Southern origins and recent admixture of Siberian populations

bioRxiv http://dx.doi.org/10.1101/018770

The complex admixture history and recent southern origins of Siberian populations

Irina Pugach , Rostislav Matveev , Viktor Spitsyn , Sergey Makarov , Innokentiy Novgorodov , Vladimir Osakovsky , Mark Stoneking , Brigitte Pakendorf

Although Siberia was inhabited by modern humans at an early stage, there is still debate over whether this area remained habitable during the extremely cold period of the Last Glacial Maximum or whether it was subsequently repopulated by peoples with a recent shared ancestry. Previous studies of the genetic history of Siberian populations were hampered by the extensive admixture that appears to have taken place among these populations, since commonly used methods assume a tree-like population history and at most single admixture events. We therefore developed a new method based on the covariance of ancestry components, which we validated with simulated data, in order to investigate this potentially complex admixture history and to distinguish the effects of shared ancestry from prehistoric migrations and contact. We furthermore adapted a previously devised method of admixture dating for use with multiple events of gene flow, and applied these methods to whole-genome genotype data from over 500 individuals belonging to 20 different Siberian ethnolinguistic groups. The results of these analyses indicate that there have indeed been multiple layers of admixture detectable in most of the Siberian populations, with considerable differences in the admixture histories of individual populations, and with the earliest events dated to not more than 4500 years ago. Furthermore, most of the populations of Siberia included here, even those settled far to the north, can be shown to have a southern origin. These results provide support for a recent population replacement in this region, with the northward expansions of different populations possibly being driven partly by the advent of pastoralism, especially reindeer domestication. These newly developed methods to analyse multiple admixture events should aid in the investigation of similarly complex population histories elsewhere.

Link

Turkic language family time depth: 204BC

From the paper:

The regular-sound-change tree estimates a mean divergence time between the outgroup Chuvash and other Turkic languages of 204 BCE, with a 95% credible interval of 605 BCE to 81 CE. This compares to proposals from glottochronological analyses that suggest dates of 30 BCE to 0 CE [21] and 500 BCE to 50 CE from historical data [18, 21 and 22]. The sporadic-sound-change model estimates the mean age of the tree to be more than two millennia older (2408 BCE, 95% CI = 3994–1279 BCE), because it wrongly assumes that the many occurrences of regular sound change along the outgroup Chuvash branch are multiple instances of independent phonological change.

Current Biology Volume 25, Issue 1, 5 January 2015, Pages 1–9

Detecting Regular Sound Changes in Linguistics as Events of Concerted Evolution

Daniel J. Hruschka et al.

Summary

Background

Concerted evolution is normally used to describe parallel changes at different sites in a genome, but it is also observed in languages where a specific phoneme changes to the same other phoneme in many words in the lexicon—a phenomenon known as regular sound change. We develop a general statistical model that can detect concerted changes in aligned sequence data and apply it to study regular sound changes in the Turkic language family.

Results

Linguistic evolution, unlike the genetic substitutional process, is dominated by events of concerted evolutionary change. Our model identified more than 70 historical events of regular sound change that occurred throughout the evolution of the Turkic language family, while simultaneously inferring a dated phylogenetic tree. Including regular sound changes yielded an approximately 4-fold improvement in the characterization of linguistic change over a simpler model of sporadic change, improved phylogenetic inference, and returned more reliable and plausible dates for events on the phylogenies. The historical timings of the concerted changes closely follow a Poisson process model, and the sound transition networks derived from our model mirror linguistic expectations.

Conclusions

We demonstrate that a model with no prior knowledge of complex concerted or regular changes can nevertheless infer the historical timings and genealogical placements of events of concerted change from the signals left in contemporary data. Our model can be applied wherever discrete elements—such as genes, words, cultural trends, technologies, or morphological traits—can change in parallel within an organism or other evolving group.

Link

Indo-Europeans in Journal of Language Relationship

I had referred to this collection of papers before,  and now all the PDFs appear to be available free of charge.

This seems fairly interesting:

Language and archeology: some methodological problems.
1. Indo-European and Altaic landscapes

Anna Dybo

The article is the first part of a larger work that represents an attempt to systematize our
ideas on the natural environment and material culture of the Proto-Indo-Europeans. It is
based on a more or less complete selection of reconstructed words from the appropriate semantic areas and on their comparison with a similar selection performed for a protolanguage of similar time depth, whose speakers evidently inhabited a territory that was not
in contact with the Proto-Indo-European one — Proto-Altaic. In this part, only the words that
belong to the semantic field of landscape terms are analyzed. The main conclusion is that thehypothesis of a steppe environment is more applicable for the Proto-Altaic population,whereas for Proto-Indo-Europeans a mountainous region seems more appropriate. As for
the water bodies, for Proto-Indo-Europeans we should suppose the existence of a sea (or of a
very big lake), and for speakers of Proto-Altaic, the existence of very big rivers with season
floods

Mallory's article is also interesting as the latest public take on the PIE origins issue by the prominent champion of the Pontic-Caspian steppe hypothesis. It also alerted me to a study in Russian on the problem of Tocharian origins by Leonid Sverchkov. Sadly, I don't read Russian, but Mallory has a nice review of it in the Journal of Indo-European Studies, from which comes the following excerpt:

 The second section of the book investigates Central
Asia as a cultural historical region. It briefly summarizes the
major Palaeolithic influences, then provides more detail
about the Mesolithic cultures of the region before settling
down to a much more thorough description of the
Neolithic cultures, among which much time is devoted to
the Kelteminar culture that occupied a broad area of
Central Asia and which many earlier authors saw as critical
in explaining the origins of many of the neighboring
cultures, among which would be included the Afanasievo
culture of the Altay and Minusinsk Basin. The author
continues laying out the cultural-historical development of
Central Asia up to the early Middle Ages.
 The third part is titled ‘Tokharians and the IndoEuropean problem” and the archaeological evidence seen
earlier is then recast to provide arguments for a Central
Asian homeland for the Indo-Europeans. One of the
perennial problems with searching out the origins of any
particular Indo-European group is that all too often
proponents of a particular theory provide an isolated
‘solution’ divorced from the fact that it is only part of a
larger puzzle and its pieces must make joins with the rest
of the Indo-European world. I have termed this the ‘total
distribution principle’ and it is one of the tests of how
serious we should deal with any partial solution to IndoEuropean expansions. In attempting to meet this
principle, one can hardly criticize the author as his final
section is essentially a very detailed proposal for a ‘new’
Indo-European homeland in Central Asia. Geographically
situated not far from the earlier proposals of Gamkrelidze
and Ivanov, it does provide some legs to their general
positioning of the Indo-European homeland but in a novel
fashion. Sverchkov’s solution also embraces a series of
earlier suggestions or models but is truly his own in terms
of its implementation.
 Sverchkov’s solution is fundamentally a rejection of
those who would normally dismiss Central Asia as merely a
transition zone across which migrating populations passed
through. During the transition between the Mesolithic
and Neolithic we find a vast Keltiminar culture occupying
the entire region from the Urals and Caspian east to the
Altay, and north of the Kopetdagh and northern
Afghanistan. This region matches at least in areal extent
the type of homelands anchored in Europe such as those
who have sought the Urheimat in the area of the
Linearbandkeramik. To these Sverchkov also includes the
southern agricultural regions of Jarmo and later Jeitun
which would appear to lie outside the area normally
ascribed to other non-Indo-European languages (Semitic,
Elamite, Dravidian, Altaic, Uralic). This entire region then
functions as a broad Indo-European homeland. He suggests
that the westward movement of the Halaf culture accounts
for the separation of the Anatolian branch. The ProtoTocharians begin within the Jeitun region and moved
eastwards to arrive in Ferghana by the Bronze Age. The
archaeological discussion emphasizes the presence of
painted wares in both the Tarim Basin, especially in the
region where we find Tocharian B, and Ferghana, and
these persistent contacts are seen as indicating the spread
of the Tokharian languages. This pattern of Central Asian
contacts is seen even in the earliest cemeteries of the
region (Xiaohe, Gumagou) which, although lacking
ceramics altogether, possessed abundant evidence for bagshaped baskets which have been compared to the shape
and decorations of Kelteminar vessels. It might be noted
that precisely the same pot-to-basket argument has been
employed by those who support a connection between the
Tarim Basin and the steppelands.
 The other Indo-European languages are accounted
for by very early (Neolithic) movements from Central Asia
into the Pontic-Caspian region. The Ayderbol culture of
Kazakhstan, for example, is proposed as underlying the
formation of the Dnieper-Donets culture of the Ukraine
and as seen as the initial wave (roughly in the sense of
Marija Gimbutas) of the Italo-Celtic-Illyrians. The Neolithic
and Eneolithic developments of the Volga-Ural region are
under the Kelteminar aegis and yield the later GermanicBalto-Slavic branches. Out of the steppe cultures (Sredny
Stog and Khvalynsk) and the neighboring Maykop culture
he derives the Yamnaya which in the guise of the
Andronovo culture sets off the Aryanization of southern
Central Asia. Throughout this archaeological discussion the
author relates his theories to a variety of linguistic
proposals, e.g., Henning’s famous argument tying the
names of cultures on the frontiers of Mesopotamia with
those of the Tarim Basin

It seems that the PIE urheimat debate is alive and well.

Complete mtDNA sequences and the history of Slavs

PLoS ONE 8(1): e54360. doi:10.1371/journal.pone.0054360

The History of Slavs Inferred from Complete Mitochondrial Genome Sequences

Marta Mielnik-Sikorska et al.

To shed more light on the processes leading to crystallization of a Slavic identity, we investigated variability of complete mitochondrial genomes belonging to haplogroups H5 and H6 (63 mtDNA genomes) from the populations of Eastern and Western Slavs, including new samples of Poles, Ukrainians and Czechs presented here. Molecular dating implies formation of H5 approximately 11.5–16 thousand years ago (kya) in the areas of southern Europe. Within ancient haplogroup H6, dated at around 15–28 kya, there is a subhaplogroup H6c, which probably survived the last glaciation in Europe and has undergone expansion only 3–4 kya, together with the ancestors of some European groups, including the Slavs, because H6c has been detected in Czechs, Poles and Slovaks. Detailed analysis of complete mtDNAs allowed us to identify a number of lineages that seem specific for Central and Eastern Europe (H5a1f, H5a2, H5a1r, H5a1s, H5b4, H5e1a, H5u1, some subbranches of H5a1a and H6a1a9). Some of them could possibly be traced back to at least ~4 kya, which indicates that some of the ancestors of today's Slavs (Poles, Czechs, Slovaks, Ukrainians and Russians) inhabited areas of Central and Eastern Europe much earlier than it was estimated on the basis of archaeological and historical data. We also sequenced entire mitochondrial genomes of several non-European lineages (A, C, D, G, L) found in contemporary populations of Poland and Ukraine. The analysis of these haplogroups confirms the presence of Siberian (C5c1, A8a1) and Ashkenazi-specific (L2a1l2a) mtDNA lineages in Slavic populations. Moreover, we were able to pinpoint some lineages which could possibly reflect the relatively recent contacts of Slavs with nomadic Altaic peoples (C4a1a, G2a, D5a2a1a1).

Link

Iron Age Pazyryk mtDNA

The term "Scythian" is often used to describe a whole host of unrelated peoples across time periods, a practice that is not new but was also applied by the classical writers who were not well acquainted with the world of Eurasian nomads.

The distinction between "west" and "east" in terms of genetics and geography was not always very concordant. East Eurasian mtDNA has been uncovered as far west as Ukraine, and West Eurasian mtDNA well to the east of Europe, in Siberia and eastern Central Asia. The former was extended in the boreal zone of north Eurasian hunter-gatherers, while the latter in the intermediate steppe zone. The results of this paper might suggest that the Europeoid zone extended only up to the Altai, but a previous study discovered mtDNA U5a in Lake Baikal, well to the east of this region. A temporal transect of a particular region, such as the one reported here may help  elucidate not only the mixing of west/east types --which seems to be ancient across the northern parts of Eurasia-- but also the kinds of elements involved. For example, haplogroups K and J which are well-represented in the Iron Age results presented in this paper (especially the former), made their first appearance in the transition to the Iron Age in the Baraba forest-steppe zone to the west during the same time. The picture is still muddy, but a few patterns have begun to emerge: first U's, followed by T's during Andronovo horizon, followed by a wide assortment of lineages during the "Scythian" Iron Age. As I've written before, I strongly suspect that the last stratum originated in the area east of the Caspian sea, where the likely Proto-Indo-Iranian homeland existed, and where a segment of the BMAC population "went nomad" after the desiccation of their homeland.

PLoS ONE 7(11): e48904. doi:10.1371/journal.pone.0048904

Tracing the Origin of the East-West Population Admixture in the Altai Region (Central Asia)

Mercedes González-Ruiz et al.

