Ust'-Ishim: Ancient DNA offers the first of what I expect in the coming years will be many disappointments to those emotionally invested in a SE Asian origin for K-M526

It's been asserted, on crude phylogeographic grounds, that K-M526 originated in South East Asia. A SE Asian origin for K-M526 is credible if you ignore the rest of the Y phylogeny, starting with K-M9, and all other available information. Sadly for Hector, reality, with this recent publication, has again chosen to side with "Eurocentrists".

I don't expect the Hectors will gracefully accept their beating, but to others the presence of a previously unknown branch of K(xLT) in Siberia 45,000 years ago should be a pretty clear signal that the idea of a 500 year sprint from West or Central Asia to an already-inhabited SE Asia, followed, after an indefinite pause, by a repopulating of the world from Sundaland (if not the islands of Wallacea), all while failing to carry any trace of Denisovan admixture back to the future civilized world is an unnecessary and improbable fantasy.

The cline of Denisovan admixture, from faint, highly-selected remnants in mainland SE Asia to maxima among Melanesians and Australian Aborigines, has always pointed to gene flow into the region after its initial settlement rather than out of it, the K-bearers being one obvious candidate for the major source of this dilution. I'd also say it's more likely than not that they (an M526-carrying population of Central Asian origin) are the ones who brought culture to Hector's ancestors.

ESHG 2014: Genetic landscape of populations along the Silk Road

Title: P17.64-M - Genetic landscape of populations along the Silk Road reveals a haplotype associated with hyposmia in Tajikistan's population
Keywords: olfactory receptor clusters; Silk Road; population structure
Authors: M. Mezzavilla1,2, S. Ulivi2, P. Gasparini1,2, V. Colonna3; 1University of Trieste, Trieste, Italy, 2Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, Trieste, Italy, 3Institute of Genetics and Biophysics "A. Buzzati-Traverso", National Research Council (CNR), Napoli, Italy.

Abstract: Smell is a versatile mechanism for recognizing different odours and is mediated by olfactory receptors. While collecting phenotypes related to smell in six countries along the Silk Road, we found an increased rate of failure to discriminate odorants in individuals from Tajikistan respect to the other countries. Using haplotype-based association we linked this to a 15 kb region within olfactory receptor gene cluster on chromosome 6 (p-value 3.86e-05). This region is embedded in the largest intron of OR5V1 and is downstream OR11A1 and upstream OR12D3. We also analysed genetic variability in 1,114 unrelated samples either from the Silk Road and ten other worldwide populations at over 300,000 polymorphic sites and characterized population genetic structure of the Silk Road within a worldwide context with a resolution never obtained before. We identified genetic components peculiar to Central Asia and observed that Tajikistan behaves as an outlier population. Indeed Tajiks share a consistent number of unusually large stretches of homozygosity and have the lowest effective population size (Ne) among the studied populations, most likely as the result of past isolation and/or consanguinity. Altogether these novel findings clarify the complex genetic patterns of the Silk Road populations and suggest that the smell misperception phenotype observed in Tajikistan might be the result of a combination of genetic drift and relaxed selection at the olfactory receptors genes.

ESHG 2014: Y chromosome haplogroups C, N and Q in Eurasian populations for the perspectives of proto-Bulgarian ancestry

Title: P17.92-M - Meta-analysis of Y chromosome haplogroups C, N and Q in Eurasian populations for the perspectives of proto-Bulgarian ancestry
Keywords: Y-chromosome; haplogroup; proto-Bulgarians
Authors: S. Karachanak1, D. Nesheva1, V. Grugni2, N. Al-Zahery2, V. Battaglia,2, A. S. Galabov3, D. Toncheva1; 1Department of Medical Genetics, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria, 2Department of Biology and Biotechnologies “Lazzaro Spallanzani”. University of Pavia, Pavia, Italy, 3The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria.

Abstract: Bulgaria is situated on the presumed trajectory of the pioneer colonization of Europe. Since then it has been subjected to a series of demographic events with disputable impact on the contemporary Bulgarian gene pool. One of the most controversial issues of the Bulgarian past is the origin of the proto-Bulgarians, which were previously considered as a sparse Turkic population.

