Incipient Mongoloids (or elusive Denisovans) 105-125kya in China?

The authors claim that these archaic humans from China show parallels to both modern eastern Eurasians (Mongoloids) and to Neandertals. The relationship with the Neandertals makes them prime candidates for the elusive Denisovans who were a sister group to Neandertals but are morphologically unknown (since all we've got is a genome, teeth, and a pinky). The relationship with Mongoloids suggest an appearance of Mongoloid morphology pre-dating the transition to sapiens, and brings to mind past claims about incipient Caucasoid morphology in Neandertals. Did aspects of modern Eurasian morphology originate in pre-sapiens archaic Eurasians? Hopefully someone's studying DNA from these crania as we speak.

Science 03 Mar 2017: Vol. 355, Issue 6328, pp. 969-972 DOI: 10.1126/science.aal2482

Late Pleistocene archaic human crania from Xuchang, China 

Zhan-Yang Li et al.

Two early Late Pleistocene (~105,000- to 125,000-year-old) crania from Lingjing, Xuchang, China, exhibit a morphological mosaic with differences from and similarities to their western contemporaries. They share pan–Old World trends in encephalization and in supraorbital, neurocranial vault, and nuchal gracilization. They reflect eastern Eurasian ancestry in having low, sagittally flat, and inferiorly broad neurocrania. They share occipital (suprainiac and nuchal torus) and temporal labyrinthine (semicircular canal) morphology with the Neandertals. This morphological combination reflects Pleistocene human evolutionary patterns in general biology, as well as both regional continuity and interregional population dynamics.

Link

East Eurasian-like ancestry in Northern Europe (part 3)

(This is the third part of the series. See part 1 and part 2.)

In the first two parts of the series, I showed that northern European populations show hints of East Eurasian ancestry when compared against Sardinians. I used Dai, Han, and Karitiana as reference populations for East Eurasia. In the current post, I extend this analysis by using HGDP Papuans and the Onge (Reich et al. 2009) from the Andaman Islands.

The f4 statistics using Karitiana, Papuan, and Onge populations can be found in this spreadsheet.

Below, you can see that they are all near perfectly correlated with each other.

The visual appraisal is confirmed when we calculate the correlation coefficients:

The fact that all three populations track the same signal is strong evidence for the direction of gene flow: from Asia into northern Europe. If the signal was present in only one of the three populations, then it could conceivably be an artefact of gene flow in the opposite direction (from northern Europeans to the affected population). But, the fact that all three populations show the same pattern would require northern European-like admixture in the Andaman Islands, Papuan New Guinea and South America, which does not appear very parsimonious.

While the signals from the three populations are correlated, their intensity varies. The Z-scores provide a measure of this intensity. The mean Z-scores using a Karitiana, Papuan, and Onge reference across all populations are respectively -17.7, -8.0, and -6.0.

While I did not include the Han reference of part 1 in this analysis, inspection of the f4 statistics (which can be obtained at the bottom of that part), suggests that the Z-scores become more significant when using an Onge, Papuan, Han, and Karitiana reference in that order. For example, for the Finnish_D population, they are: -10.037, -13.2949, -23.9305, and -27.764 respectively.

It thus appears that the element contributing East Eurasian-like ancestry in northern Europeans was derived from the northern spectrum of East Eurasians; the Karitiana may live in South America today, but they trace their ancestors to northern Eurasia, having entered the Americas c. 15ka.

In my opinion, the signal has been formed by a superposition of a few factors:

1. The fact that Y-haplogroup R, the main lineage in modern northern Europeans has a common origin (Y-haplogroup P) with haplogroup Q, the main lineage in modern Amerindians, and many Siberians. We can hypothesize that the population that brought R into Europe was intermediate genetically across the Caucasoid-Mongoloid spectrum. In West Eurasia, this population admixed with the Palaeo-West Eurasians (Y-haplogroups IJ, G, and possibly LT), and contributed their DNA primarily to the northern Europeoids.
2. Other population movements of more regional impact, such as Y-haplogroup N, which affected mainly Uralic, Baltic, and East Slavic populations, as well as elements from the mixed West/East Eurasian mtDNA contact zone that ancient DNA analysis has revealed in Eastern Europe and Siberia.

The raw dumps of fourpop output for Papuan and Onge reference can be found here.

East Eurasian-like admixture in Northern Europe (part 2)

This is a continuation of my earlier post. Please refer to it for the methodology. A new part 3 can be found here.

I have repeated the experiment with a much larger set of populations:

English_D, British_D, Ukranians_Y,  Karitiana, Spaniards, Sardinian,  Serb_D, Mordovians_Y, Irish_D,  French, Finnish_D, Chuvashs_16,  Romanian_D, N_Italian_D, French_Basque,  Austrian_D, Russian_D, Hungarians_19,  Kent_1KG, German_D, Belorussian,  Tuscan, Lithuanian_D, Orkney_1KG,  Dutch_D, TSI30, Ukrainian_D,  Bulgarians_Y, Bulgarian_D, Russian,  Swedish_D, Pais_Vasco_1KG, French_D,  Castilla_Y_Leon_1KG, Lithuanians, San,  Polish_D, Romanians_14, Orcadian,  Cornwall_1KG, Valencia_1KG, North_Italian,  FIN30, Norwegian_D, CEU30

I used Sardinians as the Caucasoid reference population, Karitiana for Mongoloids, and San for Africans. The latter two were chosen because they live at maximally opposite corners of the Earth (South America vs. South Africa).

A first plot of the f4 statistics used for f4 regression ancestry estimation is seen below:

Clearly, some evidence of a cline is present, but several populations appear to deviate from it. In order to get the cleanest possible cline, I carried out the following greedy procedure: I calculate the correlation coefficient of this set, and iteratively remove one population that leads to the maximum improvement of the correlation, until no further improvement takes place. The following populations were removed with this procedure:

Spaniards, Serb_D, Romanian_D, N_Italian_D, Tuscan, TSI30, Bulgarians_Y, Bulgarian_D, Castilla_Y_Leon_1KG, Romanians_14, Valencia_1KG

This seems to make sense, as all these are southern European populations. Note that their removal does not mean that they do not partake in the same phenomenon as northern Europeans: they also exhibit Karitiana-shift relative to the Sardinians, but there are probably other confounding factors that make them fall "off-cline". Including them would diminish the clarity of the cline for Northern European populations. The regression of the remaining populations can be seen on the right:

f4 regression ancestry estimation results are shown on the left. These appear to be much higher than was the case with the Han and Dai in the previous experiment.

I can't say that I've made any obvious mistakes, but these admixture proportions are substantial, and call for an explanation. Whatever their true levels, I am fairly confident on at least a few points:

First, it is evident that northern Europeans have higher levels of this element than southern Europeans; the latter are not altogether deficient in it, but they fall "off-cline", making estimation of their admixture proportions more difficult.

