BACKGROUND: From Paleo-Indian times to recent historical episodes, the Mesoamerican isthmus played an important role in the distribution and patterns of variability all around the double American continent. However, the amount of genetic information currently available on Central American continental populations is very scarce. In order to shed light on the role of Mesoamerica in the peopling of the New World, the present study focuses on the analysis of the mtDNA variation in a population sample from El Salvador. METHODOLOGY/PRINCIPAL FINDINGS: We have carried out DNA sequencing of the entire control region of the mitochondrial DNA (mtDNA) genome in 90 individuals from El Salvador. We have also compiled more than 3,985 control region profiles from the public domain and the literature in order to carry out inter-population comparisons. The results reveal a predominant Native American component in this region: by far, the most prevalent mtDNA haplogroup in this country (at approximately 90%) is A2, in contrast with other North, Meso- and South American populations. Haplogroup A2 shows a star-like phylogeny and is very diverse with a substantial proportion of mtDNAs (45%; sequence range 16090-16365) still unobserved in other American populations. Two different Bayesian approaches used to estimate admixture proportions in El Salvador shows that the majority of the mtDNAs observed come from North America. A preliminary founder analysis indicates that the settlement of El Salvador occurred about 13,400+/-5,200 Y.B.P.. The founder age of A2 in El Salvador is close to the overall age of A2 in America, which suggests that the colonization of this region occurred within a few thousand years of the initial expansion into the Americas. CONCLUSIONS/SIGNIFICANCE: As a whole, the results are compatible with the hypothesis that today's A2 variability in El Salvador represents to a large extent the indigenous component of the region. Concordant with this hypothesis is also the observation of a very limited contribution from European and African women ( approximately 5%). This implies that the Atlantic slave trade had a very small demographic impact in El Salvador in contrast to its transformation of the gene pool in neighbouring populations from the Caribbean facade.
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Several suggestions have been made for avoiding errors in mitochondrial DNA (mtDNA) sequencing and documentation. Unfortunately, the current clinical, forensic, and population genetic literature on mtDNA still delivers a large number of studies with flawed sequence data, which, in extreme cases, damage the whole message of a study. The phylogenetic approach has been shown to be useful for pinpointing most of the errors. However, many geneticists, especially in the forensic and medical fields, are not familiar with either effective search strategies or the evolutionary terminology. We here provide a manual that should help prevent errors at any stage by re-examining data fresh from the sequencer in the light of previously published data. A fictitious case study of a European mtDNA data set (albeit composed from the literature) then demonstrates the steps one has to go through in order to assess the quality of sequencing and documentation. (C) 2005 Elsevier Inc. All rights reserved.
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We have analyzed and compared mitochondrial DNA variation of populations from the Near East and Africa and found a very high frequency of African lineages present in the Yemen Hadramawt: more than a third were of clear sub-Saharan origin. Other Arab populations carried approximately 10% lineages of sub-Saharan origin, whereas non-Arab Near Eastern populations, by contrast, carried few or no such lineages, suggesting that gene flow has been preferentially into Arab populations. Several lines of evidence suggest that most of this gene flow probably occurred within the past approximately 2,500 years. In contrast, there is little evidence for male-mediated gene flow from sub-Saharan Africa in Y-chromosome haplotypes in Arab populations, including the Hadramawt. Taken together, these results are consistent with substantial migration from eastern Africa into Arabia, at least in part as a result of the Arab slave trade, and mainly female assimilation into the Arabian population as a result of miscegenation and manumission.
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Previous studies of mitochondrial DNA (mtDNA) in Europe and the Near East have suggested that, in contrast with classical markers and the Y chromosome, mtDNA does not exhibit significant geographical structuring. Here, we show that, with a sufficiently large sample size and a better resolved mtDNA tree, clades of mtDNA do indeed exhibit gradients similar to those of other marker systems. However, the more detailed analyses afforded by molecular sequence data suggest that the explanations for these gradients are likely to be much more complex than those proposed for classical markers.
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We have analyzed the maternally inherited mitochondrial DNA from each of nine geographically separated Jewish groups, eight non-Jewish host populations, and an Israeli Arab/Palestinian population, and we have compared the differences found in Jews and non-Jews with those found using Y-chromosome data that were obtained, in most cases, from the same population samples. The results suggest that most Jewish communities were founded by relatively few women, that the founding process was independent in different geographic areas, and that subsequent genetic input from surrounding populations was limited on the female side. In sharp contrast to this, the paternally inherited Y chromosome shows diversity similar to that of neighboring populations and shows no evidence of founder effects. These sex-specific differences demonstrate an important role for culture in shaping patterns of genetic variation and are likely to have significant epidemiological implications for studies involving these populations. We illustrate this by presenting data from a panel of X-chromosome microsatellites, which indicates that, in the case of the Georgian Jews, the female-specific founder event appears to have resulted in elevated levels of linkage disequilibrium.
