Ancestors of Eastern Neandertals admixed with modern humans 100 thousand years ago

If true, this is very hard to reconcile with late (60kya) out of Africa and may be a smoking gun for pre-100kya presence of anatomically modern humans in Eurasia. From the paper:

The inferred demographic model confirms and provides quantitative estimates of previously inferred gene flow events among modern and archaic humans2, 3 (Extended Data Fig. 1). These include Neanderthal gene flow into modern humans outside Africa (3.3–5.8%) and gene flow from an unknown archaic hominin into the ancestors of Denisovans (0.0–0.5%). Interestingly, we also detect a signal of gene flow from modern humans into the ancestors of the Altai Neanderthal (1.0–7.1%). The precise source of this gene flow is unclear, but it appears to come from a population that either split from the ancestors of all present-day Africans or from one of the early African lineages, as significant admixture rates are estimated from San as well as Yoruba individuals. This introgression thus occurred in the opposite direction from the previously reported gene flow from Neanderthals to modern humans outside Africa

And:

However, it is clear that the source of the gene flow is a population equally related to present-day Africans and non-Africans (Extended Data Fig. 3). We conclude that the introgressing population diverged from other modern human populations before or shortly after the split between the ancestors of San and other Africans (Fig. 3a), which occurred approximately 200,000 years ago11.

The implications of this inference (if correct) for modern human origins are potentially monumental as they suggest a Eurasian modern human lineage (only detected in the Altai Neandertal) that diverges from other modern humans as early (if not earlier) than any two African ones.

If the new discovery checks out, it will no longer be possible to assert that the deepest split in our species, H. sapiens, involves African populations. A modest interpretation of these results would assert an earlier (pre-100kya) exodus of our species from Africa, and a more bold one would seek to re-examine the geographical origin of H. sapiens itself. I don't know if anyone is working on getting DNA from the progressive Neandertals of the Near East, but they should.

Things are bound to get more interesting.

Nature (2016) doi:10.1038/nature16544

Ancient gene flow from early modern humans into Eastern Neanderthals

Martin Kuhlwilm, Ilan Gronau, Melissa J. Hubisz, Cesare de Filippo, Javier Prado-Martinez, Martin Kircher, Qiaomei Fu, Hernán A. Burbano, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Pavao Rudan, Dejana Brajkovic, Željko Kucan, Ivan Gušic, Tomas Marques-Bonet, Aida M. Andrés, Bence Viola, Svante Pääbo, Matthias Meyer, Adam Siepel & Sergi Castellano

It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.

Link

Humans in the central Siberian Arctic ~45,000 years ago

The lack of such northerly sites prior to 45,000 years ago makes it quite likely that this mammoth kill was made by modern humans (it would be quite a coincidence if it was made by Neandertals at the same time as the expansionary Homo sapiens make their appearance all over the rest of Eurasia). If this is right, it's quite remarkable that by the mid to late 40,000s, modern humans were at ease from the equator to the arctic and from Europe to the remotest parts of Asia.

Science 15 Jan 2016:
Vol. 351, Issue 6270, pp. 260-263

Early human presence in the Arctic: Evidence from 45,000-year-old mammoth remains

Vladimir V. Pitulko, Alexei N. Tikhonov et al.

Archaeological evidence for human dispersal through northern Eurasia before 40,000 years ago is rare. In west Siberia, the northernmost find of that age is located at 57°N. Elsewhere, the earliest presence of humans in the Arctic is commonly thought to be circa 35,000 to 30,000 years before the present. A mammoth kill site in the central Siberian Arctic, dated to 45,000 years before the present, expands the populated area to almost 72°N. The advancement of mammoth hunting probably allowed people to survive and spread widely across northernmost Arctic Siberia.

Link

Genome of Kostenki-14, an Upper Paleolithic European (Seguin-Orlando, Korneliussen, Sikora, et al. 2014)

A new paper in Science reports on the genome of Kostenki-14 (K14), an Upper Paleolithic European from Russia. This is now the third oldest Homo sapiens for which we have genetic data, after Ust'-Ishim (Siberia, 45 thousand years), Tianyuan (China, 40 thousand years), and now Kostenki (European part of Russia, 37 thousand years). Of these three genomes, the Ust'-Ishim is both the highest coverage and earliest (Siberia is the gift that keeps on givin'), Tianyuan only has its chromosome 21 known, and K14, a complete 2.42x coverage sequence (and, apparently, good teeth, after all these years; left).

The publication of the Tianyuan genome showed that populations related to East Asians and Oceanians existed in the world 40 thousand years ago. So, models based on modern humans that put the split of East Asians from Europeans to a much more recent time period were basically wrong (more on this a little below). The Ust'-Ishim genome showed that populations basal to both East Asians and Europeans existed in the world 45 thousand years ago. So, either East Asians and Europeans hadn't gone along their different paths yet, or, if they had, Ust'-Ishim happened to be a side branch and not the major East Asian and European lineages.

K14 may not be the older Upper Paleolithic human, but as of this writing it is the only Upper Paleolithic European that has been published so far, the next ones being the Loschbour, Motala, and La Brana Mesolithic Europeans who who have about 1/5 of its age. The new paper shows that K14 was definitely European (or more correctly West Eurasian or Caucasoid), as it was more similar to modern Europeans than to East Asians or other non-West Eurasian populations. Thus, the morphological description of the sample as "Australoid" by some early anthropologists did not reflect its ancestral makeup. Also, this proves that Caucasoids existed 37,000 years ago, which most physical anthropologists would believe, but it is nice to have direct confirmation. This pushes the lower bound from 24,000 years ago (because MA-1 was West Eurasian according to the results of Raghavan et al.). It will be nice to push the lower bound further to the past as there are much older bones (and plenty of teeth) from earlier Upper Paleolithic Europeans.