Second, within northern Europe, there is a fairly clear east-west cline of diminishing Amerasian-like admixture. The minimum occurs in Sardinians and secondarily in Southwest Europe. Romance, Celtic, and Germanic populations all have less of it than Balto-Slavic and Uralic ones. And, some populations of northeastern Europe seem to have a noticeable excess of it.

The groups with the most Amerasian-like admixture possess Y-haplogroup N, a clear trace of eastern ancestry that is not shared by most Europeans. The arrival of this haplogroup, either with Comb Ceramic of the Baltic Neolithic or later with Seima Turbino Bronze Age expansions is probably responsible for the local excess in Northeastern Europe. The Chuvash are, of course, a Turkic population but of Finno-Ugrian genetic origin.

But, the presence of this element even in Western Europe cannot be explained on the basis of typically Mongoloid elements which are almost completely lacking there. If Mesolithic Europeans were themselves Asian-shifted, then this would account for the presence of the element, but not necessarily for its clinal manifestation. The double (north-south and east-west) cline indicates every sign of an intrusive element. So, for the time being, I will propose that this is associated with late (e.g., Copper and Bronze Age) phenomena, such as the northern stream of the Bronze Age Indo-European invasion of Europe.

This may be due to the

• (i) northern Indo-European groups picking up some native east European or Siberian elements as they made their way into Europe, 
• or (ii), more likely, in my opinion, that the Y-haplogroup R1 group of people, whose closest relatives are in Central/South Asia (R2) , and whose more distant relatives (Q) are in Siberia and the Americas, were from the beginning an "intermediate population" between West and East Eurasia. The R1 group of people in its R1b and R1a varieties first appear in Europe during the Copper Age, and they are lacking in early Neolithic sites.

Eight years ago, and in a totally different context, I wrote:

Similarly, 9 out of 10 Basques are descended from a man who has also fathered 9 out of 10 Kets from Siberia and 9 out of 10 Maya Indians from America. That man, founder of haplogroup P thus has descendants who belong to two of the major human races (or three, if Amerindians are considered as separate from Asian Mongoloids)   

... 

In conclusion, human continental populations form groups of genetic and phenotypic similarity, and these groups can be considered races in the phenetic sense. However, these groups are not monophyletic, hence in the cladistic sense they should not be considered as valid taxa. Since the principle of common descent is generally applied in modern systematics (or at least it should!), I think it's best not to recognize human subspecies. 

If these data pan out, it may be revealed that the European branch of the Caucasoids is actually a product of admixture too, with at least two of its constituent elements being the "Palaeo-West Eurasians" (Y-haplogroups G, IJ, possibly LT) and the "Neo-NW Eurasians" (Y-haplogroups N1 and R1), with the "Neo-Afrasians" (Y-haplogroup E1b1b) forming a third element.

(A raw dump of fourpop output can be found here).

4-population test and East Eurasian-like ancestry in Northern Europe

Update: This is the first part of my discussion on the topic. For part 2 go here; for part 3 here.

I decided to follow up on a hint in the recent Reich et al. (2012) paper on Native Americans to the effect that:

... east/central Asian admixture has affected northern Europeans to a greater extent than Sardinians (in our separate manuscript in submission, we show that this is a result of the different amounts of central/east Asian-related gene flow into these groups).

 I used the implementation of the 4-population test of Reich et al. (2009) in the fourpop program of  TreeMix. 255,020 SNPs common in the various datasets were used throughout, and blocks of 200 SNPs for standard error estimation.

I used HGDP Sardinian, X, Han, San, with X being one of the following:

Armenian_D, Turkish_D, Russian_D, Polish_D, German_D, Irish_D, Greek_D, Finnish_D, Sicilian_D, Swedish_D, Portuguese_D, Lithuanian_D, Somali_D, AMHARA_Pa, Dai, Japanese, Kyrgyz_Bishkek_Ho, Mozabite, Bedouin, North_Italian, French_Basque, Tuscan, Russian, Orkney_1KG, Kent_1KG, Cornwall_1KG, Yoruba, Mbuti_Pygmies

As always, you can find a list of population sources at the bottom of the Dodecad blog.

As I have noted in my review of Moorjani et al., this test shows a superposition of a set of populations on the African-East Asian axis, so populations occupy different positions depending on whether they have African or East Asian admixture. It's a palimpsest. That paper ignored the Eastern ancestry in North Europeans, and used the CEU (a population of mainly North European origin) instead of Sardinians, hence generating inflated estimates of African ancestry in Southern Europeans.

Now that the Central/East Asian ancestry in northern Europeans seems to be recognized by some of the co-authors of the earlier paper, and using the Reich et al. (2012) framework, the different processes superimposed on the African-East Asian axis can probably be disentangled. Hopefully, we won't have to wait too long for the full treatment. Maybe it can go to the arXiv too!

In any case, here are the f4(Sardinian, X; Han, San) values for the different populations:

It is quite clear that North European populations are shifted towards East Asians, with the exception of the Turkish_D sample which is also so shifted, due to its Central Asian Turkic admixture. There are also a few cases of substantial African shift, such as the Bedouin and Mozabite Berbers.

I have also rescaled the f4 statistics on a 0: Sardinian to 100: Japanese scale, including only West Eurasian populations that are East Asian-shifted relative to Sardinians:

I have calculated the correlation coefficient between the f4 statistics for this set of West_Eurasian populations and the sum of the Siberian+East Asian components of my K7b calculator on the same set of populations. This is +0.85, highly significant, and consistent with the idea that ADMIXTURE software and formal tests of admixture capture the same phenomenon. I also calculated the correlation coefficient with the Atlantic_Baltic component that is modal in Europeans, which is equal to +0.56 and confirms the higher East Eurasian shift in  European populations.

(I have also repeated the above with the K12b calculator; the correlation between the f4 statistics and the Siberian+East Asian+Southeast Asian components is +0.76, and the North_European +0.84. The latter is higher than with the Atlantic_Baltic component (+0.56) which combines North and West European ancestry. It thus appears that the East Eurasian admixture in Europe is not a general feature of the oldest Europeans, but reflects a more recent phenomenon.)

Furthermore, I have carried out f4 regression ancestry estimation (Reich et al. 2009) using the f4(Sardinian, San; X, Han), in the horizontal axis, and f4(Sardinian, X; San, Han) statistics, in the vertical. An initial plot shows that while northern Europeans fall precisely on a line in this space, Turks and Armenians deviate substantially, while Greeks, Tuscans, and Basques less noticeably so:

The regression analysis shows a weak correlation (R^2=0.149). The southern Caucasoid populations from Armenia to Iberia appear roughly perpendicular to the north European cline, suggesting that they do not significantly partake in the same phenomenon as the northern groups.