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Human history is punctuated by periods of rapid cultural change. Although archeologists have developed a range of models to describe cultural transitions, in most real examples we do not know whether the processes involved the movement of people or the movement of culture only. With a series of relatively well defined cultural transitions, the British Isles present an ideal opportunity to assess the demographic context of cultural change. Important transitions after the first Paleolithic settlements include the Neolithic, the development of Iron Age cultures, and various historical invasions from continental Europe. Here we show that patterns of Y-chromosome variation indicate that the Neolithic and Iron Age transitions in the British Isles occurred without large-scale male movements. The more recent invasions from Scandinavia, on the other hand, appear to have left a significant paternal genetic legacy. In contrast, patterns of mtDNA and X-chromosome variation indicate that one or more of these pre-Anglo-Saxon cultural revolutions had a major effect on the maternal genetic heritage of the British Isles.
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Modern humans reached Southeast Asia and Oceania in one of the first dispersals out of Africa. The resulting temporal overlap of modern and archaic humans-and the apparent morphological continuity between them-has led to claims of gene flow between Homo sapiens and H. erectus. Much more recently, an agricultural technology from mainland Asia spread into the region, possibly in association with Austronesian languages. Using detailed genealogical study of Y chromosome variation, we show that the majority of current Austronesian speakers trace their paternal heritage to Pleistocene settlers in the region, as opposed to more-recent agricultural immigrants. A fraction of the paternal heritage, however, appears to be associated with more-recent immigrants from northern populations. We also show that the northern Neolithic component is very unevenly dispersed through the region, with a higher contribution in Southeast Asia and a nearly complete absence in Melanesia. Contrary to claims of gene flow (under regional continuity) between H. erectus and H. sapiens, we found no ancestral Y chromosome lineages in a set of 1,209 samples. The finding excludes the possibility that early hominids contributed significantly to the paternal heritage of the region.
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Founder analysis is a method for analysis of nonrecombining DNA sequence data, with the aim of identification and dating of migrations into new territory. The method picks out founder sequence types in potential source populations and dates lineage clusters deriving from them in the settlement zone of interest. Here, using mtDNA, we apply the approach to the colonization of Europe, to estimate the proportion of modern lineages whose ancestors arrived during each major phase of settlement. To estimate the Palaeolithic and Neolithic contributions to European mtDNA diversity more accurately than was previously achievable, we have now extended the Near Eastern, European, and northern-Caucasus databases to 1,234, 2, 804, and 208 samples, respectively. Both back-migration into the source population and recurrent mutation in the source and derived populations represent major obstacles to this approach. We have developed phylogenetic criteria to take account of both these factors, and we suggest a way to account for multiple dispersals of common sequence types. We conclude that (i) there has been substantial back-migration into the Near East, (ii) the majority of extant mtDNA lineages entered Europe in several waves during the Upper Palaeolithic, (iii) there was a founder effect or bottleneck associated with the Last Glacial Maximum, 20,000 years ago, from which derives the largest fraction of surviving lineages, and (iv) the immigrant Neolithic component is likely to comprise less than one-quarter of the mtDNA pool of modern Europeans.
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Recombination has recently been invoked as an explanation for the large amount of homoplasy observed in a collection of complete or nearly complete human mitochondrial sequences. Here we show that some of the data on which this conclusion was based are likely to be unreliable and that if these data are excluded, the results are no longer significant.
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Variation in the human mitochondrial genome (mtDNA) is now routinely described and used to infer the histories of peoples, by means of one of two procedures, namely, the assaying of RFLPs throughout the genome and the sequencing of parts of the control region (CR). Using 95 samples from the Near East and northwest Caucasus, we present an analysis based on both systems, demonstrate their concordance, and, using additional available information, present the most refined phylogeny to date of west Eurasian mtDNA. We describe and apply a nomenclature for mtDNA clusters. Hypervariable nucleotides are identified, and the relative mutation rates of the two systems are evaluated. We point out where ambiguities remain. The identification of signature mutations for each cluster leads us to apply a hierarchical scheme for determining the cluster composition of a sample of Berber speakers, previously analyzed only for CR variation. We show that the main indigenous North African cluster is a sister group to the most ancient cluster of European mtDNAs, from which it diverged approximately 50,000 years ago.
