Afanasievo, Okunev, Andronovo, Sintashta DNA?

A reader alerts me to this article in Russian, but you can use Google Translate to get the gist of it. Some interesting bits (note that "pit"=Yamna):

I can not ignore the question I now have is particularly exciting - the origin of the Indo-Europeans. Community Indo-Europeists animatedly discussing just appeared as a preprint work of David Raika and his colleagues discovered by studying the genomes of people Neolithic and Bronze Age that a decisive influence on the genetic landscape of Europe has had a migration of people pit culture to the north and west in the middle of the III millennium. BC .e. As a result, according to geneticists, there was a population associated with the Corded Ware culture, and from it are the origin of the later Indo-European. By the same conclusions about the same time came the other team's leading geneticists led by Eske Villerslevom.
...

A steppe, we thought had long been a special world, and differs sharply from the Middle East, and from the European. Migration from there - so it seemed - were mainly directed not to the west and to the east, along the steppes, in the direction of Central Asia, which the ancient Indo-Europeans, Afanasiev media culture (descendants of the people of the pit culture or their ancestors steppe) reached no later turn IV- III millennium BC. It is now confirmed and the group Villersleva.
...

By the way, it also happens that paleoanthropologists prompted geneticists way of research - and turned out to be right. As it happens, for example, with native Okunevskaya culture of South Siberia. When 20 years ago, we found that craniologically (by a combination of traditional measurement and we proposed new informative features of the structure of the cranial sutures and holes) okunevtsy - "cousins" of American Indians, few believed us. Firstly, in okunevtsah ever seen Caucasoid-Mongoloid Métis like the Kazakhs, and secondly, the ancestors of the Indians withdrew from Siberia to the New World at least 10 thousand. Before the Yenisey there Okunevskaya culture.

Eske Willerslev Now and his colleagues have fully confirmed our conclusion. They confirmed the close relationship between the carriers and the pit Afanasiev cultures and migration ancestors sintashtintsev and Andronov from Europe in the Urals and further to Siberia - but this is already a long time, few archaeologists and anthropologists doubted.

I hope more details will appear soon on what promises to be a very interesting new study. The author seems to be referring to his theory of a relationship between Okunev and Amerindians, and I'm wondering if this is simply "Ancient North Eurasian" ancestry or an even more specific link. Any Russian readers who can dig up more information are invited to post in the comments.

Spread of Leprosy into Medieval Europe

Infection, Genetics and Evolution Volume 31, April 2015, Pages 250–256

A migration-driven model for the historical spread of leprosy in medieval Eastern and Central Europe

Helen D. Donoghue et al.

Leprosy was rare in Europe during the Roman period, yet its prevalence increased dramatically in medieval times. We examined human remains, with paleopathological lesions indicative of leprosy, dated to the 6th–11th century AD, from Central and Eastern Europe and Byzantine Anatolia. Analysis of ancient DNA and bacterial cell wall lipid biomarkers revealed Mycobacterium leprae in skeletal remains from 6th–8th century Northern Italy, 7th–11th century Hungary, 8th–9th century Austria, the Slavic Greater Moravian Empire of the 9th–10th century and 8th–10th century Byzantine samples from Northern Anatolia. These data were analyzed alongside findings published by others. M. leprae is an obligate human pathogen that has undergone an evolutionary bottleneck followed by clonal expansion. Therefore M. leprae genotypes and sub-genotypes give information about the human populations they have infected and their migration. Although data are limited, genotyping demonstrates that historical M. leprae from Byzantine Anatolia, Eastern and Central Europe resembles modern strains in Asia Minor rather than the recently characterized historical strains from North West Europe. The westward migration of peoples from Central Asia in the first millennium may have introduced different M. leprae strains into medieval Europe and certainly would have facilitated the spread of any existing leprosy. The subsequent decline of M. leprae in Europe may be due to increased host resistance. However, molecular evidence of historical leprosy and tuberculosis co-infections suggests that death from tuberculosis in leprosy patients was also a factor.

Link

Ancient DNA from Di-qiang populations in the Xinjiang

American Journal of Physical Anthropology DOI: 10.1002/ajpa.22690

Ancient DNA reveals a migration of the ancient Di-qiang populations into Xinjiang as early as the early Bronze Age

Shi-Zhu Gao et al.

Xinjiang is at the crossroads between East and West Eurasia, and it harbors a relatively complex genetic history. In order to better understand the population movements and interactions in this region, mitochondrial and Y chromosome analyses on 40 ancient human remains from the Tianshanbeilu site in eastern Xinjiang were performed. Twenty-nine samples were successfully assigned to specific mtDNA haplogroups, including the west Eurasian maternal lineages of U and W and the east Eurasian maternal lineages of A, C, D, F, G, Z, M7, and M10. In the male samples, two Y chromosome haplogroups, C* and N1 (xN1a, N1c), were successfully assigned. Our mitochondrial and Y-chromosomal DNA analyses combined with the archaeological studies revealed that the Di-qiang populations from the Hexi Corridor had migrated to eastern Xinjiang and admixed with the Eurasian steppe populations in the early Bronze Age.