I thus limited myself to the European populations falling on the Russian to North_Italian cline, which form a near-perfect cline (R^2= 0.9783)

Admixture estimation was performed on the triangle whose three corners were (from the regression equation):

LOW: (0.0151411, 0.0000000)
HIGH: (0.00000, 0.02049)

and

TEST: the f4 statistics for each test population

Inferred admixture proportions using this method can be seen below:

I have repeated the above experiment using French_Basque instead of Sardinian, Mbuti instead of San, and Dai instead of Han:

Now, North_Italian shows no East-Eurasian-like admixture relative to French Basque, so there is one less row. The Basques appear to be Asian-shifted relative to Sardinians, so, overall, I would trust the former results more than the latter, but, in any case, the overall pattern seems fairly solid across a choice of reference populations.

While I would not take these results very literally in the absolute sense, I think they show quite well the relative ordering of populations, and are consistent with both my initial observation...

With respect to the Asian- and African- shift of West Eurasian populations, I note that northern Europeans (and Basques) are less African-shifted than southern Europeans, and, at the same time they are more Asian-shifted: the 16 least Asian-shifted populations have a coastline in the Mediterranean (excluding the Portuguese), while the 16 least African-shifted populations do not (excluding the French).

... as well as the remark in passim in the Reich et al. (2012) supplementary material mentioned above.

The prominent position that Sardinians have assumed in the genetic history of Europe puts the discovery of Veeramah et al. that Sardinians tend to be monomorphic in sites where mainland Europeans are polymorphic into new light. It now appears that the reduced genetic polymorphism of Sardinians vis a vis mainland Europeans may not be due to them having undergone a "bottleneck" relative to mainland Europeans, but rather, at least in part, a consequence of admixture in the latter. Admixture matters.

Hopefully, geneticists will become more willing to interpret patterns of decrasing genetic diversity not only as a consequence of diversity-reducing "bottlenecks", but also of admixture in populations that are especially diverse.

In the case of Sardinians and Europeans we have been lucky in that East Asians continue to exist, helping us untangle their (or their relatives') contribution to the population history of Europe. But, in other cases (such as the introgression of archaic DNA into the modern human gene pool), latent population admixture between divergent populations may lead to misinterpretations of the direction of gene flow.

 The raw dump of fourpop output can be obtained from here (for Sardinian-Han-San) and here (for Basque-Mbuti-Dai).

East Eurasian and African fastIBD analyses

Posted over at the Dodecad blog:

• fastIBD analysis of Africans and African Americans 
• fastIBD analysis of East/Central Eurasians and select West Eurasians

5,300-year-old Mongolian statue

5,300-year-old Mongolian statue pieced back together

ARCHAEOLOGISTS of the Chinese Academy of Social Sciences have finished reconstructing a 5,300-year-old pottery statue from fragments unearthed in North China’s Inner Mongolia Autonomous Region, it was announced Saturday. 

The debris of the pottery statue were found at the Xinglonggou relics site in Aohan Banner of Chifeng City in May. 

Experts began to excavate the debris June 30, and finished restoring the statue on Friday, said Liu Guoxiang, leader of the first archaeology team of Inner Mongolia. 

The restored seated figure is 55cm high with bulging eyes, a high nose and vivid facial expression. It was pieced together from 65 fragments. 

“The statue may be of a wizard or leader in the famous Hongshan Culture period (a Neolithic culture dating back 5,000-6,000 years),” added Liu.

Hints of East/Central Asian admixture in Northern Europe

A little more than a year ago, I noticed an interesting pattern in North Europeans: they all tended to be shifted towards East Asians in PCA plots:

With respect to the Asian- and African- shift of West Eurasian populations, I note that northern Europeans (and Basques) are less African-shifted than southern Europeans, and, at the same time they are more Asian-shifted: the 16 least Asian-shifted populations have a coastline in the Mediterranean (excluding the Portuguese), while the 16 least African-shifted populations do not (excluding the French).

The same pattern could also be observed in the arrangement of the ancestral components inferred by the Dodecad Project. The "Atlantic_Baltic" component, which is modal in Northern Europeans, exhibits lowered genetic divergences to the East Eurasian components (Siberian / East_Asian) relative to the "Southern" component which is modal (in Europe) in Southern Europeans.

The fact that Southern European populations were shifted towards the African side relative to Northern European ones across an African-Asian projection, was interpreted by Moorjani et al. (2011) as evidence of African admixture. As I noted at the time, this entailed the assumption that Northern European populations did not have East Asian admixture, which would also produce the observed pattern:

However, this is clearly a case of seeing the glass half full. The authors prefer the hypothesis that some Caucasoid groups have African ancestry, although the hypothesis that other Caucasoid groups have East Asian ancestry can equally well explain the observed pattern. Indeed, both hypotheses may explain the phenomenon they observe.

It now appears that some of the co-authors of the above paper have realised this, and have detected Central/East Asian admixture in northern Europeans. Writing in the supplement of the recent Reich et al. (2012) paper, we read this important aside:

A complication in computing this statistic is that Native American, Siberian, and East Asian  populations are not all equally genetically related to West Eurasian populations, as we can  see empirically from 4 Population Tests of the proposed tree (Yoruba, (French, (East Asian,  Native American))) failing dramatically whether the East Asian population is Han, Chukchi,  Naukan and Koryak. The explanation for this is outside the scope of this study (it has to do  with admixture events in Europe, as we explain in another paper in submission). In practice,  however, it means that we cannot simply use a European population like French to represent  West Eurasians in Equation S3.2, since if we do this, Equation S3.2 may have a non-zero  value for a Native American population, even without recent European admixture.    

To address this complication, we took advantage of the fact that east/central Asian admixture  has affected northern Europeans to a greater extent than Sardinians (in our separate  manuscript in submission, we show that this is a result of the different amounts of central/east  Asian-related gene flow into these groups). To quantify this, we computed the statistic f4(San,  West Eurasian; Pop1, Pop2) for West Eurasian = Sardinian and West Eurasian = French,  and for 24 Siberian and Native American populations (Pop1 and Pop2) (Figure S3.2). Figure  S3.2 shows a scatterplot for all 190=20?19/2 possible pairs of these populations. Within nonArctic Native populations, and within Arctic populations (East Greenland Inuit, Chukchi,  Naukan and Koryak), the statistics are close to zero, consistent with their being (approximate)  clades relative to West Eurasians. In contrast, there are deviations from zero when the comparisons are between non-Arctic Native and Arctic populations, with non-Arctic Native  populations showing consistent evidence of being genetically closer to West Eurasians.   

David Reich has hinted about ancient admixture in Europeans before, and is apparently working on the South Asian admixture event. It would appear that the new works might be using the newer techniques employed in the Reich et al (2012) paper, which allows one to consider multiple admixture events rather than the more simple ones of Reich et al. (2009) and Moorjani et al. (2011) that considered only two ancestral populations.