In order to delve into Bulgarian patrilineal origins we have performed a survey of Y-chromosome haplogroups followed by meta-analysis of haplogroups C, N and Q distinctive for Altaic populations. The analysis was performed on a sample comprising 808 Bulgarian males using RFLP and DHPLC analysis. We have found that only 1.49 % of the contemporary gene pool belongs to haplogroups C, N and Q. Our results were used to upgrade and extend the distribution maps of these haplogroups and to compare their frequency in 240 Eurasian (sub-) populations with more than 20 000 samples.

The comparison reveals a statistically significant difference in the distribution of the studied haplogroups between Bulgarians and Altaic populations as well as between Bulgarians and Eastern Slavic populations. Based on the novel historical studies which point to a substantial contribution of the proto-Bulgarians to the modern Bulgarian gene pool the obtained results suggest that there is no common genetic ancestry between proto-Bulgarians and present day Altaic populations as they reject the hypothesis of the Turkic origin of proto-Bulgarians.

ESHG 2014: Y-chromosome Polymorphisms in Kazakh Populations from the Perspective of Tribal-clan structure

Title: J17.65 - Characteristics of Y-chromosome Polymorphisms in Kazakh Populations from the Perspective of Tribal-clan structure
Keywords: Y-chromosome Polymorphisms; Kazakh Populations; Tribal-clan structure
Authors: M. Zhabagin1,2, Z. Sabitov3, H. Dibirova4, E. Balanovska4, I. Zakharov2, O. Balanovsky2; 1Center for Life Sciences, Nazarbayev University, Astana, Kazakhstan, 2Vavilov Institute of General Genetics RAS, Moscow, Russian Federation, 3Gumilyov Eurasian National University, Astana, Kazakhstan, 4Research Centre of Medical Genetics RAMS, Moscow, Russian Federation.

Abstract: The characteristic feature of the Kazakh nomadic society was the presence of a hierarchically organized and widely branched tribal-clan structure called “Shezhire”, which reflected complex system of ethno-social organization. In the context of the Shezhire, Kazakh populations are divided into three ethno-territorial association of tribes called "Zhuz" (Great, Middle, and Small Zhuzes) and a group of aristocratic tribes (Tore, Kozha, Sunak).

This study aims to compare Y-chromosomal polymorphism of three Kazakh Zhuzs and group of aristocratic tribes (total sample size N= 1407). We analyzed 40 SNP and 17 STR Y-chromosomal markers. Summary statistics were calculated using Arlequin 3.5. Neighbor-joining tree was constructed by the program MEGA 5.0. Multidimensional scaling plot was drawn by the software package Statistica v.7.1.

Population pairwise FST values were calculated from the Y-chromosomal haplogroup frequencies to assess the genetic similarity among studied groups of Kazakh tribes. The most distant ones were the tribe of Sunak and the Small Zhuz (0.393), whereas the shortest distance was found between the tribe of Tore and the Great Zhuz (0,021). These genetic distances are associated with the geographic distances between studied populations. The distribution of Y-chromosomal haplogroups is strongly correlated with the tribal-clan structure of Kazakhs. Presence of certain haplogroups at high frequency at particular tribes is in favor to the hypothesis that many tribes go back to one biological founder, confirming the link between Kazakh family tree Shezhire with the genetic composition.

"New" R1a1 SNPs

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

Despite the limited data available for Z280 and Z93, some general inferences can be drawn from the geographic distributions of these two haplogroups. The R1a1- Z280 subclade is a strong candidate for covering the R1a1a* (xM458) in Eastern Europe, which was found in high frequency by Underhill et al. (2010).The tested set of 53 Malaysian Indian samples presented 100% frequency for the R1a1-Z93 subclade, without co-existence Z280 or M458 sub-haplogroups. Inner and Central Asia seem to be the overlap zones for the R1a1-Z280 and R1a1-Z93 chromosomes as both forms were observed at low frequencies. This is again consistent with the observations described for R1a1a* spread in Central Asia and in the Altai region by Underhill et al. (2010). This pattern suggests that the origin of R1a1-M198 arguably occurred somewhere between South Asia and Eastern Europe. Potential candidates could be the Eurasian Steppes (Ukraine – Southern Russia – Kazakhstan – Caucasus) or the Middle East. European populations showed higher M458 and Z280, whereas Asian populations presented higher Z93 frequencies, indicating that the new markers can be effectively used to distinguish between the European and Asian branches of the haplogroup R1a1-M198. [. . .]