Link

Where pastoralist met farmer and East met West (Spengler et al. 2014)

The paper's conclusion:

Archaeobotanical data from Central Eurasian pastoralist campsites have major implications for our understanding of late prehistoric agriculture across Asia. Sites like Tasbas and Begash illustrate the earliest acquisition of domesticated crops by mobile pastoralists and illustrate their capacity to participate in exchanges that bridged East Asian and Central Asian farming cultures by the early third millennium BC. Mobile pastoralists living in (southern) Central Asian alluvial fans and along the mountainous spine of Central Eurasia also integrated farming into their own domestic strategies (at least) by the mid second millenniumBC. Their pastoral mobility and the formation of extensive networks throughout the IAMC helped spread particular grain morphotypes and a mixed plant cohort of wheat, barley, millet and green peas through the mountains between Xinjiang, China and southwest Asia in the second millennium BC. The seasonal campsites of Begash, Tasbas, Ojakly and Site 1211/1219 are the earliest sites thus far reported to break down the strict polarization between nomads and farmers in prehistoric Central Eurasia. They also transform our comprehension of the vast arena of interaction that defines this region in ancient times. 

Related:

• Frachetti on the multiregional emergence of mobile pastoralism
• Horse not important for the emergence of steppe pastoralism
• Michael Frachetti on the Inner Asian Mountain Corridor

Proc. R. Soc. B doi:10.1098/rspb.2013.3382

Early agriculture and crop transmission among Bronze Age mobile pastoralists of Central Eurasia

Robert Spengler et al.

Archaeological research in Central Eurasia is exposing unprecedented scales of trans-regional interaction and technology transfer between East Asia and southwest Asia deep into the prehistoric past. This article presents a new archaeobotanical analysis from pastoralist campsites in the mountain and desert regions of Central Eurasia that documents the oldest known evidence for domesticated grains and farming among seasonally mobile herders. Carbonized grains from the sites of Tasbas and Begash illustrate the first transmission of southwest Asian and East Asian domesticated grains into the mountains of Inner Asia in the early third millennium BC. By the middle second millennium BC, seasonal camps in the mountains and deserts illustrate that Eurasian herders incorporated the cultivation of millet, wheat, barley and legumes into their subsistence strategy. These findings push back the chronology for domesticated plant use among Central Eurasian pastoralists by approximately 2000 years. Given the geography, chronology and seed morphology of these data, we argue that mobile pastoralists were key agents in the spread of crop repertoires and the transformation of agricultural economies across Asia from the third to the second millennium BC.

Link

Afghan mega-paper (Di Cristofaro et al.)

The admixture results nicely presented on a map:

The authors note that none of the ancestral components peaks in Central Asia, concluding that this region has been a destination rather than a source of population movements. I certainly agree that Central Asia has a lot of recent history affecting it from virtually all directions. On the other hand, we should be cautious about interpreting geographical clines in terms of directionality of population movement; a good example is Sardinia which often emerges as a "focus" of Mediterranean ancestry, but this does not mean that it is the origin of such ancestry. It would certainly be interesting to remove the layers of more recent ancestry from Central Asia to see what was there before the last few thousand years.

The PCA based on autosomal data:

The Y-chromosome haplogroup data can be found in Figure S7. The authors comment:

94% of the chromosomes are distributed within the following 9 main haplogroups: R-M207 (34%), J-M304 (16%), C-M130 (15%), L-M20 (6%), G-M201 (6%), Q-M242 (6%), N-M231 (4%), O-M175 (4%) and E-M96 (3%). Within the core haplogroups observed in the Afghan populations, there are sub-haplogroups that provide more refined insights into the underlying structure of the Y-chromosome gene pool. One of the important sub-haplogroups includes the C3b2b1-M401 lineage that is amplified in Hazara, Kyrgyz and Mongol populations. Haplogroup G2c-M377 reaches 14.7% in Pashtun, consistent with previous results [31], whereas it is virtually absent from all other populations. J2a1-Page55 is found in 23% of Iranians, 13% of the Hazara from the Hindu Kush, 11% of the Tajik and Uzbek from the Hindu Kush, 10% of Pakistanis, 4% of the Turkmen from the Hindu Kush, 3% of the Pashtun and 2% of the Kyrgyz and Mongol populations. Concerning haplogroup L, L1c-M357 is significantly higher in Burusho and Kalash (15% and 25%) than in other populations. L1a-M76 is most frequent in Balochi (20%), and is found at lower levels in Kyrgyz, Pashtun, Tajik, Uzbek and Turkmen populations. Q1a2-M25 lineage is characteristic of Turkmen (31%), significantly higher than all other populations. Haplogroup R1a1a-M198/M17 is characterized by its absence or very low frequency in Iranian, Mongol and Hazara populations and its high frequency in Pashtun and Kyrgyz populations.

PLoS ONE 8(10): e76748. doi:10.1371/journal.pone.0076748

Afghan Hindu Kush: Where Eurasian Sub-Continent Gene Flows Converge

Julie Di Cristofaro et al.

Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH). The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci.

Link

mtDNA from Nepal and Tibet (Gayden et al. 2013)

Am J Phys Anthropol. 2013 Jun;151(2):169-82. doi: 10.1002/ajpa.22240. Epub 2013 Apr 12.

The Himalayas: Barrier and conduit for gene flow.

Gayden T, Perez A, Persad PJ, Bukhari A, Chennakrishnaiah S, Simms T, Maloney T, Rodriguez K, Herrera RJ.