I will, of course, eagerly wait the publication of the mentioned manuscript, but it appears that this is not the only piece of evidence of gene flow from Central Asia into Europe. In an SMBE 2012 abstract by Palstra et al. we read:

Using an approximate Bayesian framework, we find that present patterns of genetic diversity in Central Asia may be  best explained by a demographic history which combines long-term presence of some ethnic groups (Indo-Iranians)  with a more recent admixed origin of other groups (Turco-Mongols). Interestingly, the results also provide indications  that this region might have genetically influenced Western European populations, rather than vice versa. A further  evaluation in MCMC-based Bayesian analyses of isolation-with-migration models confirms the different times of  establishment of ethnic groups, and suggests gene flow into Central Asia from the east. The results from the  approximate Bayesian and full Bayesian analyses are thus largely congruent. In conclusion, these analyses illustrate  the power of Bayesian inference on genetic data and suggest that the high genetic diversity in Central Asia reflects both  long-term presence and admixture in more recent historical times. 

Neither of these two upcoming pieces of work mention the timing of the Central Asian element in Europe: 

• One possibility is that the Mesolithic Europeans were Asian-shifted themselves. 
• Another one would relate it to the emerging ancient mtDNA picture of deep penetration of Mongoloid elements into west Eurasia at the dawn of history, although the western limit of this penetration has not been conclusively ascertained. 
• Finally, the elements may be a legacy of the Bronze Age Indo-European invasion of Europe, piggy-backing on the spread of the latter from their eastern homeland

In two of the existing models of how the latter event took place (the Armenian plateau hypothesis of Gamkrlidze and Ivanov and the Bactria Sogdiana hypothesis of Johanna Nichols), the Indo-Europeans followed separate streams from their eastern homeland into Europe, with some groups following a path north of the Black and Caspian seas, while others followed a southern path from Anatolia to the Balkans. The northern dispersal route would have brought them into contact with the mixed Caucasoid/Mongoloid population of West Siberia and Eastern Europe, and they may have carried some of this DNA across their sweep over Northern Europe.

My own working hypothesis would derive the earliest Proto-Indo-Europeans with groups living in Neolithic eastern Anatolia and northern Mesopotamia. There are details to be fleshed out, such as when this group of people reached the Balkans (pending ancient DNA from the region), and how they interfaced with the populations living in the north of the Black and Caspian seas (e.g., via a trans-Caucasus movement or a counterclockwise spread around the Caspian).

We will know soon enough how and when Northern Europeans ended up with an extra slice of Central/East Asian ancestry. Things are looking good for our understanding of events in Eurasian prehistory.

Population strata in the West Siberian plain (Baraba forest steppe)

Also from the Population Dynamics in Prehistory and Early History (2012) volume, this is an awesome ancient DNA study which dissects a succession of archaeological cultures stretching from the beginning of the metal ages to the beginning of the Iron Age in a small region of West Siberia. As the authors write:

Our work is devoted to the analysis of human migration processes that occurred during the Bronze Age (4th–early 1st millennium BC) in the forest steppe zone between the Ob and Irtysh rivers (about 800 km from west to east). This area, known as Baraba forest steppe, stretches over 200 km from the taiga zone in the north to the steppes in the south.

The careful examination of the sequence of cultures, combining ancient mtDNA and physical anthropology paints a very compelling picture of the changes that occurred in the span of a few millennia in the Baraba forest steppe. The authors give the map on the left, with the caption: "Fig. 5 | Location of ancient human groups with a high frequency of mtDNA haplogroups U5, U4 and U2e lineages. The area of Northern Eurasian anthropological formation is marked by yellow region on the map (References: 1 Bramanti et al., 2009; 2Malmstrom et al., 2009; 3 Krause et al., 2010; 4 this study)".


The northern Eurasian anthropological formation actually combines eastern and western Eurasian features and may correspond to the Proto-Uralic type. Researchers have clashed about the origins of this population element, with some considering it a third Eurasian race that evolved independently of Caucasoids and Mongoloids, others assigning it to a much diverged branch of one of the two major Eurasian races, and still others considering it the product of admixture between east and west.


All indications are that the type, unlike the Caucasoid-Mongoloid mixtures that took place in Central Asia in the last 2 millennia, is of more ancient vintage, and represents an anthropological element that was indeed of Caucasoid-Mongoloid origins, but in the rather remote past. The authors write with respect to the most ancient periods:

In contrast to the occupation of the southern region of West Siberia, modern humans arrived in the Ob-Irtysh interfluve relatively late, at the end of the Pleistocene, about 13–14 thousand years ago (Okladnikov, Molodin, 1983; Petrin, 1986). The absence of burials dating back to this period in the region does not allow us to conduct a biological investigation of this earliest population. The most ancient anthropological material available is from the Neolithic period (4th–5th millennium BC). 

And, what of the earliest available material?

The anthropological analysis of the material allowed us to detect a specific craniological type in the Baraba population, which was assigned to one of the anthropological formations discovered by V.V. Bunak in 1956 through the analysis of Neolithic materials from the northern forest zone of the East European Plain. Bunak called it the “northern Eurasian anthropological formation” (Bunak, 1956).

This anthropological type developed in a zone that is intermediate to the geographic areas occupied by the classic Caucasoids and the Mongoloids. The exists substantial anthropological evidence showing a wide geographic distribution of this anthropological formation: from the Trans-Urals forest and the Barabian province of Western Siberia in the east to Karelia and the Baltic in the west (Chikisheva, 2010).

The mtDNA evidence seems to support the anthropological assessment:

We have analyzed 18 mtDNA samples from the Ust-Tartas population to date (Fig. 3). The results obtained thus far allow us to draw several preliminary conclusions about the genetic background in the region in the beginning of the Bronze Age. By the Early Metal Period the mtDNA pool structure was already mixed and consisted of both Western and Eastern Eurasian haplogroups in nearly equal proportions. The eastern Eurasian mtDNA cluster was represented by Haplogroups A, C, Z, D, which are most typical of modern and perhaps ancient populations located in the east of the region studied. Haplogroups C and D were predominantly represented by widely distributed root haplotypes. A lineage of Haplogroup A that was detected in two Ust-Tartas samples represents a subcluster that is apparently characteristic of West Siberia and the Volga-Ural Region. The observed presence of Haplogroup Z lineages with a high frequency in the Ust-Tartas group was unexpected, since these lineages are nearly absent in the gene pool of modern indigenous West Siberian populations.

It is worth noting that the Western Eurasian mtDNA haplogroups in the Ust-Tartas series were represented only by Haplogroup U lineages, and specifically by the three subgroups – U2e, U4, U5a1. These results are in agreement with previous data indicating that Haplogroup U lineages (particularly Subgroups U5 and U4) predominated in Eastern, Central and Northern European hunter-gatherer groups from 14000 to 4000 years ago (Bramanti et al., 2009; Malmstrom et al., 2009), and possibly in earlier periods (Krause et al., 2010). The geographic area within which this genetic feature is observed appears to be broad (Fig. 5). Apparently, Baraba was near the eastern periphery of this area.