But there is a slight kink in the story, as K14 also belonged to Y-haplogroup C which is predominantly East Asian/Ocenian/Native American today. So, maybe there is some distant link to these populations in its ancestry. But, there is definitely a link to much more recent Europeans: the tiny percentage of living Europeans who have preserved K14's Y-chromosomal type (some of which were doubtlessly told a few years back that they were descendants of Genghis Khan, before the phylogenetic structure of C was known), the La Brana hunter-gatherer from Mesolithic Spain, as well as Neolithic Europeans from Hungary.

The authors of the current paper also date the date of Neandertal admixture to 54 thousand years. This seems very compatible with the finding of between 50 and 60 thousand years by Fu et al. (2014) based on the Ust'-Ishim genome (which is both earlier and better, so the chunks of Neandertal ancestry in it are probably be longer and more well-defined).

The authors propose the following model for how various populations are related to each other:

This model is not formally tested, but at least it seems to derive Europeans as a 3-way mixture that is basically identical to that of Lazaridis et al., with some relabeling of populations (MHG=WHG and NEOL=EEF).

The model also includes Yeniseian Siberians as a mixture of MHG and East Asians (although it does not include actual East Asians). It's strange that Yeniseians apparently are given no ANE ancestry but only WHG/MHG. Both Raghavan et al. and Lazaridis et al. mentioned that ancestry related to MA-1 in living Siberians is diminished, but none at all?

The major new finding of this paper, however, is that K14 had Basal Eurasian ancestry, which was first proposed for EEF from Germany 7,000 years ago, so now it postulated for Russian hunter-gatherers 37,000 years ago. I don't think many archaeologists would derive European farmers from Russia (Russia is actually one of the last places in Europe that became agricultural). So, maybe the hunter-gatherers from Russia had Basal Eurasian ancestry and this wasn't limited to the ancestors of the EEF? If they did, it's strange that Loschbour, La Brana, MA-1, Ust'-Ishim, Swedish Mesolithic (and maybe KO1?) didn't have it. So, either Kostenki was very unique or there is an alternative explanation for its strangeness.


The evidence for the Basal Eurasian ancestry in K14 is summarized in the figure above in bullet point (b).

• The statistic D(Mbuti, East Asia; HG, K14) is less than 0. So, there's some link between HG and East Asians. Is this because of Basal Eurasian admixture in K14 or due to some admixture between Caucasoids and Mongoloids after the time of K14? (this might cause the lower dates of European-East Asian splits alluded to above).
• The statistic D(Mbuti, East Asia; NEOL, K14) is 0. So, East Asians don't "prefer" either Neolithic Europeans (NEOL) or K14. I guess the value of this statistic depends on how much Basal Eurasian the different populations have and what's the relationship between East Asians, K14, and the non-Basal Eurasian part in K14.
• Finally, "NEOL component for K14 in ADMIXTURE". I think they are referring to the "Middle East" component (right). This may be Basal Eurasian ancestry, or maybe because K14 is so old, it pre-dates the European/Middle Eastern divide and its ancestry isn't attracted to either Europe or the Middle East, so it gets ancestry from both (and many other colors besides).

It is fascinating how many new questions are both answered and raised each time a new genome gets published (and there has been a constant stream of these over the last couple of years).

Science DOI: 10.1126/science.aaa0114

Genomic structure in Europeans dating back at least 36,200 years

Andaine Seguin-Orlando1,*, Thorfinn S. Korneliussen1,*, Martin Sikora1, et al.

The origin of contemporary Europeans remains contentious. We obtain a genome sequence from Kostenki 14 in European Russia dating to 38,700 to 36,200 years ago, one of the oldest fossils of Anatomically Modern Humans from Europe. We find that K14 shares a close ancestry with the 24,000-year-old Mal’ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a meta-population that at times stretched from Europe to central Asia.

Link

Oldest modern human genome from Siberia ~45 thousand years ago

Just a teaser from Ann Gibbons in Science:

In 2008, Siberian ivory carver Nikolay Peristov was searching for ancient mammoth tusks eroding from the banks of the Irtysh River in western Siberia, when he found fossilized bones instead. Back in his workshop in Omsk, he showed the bones to local paleontologist Aleksey Bondarev, who recognized a human thighbone. Bondarev in turn showed it to an anthropologist friend, and it was passed on up the chain to some of the world's top experts in human evolution. They dated it to 45,000 years ago, making it one of the oldest known modern humans in northern Asia and Europe.

Now, the bone has opened a window on the genetics of our species at a crucial moment: soon after their arrival in northern Eurasia. At a meeting* here last week, paleogeneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, announced that his team has sequenced the thighbone's entire nuclear genome to high accuracy—an astonishing 42x coverage. "This is by far the oldest sequenced genome of a modern human," he said.

Because all living people in Europe and Asia carry roughly the same amount of Neandertal DNA, Pääbo's team thought that the interbreeding probably took place in the Middle East, as moderns first made their way out of Africa. Middle Eastern Neandertal sites are close to Skhul and Qafzeh, so some researchers suspected that those populations were the ones that mingled. But the team's analysis favors a more recent rendezvous. The femur belonged to an H. sapiens man who had slightly more Neandertal DNA, distributed in different parts of his genome, than do living Europeans and Asians. His Neandertal DNA is also concentrated into longer chunks than in living people, Pääbo reported. That indicates that the sequences were recently introduced: With each passing generation, any new segment of DNA gets broken up into shorter chunks as chromosomes from each parent cross over and exchange DNA. Both features of the Neandertal DNA in the femur suggest that the Ust-Ishim man lived soon after the interbreeding, which Pääbo estimated at 50,000 to 60,000 years ago.