Abstract

A recent discovery of Iron Age burials (Pazyryk culture) in the Altai Mountains of Mongolia may shed light on the mode and tempo of the generation of the current genetic east-west population admixture in Central Asia. Studies on ancient mitochondrial DNA of this region suggest that the Altai Mountains played the role of a geographical barrier between West and East Eurasian lineages until the beginning of the Iron Age. After the 7th century BC, coinciding with Scythian expansion across the Eurasian steppes, a gradual influx of East Eurasian sequences in Western steppes is detected. However, the underlying events behind the genetic admixture in Altai during the Iron Age are still unresolved: 1) whether it was a result of migratory events (eastward firstly, westward secondly), or 2) whether it was a result of a local demographic expansion in a ‘contact zone’ between European and East Asian people. In the present work, we analyzed the mitochondrial DNA lineages in human remains from Bronze and Iron Age burials of Mongolian Altai. Here we present support to the hypothesis that the gene pool of Iron Age inhabitants of Mongolian Altai was similar to that of western Iron Age Altaians (Russia and Kazakhstan). Thus, this people not only shared the same culture (Pazyryk), but also shared the same genetic east-west population admixture. In turn, Pazyryks appear to have a similar gene pool that current Altaians. Our results further show that Iron Age Altaians displayed mitochondrial lineages already present around Altai region before the Iron Age. This would provide support for a demographic expansion of local people of Altai instead of westward or eastward migratory events, as the demographic event behind the high population genetic admixture and diversity in Central Asia.

Link

Recent admixture in Altaic populations: a legacy of Empire?

Continuing my experiments with ALDER, I took every single Altaic population publicly available, i.e., the following 25 populations:

Altai, Balkars_Y, Buryat, Chuvashs_16, Daur, Dolgan, Evenk_15, Hezhen, Kumyks_Y, Kyrgyz_Bishkek_Ho, Mongol, Mongola, Nogais_Y, Oroqen, Tu, Turkish_Aydin_Ho, Turkish_Istanbul_Ho, Turkish_Kayseri_Ho, Turkmens_Y, Turks, Tuva, Uygur, Uzbeks, Xibo, Yakut

I also took three West Eurasian populations unlikely to have historical East Asian admixture (French, French_Basque, and Sardinians), and three East Eurasian populations unlikely to have historical West Eurasian admixture (Dai, She, Miaozu). I merged all of the above in PLINK with a --geno 0.03 flag, and extracting SNPs present in the Rutgers recombination map for Illumina chips (a total of 524,822 SNPs).

I then ran ALDER for all 25 Altaic populations using any of the 3*3 West/East Eurasian reference pairs, or a total of 25*3*3= 225 runs. I retained only those 2-ref admixture analyses for which ALDER reported "success" with no warnings.

I then converted reported times to calendar dates: a generation of 29 years was assumed; lacking information about the age of the sampled individuals, I assumed that the "present" is 1980; finally, I report the earliest and latest -/+ limits of any confidence interval, as well as the median of all estimates.

The results can be seen below; for 11 of the 25 populations there was at least one test which was successful with no warnings. This does not mean that the other populations are unadmixed, but the following cases appear to be most "well-behaved":

Now, these appear to make excellent sense.

Of the Dolgans:

There also existed a group of Russian settlers on the River Heta, who, by the end of the 19th century, had become Dolganized and had gradually adopted the way of life of nomadic reindeer breeders. ... The tribes forming the nucleus of the Dolgans migrated from the banks of the River Lena at the end of the 17th century. One of the reasons for migration was the fact that Russian goods, flour, for instance, were coming to the Taimyr Peninsula by the boats on the Lena.

The 1770-1860AD range for the admixture appears to coincide with the period where the Dolgans came under Russian influence.

Of the Evenks:

The history of the Evenks' habitation can be traced in detail from the 17th century on. At that time the Evenks left several of their previous territories, for instance, the River Angara, when the Yakut, the Buryat and the Russians appeared in the province. The Evenks had especially bad relations with the Yakuts, who had settled in the river basin of the Lena in the 13th century. In the 18th and 19th centuries the Evenks living there adopted the Yakut language. In the Baikal area the Evenks began to speak the Buryat and the Mongolian languages, and even converted to lamaism. The southern Evenk -- the Manegir, the Birar, the Solon -- were influenced by the Manchu, Daur and Chinese cultures. The arable lands in Siberia were occupied by Russian settlers, migrating there in the 17th century, and those Evenks, living in the vicinity on the upper reaches of the Lena and near Baikal, were russified.

Again, the  1630-1800AD admixture range seems consistent with the time when Evenks came into contact with Russians.

Of the Nogais:

 In the first half of the 17th century a number of Nogay tribes were nomadic on the steppes between the Danube and the Caspian. The invasion of the warlike Kalmyks forced several of the Nogay tribes to leave their home steppes and withdraw to the foothills of the North Caucasus. By the River Kuban they met with the Cherkess.  In the Moscow chronicles from the 16th and 17th centuries there are several mentions of the Nogay, including the two Nogay Hordes, the Great and the Small. The former roamed beyond the River Volga, the latter somewhat to the west. Both had numerous military encounters with the Russians. In the 17th century some of the Nogay chiefs entered into an alliance with Moscow and fought at times together with the Russians against the Kabardians, the Kalmyks and peoples of Dagestan. 

 The 1610-1730AD range intersects the period when the Nogais settled in the North Caucasus and interacted with North Caucasians and Russians.

Not much needs to be said for the admixture signal in the Uygur, Uzbek, Kyrgyz, and Mongols which collectively ranges from 1260-1500AD. This was a period of Mongol power when Mongolian and Turkic speaking peoples assumed control over Central Asia and replaced to a great degree the previous inhabitants of the area.

The origin of the Balkars is less certain, because they are an old Turkic group that settled in the Caucasus, but the admixture (830-1220AD) date seems plausible. So does, of course, that of the Turks from Caesaria (990-1260AD) which parallels those of my recent experiment, and can be associated with the takeover of Anatolia following the Battle of Manzikert. Finally, I don't have a read explanation for the 11-12th century signal of admixture in the Siberian Altai and Buryat, but presumably it has something to do with the expansions of Altaic peoples around that time that were also felt in the west during this period; presumably, this involved some type of mixture with Caucasoid groups in Siberia.

The admixture dates are quite helpful in helping us better interpret other signals of admixture such as those of ADMIXTURE analyses (e.g., globe13). For example, the Dolgan have 13.1% North_European in that experiment, and the Altai have 13.2%, but apparently this occurred centuries apart and may have involved different groups of West Eurasian people.