We now have evidence of the zone of U dominance extending from Iberia in the west and all the way to Lake Baikal in the east. But, this zone is not homogeneous: its western, European, end appears to have lacked the East Eurasian lineages, while starting from Ukraine and to the East the U types were supplemented by the Mongoloid lineages.

But, there was structure within the U zone itself: according to Lillie et al. (same volume) in Ukraine during the 6th millennium BC, the West Eurasian types were represented by U1 and U3, a different mix than in the Baraba forest steppe, and haplogroup T was also present, while of the Mongoloid haplogroups only C was present.

As we head into the Bronze Age, the population of the region displayed signs of continuity:

The genetic analysis of the Odinovo and Krotovo groups (10 and 6 samples, respectively) (Fig. 3) did not reveal any differences between them and the previous Ust-Tartas group, such as the presence of new mtDNA haplogroups. The mtDNA pool structure was still mixed. The East Eurasian haplogroups were represented by the D, C, Z (in both the Odinovo and Krotovo groups) and A (in the Krotovo group) haplogroups. The East Eurasian lineages identified were phylogenetically close (lineages of haplogroups A, C, Z) or even identical (D haplogroup, 16223–16362 lineages) to the samples from the Ust-Tartas group. The West Eurasian part of the samples were represented by the U5a1 (Odinovo group) and U2e (Krotovo group) haplogroup lineages.  

Although only a small series of samples have been investigated thus far, the data obtained reveal continuity between the Odinovo and Krotovo populations and the earlier Ust-Tartas group. These findings are consistent with the autochthonous development of the Baraba populations during the Early and the beginning of the Middle Bronze Age, as well as with the anthropological evidence.  

It is during the Middle and Late Bronze ages that we begin to say the first intrusive lineage into the native population mix:

The anthropological analysis of the West Siberian Andronovo population shows at least four craniological types. Three types are related to the Palaeocaucasian race and are represented by proto-European anthropological type variants. The fourth, Mongoloid, component is autochthonous. The most intensive interactions between the Andronovo migrants and the indigenous populations apparently occurred in the Baraba forest steppe and the right bank of the upper Ob River (Chikisheva and Pozdnyakov, 2003).  

To investigate the putative impact of Andronovo migrants on the mtDNA pool structure of the indigenous populations in Baraba, mtDNA samples from the Late Krotovo (n=20) and Andronovo (n=20) groups in this region were analyzed (Fig. 3) and compared to recently published data (n=10) (Keyser et al., 2009) and our own unpublished data (n=6) on mtDNA lineages from West Siberian Andronovo populations located outside the Baraba forest steppe.  

The genetic influence of migrants can be detected by the appearance of a new mtDNA haplogroup that was absent in the populations preceding the migration wave. This new mtDNA haplogroup, a West Eurasian T haplogroup, was detected in the Late Krotovo population. The T haplogroup appears simultaneously (with a 15 % frequency) in the Krotovo and Andronovo groups, but was completely absent in all preceding Baraba populations. We therefore consider the appearance of the Haplogroup T-lineage as the most likely genetic marker of the Andronovo migration wave to the region.  

This assumption is confirmed by mtDNA studies of Andronovo groups from other West Siberian areas. Haplogroup T lineages were found, with a frequency of 25 %, in the samples (n=16) taken from two Andronovo groups from the Krasnoyarsk and upper Ob River areas.  

We also detected another remarkable feature in the mtDNA pool of the Andronovo group from Baraba. Most mtDNA samples belonged to haplogroups, such as the East Eurasian A and C haplogroups, that are typical of preceding Baraba indigenous populations. Still, these haplogroups were not found in the other West Siberian Andronovo groups. Apparently, the Andronovo group from Baraba assimilated the aboriginal Krotovo population, from which it obtained these East-Eurasian mtDNA haplogroups. Obviously, there was reciprocal genetic contact between the migrant and indigenous groups in the region. 

...

A small but informative series of mtDNA samples from the Baraba Late Bronze Age culture population (n=5) was analyzed (Fig. 3), revealing the presence of MtDNA lineages (East Eurasian A and C lineages) that mark the genetic continuity with aboriginal Baraba groups. At the same time, the series includes the Haplogroup-T lineage, which we believe marks the Andronovo migration wave to West Siberia. Our data is therefore consistent with the putative origin of the West Siberian Late Bronze Culture population as the result of interaction between the Baraba indigenous genetic substrate and the newly arrived group.

It is now clear that the Andronovo groups moving into the area possessed mtDNA haplogroup T and assimilated the locals with their U+East Eurasian mix. It is of course interesting that haplogroup T is the only non-U lineage found in the aforementioned study of Mariupol-type cemeteries from Neolithic Ukraine.

The earliest occurrence of haplogroup T is in the Pre-Pottery Neolithic B of the Near East (Tell Hallula), and this haplogroup appears all over the place in Neolithic Europe. While a recent article has suggested a pre-Neolithic dispersal of T subclades into Europe, on the basis of modern populations, this hypothesis is difficult to reconcile with the ancient DNA data.


Pending new discoveries, it appears likely that mtDNA haplogroup T represents a Neolithic entrant into the boreal zone of U dominance. This has, of course, substantial implications in the context of J.P. Mallory's concept of fault lines, as it demonstrates that the steppe populations did not evolve in isolation, but the dominant lineage in the Andronovo groups was a late entrant into the indigenous U-zone of the eastern European plain.

But, the story doesn't end here:

The analysis of mtDNA samples from the Chicha-1 population revealed some interesting patterns. Crucial changes in the composition of mtDNA haplogroups in the gene pool were observed as compared to the earlier Baraba groups studied (Fig. 3). Dominance of Western Eurasian haplogroups and the near absence of East Eurasian were observed. Additionally, several new West Eurasian haplogroups appeared in the region, including Haplogroups U1a, U3, U5b, K, H, J and W.  

The phylogeographic analysis suggests that the distribution and diversification centres of several of these mtDNA haplogroups and specific lineages are located on the west and south west of the Baraba forest steppe region, on the territory corresponding to modern-day Kazakhstan and Western Central Asia (Fig. 10). Apparently, the migration wave from the south strongly influenced the gene pool of the Baraba population in the transitional period from the Bronze to the Early Iron Age. The impact of the northern human groups was probably less evident in the south of the Baraba forest steppe, at least at the mtDNA level. 

The drastic appearance of a purely Caucasoid population at the Iron Age from a southern, east-Caspian origin perhaps corresponds to the arrival of the first steppe Iranians. The vector of proposed migration is reasonable, if we consider both the likely Indo-Iranian homeland east of the Caspian, as well as the literary evidence for Scythian mobility during this period.

