Population Genetics Quick Hits

Excerpts from abstracts of papers to be presented at aa population genetics conference this summer here and here via Dienekes' Anthropology blog:

Wheat domestication:

The past 15 years have witnessed a notable scientific interest in the topic of crop domestication and the emergence of agriculture in the Near East. . . . some seemingly conflicting evidence, especially in the case of emmer wheat, caused certain controversy and a broad scientific consensus on the circumstances of the wheat domestication has not been reached. . . . the main cause of the above mentioned inconsistencies might lie in the inadequacy of the divergent, tree-like evolutional model. The inconsistent phylogenetic results and implicit archaeological evidence indicate a reticulate (rather than divergent) origin of domesticated emmer. Reticulated genealogy cannot be properly represented on a phylogenetic tree. . . . On a genome-wide super-tree, the conflicting phylogenetic signals are suppressed and the origin of domesticated crop may appear monophyletic, leading to misinterpretations of the circumstances of the Neolithic transition. The network analysis of multi-locus sequence data available for tetraploid wheat clearly supports the reticulated origin of domesticated emmer and durum wheat.

In other words, when hybrids are involved, phylogenetic trees start to look like Ewok villages.

Global population genetics:

There has been recent excitement and debate about the details of human demographic history, involving gene flow that has occurred between populations as well as the extent and timing of bottlenecks and periods of population growth. Much of the debate concerns the timing of past admixture events; for example, whether Neanderthals exchanged genetic material with the ancestors of non-Africans before before or after they left Africa. . . . [W]ithin the populations sequenced by the 1000 Genomes consortium, we find evidence that there was no significant gene flow between Europeans and Asians within the past few hundred generations. It also looks unlikely that the Yorubans of Nigeria interbred with Europeans or Asians in a population-specific way, though there may have been admixture between [some] Africans and an ancestral non-African population.

Put another way, the genetic exchanges between Africa and Europe probably post-date the non-Paleoafrican West African founding population and did not extend as far as West Africa (or Southern Africa) until the European colonial era. These empirical results, taken together with statistical models that show that even very slight gene flow can dramatically link large populations surprisingly quickly, suggest that the level of regional population isolation until very recently was very extreme.

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We applied our method to polymorphism data in European and East Asian individuals from the 1000 genomes project, in conjunction with the draft sequence of the Neandertal genome, to obtain the first genomewide map of Neandertal ancestry. Analysis of this map reveals several findings: 1. We identify around 35,000 Neandertal-derived alleles in Europeans and 21,000 in East Asians. 2. The map allows us to identify Neandertal alleles that have been the target of selection since introgression. We identified over 100 regions in which the frequency of Neandertal ancestry is extremely unlikely under a model of neutral evolution. The highest frequency region on chromosome 4 has a frequency of Neandertal ancestry of about 85% in Europe and overlaps CLOCK, a key gene in Circadian function in mammals. The high frequency, Neandertal-derived variant is specific to Europeans; it is not very common in East Asians. This gene has been found in other selection scans in Eurasian populations, but has never before been linked to Neandertal gene flow. 3. Several of the Neandertal-derived alleles identified in 1) above are found in the >6,000 SNPs associated with common diseases listed in the NHGRI catalog. These Neandertal derived variants are found to be risk variants associated with obesity and protective variants against breast cancer. 4. We also investigate the possibility of using this map to reconstruct the genome of the introgressing Neandertal. Using the ancestries in Europe and East Asia, we can reconstruct about 600 Mb which we expect to increase with larger samples and additional populations.

The West Eurasian v. East Eurasian differences in Neanderthal admixture must have occured separately but comparably in West Eurasians and East Eurasian founding populations (both not long after that basic West-East split of the respective founding populations), or must have resulted from a pretty complete fission of a Eurasian founding population at a time when genes introgressed from Neanderthals had not yet reached fixation on the original Out of Africa population.

Either way, the West Eurasian v. East Eurasian split in the Out of Africa population has to come very early, and the notion of a many millenia long Eurasian Eden period prior to this split and after Neanderthal admixture is disfavored. In an unstructured population of tens of thousands of people, which is approximately the size of the Eurasian founding population on a census basis, which probably did not exceed a few hundred thousand for many millenia, it would have taken only a dozen or few generations (a few centuries) for the West Eurasian and East Eurasian components of Neanderthal admixture to be much more similar than they are in reality.