Abstract

The Himalayan mountain range is strategically located at the crossroads of the major cultural centers in Asia, the Middle East and Europe. Although previous Y-chromosome studies indicate that the Himalayas served as a natural barrier for gene flow from the south to the Tibetan plateau, this region is believed to have played an important role as a corridor for human migrations between East and West Eurasia along the ancient Silk Road. To evaluate the effects of the Himalayan mountain range in shaping the maternal lineages of populations residing on either side of the cordillera, we analyzed mitochondrial DNA variation in 344 samples from three Nepalese collections (Newar, Kathmandu and Tamang) and a general population of Tibet. Our results revealed a predominantly East Asian-specific component in Tibet and Tamang, whereas Newar and Kathmandu are both characterized by a combination of East and South Central Asian lineages. Interestingly, Newar and Kathmandu harbor several deep-rooted Indian lineages, including M2, R5, and U2, whose coalescent times from this study (U2, >40 kya) and previous reports (M2 and R5, >50 kya) suggest that Nepal was inhabited during the initial peopling of South Central Asia. Comparisons with our previous Y-chromosome data indicate sex-biased migrations in Tamang and a founder effect and/or genetic drift in Tamang and Newar. Altogether, our results confirm that while the Himalayas acted as a geographic barrier for human movement from the Indian subcontinent to the Tibetan highland, it also served as a conduit for gene flow between Central and East Asia.

Link

Y chromosomes in Iranians and Tajiks (Malyarchuk et al. 2013)

An interesting paper on Iranian and Tajik Y chromosomes. Iranian Y chromosomes were comprehensively studied by Grugni et al. but it is always good to have additional samples.

I have mentioned before the apparent distinction between west and east Iranians in terms of haplogroup J/R1a frequencies, with high ratios in Persians and Kurds, and low ones in Pathans, and this seems to be reinforced here; the Tajiks are speakers of Persian (hence "western") but trace their ancestry to the east of the modern country of Iran, and in-between Persians and eastern Iranians.

The absence of R1a in this Kurdish sample, coupled with high J frequency parallels the situation in the Kurdish Anatolian settlement studied by Gokcument et al., as well as the Georgian Kurmanji sample studied by Nasidze et al. On the other hand, R1a is present in the Kurmanji samples from Turkey and Turkmenistan in the latter study, as well as in the aforementioned Kurdish sample from Iran by Grugni et al. and the Kurdish sample from Turkmenistan studied by Wells et al. I'd say that there is potential variation of this haplogroup within Kurdish groups, which might be worth further exploration.

It would also be very interesting to study the haplogroup I chromosomes from this region. Do they represent historical introgression from Europe, or are they, perhaps, local basal clades that reinforce the idea of a relic distribution of I in West Asia, prior to the migration into Europe, that was recently suggested by the discovery of IJ* chromosomes in Iran by Grugni et al.?

Annals of Human Biology, 2013; Early Online: 1–7

Y-chromosome variation in Tajiks and Iranians

Boris Malyarchuk et al.

Aim: The purpose of this study was to characterize Y-chromosome diversity in Tajiks from Tajikistan and in Persians and Kurds from Iran.

Method: Y-chromosome haplotypes were identified in 40 Tajiks, 77 Persians and 25 Kurds, using 12 short tandem repeats (STR) and 18 binary markers.

Results: High genetic diversity was observed in the populations studied. Six of 12 haplogroups were common in Persians, Kurds and Tajiks, but only three haplogroups (G-M201, J-12f2 and L-M20) were the most frequent in all populations, comprising together 60% of the Y-chromosomes in the pooled data set. Analysis of genetic distances between Y-STR haplotypes revealed that the Kurds showed a great distance to the Iranian-speaking populations of Iran, Afghanistan and Tajikistan. The presence of Indian-specific haplogroups L-M20, H1-M52 and R2a-M124 in both Tajik samples from Afghanistan and Tajikistan demonstrates an apparent genetic affinity between Tajiks from these two regions.

Conclusions: Despite the marked similarities between Y-chromosome gene pools of Iranian-speaking populations, there are differences between them, defined by many factors, including geographic and linguistic relationships.

Link

Mitochondrial DNA in Ancient Human Populations of Europe (der Sarkissian 2011)

Going over the 322 pages of thesis may take a while, but feel free to comment on it if you discover any interesting nuggets in the text. The following view of West/East Eurasian mtDNA surrounding the beginning of the Iron Age may be useful, and seems to parallel the results of a recent paper on Pazyryk mtDNA:

Of course, since the thesis was published we have new data from West Siberia/Ukraine that suggest that the penetration of east Eurasian lineages covered a great area to the west of the indicated region even prior to the Iron Age.

We can be fairly sure that "non-East Eurasian admixed" populations existed during the Bronze Age in three portions of the Eurasian landmass, separated by the Black and Caspian Seas: west of the Black Sea (Balkans/Central Europe); between Black and Caspian Seas (Caucasus) and east of the Caspian Sea (Kazakhstan and Turkmenistan). But how did these three regions contribute to the West Eurasian elements found on a west-east axis across Eurasia today? And, to what extent did the early east Eurasian elements that penetrated well into eastern Europe in the Neolithic-to-Bronze Age contribute to latter populations of the area vs. more recent expansions from the Altai and Central Asia during the Iron Age?

Here is a PCA of the pre-Iron Age individuals, compared with modern populations:

Both "Tarim" (TAR) and "Neolithic Lake Baikal" (LOK) appear well within east Eurasian variation. But, of the West Eurasian groups, Pitted Ware Complex (PWC), i.e., Neolithic hunter-gatherers from NE Europe and Bronze Age Altai (ALT-BA) appear clearly "northern Europeoid" across the 2nd PC, as do, to a lesser extent, C/N European Hunter-Gatherers (HG) and Kurgan burials from south Siberia (KUR-BA), but Bronze Age Kazakhstan (KAZ-BA) appear to be southern Europeoid, and, also, noticeably more "West Eurasian" than the others. Clearly, the West Eurasian elements were not homogeneous, with some of them (such as KAZ-BA) apparently derived from the southern Caucasoid zone -which largely did not experience east Eurasian admixture- and others from the northern Caucasoid zone that did.