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We have developed a typing system using natural sequence variation in the thrombospondin-related adhesive protein (TRAP) gene of Plasmodium falciparum. This method permits a haplotype to be assigned to any particular TRAP gene. We have applied this method to a hospital-based, case control-study in Mali. Previous sequence variation and conservation in TRAP has been confirmed. Particular TRAP haplotypes can be used as geographic hallmarks. Because of the high level of conflict between characters, we have examined the phylogenetic relationships between parasites using a network approach. Having received patient samples from urban and periurban areas of Bamako, the majority of haplotypes were closely related and distinct from TRAP sequences present in other continents. This suggests that the structure of TRAP can only tolerate a limited number of sequence variations to preserve its function but that this is sufficient to allow the parasite to evade the host's immune system until a long-lived immune response can be maintained. It may also reflect host genetics in that certain variants may escape the host immune response more efficiently than others. For vaccine design, sequences from the major regional variants may need to be considered in the production of effective subunit vaccines.
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For most of the past century, prehistorians have had to rely on the fossil and archaeological records in order to reconstruct the past. In the last few decades, this evidence has been substantially supplemented from classical human genetics. More recently, phylogenetic analyses of DNA sequences that incorporate geographical information have provided a high-resolution tool for the investigation of prehistoric demographic events, such as founder effects and population expansions. These events can be dated using a molecular clock when the mutation rate and founder haplotypes are known. We have previously applied such methods to sequence data from the mitochondrial DNA control region, to suggest that most extant mitochondrial sequences in western Europe have a local ancestry in the Early Upper Palaeolithic, with a smaller proportion arriving from the Near East in the Neolithic. Here, we describe a cladistic notation for mitochondrial variation and expand upon our earlier analysis to present a more detailed portrait of the European mitochondrial record.
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Phylogenetic and diversity analysis of the mtDNA control region sequence variation of 821 individuals from Europe and the Middle East distinguishes five major lineage groups with different internal diversities and divergence times. Consideration of the diversities and geographic distribution of these groups within Europe and the Middle East leads to the conclusion that ancestors of the great majority of modern, extant lineages entered Europe during the Upper Paleolithic. A further set of lineages arrived from the Middle East much later, and their age and geographic distribution within Europe correlates well with archaeological evidence for two culturally and geographically distinct Neolithic colonization events that are associated with the spread of agriculture. It follows from this interpretation that the major extant lineages throughout Europe predate the Neolithic expansion and that the spread of agriculture was a substantially indigenous development accompanied by only a relatively minor component of contemporary Middle Eastern agriculturalists. There is no evidence of any surviving Neanderthal lineages among modern Europeans.
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We have analysed 302 bp of the first hypervariable region of the mitochondrial D-loop in 271 individuals from different regions of the Iberian Peninsula and 85 individuals from Algeria. The Basque population is significantly different from neighbouring populations in terms of overall levels of diversity. This is because the majority of sequences in the Basques are restricted to the lineage group defined by the CRS (Cambridge Reference Sequence) and its derivatives although, like other Iberian populations, they showed a unimodal distribution of pairwise sequence differences. The timing of divergence of populations within Iberia points to a shared ancestry of all populations in the Upper Palaeolithic. Further genetic subdivision is apparent in Catalonia and Andalusia, with increased genetic diversity in the latter. Lineage diversity comparisons of Iberian populations with European (Tuscan) and North African (Algerian) populations shows the Iberian Peninsula to be more similar to other European populations, although a small number of Iberian lineages can be traced to North Africa.
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A total of 11 Bos primigenius and Bos taurus bones from archaeological sites between 500 and 12000 years old were examined for the presence of DNA. It was possible to amplify and sequence mitochondrial control region DNA extracted from seven of the 11 samples, including two Pleistocene B. primigenius samples. We compared the results with published data by constructing phylogenetic networks. The two B. primigenius samples clustered with the extant B. taurus samples in the networks. The similarity between B. primigenius and modern taurine cattle confirms that these should be considered members of a single species. The sequences obtained from the B. taurus specimens were either identical to the reference sequence for modern European cattle or closely related to it. They included two sequences not previously documented. The network analysis of the ancient data highlights the intermediary nature of the B. primigenius sequences between modern European and African B. taurus and the proximity of the ancient DNA B. taurus sequences to modern European B. taurus. Further analysis of the extant data in the light of the ancient DNA results suggests that a degree of Pleistocene diversity survives in the extant European Bos population that is mainly derived from a more recent population expansion.
