Eswaran Vinayak - Harpending Henry - Rogers Alan R. - Genomics refutes an exclusively African origin of humans

Authors : Eswaran Vinayak - Harpending Henry - Rogers Alan R.
Title : Genomics refutes an exclusively African origin of humans
Year : 2005

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Ten years ago, evidence from genetics gave strong support to the ‘‘recent Africa origin’’ view of the evolution of modern humans, which posits that Homo sapiens arose as a new species in Africa and subsequently spread, leading to the extinction of other archaic human species. Subsequent data from the nuclear genome not only fail to support this model, they do not support any simple model of human demographic history. In this paper, we study a process in which the modern human phenotype originates in Africa and then advances across the world by local demic diffusion, hybridization, and natural selection. While the multiregional model of human origins posits a number of independent single locus selective sweeps, and the ‘‘out of Africa’’ model posits a sweep of a new species, we study the intermediate case of a phenotypic sweep. Numerical simulations of this process replicate many of the seemingly contradictory features of the genetic data, and suggest that as much as 80% of nuclear loci have assimilated genetic material from non-African archaic humans. Introduction. Since the discovery of apparent signals of strong late Pleistocene population expansions (Rogers and Harpending, 1992; Harpending et al., 1993) in human mitochondrial DNA (mtDNA), a number of studies have sought similar signs in other genetic polymorphisms. Among the data so analyzed have been nuclear sequences, short tandem repeat polymorphisms (STRs), and single nucleotide polymorphisms (SNPs). While mtDNA shows signals of recent expansions in almost every human population, it has by now become clear that the nuclear data do not present an unambiguous picture regarding population expansion associated with the spread of anatomically modern humans. For example, various analyses of STR data using different statistics have given contradictory signals of expansions, their timing, and the sub-populations involved (Di Rienzo et al., 1998; Reich and Goldstein, 1998; Kimmel et al., 1998; Zhivotovsky et al., 2000). The first detailed evidence from the nuclear genome also showed no evidence at all of expansion (Harris and Hey, 1999). To explain low interpopulation diversity in humans, it has been suggested that humans passed through a bottleneck (Haigh and Maynard Smith, 1972). It has also been proposed that there was a bottleneck associated with the emergence of modern humans in Africa and their spread throughout the world (Jones and Rouhani, 1986). For example, SNP haplotype block data show a signature of bottlenecks at vastly differing times in the prehistory of African and non-African populations (Reich et al., 2001; Gabriel et al., 2002), even if their cause as yet remains unclear. These bottlenecks would need to have been of extraordinary severity and/or duration to explain some of the data, e.g., for Europeans, Reich et al. (2001) suggested a pre-expansion bottleneck size of 50 individuals for 20 generations (or any size and duration of the same ratio), while Marth et al. (2003) obtained their best fit with size-duration ratios between 1000 to 2500 individuals for, respectively, 240 to 550 generations. Yet, single locus studies (e.g., Harding et al., 1997, 2000; Zhao et al., 2000; Yu et al., 2001, 2002) often find at most mild bottlenecks, or none, in non-Africans, resulting in an overall picture that is puzzling. A recent study by Marth et al. (2003) used 500,000 SNPs to conclude that the dominant population history of humans was a Pleistocene population collapse followed by a mild post-Pleistocene recovery. The importance of these varied signals of bottlenecks and expansions is the subject of this paper. ...

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