The Rostov Scythian sample (in red) appears to belong to the southern Caucasoid zone (across PC2), but East Eurasian-shifted relative to modern Europeans and Bronze Age Kazakhstan.

Now, let's look at the Iron and post-Iron Age samples:

Egyin Gol (EG) from Mongolia and Sargat Siberians appear clearly as East Eurasians; Pazyryk Altai (ALT-IA), Iron Age Kazakhstan (KAZ-IA) and South Siberia Kurgan (KUR-IA) show decreasing East Eurasian influence; also notice the decidedly "southern" shift of the West Eurasian element among them.

This seems broadly consistent with the ideas of Molodin et al. about the gradual appearance (in their Siberian sample) of Caucasoid mtDNA types from the Neolithic to the Iron Age, with the early Neolithic U-dominated population finally receiving a full set of diverse West Eurasian lineages only during the Iron Age from the south.

It will certainly be very exciting when samples such as these can be tested for autosomal or Y-chromosome DNA, and I'm looking forward to the day when this can be done on a large scale.

Type: Thesis
Title: Mitochondrial DNA in ancient human populations of Europe.
Author: Dersarkissian, Clio Simone Irmgard
Issue Date: 2011
School/Discipline: School of Earth and Environmental Sciences

Abstract: The distribution of human genetic variability is the result of thousand years of human evolutionary and population history. Geographical variation in the nonrecombining maternally inherited mitochondrial DNA has been studied in a wide array of modern populations in order to reconstruct the migrations that have participated in the spread of our ancestors on the planet. However, population genetic processes (e.g., replacement, genetic drift) can significantly bias the reconstruction and timing of past migratory and demographic events inferred from the analysis of modern-day marker distributions. This can lead to erroneous interpretations of ancient human population history, a problem that potentially could be circumvented by the direct assessment of genetic diversity in ancient humans. Despite important methodological problems associated with contamination and post-mortem degradation of ancient DNA, mitochondrial data have been previously obtained for a few spatially and temporally diverse European populations. Mitochondrial data revealed additional levels of complexity in the population history of Europeans that had remained unknown from the study of modern populations. This justifies the relevance of broadening the sampling of ancient mitochondrial DNA in both time and space. This study aims at filling gaps in the knowledge of the genetic history of eastern Europeans and of European genetic outliers, the Saami and the Sardinians. This study presents a significant extension to the knowledge of past human mitochondrial diversity. Ancient remains temporally-sampled from three groups of European populations have been examined: north east Europeans (200 – 8,000 years before present; N = 76), Iron Age Scythians of the Rostov area, Russia (2,300 – 2,600 years before present; N = 16), Bronze Age individuals of central Sardinia, Italy (3,200 – 3,400 years before present; N = 16). The genetic characterisation of these populations principally relied on sequencing of the mitochondrial control region and typing of single nucleotide polymorphisms in the coding region. Changes in mitochondrial DNA structure were tracked through time by comparing ancient and modern populations of Eurasia. Analysis of haplogroup data included principal component analysis, multidimensional scaling, fixation index computation and genetic distance mapping. Haplotypic data were compared by haplotype sharing analysis, phylogenetic networks, Analysis of the Molecular Variance and coalescent simulations. The sequencing of a whole mitochondrial genome in a north east European Mesolithic individual lead to defining a new branch within the human mitochondrial tree. This work presents direct evidence that Mesolithic eastern Europeans belonged to the same Palaeolithic/Mesolithic genetic background as central and northern Europeans. It was also shown that prehistoric eastern Europeans were the recipients of multiple migrations from the East in prehistory that had not been previously detected and/or timed on the basis of modern mtDNA data. Ancient DNA also provided insights in the genetic history of European genetic outliers; the Saami, whose ancestral population still remain unidentified, and the Sardinians, whose genetic differentiation is proposed to be the result of mating isolation since at least the Bronze Age. This study demonstrates the power of aDNA to reveal previously unknown population processes in the genetic history of modern Eurasians.

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

Improved phylogenetic resolution within Y-haplogroup R1a1

Here is the table of haplogroup frequencies:

I have written before that I envision R1a1 to have been anciently distributed in the wide arc of "flatlands" north and east of the Caspian sea, complementing R-M269 whose distribution is suggestive of the short arc of "highlands" west and south of it.

The current distribution is strongly geographically bimodal, with peaks in eastern Europe and South Asia. The phylogeny of this group is continuously refined, but one of the problems with the "commercial" studies of haplogroups is that they tend to consist of samples drawn primarily of the groups of people who are likely to have heard of DNA testing, and this excludes large regions within the Eurasian heartland. For example, Z280 is listed as "Central and Eastern Europe Western Asia" in the R1a1a and subclades project, but here makes up 2/9 R-M198 related samples from the Central Asian Uzbek sample. Similarly, M458 is listed as Central Europe, but occurs in 1/9 Uzbek. We can't know for sure which SNP occurs where until we test large representative samples.

