R1ans still at large (or, the story of India)

Ten ago, in the pre-ancient DNA "Dark Ages" a big debate raged on about the origin of R1a  men in India. The stage had been set even earlier, by the pioneering Eurasian heartland paper which was the first (to my memory) to link M17 with steppe migrations and Indo-Iranians. Yet, there was pushback as the distribution of M17 was better described, and people started using Y-STRs to try to date and place phylogeographically its migrations.

The two poles of the debate were the "Out-of-India", which relied primarily on Y-STR based time estimates that seemed very old (even Paleolithic, if one used the wrong mutation rate) in India, and the "Into-India" which thought that the R1a distribution pointed to its being brought into India by the Indo-Aryans in the conventional ~3,500BC time frame of the "Aryan Invasion Theory" (AIT).

AIT has been much maligned because it has been received as a Western colonialist imposition on Indian history: a way to claim that Indian civilization was not native but European in origin. Europeans were certainly guilty of misusing AIT: for British colonials it represented a precedent for their colonization of India; for German National Socialists it was evidence for the greatness of the Aryan race and its past expansions eastward. It also played into internal Indian politics, espoused by some as a means of furthering their superiority as either descendants of "Aryan conquerors" or as oppressed victims of the same.

Of course, a misuse of a theory does not mean it is wrong, and if a new preprint based on ancient and modern DNA is correct, it means that AIT was basically correct: Indo-Aryans did come to India in the Late Bronze Age, via the steppe, and ultimately from central Europe.

The opposing Out-of-India theory is all but dead, although failed theories often have a long half-life, especially if they are espoused for psycho-political reasons. I would argue that Out-of-India was dead for thousands of years before it was conceived, since even in Homer's time it was known that "India" was not "one thing" but was peopled by Indians in the north and "Eastern Ethiopians" in the south (which differed from their western "actual" Ethiopians of Africa by their possession of straight rather than curly hair). These were the "Ancestral North Indians" and "Ancestral South Indians" that modern science has revealed. Out-of-India is little more than a nationalistic myth functioning as an antidote to this basic dichotomy, a way to imbue India's diverse citizens with a myth of common origins.

Yet, proponents of AIT (who have a non-trivial overlap with R1an enthusiasts) are also scratching their heads because of the 27 ancient South Asian males from South Asia studied in the preprint there is exactly one R1a, who also happened to live after the time of the Buddha and not during the Bronze Age.

Both OIT enthusiasts (who expected copious and abundant R1a in India and its environs since the Paleolithic) and AIT/R1an enthusiasts (who expected to see it come in c. 3,500BC) are bound to be disappointed.

Perhaps the R1a Indo-Aryans did come to South Asia in a conventional AIT time frame and they haven't been sampled. Or, maybe they were, indeed, there, but were not R1ans. Or, maybe both sides missed the bigger story which is that the Indo-Aryans (so closely associated with India today) were simply not there as early as people have thought. 

bioRxiv: doi: https://doi.org/10.1101/292581

The Genomic Formation of South and Central Asia

Vagheesh M Narasimhan, Nick J Patterson et al.

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia — consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC — and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.

Link

More Y-chromosome super-fathers

The time estimates are based on a mutation rate of 1x10-9 mutations/bp/year which is ~1/3 higher than mutation rate of Karmin et al.  So the values on the table may be a little lower.

There may be additional founders with recent time depths than shown in the table, e.g., a very shallow clusters within E-M35 (probably E-V13?) and a couple of shallow clusters within I-P215

Also of interest is the fact that Greeks and Anatolian Turks do not show evidence of the recent Y-chromosomal bottleneck:

The plots are consistent with patterns seen in the relative numbers of singletons, described above, in that the Saami and Palestinians show markedly different demographic histories compared with the rest, featuring very recent reductions, while the Turks and Greeks show evidence of general expansion, with increased growth rate around 14 KYA. A different pattern is seen in the remaining majority (13/17) of populations, which share remarkably similar histories featuring a minimum effective population size ~2.1–4.2 KYA (considering the 95% confidence intervals (CIs) reported in Supplementary Table 4), followed by expansion to the present.

Related:

• Y chromosome super-fathers 
• Bottleneck in human Y-chromosomes in the last 10,000 years

Nature Communications 6, Article number: 7152 doi:10.1038/ncomms8152

Large-scale recent expansion of European patrilineages shown by population resequencing

Chiara Batini, Pille Hallast et al.

The proportion of Europeans descending from Neolithic farmers ~10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Y chromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7 Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting ~2.1–4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.

Link

Scandinavian team looking for Indo-Europeans in Kazakhstan

An article in the Astana Times. If anyone has any additional information via Kazakh or Scandinavian media, or can find the press release referred to in the article, feel free to share.

  Scandinavian Team Searches for Indo-European Homeland through Kazakhstan DNA

A Scandinavian team has come to Kazakhstan in search of the common homeland of all Indo-European peoples, collecting bone fragments for analysis in the Centre for Geogenetics at the University of Copenhagen.

The researchers are looking for a genetic connection to match the linguistic connections that have already been drawn, Norwegian historian Sturla Ellingvag of the Explico Historical Research Foundation told The Astana Times on Feb. 20. “We’re trying to find a connection in science, in our DNA, to prove that there is indeed a connection, between, for example, Norwegians and the people in Kazakhstan. And also we are looking for a homeland, which is somewhere on the Caspian steppe, or in Russia, or some say it’s in Armenia or Ukraine. There are many different theories.”

The researchers collected about 120 Bronze and early Iron Age bone samples in total from Pavlodar, Kostanai and Karaganda during their week-long trip to Kazakhstan, from Feb. 14 – 21. Kazakhstan is fascinating, the researcher says, because it contains human remains that are “so far back on the DNA map.”

The 4,000 year old samples they’ve found have been very well preserved, Ellingvag said. “I can only speak from meeting archaeologists in Astana and here in Karaganda, but I’m very much impressed by the professionalism and also by the exhibitions they have,” he said.

The project to search for the ancestral homeland of the Indo-European peoples falls under the umbrella of a large grant from the Danish government and is being supported by the Kon-Tiki Museum in Oslo, Gotenburg University in Sweden and the University of Copenhagen in Denmark, which has one of the best historical DNA analysis labs in the world and which is where the analysis on the Kazakh remains will actually be done. Universities in Karaganda, Pavlodar and Kostanai are also involved.

The Kurgan hypothesis posits that the speakers of proto-Indo-European, the hypothesized common ancestor of the massive Indo-European language group, originally lived on the Pontiac-Caspian steppe, an area of land stretching from the Black Sea to the Caspian Sea and including parts of Russia, Ukraine and northwest Kazakhstan, beginning around the fifth millenium B.C. The hypothesis describes the spread of the language family from the steppe in every direction. “Kurgan” is a term for a type of burial mound common in the Caucasus, across Kazakhstan and beyond.

“Two thousand years ago, we started having Kurgan graves in Scandinavia,” said Ellingvag. The commonalities between burial mounds in Norway and Scythian/Saka mounds in Kazakhstan are striking, he said. “[The Scythian people] had these ornaments, these animal ornaments, which are very, very important in Scandinavian art … and the ornaments are actually quite similar, which is striking, it’s very special.”

The Kurgan hypothesis has been somewhat substantiated by genetic evidence so far, according to a press release by the Kon-Tiki Museum on the project, and advances in the technology for doing historical DNA research over the past few years means it is now possible to get closer to finding this genetic and linguistic starting point for most of the peoples of Europe.

“During the past 15 years, the Y-DNA R1a haplogroup has been characterised as a genetic signal of the Proto-Indo-Europeans. The theory now looks more plausible than ever, thanks to recent discoveries about its structure and phylogeography. Moreover, the Y-DNA R1a haplogroup has been found in numerous ancient remains supposedly belonging to early Indo-Europeans,” the press release explains.

A separate but related project is looking into the DNA of ancient horses. The Kurgan culture is credited with being the first to domesticate the horse.

The research team includes Ellingvag, Danish DNA-scientist Peter Damgaard and Bettina Heyerdahl, daughter of Norwegian archaeologist and explorer Thor Heyerdahl. They are also working with Kazakh researcher Emma Usmanova.

