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  1. The genetic structure of Pacific islanders
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  4. Who are we?: The Human Genome Project, Race and Ethnicity - Ministry of Social Development

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The genetic structure of Pacific islanders

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CARTA: Ancient DNA and Human Evolution – María C. Ávila-Arcos: The Genetic History of the Americas

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5 Takeaways From the Ancient DNA Research Story

ABAEnrichment: An R package to test for gene set expression enrichment in the adult and developing human brain. Bioinformatics, 32 20 , Human adaptation in the light of ancient and modern genomes. Human adaptation and population differentiation in the light of ancient genomes. Nature Communications, 7 : Krause, J. Genetic time travel. Genetics, 1 , Kuhlwilm, M. Ancient gene flow from early modern humans into Eastern Neanderthals. Lazaridis, I. Genomic insights into the origin of farming in the ancient Near East.

Le Duc, D. Adaptation to nocturnality — learning from avian genomes. Genome-wide single nucleotide polymorphism SNP genotyping studies largely supported these observations 13 — The findings of these and other studies indicate that African populations have maintained a large and subdivided structure throughout their evolutionary history 16 , 19 and that the deepest splits between human populations lie in sub-Saharan Africa 18 , There is also evidence of both ancient and modern migration events across sub-Saharan Africa, as well as extensive admixture in the region Other important migration events include the migration of pastoralist populations, which comprise farmers raising livestock, from their southern Sudanese homeland to eastern and central Africa about 7 kyr ago, and the migration of agropastoralists who engage in both raising livestock and growing crops from Ethiopia to Kenya and Tanzania about 5 kyr ago Some migration routes remain under debate.

For example, there is still some uncertainty regarding the migration routes used to populate the Americas. Genomic data are limited in their resolution to determine paths of migration because further population movements, subsequent to the initial migrations, may obscure the geographic patterns that can be discerned from the genomic data. Proposed routes of migration that remain controversial are indicated by dashed lines. Analysis of whole-genome sequencing and SNP array data found that the genetic lineages of click-language-speaking San populations of southern Africa capture the deepest split between populations of humans, with their divergence estimated to have occurred around — kyr ago 15 , 18 , 20 — 22 Fig.

However, genetic markers with uniparental inheritance and linguistic studies suggest that click-language-speaking hunter-gatherer populations may originally have been more widespread and were replaced in areas other than southern Africa or, alternatively, that they may have originated in eastern Africa and then migrated to southern Africa in the past 50 kyr 13 , Indeed, other hunter-gatherer populations that speak languages that use clicks, including the Hadza people and the Sandawe people, currently reside in Tanzania in eastern Africa, although they display limited genomic affinity with the San people of southern African 15 , The exact origin of anatomically modern humans in Africa remains unknown, mainly because of the scarcity of fossil and archaeological data in the tropical regions of the continent.

However, a multiregional origin of modern humans in Africa 24 , in which modern features evolved in a fragmented manner in several areas connected by gene flow, is still possible, especially given the opportunity for migration and admixture across the continent. Indeed, there is evidence for the admixture of anatomically modern humans with archaic populations in Africa 25 — The characterization of genomes from individuals who lived in Africa more than 10 kyr ago is challenging because the environment of the samples from which DNA is extracted, including the local climatic conditions, is not favourable to the preservation of genetic material.

However, the statistical analysis of whole-genome sequencing data from geographically diverse hunter-gatherer populations provides evidence of archaic human lineages that have undergone introgression the exchange of genetic material through interbreeding and that diverged from modern human lineages as long ago as 1. The degree of archaic admixture in Africa therefore remains controversial, and many ongoing efforts are aiming to resolve this question. However, the number, the geographic origin and migratory routes and the timing of major dispersals remains elusive. For instance, there is evidence to support the origins of modern humans in eastern, central and southern Africa 18 , 31 — 33 , single and multiple dispersals out of Africa 7 , 34 — 36 , a north or south dispersal route 37 , 38 and estimates for the timing of dispersals occurring about 50 kyr— kyr ago 20 , 39 — Three studies 44 — 46 that leverage fresh, high-quality whole-genome sequencing data from geographically diverse individuals from more than locations worldwide help to resolve some of these questions.