There are various aspects of the problem that need to be considered: the absence of R1a-related lineages in pre-Copper Age Europe, and of the distant R1b relative, together with the firm rooting of the R1 clade in Asia indicate that the lineage leading to R1a1 traces its ancestry to a migration into Europe. How and when that migration occurred is an open problem. The paucity of SNP diversity in South Asia, at least in the available samples, indicates that a migration into South Asia also occurred. So, I agree with the authors "that an early differentiation zone of R1a1-M198 conceivably occurred somewhere within the Eurasian Steppes or the Middle East and Caucasus region as they lie between South Asia and Eastern Europe."

My working hypothesis is that the bimodal distribution of R1a1-related lineages in Eurasia can be explained on the basis of two expansions involving largely Z283 in Europe and Z93 in Asia. The source of those expansions may have been Central Asia, and the relative scarcity of R1a1 in that region (relative to Europe and South Asia) may be the result of a subsequent movement of East Eurasians into it, at the same time as the expansion of Altaic speakers. The Uzbek sample in this paper give us a strong hint about the existence of an overlap zone in Central Asia, but the SNP diversity is little studied in the populations of the -stan states, and ancient DNA samples are missing.

The issue of time depth is also relevant, as it will anchor in time the evolutionary relationships between different populations of R1a1 descendants. This can be achieved both by (i) typing ancient samples for the relevant markers, which will provide -assuming a positive result- a terminus ante quem for the appearance of particular SNP, and (ii) sequencing modern Y-chromosomes to determine their TMRCA.

AJPA DOI: 10.1002/ajpa.22167

Brief communication: New Y-chromosome binary markers improve phylogenetic resolution within haplogroup R1a1

Horolma Pamjav et al.

Abstract

Haplogroup R1a1-M198 is a major clade of Y chromosomal haplogroups which is distributed all across Eurasia. To this date, many efforts have been made to identify large SNP-based subgroups and migration patterns of this haplogroup. The origin and spread of R1a1 chromosomes in Eurasia has, however, remained unknown due to the lack of downstream SNPs within the R1a1 haplogroup. Since the discovery of R1a1-M458, this is the first scientific attempt to divide haplogroup R1a1-M198 into multiple SNP-based sub-haplogroups. We have genotyped 217 R1a1-M198 samples from seven different population groups at M458, as well as the Z280 and Z93 SNPs recently identified from the “1000 Genomes Project”.

The two additional binary markers present an effective tool because now more than 98% of the samples analyzed assign to one of the three sub-haplogroups. R1a1-M458 and R1a1-Z280 were typical for the Hungarian population groups, whereas R1a1-Z93 was typical for Malaysian Indians and the Hungarian Roma. Inner and Central Asia is an overlap zone for the R1a1-Z280 and R1a1-Z93 lineages. This pattern implies that an early differentiation zone of R1a1-M198 conceivably occurred somewhere within the Eurasian Steppes or the Middle East and Caucasus region as they lie between South Asia and Eastern Europe. The detection of the Z93 paternal genetic imprint in the Hungarian Roma gene pool is consistent with South Asian ancestry and amends the view that H1a-M82 is their only discernible paternal lineage of Indian heritage.

Link

Archaeometallurgy in the Mediterranean

Continuing a discussion on metallurgical innovation which I began here.

Some interesting excerpts from a book chapter:

Tin bronze first appeared in Mesopotamia and Anatolia during the third millennium B.C., or Early Bronze Age (Pare 2000a:6–7). In the Mediterranean,the transition from arsenical to tin bronze took place during the course of the Middle Bronze Age (late third to early second millennium B.C.in the eastern Mediter-ranean, somewhat later in the west). The implication (Renfrew 1972:313–319) that tin bronze was an independent development in the northeast Aegean is contradicted by lead isotope analyses which show that most copper or bronze objects from sites such as Troy, Poliochni, and Kastri were not produced from local ores (Muhly and Pernicka 1992; Pernicka 1998:140–141). Exactly what caused the transition from arsenical to tin bronze is not well understood: as an alloy, tin bronze is not mechanically superior to arsenical copper (Pernicka 1998:135–136).Unlike arsenic, moreover, tin is not widely available as a mineral, and new trade networks would have been required to enable its distribution. However, it may have been easier to control the quality of tin bronze, and the production of tin bronze would have overcome the problem of working with toxic arsenic fumes (Charles 1978:30;Pare 2000a:7).

Given the limited number of tin deposits in the region, the source(s) of tin usedin the prehistoric eastern Mediterranean has always been a highly controversial issue. The suggestion that Afghanistan served as a prime source of tin for Bronze Age eastern Mediterranean societies is based in part on the existence of its rich tin resources (Muhly and Pernicka 1992:315;Weeks 1999:60–61).Muhly (1999:21) recently argued that Afghanistan or central Asia provided the tin that supplied the bronze industries of Mesopotamia, Anatolia, and the eastern Mediterranean, including Cyprus. Cuneiform documents from the early second millennium B.C., moreover, point to a trade network that brought tin from the east to the early states of Anatolia and Mesopotamia (Maddin et al.1977:41:Weeks 1999),and thence to the Mediterranean. Weisgerber and Cierny (2002,with fuller references) now maintain that prehistoric tin mining (second millennium B.C.), attested at the sites of Karnab (Uzbekhistan) and Musciston (Tajikistan), provided an important source of tin for Anatolia and Mesopotamia, if not for the Mediterranean. In contrast, Yener and Vandiver (1993) have argued that (very limited) tin deposits in the Taurus Mountains of southern Turkey were exploited during the Early Bronze Age. Their argument has been challenged by several scholars (e.g.,Muhly 1993;Weisgerberand Chierny 2002:180–181;papers in Journal of Mediterranean Archaeology 5[1995]) who maintain that the archaeological evidence is unclear,and far too limited to demonstrate anything beyond local use. Even if tin from the Taurus were mined during the Early Bronze Age, it now seems more likely that central Asia provided at least some of the tin used during the Middle-Late Bronze Ages,when tin bronze was far more widely produced, traded, and consumed in the Mediterranean. 