I could also find this Youtube video from this expedition.

A story of 69 ancient Europeans

A new study on the bioRxiv includes data on 69 ancient Europeans (remember when we got excited in anticipation for the single genome of the Iceman? that was only three years ago) and adds plenty of new info to chew on for those of us interested in prehistory. 

Two Near Eastern migrations into Europe

In 2011, I observed that West Eurasian populations were too close (measured by Fst) to allow for long periods of differentiation between them. By implication, there must have been a "common source" of ancestry uniting them, which I placed in a "womb of nations" of the Neolithic Near East. I proposed that migrations out of this core area homogenized West Eurasians, writing:

In Arabia, the migrants would have met aboriginal Arabians, similar to their next door-neighbors in East Africa, undergoing a subtle African shift (Southwest_Asians). In North Africa, they would have encountered denser populations during the favorable conditions of MIS 1, and by absorbing them they would became the Berbers (Northwest_Africans). Their migrations to the southeast brought them into the realm of Indian-leaning people, in the rich agricultural fields of the Mehrgarh and the now deserted oases of Bactria and Margiana. Across the Mediterranean and along the Atlantic facade of Europe, they would have encountered the Mesolithic populations of Europe, and through their blending became the early Neolithic inhabitants of the Mediterranean and Atlantic coasts of Europe (Mediterraneans). And, to the north, from either the Balkans, the Caucasus, or the trans-Caspian region, they would have met the last remaining Proto-Europeoid hunters of the continental zone, becoming the Northern Europeoids who once stretched all the way to the interior of Asia.

The new paper confirms the last two of these migrations. The remainder involve parts of the world from which no ancient DNA has been studied.

The first migration (early Neolithic) is already uncontroversial, but the paper includes data from Spanish early farmers that are also Sardinian- and LBK-like. The "Sardinian" Iceman was no fluke. It is now proven that not only the LBK but also the Spanish Neolithic came from the same expansion of Mediterranean populations which survives in Sardinia. The authors write:

Principal components analysis (PCA) of all ancient individuals along with 777 present-day West Eurasians4 (Fig. 2a, SI5) replicates the positioning of present-day Europeans between the Near East and European hunter-gatherers4,20, and the clustering of early farmers from across Europe with present day Sardinians3,4,27, suggesting that farming expansions across the Mediterranean to Spain and via the Danubian route to Hungary and Germany descended from a common stock.

The second migration went into eastern Europe:

The Yamnaya differ from the EHG by sharing fewer alleles with MA1 (|Z|=6.7) suggesting a dilution of ANE ancestry between 5,000-3,000 BCE on the European steppe. This was likely due to admixture of EHG with a population related to present-day Near Easterners, as the most negative f3-statistic in the Yamnaya (giving unambiguous evidence of admixture) is observed when we model them as a mixture of EHG and present-day Near Eastern populations like Armenians (Z = -6.3; SI7).

The EHG (Eastern European Hunter-Gatherers) are likely Proto-Europeoid foragers and the Yamnaya (a Bronze Age Kurgan culture) were a mixture of the EHG and something akin to Armenians.The "attraction" of later groups to the Near East is clear in the PCA: hunter-gatherers on the left side, the Near East (as grey dots) on the right side, and Neolithic/Bronze Age/modern Europeans in the middle. The second migration may very well be related to the Uruk expansion and the presence of gracile Mediterranoids and robust Proto-Europeoids in the Yamna:

The Yamna population generally belongs to the European race. It was tall (175.5cm), dolichocephalic, with broad faces of medium height. Among them there were, however, more robust elements with high and wide faces of the proto-Europoid type, and also more gracile individuals with narrow and high faces, probably reflecting contacts with the East Mediterranean type (Kurts 1984: 90).

The authors present a table of Fst values which confirms the homogenizing influence of migrations from the Near East. The WHG group has an Fst=0.086 with Armenians, but the LBK farmers have only 0.023. The EHG group has an Fst=0.067 with Armenians, but the Yamnaya steppe people have only 0.030. Someone might argue that it is the Armenians that are receiving genes from Europe, but the same pattern holds even for the Bedouins, for which admixture with Europeans seems far-fetched: 0.106 to 0.043 and 0.093 to 0.060. It is now clear that the "glue" that did not allow West Eurasian populations to drift very far apart were migrations from the Near East.

The (partial) demise of the farmers

It seems that the legacy of the early farmers suffered two hits, which is why only in Sardinia and (to a lesser degree) in southern Europe that they have persisted as the major component of ancestry. The first blow came during the Neolithic:

Middle Neolithic Europeans from Germany, Spain, Hungary, and Sweden from the period ~4,000-3,000 BCE are intermediate between the earlier farmers and the WHG, suggesting an increase of WHG ancestry throughout much of Europe.

And the coup de grâce after the 5kya mark:

We estimate that these two elements each contributed about half the ancestry each of the Yamnaya (SI6, SI9), explaining why the population turnover inferred using Yamnaya as a source is about twice as high compared to the undiluted EHG. The estimate of Yamnaya related ancestry in the Corded Ware is consistent when using either present populations or ancient Europeans as outgroups (SI9, SI10), and is 73.1 ± 2.2% when both sets are combined (SI10). [...] The magnitude of the population turnover that occurred becomes even more evident if one considers the fact that the steppe migrants may well have mixed with eastern European agriculturalists on their way to central Europe. Thus, we cannot exclude a scenario in which the Corded Ware arriving in today’s Germany had no ancestry at all from local populations.

Confirmation of the Bronze Age Indo-European invasion of Europe

In 2012 I had used the paltry data on a handful ancient DNA samples to observe that in ADMIXTURE modern Europeans had a West Asian genetic component (peaking in "Caucasus" and "Gedrosia") that pre-5kya Europeans didn't. I proposed that the Bronze Age migration of the Indo-Europeans spread this component:

But there is another component present in modern Europe, the West_Asian which is conspicuous in its absence in all the ancient samples so far. This component reaches its highest occurrence in the highlands of West Asia, from Anatolia and the Caucasus all the way to the Indian subcontinent. [...] Nonetheless, some of the legacy of the earliest Indo-European speakers does appear to persist down to the present day in the genomes of their linguistic descendants, and I predict that when we sample later (post 5-4kya) individuals we will finally find the West_Asian piece that is missing from the European puzzle.

This prediction is now confirmed:

This pattern is also seen in ADMIXTURE analysis (Fig. 2b, SI6), which implies that the Yamnaya have ancestry from populations related to the Caucasus and South Asia that is largely absent in 38 Early or Middle Neolithic farmers but present in all 25 Late Neolithic or Bronze Age individuals. This ancestry appears in Central Europe for the first time in our series with the Corded Ware around 2,500 BCE (SI6, Fig. 2b, Extended Data Fig. 1).

I was a little puzzled with the "Ancient North Eurasians" recently proposed as a "third ancestral population" for Europeans: it seemed to be a tertium quid that spread after 5kya, but very different geographically than the "West Asian" component. But:

These results can be explained if the new genetic material that arrived in Germany was a composite of two elements: EHG and a type of Near Eastern ancestry different from that which was introduced by early farmers (also suggested by PCA and ADMIXTURE; Fig. 2, SI5, SI6).

So, it seems that there is no contradiction after all and both EHG (which is related to "Ancient North Eurasians") and another type of Near Eastern ancestry (=West_Asian) arrived after 5kya.

1939 strikes back

It is amazing how well this was anticipated by Carleton Coon in 1939. Back then much of West Eurasia was an archaeological/anthropological terra incognita, there was no radiocarbon dating, no DNA, no computers, not even serious multivariate statistics. And yet:

We shall see, in our survey of prehistoric European racial movements, 8 that the Danubian agriculturalists of the Early Neolithic brought a food-producing economy into central Europe from the East. They perpetuated in the new European setting a physical type which was later supplanted in their original home. Several centuries later the Corded people, in the same way, came from southern Russia but there we first find them intermingled with other peoples, and the cul-tural factors which we think of as distinctively Corded are included in a larger cultural equipment. [...] On the basis of the physical evidence as well, it is likely that the Corded people came from somewhere north or east of the Black Sea. The fully Neolithic crania from southern Russia which we have just studied include such a type, also seen in the midst of Sergi's Kurgan aggregation. Until better evidence is produced from elsewhere, we are entitled to consider southern Russia the most likely way station from which the Corded people moved westward.