The higher Neandertal DNA in the Ust-Ishim sample might be explainable by the negative selection against Neandertal material recently documented.  At 45kya, this sample is right around the time of the Early Upper Paleolithic at Kara-Bom in Siberia (and indeed anywhere), so this will be a hugely interesting sample when it is finally published.

Here is the program of the symposium on which this was apparently discussed (pdf). There seem to be quite a few interesting titles (but no abstracts).

mtDNA of Okladnikov Neandertal

PNAS February 11, 2014 vol. 111 no. 6

Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal

Pontus Skoglund et al.

One of the main impediments for obtaining DNA sequences from ancient human skeletons is the presence of contaminating modern human DNA molecules in many fossil samples and laboratory reagents. However, DNA fragments isolated from ancient specimens show a characteristic DNA damage pattern caused by miscoding lesions that differs from present day DNA sequences. Here, we develop a framework for evaluating the likelihood of a sequence originating from a model with postmortem degradation—summarized in a postmortem degradation score—which allows the identification of DNA fragments that are unlikely to originate from present day sources. We apply this approach to a contaminated Neandertal specimen from Okladnikov Cave in Siberia to isolate its endogenous DNA from modern human contaminants and show that the reconstructed mitochondrial genome sequence is more closely related to the variation of Western Neandertals than what was discernible from previous analyses. Our method opens up the potential for genomic analysis of contaminated fossil material.

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. 

Ancient steppe populations: hints of things to come

A reader alerts me to this research summary from a German government site (pdf). The research covered seems to be that of Joachim Burger's group.

The relevant chapter is:

Schritte im weiten Raum: Neue Blicke auf Zivilisationen der Eurasischen Steppe
[steps in the vast space: New Views on civilizations of the Eurasian steppe]

I invite my German readers to translate the most interesting parts of the chapter in the comments (or at least to summarize them). A few observations on what I've been able to make sense of:

• Heterogeneity of North Pontic steppe groups with differences between Catacomb culture and earlier Yamnaya individuals
• "European" light pigmentation but with darker eyes 
• Iron Age nomadic horsemen of Central Asia/South Siberia were mixed West/East Eurasian

Here are some (little) processed Google Translate portions to whet your appetite:

[The first part of the project looked for copper and Bronze Age cultures of the steppe west and north of the Black Sea (Fig. 1). In the Late Bronze Age (around 3000 BC) came here the very mobile Yamnaya culture in appearance, their population and influence radius - as the investigations showed - apparently at the same time expanding consolidated. With the Yamnaya culture is a single burial rites used in so-called pit graves under kurgans (grave mound). Also this wont Halbno addition maggots strong trading relationships across the steppe. Around 2500 BC, they were replaced by the less mobile Katakombengrab-culture whose dissemination conduction region was significantly smaller. Population genetic analyzes of DNA occupied by the late copper to the Middle Bronze Age, a steadily increasing genetic distance between those cul tures. Between copper and time Katakombengrab culture is the genetic distance is greatest. Here the differences are much more pronounced than between early Chalcolithic cultures and Yamnaya population. This population genetic change could be an indication of discontinuity and population changes due to migration. An archaeological site of suspected immigration from eastern steppe areas but at least on the female side hardly taken place: For Central Asia typical DNA lines do not occur in the studied populations. Despite the genetic differences within the un the investigated groups are with them to popu lations, which are without doubt be described as European.Here the differences are much more pronounced than between early Chalcolithic cultures and Yamnaya population. This population genetic change could be an indication of discontinuity and population changes due to migration. An archaeological site of suspected immigration from eastern steppe areas but at least on the female side hardly taken place: For Central Asia typical DNA lines do not occur in the studied populations. Despite the genetic differences within the un the investigated groups are with them to popu lations, which are without doubt be described as European. DNA markers with known phenotype suggest a continuity between the North Pontic area of ​​4 / 3 Millennium BC and today's Europeans out. For instance, have all examined individuals tierungstyp on a bright pigments, as is prevalent in Europe today. Only the eye color has been dark in comparison to today.]

[The second part of the project was devoted to the population dynamics of early Iron Age peoples of nomadic horsemen in the Eurasian steppe belt. Here were 900-300 BC disseminated numerous highly mobile populations that are associated with the so-called Scythian or Sakian culture (Fig. 2). The groups studied are from the areas of eastern Kazakhstan, Altai mountains, Minusinsk Basin and Tuva. They all consist of a mixture of DNALinien, which today is a part of Central and East Asia and the other in Europe. Ity of the ground because this way the populations have a remarkably high level of genetic diversity that characterizes the Altai population today.

...

The Tagar Culture (Minusinsk Basin) this shows the greatest genetic - but also cultural - distance to all other groups. Although it chronologically corresponds to the Pazyryk culture of the Altai (5th-3rd century BC) seems to be present here genetic isolation. Between the Pazyryk culture and the significantly older findings from Tuva (7 / 6th century BC), however, the genetic distance in spite of the time interval is very small. Amazingly, has the Pazyryk culture also within its range a geographic substructure: Divided into Kazakh Altai, and Cuja Ukok plateau region, show the nomadic horsemen of Cuja region in relation to the other two groups increased genetic distance.]