In conclusion, ALDER seems to find some quite plausible dates for major admixture episodes in the history of Altaic populations that are compatible with fairly recent historical events.

ALDER estimates of East Eurasian admixture in Europe

I used the 1-reference method of ALDER to infer lower bounds of East Eurasian admixture in a few European populations. This method does not include a statistical test of admixture (as does the 2-reference one or the f3 test), but we can probably reasonably suppose that some such admixture did take place on the combined evidence of the f3 test and ADMIXTURE evidence.

In any case, I took the East Asian populations of Loh et al. (2012) which had no evidence of admixture with either ALDER or the f3 test, and also a few populations from Rasmussen et al. (2010) that included representatives of Siberian Uralic speakers, as well as the three main branches of narrow-sense Altaic (Turkic, Mongolian, Tungusic), and estimated lower bounds of admixture for a set of European populations. Results can be seen below:

The evidence for admixture appears most convincing in the 1000 Genomes Finns and HGDP Russians where the +/- interval does not intersect or approach zero irrespective of the Asian population chosen. For these populations, the percentages vary from ~4-5% for the "pure" East Eurasians to ~10% for some Siberian groups such as Selkup and Altai. Thes latter carry some West Eurasian admixture, so it makes sense that a greater deal of admixture with them is necessary to account for the observed "East Eurasian" influence. And, indeed, it is probably via such "intermediate" Siberian populations that some East Eurasian ancestry flowed into Europe, rather than via the relatively untouched populations of the Far East.

PS: Note that this probably represents the most recent signal of admixture, and not the older and more general "North Eurasian"/Amerindian-like admixture that, as Loh et al. mention in their paper cannot be captured with ALDER.

Structural stability and ancient connections between languages

From the press release:

Using a large database and many alternative methods Dediu and Levinson show that both positions are right: there are universal tendencies for some features to be more stable than others, but individual language families have their own distinctive profile. These distinctive profiles can then be used to probe ancient relations between what are today independent language families.  

"Using this technique we find for instance probable connections between the languages of the Americas and those of NE Eurasia, presumably dating back to the peopling of the Americas 12,000 years or more ago," Levinson explains. "We also find likely connections between most of the Eurasian language families, presumably pre-dating the split off of Indo-European around 9000 years ago."

From the paper:

Quite convincing is the evidence that Core Eurasian families (comprising Altaic – or Mongolic + Turkic –, Dravidian, Indo-European, Uralic and the Caucasian families) might form a group (p=0.0013, 5 methods, and , p=0.094, 4 methods, when controlling for geography).

The authors were also able to reject the "broad" Afroasiatic group "comprising Afro-Asiatic, Indo-European, Dravidian and Uralic". I think this makes some sense, since Afroasiatic is basically an African language family with a Near Eastern offshoot, so I did not expect it to group with the Eurasian language families.

The Core Eurasian group seems very interesting in light of accumulating evidence about contacts between human groups across Eurasia. Such a group is pushing the limits of what can be inferred using linguistic data, and, perhaps, archaeogenetics might provide some evidence that might be used to plausibly argue for such a relatively broad group.

PLoS ONE 7(9): e45198. doi:10.1371/journal.pone.0045198

Abstract Profiles of Structural Stability Point to Universal Tendencies, Family-Specific Factors, and Ancient Connections between Languages

Dan Dediu, Stephen C. Levinson

Language is the best example of a cultural evolutionary system, able to retain a phylogenetic signal over many thousands of years. The temporal stability (conservatism) of basic vocabulary is relatively well understood, but the stability of the structural properties of language (phonology, morphology, syntax) is still unclear. Here we report an extensive Bayesian phylogenetic investigation of the structural stability of numerous features across many language families and we introduce a novel method for analyzing the relationships between the “stability profiles” of language families. We found that there is a strong universal component across language families, suggesting the existence of universal linguistic, cognitive and genetic constraints. Against this background, however, each language family has a distinct stability profile, and these profiles cluster by geographic area and likely deep genealogical relationships. These stability profiles seem to show, for example, the ancient historical relationships between the Siberian and American language families, presumed to be separated by at least 12,000 years, and possible connections between the Eurasian families. We also found preliminary support for the punctuated evolution of structural features of language across families, types of features and geographic areas. Thus, such higher-level properties of language seen as an evolutionary system might allow the investigation of ancient connections between languages and shed light on the peopling of the world.

Link

Words denoting pulse crops in European languages

From the paper:

The attested Proto-Indo-European root-words directly linked to pulse crops are further testimony that Proto-Indo-European society was well-acquainted with agriculture (47), and was not predominantly nomadic and pastoral, as initially thought by the proposers of the Kurgan hypothesis (48).

PLoS ONE 7(9): e44512. doi:10.1371/journal.pone.0044512

Origin of the Words Denoting Some of the Most Ancient Old World Pulse Crops and Their Diversity in Modern European Languages

Aleksandar Mikic

This preliminary research was aimed at finding the roots in various Eurasian proto-languages directly related to pulses and giving the words denoting the same in modern European languages. Six Proto-Indo-European roots were indentified, namely arnk(')- (‘a leguminous plant’), *bhabh- (‘field bean’), * (‘a kernel of leguminous plant’, ‘pea’), ghArs- (‘a leguminous plant’), *kek- (‘pea’) and *lent- (‘lentil’). No Proto-Uralic root was attested save hypothetically *kaca (‘pea’), while there were two Proto-Altaic roots, *bukrV (‘pea’) and *(‘lentil’). The Proto-Caucasianx root * denoted pea, while another one, *howl(a)(‘bean’, ‘lentil’) and the Proto-Basque root *ilha-r (‘pea’, ‘bean’, ‘vetch’) could have a common Proto-Sino-Caucasian ancestor, *hVwlV (‘bean’) within the hypothetic Dene-Caucasian language superfamily. The Modern Maltese preserved the memory of two Proto-Semitic roots, *'adas- (‘lentil’) and *pul- (‘field bean’). The presented results prove that the most ancient Eurasian pulse crops were well-known and extensively cultivated by the ancestors of all modern European nations. The attested lexicological continuum witnesses the existence of a millennia-long links between the peoples of Eurasia to their mutual benefit. This research is meant to encourage interdisciplinary concerted actions between plant scientists dealing with crop evolution and biodiversity, archaeobotanists and language historians.

Link

Clarifying the phylogeny of Y-chromosome haplogroup C3c

A short and to the point paper that addresses the issue of classification within Y-haplogroup C3c and refines our knowledge about the distribution of both C3c* and C3c1. I wish more researchers would publish such short technical papers that refine the classification of their Y-chromosome samples as more phylogenetic information becomes available.