And in 2015:

Our results support a view of European pre-history punctuated by two major migrations: first, the arrival of first farmers during the Early Neolithic from the Near East, and second of Yamnaya pastoralists during the Late Neolithic from the steppe (Extended Data Fig. 5).

In 1939:

Linguistically, Indo-European is probably a relatively recent phenomenon, which arose after animals had been tamed and plants cultivated. The latest researches find it to be a derivative of an initially mixed language, whose principal elements were Uralic, called element A, and some undesignated element B which was probably one of the eastern Mediterranean or Caucasic languages. 5 The plants and animals on which the Somewhere in the plains of southern Russia or central Asia, the blending of languages took place which resulted in Indo-European speech. This product in turn spread and split, and was further differentiated by mixture with the languages of peoples upon whom it, in one form or other, was imposed. Some of the present Indo-European languages, in addition to these later accretions from non-Indo-European tongues, contain more of the A element than others, which contain more of the B. The unity of the original " Indo- Europeans," could not have been of long duration, if it was ever complete. 

In 2015:

These results can be explained if the new genetic material that arrived in Germany was a composite of two elements: EHG and a type of Near Eastern ancestry different from that which was introduced by early farmers (also suggested by PCA and ADMIXTURE; Fig. 2, SI5, SI6). We estimate that these two elements each contributed about half the ancestry each of the Yamnaya (SI6, SI9), explaining why the population turnover inferred using Yamnaya as a source is about twice as high compared to the undiluted EHG.

The EHG is still flimsy as it's only two individuals from Karelia and Samara who are very similar to each other. It's hard not to imagine that the hunter-gatherer from Russian Karelia (outside any proposed PIE homeland) would be speaking a similar language as his Samara counterpart. Did they both speak "element A" and was PIE formed when the "southern" steppe hunter-gatherers came into contact with "element B" people from the Caucasus? Short of a time machine, we can never say for sure. This might very well be an answer to the conundrum of Uralic/Proto-Kartvelian borrowings. There is simply no geographical locale in which these two language families neighbor each other: Northwest, Northeast Caucasian speakers and the pesky Greater Caucasus intervene. But, maybe there was no such locale, and these borrowings aren't due to some "PIE people" living adjacent to Uralic and Proto-Karvelian speakers but the "PIE people" being a mix of an element A (EHG) that was (or interacted with) Uralic and another element B (Armenian-like) that was (or interacted with) Proto-Kartvelian.

Urheimat (or not?)

The authors of the current paper are agnostic about the PIE homeland:

We caution that the location of the Proto-Indo-European9,27,29,30 homeland that also gave rise to the Indo-European languages of Asia, as well as the Indo-European languages of southeastern Europe, cannot be determined from the data reported here (SI11). Studying the mixture in the Yamnaya themselves, and understanding the genetic relationships among a broader set of ancient and present-day Indo-European speakers, may lead to new  insight about the shared homeland.

Whatever the ultimate answer will be, it seems that Coon was right that "The unity of the original " Indo- Europeans," could not have been of long duration, if it was ever complete." If PIE=EHG (as Anthony and Ringe suggest), then "from the crib", PIE got half its ancestry from a non-IE, Near Eastern source. Conversely, if PIE=Near East (as I suggested) then "from the crib", PIE got half of its ancestry from a non-IE, Eastern European source. The "Yamnaya" seems to max out in Norwegians at around half, which means that they are about a quarter Proto-Indo-European genetically, regardless of which theory is right.

These two possibilities (as well as the third one of PIE being neither-nor, but rather a linguistic mixture of the languages of the EHG and Near East) are testable. The Anthony/Ringe version of the steppe hypothesis predicts pre-Yamnaya expansions from the steppe. Whether these happened and what was their makeup can be tested: if they did occur and they did lack "Near Eastern" ancestry, then the steppe hypothesis will be proven. PIE in the Near East, on the other hand, predicts that some PIE languages (certainly the Anatolian ones) will be a "within the Near East" expansion. If such migrations did occur and they lacked "EHG" ancestry, then some variant of the Gamkrelidze/Ivanov model will be proven. Or, the truth might be that everywhere where Indo-Europeans arrive they carry a blend of "West Asian" and "EHG", supporting the third possibility. Time will tell.

In the interim, I am curious about how much Yamnaya ancestry existed in different parts of Europe (all of the post-5kya samples in this study come from Germany, with a couple from Hungary). In northern Europe, all populations seem to have less Yamnaya ancestry than the Corded Ware: there it must have declined. But, modern Hungarians have more than Bronze Age Hungarians: there it must have increased.

Germany and a slice of Hungary is a very narrow window through which to see the whole of Europe and these results must be tested by looking at samples from beyond the "heartland". I do hope that some kind of Moore's law operates in the world of ancient DNA, and in three more years we'll be reading studies about thousands of ancient individuals.

bioRxiv doi: http://dx.doi.org/10.1101/013433
Massive migration from the steppe is a source for Indo-European languages in Europe

Wolfgang Haak , Iosif Lazaridis , Nick Patterson , Nadin Rohland , Swapan Mallick , Bastien Llamas , GuidoBrandt , Susanne Nordenfelt , Eadaoin Harney , Kristin Stewardson , Qiaomei Fu , Alissa Mittnik , Eszter Banffy ,Christos Economou , Michael Francken , Susanne Friederich , Rafael Garrido Pena , Fredrik Hallgren , ValeryKhartanovich , Aleksandr Khokhlov , Michael Kunst , Pavel Kuznetsov , Harald Meller , Oleg Mochalov ,Vayacheslav Moiseyev , Nicole Nicklisch , Sandra L. Pichler , Roberto Risch , Manuel A. Rojo Guerra , ChristinaRoth , Anna Szecsenyi-Nagy , Joachim Wahl , Matthias Meyer , Johannes Krause , Dorcas Brown , DavidAnthony , Alan Cooper , Kurt Werner Alt , David Reich

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6. By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe.

Link

Y chromosome super-fathers

This is a very exciting paper. Most of these lineages are so young that there are good chances that their founders were figures from history or mythology.

The most interesting one is DC2 which was also found in south Siberian Kurgans, belongs to haplogroup R1a1 and is given an age of 3,284 years by the authors (with some almost impossibly wide confidence intervals). Based on its distribution, and if a Bronze Age date is right, it is difficult to see in it anything other than a patrilineage that was present in Proto-Indo-Iranians.

European Journal of Human Genetics advance online publication 14 January 2015; doi: 10.1038/ejhg.2014.285

Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations

Patricia Balaresque et al.

High-frequency microsatellite haplotypes of the male-specific Y-chromosome can signal past episodes of high reproductive success of particular men and their patrilineal descendants. Previously, two examples of such successful Y-lineages have been described in Asia, both associated with Altaic-speaking pastoral nomadic societies, and putatively linked to dynasties descending, respectively, from Genghis Khan and Giocangga. Here we surveyed a total of 5321 Y-chromosomes from 127 Asian populations, including novel Y-SNP and microsatellite data on 461 Central Asian males, to ask whether additional lineage expansions could be identified. Based on the most frequent eight-microsatellite haplotypes, we objectively defined 11 descent clusters (DCs), each within a specific haplogroup, that represent likely past instances of high male reproductive success, including the two previously identified cases. Analysis of the geographical patterns and ages of these DCs and their associated cultural characteristics showed that the most successful lineages are found both among sedentary agriculturalists and pastoral nomads, and expanded between 2100 BCE and 1100 CE. However, those with recent origins in the historical period are almost exclusively found in Altaic-speaking pastoral nomadic populations, which may reflect a shift in political organisation in pastoralist economies and a greater ease of transmission of Y-chromosomes through time and space facilitated by the use of horses.

