Post by Admin on Aug 25, 2013 8:37:45 GMT
Until recently, the out-of-Africa model of human evolution was favoured by most genetic analyses, but this model collapsed when the sequencing of the Neanderthal genome revealed that 1%–3% of the genome of Eurasians was of Neanderthal origin. At the same time, refined analyses of modern human genomic data [1]–[3] have changed our view of evolutionary forces acting on our genome. While most people assumed that the out-of-Africa expansion had been characterized by a series of adaptations to new environments [4]–[6] leading to recurrent selective sweeps [7], our genome actually contains little trace of recent complete sweeps [2], [3], [8] and the genetic differentiation of human population has been very progressive over time, probably without major adaptive episodes [9]. In this review, we detail these changes of paradigm and we discuss their implication for future studies of human diversity.
In line with previous studies [10]–[12] which suggested that some aspects of human genomic diversity were incompatible with a complete replacement of archaic hominins, evidence for admixture between humans and Neanderthals emerged from the first analysis of a complete Neanderthal genome [13]. Indeed, the presence of a significant excess of Neanderthal-derived alleles in Eurasian populations as compared to Africans has been interpreted as resulting from an admixture episode between the ancestors of Eurasians and Neanderthals somewhere in the Middle East [13] (Figure 1A). Even though the existence of a very ancient population subdivision in Africa from which both Neanderthals and Eurasians would have emerged could lead to similar patterns [14], the maintenance of such a subdivision over tens of thousands of generations seems unlikely.
The sequencing of another archaic hominin from the Denisova cave in the Altaï mountains in Siberia has further revealed that Papua New Guineans showed signs of introgression from this archaic human [15]. Further studies of 33 populations from Southeast Asia and Oceania [16] showed that Denisovan admixture was actually present in other Oceanians, Melanesians, Polynesians, and east Indonesians but was virtually absent in mainland east Asians (but see [17] for evidence of possible Denisovan introgression on the Asian continent). Overall, these genomic analyses of admixture suggest that 1%–3% of the genome of all Eurasians and native Amerindians is of Neanderthal origin [15], and that Papua New Guineans and Australians have another 3.5% of their genome of Denisovan origin [16]. The out-of-Africa model of human evolution, which posited a complete replacement of archaic by modern humans in Eurasia, thus needs to be modified to include a limited assimilation of archaic genes, but the fact that most of the genetic variation observed in extant non-African populations comes from Africa remains true.
There is thus both direct [13], [15] and indirect [11], [18] evidence for archaic admixture on four continents, suggesting that modern humans have not been totally genetically isolated since their emergence, some 150–200 Kya in East Africa [22], [23]. However, there is still quite some discussion about the place, the timing, the exact numbers of admixture events, and the biological implications of these interbreeding events (see Figure 1). The finding of almost equal levels of Neanderthal introgression in all Eurasians has been interpreted as evidence for a unique pulse of admixture in the Middle East between Neanderthals and the ancestors of Eurasians [13] (Figure 1A). The fact that Denisovan admixture had been first evidenced in Papua New Guineans suggested that admixture had occurred as a single pulse in Southeast Asia, after the separation of the ancestors of Oceanians and other Asians [15], [16] (Figure 1A). The analysis of an Australian genome has confirmed the presence of Denisovan admixture in Australians [24] and suggested that admixture occurred during a first early wave of colonization towards Oceania, either in Southeast Asia or earlier in Eurasia (Figure 1B). A reanalysis of a large human SNP database and its comparison with Denisovan-derived alleles has suggested the presence of Denisovan admixture in East Asians, albeit at lower levels than in Oceanians [17], which could have occurred at a different place than for Oceanians, somewhere in East Asia (Figure 1C).
Contrastingly, Currat and Excoffier [25] introduced a spatially explicit model of interbreeding between Neanderthals and Eurasians that could occur over the whole Neanderthal range (Figure 1D). They obtained similarly low levels (1%–3%) of Neanderthal introgression in both Europe and China if interspecific exchanges were locally extremely limited (only 200–400 interbreeding events over the >6,000 years of co-existence between the two species). An extension of this scenario to Denisovan admixture would imply that modern humans could have hybridized along all migration routes overlapping with the range(s) of archaic humans (Figure 1D). The fact that the largest levels of Denisovan introgression are found in Oceanians raises the question of a potential discontinuity in the Denisovan range (Figure 1A, 1B) or of a genetic differentiation of archaic hominins living in different ecosystems (Figure 1D). Alternatively, modern humans could have admixed with other hominins [26], and/or inferred hominin introgression could result from the sharing of some derived sites between Neanderthals, Denisovans, and unidentified archaic hominins. A scenario involving an unsampled Eurasian archaic hominin has received support from a recent study [27] showing the presence of a highly divergent (>3 Mya) haplotype of the innate immune gene OAS1. This deep lineage is found at high frequencies in Oceania (and at lower frequencies up to Pakistan). This DNA segment is more closely related (0.6 Mya divergence) to the Denisova sequence than to the Neanderthal sequence, which is itself closer to the human reference sequence. It has been speculated [27] that this fragment had introgressed from a more archaic hominin than Denisovans, who could have been themselves introgressed earlier.