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The majority of published human mitochondrial DNA sequence data are confined to hypervariable region I in the control region. By contrast, this paper focuses on a nucleotide site in hypervariable region II. Unlike most non-European populations whose mtDNA sequences have been studied in the literature, the British 'white Caucasian' population has a high level of variation at site 73 (following the site numbering by Anderson et al. 1981). This variation appears to have its origin largely in a mutation from guanine to adenine at that site with an estimated minimum age between 15,000 and 25,000 years. The data of Piercy et al. (1993) suggest that roughly half of the British 'white Caucasian' mitochondrial gene pool is descended from a common maternal ancestor who carried this mutation at site 73. This site also plays a central role in distinguishing the five major European mtDNA clusters identified in Richards et al. (1996). We suggest that the lineages carrying an A at site 73, together with some other lineages, may have their origins in a small founder population which expanded after the last glacial maximum about 20,000 years ago. We conclude that, in addition to region I sequences, site 73 is worth determining in studies of Caucasian populations.
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Using mitochondrial lineage analysis of 1,178 individuals from Polynesia, the western Pacific, and Taiwan, we show that the major prehistoric settlement of Polynesia was from the west and involved two or possibly three genetically distinct populations. The predominant lineage group, accounting for 94% of Polynesian mtDNA, shares a 9-bp COII/tRNA(Lys) intergenic deletion and characteristic control region transition variants, compared to the Cambridge reference sequence. InPolynesia, the diversity of this group is extremely restricted, while related lineages in Indonesia, the Philippines, and Taiwan are increasingly diverse. This suggests a relatively recent major eastward expansion into Polynesia, perhaps originating from Taiwan, in agreement with archeological and linguistic evidence, but which experienced one or more severe population bottlenecks. The second mitochondrial lineage group, accounting for 3.5% of Polynesian mtDNA haplotypes, does not have the 9-bp deletion and its characterized by an A-C transversional variant at nt position 16265. Specific oligonucleotides for this variant were used to select individuals from the population sample who, with other sequences, show that the Polynesian lineages were part of a diverse group in Vanuatu and Papua New Guinea. The very low overall diversity of both lineage groups in Polynesia suggests there was severe population restriction during the colonization of remote Oceania. A third group, represented by only four individuals (0.6%) in Polynesia but also present in the Philippines, shares variants at nt positions 16172 and 16304. Two Polynesians had unrelated haplotypes matching published sequences from native South Americans, which may be the first genetic evidence of prehistoric human contact between Polynesia and South America.
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This talk will summarise the genetic composition of the human populations of the British Isles, focusing especially on the phylogeographically informative non-recombining marker systems of the maternally inherited mitochondrial DNA and the paternally inherited Y chromosome. Whilst much of the signal in these marker systems seems to be due to re-colonisation at the end of the last glaciation, there has been controversy over the demic impact of putative subsequent immigration events, including those from continental Europe traditionally thought to have taken place in the fifth century. Although some have argued from Y-chromosome evidence for a very heavy component at this time, others have questioned this view to a lesser of greater extent. The talk will discuss these various alternative perspectives.