... 

By the Late Neolithic period (ca.4800–3100 B.C.), most people living in the Mediterranean region produced their own food, lived the year round in sedentary communities and increasingly were involved in intricate social and economic exchanges. By the beginning of the Bronze Age, certain alliances, special-interest groups, or even individual local leaders came to control access to raw materials in demand: obsidian, precious or semi-precious stones, metals such as gold, silver, copper, and tin, and a range of more perishable goods. From about 3000 B.C.onward – corresponding to the Chalcolithic period (Argaric culture) in Spain, the Final Neolithic in Italy, and the Early Bronze Age in the Aegean and eastern Mediterranean – the production and trade in metals increasingly became a key factor in promoting social change (Giardino 2000b;Knapp 1990a;Levy et al.2002;Manning 1994;Ruiz Taboada and Montero Ruiz 1999).  

...  

Technological innovations may be seen as progressive by managers and elites, but for the people who mined ores or smelted metals they were also potentially disruptive, forming the backdrop for social change as well as social abuse (Heskel andLamberg-Karlovsky 1980:260–261;Stollner 2003:427–429). Miners and metal-smiths often use ideology as a means to maintain, resist,or change their power base within society. Because elites who control and organize metallurgical produc-tion often use material culture to restructure relations of power (Gamble 1986:39), we may also expect such transformations to be visible in the archaeological record. 

...  

Consequently, there is little room to doubt that innovations in technology had deep-seated and long-lasting social and ecological effects, placing constraints as well as conferring benefits on Bronze Age mining and metallurgical production. In social terms, whereas the intensified production of copper employing an advanced technology did not preclude a strong sense of local community, such factors served to increase social distinctions between those at the top of the control structure and those at the bottom (Hardesty 1988:102,116;Knapp 1986b;2003). 

...  

The trade in metals during the Chalcolithic period was carried out on a very limited scale, and most metals were certainly consumed in the same area where they were produced (cf.Gale 1991). During the Early Bronze Age (third millennium B.C.), technological innovations like the longboat and sail facilitated the bulk transport of raw materials or manufactured goods on a much larger scale than ever before (Broodbank 1989). 

... 

Metals and metallurgy wielded an immense impact on Mediterranean Bronze Age societies, clearly evident in all the fundamental changes seen in the archaeological record from the end of the Chalcolithic period (Copper Age) onward. During the Bronze Age,innovations in maritime transport and the earliest cultivation of olives and vines stimulated the economy of the Mediterranean region and spurred some of its inhabitants to produce metals, take part in maritime trade, manufacture distinctive artifacts, and build domestic and public structures that represented the earliest towns and ceremonial complexes in the Mediterranean. The advent and spread of metallurgy promoted greater social distinctions,as certain individuals or groups acquired new wealth and prestige items. Because tin had to be imported in order to produce bronze, long-distance trade was stimulated. Duringthe second millennium B.C., gold, silver, copper, and tin came to represent what Sherratt (2000:83) has termed “convertible”value, both in an economic sense and in the literal sense that they could be consumed, stored, redistributed, or recycled in diverse forms and for various symbolic or ideological ends.Such documentary evidence as exists, exclusively in the eastern Mediterranean, is frequently preoccupied with these self-same metals (Liverani 1990:205–223,247–266;Moran,inKnapp 1996:21–25).

A remarkable series of social and economic changes thus were linked closely to all the innovative developments in extractive and metallurgical technologies,and tothe increasingly widespread and intensified production and distribution of metalsand metal objects. These changes include but are not limited to: (1) the proliferation of settlements and the emergence of town centers;(2) the development and expansion in interregional trade;(3) the growth of palatial regimes and city-state kingdoms,with their attendant writing systems (notably in the eastern Mediterranean);(4) the development and refinement of craft specialization and the spread of an iconographic koine;(5) the elaboration of mortuary rituals and burials with large quantities of precious metal goods;(6) the widespread occurrence of metal hoards and the related trade in recycled and scrap metal. The circulation of goods, ideas, and ideologies across geographic,cultural,and economic boundaries represents a social transaction,one that entangled producers, distributors, and consumers in wider relations of alliance and dependence, patronage and privilege, prestige and debt (Thomas 1991:123–124). Certain occupational identities came to be focused around metallurgical production and trade, and Cyprus even gave its name to the island’s most prominent product: copper ore (Muhly 1973:174–175).The coming of the Age of Iron, subsequent to all the developments discussed in this study, itself relied on extractive and smelting technologies developed during theBronze Age,together with the use of carburization, all of which are linked directly(albeit over the millennia) to the dramatic social and economic changes that ushered in the Industrial Revolution and the beginnings of the modern era.If it is indeed the case that “metals make the world go round” (Pare 2000b),nowhere can this slogan be better and more widely illustrated than in the prehistoric Bronze Age of the Mediterranean.