Link

Paternal lineages and languages in the Caucasus

An interesting new study on Y chromosome and languages in the Caucasus. The distribution of haplogroups is on the left. The authors make some associations of haplogroups with language families:

• R1b: Indo-European
• R1a: Scytho-Sarmatian
• J2: Hurro-Urartian
• G2: Kartvelian

Hum Biol. 2014 May;86(2):113-30.

Human paternal lineages, languages, and environment in the caucasus.

Tarkhnishvili D1, Gavashelishvili A1, Murtskhvaladze M1, Gabelaia M1, Tevzadze G2.

Abstract

Publications that describe the composition of the human Y-DNA haplogroup in diffferent ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus, a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. We genotyped 224 men that identified themselves as ethnic Georgian for 23 Y-chromosome short tandem-repeat markers and assigned them to their geographic places of origin. The genotyped data were supplemented with published data on haplogroup composition and location of other ethnic groups of the Caucasus. We used multivariate statistical methods to see if linguistics, climate, and landscape accounted for geographical diffferences in frequencies of the Y-DNA haplogroups G2, R1a, R1b, J1, and J2. The analysis showed significant associations of (1) G2 with wellforested mountains, (2) J2 with warm areas or poorly forested mountains, and (3) J1 with poorly forested mountains. R1b showed no association with environment. Haplogroups J1 and R1a were significantly associated with Daghestanian and Kipchak speakers, respectively, but the other haplogroups showed no such simple associations with languages. Climate and landscape in the context of competition over productive areas among diffferent paternal lineages, arriving in the Caucasus in diffferent times, have played an important role in shaping the present-day spatial distribution of patrilineages in the Caucasus. This spatial pattern had formed before linguistic subdivisions were finally shaped, probably in the Neolithic to Bronze Age. Later historical turmoil had little influence on the patrilineage composition and spatial distribution. Based on our results, the scenario of postglacial expansions of humans and their languages to the Caucasus from the Middle East, western Eurasia, and the East European Plain is plausible.

Link (pdf)

Ancient DNA from Bronze Age Altai

UPDATE:

Two observations: it seems that West/East Eurasian Y chromosomes were sometimes associated with East/West mtDNA and vice versa, so these samples don't appear to be two disjoint West/East Eurasian populations, but some mixing took place. Also, the pigmentation estimates are mainly brown eyes (one blue-eyed individual) and black/dark brown hair (although both brown/dark blond were present).

The STRUCTURE results (which should be interpreted with great caution because of the small number of autosomal loci used) do suggest that this was a population that was more West than East Eurasian autosomally.

Forensic Science International: Genetics Received 2 January 2014; received in revised form 21 May 2014; accepted 25 May 2014. published online 04 June 2014.

Strong genetic admixture in the Altai at the Middle Bronze Age revealed by uniparental and ancestry informative markers

Clémence Hollard et al.

The Altai Mountains have been a long term boundary zone between the Eurasian Steppe populations and South and East Asian populations. To disentangle some of the historical population movements in this area, 14 ancient human specimens excavated in the westernmost part of the Mongolian Altai were studied. Thirteen of them were dated from the Middle to the End of the Bronze Age and one of them to the Eneolithic period. The environmental conditions encountered in this region led to the good preservation of DNA in the human remains. Therefore, a multi-markers approach was adopted for the genetic analysis of identity, ancestry and phenotype markers. Mitochondrial DNA analyses revealed that the ancient Altaians studied carried both Western (H, U, T) and Eastern (A, C, D) Eurasian lineages. In the same way, the patrilineal gene pool revealed the presence of different haplogroups (Q1a2a1-L54, R1a1a1b2-Z93 and C), probably marking different origins for the male paternal lineages. To go further in the search of the origin of these ancient specimens, phenotypical characters (ie: hair and eye colour) were determined. For this purpose, we adapted the HIrisPlex assay recently described to MALDI-TOF mass spectrometry. In addition, some ancestry informative markers were analyzed with this assay. The results revealed mixed phenotypes among this group confirming the probable admixed ancestry of the studied Altaian population at the Middle Bronze Age. The good results obtained from ancient DNA samples suggest that this approach might be relevant for forensic casework too.

Link

Major new article on the deep origins of Y-haplogroup R1a (Underhill et al. 2014)

Five years ago, Underhill et al. (2009) presented a major advance in the study of haplogroup R1a. Much new knowledge was added in the interim by genetic genealogists and some scientists,  and now a major new paper by Peter Underhill comes to update our knowledge of this important and widely spread human lineage.

The shallow coalescence time within R1a will not surprise many genetic genealogists while its diversification in the vicinity of present-day Iran might. A ~5-7kyBP coalescence would make the expansion of R1a lineages presumably visible to future ancient DNA studies which will probably be the final arbiter of the veracity of the date estimate in this paper and its postulated place of origin.

I'll try to digest what the new information has to say about Eurasian prehistory, but in the meantime...

... I will, however, take some time to highlight the passing of the guard from Y-STRs to Y-SNPs which I had long ago anticipated. There is some lingering controversy about the substitution rate on the Y chromosome is, but it is hopeful that this will be resolved before not too long as the price of whole genome sequencing is always dropping and the samples sequenced in this study are probably the first of many to come.

In any case:

Our phylogeographic data lead us to conclude that the initial episodes of R1a-M420 diversification occurred in the vicinity of Iran and Eastern Turkey, and we estimate that diversification downstream of M417/Page7 occurred ~5800 years ago. This suggests the possibility that R1a lineages accompanied demic expansions initiated during the Copper, Bronze, and Iron ages, partially replacing previous Y-chromosome strata, an interpretation consistent with albeit limited ancient DNA evidence.54, 60 However, our data do not enable us to directly ascribe the patterns of R1a geographic spread to specific prehistoric cultures or more recent demographic events. High-throughput sequencing studies of more R1a lineages will lead to further insight into the structure of the underlying tree, and ancient DNA specimens will help adjudicate the molecular clock calibration. Together these advancements will yield more refined inferences about pre-historic dispersals of peoples, their material cultures, and languages.

It would of course be great to get some ancient DNA data from Iran and Eastern Turkey:

Among the 120 populations with sample sizes of at least 50 individuals and with at least 10% occurrence of R1a, just 6 met these criteria, and 5 of these 6 populations reside in modern-day Iran. Haplogroup diversities among the six populations ranged from 0.78 to 0.86 (Supplementary Table 4). Of the 24 R1a-M420*(xSRY10831.2) chromosomes in our data set, 18 were sampled in Iran and 3 were from eastern Turkey. Similarly, five of the six observed R1a1-SRY10831.2*(xM417/Page7) chromosomes were also from Iran, with the sixth occurring in a Kabardin individual from the Caucasus. Owing to the prevalence of basal lineages and the high levels of haplogroup diversities in the region, we find a compelling case for the Middle East, possibly near present-day Iran, as the geographic origin of hg R1a.

Also, the finding that...

The four subhaplogroups of Z93 (branches 9-M582, 10-M560, 12-Z2125, and 17-M780, L657) constitute a multifurcation unresolved by 10 Mb of sequencing; it is likely that no further resolution of this part of the tree will be possible with current technology. Similarly, the shared European branch has just three SNPs.

... seems to imply some Copper-to-Bronze Age guys did more than their fair share of fathering.

European Journal of Human Genetics , (26 March 2014) | doi:10.1038/ejhg.2014.50

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

Peter A Underhill et al.

R1a-M420 is one of the most widely spread Y-chromosome haplogroups; however, its substructure within Europe and Asia has remained poorly characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-chromosomes and analyzed them to a highly granular phylogeographic resolution. Whole Y-chromosome sequence analysis of eight R1a and five R1b individuals suggests a divergence time of ~25 000 (95% CI: 21 300–29 000) years ago and a coalescence time within R1a-M417 of ~5800 (95% CI: 4800–6800) years. The spatial frequency distributions of R1a sub-haplogroups conclusively indicate two major groups, one found primarily in Europe and the other confined to Central and South Asia. Beyond the major European versus Asian dichotomy, we describe several younger sub-haplogroups. Based on spatial distributions and diversity patterns within the R1a-M420 clade, particularly rare basal branches detected primarily within Iran and eastern Turkey, we conclude that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran.