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Global patterns of human genetic diversity suggest that modern human variation is broadly (albeit shallowly) structured at the continental level, with South Asia and East Asia (and probably also Southeast Asia) forming genetic clusters or domains distinct both from each other and from (Native) America, Australasia, west Eurasia and sub-Saharan Africa. This has been shown by analysing multiple autosomal microsatellites using the STRUCTURE software (Rosenberg et al. 2006). However, evidence is accumulating, especially from the non-recombining marker systems, mitochondrial DNA (mtDNA) and the non-recombining part of the Y chromosome (NRY), that this is the result of sequential colonisation and expansion from very small founder groups who dispersed from an East African homeland within the last 70,000 years (ky) or so (Macaulay et al. 2005; Metspalu 2006; Richards et al. 2006). Recent archaeological and fossil evidence suggests that anatomically modern humans were settled in Southeast Asia by at least 50 kya, implying that South Asia was already settled by this time, although unequivocal evidence from the Subcontinent is more recent. Genetic estimates are much less precise, but a recent new calibration of the mtDNA mutation rate, which employs the entire variation in the mtDNA genome for maximum precision and makes allowance for the action of purifying selection, therefore also maximising accuracy, provides at least one molecular clock that can be employed for phylogeographic reconstructions (Soares et al. 2009). This suggests that Asia was first settled by modern humans 60¬–70 kya – somewhat earlier than the earliest widely accepted archaeological evidence, but matching some evidence from Australia and perhaps also China that is less widely accepted. It was initially assumed that Eurasia had been settled by modern humans via northeast Africa and the Levant, ~50 kya, and Y-chromosome evidence has been used to argue for a Central Asian “heartland” from which much of the Old World was settled (Wells et al. 2001). However, the aforementioned dating evidence from Australia suggested an earlier dispersal from the Horn of Africa across the Red Sea and along the tropical southern Asian coastline. This was supported by the extremely high number of basal mtDNA haplogroup R and M lineages in India (Sun et al. 2006), and by similarities between industries associated with modern humans in South Africa ~60 kya and South Asia at least 35 kya (Mellars 2006).Analysis of complete mtDNA genomes sequences from so-called “relict” populations in South Asia, Southeast Asia and Australasia have been used to address this question. Modern non-African populations throughout the world, with the exception of populations or regions with a recent African ancestry, harbour mtDNAs from just three major founder clades, M, N and (nested closely within N) R, all of which belong to the L3 clade, which is of sub-Saharan African origin ~70 kya. Aboriginal populations in South Asia, Southeast Asia and Australasia display mtDNA profiles that include basal lineages belonging to all three of the mtDNA founder clades, indicating that even the most ancient populations on the southern coast of Asia were part of the same, single dispersal out of Africa (Macaulay 2005). This pattern, and the molecular-clock timing of the dispersal to at least 60 kya, suggest that the primary expansion was along the southern coastal route, with the Asian continental heartland (including Southwest Asia, and ultimately Europe) taking place subsequently along various corridors as climatic conditions allowed, most likely after 50 kya. These dates seem to exclude the possibility, suggested on archaeological grounds as well as on earlier genetic analyses, that the dispersal into South and Southeast Asia took place before the volcanic eruption of Toba in Sumatra ~74 kya, which is therefore unlikely to have impacted on Asian populations. Moreover, the dispersal seems to have beenextremely rapid, within the space of a few thousand years, since it led to the divergence of the distinct domains of basal mtDNA lineages in each region, rather than a pattern of nesting (such as occurred in the settlement of the Americas from East Asia and the Remote Pacific from Southeast Asia/Near Oceania). There is relatively little differentiation between ethnic and language groups within South Asia, similar to other parts of Eurasia. The Indian Subcontinent has long been seen as having been deeply affected by migrations from the north, and the non-recombining markers and autosomal SNPanalysis indeed suggest genetic gradients, but these have arisen from a variety of distinct prehistoric dispersals, with little or no impact attributable to the putative Aryan migrations that are thought to have led to the establishment of the caste system. There are mtDNAs in India that originatedin Southwest Asia but probably arrived not long from the time of first settlement, and only atiny minority that appear to have arrived during