Improved analyses of human mtDNA sequence support a recent African origin for Homo sapiens
Degree GrantorUniversity of Canterbury
Degree NameResearch report
New quantitative methods including several new techniques are reported for the 135 human mitochondrial sequences from Vigilant et al. (1991 ). General problems in analyzing large numbers of short sequences are discussed and an improved strategy suggested. A key feature is to focus, not on individual trees, but on the general 'landscape' of trees. Over 1000 searches were made from random starting trees with only one tree (a local optimum) being retained each time, thereby ensuring optima were found independently. A new tree comparison metric was developed that is unaffected by rearrangements of trees around many very short internal edges. Use of this metric showed that downweighting hypervariable sites revealed more evolutionary structure than studies that weighted all sites equally. Our results are consistent with convergence toward a global optimum. A crucial feature is that the best optima show very strong regional differentiation, a common group of african 49 sequences is found in all the best optima, and contain the 16 !Kung sequences in a separate group of San people. The other 86 sequences form a heterogeneous mixture of africans, europeans, australopapuans and asians. Thus all major human lineages occur in Africa but only a subset in the rest of the world. The existence of these African-only groups strongly contradicts multiregional theories for the origin of Homo sapiens that require widespread migration and interbreeding over the entire range of H. erectus. Only when the multiregional model is rejected is it appropriate to consider the root, based on a single locus, to be the center of origin of a population (otherwise different loci could give alternative geographic positions for the root). For this data, several methods locate the root within the group of 49 african sequences and are thus consistent with the recent African origin of H. sapiens. We demonstrate that the time of the last common ancestor cannot be the time of major expansion in human numbers and our results are thus also consistent with recent models that differentiate between the last common ancestor, expansion out of Africa, and the major expansion in human populations. Such a two-phase model is consistent with a wide range of molecular and archeological evidence.
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