From the paper:

In our study, the highest frequencies of subhaplogroup C3c1-(M77, M86) were observed in Tungusic-speaking people of North-Eastern Asia, such as Evens and Evenks, as well as in Turkic-speaking Altaian Kazakhs and Mongolic-speaking Kalmyks. These results are in agreement with previous observations based on separate or joint genotyping of M77 and M86 markers.3,9,12,16

C3c* haplotypes were detected in aboriginal populations of North- Eastern Asia—Koryaks (28.2%) and Evens (1.6%) from the Sea of Okhotsk coast (Magadan region) and West Evenks (2.4%) from Central Siberia (Evenki Autonomous District) (Table 1). Earlier, two Evenk individuals from southern part of Yakutia, one Yakut-speaking Evenk and one Yukaghir were found to belong to C3c*.2,3 Therefore, the geographic distribution of subhaplogroup C3c* is limited to the eastern part of Siberia.

The authors apply the evolutionary mutation rate -although they acknowledge that molecular dating is controversial- to obtain ages of 9.9 (C3c), 6.5 (C3c1), and 4.5 (C3c*). While I don't trust the ability of Y-STR-based molecular dating to provide reasonably accurate age estimates, I would not be surprised if C3c1 was somehow implicated in the deeper origins of the Altaic language family, at least in the "narrow-sense" (Mongolian-Tungusic-Turkic).

J Hum Genet. 2012 Jul 19. doi: 10.1038/jhg.2012.93. [Epub ahead of print]

On the Y-chromosome haplogroup C3c classification.

Malyarchuk BA, Derenko M, Denisova G.

Abstract As there are ambiguities in classification of the Y-chromosome haplogroup C3c, relatively frequent in populations of Northern Asia, we analyzed all three haplogroup-defining markers M48, M77 and M86 in C3-M217-individuals from Siberia, Eastern Asia and Eastern Europe. We have found that haplogroup C3c is characterized by the derived state at M48, whereas mutations at both M77 and M86 define subhaplogroup C3c1. The branch defined by M48 alone would belong to subhaplogroup C3c*, characteristic for some populations of Central and Eastern Siberia, such as Koryaks, Evens, Evenks and Yukaghirs. Subhaplogroup C3c* individuals could be considered as remnants of the Neolithic population of Siberia, based on the age of C3c*-short tandem repeat variation amounting to 4.5±2.4 thousand years.

Link

SMBE 2012 abstracts (Part II)

Some more abstracts from SMBE 2012.

The Neolithic trace in mitochondrial haplogroup U8 

Joana Barbosa Pereira 1,2 , Marta Daniela Costa 1,2 , Pedro Soares 2 , Luísa Pereira 2,3 , Martin Brian Richards 1,4 1 Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, 2 Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,  3 Faculdade de Medicina da  Universidade do Porto, Porto, Portugal,  4 School of Applied Sciences, University of Huddersfield, Huddersfield, UK  

The mitochondrial DNA (mtDNA) still remains an important marker in the study of human history, especially if  considering the increasing amount of data available. Among the several questions regarding human history that are  under debate, the model of expansion of agriculture into Europe from its source in the Near East is still unclear. Recent  studies have indicated that clusters belonging to haplogroup K, a major clade from U8, might be related with the  Neolithic expansions. Therefore, it is crucial to identify the founder lineages of the Neolithic in Europe so that we may  understand the real genetic input of the first Near Eastern farmers in the current European population and comprehend  how agriculture spread so quickly throughout all Europe.  In order to achieve this goal, a total of 55 U8 samples from the Near East, Europe and North Africa were selected for  complete characterisation of mtDNA. A maximum-parsimonious phylogenetic tree was constructed using all published  sequences available so far. Coalescence ages of specific clades were estimated using ρ statistic, maximum likelihood  and Bayesian methods considering a mutation rate for the complete molecule corrected for purifying selection.   Our results show that U8 dates to ~37-54 thousand years ago (ka) suggesting that this haplogroup might have been  carried by the first modern humans to arrive in Europe, ~50 ka. Haplogroup K most likely originated in the Near East  ~23-32 ka where it might have remained during the Last Glacial Maximum, between 26-19 years ago. The majority of K  subclades date to the Late Glacial and are related with the repopulation of Europe from the southern refugia areas. Only  a few lineages appear to reflect post glacial, Neolithic or post-Neolithic expansions, mostly occurring within Europe. The  major part of the lineages dating to the Neolithic period seems to have an European origin with exception of haplogroup  K1a4 and K1a3. Clade K1a4 appears to be originated from the Near East where it also reaches its highest peak of  diversity. Despite the main clades of K1a4 arose in the Near East during the Late Glacial, its subclade K1a4a1 dates to  ~9-11 ka and is most likely related with the Neolithic dispersal to Europe. Similarly, K1a3 probably originated in the Near  East during the Late Glacial and its subclade K1a1a dispersed into Europe ~11-13 ka alongside with the expansion of  agriculture. 

Late Glacial Expansions in Europe revealed through the fine-resolution characterisation of mtDNA haplogroup  U8 

Marta Daniela Costa 1,2 , Joana Barbosa Pereira 1,2 , Pedro Soares 2 , Luisa Pereira 2,3 , Martin Brian Richards 1,4 1 Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, 2 IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,  3 Faculdade de  Medicina, Universidade do Porto, Porto, Portugal,  4 School of Applied Sciences, University of Huddersfield, Huddersfield,  UK  

The maternally inherited and fast evolving mitochondrial DNA (mtDNA) molecule is a highly informative tool with which  to reconstruct human prehistory. This has become even more true in recent years, as mtDNA based studies are  becoming more robust and powerful due to the availability of complete mtDNA genomes. These allow better mutation  rate estimates and fine-resolution characterisation of the phylogeography of mtDNA haplogroups, or named  clades.  MtDNA haplogroup K, the major subclade of U8, occurs at low frequencies through West Eurasian populations,  and is much more common in Ashkenazi Jews. However, the lack of variation on the first hypervariable segment (HVSI) has precluded any meaningful phylogeographic analysis to date. We therefore completely sequenced 50 haplogroup  K and 5 non-K U8 mtDNA samples from across Europe and the Near East, and combined them with 343 genomes  previously deposited in GenBank, in order to reconstruct a detailed phylogenetic tree. By combining several inference  methods, including maximum parsimony, maximum likelihood and Bayesian inference it was possible to trace the  timescale and geography of the main expansions and dispersals associated with this lineage. We confirmed that  haplogroup K, dating to ~32 thousand years (ka) ago, descended from the U8 clade, which coalesces ~48 ka ago. The  latter is close to the timing of the first arrival of modern humans in Europe and U8 could be one of the few surviving  mtDNA lineages brought by the first settlers from the Near East. U8 split into the widespread U8b, at ~43 ka, and U8a,  which seems to have expanded only in Europe ~24 ka ago. Considering the pattern of diversity and the geographic  distribution, haplogroup K is most likely to have arisen in the Near East, ~32 ka ago. However, some subclades were  evidently carried to Europe during the Last Glacial Maximum (LGM). We observed significant expansions of haplogroup  K lineages in the Late Glacial period (14-19 ka), reflecting expansions out of refuge areas in southwest and possibly  also southeast Europe. 