www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002837
In line with previous studies [10]–[12] which suggested that some aspects of human genomic diversity were incompatible with a complete replacement of archaic hominins, evidence for admixture between humans and Neanderthals emerged from the first analysis of a complete Neanderthal genome [13]. Indeed, the presence of a significant excess of Neanderthal-derived alleles in Eurasian populations as compared to Africans has been interpreted as resulting from an admixture episode between the ancestors of Eurasians and Neanderthals somewhere in the Middle East [13] (Figure 1A). Even though the existence of a very ancient population subdivision in Africa from which both Neanderthals and Eurasians would have emerged could lead to similar patterns [14], the maintenance of such a subdivision over tens of thousands of generations seems unlikely.
The sequencing of another archaic hominin from the Denisova cave in the Altaï mountains in Siberia has further revealed that Papua New Guineans showed signs of introgression from this archaic human [15]. Further studies of 33 populations from Southeast Asia and Oceania [16] showed that Denisovan admixture was actually present in other Oceanians, Melanesians, Polynesians, and east Indonesians but was virtually absent in mainland east Asians (but see [17] for evidence of possible Denisovan introgression on the Asian continent). Overall, these genomic analyses of admixture suggest that 1%–3% of the genome of all Eurasians and native Amerindians is of Neanderthal origin [15], and that Papua New Guineans and Australians have another 3.5% of their genome of Denisovan origin [16]. The out-of-Africa model of human evolution, which posited a complete replacement of archaic by modern humans in Eurasia, thus needs to be modified to include a limited assimilation of archaic genes, but the fact that most of the genetic variation observed in extant non-African populations comes from Africa remains true.
There is thus both direct [13], [15] and indirect [11], [18] evidence for archaic admixture on four continents, suggesting that modern humans have not been totally genetically isolated since their emergence, some 150–200 Kya in East Africa [22], [23]. However, there is still quite some discussion about the place, the timing, the exact numbers of admixture events, and the biological implications of these interbreeding events (see Figure 1). The finding of almost equal levels of Neanderthal introgression in all Eurasians has been interpreted as evidence for a unique pulse of admixture in the Middle East between Neanderthals and the ancestors of Eurasians [13] (Figure 1A). The fact that Denisovan admixture had been first evidenced in Papua New Guineans suggested that admixture had occurred as a single pulse in Southeast Asia, after the separation of the ancestors of Oceanians and other Asians [15], [16] (Figure 1A). The analysis of an Australian genome has confirmed the presence of Denisovan admixture in Australians [24] and suggested that admixture occurred during a first early wave of colonization towards Oceania, either in Southeast Asia or earlier in Eurasia (Figure 1B). A reanalysis of a large human SNP database and its comparison with Denisovan-derived alleles has suggested the presence of Denisovan admixture in East Asians, albeit at lower levels than in Oceanians [17], which could have occurred at a different place than for Oceanians, somewhere in East Asia (Figure 1C).
Contrastingly, Currat and Excoffier [25] introduced a spatially explicit model of interbreeding between Neanderthals and Eurasians that could occur over the whole Neanderthal range (Figure 1D). They obtained similarly low levels (1%–3%) of Neanderthal introgression in both Europe and China if interspecific exchanges were locally extremely limited (only 200–400 interbreeding events over the >6,000 years of co-existence between the two species). An extension of this scenario to Denisovan admixture would imply that modern humans could have hybridized along all migration routes overlapping with the range(s) of archaic humans (Figure 1D). The fact that the largest levels of Denisovan introgression are found in Oceanians raises the question of a potential discontinuity in the Denisovan range (Figure 1A, 1B) or of a genetic differentiation of archaic hominins living in different ecosystems (Figure 1D). Alternatively, modern humans could have admixed with other hominins [26], and/or inferred hominin introgression could result from the sharing of some derived sites between Neanderthals, Denisovans, and unidentified archaic hominins. A scenario involving an unsampled Eurasian archaic hominin has received support from a recent study [27] showing the presence of a highly divergent (>3 Mya) haplotype of the innate immune gene OAS1. This deep lineage is found at high frequencies in Oceania (and at lower frequencies up to Pakistan). This DNA segment is more closely related (0.6 Mya divergence) to the Denisova sequence than to the Neanderthal sequence, which is itself closer to the human reference sequence. It has been speculated [27] that this fragment had introgressed from a more archaic hominin than Denisovans, who could have been themselves introgressed earlier.
www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002837