ISABS 2013 abstracts

From the book of abstracts (pdf):

MITOCHONDRIAL DNA AND PHYLOGENETIC ANALYSIS OF PREHISTORIC NORTH AFRICAN POPULATIONS

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

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

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

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

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

MATERNAL GENETIC PROFILE OF A NORTHWEST ALGERIAN POPULATION

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

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

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

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

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

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

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

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

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

rolloff and ALDER analysis of Turks

I carried out rolloff analysis of the Behar et al. (2010) sample of Turks together with the sample of Uzbeks from the same, and the Yunusbayev et al. (2011) sample of Armenians. A --geno 0.03 flag was applied for merging and SNPs available in the Rutgers recombination map for Illumina chips were used.

The exponential decay can be seen below:

The signal of admixture seems pretty clear and extends up to several cM. Of course, as always, this does not mean that exactly these two populations mixed to form the Turks sample, but it does mean that they are reasonable standins.

The jackknife gives an admixture time estimate of 27.622 +/- 5.348 generations or 800 +/- 160 years, which of course makes perfect historical sense as it is a date between the first arrival of the Seljuks in Anatolia and the final consolidation of power by the Ottomans. Note also that this probably applies principally to this particular sample (which I believe is from Cappadoccia) and there were perhaps different admixture dynamics elsewhere.

I had started this analysis before the announcement of ALDER, but since it is very fast, I decided to give it a go as well. Below is the raw output:




                    *** Admixture test summary ***

Weighted LD curves are fit starting at 1.45 cM

Pre-test: Does Turks have a 1-ref weighted LD curve with Armenians_Y?
   1-ref decay z-score:    0.09
   1-ref amp_exp z-score: -0.01
                                  NO: curve is not significant

Pre-test: Does Turks have a 1-ref weighted LD curve with Uzbeks?
   1-ref decay z-score:    6.56
   1-ref amp_exp z-score:  5.02
                                  YES: curve is significant

Does Turks have a 2-ref weighted LD curve with Armenians_Y and Uzbeks?
   2-ref decay z-score:    5.61
   2-ref amp_exp z-score:  5.58
                                  YES: curve is significant

Do 2-ref and 1-ref curves have consistent decay rates?
   1-ref Armenians_Y - 2-ref z-score:                  0.01   ( 13%)
   1-ref Uzbeks - 2-ref z-score:                       0.69   ( 11%)
   1-ref Uzbeks - 1-ref Armenians_Y z-score:          -0.00   ( -1%)
                                  YES: decay rates are consistent

Test FAILS (z=5.58, p=2.4e-08) for Turks with {Armenians_Y, Uzbeks} weights

DATA: failure 2.4e-08 Turks Armenians_Y Uzbeks 5.58 -0.01 5.02 13% 23.92 +/- 4.26 0.00002930 +/- 0.00000525 27.18 +/- 302.36 -0.00000082 +/- 0.00013129 26.84 +/- 4.09 0.00002316 +/- 0.00000461

DATA: test status p-value test pop ref A ref B 2-ref z-score 1-ref z-score A 1-ref z-score B max decay diff % 2-ref decay 2-ref amp_exp 1-ref decay A 1-ref amp_exp A 1-ref decay B 1-ref amp_exp B

The age estimate appears to be very similar, and most curves appear to be significant, except the one with Armenians_Y. This makes good sense. From Loh et al. (2012):

Also, if a reference A' shares some of the same admixture history as C or is simply very closely related to C, the pre-test will typically identify long-range correlated LD and deem A' an unsuitable reference to use for testing admixture.

In our case, A'=Armenians and C=Turks. We can be fairly sure that Armenians lack the same admixture history as Turks (because they were not affected by Central Asian Turkic invasions), but we can try a 1-ref analysis of Armenians with Uzbeks to substantiate it. The admixture lower bound estimate is a huge interval 7.6 +/- 88.2 and the jackknife is unable to estimate the admixture time. Thus, more plausibly, the second explanation applies, and because Armenians_Y are very closely related to Turks, they are deemed as an inappropriate reference to test admixture.