Any extended Eurasian Eden period, during which non-Africans grew genetically distinct from Africans before splitting into West Eurasian and East Eurasian branches, would have had to have taken place before any significant Neanderthal admixture in that population.

The earliest archaeological evidence for modern humans outside Africa, which is more than 100,000 years ago, and even the earliest evidence of continuous modern human presence of modern humans outside Africa, which is more than 75,000 years ago, far precedes the arrival of modern humans in Europe (ca. 40,000 years ago) or Neanderthal extinction (ca. 29,000 years ago). Both the 100,000 year ago evidence from the Levant and the 75,000 year ago evidence from the Levant suggests that modern humans were contemporaneous with Neanderthals there at these times (with a possible absence of more than twenty-millenia in between these time periods).

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A draft genome sequence was determined in 2010 from a small finger bone found in Denisova Cave in southern Siberia and was recently completed to 30-fold coverage. Its analysis reveals that it derived from an individual that belonged to a population related to, but distinct from, Neandertals. A large molar has also been described from Denisova Cave and shown to carry an mtDNA genome closely related to that of the finger bone.

A second molar was found in Denisova Cave in 2010. We have captured and sequenced the complete mitochondrial genome of this tooth. While the mtDNAs of the finger bone and the first molar differ at only two nucleotide positions, they carry 86 and 84 differences, respectively, to the second molar. Thus, the maximum amount of mtDNA differences observed among these three Denisovans found within one cave is almost twice as large as the maximum differences seen among six Neandertals for which complete mtDNAs are available. Interestingly, the mtDNA of the second molar has a shorter branch than the other two Denisovan mtDNAs, suggesting that it may be older than the others.

If, as I suspect, Denisovians have a significant Asian Homo Erectus descent, then we would expect more genetic diversity in their nearly two million year old Out of Africa lineage than in Neanderthals whose emergence is not more than about six hundred thousand years old and perhaps considerably more recent than that date.

Paleoafrican genetics:

[W]e sequenced the whole genomes of five individuals in each of three geographically and linguistically diverse African hunter-gatherer populations. . . . In these 15 genomes we identify 13.4 million variants, many of which are novel, substantially increasing the set of known human variation. These variants result in allele frequency distributions that are free of SNP ascertainment bias. This genetic data is used to infer population divergence times and demographic history (including population bottlenecks and inbreeding). . . . These highly-divergent genomic regions include genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing.

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Previous studies have shown an ancient divergence (~60,000 years ago) of the ancestors of modern day Pygmies from non-Pygmies, and a more recent split of the Eastern and Western Pygmy groups. . . . we sequenced the [whole] genomes of 47 individuals from three populations: 20 Baka, a Pygmy hunter-gatherer population from the Western subgroup of the African Pygmies; 20 Nzebi, a neighboring non-Pygmy agriculturist population from the Bantu ethnolinguistic group; as well as 7 Mbuti, Eastern Pygmy population, from the Human Genome Diversity Project (HGDP). . . . we call over 17 Million SNPs across the three populations, 32% of them novel. . . . Preliminary results show relatively low genetic differentiation between the Baka and the Nzebi (mean FST = 0.026), whereas the Mbuti show higher differentiation to both Baka and Nzebi (mean FST = 0.060 and 0.070, respectively).

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The San and Khoe people currently represent remnant groups of a much larger and widely distributed population of hunter-gatherers and pastoralists who had exclusive occupation of southern Africa before the arrival of Bantu-speaking groups in the past 1,200 years and sea-borne immigrants within the last 350 years. Mitochondrial DNA, Y-chromosome and autosomal studies conducted on a few San groups revealed that they harbour some of the most divergent lineages found in living peoples throughout the world. . . . we successfully genotyped . . . 220 individuals, comprising seven Khoe-San, two Coloured and two Bantu-speaking groups from southern Africa. . . .