All in all, this is commendable research which allows us to intuit a sequence of events:

• An early mixture zone between Caucasoids and Mongoloids
• The Bronze Age arrival of mtDNA-T bearing Andronovo groups, the first pastoralists entering the zone of U+East Eurasian boreal hunter-gatherers; these Caucasoid peoples admixed with the natives of the mixture zone.
• The early Iron Age arrival of a full-blown set of Caucasoid mtDNA lineages from the south paving the way for the Iranian Scytho-Sarmatian period

Human migrations in the southern region of the West Siberian Plain during the Bronze Age: Archaeological, palaeogenetic and anthropological data


Molodin, Vyacheslav I. et al.


In this paper we present archaeological and anthropological data on human migrations in the Western Siberian foreststeppe region during the Bronze Age (4th–beginning of 1st millennium BC). These data, accumulated over forty years of intensive research in the region, are compared to new results showing the diversity of mitochondrial DNA (mtDNA) lineages in this region during that period (92 mtDNA samples from seven ancient human groups). Preliminary analyses have demonstrated the usefulness of ancient DNA in tracing and unravelling patterns of past human migrations.  


Link


Prehistoric populations of Ukraine: Migration at the later Mesolithic to Neolithic transition


Lillie, Malcolm C. et al.


This paper focuses on the identification of population movements during the Mesolithic and Neolithic periods in the Dnieper Basin region of Ukraine. We assess the evidence for migration from the perspective of individual life histories using a combination of palaeoanthropology/pathology, radiocarbon dating, stable isotopic studies of diet, and mtDNA. 


Link

East Eurasian mtDNA in Ukrainian Neolithic and Bronze Age

Jean M links to a Master's thesis, which discovered the following:

While most of our samples possessed mtDNA haplotypes that can be linked to European and Near Eastern populations, three Neolithic and all three Bronze Age individuals belonged to mtDNA haplogroup C, which is common in East Eurasian, particularly South Siberian, populations but exceedingly rare in Europe. Phylogeographic network analysis revealed that our samples are located at or near the ancestral node for haplogroup C and that derived lineages branching from the Neolithic samples were present in Bronze Age Kurgans. In light of the numerous examples of mtDNA admixture that can be found in both Europe and Siberia, it appears that the NPR and South Siberia are located at opposite ends of a genetic continuum established at some point prior to the Neolithic. This migration corridor may have been established during the Last Glacial Maximum due to extensive glaciation in northern Eurasia and a consequent aridization of western Asia. This implies the demographic history for the European gene pool is more complex than previously considered and also has significant implications regarding the origin of Kurgan populations.

Unfortunately the thesis is under embargo until next year. We'll have to wait and see whether this research stands up to closer scrutiny by ancient DNA experts. The detection of a haplogroup that is quite rare in Europe today makes it difficult to envision a scenario in which contamination may have produced a spurious result, however.

The Dnieper-Donets population was described as robust Europeoid by Soviet anthropologists as was the Andronovo/Afanasevo tradition further east. It is interesting that Mongoloid admixture has been detected in both groups. I would not have guessed that this would have extended that far west and south. It seems that M. G. Levin may have been right when he stated that the Mongoloid elements penetrated far into eastern Europe.

It will certainly be interesting to discover how the Mongoloid component in the gene pool of the Northern Pontic steppe became diluted until the present. James Mallory argued at great length in a recent talk about the impossibility of Balkan influences on the steppe. I would bet that there were influences from the both the Balkans and the Caucasus, as well as the Transcaspian arrival of Iranic speakers in the 1st millennium BC, ultimately from their Bactria-Margiana source.

UPDATE:

On the Origin of Mongoloid Component in the Mitochondrial Gene Pool of Slavs, B. A. Malyarchuk, M. A. Perkova, and M. V. Derenko (pdf)

Concerning the population of Eastern Europe, it should be noted that the forest zone of Eastern Europe was the area of intense population admixture [35]. It seems likely, that formation of the complex of Mongoloid traits happened not later than in Upper Paleolithic. For this reason, it is suggested that East Siberian populations could have much time for migration to Eastern Europe [35]. The number of such migrations still remains unclear, since in the northwest of Eastern Europe Mongoloid component is detected 10000–8000 years ago; in Dnepr–Donetsk tribes, 7000–6000 years ago, and on the territory of Ivanovo oblast (Sakhtysh), 6000–5000 years ago [35, 36].

It seems, once again, that physical anthropology and genetics are consistent with each other.

An updated tree of Y-chromosome Haplogroup O (Yan et al. 2011)

European Journal of Human Genetics advance online publication 20 April 2011; doi: 10.1038/ejhg.2011.64

An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4

Shi Yan et al.

Y-chromosome Haplogroup O is the dominant lineage of East Asians, comprising more than a quarter of all males on the world; however, its internal phylogeny remains insufficiently investigated. In this study, we determined the phylogenetic position of recently defined markers (L127, KL1, KL2, P164, and PK4) in the background of Haplogroup O. In the revised tree, subgroup O3a-M324 is divided into two main subclades, O3a1-L127 and O3a2-P201, covering about 20 and 35% of Han Chinese people, respectively. The marker P164 is corrected from a downstream site of M7 to upstream of M134 and parallel to M7 and M159. The marker PK4 is also relocated from downstream of M88 to upstream of M95, separating the former O2* into two parts. This revision evidently improved the resolving power of Y-chromosome phylogeny in East Asia.

Link

East Eurasian population structure as a window into the human past

Here is an MDS plot of 454 individuals from 32 East Eurasian/substantially East Eurasian populations:

Population labels have been placed in the (x,y) spot of the population averages. This corresponds -usually- to the midpoint of blobs of individuals from that population, but some populations have a few European-admixed individuals, and hence their population average is transposed. Consult the legend for color/point information for the 32 populations.

The most striking feature of this plot is the extreme homogeneity of the vast majority of East Eurasians. They may occupy a tiny blob on the left of the plot, but the various ethnic groups of China, the Japanese, and the Cambodians all appear to be very close to each other; indeed you can hardly see their labels in the mass of points. Here is a blowup of that part of the plot.

These dots represent the overwhelming mass of East Eurasians, and indeed the biggest single set of human groups. The scattering of populations to the right of the main MDS plot are, in comparison, demographically insignificant, some of them numbering less than 1,000 individuals.

What this plot shows, in tangible form, is a picture of mankind's past: before the invention of agriculture, most humans lived in small tribes, scattered across the world. We can be fairly certain that the action of genetic drift and natural selection would have created a cornucopia of human diversity, with high between-group diversity due to high levels of genetic drift.

Out of all this variety, some tribes of hunters made the transition to agriculture, growing in numbers, filling the areas they exploited, and expanding into new ones. The hunters were on their way to extinction, but new tribes formed at the fringes, those of pastoral nomads exploiting animals to thrive where neither farmer nor hunter could.

In the world of farmers, with growing population densities and expansion came the breakdown of isolates: this led to a further homogenization of the farmers' gene pool, as different tribes that had adopted the new way of life lost all trace of their past tribal identities and formed new ones based on the common language of the agriculturalists and the new way of life.