historical times. The demic impact of the Southwest Asian Neolithic appears to have been similarly minor for most of the Subcontinent, despite some claims to the contrary (Chaubey et al. 2006). Southeast Asia was settled by the southern coastal route by ~55 kya according to the mtDNA clock, when much of Island Southeast Asia formed part of the mainland as the Sunda continent. Dental patterns, as well as genetic diversity, suggest that East Asia was initially settled from the south, although there is a suggestion in Y-chromosome patterns of an early offshoot from the southern route east of the Himalayas into the region of the Tibetan plateau, sometime referred to as the“mammoth steppe”. The northeast Asian coast was reached at least 30 kya; some mtDNA and Y-chromosome lineages in Japan appear to trace to this time. Genetic and fossil data indicate discontinuities in the prehistory of East Asia; there are suggestions of subsequent re-dispersals from south to north, which may be in part due to Neolithic expansions, but seem likely to also reflect the expansion of Han Chinese people within the last 1500 years or so. The impact of the Last Glacial Maximum is also likely to have been severe in continental East Asia, whereas refugial areas existed within Southeast Asia. Sea-level rises beginning ~19 kya had their maximal impact, however, in Southeast Asia; the Sunda continent was inundated leading to wide scale dispersals of lineages across what is now Island Southeast Asia which may have had a much greater demographic impact than the subsequent Holocenespread of the Neolithic across Southeast Asia and into the Pacific islands (Soares et al. 2008). References Chaubey, G., M. Metspalu, T. Kivisild and R. Villems. 2006. Peopling of South Asia: investigating the caste-tribe contimuum in India. Bioessays 29: 91-100. Macaulay, V., C. Hill, A. Achilli, C. Rengo, D. Clarke, W. Meehan, J. Blackburn, O. Semino, R. Scozzari, F. Cruciani, A. Taha, N. K. Shaari, J. M. Raja, P. Ismail, Z. a. Zainuddin, W. Goodwin, D. Bulbeck, H.-J. Bandelt, S. Oppenheimer, A. Torroni and M. Richards. 2005. Single, rapid coastal settlement of Asia revealed by analysisof complete mitochondrial genomes. Science 308: 1034-1036. Mellars, P. 2006. Going East: New genetic and archaeological perspectives on the modern human colonization of Eurasia. Science 313: 796-800. Metspalu, M., Kivisild, T., Bandelt, H.-J., Richards, M., Villems, R. 2006. The pioneer settlement of modern humans in Asia. Mitochondrial DNA and the evolution of Homo sapiens. H. J. Bandelt, Macaulay, V., Richards, M. Berlin, Springer–Verlag: 181–199. Richards, M., H. J. Bandelt, T. Kivisild and S. Oppenheimer 2006. A model for the dispersal of modern humans out of Africa. Mitochondrial DNAand the evolution of Homo sapiens. H. J. Bandelt, V. Macaulay and M. Richards. Berlin, Springer–Verlag: 225–265. Rosenberg, N. A., S. Mahajan, C. Gonzalez-Quevedo, M. G. Blum, L. Nino-Rosales, V. Ninis, P. Das, M. Hegde, L. Molinari, G. Zapata, J. L. Weber, J. W. Belmont and P. I. Patel. 2006. Low levels of genetic divergence across geographically and linguistically diverse populations from India. PloS Genet. 2: e215. Soares, P., L. Ermini, N. Thomson, M. Mormina, T. Rito, A. Röhl, A. Salas, S. Oppenheimer, V. Macaulay and M. B. Richards. 2009. Correcting for purifying selection: an improved human mitochondrial molecular clock. Am. J. Hum. Genet. 84: 740-759. Soares, P., J. A. Trejaut, J.-H. Loo, C. Hill, M. Mormina, C.-L. Lee, Y.-M. Chen, G. Hudjashov, P. Forster, V. Macaulay, D. Bulbeck, S. Oppenheimer, M. Lin and M. B. Richards. 2008. Climate change and post-glacial human dispersals in Southeast Asia. Mol Biol. Evol. 25: 1209–1218. Sun, C., Q.-P. Kong, M. g. Palanichamy, S. Agrawal, H.-J. Bandelt, Y.-G. Yao, F. Khan, C.-L. Zhu, T. K. Chaudhuri and Y.-P. Zhang. 2006. The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes. . Mol Biol. Evol. 23: 683–690. Wells, R. S., N. Yuldasheva, R. Ruzibakiev, P. A. Underhill, I. Evseeva, J. Blue-Smith, L. Jin, B. Su, R. Pitchappan, S. Shanmugalakshmi, K. Balakrishnan, M. Read, N. M. Pearson, l. T. Zerja, M. T. Webster, I. Zholoshvili, E. Jamarjashvili, S. Gambarov, B. Nikbin, A. Dostiev, O. Aknazarov, P. Zalloua, I. Tsoy, M. Kitaev, M. Mirrakhimov, A. Chariev and W. F. Bodmer. 