The coalescent time calculated by us for R1a1-M458 carriers is consistent with the age calculated by Underhill et al. (2010) in Europe yielding 7.3 KYA versus 7.9 KYA (thousands of years ago). Underhill et al. (2010) also noted the potential association of R1a1-M458 with the Linear Pottery Neolithic culture in the territory of present-day Hungary—this observation is supported by our data. The TMRCA calculated for R1a1-Z280 diversification (10.3 KYA) is approximately in agreement with the estimation of Underhill et al. (2010) for R1a1a*(xM458) chromosomes in Eastern Europe ( 11 KYA). However, the coalescent age of 10.3 KYA for R1a1- Z93 chromosomes in this study is lower than that of populations of the Indus Valley (14 KYA) for the STR associated diversity of R1a1a*(xM458) chromosomes calculated by Underhill et al. (2010).

Of course, these markers and other markers defining additional layers of structure under M417 have been known for over a year. Budgetary constraints and the magic of peer review combine to render this paper relatively uninformative. One of the authors explains:

I have to agree with all, but those who never tried to push an article through a serious academic journal has no idea how difficult this is. The first version was submitted like 1 year ago, and also contained pedigree rates plus 500+ FTDNA samples from different ethnic groups. But unfortunately the reviewers were so narrow-minded that we had finally to drop all FTDNA samples plus the pedigree calcs.

Personally I also do not consider Zhiv. rate valid, but I had to accept this compromise to get the paper accepted. Anyway, as Lukasz pointed out, the main goal was to introduce Z93 and Z280 into the "academic circles" so in the future we may have a comprehensive paper from a more wealthy lab. The Budapest forensics are not full of money so we had no chance to have more than 12 markers tested and "low-chance SNPs" like Z284 in Hungary. Actually we submitted the first draft before Z283 was established securely on the FTDNA tree so we could not include it later...

My comments from last year on the dna-forums postings of an Underhill(lab that brought us Zhivotovsky "evolutionary" mutation rates)-affiliated academic stand:

Another poster points out: "Dividing by 3 [to bring the estimate more in line with real mutation rates] gives an age of 3300 years, almost exactly the estimate from Nordtvedt's spreadsheet." Someone else recently estimated the TMRCA for L342.2+ at around 3,600 years. So: if current patterns hold, the bulk of South Asian R1a unambiguously falls within European R1a variation. While I fully expect, when we eventually see results for these markers in large academic samples published, the papers will feature evolutionary mutation rates and less than parsimonious attempts to fit the distribution of M417 sublineages to archaeology, it's pretty clear to me Z93 and L342.2 originated on the Steppe within the past 4000 years or so and spread with Indo-Iranian.

Again: the most straightforward interpretation of the evidence is that Z93 is a relatively young branch of an evidently European lineage. Accurate, unbiased dates using SNPs instead of STRs should be here soon enough, definitively settling this and other issues.

Victor Mair talk on Tarim Basin Mummies

Part of a series of lectures related to the "Secrets of the Silk Road" exhibition at the University of Pennsylvania Museum of Archaeology and Anthropology. The mummy and artifacts abruptly pulled from the exhibition by the Chinese government before it opened are back for now.

Two old papers on Tarim Basin mummies / crania

Now available online at the Sino-Platonic Papers website.

Dolkun Kamberi, "The Three Thousand Year Old Charchan Man" Sino-Platonic Papers, 44 (January, 1994)

The male would have been two meters tall when living (see color plates I and IIa); the corpse was lying on its right side with legs bent and propped up by a small piece of wood (perhaps to promote preservation by means of circulation of air around the corpse). The hair, eyelashes, beard and chest hair were intact and traces of makeup (ocher spiral sun-symbols) could be seen on the face. The presence in the tomb of two small bone spoons with dried ocher pigment in them may indicate that the makeup was applied after death. The male's head hair was yellowish brown half gone to white;

Note: More recent estimates put Cherchen Man's height closer to 5'9".