They also point to the occurrence of a single out-of-Africa dispersal in which all contemporary non-African peoples branched off from the same ancestral population that left Africa, possibly with minor genetic contributions from an earlier modern human migration wave into Oceania Furthermore, on leaving Africa, modern humans may have immediately separated into two waves of dispersal As proposed in refs 36 and 47 , one wave led ultimately to the founding of Australasia and New Guinea and the other contributed to the ancestry of present-day mainland Eurasians.

However, the exact routes of migration in the early diversification of people outside Africa remain a topic of research and controversy. It is now clear that the ancestors of all contemporary non-African people encountered, and admixed with, Neanderthals On the basis of patterns of linkage disequilibrium, the date of hybridization has been estimated to be approximately 50—65 kyr ago 52 , and knowledge of the timing of admixture with Neanderthals helps to bound estimates of when the ultimately successful out-of-Africa dispersal occurred.

Estimates of the proportion of Neanderthal ancestry that persists in the genomes of modern humans 51 , 53 points towards a more complex history of interaction between Neanderthals and modern humans. Strikingly, SNP genotyping in an early modern human from Romania who lived about 40 kyr ago provided further evidence that introgression occurred at several times and locations in Eurasia 55 , although the individual did not contribute detectable ancestry to present-day populations.

Recent studies 50 have suggested a more complex admixture history than previously thought, and we caution that our understanding of admixture models is fluid at present and that further demographic models are also compatible with the observed. The first anatomically modern humans lived in Europe as early as 43 kyr ago 11 , These early Paleolithic Europeans have probably made little genetic contribution to the European people of today 61 as there is evidence of turnover in the genetic composition of Europeans before the Last Glacial Maximum LGM , possibly in relation to climate oscillations 63 — although the exact contributions from early Europeans is still under debate Around 11 kyr ago, after the LGM had passed, a new way of life based on animal husbandry, agriculture and sedentarism — and known as a Neolithic lifestyle — started to emerge in several subregions of the Fertile Crescent 64 Fig.

Analyses of ancient DNA showed that this population of farmers expanded from Central Anatolia into Europe; however, other regions of the Fertile Crescent contributed only limited genetic material to the early European farmers They reached the Iberian Peninsula Fig. Genomic data from the remains of Neolithic humans have shown that this process was driven by the mass migration of groups of farmers 61 and the assimilation of local hunter-gatherers 65 , demonstrating that the Neolithic way of life spread across Europe through the migration of people rather than solely as an idea or a culture.

The Neolithic lifestyle helped to increase the size of populations, as seen in the estimates of effective population sizes that were generated from genomic data 66 , although archaeological data suggests that the health of the individuals who lived as farmers was sometimes poor as there were ample signs of malnutrition and caries 66 , Another wave of migration into Europe, which introduced the third European genetic component, occurred during the late Neolithic period and the early Bronze Age.

Herders from the Pontic—Caspian steppe who belonged to the Yamnaya culture were involved in a migration to central Europe about 4. The herders themselves were descendants of various hunter-gatherer groups from modern Russia 58 and the Caucasus This migration was probably linked to conquests and technological innovations such as horseback riding and may have spread Indo-European languages to Europe 58 , 60 , although some linguistics researchers suggest that these languages were already spoken by Neolithic farmers Clearly, the late Neolithic period and the Bronze Age were dynamic times that led to the spread of the genetic material of the steppe herders across western and northern Europe 58 , The three main genetic components of modern-day European populations reflect the contributions of hunter-gatherers to the recolonization of Europe after the LGM, the migration of Neolithic farmers from Anatolia to Europe and the late-Neolithic period and Bronze Age migration to Europe from the east.

These components can explain much of the genetic diversity found in present-day Europe For example, the Neolithic genetic component seems to be most dominant in southern European populations such as the Sardinian people 56 , 57 , Genetic variation among modern-day Europeans is strongly correlated with geography 70 , 71 and shows a gradient of decreasing diversity with increasingly northern latitudes Although the main components of genetic diversity were introduced into Europe in separate waves of migration, subsequent processes of gene flow that were limited by geography have shaped the present genetic landscape.