2001. The Eurasian heartland: a continental perspective on Y-chromosome diversity. Proc. Natl Acad. Sci. USA 98: 10244-10249. Archaeogenetics and the peopling of Asia * Institute of Integrative&Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK Global patterns of human genetic diversity suggest that modern human variation is broadly (albeit shallowly) structured at the continental level, with South Asia and East Asia (and probably also Southeast Asia) forming genetic clusters or domains distinct both from each other and from (Native) America, Australasia, west Eurasia and sub-Saharan Africa. This has been shown by analysing multiple autosomal microsatellites using the STRUCTURE software (Rosenberg et al. 2006). However, evidence is accumulating, especially from the non-recombining marker systems, mitochondrial DNA (mtDNA) and the non-recombining part of the Y chromosome (NRY), that this is the result of sequential colonisation and expansion from very small founder groups who dispersed from an East African homeland within the last 70,000 years (ky) or so (Macaulay et al. 2005; Metspalu 2006; Richards et al. 2006). Recent archaeological and fossil evidence suggests that anatomically modern humans were settled in Southeast Asia by at least 50 kya, implying that South Asia was already settled by this time, although unequivocal evidence from the Subcontinent is more recent. Genetic estimates are much less precise, but a recent new calibration of the mtDNA mutation rate, which employs the entire variation in the mtDNA genome for maximum precision and makes allowance for the action of purifying selection, therefore also maximising accuracy, provides at least one molecular clock that can be employed for phylogeographic reconstructions (Soares et al. 2009). This suggests that Asia was first settled by modern humans 60¬–70 kya – somewhat earlier than the earliest widely accepted archaeological evidence, but matching some evidence from Australia and perhaps also China that is less widely accepted. It was initially assumed that Eurasia had been settled by modern humans via northeast Africa and the Levant, ~50 kya, and Y-chromosome evidence has been used to argue for a Central Asian “heartland” from which much of the Old World was settled (Wells et al. 2001). However, the aforementioned dating evidence from Australia suggested an earlier dispersal from the Horn of Africa across the Red Sea and along the tropical southern Asian coastline. This was supported by the extremely high number of basal mtDNA haplogroup R and M lineages in India (Sun et al. 2006), and by similarities between industries associated with modern humans in South Africa ~60 kya and South Asia at least 35 kya (Mellars 2006).Analysis of complete mtDNA genomes sequences from so-called “relict” populations in South Asia, Southeast Asia and Australasia have been used to address this question. Modern non-African populations throughout the world, with the exception of populations or regions with a recent African ancestry, harbour mtDNAs from just three major founder clades, M, N and (nested closely within N) R, all of which belong to the L3 clade, which is of sub-Saharan African origin ~70 kya. Aboriginal populations in South Asia, Southeast Asia and Australasia display mtDNA profiles that include basal lineages belonging to all three of the mtDNA founder clades, indicating that even the most ancient populations on the southern coast of Asia were part of the same, single dispersal out of Africa (Macaulay 2005). This pattern, and the molecular-clock timing of the dispersal to at least60 kya, suggest that the primary expansion was along the southern coastal route, with the Asian continental heartland (including Southwest Asia, and ultimately Europe) taking place subsequently along various corridors as climatic conditions allowed, most likely after 50 kya. These dates seem to exclude the possibility, suggested on archaeological grounds as well as on earlier genetic analyses, that the dispersal into South and Southeast Asia took place before the volcanic eruption of Toba in Sumatra ~74 kya, which is therefore unlikely to have impacted on Asian populations. Moreover, the dispersal seems to have been extremely rapid, within the space of a few thousand years, since it led to the divergence of the distinct domains of basal mtDNA lineages in each region, rather than a pattern of nesting (such as occurred in the settlement of the Americas from East Asia and the Remote Pacific from Southeast Asia/Near Oceania). There is relatively little differentiation between ethnic and language groups within South Asia, similar to other parts of Eurasia. The Indian Subcontinent has long been seen as having been deeply affected by migrations from the north, and the non-recombining markers and autosomal SNP analysis indeed suggest genetic gradients, but these have arisen from a variety of distinct prehistoric dispersals, with little or no impact attributable to the putative Aryan migrations that are thought to have led to the establishment of the caste system. There are mtDNAs in India that originated in Southwest Asia but probably arrived not long from the time of first settlement, and only a tiny minority that appear to have arrived during historical times. The demic impact of the Southwest Asian Neolithic appears to have been similarly minor for most of the Subcontinent, despite some claims to the contrary (Chaubey et al. 2006). Southeast Asia was settled by the southern coastal route by ~55 kya according to the mtDNA clock, when much of Island Southeast Asia formed part of the mainland as the Sunda continent. Dental patterns, as well as genetic diversity, suggest that East Asia was initially settled from the south, although there is a suggestion in Y-chromosome patterns of an