Finally, the lower bound of the admixture fraction for Turks with an Uzbek reference is estimated as:

Mixture fraction % lower bound (assuming admixture): 29.8 +/- 4.0

This is a very interesting number. We can be fairly sure that Central Asian Turkic people who invaded Anatolia carried with them an East Eurasian component, but in what proportion to their West Eurasian one? The East Eurasian element in Turks has been rather consistently estimated at ~5-7% with various methods, so perhaps this formed the minority element in the Turkic people who arrived in Anatolia. 

On the other hand, this case is rather muddled by the occurrence of by-directional gene flow: Uzbeks may have West Eurasian ancestry of ultimate West Asian origin, just as Turks have Central Asian ancestry. And, indeed, when we estimate the admixture fraction of Uzbeks with the Turks as a reference, we obtain:

Mixture fraction % lower bound (assuming admixture): 46.7 +/- 2.4

The age estimate for this is ~16 +/- 2 generations = 460 +/- 60 years. Very similar time estimates appear when Armenians are used as a West Eurasian reference. So, this might indicate that the Uzbek population was formed by admixture after the Anatolian Turks were so formed.

I see no easy way to solve the problem of estimating admixture proportions when both extant populations have been both donors and recipients of gene flow, but in any case, these numbers are something to think about.

Analysis of Turks with a variety of Turkic and East Asian populations

I subsequently formed a new dataset by merging the sample of Turks with a variety of Turkic and East Asian populations (same procedure for SNP choice).

For the calendar year calculation, I arbitrarily set the birthdate of the modern sampled individuals at 1980; I have no idea on the age profile of the individuals comprising the Behar et al. sample of Turks. I have also used a mindis=0.5cM which facilitated the convenient automated extraction of the dates from the ALDER output and also gave a level playing field for all the reference populations. The age picked by ALDER using its own adaptive threshold did not usually differ from the reported one by more than a few generations.

The results indicate two things:

• The % of admixture depends on the choice of population, with highest amount using Uzbeks  as a reference, and lowest using the far Asian populations from China. This indicates our uncertainty regarding the East/West Eurasian-ness of the people who settled in Anatolia.
• Admixture times, on the other hand appear to be fairly constant and appear to frame an important watershed moment of Anatolian history, the Battle of Manzikert which paved the way for the eventual Turkification of the peninsula. The Turkmen sample appears as an outlier in this respect, which might indicate that limited migration of Turkmen tribes may have occurred at a later date.

Uzbeks as the nexus, Altai as the source of Turkic expansions

I have often used Uzbeks as a convenient population to assess the extent of Central Asian Turkic admixture in West Eurasia. The recent Yunusbayev et al. (2011) paper has provided some interesting supporting evidence for that use:


I have extended lines from Uzbeks through the four different western Eurasians Turkic populations: Turks, Turkmen, Nogais, and Chuvashs. It is interesting that these lines intersect West Eurasians at different points:

• The line of Turks (Anatolia) with Armenians and Georgians
• The line of Turkmen (Iran) with Iranians
• The line of Nogais (North Caucasus) with Chechens
• The line of Chuvashs (far eastern Europe) beyond Russians

These are what we expect if ancestral Turkic speakers en route from their ultimate eastern homeland were roughly like modern-day Uzbeks at some stage before their settlement in west Eurasia. The linearity of the Uzbek-Turkic population-Native population triples is striking

The only case where the fit is not almost perfect is that of the Chuvashs, who are the most northern population. It is easy enough to discover the cause of this. Chuvash have ~1.1% South Asian, as opposed to ~8.2% in the Uzbeks. There is a north-south latitudinal cline of the "South Asian" component in middle Eurasia, and the ancestors of the Chuvash moved at the northern end of that cline; of the Uzbeks at the middle.

If we add a line linking Russians with Chuvashs, we can reconstruct the hypothetical Proto-Chuvashs as a population that differed from Uzbeks in being less "South Asian", which confirms the Dodecad admixture data:

The mystery is further resolved once we look at the following PCA plot from my article On the northern/southern Caucasoid contributions to Asia


Notice that Turks, Uzbeks and the pair of Altai and Dolgan fall along one line, while Chuvashs, Russians, and the pair of Altai/Dolgan along another.

So, the data seems consistent with the idea that the primary source of the westward Turkic expansions was something like the Altai (pics) and Dolgan, undergoing transformations and successive admixtures all the way to the Mediterranean and eastern Europe.

