, respectively, in a population sample and in part because they do not undergo recombination and, therefore, lineages can be more easily traced back to a single common ancestor. Unfortunately, the mtDNA and NRY loci are single loci, which are susceptible to the effects of natural selection and genetic drift because they have smaller effective population sizes relative to the autosomes and because any selective pressure will impact the entire locus. Thus, combined mtDNA, NRY, and autosomal data are necessary for a thorough understanding of any population history.
The mtDNA, NRY, and autosomal DNA studies demonstrate that the highest levels of genetic variation are present in African samples relative to non-Africans, consistent with a model of African ancestry for all modern humans [e.g., Cann et al. (1987), Underhill et al. (2001), International HapMap Consortium (2003), Akey et al. (2004); Frazer et al. (2007), Garrigan et al. (2007), Li et al. (2008), Tishkoff et al. (2009)]. Further, phylogenetic analysis of mtDNA and NRY variation reveals that the deepest phylogenetic clades are found exclusively in African samples and all