Link

Near Eastern origin of R1a in Ashkenazi Levites

This paper is a nice cautionary tale. R1a is very common in eastern Europe and less so in the Near East. Ashkenazi Jews lived in Eastern Europe, and one group of them (Levites) had high frequency of R1a than the rest. It seemed that an eastern European patrilineage had inserted itself into the Ashkenazi Levite gene pool.

It turns out that this is not the case. The specific clade R-M582 to which Ashkenazi Levites (and other non-Levites) belong to is absent in eastern Europeans and present in non-Jewish Near Easterners, making it more likely that Jews did not pick it up from eastern Europeans, but rather from some Near Eastern population. A look at the table of frequencies suggests to me an Iranic source, but I doubt that modern populations will ever allow a full resolution of such questions.

Nature Communications 4, Article number: 2928 doi:10.1038/ncomms3928

Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites

Siiri Rootsi et al.

Previous Y-chromosome studies have demonstrated that Ashkenazi Levites, members of a paternally inherited Jewish priestly caste, display a distinctive founder event within R1a, the most prevalent Y-chromosome haplogroup in Eastern Europe. Here we report the analysis of 16 whole R1 sequences and show that a set of 19 unique nucleotide substitutions defines the Ashkenazi R1a lineage. While our survey of one of these, M582, in 2,834 R1a samples reveals its absence in 922 Eastern Europeans, we show it is present in all sampled R1a Ashkenazi Levites, as well as in 33.8% of other R1a Ashkenazi Jewish males and 5.9% of 303 R1a Near Eastern males, where it shows considerably higher diversity. Moreover, the M582 lineage also occurs at low frequencies in non-Ashkenazi Jewish populations. In contrast to the previously suggested Eastern European origin for Ashkenazi Levites, the current data are indicative of a geographic source of the Levite founder lineage in the Near East and its likely presence among pre-Diaspora Hebrews.

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

Y chromosomes of Slavic minorities inhabiting Vojvodina, Serbia

From the paper:

Scrutiny of predicted haplogroups revealed high incidence of haplogroup R1a in both Northern Slavic minorities inhabiting Serbia (42.0% and 44.0% in Slovaks and Ruthenians, respectively), which was comparable to its prevalence in the two Northern Slavic reference populations (45.1% and 43.5% in Slovaks and Ukrainians, respectively), but considerably higher than the one observed in Southern Slavic Serbs (15.1%, Table S4).

Forensic Science International: Genetics Volume 8, Issue 1, January 2014, Pages 126–131

Northern Slavs from Serbia do not show a founder effect at autosomal and Y-chromosomal STRs and retain their paternal genetic heritage

Krzysztof Rębała et al.

Studies on Y-chromosomal markers revealed significant genetic differentiation between Southern and Northern (Western and Eastern) Slavic populations. The northern Serbian region of Vojvodina is inhabited by Southern Slavic Serbian majority and, inter alia, Western Slavic (Slovak) and Eastern Slavic (Ruthenian) minorities. In the study, 15 autosomal STR markers were analysed in unrelated Slovaks, Ruthenians and Serbs from northern Serbia and western Slovakia. Additionally, Slovak males from Serbia were genotyped for 17 Y-chromosomal STR loci. The results were compared to data available for other Slavic populations. Genetic distances for autosomal markers revealed homogeneity between Serbs from northern Serbia and Slovaks from western Slovakia and distinctiveness of Serbian Slovaks and Ruthenians. Y-STR variation showed a clear genetic departure of the Slovaks and Ruthenians inhabiting Vojvodina from their Serbian neighbours and genetic similarity to the Northern Slavic populations of Slovakia and Ukraine. Admixture estimates revealed negligible Serbian paternal ancestry in both Northern Slavic minorities of Vojvodina, providing evidence for their genetic isolation from the Serbian majority population. No reduction of genetic diversity at autosomal and Y-chromosomal markers was found, excluding genetic drift as a reason for differences observed at autosomal STRs. Analysis of molecular variance detected significant population stratification of autosomal and Y-chromosomal microsatellites in the three Slavic populations of northern Serbia, indicating necessity for separate databases used for estimations of frequencies of autosomal and Y-chromosomal STR profiles in forensic casework. Our results demonstrate that regarding Y-STR haplotypes, Serbian Slovaks and Ruthenians fit in the Eastern European metapopulation defined in the Y chromosome haplotype reference database.

Link

ISABS 2013 abstracts

From the book of abstracts (pdf):

MITOCHONDRIAL DNA AND PHYLOGENETIC ANALYSIS OF PREHISTORIC NORTH AFRICAN POPULATIONS

North Africa is located at a crossroad between Europe, Africa and Asia and has been inhabited since the Prehistoric time. In the Epipaleolithic period (23.000 years to 10.000 years BP), the Western North Africa has been occupied by Mecha- Afalou Men, authors of the Iberomaurusian industry. The origin of the Iberomaurusians is unresolved, several hypotheses have been forwarded. With the aim to contribute to a better knowledge of the Iberomaurusian settlement we analysed the mitochondrial DNA (mtDNA) of skeletons exhumed from the prehistoric site of Taforalt in Morocco (23.000-10.800 years BP) and Afalou in Algeria (11.000 to 15.000 BP -Algeria). Hypervariable segment 1 of mtDNA from 38 individuals were amplified by Real-Time PCR and directly sequenced. Sequences were aligned with the reference sequence to perform the mtDNA classification within haplogroups. Phylogenetic analysis based on mitochondrial sequences from Mediterranean populations was performed using Neighbor-Joining algorithm implemented in MEGA program. mtDNA sequences from Afalou and Taforalt were classified in Eurasiatic and North African haplogroups. We noted the absence of Sub-Saharan haplotypes. Phylogenetic tree clustered Taforalt with European populations. Our results excluded the hypothesis of the sub-Saharan origin of Iberomaurusians populations and highlighted the genetic flow between Northern and Southern cost of Mediterranean since Epipaleolithic period.

DISCONTINUITY SCREENING OF THE EARLY FARMERS’ MT-DNA LINEAGES IN THE CARPATHIAN BASIN

Discontinuous mitochondrial (mt) haplotype data between Central-Europe’s first farmers and contemporary Europeans have been described before. Hungary was a key-area of the Neolithisation, in the route of Neolithisation following the River Danube, and that was also the birthplace of the Linear Pottery Culture, which later colonised Western and Northern Europe. Neolithic and post-Neolithic human remains as well as contemporary population of Hungary is involved in our project to gain information on their mt-haplotype pattern and especially on the frequency of Asian haplotypes in the Carpathian Basin. HVS-I sequences from nt15977 to nt16430 of Neolithic specimens with sufficient mtDNA preservation among an extended Neolithic collection were analysed for polymorphisms, identifying 23 different ones. A novel, N9a, N1a, C5, D1/G1a, M/R24 haplogroups were determined among the pre-industrial Hungarians. The presence of Asian haplotypes in the ancient populations must be taken into consideration when reconstructing the population history of Europe and Asia, so a survey of the recent Asian haplotype frequency in Europe is unavoidable. The ancient and recent haplotype pattern of Hungary is definitely worth further investigation to test a theory on the continuous population history of Europe, wheter genetic gaps between ancient and recent human populations of Europe were more likely to be detected. 

ANTHROPOLOGIC AND MITOCHONDRIAL DNA ANALYSIS OF A MEDIEVAL GRAVEYARD FROM SOPOT (CROATIA)

Anthropologic and DNA analysis of human remains recovered from a graveyard in ©opot near Benkovac (Croatia) dating to the 14th/15th century was conducted in order to reconstruct the origin and life conditions of the people populating the region at that time. The dynamics of the population represented in this graveyard are important for understanding Croatian history because the deceased individuals were buried according to pagan ritual which was uncommon in a post Christianization period. Human remains from a total of 31 graves were analyzed, in which 47 individuals were found (9 female, 23 male and 15 children). Average age at death for adults was lower than expected (for female 28.9, male 32.4 years), suggesting that the living conditions of these individuals were poor. In addition, 10 antemortem traumas were visible on 6 adults, which is a higher rate than expected, and indicates potential violence within the population group. Finally, mitochondrial DNA (mtDNA) analysis was performed on hypervariable regions one and two for 46 of the individuals. Due to the age and condition of the remains, only 19 of the samples yielded full sequence profiles. Haplogroup analysis was performed for these 19 individuals, with the majority of the results falling within the most common groups in present-day Croatia. However, examination of the lesscommon haplogroups suggested a possible migration of individuals from Asia. Collectively, the physical and molecular results from this study provide evidence to suggest that individuals recovered from this gravesite are not from the current indigenous population.