Sakha origins

An interesting quote from the paper:

Although the genetic heritage of the native populations of Sakha is mostly of East Asian ancestry, analyses of autosomal SNP data as well as haploid loci also show a minor West  Eurasian genetic component. The patchy presence of the “European” (blue) component in the  ADMIXTURE plot (Figure 6), most pronounced in Yukaghirs, probably testifies to recent  admixture with Europeans. In addition, the presence of European-specific paternal lineages  R1a-M458, I1 and I2a among Yakuts, Dolgans, Evenks and Yukaghirs likely points to a  recent gene flow from East Europeans. Although only individuals with self-reported unadmixed ancestry for at least two generations were included in the study of haploid loci,  mistakes in ethnic self-identification cannot be entirely excluded. One of the main sources of  gene flow has likely been Russians who accounted for 37.8% of the population of Sakha in  2010 [61]. The migration of Russians (at first mainly men) to eastern Siberia started already  in the 17th century, when Yakutia was incorporated into the Russian Empire [62]. 

But:

The mtDNA haplogroup J detected in the remains from a Yakut burial site dated to the  beginning of the 17th century [41], long before the beginning of the settlement of Russian  families in the 18th century [63], clearly points to more ancient gene flow from western  Eurasia. The presence of haplogroups H8, H20 and HV1a1a among the Yakuts, Dolgans and  Evenks (Figure 1) also suggests gene flow other than from Russians, because these  haplogroups are rare (H8 and H20) or even absent (HV1a1a) among Russians [64-67], but are  common among southern Siberian populations as well as in the Caucasus, the Middle and  Near East [19,68-70]. Moreover, the HVSI haplotypes of H8, H20a and HV1a1a in our  sample exactly match those in the Buryats from the Buryat Republic [19]. Similarly, the Ychromosome haplogroup J in Dolgans and Evens very likely testifies to gene flow through  South Siberia, as it is present among native South Siberian populations [47,71]. The scenario  of ancient gene flow from West Eurasia is supported by ancient DNA data, which show that  in the Bronze and Iron Ages, South Siberia, including the Altai region, was an area of  overwhelmingly predominant western Eurasian settlement [72,73], and the Indo-European  migration even reached northeastern Mongolia [74]. To summarize, the West Eurasian  genetic component in Sakha may originate from recent admixture with East Europeans,  whereas more ancient gene flow from West Eurasia through Central Asia and South Siberia is  also probable. 

BMC Evolutionary Biology 2013, 13:127 doi:10.1186/1471-2148-13-127

Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia

Sardana A Fedorova et al.

Abstract (provisional)

Background

Sakha -- an area connecting South and Northeast Siberia -- is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia.

Results

We report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages D5a2a2, C4a1c, C4a2, C5b1b and the Yakut-specific STR sub-clade of Y-chromosome haplogroup N1c can be linked to a migration of Yakut ancestors, while the paternal lineage C3c was most likely carried to Sakha by the expansion of the Tungusic people. MtDNA haplogroups Z1a1b and Z1a3, present in Yukaghirs, Evens and Dolgans, show traces of different and probably more ancient migration(s). Analysis of both haploid loci and autosomal SNP data revealed only minor genetic components shared between Sakha and the extreme Northeast Siberia. Although the major part of West Eurasian maternal and paternal lineages in Sakha could originate from recent admixture with East Europeans, mtDNA haplogroups H8, H20a and HV1a1a, as well as Y-chromosome haplogroup J, more probably reflect an ancient gene flow from West Eurasia through Central Asia and South Siberia.

Conclusions

Our high-resolution phylogenetic dissection of mtDNA and Y-chromosome haplogroups as well as analysis of autosomal SNP data suggests that Sakha was colonized by repeated expansions from South Siberia with minor gene flow from the Lower Amur/Southern Okhotsk region and/or Kamchatka. The minor West Eurasian component in Sakha attests to both recent and ongoing admixture with East Europeans and an ancient gene flow from West Eurasia.

Link

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.

Genomewide structure of populations from European Russia (Khrunin et al. 2013)

Notice:

1. The intermediate position of Estonians between Balts and Finns
2. The intermediate position of some Russian groups between Komi and the main body of Europeans.

PLoS ONE 8(3): e58552. doi:10.1371/journal.pone.0058552

A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe

Andrey V. Khrunin et al.

Several studies examined the fine-scale structure of human genetic variation in Europe. However, the European sets analyzed represent mainly northern, western, central, and southern Europe. Here, we report an analysis of approximately 166,000 single nucleotide polymorphisms in populations from eastern (northeastern) Europe: four Russian populations from European Russia, and three populations from the northernmost Finno-Ugric ethnicities (Veps and two contrast groups of Komi people). These were compared with several reference European samples, including Finns, Estonians, Latvians, Poles, Czechs, Germans, and Italians. The results obtained demonstrated genetic heterogeneity of populations living in the region studied. Russians from the central part of European Russia (Tver, Murom, and Kursk) exhibited similarities with populations from central–eastern Europe, and were distant from Russian sample from the northern Russia (Mezen district, Archangelsk region). Komi samples, especially Izhemski Komi, were significantly different from all other populations studied. These can be considered as a second pole of genetic diversity in northern Europe (in addition to the pole, occupied by Finns), as they had a distinct ancestry component. Russians from Mezen and the Finnic-speaking Veps were positioned between the two poles, but differed from each other in the proportions of Komi and Finnic ancestries. In general, our data provides a more complete genetic map of Europe accounting for the diversity in its most eastern (northeastern) populations.