With more human bodies in the farming communities, came more novel mutations, and hence more of the raw materials of selection.

Coupled with the new challenges of agriculture, for which man is unaccustomed to, the social challenges of living close to many others in villages, and, later, cities, the cognitive challenges of new symbolic systems of communication, selection further reduced diversity in key aspects of human appearance and behavior, while maintaining it, or even increasing it in others, such as resistance to pathogens.

In western Eurasia this process was pushed to its limits, and there are virtually no nomads or hunters to be found there anymore. Africa was explored by Europeans just in time to find living hunters such as the San and Pygmies still in existence there. A few centuries more, and perhaps they, too, would have beeen absorbed into the mass of expanding farmers.

The few dots of European- and Chinese-admixed individuals that deviate from their own populations are a reminder of what would have happened if genetic science had not arrived at the scene when it did. For better or worse, the odds are stacked against most of these peoples surviving as distinct entities. The numbers are against them, and, sooner, or later, they will be assimilated.

Some ADMIXTURE estimates in Eurasia

(Last Update: Sep 29)

Continuing my exploration of ADMIXTURE, I turned to the HGDP data, which has 660,918 SNPs for a wide assortment of worldwide populations. After pruning 12,086 SNPs with more than 1% missing genotypes, I was still left with ~650k SNPs.

Here are some experiments on this dataset. First, a clustering with K=2 of Han Chinese, Russians, and Orcadians (left to right)

The emergence of 2 clusters (red=Mongoloid, blue=Caucasoid) is as expected, with Russians showing a small participation in the red cluster (7.2%). These northern Russians are believed to have a substantial Finno-Ugric genetic origin, so this is inline with a recent estimate for the eastern component in the westernmost Finno-Ugric speakers being less than 10% (but see below).

Notice a couple of Chinese individuals with a small Caucasoid component: as I've mentioned before Mongolians, and presumably northern Han have a small Caucasoid component from early movements of Iranian speakers from the west. That's an advantage of doing your own admixture analysis, that you can look at the data at a fine detail, and not rely on the published figures.

Next, a clustering of Orcadians, Uygur, and Han Chinese:
The variable admixture in Uygurs is evident (47.2-63.7%, mean: 54.2%)

Next, a clustering of Druze, Bedouin, and Bantu from Kenya.

Druze appear complete Caucasoid (red), Bantu completely Negroid (save for a couple of individuals), while Bedouins show a quite variable minor Negroid component. This variable African contribution (0-17.6%) makes an elongated cluster out of Bedouins in a recent analysis, pulling them away from other Middle Eastern populations in a Sub-Saharan direction.

Finally, I clustered European populations together with Mandenka and Han Chinese:

The populations are in the following order: Han, Mandenka, Orcadian, French Basque, French, North Italian, Tuscan, Sardinian, Russian.

Here are the admixture proportions:

Notice how the eastern component in Russians is now estimated as 10.9%. This probably reflects the inclusion of French Basque and Sardinians, i.e., populations which have historically no opportunity for eastern Eurasian admixture, rather than only Orcadians. This underscores the importance of having appropriate poles in inter-continental admixture estimates (see Appendix I).

Note also that the 100% value for the Han Chinese is not incompatible with the presence of the two aforementioned Caucasoid-admixed individuals, who are present here with an estimated 1.9% and 0.5% such admixture. However, this contributes little to the sample average of 40+ individuals.

The minor (0.1%) Sub-Saharan admixture in Tuscans and Sardinians is also interesting. As you can guess from the figure, this stems from a handful of individuals (green specks) with less than 1% admixture, which is, however more than the numerical low of 0.001% inferred for most Europeans by the software.

UPDATE I: Eurasian Cline

Below is a run for the following populations (left-to-right: French Basque, Russians, Uygur, Mongolians, Daur, Han Chinese). Notice that the Mongolic-speakers (Mongolian and Daur from HGDP have a small Caucasoid admixture, as I have mentioned before.

APPENDIX I: The importance of choosing poles

The choice of appropriate poles in the estimation of inter-continental admixture is extremely important.

If there is a racial admixture continuum between two major races, such as we observe in Eurasia, then we can express each intermediate population as a weighted sum of populations that live to the east and west of it.

For example, I will use a variable in interval [0, 1] to represent the position in the continuum, with 0: pure western, and 1: pure eastern.

A population at 0.4 can be expressed as the following weighted sum:

0.4 = 0.6*0 + 0.4*1

i.e., as an admixture of 60% western, and 40% eastern.

But, it can also be expressed as e.g.,

0.4 = 0.612*0.02 + 0.388*1

Notice that the choice of a slightly eastward-tilted "western pole" (at position 0.02 in the continuum) has resulted in a reduction of the inferred eastern component (from 40% to 38.8%).

This is exactly what happened in our example: Russian eastern admixture reduced when we used Orcadians, rather than French Basque as the western pole.

Note also, that this is all done automatically: no one told ADMIXTURE to identify these two poles: it was the presence of unlabeled individuals from different ends of the spectrum that influenced the admixture estimates for the rest.

APPENDIX II: Latent populations

Another important point that needs to be remembered has to do with the possible existence of latent ancestral populations.

For example, it is true that Eurasia (minus South Asia) is economically described as a continuum from the Caucasoids of the Atlantic coast to the Mongoloids of the Pacific, with a transition zone in Central Asia and Siberia, and spillovers on either side. But, we cannot exclude the prehistoric existence of other races in the Eurasian landmass that do not exist today in a relatively unadmixed form.

In Eurasia, the Proto-Uralic race was postulated as such a "third race" with features of its own and not reducible to simple Caucasoid-Mongoloid admixture. It is difficult to see whether these features are ancestral peculiarites (prior to admixture with Caucasoids and Mongoloids), or if they have arisen in a mixed Caucasoid-Mongoloid population.

It is also important to understand how such latent populations affect genetic continua:

First, if the latent population is equidistant from the two major races, then its admixture has no effect on an individual's position in the continuum between the two races. However, it is possible that the latent population was more related to one of the two major races. In that case, admixture with it will move a population towards that race.

So while the jury is still out about the existence of a Proto-Uralic race in Eurasia, its effects on admixed populations indicates that if it had existed it was genetically closer to Mongoloids than to Caucasoids.

Major study of Central Asian populations (Martinez-Cruz et al. 2010)

I have often commented on the fact that Central Asians were mainly formed by the pendulum of Western Eurasians (Caucasoids) moving east with Indo-Iranian languages during prehistory and the later historical westward movement of Turkic speakers. There were other movements besides these, e.g., the Tocharians represent a non-Indo-Iranian eastward Caucasoid movement, while the Mongols represent a non-Turkic westward Mongoloid movement.