We found that six of the seven Khoe-San populations form a common population lineage basal to all other modern human populations. The studied Khoe-San populations are genetically distinct, with diverse histories of gene flow with surrounding populations. A clear geographic structuring among Khoe-San groups was observed, the northern and southern Khoe-San groups were most distinct from each other with the central Khoe-San group being intermediate. The Khwe group contained variation that distinguished it from other Khoe-San groups. Population divergence within the Khoe-San group is approximately 1/3 as ancient as the divergence of the Khoe-San as a whole to other human populations (on the same order as the time of divergence between West Africans and Eurasians). Genetic diversity in some, but not all, Khoe-San populations is among the highest worldwide, but it is influenced by recent admixture. We furthermore find evidence of a Nilo-Saharan ancestral component in certain Khoe-San groups, possibly related to the introduction of pastoralism to southern Africa.

The latest information on Paleoafrican genetics refines, but largely confirms the status quo pre-history of Africa. Genetic data suggest that African hunter-gatherer populations diverged from other Africans at roughly the same time as indicated by mutation and recombination rates as the Out of Africa event, and at the very least, in the Mesolithic era prior to modern human presence in Europe, Australia, Papua New Guinea, Japan, Tibet, or the Americas. These small populations have many genetic variations found nowhere else, some of which are probably basal and provide unique insights into early modern human genetics, and others of which probably reflect selective evolution for their circumstances as hunter-gatherers in marginal territories. Their Bantu and European and Asian ancestries, when observed, are well understood in the historic context of colonialism, and the near pre-historic context of Bantu expansion.

These studies reinforce the notion that these populations have highly substructured population genetics, rather than being drawn from a homogeneous Paleoafrican population. This contrasts sharply with population like those of indigeneous North and South Americans, indigneous Papuan and Australian populations, Jomon Japan, the Andaman Islands, and Arctic Finland's Saami population (one of Europe's last populations to transition from hunting and gathering to pastoralism), whose population genetics are all show characteristic signs of being derived from small founding populations that placed a bottleneck on subsequent genetic diversity. Indeed, non-African population genetics, in general, show a derivation from a relatively modest sized founding population.

The evidence of a Nilo-Saharan ancestral component in certain Khoe-San groups is also new.

West African genetics:

The Niger-Congo phylum encompasses more than 1500 languages spread over sub-Saharan Africa. This current wide range is mostly due to the spread of Bantu-speaking people across sub-equatorial regions in the last 4000-5000 years. Although several genetic studies have focused on the evolutionary history of Bantu-speaking groups, much less effort has been put into the relationship between Bantu and non-Bantu Niger-Congo groups. Additionally, archaeological and linguistic evidence suggest that the spread of these populations occurred in distinct directions from the core region located in what is now the border between Nigeria and Cameroon towards West and South Africa, respectively. We have performed coalescent simulations . . . in order to statistically evaluate the relative probability of alternative models of the spread of Niger-Congo speakers and to infer demographic parameters underlying these important migration events.

We have analysed 61 high-quality microsatellite markers, genotyped in 130 individuals from three Bantu and three non Bantu-speaking populations, representing a "Southern wave" or the Bantu expansion, and a "Western wave", respectively. Preliminary results suggest that models inspired by a spatial spread of the populations are better supported than classical isolation with migration (IM) models. We also find that Niger-Congo populations currently maintain high levels of gene flow with their neighbours, and that they expanded from a single source between 200 and 600 generations[.]

I would quarrel with the claim that the lingustic evidence supports a non-Bantu expansion was centered at a place more or less identical to the Bantu expansion. The Niger-Congo expansion is widely viewed in linguistic circles as happening earlier than Bantu expansion from a location to the North of this location. The archaeological record is thin, any way you cut it.

A Niger-Congo expansion time of 200 to 600 generations sounds more precise than it seems - this covers a period from about 18,000 years ago to the eve of Bantu expansion, depending on the demographic parameters applied. All this shows is that Niger-Congo expansion did not happen in the early Upper Paleolithic, which the reasonable coherence of most of the Niger-Congo language family has always suggested was probably the case.

Mediterranean genetics:

We identify a complex pattern of autochthonous, European, Near Eastern, and sub-Saharan components in extant North African populations; where the autochthonous component diverged from the European and Near Eastern component more than 12,000 years ago, pointing to a pre-Neolithic ‘‘back-to-Africa’’ gene flow.

To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the frequency and length distribution of migrant tracts, which has suggested a migration of western African origin into Morocco ~1,200 years ago and a migration of individuals with Nilotic ancestry into Egypt ~ 750 years ago.