Archaeometallurgy in the Mediterranean: The Social Context of Mining, Technology, and Trade

Vasiliki Kassianidou and A.Bernard Knapp

Link

Huge study on Y-chromosome variation in Iran (Grugni et al. 2012)

This is the equivalent of a box of candy for anyone interested in Eurasian (pre-)history. I will have digest all the goodies within, and post any of my comments as updates to this post.

UPDATE I: Here is the table of haplogroup frequencies for easy reference:

One of the most interesting finds is the presence of a few IJ-M429* chromosomes  in the sample. Haplogroup IJ encompasses the major European I subclade, and the major West Asian J subclade. The discovery of IJ* chromosomes is consistent with the origin of this haplogroup in West Asia; it is widely believed that haplogroup I represents a pre-Neolithic lineage in Europe, although at present there are no Y chromosome-tested pre-Neolithic remains.

There is also a wide assortment of Q and R in Iran. While some of these may be intrusive (e.g., the 42.6% of Q1a2 in Turkmen, likely a legacy of their Central Asian origins), the overall picture appears consistent with a deep presence of these lineages in Iran. This is especially true for haplogroup R where pretty much every paragroup and derived group is present, excepting those likely to have originated recently elsewhere.

UPDATE II: From the paper:

Although accounting only for 25% of the total variance, the first two components (Figure 3) separate populations according to their geographic and ethnic origin and define five main clusters: East-African, North-African and Near Eastern Arab, European, Near Eastern and South Asian. The 1stPC clearly distinguishes the East African groups (showing a high frequency of haplogroup E) from all the others which distribute longitudinally along the axis with a wide overlapping between European and Arab peoples and between Near Eastern and South Asian groups. The 2ndPC separates the North-African and Near Eastern Arabs (characterized by the highest frequency of haplogroup J1) from Europeans (characterized by haplogroups I, R1a and R1b) and the Near Easterners from the South Asians (due to the distribution of haplogroups G, R2 and L). Iranian groups do not cluster all together, occupying intermediate positions among Arab, Near Eastern and Asian clusters. In this scenario, it is worth of noticing the position of three Iranian groups: (i) Khuzestan Arabs (KHU-Ar) who, despite their Arabic origin, are close to the Iranian samples; (ii) Armenians from Tehran (THE-Ar), whose position, in the upper part of the Iranian distribution, indicates a close affinity with the Near Eastern cluster, while their position near Turkey and Caucasus groups, due to the high frequency R1b-M269 and other European markers (eg: I-M170), is in agreement with their Armenia origin; (iii) Sistan Baluchestan (SB-Ba) that clusters with its neighbouring Pakistan.

UPDATE III: There are lots of little details in the haplogroup distribution that make historical sense. For example, C3 exists in Assyrians from Azarbaijan, and both C*, C3, and O exists in Zoroastrians from Yazd. It is often forgotten that before the spread of Islam, and quite time thereafter, Inner Asia was teeming with Zoroastrians and Nestorian Christians. It seems quite likely that these outliers represent a legacy of these communities.

UPDATE IV: I have a feeling that Razib will take exception with this statement: "Ancient Persian people were firstly characterized by the Zoroastrianism. After the Islamization, Shi'a became the main doctrine of all Iranian people."


UPDATE V: This confirms my observation from the recent studies in Afghanistan, that there is an inverse relationship of J2a and R1a in Iranian-speaking groups, with an excess of the latter among the eastern Iranians, and of the former among the Persians. From the paper:

Among the different J2a haplogroups, J2a-M530 [46] is the most informative as for ancient dispersal events from the Iranian region. This lineage probably originated in Iran where it displays its highest frequency and variance in Yazd and Mazandaran (Figure 2). Taking into account its microsatellite variation and age estimates along its distribution area (Tables S3 and S7), it is likely that its diffusion could have been triggered by the Euroasiatic climatic amelioration after the Last Glacial Maximum and later increased by agriculture spread from Turkey and Caucasus towards southern Europe. The high variance observed in the Italian Peninsula is probably the result of stratifications of subsequent migrations and/or of the presence of sub-lineages not yet identified. Of interest in the M530 network (Figures 2 and S3) is the presence of a lateral branch that is characterized by a DYS391 repeat number equal to 9. Differently from previous observations [46], this branch is not restricted to Anatolian Greek samples being shared with different eastern Mediterranean coastal populations. The M530 diffusion pattern seems to be also shared by the paragroups J2a-M410* and J2a-PAGE55*. In addition, the variance distribution of the rare R1b-M269* Y chromosomes, displaying decreasing values from Iran, Anatolia and the western Black Sea coastal region, is also suggestive of a westward diffusion from the Iranian plateau, although more complex scenarios can be still envisioned because of its non-star like structure.

Of course, the idea that the diffusion of J2a related lineages ties in with early agricultural expansions has been with us for a long time, but it is time to abandon it. First of all, as we have seen, J2a diminishes greatly as we head towards South Asia; it certainly doesn't look like the lineage of the multitude of agricultural settlements that sprang up along the southeastern vector soon after the invention of agriculture. Second, it is lacking so far in all ancient Y chromosome data from Europe down to 5,000 years ago. It seems much more probably that J2 related lineages spread from the highlands of West Asia much later. 


The "age estimates" are the result of using the inappropriate "evolutionary mutation rate", and become even older because of the inclusion of the DYS388 marker that is very stable in many haplogroups but very mutable within haplogroup J. On the left you can see frequency, Y-STR variance, and haplotype network structures for various J-related groups.