MATERNAL GENETIC PROFILE OF A NORTHWEST ALGERIAN POPULATION

The North African population gene pool based on mitochondrial DNA (mtDNA) polymorphisms has been shaped by the back-migration of several Eurasian lineages in Paleolithic and Neolithic times. Recent influences from sub-Saharan Africa and Mediterranean Europe are also evident. The presence of East-West and North- South haplogroup frequency gradients strongly reinforces the genetic complexity of this region. However, this genetic scenario is beset with a notable gap, which is the lack of consistent information for Algeria, the largest country in the continent. To fill this gap, we analyzed a sample of 240 unrelated subjects from a northwest Algeria cosmopolitan population. mtDNA sequences analysis was performed on the regulatory hypervariable segment I region (HVSI). Haplogroup diagnostic mutations were analyzed using PCR-RFLPs and/or SNaPshot multiplex reactions. Of all North African populations, Eurasian lineages are the most frequent in Algeria (80%) while sub-Saharan Africa origin accounts for the remaining (20%). Within them, the North African genetic component U6 and M1 count for 20%. Indeed, the U6 haplogroup, highly distributed in Northwestern African populations, show a high frequency in Algeria (11.83%), while, the M1 frequency (7.1%) raises an anomalous peak in its decreasing Northeast - Northwest gradient. Moreover, the high frequency of HV subgroups (38.33%) point to direct maritime contacts between the European and North African western sides of the Mediterranean. Besides, the most common western H subgroups, H1 (47.8%) and H3 (10.1%), represent 60% of H lineages. These frequencies and HV0 (7.5%) lie well within the observed Northwestern to Northeastern African decreasing gradients.

MATERNAL GENETIC VARIATION OF THE SLOVENIAN POPULATION IN A BROADER EUROPEAN CONTEXT AND COMPARED TO ITS PATERNAL COUNTERPART

Slovenia is a European country situated at the crossroads of main European cultural and trade routes. It is geographically more linked to Central Europe, but history draws it closer together to its ex-Yugoslavian, Southeast European (SEE) neighbors. Slovenian maternal heritage has not been analyzed since 2003 and our aim was to analyze SNP markers of 97 Slovenian mtDNAs in high resolution to see where this population fits according to its maternal genetic variation. We compared the Slovenian sample with the neighboring SEE populations, as well as with other published European population datasets. Also, we compared the obtained mtDNA variation results with the available Slovenian Y chromosome data to see how these two uniparental marker systems correspond to each other. In the PC plot based on mtDNA haplogroups frequencies, Slovenian population has an outlying position mostly due to the increased prevalence of J (14.4%) and T (15.4%) clade and especially because of the abundance and diversity of J1c samples in Slovenia, represented with 8 haplotypes and in a percentage of >11%. Although in an outlying position, Slovenian mtDNA variation still shows a certain degree of affinity to SEE. On the contrary, Slovenia’s paternal genetic heritage yielded results that correspond to the population’s geographic location and groups Slovenian population considerably closer to Central European countries, based on increased prevalence of Northern/Central European R1a-M198 and decreased frequency of Balkan-specific I2a2-M423. Such differences in maternal and paternal marker systems could indicate that Slovenian genetic variation was influenced by sex-biased demographic events.

AN ASIAN TRACE IN THE GENETIC HERITAGE OF THE EASTERN ADRIATIC ISLAND OF HVAR

The Island of Hvar is situated in the central eastern Adriatic, and its relatively small rural population has been reproductively isolated thought history. Therefore, founder effects, genetic drift and inbreeding have had significant role in the shaping of current genetic diversity of Hvar Islanders. We analyzed Y-chromosome SNP markers of 412 Hvar islanders in high resolution, with the aim to investigate the current paternal genetic diversity. We found a relatively high frequency (6.1%) of unrelated male samples belonging to the Q*-M424 haplogroup, which is unusual for European populations. Interestingly, a previous study showed 9 individuals from Hvar with mitochondrial haplogroup F, which is almost absent in Europe. Both findings could indicate a certain connection with Asian populations, where these haplogroups are most common. This might be a result of several migratory events in the history, one of which could be linked to the ancient Silk Road, the other a consequence of the arrival of the Slavs, following the Avars, to the eastern Adriatic in the 6th century or due to the expansion of the Ottoman Empire in 16th to 18th century. The presence of these rare mitochondrial and Y-chromosome lineages are an example of founder effect and random genetic drift which, in this small island with a high degree of isolation and endogamy, had a strong impact on shaping the genetic diversity of the population. 

GENETIC PORTRAIT OF THE BESERMYAN ETHNIC GROUP BASED ON MTDNA HAPLOGROUP STUDY

Besermyan are a small ethnic group living in the Volga-Ural region of Russia. They belong to Finno-Ugric language group, but speak a special dialect. There are some Bulgar-Chuvash borrowings in their adverb vocabulary that are absent in other dialects of the Udmurt language. Besermyan live in the northwestern part of modern Udmurtia in the Cheptsa basin. In 2002 their number was about three thousand. The Besermyan origin is a very interesting issue. There is a view that the endonym Besermyan (beserman) is derived from the Turkic word which means flMuslim« in Arabic. This hypothesis, along with their language, hints at the origin of this ethnic group; however the genetic portrait of Besermyan has not been described yet. In our study we used the data of mitochondrial DNA (mtDNA) HVSI sequencing from 98 Besermyans representing 10 villages in Udmurtia Republic of Russia. The prevalence of Western Eurasian mtDNA lineages (91.7%) over Eastern Eurasian ones (9.2%) was shown in the studied population which is consistent with the structure of mtDNA pool of Finno-Ugric ethnic groups of the Volga-Ural region. Some Eastern Eurasian lineages in Besermyan are represented by haplogroups D4b, A4b and Z1a which are also common in Udmurts. It is important to note though that the share of Western Eurasian component in Udmurts according to previous study by Bermisheva et al. (2002) is about 74.5% so mtDNA haplogroup distribution in Besermyans is closer to other Finno-Ugric people of the Volga-Ural region: Mordvins and Maris.

COSMOPOLITAN CENTRAL ASIA: TAJIK MTDNA TRACES THE EASTWEST MOVEMENT OF ANCIENT NOMADS 

Tajikistan is a country in the mountains of southeast Central Asia. Due to its isolation, mtDNA variation in the Tajiks has been fragmentary studied on a limited number of samples. In 1997 saliva samples were collected from unrelated Tajiks across Tajikistan. After long-term preservation DNA was extracted from 2 mm FTA discs. Due to degradation mtDNA was amplified using the primary and secondary PCRs with nested primers in the multiplex format. The origin of 91 mitochondrial genomes from Tajikistan traced from western Eurasia (62.6%), eastern Eurasia (25.3%), south Asia (11.0%), and North Africa (1.1%). Significant population structure in the distribution of these mtDNA lineages was revealed within the regional groups in Tajikistan. The mtDNA variation was compared between the Tajiks and 45 populations of Eurasia. Pairwise Fst comparisons and the correspondence analysis revealed non-significant differences between the Tajik and Uzbek populations. Although both nations speak languages belonging to different linguistic groups, this result corresponds to their cultural and economic proximity. Surprisingly, after the Uzbeks, the Tajik mtDNA pool most closely resembles to the Ossetians, an Indo-Iranian people from the North Caucasus. The Tajiks also display intensive gene flow and admixture with some other populations of Central Asia and the Iranian Plateau living along the centers and crossroads of the earliest civilizations and belonging to different linguistic groups including the Uyghur, Kazakh, Karakalpak, Turkmen, Pathans, Iranian Arabs, and Gilaki. This study demonstrates an impact of ancient nomad migrations and invasions on the distribution of mtDNA variation in Eurasia. 