Reticulated origin of domesticated tetraploid wheat 

Peter Civan Centro de Ciencias do Mar, Universidade do Algarve, Faro, Portugal  

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. Multi-disciplinary approaches brought a significant amount of new data and a multitude of  hypotheses and interpretations. However, 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, yet.  The past phylogenetic research has translated the issue of wheat domestication into somewhat simplistic mono- /polyphyletic dilemma, where the monophyletic origin of a crop signalizes rapid and geographically localized  domestication, while the polyphyletic evidence suggests independent, geographically separated domestication events.  Interestingly, the genome-wide and haplotypic data analyzed in several studies did not yield consistent results and the  proposed scenarios are usually in conflict with the archaeological evidence of lengthy domestication.  Here I suggest that 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; hence different sets of samples and genetic loci are prone to conclude different domestication  scenarios. 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. The concept of reticulated genealogy of domesticated wheat sheds new light  onto the emergence of Near-Eastern agriculture and is in agreement with current archaeological evidence of protracted  and dispersed emmer domestication.

High-coverage population genomics of diverse African hunter-gatherers 

Joseph Lachance 1 , Benjamin Vernot 2 , Clara Elbers 1 , Bart Ferwerda 1 , Alain Froment 3 , Jean-Marie Bodo 4 , Godfrey  Lema 5 , Thomas Nyambo 5 , Timothy Rebbeck 1 , Kun Zhang 6 , Joshua Akey 2 , Sarah Tishkoff 1 1 University of Pennsylvania, Philadelphia, PA, USA,  2 University of Washington, Seattle, WA, USA,  3 IRD-MNHN, Musee  de l'Homme, Paris, France,  4 Ministere de la Recherche Scientifique et de l’Innovation, Yaounde, Cameroon,  5 Muhimbili  University College of Health Sciences, Dar es Salaam, Tanzania,  6 University of California at San Diego, San Diego, CA,  USA     

In addition to their distinctive subsistence patterns, African hunter-gatherers belong to some of the most genetically  diverse populations on Earth.  To infer demographic history and detect signatures of natural selection, we sequenced  the whole genomes of five individuals in each of three geographically and linguistically diverse African hunter-gatherer  populations at >60x coverage.  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).  We find that natural selection continues to shape the genomes of  hunter-gatherers, and that deleterious genetic variation is found at similar levels for hunter-gatherers and African  populations with agricultural or pastoral subsistence patterns.  In addition, the genomes of each hunter-gatherer  population contain unique signatures of local adaptation.  These highly-divergent genomic regions include genes  involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing.

Reconstructing past Native American genetic diversity in Puerto Rico from contemporary populations Marina Muzzio 1,2 , Fouad Zakharia 1 , Karla Sandoval 1 , Jake K. Byrnes 3 , Andres Moreno-Estrada 1 , Simon Gravel 1 , Eimear  Kenny 1 , Juan L. Rodriguez-Flores 5 , Chris R. Gignoux 6 , Wilfried Guiblet 4 , Julie Dutil 7 , The 1000 Genomes Consortium 0 ,  Andres Ruiz-Linares 8 , David Reich 9,10 , Taras K. Oleksyk 4 , Juan Carlos Martinez-Cruzado 4 , Esteban Gonzalez  Burchard 6 , Carlos D. Bustamante 1 1 Department of Genetics, Stanford University School of Medicine, Stanford, California, USA,  2 Facultad de Ciencias  Naturales, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina,  3 Ancestry. com®, San Francisco,  California, USA,  4 Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico,  5 Department  of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA,  6 Institute for Human Genetics,  University of California San Francisco, San Francisco, California, USA,  7 Ponce School of Medicine, Ponce, Puerto Rico, 8 Department of Genetics, Evolution and Environment. University College London, London, UK,  9 Department of  Genetics, Harvard Medical School, Boston, Massachusetts, USA,  10 Broad Institute of MIT and Harvard, Cambridge,  Massachusetts, USA  

The Caribbean region has a rich cultural and biological diversity, including several countries with different languages,  and important historical events like the arrival of the Europeans in the late fifteenth century affected it deeply. Although it  has been said that two main Native American groups peopled the Caribbean at the time of Columbus’s voyages—the  Arawakan-speaking Tainos and the Caribs—this model has been questioned because it comes from the descriptions  written by the conquerors. The archaeological record shows a richer picture of trade among the islands, cultural change  and diversity than what colonial documents depict, from the early settlements around 8000 B.P. to the chiefdoms and  towns at the time of contact. How this area was peopled and how its inhabitants interacted with the surrounding  continent are questions that remain to be answered due to the fragmentary nature of the historical and archaeological  records.   
We aim to reconstruct the Native American genetic diversity from the time of the Spanish arrival at the island of Puerto  Rico from its contemporary population. We seek to find out how the original peopling of Puerto Rico occurred, along  with which contemporary Native American populations are the most closely related to the Native tracks found. We used  PCAdmix to trace Native American segments in admixed individuals, thus enabling us to reconstruct the original native  lineages previous to the European and African contact.   

Specifically, we generated local ancestry calls for the 70 parents of the 35 complete Puerto Rican trios from the wholegenome and Illumina Omni 2.5M chip Genotype data of the 1000 Genomes Project, both to examine genome-wide  admixture patterns and to infer demographic historical events from ancestry tract length distributions and an ancestryspecific PCA approach, adding 55 Native American groups as potential source populations (N=475 genotyped through  Illumina’s 650K array) and 15 selected Mexican trios (genotyped on Affymetrix’s 6.0 array, including about 906,000  SNPs) to provide population context. ADMIXTURE analysis has shown that in Puerto Rico there is no single source of  contribution for the Native component. Rather, this component seems to include a mixture of major Mexican and  Andean components with little contributions from the Amazonian isolates. On the other hand, the 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.

