Gene Flow, Haplotype Patterns and Modern Human Origins


Gene flow is a genetic interchange between local populations within a species. Information about past gene flow patterns can be extracted from haplotypes, which are the multisite nucleotide states of a stretch of deoxyribonucleic acid (DNA) in the genome. Such studies reveal that gene flow has and continues to play an important role in human evolution, causing all modern humans to represent a single evolutionary lineage. These studies also revealed that when anatomically modern humans first expanded out of sub‐Saharan Africa starting 130 000 years ago, they interbred at low levels with the archaic Eurasian populations that they encountered, thereby falsifying the hypothesis that anatomically modern humans completely replaced genetically the archaic populations that they encountered. This conclusion has been confirmed by direct studies on ancient DNA and fossils.

Key Concepts:

  • Gene flow occurs when individuals move out of their population of birth and reproduce in a different geographical population.

  • Admixture is a special case of gene flow in which a whole group of individuals moves as a population and interbreeds with other, genetically distinct populations that they encounter.

  • When a new genetic variant (mutation) arises, its spatial distribution is affected by the movement of individuals and/or populations that bear this mutation.

  • Many different mutations that occur close together in a genomic region with little or no recombination can be ordered together into a multisite haplotype, and haplotypes can then be used to estimate an evolutionary tree that displays the temporal order and genetic background upon which each mutation occurred.

  • By overlaying geographical information upon the haplotype tree, the pattern of spatial and temporal spread of mutations and haplotypes can be estimated, thereby allowing inference about past patterns of gene flow and of historical events such as range expansions or population fragmentation events.

  • An analysis of human haplotype trees shows with strong statistical significance that there were three major expansion events out of Africa into Eurasia during the Pleistocene, all corraborated by fossil and archaelogical evidence and occurring during climatically favourable periods; an expansion 1.9 million years ago corresponding to the initial spread of Homo erectus out of Africa; a mid‐Pleistocene expansion corresponding to the spread of the Acheulean culture out of Africa, and a recent expansion 130 000 years ago corresponding to the spread of anatomically modern humans out of Africa.

  • The haplotype tree analysis indicates that the last two out‐of‐Africa expansion events were marked by low levels of admixture between the expanding African populations with Eurasian populations that had been established by the first out‐of‐Africa expansion of H. erectus, and this conclusion of limited admixture has been confirmed by studies on ancient DNA.

  • The haplotype tree analysis indicates that recurrent gene flow occurred between African and Eurasian populations at least since the Acheulean expansion, and that gene flow and admixture have played an even more important role in human evolution as humans became more mobile after the most recent out‐of‐Africa expansion 130 000 years ago.

  • Because of historic and ongoing gene flow and admixture, the human species today behaves as a single evolutionary lineage with modest levels of genetic differentiation across the world.

Keywords: human evolution; gene flow; replacement; admixture; haplotype

Figure 1.

The multiregional (a) and candelabra (b) models of human evolution. In the multiregional model, key fossils and sites are placed in a trellis, with vertical lines indicating regional descent, and diagonal and horizontal lines representing genetic exchange between regions. In the candelabra model, the vertical lines represent separate evolutionary lineages of hominins with no significant gene flow between them.

Figure 2.

The out‐of‐Africa replacement (a) and candelabra with weak gene flow (b) models of human evolution. The broken vertical lines in panel (a) represent the replacement of Eurasian populations by the expanding African population. The thin double‐headed arrows in panel (b) indicate weak and sporadic gene flow among the continental hominin populations.

Figure 3.

A model of recent human evolution as inferred from a multilocus nested‐clade analysis. All inferences are cross‐validated by the indicated gene name abbreviations. Major expansions of human populations are indicated by arrows, along with their estimated times and 95% confidence limits using a molecular clock with a 6 Ma calibration for the split of humans and chimpanzees. Regional descent is indicated by thin vertical lines, and gene flow (mostly constrained by isolation‐by‐distance) between regions is indicated by thin diagonal lines.



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Further Reading

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Templeton, Alan R(Nov 2012) Gene Flow, Haplotype Patterns and Modern Human Origins. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0020795.pub2]