Thesis of Oleg Balonovsky

is available here as pdf. Lots of interesting information, and a few striking maps. Hopefully, the fact that it's all in Russian won't be much of a problem in this day and age.

I will highlight a few pieces of information. First, a distribution of Y-chromosome haplogroups in Russian groups:

Notice:

• N1c-Tat is a general feature of the Russians, but N1b-P43 is only really found at any significant frequency in the northern groups.
• A strong contrast of E-M78 between central (present) and northern (absent) groups, consistent with a late introduction of this haplogroup in easternmost Europe.
• South-Central-North decreasing frequency of R1a; now, it's not clear how R1a came to be in Russians: some of it may be legacy of its initial entry into Europe from the east, other could be of historical import, and may have even arrived during the Slavic expansion from Central Europe. The pattern probably is the reverse of the high frequency of N1, indicating increasing importance of Finno-Ugric substratum in the north.
• Fairly interesting that of the two likely "Balkan" haplogroups E-M78 and I-P37, the former is modal in central region, the latter in southern one. The absence of both in "deep Asia" suggests a late introduction, as mentioned before, but when?

Also of interest a haplotype analysis within R1a1a-M198:

My most immediate observation is the set of mainly Indian highly divergent haplotypes on the left. There has been (well-deserved) excitement about recent Y-SNP progress within this haplogroup, but we should not neglect the occurrence of outliers/relics in our reconstruction of a haplogroup's history. I'd love to see those few Indian haplotypes SNP-tested using the currently available SNPs, or even used to develop new SNPs for this important Eurasian haplogroup.

Y chromosomes of Bulgarians (Karachanak et al. 2013)

Bulgaria had been something of a blank area in studies of uniparental markers, so it's nice to finally see a comprehensive Y-chromosome study of the country.

The dates in the paper are based on the "evolutionary mutation rate". I suspect that ancient DNA will be the final arbiter in this issue, because, for example, a Mesolithic TMRCA of E-V13 in Bulgaria implies that we'll find a lot of it in Neolithic contexts, whereas a Bronze Age one implies that we'll find a little if any of it, and a discontinuity across time.

Of interest is the occurrence of some E*(xM35, M2) in this sample in Burgas, Varna, and Plovdiv. It would be interesting to trace the ancestry of the bearers of these Y-chromosomes. I know that there still exists a minority-within-a-minority of Black Muslims in Greek Thrace, and it's not inconceivable that these Y-chromosomes may represent the legacy of a similar population; in any case, their haplotypes can be found in Table S5 for anyone wanting to investigate.

SNP Diversity within R seems substantial, and as always, it is difficult to say much, since this may be a consequence of either (i) a plausible role of the Balkans as a staging point of the likely invasion of Europe in late prehistory, or (ii) back-migration of derived R-bearers into the Balkans, be them Slavs or Goths or "eastern" folks of various stripes during history. Once again, I suspect that ancient DNA might solve this riddle, or, alternatively, routine high-coverage sequencing of the Y chromosome that might inform us, e.g., about the TMRCA of a Bulgarian and a German R-U152 or a Bulgarian and Polish R-M458.

PLoS ONE 8(3): e56779. doi:10.1371/journal.pone.0056779

Y-Chromosome Diversity in Modern Bulgarians: New Clues about Their Ancestry

Sena Karachanak et al

To better define the structure and origin of the Bulgarian paternal gene pool, we have examined the Y-chromosome variation in 808 Bulgarian males. The analysis was performed by high-resolution genotyping of biallelic markers and by analyzing the STR variation within the most informative haplogroups. We found that the Y-chromosome gene pool in modern Bulgarians is primarily represented by Western Eurasian haplogroups with ~ 40% belonging to haplogroups E-V13 and I-M423, and 20% to R-M17. Haplogroups common in the Middle East (J and G) and in South Western Asia (R-L23*) occur at frequencies of 19% and 5%, respectively. Haplogroups C, N and Q, distinctive for Altaic and Central Asian Turkic-speaking populations, occur at the negligible frequency of only 1.5%. Principal Component analyses group Bulgarians with European populations, apart from Central Asian Turkic-speaking groups and South Western Asia populations. Within the country, the genetic variation is structured in Western, Central and Eastern Bulgaria indicating that the Balkan Mountains have been permeable to human movements. The lineage analysis provided the following interesting results: (i) R-L23* is present in Eastern Bulgaria since the post glacial period; (ii) haplogroup E-V13 has a Mesolithic age in Bulgaria from where it expanded after the arrival of farming; (iii) haplogroup J-M241 probably reflects the Neolithic westward expansion of farmers from the earliest sites along the Black Sea. On the whole, in light of the most recent historical studies, which indicate a substantial proto-Bulgarian input to the contemporary Bulgarian people, our data suggest that a common paternal ancestry between the proto-Bulgarians and the Altaic and Central Asian Turkic-speaking populations either did not exist or was negligible.

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Ancient Y chromosomes from China

This appears to be an abstract of a 2012 dissertation from Jilin University (using Google Translate):

Northern China is the hub of East Asia connecting North Asia, Central Asia and the European civilization, it is a vast variety of natural ecological environment, suitable for farming, nomadic, hunting and fishing and other economic lifestyle coexist, since ancient times is fertile ground for human life, many ancient ethnic groups in here thrive and leave a valuable intangible cultural heritage. Ancient ancestors of the region but also a number of occasions by force to seize power, large-scale war had thrown the history of the North China southward to accelerate China Southern, northern populations gene fusion. Part of the ancient nation even Expeditionary Europe, its descendants across the country to play a role in promoting the exchange of population of the entire Eurasian continent. These events northern populations occupy an important position in the history of human migration. Therefore, this region of the ancient population genetics research for the original genetic retrospective of the Chinese nation, and speculated Eurasia population migration, fusion mode has great significance. This study of 13 archaeological sites in northern China - Xinjiang river cemetery, Hami Tianshan Road cemetery, Barkol the black Gouliang cemetery, the Ning Xia Pengyang cemetery, Xining Tao Wangjiazai cemetery, of Shanxi Jiangxian cross Kitamura cemetery, Hebei Yuxian three hurdles cemetery, Temple Zaigou site Niuheliang site, Sahara Trench cemetery, DADIANZI site, large piedmont ruins, wells ditch sub cemetery - human remains unearthed parent molecular genetics research, summed up the various ancient population Y chromosome haplotype groups paternal genetic diversity of the distribution rules and characteristics, combined with related ancient the modern crowd molecular genetics data reveal ancient population of the different regions of northern China, to explore the genetic makeup of the different periods of the ancient population dynamic process, in order to clarify the north fusion between ethnic origin, flow and crowd differentiation provides evidence of molecular genetics. The results are as follows: First, five archaeological site northeast western Liaoning Province 78 males unearthed ancient human remains of 44 cases of samples Y-DNA results are attributed to the C, N and O three single haplotype groups. Haplogroup N in western Liaoning Province the ancient population for a long, extensive presence, and account for a large proportion, dated to 5500-3000 years ago, is the most important ingredient in the genetic composition of the area of the ancient population paternal; based on single frequency of the haplotype groups O ancient population of western Liaoning Province and their cultural attributes and lifestyle of the crowd, and the combination of the relevant ancient population Y-SNP findings, we speculate that the haplogroup O northward by the Central Plains, emigrated to the the ancient agricultural population of western Liaoning Province carried haplogroup. The emergence of haplogroup C may be related to the nomads of the south of the North Asia. These data suggest that paternal genetic structure of the indigenous populations of the western Liaoning Province while maintaining continuity, integration into the ancient Central Plains and North Asian populations paternal genetic component. , From 64 cases of the Northwest men of ancient human remains successful Y-DNA results of 46 cases of samples, attributable to four single haplotype N, O, Q and R groups. Paternal genetic make-up of the ancient population of the Northwest Territories has obvious geographical specificity, for example, the westernmost Creek crowd as the main western lineage of R1a1 haplogroup; the adjoining Inner Mongolia Pengyang crowd all individuals can be attributed to a single type groups Q, North Asian populations in the high-frequency haplogroup; while the the approaching the Central Plains Dow Wangjiazai crowd of paternal Y-DNA to the East Asian haplogroup O, similar to the modern Han population. Comprehensive analysis of the ancient population of the Northwest Territories paternal genetic structure, in the paternal genetic form of the ancient population of the Northwest Territories there are significantly different, the reason for these different genetic data obtained speculated, is mainly due to the different groups of people have different paternal origin, everyone group accepted by the ancestors of the crowd gene contribution is different, and the from Sire terms, fewer exchanges between people own unique genetic component, so that it is preserved. Third, the success obtained from ancient human remains of the 48 cases in North China's male Y-DNA results of 29 cases of samples, attributable to the N, O and Q three single haplotype groups. The largest proportion of haplogroup O, diversity highest in two archaeological sites of the ancient Central Plains region of North China have been found; the haplogroup Q high frequency existence of Shanxi was the ancient nomads " Di "active area; haplogroup N appears that there may be the exchange of genes between populations in the Central Plains and western Liaoning Province. Comprehensive analysis of the Y-DNA of the various regions of the ancient population study results, northwest and northeast regions of the ancient population of most East Asian specific single haplotype groups can be found in the ancient population of the Central Plains, Ancient crowd paternal genetic diversity high. Central Plains region, since the Shang and Zhou dynasties is the Huaxia their descendants Han settlements, so the characteristics of the ancient population genetic structure in the Central Plains region of North China from one side of corroboration ancestors of the Han - Huaxia the Source is diverse rather than a single the integration of the different sources of the ancient population genetic component in the process of its formation. Based on the above analysis of the results, the paternal genetic structure of the ancient population in northern China in different regions have different distribution patterns: Northeast western Liaoning Province, while maintaining continuity in the of indigenous populations paternal genetic, you can see that the foreign genetic component exists in the population of the region, the foreign genetic component is likely to come from the Central Plains and North Asia and other regions. About 3000-2500 years ago, and the increasing trend of foreign genetic component. Northwest Territories of paternal inheritance there are significant differences between different geographical area of ancient population. 5 northwest of the ancient population of this study, Y chromosome genetic data, the reasons for these differences may be due to different populations have different sources of paternal and less genetic exchange between different populations, so that the the inherent genetic structure is maintained; in North China, the the patrilineal genetic structure is located in the ancient Central Plains region of the ancient population with modern Han closest, the modern Han paternal genes contributors.