 Inference of demographic history and natural selection in African Pygmy populations from whole-genome  sequencing data

 Martin Sikora 1 , Etienne Patin 2 , Helio Costa 1 , Katherine Siddle 2 , Brenna M Henn 1 , Jeffrey M Kidd 1,3 , Ryosuke Kita 1 ,  Carlos D Bustamante 1 , Lluis Quintana-Murci 2 1 Department of Genetics, School of Medicine, Stanford Uni, Stanford, CA, USA,  2 Unit of Human Evolutionary Genetics,  Institut Pasteur, CNRS URA3012, Paris, France,  3 Departments of Human Genetics and Computational Medicine and  Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA     

The Pygmy populations of Central Africa are some of the last remaining hunter-gatherers among present-day human  populations, and can be broadly classified into two geographically separated groups, the Western and Eastern Pygmies.  Compared to their neighboring populations of predominantly Bantu origin, Pygmy populations show distinct cultural and  physical characteristics, most notably short stature, often referred to as the “Pygmy phenotype”. Given their distinct  physical characteristics, the questions of the demographic history and origin of the Pygmy phenotype have attracted  much attention. Previous studies have shown an ancient divergence (~60,000 years ago) of the ancestors of modernday Pygmies from non-Pygmies, and a more recent split of the Eastern and Western Pygmy groups. However, these  studies were generally based on a relatively small set of markers, precluding accurate estimations of demographic  parameters. Furthermore, despite the considerable interest, to date there is still little known about the genetic basis of  the small stature phenotype of Pygmy populations.   

In order to address these questions, we sequenced the 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 nonPygmy agriculturist population from the Bantu ethnolinguistic group; as well as 7 Mbuti, Eastern Pygmy population, from  the Human Genome Diversity Project (HGDP). We performed whole-genome sequencing using Illumina Hi-Seq 2000 to  a median sequencing depth of 5.5x per individual. After stringent quality control filters, we call over 17 Million SNPs  across the three populations, 32% of them novel (relative to dbSNP 132). Genotype accuracy after imputation was  assessed using genotype data from the Illumina OMNI1 SNP array, and error rates were found to be comparable to  other low-coverage studies (< 3% for most individuals). 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). Furthermore, we find that alleles previously found to be associated with height in other populations are not enriched for the “small” alleles in the Pygmy populations. We find a number of  highly differentiated genomic regions as candidate loci for height differentiation, which will be verified using simulations  under the best-fit demographic model, inferred from multi-dimensional allele frequency spectra using DaDi. Our dataset  will allow a detailed investigation of the demographic history and the genomics of adaptation in these populations.

Genetic structure in North African human populations and the gene flow to Southern Europe

Laura R Botigué 1 , Brenna M Henn 2 , Simon Gravel 2 , Jaume Bertranpetit 1 , Carlos D Bustamante 2 , David Comas 1 1 Institut de Biologia Evolutiva (IBE, CSIC-UPF), Barcelona, Spain,  2 Stanford University, Stanford CA, USA Despite being in the African continent and at the shores of the Mediterranean, North African populations might have  experienced a different population history compared to their neighbours. However, the extent of their genetic divergence  and gene flow from neighbouring populations is poorly understood. In order to establish the genetic structure of North  Africans and the gene flow with the Near East, Europe and sub-Saharan Africa, a genomewide SNP genotyping array  data (730,000 sites) from several North African and Spanish populations were analysed and compared to a set of  African, European and Middle Eastern samples. 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

Estimating a date of mixture of ancestral South Asian populations

Priya Moorjani 1,2 , Nick Patterson 2 , Periasamy Govindaraj 3 , Danish Saleheen 4 , John Danesh 4 , Lalji Singh* 3,5 ,  Kumarasamy Thangaraj* 3 , David Reich* 1,2 1 Harvard University, Boston, Massachusetts, USA,  2 Broad Institute, Cambridge, Massachusetts, USA,  3 Centre for  Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India,  4 Dept of Public Health and Care, University of  Cambridge, Cambridge, UK,  5 Genome Foundation, Hyderabad, Andhra Pradesh, India 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.   

Long IBD in Europeans and recent population history 

Peter Ralph, Graham Coop  UC Davis, Davis, CA, USA  

Numbers of common ancestors shared at various points in time across populations  can tell us about recent demography, migration, and population movements.  These rates of shared ancestry over tens of generations can be inferred from  genomic data, thereby dramatically increasing our ability to infer population  history much more recent than was previously possible with population genetic  techniques.  We have analyzed patterns of IBD in a dataset of thousands of  Europeans from across the continent, which provide a window into recent  European geographic structure and migration.   

Gene flow between human populations during the exodus from Africa, and the timeline of recent human  evolution  

Aylwyn Scally, Richard Durbin  Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK 

We present a novel test for historical gene flow between populations using unphased genotypes in present-day  individuals, based on the sharing of derived alleles and making a minimal set of assumptions about their demographic  history. We apply this test to data for three human individuals of African, European and Asian ancestry. We find that the  joint distribution of European and Asian genotypes is compatible with these populations having separated cleanly at  some time in the past without subsequent genetic exchange. However the same is not true of the European-African and  Asian-African distributions, which instead suggest an extended period of continued exchange between African and nonAfrican populations after their initial separation. 

We discuss this in comparison with recent models and estimates of separation time between these populations. We  also consider the impact of recent direct experimental studies of the human mutation rate, which suggest rates of  around 0.5 × 10 -9  bp -1  y -1 , substantially lower than prior estimates of 1 × 10 -9  bp -1  y -1  obtained from calibration against  the primate fossil record. We show that in several places the lower rate, implying older dates, yields better agreement  between genetic and non-genetic (paleoanthropological and archaeological) evidence for events surrounding the  exodus of modern humans from Africa and their dispersion worldwide.

Long-term presence versus recent admixture: Bayesian and approximate-Bayesian analyses of genetic  diversity of human populations in Central Asia 

Friso Palstra, Evelyne Heyer, Frederic Austerlitz  Eco-anthropologie et Ethnobiologie UMR 7206 CNRS, Equipe Genetique des Populations Humaines, Museum National  d'Histoire Naturelle, Paris, France 

A long-standing goal in population genetics is to unravel the relative importance of evolutionary forces that shape  genetic diversity. Here we 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. For this purpose we employ both full Bayesian and  approximate-Bayesian analyses of nuclear genetic diversity in 20 unlinked non-coding resequenced DNA regions,  known to be at least 200 kb apart from any known gene, mRNA or spliced EST (total length of 24 kb), and 22 unlinked  microsatellite loci.   