Link

Recent admixture in Altaic populations: a legacy of Empire?

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

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

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

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

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

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

Now, these appear to make excellent sense.

Of the Dolgans:

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

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

Of the Evenks:

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

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

Of the Nogais:

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

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

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

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

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

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

ADMIXTURE tracks Amerindian-like admixture in northern Europe

I have recently assembled a new "world" dataset of 4,280 individuals that I am currently incrementally analyzing with ADMIXTURE. But, I noticed an interesting pattern at K=4 that I wanted to share right away.

4 ancestral populations emerge at this level of resolution, which I have named: European, Asian, African, Amerindian. The names aren't important, and you can replace them with whatever you prefer. 

The interesting thing about this K=4 analysis is that European populations show evidence of Amerindian admixture, consistent with the pattern inferred using f-statistics, where European populations show admixture between Sardinians and a Karitiana-like population.

This pattern may have emerged at previous ADMIXTURE analyses at this level of resolution, but thanks to the f3 evidence presented in previous posts, it is now clear that it is no quirk of ADMIXTURE, but indicative of a real (albeit still rather mysterious) pattern of gene flow that differentially affected European populations.

For example, the Irish_D population has 7.6% of the Amerindian component, and so do HGDP Orcadians. HGDP Sardinians have only 1.7% of it, which appears to be the minimum in Europe, with French_Basque having more at 4.6%.

Another interesting observation is that West Eurasian populations that show an excess of East Eurasian-like admixture appear to be doing so for two separate reasons. For example, HGDP Russians have 11.7% of Amerindian component, but also 4.5% of "Asian", and 1000 Genomes Finns have 3.3% Asian and 12% Amerindian. Behar et al. (2010) Turks, on the other hand, have 9.9% Asian and 2.2% Amerindian. All these populations are East Eurasian-shifted relative to Sardinians, a pattern which can also be observed by looking at the K=3 analysis, but for apparently different reasons.

The pattern for Near Eastern populations is also interesting. For example, Yunusbayev et al. (2011) Armenians have 0% of the Amerindian component, and 5.7% of the Asian, and all three HGDP Arab populations (Druze, Palestinian, Bedouin) also have 0% of the Amerindian component, with variable levels of the Asian.

It would appear that whatever process contributed Amerindian-like admixture in Europeans, minimally affected Near Eastern populations, with Sardinians being demonstrably related to Neolithic Europeans (thanks to ancient DNA evidence), tilting towards the Near Eastern pattern. On the other hand, Near Eastern populations show evidence of Asian admixture, which probably involves unresolved East Asian/ASI ancestry, and will be resolved at higher K. Sardinians appear to be at the end of three clines: (i) Amerindian-like cline of Europe-Siberia-Americas, (ii) East Asian-like cline of Europe-Central Asia/Siberia-East Asia, (iii) ASI-like cline of Europe-Near East-South Asia. These are separate, but not independent phenomena.

To confirm that the signal picked up by ADMIXTURE tracks the signal picked up by ADMIXTOOLS formal tests, I calculated the following D-statistic:

D(Sardinian, European, Karitiana, San)

where European is any population with a sample size of at least 10, and which belonged at 99% in the European+Amerindian components:

And, here is a scatterplot:

The correlation is clear, and the Pearson coefficient is -0.96. This means that populations with higher % Amerindian, as estimated by ADMIXTURE, also show higher D-statistic evidence for admixture.

What of the actual estimates of admixture produced by ADMIXTURE? Using the F4 ratio test, I recently showed that African admixture in Sardinians confounds estimates of Amerindian-like admixture in northern Europeans and vice versa (Amerindian-like admixture in northern Europeans confounds African admixture in Sardinians).

In that experiment, I "scrubbed" Sardinians to remove segments of African ancestry, and showed that estimates of Amerindian-like admixture in the CEU population diminished from 13.9% to 8.8%. The latter seems reasonably close to the 7.1% inferred by ADMIXTURE.

On balance, I would say that ADMIXTURE at K=4 provides a good proxy for the effect described in Patterson et al. (2012). Its results are more difficult to interpret, because its underlying model does not take into account evolutionary relationships between populations. On the other hand, it has the advantage of being able to handle multiple ancestral populations, and has consistently proven able to generate useful data that correlate well with those from other techniques of population genetics.

The tangled web of humanity

Indian populations are composed of two ancestral components: Ancestral North Indians (ANI) and Ancestral South Indians (ASI), discovered by Reich et al. (2009). In that paper, it was also shown that ASI forms a clade with East Eurasians, while ANI does so with West Eurasians.

Patterson et al. (2012) published a different pattern: non-Sardinian Europeans have North Eurasian-like ancestry that links them to Amerindian populations. It is thus possible that ASI and the East Eurasian-like admixture in North Europeans may share a common evolutionary history:

Now, consider a hypothetical population of the Indian Cline. A European population is related to it both via its ANI/West Eurasian ancestry, but also via its ASI ancestry, because the East_Eurasian component in Europeans shares a portion of ancestry (indicated by the red arrow) with ASI.

Sardinians lack (or have less of) this "red arrow" portion of ancestry. 

It is also possible that ANI itself may have some East_Eurasian ancestry, like Europeans do; this is not indicated in the figure. More on this later.

Consider the following D-statistic:

D(European, Sardinian, Indian, San)

As we shall see, this takes positive values, consistent with the idea of gene flow between Europeans and Indians at the exclusion of Sardinians. However, this gene flow may involve either the West Eurasian component in the ancestry of Indians (i.e., this component is more related to Europeans than to Sardinians), or to the ASI component (which is related to Europeans via the common "red arrow" portions of ancestry).