We characterize broad patterns of recent gene flow between Europe and Africa, with a gradient of recent African ancestry that is highest in southwestern Europe and decreases in northern latitudes. The elevated shared African ancestry in SW Europe (up to 20% of the individuals’ genomes) can be traced to populations in the North African Maghreb. Our results, based on both allele-frequencies and shared haplotypes, demonstrate that recent migrations from North Africa substantially contribute to the higher genetic diversity in southwestern Europe.

Central Asian genetics:

[W]e focus on human populations in Central Asia, a region that has long been known to contain the highest genetic diversity on the Eurasian continent. However, whether this variation principally reflects long-term presence, or rather the result of admixture associated with repeated migrations into this region in more recent historical times, remains unclear. Here we investigate the underlying demographic history of Central Asian populations in explicit relation to Western Europe, Eastern Asia and the Middle East. . . . we find that present patterns of genetic diversity in Central Asia may be best explained by a demographic history which combines long-term presence of some ethnic groups (Indo-Iranians) with a more recent admixed origin of other groups (Turco-Mongols). Interestingly, the results also provide indications that this region might have genetically influenced Western European populations, rather than vice versa.

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Kyrgyzstan . . . we focused on two populations in Central Asia with long-term contrasted lifestyles: Kyrgyz’s that are traditionally nomadic herders, with a traditional diet based on meat and milk products, and Tajiks that are traditionally agriculturalists, with a traditional diet based mostly on cereals. . . . Tajiks display a much larger proportion of common ancestry with European populations while Kirgiz’s share a larger common ancestry with Asiatic populations.

South Asian genetics:

Linguistic and genetic studies have demonstrated that almost all groups in South Asia today descend from a mixture of two highly divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners and Europeans, and Ancestral South Indians (ASI) not related to any populations outside the Indian subcontinent. ANI and ASI have been estimated to have diverged from a common ancestor as much as 60,000 years ago, but the date of the ANI-ASI mixture is unknown.

Here we analyze data from about 60 South Asian groups to estimate that major ANI-ASI mixture occurred 1,200-4,000 years ago. Some mixture may also be older—beyond the time we can query using admixture linkage disequilibrium—since it is universal throughout the subcontinent: present in every group speaking Indo-European or Dravidian languages, in all caste levels, and in primitive tribes. After the ANI-ASI mixture that occurred within the last four thousand years, a cultural shift led to widespread endogamy, decreasing the rate of additional mixture.

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Human skin colour is a polygenic trait that is primarily determined by the amount and type of melanin produced in the skin. The pigmentation variation between human populations across the world is highly correlated with geographic latitude and the amount of UV radiation. Association studies together with research involving different model organisms and coat colour variation have largely contributed to the identification of more than 378 pigmentation candidate genes. These include TYR OCA2, that are known to cause albinism, MC1R responsible for the red hair phenotype, and genes such as MATP, SLC24A5 and ASIP that are involved in normal pigmentation variation. In particular, SLC24A5 has been shown to explain one third of the pigmentation difference between Europeans and Africans. However, the same gene cannot explain the lighter East Asian phenotype; therefore, light pigmentation could be the result of convergent evolution.

A study on UK residents of Pakistani, Indian and Bangladeshi descent found significant association of SLC24A5, SLC45A2 and TYR genes with skin colour. . . . We have tested 15 candidate SNPs for association with melanin index in a large sample of 1300 individuals, from three related castes native to South India. Using logistic regression model we found that SLC24A5 functional SNP, rs1426654, is strongly associated with pigmentation in our sample and explains alone more than half of the skin colour difference between the light and the dark group of individuals. Conversely, the other tested SNPs fail to show any significance; this strongly argues in favour of one gene having a major effect on skin pigmentation within ethnic groups of South India, with other genes having small additional effects on this trait. We genotyped the SLC24A5 variant in over 40 populations across India and found that latitudinal differences alone cannot explain its frequency patterns in the subcontinent.

The proposed ANI-ASI admixture date is not inconsistent with a proposed time frame for an Indo-Aryan migration into India, although it is suspiciously young and may conceal pre-existing ANI-ASI divisions due to inadequacies of the model.