Using an approximate Bayesian framework, 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. A further  evaluation in MCMC-based Bayesian analyses of isolation-with-migration models confirms the different times of  establishment of ethnic groups, and suggests gene flow into Central Asia from the east. The results from the  approximate Bayesian and full Bayesian analyses are thus largely congruent. In conclusion, these analyses illustrate  the power of Bayesian inference on genetic data and suggest that the high genetic diversity in Central Asia reflects both  long-term presence and admixture in more recent historical times. 

Population structure and evidence of selection in the Khoe-San and Coloured populations from southern Africa 

Carina Schlebusch 1 , Pontus Skoglund 1 , Per Sjödin 1 , Lucie Gattepaille 1 , Sen Li 1 , Flora Jay 2 , Dena Hernandez 3 , Andrew  Singleton 3 , Michael Blum 2 , Himla Soodyall 4,5 , Mattias Jakobsson 1 1 Uppsala University, Uppsala, Sweden,  2 Université Joseph Fourier, Grenoble, France,  3 National Institute on Aging (NIH),  Bethesda, USA,  4 University of the Witwatersrand, Johannesburg, South Africa,  5 National Health Laboratory Service,  Johannesburg, South Africa  

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 used autosomal data to characterize patterns of genetic variation among southern African individuals in order to  understand human evolutionary history, in particular the demographic history of Africa. To this end, we successfully  genotyped ~ 2.3 million genome wide SNP markers in 220 individuals, comprising seven Khoe-San, two Coloured and  two Bantu-speaking groups from southern Africa. After quality filtering, the data were combined with publicly available  SNP data from other African populations to investigate stratification and demography of African populations.  

We also  applied a newly developed method of estimating population topology and divergence times. Genotypes and inferred  haplotypes were used to assess genetic diversity, patterns of haplotype variation and linkage disequilibrium in different  populations.  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.   

We searched for signatures of selection in the different population groups by scanning for differentiated genome-regions  between populations and scanning for extended runs of haplotype homozygosity within populations. By means of the  selection scans, we found evidence for diverse adaptations in groups with different demographic histories and modes of  subsistence. 

Impacts of life-style on human evolutionary history: A genome-wide comparison of herder and farmer  populations in Central Asia 

Michael C. Fontaine 1,2 , Laure Segurel 2,3 , Christine Lonjou 4 , Tatiana Hegay 5 , Almaz Aldashev 6 , Evelyne Heyer 2 , Frederic  Austerlitz 1,2 1 Ecology, Systematics & Evolution. UMR8079 Univ. Paris Sud - CNRS - AgroParisTech, Orsay, France,  2 EcoAnthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cite, Paris, France, 3 Department of Human Genetics, University of Chicago, Chicago, USA,  4 C2BiG (Centre de  Bioinformatique/Biostatistique Genomique d’Ile de France), Plateforme Post-genomique P3S, Hopital Pitie Salpetriere,  Paris, France,  5 Uzbek Academy of Sciences, Institute of Immunology, Tashkent, Uzbekistan,  6 Institute of Molecular  Biology and Medicine, National Center of Cardiology and Internal Medicine, Bishkek,  

Kyrgyzstan Human populations use a variety of subsistence strategies to exploit an exceptionally broad range of habitats and  dietary components. These aspects of human environments have changed dramatically during human evolution, giving  rise to new selective pressures. Here 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. We genotyped 93 individuals for more  than 600,000 SNP markers (Human-660W-Quad-V1.0 from Illumina) spread across the genome. We first analysed the  population structure of these two populations in the world-wide context by combining our results with other available  genome-wide data. Principal component and Bayesian clustering analyses revealed that Tajiks and Kirgiz’s are both  admixed populations which differed however from each other with respect to their ancestry proportions: Tajiks display a  much larger proportion of common ancestry with European populations while Kirgiz’s share a larger common ancestry  with Asiatic populations. We then examined the region of the genome displaying unusual population differentiation  between these two populations to detect natural selection and checked whether they were specific to Central Asia or  not. We complemented these analyses with haplotype-based analyses of selection. 

Bayesian inference of the demographic history of Niger-Congo speaking populations 

Isabel Alves 1,2 , Lounès Chikhi 2,3 , Laurent Excoffier 1,4 1 CMPG, Institute of Ecology and Evolution, Berne, Switzerland,  2 Population and Conservation Genetics Group, Instituto  Gulbenkian de Ciência, Oeiras, Portugal,  3 CNRS, Université Paul Sabatier, ENFA, Toulouse, France,  4 Swiss Institute of  Bioinformatics, Lausanne, Switzerland  

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 within an approximate Bayesian computation (ABC) framework 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, even though available genetic data do not  provide enough information to accurately infer these demographic parameters.

A genetic study of skin pigmentation variation in India  

Mircea Iliescu1 , Chandana Basu Mallick 2,3 , Niraj Rai 4 , Anshuman Mishra 4 , Gyaneshwer Chaubey 2 , Rakesh Tamang 4 ,  Märt Möls 3 , Rie Goto 1 , Georgi Hudjashov 2,3 , Srilakshmi Raj 1 , Ramasamy Pitchappan 5 , CG Nicholas Mascie-Taylor 1 , Lalji  Singh 4,6 , Marta Mirazon-Lahr 7 , Mait Metspalu 2,3 , Kumarasamy Thangaraj 4 , Toomas Kivisild 1,3 1 Division of Biological Anthropology, University of Cambridge, Cambridge, UK,  2 Evolutionary Biology Group, Estonian  Biocentre, Tartu, Estonia,  3 Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia,  4 Centre for Cellular  and Molecular Biology, Hyderabad, India,  5 Chettinad Academy of Research and Education, Chettinad Health City,  Chennai, India,  6 Banaras Hindu University, Varanasi, India,  7 Leverhulme Centre for Human Evolutionary Studies,  Division of Biological Anthropology, University of Cambridge, Cambridge, UK  

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. While these genes may explain a significant proportion of  interethnic differences in skin colour, it is not clear how much variation such genes explain within Indian populations  who are known for their high level of diversity of pigmentation. 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. Key questions arising from this research are  when and where did the light skin variant enter South Asia and the manner and reason for it spreading across the Indian  sub-continent. Hence, a comprehensive view of skin colour evolution requires that in depth sequence information be  corroborated with population (genetic) history and with ancient DNA data of past populations of Eurasia.