The full text appears to be behind a paywall. Any native speakers who can add some information and/or correct possible mistranslations, feel free to do so in the comments.

Y chromosome study of Italy (Brisighelli et al. 2012) incl. sample of Greek speakers from Salento

This is a wonderful new source of information on Y-chromosome variation in Italy, that also includes some samples of the linguistic minorities of Ladins and Griko speakers.

The latter is particularly interesting to me, because, these last Greeks of Magna Graecia are descended either from the ancient colonists or medieval Eastern Roman settlers, and as such may represent a group of Greek descendants that (i) may have admixed to some extent with local Italic speakers, but (ii) will not have had an opportunity to experience much post-medieval gene flow that may have affected Greeks from the Aegean.

There may be something wrong with the presentation of the haplogroup frequencies on the left; in particular, based on the text, I think that what appears as R1* is in fact R1*(xR1a1).

In any case, here are my observations on the Grecani Salentini sample:

• They, as well as the Messapi, possess the highest frequencies of E-M78. This ties them to the Balkans in a very obvious way; this haplogroup was also interpreted as a signal of Greek colonization in Sicily and Massalia. This seems like the most obvious explanation; note that Salento is in Messapia, so the high frequency in the non-Greek denizens of the region may be simply the result of language shift, since the remaining Greek speakers are presumably the last remnant of a once much more numerous population that was linguistically Italicized as have most other Greek speaking populations of Italy and Sicily.
• Their highest frequency haplogroups are R1*(xR1a1) and J2. Both are fairly common haplogroups in both Greece and Italy, so only a fine-scale analysis would be able to differentiate between what might be pre-Greek and what is Greek in origin. In any case, I have proposed that these two haplogroups were typical of (albeit not limited to) the Graeco-Phrygo-Armenian clade, so their occurrence in this sample is not surprising.
• There is an occurrence of I*(xM26) chromosomes. This requires finer phylogenetic resolution, but certainly the absence of M26 -which has a SW European distribution- is interesting to note.
• Haplogroup G-M201 again requires finer-scale resolution, and could be anything from a relative of the Neolithic Italians (having been found in the Tyrolean Iceman) to much more recent events.
• Within haplogroup J, the majority of the chromosomes belong to clade J2, with about a tenth of the frequency made up of J*(xM62, M172). Note that these are not necessarily J*(xJ1,J2) as indicated in the figure, since M62 defines only a part of the J1 lineage.
• The absence of haplogroup R1a1 in this sample is perhaps the most interesting finding. This occurs at a frequency of ~10% in Greek samples from Greece and is fairly variable. I have previously observed that it was absent in the south stream of Indo-European based on its paucity in Armenians, Albanians, and its uneven distribution in Greeks. Its absence in the Italian Griko sample reinforces this idea. A caveat, however, is that the origin of the Greek settlement of Italy can be traced to southern Greece and western Anatolia, so it's still possible that some R1a1 was present in other areas of the Aegean basin since pre-medieval times.

The authors of the paper use many conventional labels of what is "Neolithic" and what is not (e.g., R1*(xR1a1) is claimed as Mesolithic). But, certainly, both age estimation of modern chromosomes (e.g., Wei et al. 2012) and the ancient Y chromosome studies cast doubt on this association. I would say that rather than being predominantly pre-Neolithic, it might appear that the Y-chromosome gene pool of Italy may have been formed in late Neolithic to medieval times, with the only lineages that can convincingly trace their ancestry to the Neolithic or earlier epochs being G and I-M26.

As for the Ladins, the high frequency (67.7%) of R1*(xR1a1) is consistent with what I believe to have been the main Italo-Celtic lineage.

Finally, I should point out the occurrence of a couple of haplogroup L samples; this haplogroup is more typical of populations much to the east, being the "eastern" cousin of the more "western" haplogroup T within the LT clade. Certainly a finer-scale resolution of these two L samples might be informative about their potential origins and/or the ancient distribution of this rather mysterious haplogroup.

PLoS ONE 7(12): e50794. doi:10.1371/journal.pone.0050794

Uniparental Markers of Contemporary Italian Population Reveals Details on Its Pre-Roman Heritage

Francesca Brisighelli et al.

Abstract
Background

According to archaeological records and historical documentation, Italy has been a melting point for populations of different geographical and ethnic matrices. Although Italy has been a favorite subject for numerous population genetic studies, genetic patterns have never been analyzed comprehensively, including uniparental and autosomal markers throughout the country.

Methods/Principal Findings

A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities — and from two linguistic isolates (Ladins, Grecani Salentini). All samples were first typed for the mitochondrial DNA (mtDNA) control region and selected coding region SNPs (mtSNPs). This data was pooled for analysis with 3,778 mtDNA control-region profiles collected from the literature. Secondly, a set of Y-chromosome SNPs and STRs were also analyzed in 479 individuals together with a panel of autosomal ancestry informative markers (AIMs) from 441 samples. The resulting genetic record reveals clines of genetic frequencies laid according to the latitude slant along continental Italy – probably generated by demographical events dating back to the Neolithic. The Ladins showed distinctive, if more recent structure. The Neolithic contribution was estimated for the Y-chromosome as 14.5% and for mtDNA as 10.5%. Y-chromosome data showed larger differentiation between North, Center and South than mtDNA. AIMs detected a minor sub-Saharan component; this is however higher than for other European non-Mediterranean populations. The same signal of sub-Saharan heritage was also evident in uniparental markers.

Conclusions/Significance

Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times.

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