It is unfortunate that there is no progress in the phylogeographic assessment of R1a in this paper. There have been substantial discoveries of SNPs within this haplogroup as a result of commercial testing; however there is clearly an ascertainment bias in the newer discoveries, as almost all these SNPs have been detected in Europeans. The new paper confirms the high levels of Y-STR variance in India, Pakistan, and Iran. Together with the cornucopia of related paragroups in Iran, there is little doubt that this haplogroup originated in the general area of Central/South Asia.


Personally, as I have stated before, I would relate this R1a with Neolithic peoples living east of the Caspian, in contrast to the R1b bearers who lived west and south of it. These two populations came under the influence of the Indo-Europeans and spread in different directions. The Indo-Iranians were then initially the mixed descendants of the Indo-Europeans and the R1a old agricultural population, and were formed in the territory of the Bactria-Margiana Archaeological Complex. 


This also explains the contrast between Iranian and Armenian groups: the latter mostly lack the R1a lineage, contrasting with all Iranian groups (even their Kurdish neighbors) who possess it. Conversely, Iranian groups, and especially eastern Iranians and Indo-Ayrans lack the R1b lineage. This is due to the fact that neither R1a nor R1b were originally part of the Indo-European community, but their geographical position was such that they came under the influence of the Indo-Europeans when the latter began their expansion.


UPDATE VI: I have created my own dendrogram using the Y-haplogroup frequencies and the hclust package of R (default parameters):

From top to bottom, one can identify some clusters:

• Eastern Europe, further broken down into Balkans and Slavic+Hungary
• West Asian/Caucasus
• Iranian Proper
• Arab

These correspond largely to the clusters identified by the authors, with India and the Turkmen sample emerging as the clear outliers. I omitted the Ethiopian samples, since E-M78 was not resolved phylogenetically, causing the Ethiopians to group with the likely E-V13 from the Balkans.

UPDATE VII: I have also run MCLUST over the haplogroup frequency data over the MDS representation of the distance matrix. The maximum number of 10 clusters occurred with 5 MDS dimensions retained. Population assignments in the 10 clusters can be found in the table below:

Iran/Azerbaijan_Gharbi+Tehran_(Assyrian)	1
Iran/Lorestan_(Lur)	1
Iran/Tehran_(Armenian)	1
Iran/Azerbaijan_Gharbi_(Azeri)	2
Iran/Hormozgan_(Bandari+Afro-Iranian)	2
Iran/Hormozgan/Qeshmi	2
Iran/Khorasan_(Persian)	2
Iran/Kurdistan_(Kurd)	2
Iran/Sistan_Baluchestan_(Baluch)	2
Pakistan	2
Iran/Fars+Isfahan_(Persian)	3
Iran/Gilan_(Gilak)	3
Iran/Yazd+Tehran_(Zoroastrian)	3
Turkey/Central	3
Turkey/East	3
Turkey/West_	3
Iran/Golestan_(Turkmen)	4
India	4
Iran/Khuzestan_(Arab)	5
Egypt_(Arab)	5
Iraq/Baghdad	5
Oman	5
Saudi_Arabia	5
Tunisia	5
United_Arab_Emirates	5
Iran/Mazandaran_(Mazandarani)	6
Iran/Yazd_(Persian)	6
Balkarian	6
Georgia	6
Albania	7
Greece	7
Bosnia	8
Croatia	8
Slovenia	8
Czech_Republic	9
Hungary	9
Poland	9
Ukraine	9
Iraq_(Marsh_Arab)	10
Qatar	10
Yemen	10

We can ignore cluster #4 which consists of the two outliers (India + Turkmen). The rest of the clusters seem relatively coherent. Notice, for example, the Arabian cluster #10, Balkan cluster #8, Eastern European cluster #9, Greek-Albanian cluster #7, Mixed Arab cluster #5.

PLoS ONE 7(7): e41252. doi:10.1371/journal.pone.0041252

Ancient Migratory Events in the Middle East: New Clues from the Y-Chromosome Variation of Modern Iranians

Viola Grugni et al.


Knowledge of high resolution Y-chromosome haplogroup diversification within Iran provides important geographic context regarding the spread and compartmentalization of male lineages in the Middle East and southwestern Asia. At present, the Iranian population is characterized by an extraordinary mix of different ethnic groups speaking a variety of Indo-Iranian, Semitic and Turkic languages. Despite these features, only few studies have investigated the multiethnic components of the Iranian gene pool. In this survey 938 Iranian male DNAs belonging to 15 ethnic groups from 14 Iranian provinces were analyzed for 84 Y-chromosome biallelic markers and 10 STRs. The results show an autochthonous but non-homogeneous ancient background mainly composed by J2a sub-clades with different external contributions. The phylogeography of the main haplogroups allowed identifying post-glacial and Neolithic expansions toward western Eurasia but also recent movements towards the Iranian region from western Eurasia (R1b-L23), Central Asia (Q-M25), Asia Minor (J2a-M92) and southern Mesopotamia (J1-Page08). In spite of the presence of important geographic barriers (Zagros and Alborz mountain ranges, and the Dasht-e Kavir and Dash-e Lut deserts) which may have limited gene flow, AMOVA analysis revealed that language, in addition to geography, has played an important role in shaping the nowadays Iranian gene pool. Overall, this study provides a portrait of the Y-chromosomal variation in Iran, useful for depicting a more comprehensive history of the peoples of this area as well as for reconstructing ancient migration routes. In addition, our results evidence the important role of the Iranian plateau as source and recipient of gene flow between culturally and genetically distinct populations.

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.