We can figure out what is going on by trying different Indian populations along the Indian Cline, and seeing whether the D-statistic is inflated/deflated in populations of greater ANI/ASI ancestry.

Here are the results:


                Russian Orcadian French Lithuanians   ANI
Mala             0.0153   0.0120 0.0088      0.0131 38.86
Madiga           0.0153   0.0122 0.0091      0.0111 40.66
Chenchu          0.0157   0.0108 0.0088      0.0115 40.76
Bhil             0.0149   0.0115 0.0086      0.0124 42.96
Satnami          0.0166   0.0125 0.0091      0.0126 43.06
Kurumba          0.0156   0.0117 0.0095      0.0121 43.26
Kamsali          0.0139   0.0105 0.0088      0.0098 44.56
Vysya            0.0130   0.0099 0.0083      0.0102 46.26
Lodi             0.0143   0.0124 0.0092      0.0125 49.96
Naidu            0.0138   0.0104 0.0092      0.0108 50.16
Tharu            0.0150   0.0112 0.0095      0.0118 51.06
Velama           0.0126   0.0107 0.0083      0.0095 54.76
Srivastava       0.0144   0.0124 0.0091      0.0116 56.46
Meghawal         0.0131   0.0107 0.0088      0.0117 60.36
Vaish            0.0143   0.0144 0.0099      0.0128 62.66
Kashmiri_Pandit  0.0119   0.0116 0.0090      0.0116 70.66
Sindhi           0.0106   0.0112 0.0095      0.0111 73.76
Pathan           0.0098   0.0114 0.0087      0.0106 76.96

For each Indian Cline population, I list the ANI percentage, as estimated by Reich et al. (2009) in the last column, and the D-statistic of the above given form for different pairs of Indian and European populations.

We can plot the D-statistic vs. ANI for each of our European populations:

The correlation coefficients confirm the visual impression, that for the HGDP Russians there is a significantly negative relationship between ANI admixture in an Indian Cline population and the D-statistic:

Russian   Orcadian    French Lithuanians

-0.8631118 0.08670188 0.1870127  -0.1889908

In other words, the evidence for gene flow between Russians and Indians is maximized when south Indian (ASI-rich) populations are used.

The lack of a clear pattern in the other three populations is itself interesting. One possible explanation involves East Eurasian-like admixture in the ANI, a conjecture which would make sense, given that all non-Sardinian continental West Eurasians seem to possess it.

If that is true, then as we go "south" along the Indian Cline, ASI related admixture inflates the D-statistic by increasing the "red arrow" overlap with the East Eurasian-like admixture in Europeans. As we go "north" along this cline, then the D-statistic decreases, due to ASI-reduction, but also increases, due to East Eurasian-like admixture in ANI, with an end result of no clear pattern in the superposition of processes.

In any case, this is an interesting example of a crisscrossing type of admixture where unrelated processes (east Eurasian-like admixture in Russians and ASI admixture in Indians) combine to present an unusual effect.

Visualizing admixture differences with ACD tool

Vaêdhya has created a new ACD tool that allows one to visualize differences between sets of populations in terms of admixture components. He also posts two examples of the application of his tool on data generated by myself in the Dodecad Project, as well as by the Harappa Project.

 I have speculated about the origins of Indo-Iranians before, noting that the evidence links even the Kurds with a "South Asian" component; in subsequent higher-resolution analysis, such as the K12b, it appeared that this component was related to the Gedrosia component. In any case, the evidence is clear about the links of different Iranian and Indo-Aryan groups, so it is nice that this can be made evident with the ACD tool and data from the Harappa Project. Notice the excess of the Baloch (~Gedrosia) component in Kurds and Iranians in contradistinction to the Indo-European Armenians and Semitic Assyrians. It is fairly clear to me that the Iranian ancestral homeland is to be sought to the east, with the Bactria-Margiana Archaeological Complex (BMAC) being a good candidate for its location.

In a second plot, Vaêdhya uses Dodecad data to contrast patterns of differences in Northeastern Europe. Here, too, the patterns are clear, with Finns, and secondarily Russians showing an excess of Siberian ancestry relative to Poles. This is, no doubt, due to the Finnic element, which links Finns, and the Uralic substratum in Russians with Siberia. A second contrast is between Finns and Russians/Poles. The latter have more of the Caucasus component, a probable legacy of the Bronze Age Indo-European invasion of Europe. A final contrast is the higher Atlantic_Med element in Poles, which suggests an excess of early Neolithic farmer ancestry, or, admixture with West European populations such as Germans and others who possess more of this component than Slavs.

~9ky old textiles from Russian Far East

Antiquity Volume: 86 Number: 332 Page: 325–337

The earliest surviving textiles in East Asia from Chertovy Vorota Cave, Primorye Province, Russian Far East

Yaroslav V. Kuzmin et al.

Carbonised textiles were found in a burnt down building inside a cave 30km from the far eastern coast of Russia. The textiles were made from untwisted or hand-twisted blades of sedge grass to form ropes, nets and woven mats. Dated by AMS to c. 9400–8400 cal BP these are the earliest textiles so far known from East Asia.

Link

Horse domestication mystery solved (?)

I will add the abstract of the paper later when it is "live" on the PNAS site. For the moment, a link to the press release:

New research indicates that domestic horses originated in the steppes of modern-day Ukraine, southwest Russia and west Kazakhstan, mixing with local wild stocks as they spread throughout Europe and Asia. The research was published today, 07 May, in the journal PNAS.