Culture and lifestyle were therefore more important determinants of genomic differentiation and similarity in many periods during Prehistoric Europe than geography Most evidence indicates that Asia was colonized through at least two early waves of migration. However, the details of how Asia was first colonized remain largely unknown. Two early modern human genomes from Asia have been sequenced. Together with evidence from the 36—kyr-old genome of the Kostenki 14 individual from European Russia 75 , showing a close affinity to contemporary western Eurasians but not East Asians, this points to the occurrence of a divergence between East Asians and western Eurasians around 36—45 kyr ago.

The first event was an expansion of Yamnaya herders into Asia about 5 kyr ago, which occurred at the same time as the Yamnaya expansion into Europe. Subsequently, between 2. Archaeological evidence shows that humans were present in Oceania around Morphological variation in ancient human skeletons from Australia has been used to propose that there were at least two independent migrations to the ancient continent of Sahul, which is comprised of modern Australia, New Guinea and Tasmania Similar claims have been put forward on the basis of linguistic data and lithic technology or the introduction of domesticated species such as the dingo However, the only extensive population genomic study so far on Aboriginal Australians and Papuans 44 finds evidence for only a single founding event in Sahul, which was followed by a divergence of the Papuan and Aboriginal Australian ancestral population and further genetic diversification in the Aboriginal Australian population that could have coincided with environmental changes such as desertification.

Aboriginal Australians therefore seem to have been living in a high level of isolation until only relatively recent times. A study 79 of genome-wide SNP data from modern people in Oceania confirmed archaeological predictions that Polynesians, who are distributed across a triangle of islands in the South Pacific that is bounded by Rapa Nui also known as Easter Island to the east, represent an expansion into Oceania of individuals with mixed Melanesian and East Asian ancestry.

The Melanesian ancestry was added to the original East Asian ancestry after the initial Polynesian expansion had begun Whether Polynesians reached the Americas and admixed with Native Americans during their eastward expansion that ended about 1 kyr ago remains controversial.

A genetic study of ancient chicken remains from South America supports this scenario 81 but has also been questioned Genome sequencing of the remains of humans from Brazil that date to around , and therefore pre-date the recorded trade of Polynesian slaves to South America 83 , shows that the individuals are closely related to contemporary Polynesians. These data potentially provide further support for early contact between Polynesians and Native Americans but they could also be the result of the European-mediated transportation of people.

More convincing are the results of a genome-wide study of the modern-day inhabitants of Easter Island 84 , which provided statistical support for Native American admixture that can be dated to —, several hundred years before Europeans reached the islands in However, only evidence of Polynesian and Native American admixture in human remains that pre-date colonization in the Americas would settle the debate. The oldest most widely accepted evidence of humans in the Americas dates to about 15—14 kyr ago 85 , and widespread settlement of the Americas appeared with the emergence of the Clovis complex around However, until around 13 kyr ago, much of North America was covered by a large ice sheet, which would have made it difficult for people to move from Beringia now northeastern Siberia and northwestern North America to the southern parts of the Americas.

After the ice melted, a roughly 1, km interior ice-free corridor formed 3. Metagenomic analyses of lake cores from Canada 86 have estimated that this corridor first became biologically viable around How and when the earliest ancestors of Americans crossed the Pleistocene ice sheets into southern North America is unknown, as is whether movement of the pre-Clovis and Clovis groups represents the same migration. However, a movement towards the south along the west coast of North America that occurred more than 14 kyr ago, and that was possibly followed by southerly or northerly back-migrations through the interior, seems to be the most plausible scenario Fig.

On the basis of cranial morphology and lithic analysis, it has been proposed that early Americans were not direct ancestors of contemporary Native Americans, but instead were related to Australo-Melanesians, Polynesians, the Ainu people of Japan or Europeans who were later replaced or assimilated by ancestors of Native Americans from Siberia 88 — However, several genomic studies have largely rejected these models.

In , the oldest and the only Clovis-associated human genome from the Americas found in Montana, United States , which belonged to an individual who lived about Analyses suggested that the Clovis population from which the genome came was directly ancestral to many contemporary Native Americans. Similarly, analysis of the genome sequence of the roughly 9.

Moreover, populations that were considered to be relicts of an early migration into the Americas and closely related to Australo-Melanesians have been shown to be genetically related to contemporary Native Americans 93 , Estimates of the time of divergence between Siberians and Native Americans, based on whole-genome sequences, point to the formation of the Native American gene pool as early as around 23 kyr ago 93 , which lends further support to the early entrance of ancestors of Native Americans into the Americas.