HAN Kangxin: "The Study of Ancient Human Skeletons from Xinjiang, China" Sino-Platonic Papers, 5 1 (November, 1994)

Between 1920 and 1940, only three foreign scientists published completed research in this area. They are: Arthur Keith of England (1929), Carl-Herman Hjortsjo and Ander Walander of Germany (1924) and A.N. Iuzefovich of the USSR (1949). A total of twenty skulls were described. Five came from the northern part of the Taklamakan Desert and Keith thought they characterized the "Loulan racial type." Eleven skulls were collected by Sven Hedin from near Luobubo (Lopnor) in 1928 and 1934, and have been subdivided into three groups (Nordic, Chinese, and Alpine) by Hjortsjo and Walander. The remaining skulls also came from the Luobubo (Lopnor) area and exhibit Mongoloid characteristics. Iuzefovich considered these to be of Tujue (Turkish) origin (Keith, A., 1929; Hjortsjo, C.H. and A. Walander, 1942; Iusefovich, A.N., 1949). [. . .]

Chinese scientists have conducted systematic excavations in this region since 1940. I have studied all the skeletal material housed at the Institute of Archeology of Xinjiang and analyzed the physical and racial characteristics of these human bones. The materials included about 274 skulls which were collected from nine ancient cemeteries in Xinjiang. The cemeteries range in age from about 1800 B.C.E. to 300 C.E.

Ancient DNA from Small River Cemetery Number 5

Someone asked about the reference to Siberian admixture in the NYT article on Ordek's necropolis. According to the paper reporting the DNA results, the majority of individuals tested belonged to a branch of haplogroup C4 that shows some similarities to one found among "Evenks and Udegeys of southeastern Siberia". Other mtDNA lineages detected include H and K. All Y chromosomes tested belonged to haplogroup R1a1a.

The shared sequences of the Xiaohe C haplotype (S1) were distributed in southeastern Siberia. It implies that the east Eurasian component in the Xiaohe people originated from the Siberian populations, especially the southern or eastern Siberian populations.

The mtDNA haplogroup H is the most common mtDNA haplogroup in Europe, especially in northwestern Europe, and its frequency can be as high as 65% in Iberia. Frequencies gradually decrease from the northwest to the southeast of Europe. By contrast, the frequency of haplogroup H rises to only 20% in the Near East, and to less than10% in Central Asia, and is very low in East Asia [33,34]. All of the shared sequences of the Xiaohe H haplotype, however, were distributed in Western Europe. Haplogroup K is also common in Europe, particularly around the Alps and the British Isles. It is found with less frequency in North Africa, the Middle East, and South Asia [21,35-37]. Considering the presence of haplogroups H and K in the Xiaohe people and the geographical distribution of shared sequences, we conclude that the west Eurasian component observed in the Xiaohe people originated from western European, and maternal ancestry of the Xiaohe people might have close relationship with western European.

Regarding the Y chromosomal DNA analyses, the seven males identified all belonged to haplogroup R1a1a. It is most frequently found in Eastern Europe, South Asia and Siberia. In contrast, it is relatively uncommon in Middle Easterners and rare in East Asian [22-24]. It is thought to be a trace of the migration events of early Indo-European [38,39]. The presence of haplogroup R1a1a in the ancient Xiaohe people implies that the parental ancestry of the Xiaohe people originated from somewhere in Siberia or Europe, which is consistent with the origin of maternal ancestry.

[Chunxiang Li et al. Evidence that a West-East admixed population lived in the Tarim Basin as early as the early Bronze Age. BMC Biology 2010, 8:15doi:10.1186/1741-7007-8-15.]

Small River Cemetery Number 5

A New York Times article from last month on Ördek's Necropolis:

All the men who were analyzed had a Y chromosome that is now mostly found in Eastern Europe, Central Asia and Siberia, but rarely in China. The mitochondrial DNA, which passes down the female line, consisted of a lineage from Siberia and two that are common in Europe. Since both the Y chromosome and the mitochondrial DNA lineages are ancient, Dr. Zhou and his team conclude the European and Siberian populations probably intermarried before entering the Tarim Basin some 4,000 years ago.