For several decades scientists puzzled over the origin of domesticated horses. Based on archaeological evidence, it had long been thought that horse domestication originated in the western part of the Eurasian Steppe (Ukraine, southwest Russia and west Kazakhstan); however, a single origin in a geographically restricted area appeared at odds with the large number of female lineages in the domestic horse gene pool, commonly thought to reflect multiple domestication "events" across a wide geographic area.

In order to solve the perplexing history of the domestic horse, scientists from the University of Cambridge used a genetic database of more than 300 horses sampled from across the Eurasian Steppe to run a number of different modelling scenarios.

Their research shows that the extinct wild ancestor of domestic horses, Equus ferus, expanded out of East Asia approximately 160,000 years ago. They were also able to demonstrate that Equus ferus was domesticated in the western Eurasian Steppe, and that herds were repeatedly restocked with wild horses as they spread across Eurasia.

ScienceNOW also covers the new research, and reports on a contrasting viewpoint:

Not all researchers are convinced, however. Archaeologist Marsha Levine of the University of Cambridge thinks using modern genetic samples to retrace horses' evolution is a dead end. "There's been mixing of cultures and mixing of horses in this region for many thousands of years," she says. "And so when you're looking at any modern horse, you just don't know where it's from."

Bringing together many kinds of evidence is what will ultimately answer the whens and wheres of horse domestication, Levine says. "What we need to be doing is using material from excavations, sequencing ancient genes, and combining that with what we know from archaeological evidence about how animals were used in the past."

I agree with the idea that ancient DNA will ultimately confirm/reject the model presented in the paper. Of course, it may be the case that the west Eurasian steppe was the place where horse domestication happened, but it is also the place where local horses may be descended from European, West Asian, and Central Asian breeds. I'll have to read the paper to see how the problem of possible admixture between western and eastern horse breeds on the steppe is accounted for in the paper.

PNAS doi: 10.1073/pnas.1111122109

Reconstructing the origin and spread of horse domestication in the Eurasian steppe

Vera Warmuth et al.

Despite decades of research across multiple disciplines, the early history of horse domestication remains poorly understood. On the basis of current evidence from archaeology, mitochondrial DNA, and Y-chromosomal sequencing, a number of different domestication scenarios have been proposed, ranging from the spread of domestic horses out of a restricted primary area of domestication to the domestication of numerous distinct wild horse populations. In this paper, we reconstruct both the population genetic structure of the extinct wild progenitor of domestic horses, Equus ferus, and the origin and spread of horse domestication in the Eurasian steppes by fitting a spatially explicit stepping-stone model to genotype data from >300 horses sampled across northern Eurasia. We find strong evidence for an expansion of E. ferus out of eastern Eurasia about 160 kya, likely reflecting the colonization of Eurasia by this species. Our best-fitting scenario further suggests that horse domestication originated in the western part of the Eurasian steppe and that domestic herds were repeatedly restocked with local wild horses as they spread out of this area. By showing that horse domestication was initiated in the western Eurasian steppe and that the spread of domestic herds across Eurasia involved extensive introgression from the wild, the scenario of horse domestication proposed here unites evidence from archaeology, mitochondrial DNA, and Y-chromosomal DNA.

Link

Multiple origins of Russian mtDNA

First PC of mtDNA variation on the left. From the paper:

The genetic distances from the Russians to the Europeanlanguage groups indicate that the gene pool of present-day Russians bears the influence of Slavic, Baltic,Finno-Ugric and, to a lesser extent, Germanic groups, aswell as Iranian and Turkic groups. 

...

The results of this study strongly suggest that the impact of the pre-Slavic (Finno-Ugric) population on the East European Plain is the most important factor for the northward and southward differentiation of the present-day Russian gene pool. This explanation supports the view proposing the genetic influence of Finno-Ugrians on the formation of the northern regions of Russia, which was inferred from mtDNA marker studies of some Russian populations (Grzybowski et al., 2007) and Y-chromosome analysis (Balanovsky et al., 2008). 

Being quite distant from the Finno-Ugric group, the Southern Russians consequently differ from the Northern Russians in their closeness to the Germanic group. This difference indicates that the Germanic people played a significant role in the development of the southern, but not the northern segment of the Russian gene pool. In general, the Germanic influence on the formation of the Russians is not as obvious as the impact of the Slavic, Baltic, and Finno-Ugric people. However, strong interactions between the Germanic and Slavic tribes have been found in archeological materials dating from the mid-first millennium B.C. to the early first millennium A.D. These interactions were the strongest on the northern coast of the Black Sea, in the area of the multiethnic Chernyakhov archeological culture (second to fifth centuries A.D.). In the second half of the first millennium A.D., the descendants of this culture colonized the southern regions of the historical Russian area (Sedov, 1994, 1995). However, there is no evidence in the historical literature of the interaction between the Germanic tribes and the Slavs (and later, the Russians) after the Slavic colonization of the East European Plain. Therefore, the Germanic influence could not have occurred after the early part of the first millennium A.D., which was before the eastward Slavic migration (Sedov, 1994, 1995). Apparently, the impact of the Germanic people on the Chernyakhov Slavs affected the gene pool of modern Southern Russians, consequently differentiating them from the Northern Russians (Fig. 6).

Am J Phys Anthropol DOI: 10.1002/ajpa.21649


Russian ethnic history inferred from mitochondrial DNA diversity

Irina Morozova et al.