When the accepted dates for the earliest archaeological sites in the Americas are taken into consideration, ancestors of Native Americans could have remained in isolation until around 8 kyr ago in Siberia or Beringia, following the split from their Siberian ancestors, before moving eastwards into the Americas. However, whether it took place inside or outside the Americas remains unclear. In Native Americans, genomic data have been used to locate a basal division that can be dated to about 14—13 kyr ago 73 , The southern branch includes groups of Amerindian-language-speaking people and the northern branch includes groups of Athabascan-language-speaking people as well as other groups that speak languages such as Cree or Algonquin.

Divergence estimates based on analyses of whole-genome sequencing data suggest that both groups diversified from Siberians concurrently, implying that there was only one founding event for both Amerindian and Athabascan populations that was followed by subsequent gene flow from Asia Whether the divergence between the two Native American branches took place in Siberia or the north or south of the American ice sheets is still under debate, and the analysis of further ancient genomes will be needed to resolve this. Similarly, it remains undetermined whether the discovery of the Australo-Melanesian signature in some contemporary Brazilian Native Americans Fig.

So far, no studies of the genomes of ancient humans from the Americas have shown this genetic signature. The Inuit of the American Arctic have been shown to originate from a migration separate to that of other Native Americans 95 , However, it has long been discussed whether the first people to inhabit the Arctic, the now extinct Paleo-Eskimo culture, which appeared about 5 kyr ago in the Americas, represent the ancestors of the present-day Inuit or an independent founder population from Siberia 96 Fig. Sequencing of DNA from a 4-kyr-old tuft of hair from Greenland 5 showed that the population the individual belonged to had migrated from Siberia to the North American Arctic independently of the Native American and Inuit migrations The group then survived in the Arctic for about 4 kyr by reinventing their subsistence strategies and technology but were eventually replaced by the Inuit around yr ago.

As well as the Neanderthals, at least one other type of archaic human — the enigmatic Denisovans — lived in Eurasia when the first modern humans started to appear on the continent. Little is known about the morphology and distribution of Denisovans, who are known only from the genome sequences of a finger bone and three teeth that were found in the Denisova Cave in Siberia 98 — They are most closely related to Neanderthals, with a genetic differentiation that is similar to the deepest splits between modern humans 48 but an estimated time of divergence that possibly dates back — kyr Denisovans have many peculiarities; for instance, they may carry genetic material obtained through admixture from individuals related to earlier types of humans Fig.

Arguably, Denisovans can be considered to be the eastern or southern end of a spectrum of archaic humans that lived in Eurasia and possibly beyond , with Neanderthals representing the western end. Similar to Neanderthals, Denisovans interbred with anatomically modern humans. Continental southeast Asians carry genetic material on the order of 0. The genomes of both Neanderthals and Denisovans have been subjected to genetic selection on introgression. Most selection in humans seems to be directed against the introgressed DNA, because there is a paucity of introgressed DNA near functional regions of the genome Furthermore, large genomic regions that are depleted of both Neanderthal and Denisovan sequences have been identified , which is consistent with the rapid purging of deleterious sequences.

However, some of the introgressed DNA might have helped humans to adapt to the local environment, such as the adaptation to high altitudes in Tibetan people Studies of the first reliable genome data from archaic humans proposed two punctuated and very specific events for admixture between anatomically modern humans and archaic humans 6 , Since then, we have learned that such admixture is much more common, with multiple events taking place between various groups of modern and archaic humans 48 , 50 , , in both directions Fig. At present, it is unclear whether the Denisovan introgression into Melanesians and Australians occurred in Australasia or Asia, as the ancestors of modern Australasians migrated across the continent.

If it had occurred in Asia, present-day Asians would be mostly descended from other groups that arrived during subsequent waves of migration. Similarly, it is unknown whether the Denisovan admixture in East Asians is a result of the same admixture event or events that affected Australasians.

The analysis of genetic data can inform us about not only the evolutionary history of humans, but also how natural selection has affected our species.

As humans spread, first within Africa and subsequently to the rest of the world, they encountered new environmental conditions that induced selective regimes, including extreme cold in much of the Americas and Eurasia during the last ice age, altered exposure to sunlight and pathogens not previously encountered. Cultural innovations such as improved methods of hunting and fishing and the development of plant and animal domestication also induced new environmental conditions, including changes in diet. Genome-sequencing data sets have provided an opportunity to systematically scan the human genome for regions that have been targeted by selection.

