chromosome evidence for ancient human histories

Diverse African and non-African samples of the X-linked PDHA1 (pyruvate dehydrogenase E1 a subunit) locus revealed a fixed DNA sequence difference between the two sample groups. The age of onset of population subdivision appears to be about 200 thousand years ago. This predates the earliest modern human fossils, suggesting the transformation to modern humans occurred in a subdivided population. The base of the PDHA1 gene tree is relatively ancient, with an estimated age of 1.86 million years, a late Pliocene time associated with early species of Homo. PDHA1 revealed very low variation among non-Africans, but in other respects the data are consistent with reports from other X-linked and autosomal haplotype data sets. Like these other genes, but in conflict with microsatellite and mitochondrial data, PDHA1 does not show evidence of human population expansion. The estimated ages of the earliest modern human fossils from South Africa and the Levant are roughly 100–130 thousand years (1, 2), and a number of African transitional forms date from 100–200 thousand years before the present (Kyr BP) (3). The same time frame also emerges from genetic data as a period of splitting between African and non-African populations (4–9). The broad, approximate coincidence of the two types of data could have arisen from a history in which the morphological transition to modern forms occurred over a wide geographic range. The extent to which this is true and the details of such a process are issues that lie at the heart of some debates on the origins of modern humans. According to African origins models, modern humans are posited to have originated in a subpopulation of archaic hominids in sub-Saharan Africa, with the location of this subpopulation undetermined (9–11). However, transitional fossils that display near modern characteristics have been found in widely disparate regions within Africa, including South Africa, East Africa, as well as North Africa, leaving the possibility that the ancestral population covered a wide geographic area (12). In contrast, a strict multiregional view supposes that modern humans arose in multiple, different regions of the Old World (13). Between these models there lie many intermediate scenarios of the geographic spread and structure of the ancestral population at the time of the transformation to modern humans. There are three common questions to these debates (9, 14, 15). How geographically spread were ancestors of modern humans? Were they divided into subpopulations? If they were divided, how much geneflow occurred between subpopulations? One effective approach to address these questions is to generate comparative haplotype data sets for multiple regions of the genome. Multilocus data sets permit detailed historical estimates for each genomic region studied, and the comparison among genomic regions can be used to distinguish those forces that have acted on individual genomic regions (i.e., natural selection) from evolutionary forces that have affected the entire genome (e.g., population size, populations size changes, population subdivision, and gene flow) (16). We have generated a comparative DNA sequence data set from a diverse Old World sample for a portion of the X chromosome gene for the pyruvate dehydrogenase E1 a subunit, or PDHA1. We then compared our results to those reported for other X chromosome and autosomal haplotype