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Human evolution

A start for population genomics

Naturevolume 408pages652653 (2000) | Download Citation

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The most thorough analysis yet of the divergence of sequences in human mitochondrial DNA has been carried out. The results support the view that modern humans originated in Africa.

When and where did our species arise? Over the past two decades molecular evolutionists have vigorously pursued this question. DNA evidence from the cell powerhouse known as the mitochondrion has figured prominently in these studies, with mutations providing the raw data for producing evolutionary trees and molecular clocks to time sequence divergence. The mitochondrial family tree of humans has suggested that our roots lie in Africa1,2,3, but this tree has had only weak statistical support. Conversely, other researchers have proposed that modern humans arose simultaneously in different regions of the world4.

Now, on page 708 of this issue, Gyllensten and colleagues5 describe an analysis of the complete mitochondrial genomes of 53 people of diverse geographical, racial and linguistic backgrounds. At 16,500 base pairs, each sequence is much longer than those previously studied. The upshot is a robust tree rooted in Africa, which times the exodus from Africa to within the past 100,000 years (recent in evolutionary terms). With this result, the pendulum swings further towards the claim that modern humans, Homo sapiens, originated in Africa.

Our closest living relatives are African apes, so why is an African origin for modern humans controversial? The reason is that our immediate predecessors in the genus Homo, now extinct, are known to have wandered out of Africa as early as two million years ago. The main alternative to an African origin, the multiregional model, holds that modern humans arose simultaneously in Africa, Europe and Asia from these predecessors4. Proponents of this view argue that the fossil record indicates transitions between, for example, Neanderthals (H. neanderthalensis) and modern humans in Europe, and between H. erectus and modern humans in Asia. However, the existence of non-African transitional fossils is debatable6,7, and there is genetic evidence8 that Neanderthals did not widely interbreed with modern humans even though the two coexisted for at least 10,000 years. Such coexistence is the strongest evidence for recognizing the two as separate species.

The crux of the mitochondrial evidence for an African origin has been the presence of several African lineages deep in the evolutionary trees, even though they have only had weak statistical support. Gyllensten's team5 also found this pattern, but obtained a robust tree by collecting a larger data set than in previous studies. The three earliest branches in their tree lead exclusively to Africans, and two of the splits are statistically significant. Interpreted literally, the tree indicates that some Africans are closer to Europeans and Asians than to other Africans. However, the history of a single gene or molecule may not always mirror that of the population, and other molecular studies place Africans in a single group9. Together, these studies suggest that the founding population leaving Africa carried with it a subset of mitochondrial alleles — alternative forms of the same gene — and that African populations continued to interbreed after the exodus.

Gyllensten and colleagues estimate that the divergence of Africans and non-Africans occurred 52,000 ± 28,000 years ago, shortly followed by a population expansion in non-Africans. This date may even be a bit too recent. Other genetic markers indicate an exodus from Africa around 100,000 years ago9,10,11, which would be more consistent with fossil and archaeological evidence of modern humans outside Africa (Fig. 1). But no single genetic marker can time that event precisely, and the mitochondrial date is in the right ballpark. Some nuclear DNA markers have suggested earlier dates for the exodus from Africa12, so more data are needed to provide a fuller picture. Nonetheless, most of the genetic evidence indicates that there were only about 10,000 breeding individuals for a long time before the recent expansion of modern humans outside Africa13. Such a small population size is incompatible with the multiregional model, which would require many more individuals to maintain gene flow among continents.

Figure 1: The origin and dispersal of modern humans, Homo sapiens.
Figure 1

The time of origin of modern humans is not well known but may have been about 200,000 (130,000–465,000) years ago. New evidence from mitochondrial genomes5 bolsters the hypothesis that the place of origin was sub-Saharan Africa and that the dispersal from Africa occurred within the past 100,000 years. The earliest known fossil and archaeological evidence on each continent14, shown on the map, is consistent with this view.

A different question is when H. sapiens arose in the first place. Molecular clocks would be well suited to address that question if our closest relative were living. But our closest relative in the genus Homo, whether H. erectus or some other species, is unfortunately extinct. The earliest fossils of modern H. sapiens are 130,000 years old14, however, so that is the upper bound on the origin of our species. Studies of ancient DNA provide hints to a lower bound. The split between H. neanderthalensis (a species which is not necessarily our closest relative) and H. sapiens has been timed by a DNA clock at 465,000 years ago8. So our species probably arose somewhere between 130,000 and 465,000 years ago. An estimate of 200,000 years ago is not unreasonable given the transition seen in the African fossil record between archaic and modern humans around that time14.

Gyllensten and colleagues5 have used sequences from a large number of complete mitochondrial genomes to address these evolutionary questions, an approach that could be called population genomics. The number of such genome sequences will surely grow rapidly in the near future, and complete sequences of nuclear genomes, from more than one human, are to be expected. Genes responsible for physical and behavioural traits will probably be found and their allelic histories will provide additional information. Molecular evolutionary trees and time estimates will have greater precision, all of which will help to clarify our evolutionary history.

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  1. Department of Biology Institute of Molecular Evolutionary Genetics, and the Astrobiology Research Center, 208 Mueller Laboratory, Pennsylvania State University, University Park, Pennsylvania, 16802, USA

    • S. Blair Hedges

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Correspondence to S. Blair Hedges.

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