early offshoot from the southern route east of the Himalayas into the region of the Tibetan plateau, sometime referred to as the“mammoth steppe”. The northeast Asian coast was reached at least 30 kya; some mtDNA and Y-chromosome lineages in Japan appear to trace to this time. Genetic and fossil data indicate discontinuities in the prehistory of East Asia; there are suggestions of subsequent re-dispersals from south to north, which may be in part due to Neolithic expansions, but seem likely to also reflect the expansion of Han Chinese people within the last 1500 years or so. The impact of the Last Glacial Maximum is also likely to have been severe in continental East Asia, whereas refugial areas existed within Southeast Asia. Sea-level rises beginning ~19 kya had their maximal impact, however, in Southeast Asia; the Sunda continent was inundated leading to wide scale dispersals of lineages across what is now Island Southeast Asia which may have had a much greater demographic impact than the subsequent Holocenespread of the Neolithic across Southeast Asia and into the Pacific islands (Soares et al. 2008). References Chaubey, G., M. Metspalu, T. Kivisild and R. Villems. 2006. Peopling of South Asia: investigating the caste-tribe contimuum in India. Bioessays 29: 91-100. Macaulay, V., C. Hill, A. Achilli, C. Rengo, D. Clarke, W. Meehan, J. Blackburn, O. Semino, R. Scozzari, F. Cruciani, A. Taha, N. K. Shaari, J. M. Raja, P. Ismail, Z. a. Zainuddin, W. Goodwin, D. Bulbeck, H.-J. Bandelt, S. Oppenheimer, A. Torroni and M. Richards. 2005. Single, rapid coastal settlement of Asia revealed by analysisof complete mitochondrial genomes. Science 308: 1034-1036. Mellars, P. 2006. Going East: New genetic and archaeological perspectives on the modern human colonization of Eurasia. Science 313: 796-800. Metspalu, M., Kivisild, T., Bandelt, H.-J., Richards, M., Villems, R. 2006. The pioneer settlement of modern humans in Asia. Mitochondrial DNA and the evolution of Homo sapiens. H. J. Bandelt, Macaulay, V., Richards, M. Berlin, Springer–Verlag: 181–199. Richards, M., H. J. Bandelt, T. Kivisild and S. Oppenheimer 2006. A model for the dispersal of modern humans out of Africa. Mitochondrial DNAand the evolution of Homo sapiens. H. J. Bandelt, V. Macaulay and M. Richards. Berlin, Springer–Verlag: 225–265. Rosenberg, N. A., S. Mahajan, C. Gonzalez-Quevedo, M. G. Blum, L. Nino-Rosales, V. Ninis, P. Das, M. Hegde, L. Molinari, G. Zapata, J. L. Weber, J. W. Belmont and P. I. Patel. 2006. Low levels of genetic divergence across geographically and linguistically diverse populations from India. PloS Genet. 2: e215. Soares, P., L. Ermini, N. Thomson, M. Mormina, T. Rito, A. Röhl, A. Salas, S. Oppenheimer, V. Macaulay and M. B. Richards. 2009. Correcting for purifying selection: an improved human mitochondrial molecular clock. Am. J. Hum. Genet. 84: 740-759. Soares, P., J. A. Trejaut, J.-H. Loo, C. Hill, M. Mormina, C.-L. Lee, Y.-M. Chen, G. Hudjashov, P. Forster, V. Macaulay, D. Bulbeck, S. Oppenheimer, M. Lin and M. B. Richards. 2008. Climate change and post-glacial human dispersals in Southeast Asia. Mol Biol. Evol. 25: 1209–1218. Sun, C., Q.-P. Kong, M. g. Palanichamy, S. Agrawal, H.-J. Bandelt, Y.-G. Yao, F. Khan, C.-L. Zhu, T. K. Chaudhuri and Y.-P. Zhang. 2006. The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes. . Mol Biol. Evol. 23: 683–690. Wells, R. S., N. Yuldasheva, R. Ruzibakiev, P. A. Underhill, I. Evseeva, J. Blue-Smith, L. Jin, B. Su, R. Pitchappan, S. Shanmugalakshmi, K. Balakrishnan, M. Read, N. M. Pearson, l. T. Zerja, M. T. Webster, I. Zholoshvili, E. Jamarjashvili, S. Gambarov, B. Nikbin, A. Dostiev, O. Aknazarov, P. Zalloua, I. Tsoy, M. Kitaev, M. Mirrakhimov, A. Chariev and W. F. Bodmer. 2001. The Eurasian heartland: a continental perspective on Y-chromosome diversity. Proc. Natl Acad. Sci. USA 98: 10244-10249.
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A combination of archaeology and evolutionary genetics has led to a reappraisal of the major demographic transitions in British prehistory. The role of‘Celtic’ migrations has been questioned, with the aboriginal population of the islands seen largely as the result of settlement at the end of the last Ice Age, probably augmented by further settlement during the Neolithic. The demographic impact of the Anglo-Saxons, considered minor by archaeologists, has been estimated to be high by some geneticists, but this is the result of implausible assumptions about the preceding genetic composition of the islands and overinterpretation of poorly resolved genetic data.
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The strong phylogenetic signal provided by complete mitochondrial deoxyribonucleic acid (mtDNA) sequences within species is being exploited to reconstruct the maternal genealogy and anchor it in space and time. This is the starting point for interpretations of the processes in population history that led to those patterns, as illustrated here for humans.
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