Central Asians are therefore today a variable mix of Caucasoids and Mongoloids, formed over the last few millennia, although the constituent elements are still present and recognizable. The Turkicization of the region was, to a large extent, the result of language shift among Iranian populations (Sakas-Scythians), but not without some genetic contribution from the original Turks who were a Mongoloid people akin to their linguistic Altaic cousins, the Mongols. This Mongoloid component is attenuated westward, reaching its minimum among Anatolian and Balkan Turkish speakers.

With respect to the admixture proportions (figure top left) presented in the paper, I have a couple of quick comments:

• Using modern south Asians as representatives of a source population of Central Asia is problematic, as modern south Asians are admixed, comprised of Caucasoids and indigenous South Asians. While South Asia may have been a population source during remote periods of the Paleolithic, in the more recent post-Neolithic times when Central Asian populations were formed, South Asia was a population sink.
• The use of only a few autosomal markers does give a broad overview of the east-west components in these populations, but it should be noted that the use of few markers tends to overestimate minority ancestral components.

Even with such a small number of markers, it is evident that the separation of groups at the population level is possible, as the correspondence analysis indicates: green/European, red/East Asian, blue/Indo-Iranian from Central Asia, orange/Turkic from Central Asia.

UPDATE

The paper includes STRUCTURE results for K=2 to K=6. Below is the STRUCTURE run for K=6:



While less distinct than what we would get with more markers, the emergence of several clusters of individuals is apparent (from left to right: East Asian, Turkic, Central Asian Iranian, South Asian, West Eurasian, Sub-Saharan). Notice how Hazaras and Uyghurs are islands of the Turkic component in the Central/South Asian cluster, and how some Uzbeks are Iranian-like while others are Turkic-like. I am reminded of an older study which found how mythology was used among some Uzbek groups to create a common ancestry for groups of unrelated origin.

European Journal of Human Genetics , (8 September 2010) | doi:10.1038/ejhg.2010.153

In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations

Begoña Martínez-Cruz

Located in the Eurasian heartland, Central Asia has played a major role in both the early spread of modern humans out of Africa and the more recent settlements of differentiated populations across Eurasia. A detailed knowledge of the peopling in this vast region would therefore greatly improve our understanding of range expansions, colonizations and recurrent migrations, including the impact of the historical expansion of eastern nomadic groups that occurred in Central Asia. However, despite its presumable importance, little is known about the level and the distribution of genetic variation in this region. We genotyped 26 Indo-Iranian- and Turkic-speaking populations, belonging to six different ethnic groups, at 27 autosomal microsatellite loci. The analysis of genetic variation reveals that Central Asian diversity is mainly shaped by linguistic affiliation, with Turkic-speaking populations forming a cluster more closely related to East-Asian populations and Indo-Iranian speakers forming a cluster closer to Western Eurasians. The scattered position of Uzbeks across Turkic- and Indo-Iranian-speaking populations may reflect their origins from the union of different tribes. We propose that the complex genetic landscape of Central Asian populations results from the movements of eastern, Turkic-speaking groups during historical times, into a long-lasting group of settled populations, which may be represented nowadays by Tajiks and Turkmen. Contrary to what is generally thought, our results suggest that the recurrent expansions of eastern nomadic groups did not result in the complete replacement of local populations, but rather into partial admixture.

Link

Koreans in genomic context (Jung et al. 2010)

The sample codes:

A total of 320 subjects from 24 regional groups were analyzed in this study. They include Yoruba (YRI), European (CEU), Japanese (JPT), Chinese (CHB), Amerindians (AI), and several population groups from Southern and Northern Asia comprising Chinese from the Jilin area (JL), Vietnamese (VN), Cambodians (CB), Mongolians (MH), and Koreans from ten cities in South Korea

Table 1 has complete sample codes, including those for different Korean cities.

The MDS plot is shown on the left. Of interest is the Asian-specific one (right), which shows Vietnamese-Cambodians on the bottom, Mongolians on the top-left, Koreans-Japanese on top and Chinese close to them but towards the Vietnamese-Cambodian direction. Not very surprising as Koreans are basically north Mongoloid, Japanese have origins in the Korean peninsula, while Chinese are both north and south in origin.

The STRUCTURE analysis is also quite interesting: see top row which is the Korean-Chinese-Japanese only admixture analysis: clear Chinese- (green), Japanese- (red), and Korean- (yellow) centered clusters emerge, paralleling what our eyes tell us about the distinctiveness of these three ethnic groups. Notice, however, sample JJ (Jeju island) which lacks Korean yellow (K=4).

From the paper:

In addition, genetic structure analysis using the STRUCTURE method revealed the existence of five major populations, African, Caucasian, Amerindian, North-East Asian, and Southern Asian. Therefore, in between, there were significant admixtures such as Mongolian with Caucasian, Vietnamese (or Cambodian) with unknown Southern original settlers, and Amerindians with both North-East Asians and Caucasians (Fig. 2).

I have commented before on all these admixtures, so let's summarize: Mongolia represents the eastern limit of the Caucasoid expansion, where a small Caucasoid component exists in a predominantly Mongoloid population; Southeast Asians represent a fusion of Mongoloids with "Australoid"-like indigenous populations of the tropical belt from South Asia to Micronesia; Amerindians are partially admixed with Europeans, and partially admixed with NE Asians; the latter component is marked, perhaps, by Y-chromosome haplogroup C3, and may correspondto the second wave of expansion into the Americas.

PLoS ONE 5(7): e11855. doi:10.1371/journal.pone.0011855

Gene Flow between the Korean Peninsula and Its Neighboring Countries

Jongsun Jung et al.

SNP markers provide the primary data for population structure analysis. In this study, we employed whole-genome autosomal SNPs as a marker set (54,836 SNP markers) and tested their possible effects on genetic ancestry using 320 subjects covering 24 regional groups including Northern ( = 16) and Southern ( = 3) Asians, Amerindians ( = 1), and four HapMap populations (YRI, CEU, JPT, and CHB). Additionally, we evaluated the effectiveness and robustness of 50K autosomal SNPs with various clustering methods, along with their dependencies on recombination hotspots (RH), linkage disequilibrium (LD), missing calls and regional specific markers. The RH- and LD-free multi-dimensional scaling (MDS) method showed a broad picture of human migration from Africa to North-East Asia on our genome map, supporting results from previous haploid DNA studies. Of the Asian groups, the East Asian group showed greater differentiation than the Northern and Southern Asian groups with respect to Fst statistics. By extension, the analysis of monomorphic markers implied that nine out of ten historical regions in South Korea, and Tokyo in Japan, showed signs of genetic drift caused by the later settlement of East Asia (South Korea, Japan and China), while Gyeongju in South East Korea showed signs of the earliest settlement in East Asia. In the genome map, the gene flow to the Korean Peninsula from its neighboring countries indicated that some genetic signals from Northern populations such as the Siberians and Mongolians still remain in the South East and West regions, while few signals remain from the early Southern lineages.

Link