The Small River Cemetery was rediscovered in 1934 by the Swedish archaeologist Folke Bergman and then forgotten for 66 years until relocated through GPS navigation by a Chinese expedition. Archaeologists began excavating it from 2003 to 2005. Their reports have been translated and summarized by Victor H. Mair, a professor of Chinese at the University of Pennsylvania and an expert in the prehistory of the Tarim Basin. [. . .]

Several items in the Small River Cemetery burials resemble artifacts or customs familiar in Europe, Dr. Mair noted. Boat burials were common among the Vikings. String skirts and phallic symbols have been found in Bronze Age burials of Northern Europe.

Folke Bergman's 1939 report, Archaeological Researches in Sinkiang, is available online at the Digital Archive of Toyo Bunko Rare Books, along with expedition records from Sven Hedin, Aurel Stein, and others. Ördek was Sven Hedin's Turkish servant, who after being inspired by what he saw working for Hedin discovered the cemetery on a tomb robbing expedition in search of buried treasure. From Bergman:

STEIN emphasizes the non-Mongolian features of the Lop-nor mummies, and I have been able, on the whole, to confirm his statement. One or two of the mummified heads at Cemetery 5 had, however, broad cheek-bones giving them a "Mongolian" look, but this might be due to the individual variations that occur in every race or type

Cochran/Harpending on Proto-Indo-European expansion

Their book (The 10,000 Year Explosion: How Civilization Accelerated Human Evolution) hasn't yet been released, but much of it is now readable on Google Books. Here is Cochran and Harpending's take on the spread of Indo-European:

Milk and the Kurgans

Improved variants of the Kurgan hypotheses fit many facts, but what they don't do is explain why the Proto-Indo-Europeans expanded at the expense of neighboring peoples [. . .]

We suggest that the advantage driving those Indo-European expansions was biological--a high frequency of the European lactose-tolerance mutation (the 13910-T allele). The usual story about lactose tolerance is that it's the result of a cultural innovation, the domestication of cattle. That innovation led to selection for a new mutation that extended lactase production into adulthood. But there's more to the story.

Initially, selection favored individual carriers of the lactose-tolerance mutation, but the mutation was rare and had little social effect. Cattle were used for plowing and pulling wagons, for their beef, and as a source of secondary products like leather and tallow. But when the lactase persistence allele became common, so that a majority of the adult population could drink milk, a new kind of pastoralism became possible, one in which people kept cattle primarily for their milk rather than for their flesh. This change is very significant, because dairying is much more efficient than raising cattle for slaughter: It produces about five times as many calories per acre. Dairying pastoralists produce more high-quality food on the same amount of land than nondairy pastoralists, so higher frequencies of lactose tolerance among Indo-Europeans would have caused the carrying capacity of land to increase--for them.

Standard ecological theory indicates that when two similar populations use the same resources, the one with the greater carrying capacity always wins. In more familiar terms, the Proto-Indo-Europeans in our scenario could raise and feed more warriors on the same amount of land--and that is a recipe for expansion. The same basic idea is behind theories of the expansion of farming through local population growth (called demic expansion): Farming produces more food per acre, therefore farmers will outnumber foragers, and so farmers will expand at the expense of foragers.

Proto-Indo-Europeans probably were most competitive in areas where grain agriculture was marginal. In the steppe, the problem was limited rainfall. Since raising cattle there had been competitive with grain farming even before dairying arose, milk-drinking Indo-Europeans would have had an absolute advantage and should have spread rapidly over the steppe. In much of northern Europe, shorter growing seasons must have interfered with production of cereal crops such as wheat, particularly when agriculture was new there, as those crops had had little time to adapt to the local climate. Eventually, other cereal crops, such as oats and rye that could do well in those climates, were developed--probably by accident, starting as weeds in wheat or barley fields. But that happened in the Bronze Age, long after the introduction of farming. Dairying may have been more productive than grain farming in northern Europe during the late Neolithic. Even if it was not, it may have been close enough to let other advantages of the pastoral way of life tip the scales. It seems clear that the Proto-Indo-European form of patoralism did have other advantages in intergroup competition.