With the aim of gaining insight into the genetic history of the Russians, we have studied mitochondrial DNA diversity among a number of modern Russian populations. Polymorphisms in mtDNA markers (HVS-I and restriction sites of the coding region) of populations from 14 regions within present-day European Russia were investigated. Based on analysis of the mitochondrial gene pool geographic structure, we have identified three different elements in it and a vast “intermediate” zone between them. The analysis of the genetic distances from these elements to the European ethnic groups revealed the main causes of the Russian mitochondrial gene pool differentiation. The investigation of this pattern in historic perspective showed that the structure of the mitochondrial gene pool of the present-day Russians largely conforms to the tribal structure of the medieval Slavs who laid the foundation of modern Russians. Our results indicate that the formation of the genetic diversity currently observed among Russians can be traced to the second half of the first millennium A.D., the time of the colonization of the East European Plain by the Slavic tribes. Patterns of diversity are explained by both the impact of the native population of the East European Plain and by genetic differences among the early Slavs.

Link

Secular trends in some Russian populations

Anthropol Anz. 2011;68(4):367-77.

Secular trends in some Russian populations.

Godina EZ

Abstract
Secular changes of body measurements in children have been the subject of studies in many different countries. In recent years, there has been an increase in BMI associated with a significant trend towards obesity in both Europe and the US. The aim of the present study was to analyze trends in body measurements and BMI in Russia from the 1960's to the beginning of the 21st century. This was done at three locations of the Russian Federation: the city of Moscow, the cities of Saratov and Naberezhnye Chelny in the Volga-river area. In addition, data on secular changes of Abkhazian children were analyzed. A large number of anthropometric measurements were taken on each individual including height, weight, arm, leg and trunk lengths (estimated), body diameters and circumferences, skinfold thickness, head and face dimensions. Stages of secondary sex characteristics also were evaluated; data on menarcheal age were collected by status-quo and retrospective methods. Changes in hand grip strength have been evaluated in some of the samples. While stature was increasing during these years, weight, chest circumference and BMI were characterized by negative changes, which became more obvious in elder girls. Changes in handgrip strength also showed negative trends. There were noticeable changes in head and face measurements, which were expressed in more elongated head and face forms, i.e. the head became longer and narrower with narrower and higher faces. Secular changes in head and facial morphology may be considered part of the general trend.

Link

Last Neandertals of Russia's North

I am reposting this, as I don't know whether my original post has survived the recent epic #BloggerFail. I'm not going to re-write my whole text, and, besides John Hawks already has plenty on the subject.

In short: the evidence in this paper is not incompatible with the other recent paper that pushed the last Neandertals back in time due to advances in radiocarbon dating. It could very well be that Neandertals had been wiped out in most of Europe by the late 30,000s before present, but had managed to survive near the Arctic before modern humans got there.

That would not be very surprising, given that the periphery is where the last unassimilated survivors of demographic expansions are expected to be found. Today, for example, it is in northern Eurasia that one can find the few unassimilated tribes that have resisted the twin spreads out of the Fertile Crescent and the Yangtze River region that have largely shaped Eurasian demography over the last 10,000 years.


Science 13 May 2011:
Vol. 332 no. 6031 pp. 841-845
DOI: 10.1126/science.1203866

Late Mousterian Persistence near the Arctic Circle

Ludovic Slimak et al.

ABSTRACT

Palaeolithic sites in Russian high latitudes have been considered as Upper Palaeolithic and thus representing an Arctic expansion of modern humans. Here we show that at Byzovaya, in the western foothills of the Polar Urals, the technological structure of the lithic assemblage makes it directly comparable with Mousterian Middle Palaeolithic industries that so far have been exclusively attributed to the Neandertal populations in Europe. Radiocarbon and optical-stimulated luminescence dates on bones and sand grains indicate that the site was occupied during a short period around 28,500 carbon-14 years before the present (about 31,000 to 34,000 calendar years ago), at the time when only Upper Palaeolithic cultures occupied lower latitudes of Eurasia. Byzovaya may thus represent a late northern refuge for Neandertals, about 1000 km north of earlier known Mousterian sites.

Link

Breast-cancer causing mutation in Ashkenazi Jews came from Europeans

The interesting question is: why did this become frequent in AJ? If this mutation did indeed enter the AJ gene pool half a millennium ago, then it may be within the reach of genealogists and historians to uncover its origins.

European Journal of Human Genetics , (1 December 2010) | doi:10.1038/ejhg.2010.203

On the origin and diffusion of BRCA1 c.5266dupC (5382insC) in European populations

The BRCA1 mutation c.5266dupC was originally described as a founder mutation in the Ashkenazi Jewish (AJ) population. However, this mutation is also present at appreciable frequency in several European countries, which raises intriguing questions about the origins of the mutation. We genotyped 245 carrier families from 14 different population groups (Russian, Latvian, Ukrainian, Czech, Slovak, Polish, Danish, Dutch, French, German, Italian, Greek, Brazilian and AJ) for seven microsatellite markers and confirmed that all mutation carriers share a common haplotype from a single founder individual. Using a maximum likelihood method that allows for both recombination and mutational events of marker loci, we estimated that the mutation arose some 1800 years ago in either Scandinavia or what is now northern Russia and subsequently spread to the various populations we genotyped during the following centuries, including the AJ population. Age estimates and the molecular evolution profile of the most common linked haplotype in the carrier populations studied further suggest that c.5266dupC likely entered the AJ gene pool in Poland approximately 400–500 years ago. Our results illustrate that (1) BRCA1 c.5266dupC originated from a single common ancestor and was a common European mutation long before becoming an AJ founder mutation and (2) the mutation is likely present in many additional European countries where genetic screening of BRCA1 may not yet be common practice.

Link