By taking advantage of the extensive resources that are now available for the analysis of human genomes, it has been possible to determine the specific functions of individual genetic variants that were targeted by selection, thereby providing a link between the evidence of selection that was discovered through the analysis of DNA sequences and the role of these sequences in adaptation to local environments. Furthermore, studies of ancient DNA now enable the direct observation of changes in allele frequency through time , One of the most obvious changes in the environment that humans encountered as they migrated out of Africa was a reduction in exposure to sunlight at higher latitudes.

Populations that live near the equator have dark skin to protect against skin damage and the photolysis of folate by ultraviolet radiation However, ultraviolet radiation also has an important role in catalysing the production of vitamin D, which is essential for skeletal development and health.

Who are we?: The Human Genome Project, Race and Ethnicity - Ministry of Social Development

In populations that live at higher latitudes, and therefore receive lower doses of ultraviolet radiation, having lighter skin is thought to be an advantage that enables more efficient vitamin D production. Another example of the adaptation of humans to local environments is found in populations that live in hypoxic low oxygen environments at high altitude in regions such as Tibet. A study by Beall showed that Tibetans who have adapted to life at high altitudes exhibit modified regulation of red-blood-cell production in response to hypoxia.

Genomic studies have suggested that this adaptation is driven by changes in allele frequency in two genes in the hypoxia response pathway: EPAS1 and EGLN1 refs — Changes in diet, particularly those that are associated with the emergence of new hunting technologies or agricultural practices, have also had a considerable impact on the human genome. The best known example is selection for lactase persistence the avoidance of lactose intolerance , which affects regulation of the gene LCT among dairy farming populations in Europe and Africa , Similarly, genes in the FADS family, the products of which catalyse the synthesis of poly-unsaturated fatty acids, seem to have been under selection during several transitions towards or away from a vegetarian diet in humans — A more comprehensive review of adaptation to local environments can be found in ref.

Several lessons can be learned from genome-wide studies of selection in humans. First, although most of the initial scans for selection proposed that selection acts immediately on new mutations, it is becoming clear that in many cases, selection acts on standing variation — that is, alleles that were present for some time before they became favoured Furthermore, this variation has in many cases been introgressed by interbreeding with other hominins , There is a growing list of genetic variants that were identified as introgressed from Neanderthals and Denisovans that have been favoured in anatomically modern humans by natural selection For example, the adaptive EPAS1 haplotype in Tibetans seems to be introgressed from Denisovans, and the selection on the major histocompatibility complex genes and the gene MC1R is probably facilitated by introgression from Neanderthals , As humans migrated out of Africa and encountered new environments, introgression with other hominins that had already adapted to these environments seems to have been an important factor in facilitating rapid acceleration.

This might be particularly true for genes related to immunity and defence against infection, as anatomically modern humans probably encountered pathogenic agents that could jump from other hominins, and to which humans did not yet have immunity. Second, much of the selection that has affected the human genome has been in response to changes in the environment that were induced by people.

These include changes in diet that were driven by cultural innovations and an increase in the pathogen load of the population owing to changes in social structure and the emergence of cities As we modify our environment, the resulting changes in conditions induce new selective pressures. Biological evolution and cultural evolution are therefore intimately linked.

Third, a close relationship often exists between genetic variants that have been under selection and those that have a strong influence on human health. Studies of human evolution are therefore of increasing relevance for medical genetics. For example, variants found to be selected for by adaptation to high altitudes provide a model for studying hypertension Similarly, variants shown to be under selection in relation to dietary adaptation, such as those in the gene family FADS , may facilitate the development of genomics-informed personalized diets.

Fourth, the genes that show the greatest difference in allele frequency between continental groups indigenous Africans, Europeans, Americans and Australians are enriched for associations with visible traits such as skin, hair and eye pigmentation An interesting consequence is that the geographic groups are more different from each other in terms of pigmentation than they are, on average, at the level of the genome. Humans from various parts of the world are therefore more genetically similar than might be predicted on the basis of observed hair colour, skin colour or other visible traits.