South Asian skin coloration turns out to be genetically quite straight forward and to involve the same gene that is most important in distinguishing Europeans and Africans from each other in skin color. The fact that the same genetics are not at work in East Asians and do not correlate well with latitude in South Asia suggest that these skin color differences arose after the initial waves of Southern route migration into Asia and that they have a significant Holocene admixture as opposed to evolutionary selection source.

European genetics:

About 11,000 years ago, a change in human lifestyle took place in the territories of present-day western Iran, the Levant region and south-east Anatolia, which is characterised particularly by four factors: the people founded permanent settlements with buildings for various functions; plants such as Einkorn and beans were cultivated; goats, sheep, pigs and cattle were domesticated; a new kind of culture evolved, that became conspicuous with the appearance of a new material culture including ground stone tools and later, pottery products. The transition from the partly nomadic hunter-gatherer subsistence strategy to a settled lifestyle based on food production is also known as the “Neolithic Revolution”. About 8,500 years ago, the Neolithic culture spread to the southeast of Europe and later expanded episodically across central and northern Europe. The extent to which this movement of a farming culture was accompanied by a movement of people, as opposed to just a spread of ideas and skills, has been a subject of considerable debate and dispute over the last 100 years.

Population genetic computer simulations of genetic data from ancient human remains, based on coalescent theory have shown that the early Neolithic farmers could not have been descended just from the later hunter-gatherers of central Europe (Bramanti et al. 2009). As the hunter-gatherers had already been settled in Central Europe since the retreat of the glaciers 20 kya, Neolithic famers must have migrated into this area.

There is good evidence of cultural contact between hunter-gatherers and early farmers in central Europe. Whether the exchange of hunting tools also led also to the exchange of men is still not clear, as Y-chromosomal DNA has not yet been studied systematically in ancient human remains. Moreover, ancient DNA evidence is now emerging that other regions don't follow the patterns of population discontinuity observed in Central Europe. While the overall results support a model of demic diffusion of farmers from southeastern Europe, or even further East, into Central Europe, it is very likely that modern populations in most parts of Europe were formed by varying degrees of admixture between incoming farmers and indigenous hunter-gatherers.

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The Etruscan culture is documented in Etruria, Central Italy, from the 7 th to the 1 st century BC. For more than 2,000 years there has been disagreement on the Etruscans’ biological origins, whether local or in Anatolia. Genetic affinities with both Tuscan and Anatolian populations have been reported, but so far all attempts have failed to fit the Etruscans’ and modern populations in the same genealogy. We extracted and typed mitochondrial DNA of 14 individuals buried in two Etruscan necropoleis, analyzing them along with other Etruscan and Medieval samples, and 4,910 contemporary individuals. Comparing ancient and modern diversity with the results of millions of computer simulations, we show that the Etruscans can be considered ancestral, with a high degree of confidence, to the modern inhabitants of two communities, Casentino and Volterra, but not to most contemporary populations dwelling in the former Etruscan homeland. We also estimate that the genetic links between Tuscany and Anatolia date back to at least 5,000 years ago, strongly suggesting that the Etruscan culture developed locally, without a significant contribution of recent Anatolian immigrants.

This result tends to disfavor a priori the likelihood that the Etruscan and Rhaetic languages were part of the same linguistic family as pre-Indo-European Aegean languages that have been previously linked to them based on some rather thin evidence. This abstract doesn't shed much light on whether the Roman era Rhaetic Swiss from whom the Etruscans are historically attributed to have been linked ethnically and linguistically were themselves, was a refugium population displaced from Gaul by Celtic peoples. But, it does confirm that Etruscans were demically replaced in most of Tuscanny, as earlier ancient DNA studies had suggested. Earlier studies had left open the possibility that the Etruscans had been genocidally extinguished entirely by the Romans, but it now looks as if this did not happen.

Indigenous Puerto Ricans:

[T]he ancestry-specific PCA plotted the Puerto Rican Native segments tightly clustered with the Native segments of groups from the same language family as the Tainos (Equatorial-Tucanoan), showing a clear association between linguistics and genetics instead of a geographical one.

The nature of Puerto Rican indigeneous ancestry has been controversial. This finding supports the conclusion that the indigeneous ancestry of Puerto Ricans is indeed local to the island and can be traced back to the era of Columbian first contact, rather than constituting hodge podge of indigeneous roots from across the Americans that arrived via colonial era trade routes.