As the Proto-Indo-Europeans became dairymen, they should have come to rely more and more on their cattle and less on grain farming. As that happened, they would have become mobile, which is a military advantage, especially against farmers. Farmers have homes and villages that they must defend, whereas pastoralists can fight at a time and place of their choosing.

[. . .]

Back in the early days of their expansion, the Indo-Europeans appear to have encountered farmers in the Balkans who had been farming since about 6000 BC, but who weren't under a powerful central government. Around 4200 BC, things went sour. Ancient village sites were abandoned, advanced work in metals and ceramics became rare, and the inhabitants shifted to easily defended sites such as caves, hilltops, and islands. We find an increasing number of Kurgan burials similar to those found earlier on the steppe. (Interestingly, the bodies in those Kurgan burials averaged almost four inches taller than the earlier peoples of the region--milk does a body good.)

We suspect that pre-state farmers had a lot of trouble with invading Indo-European pastoralists. It wasn't just that dairying was productive and conferred increased mobility. It made cattle very valuable, and cattle are far easier to steal than heaps of grain: They can walk. It looks as if the early Indo-Europeans spent a lot of time rustling each other's cattle, fighting over cattle, planning revenge for previous raids, and in general raising hell. They became a warrior society.

So far, so plausible. Now it starts to get a bit pat.

European languages and culture spread past those regions in which dairying was favored--for example, into southern Europe and Iran--but strong states probably limited their expansion into the Middle East.

As much as anything, those peripheral expansions were probably driven by what might be called historical momentum: Peoples with a long record of success in war and raiding kept expanding even in areas where they had no special ecological advantages. Something similar happened when the Indo-Aryans moved into India: Internal weakness, possibly even collapse, of the Indus civilization may have allowed that expansion to occur.

In Understanding Human History (pdf), Michael Hart attributes conquests of more southerly peoples by Indo-Europeans to higher intelligence among the latter, which, while it may not be a complete explanation, I find more compelling than "historical momentum". Continuing:

Today the LCT 13910-T variant has reached almost 100 percent frequency in some parts of northern Europe; it is common in northern India and can even be found at low levels among some pastoral peoples of sub-Saharan Africa, such as the Fulani and Hausa.

Moreover, there is reason to think that this historical phenomenon has happened at least three times. Cattle herders of East Africa in the region of the Upper Nile and further south are lactase-tolerant[sic] milk drinkers dure to a younger mutation of their own. They, too, have expanded: They have become warlike, and there are fascinating parallels between their religions and social structure and those of the ancestral Indo-Europeans. Another separate pair of mutations causing lactose tolerance happened in the Arabian peninsula, driven in this case by the domestication of camels. This may have been an important cause of the explosive growth of Islam and the Arab conquests of the sevention century AD and later.

Ancient Mongolian mtDNA

I'd be more interested in Y-DNA results from the same time and place, which might help support or refute the "Genghis Khan" Y signature claim. The unsurprising presence of European morphological features in some skeletons is perhaps attributable to admixture by Iranian speakers, which would also likely be detected in a Y-DNA analysis.

American Journal of Physical Anthropology; Published Online: 25 Jul 2008

Ancient DNA analysis of human remains from the upper capital city of Kublai Khan

Yuqin Fu et al.

Keywords
ancient DNA • mitochondrial DNA • human origins • China

Abstract
Analysis of DNA from human archaeological remains is a powerful tool for reconstructing ancient events in human history. To help understand the origin of the inhabitants of Kublai Khan's Upper Capital in Inner Mongolia, we analyzed mitochondrial DNA (mtDNA) polymorphisms in 21 ancient individuals buried in the Zhenzishan cemetery of the Upper Capital. MtDNA coding and noncoding region polymorphisms identified in the ancient individuals were characteristic of the Asian mtDNA haplogroups A, B, N9a, C, D, Z, M7b, and M. Phylogenetic analysis of the ancient mtDNA sequences, and comparison with extant reference populations, revealed that the maternal lineages of the population buried in the Zhenzishan cemetery are of Asian origin and typical of present-day Han Chinese, despite the presence of typical European morphological features in several of the skeletons. Am J Phys Anthropol, 2008. © 2008 Wiley-Liss, Inc.

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