Last, genetic variants with large effects, such as those that influence eye colour, hair colour or lactase persistence, are unusual. Instead, such traits seem to be highly complex and may be influenced by many loci across the genome. Unlike selection at individual sites, polygenic adaptation — the result of selection acting on complex traits — can occur rapidly, even in a few generations, but the footprints of selection at individual loci are extremely weak and cannot be detected by standard methods The best characterized example of polygenic adaptation in humans is selection for an adaptive increase in the height of northern Europeans , a smaller increase in the height of Europeans compared to non-Europeans and a decrease in the height in Sardinians Selection for height may have had small effects on loci across most of the human genome Polygenic adaptation may also have influenced a variety of other morphological traits, including increases in size of the head and body of infants in northern Europe It is probable that a considerable component of selection in humans is polygenic and is yet to be discovered by studies that scan for genomic regions that are under selection.

Evolutionary and demographic inference based on genomic data from humans has often been the subject of considerable debate. Human evolution is a natural experiment that has been repeated only once, and the inference of past demography is therefore a historical science, with inherent limitations.

Furthermore, the ancestral geographic locations of humans cannot be deduced directly from the genomes of modern humans; instead, they are typically inferred indirectly from the locations in which samples are found. Genetic analyses can inform knowledge of the ancestral relationships between individuals, but ancestral DNA is not inscribed with geographic locations. Also, the dating of divergence or admixture events is only as good as the clock by which dating is measured.

Rates of mutation across the human genome and between individuals may be variable, and there has been considerably controversy regarding the mutations rates that should be used in demographic studies. Estimates of these rates vary depending on the methodology that is used for estimation, although a consensus rate of 0. It is possible that this estimate will be revised further, which would affect the dating of events inferred by genomic data in previous studies.

Despite these limitations, advances in the analysis of both modern and ancient human genomes have changed many aspects of our understanding of human evolution. The mounting evidence for interbreeding between Neanderthals, Denisovans and anatomically modern humans has put a focus on the role of introgression in human evolution.

Such studies have found that anatomically modern humans did not evolve with complete independence from other hominins outside Africa, as proposed by the strictest versions of the out-of-Africa model that were often subscribed to after the publication of mtDNA evidence almost 30 years ago 1. Levels of interbreeding suggest that the true model of human evolution — sometimes referred to as the leaky replacement model — lies between the multi-regional model and the out-of-Africa model In fact, the levels of Neanderthal admixture in modern humans are probably strong underestimates of the amount of admixture that was present at the time of introgression 55 , There is considerable evidence that substantial amounts of Neanderthal DNA was purged by selection, through genetic incompatibilities 51 or simply because the high level of inbreeding in Neanderthals caused the Neanderthal DNA to be enriched with deleterious mutations.

In other words, Neanderthals may not have become extinct because they lacked suitable ecological adaptations or through competition or warfare with humans.


Instead, they may simply have been absorbed into the human species. Testing absorption models more directly, for example by sequencing older human remains from Eurasia, may finally resolve the much-debated disappearance of Neanderthals. Similar questions remain for Denisovans. For example, what is the contribution of purifying selection negative selection against deleterious mutations to present-day levels and patterns of Denisovan-like ancestry in Australasians? What was the geographic distribution of Denisovans? And where did the introgression between humans and Denisovans occur?

The identification and genomic analysis of further Denisovan samples may help to answer these questions. Future studies of archaic hominin admixture are likely to reveal further twists in the story of human evolution. Perhaps of greatest interest is genomic data from under-sampled regions of the world, which may help to refine evolutionary theories, including the question of whether there are further, as-yet uncharacterized, lineages of archaic humans. Indeed, preliminary data from contemporary African populations suggest that gene flow occurred with at least one other archaic hominin lineage 25 — For over a century, researchers have discussed whether the biological and cultural variation that exists between groups of modern humans evolved as a result of the long-term isolation of populations, with innovation occurring through the spread of ideas , or whether genetic variation and cultural changes were driven by human migration and the mixing of populations From the analyses of genomic data obtained so far, it is clear that the migration and admixture of populations has played a much larger part in generating genetic and cultural patterns of diversity than was previously thought 56 — 58 , 60 , 66 , although some groups have remained in isolation for a long period of time 44 , The genomic studies also suggest that the geographic distribution of genetic signatures in many modern populations were established relatively late in human history