The Central Asian element in Turks (part 3)

In a previous post I summarized extensive evidence by myself and Turkish researchers to the effect that modern Turks are about 1/7 descended from Central Asian Turkic speakers, and 6/7 from pre-Turkic West Asians.

Some people have argued that Uzbeks, the best representative of the Central Asian ancestors of the Turks are inappropriate as a parental population.

Can Turks be modeled as a 1/7-6/7 simple mix of West Eurasians and Central Asians? I refer to my most recent K=11 ADMIXTURE results as useful data that can be used to test this hypothesis once again.

I will use the 4-way average of Greek_D, Armenian_D, Georgians, and Syrians as representative of the "West Eurasian" component in Turks. These 4 populations border Turks from the West, East, North, and South, and their average is expected to be a good stand-in for what pre-Turkish Anatolians were like, and probably more robust than choosing arbitrarily just one of the 4 populations.

I will use Uzbeks as representative of Central Asian Turks, and I will calculate the weighted average of the two (1/7 Uzbek + 6/7 "West Eurasian"). I will then compare this with the average of the Turks (from Behar et al. 2010)+Turkish_D combined sample.

If Turks can be modeled as the simple mix I have claimed, then the empirical Turkish average will be similar to the simulated one (1/7 Uzbek + 6/7 "West Eurasian"). Here are the actual numbers:

As you can see, the simulated average is virtually identical to the empirical one. All components do not deviate from it by more than 0.4%, and only the most important West Asian one deviates by a mere 1.8% which, in relative terms (divided by the mean of 49.2%) represents a 3.7% error.

Given the finite sample sizes, the limitations of ADMIXTURE, and the use of a 4-way average as a proxy for pre-Turkish Anatolians, I can easily claim that this does not only confirm the validity of my model but to an extraordinary degree.

A different way of testing the model's validity is the correlation between the empirical and simulated admixture proportions which is 0.99956. I don't think I need to point out how remarkable this is.

Conclusion

The empirical data are consistent with the idea that Anatolian Turks are a simple mix of a West Eurasian population element equivalent to the average of their immediate neighbors, and a Central Asian population element similar to Uzbeks in a 6:1 analogy. These results confirm and extend the extensive evidence of the previous post.

UPDATE (May 21): In a new experiment, I demonstrate that all available Turkic samples fall almost perfectly on a cline between West and East Eurasians. That experiment also shows that Uzbeks are the most West Eurasian out of the available Central Asian Turkic populations.

It is still unclear what the ratio of West/East Eurasian elements in Turkic people who entered Anatolia was, but these results certainly point out that the Uzbeks are not unusually Mongoloid in their makeup among Turkic peoples, rather the opposite.

Multidimensional scaling and ADMIXTURE across Northern Eurasia corresponds to geography and language

Here is a multi-dimensional scaling plot of a number of North Eurasian populations. In comparison to my previous post, I have excluded Americans and Greenlanders, and added several other populations from Central Asia and West Eurasia.

Population labels have been printed in the co-ordinates of the population averages; these largely correspond with identifiable blobs of colored points, but note that some populations have several outliers, so labels appear in white space. Most notable in that respect are the Koryak, Chukchi, and the Nganasan, all of whom have some apparently European-admixed individuals.

"Mongol" corresponds to Rasmussen et al. (2010) Mongol sample, while "Mongola" to the HGDP-CEPH one. The population codes on the left may not be clearly visible as they overlap with each other and are CEU, LT, HU (relatively unadmixed Caucasoids), FI/RU (Uralian-admixed northern Caucasoids), IR/TR (Altaic-admixed southern Caucasoids). The West Eurasian part of the plot can be seen blown up on the right.

The correspondence with geography and language is striking. Siberian isolates from the extreme north and east, Koryak and Chuckhi are on top; HapMap Chinese at the bottom. Between them are Uralians (Selkup, Yukagir, Nganassan) and Altaics (Mongol-Tungus-Turkic people).

Below is ADMIXTURE analysis for the same set of populations, for K=7:

Finns and Russians seem to have an excess of the "Nganasan" component over the Altaic, while Turks have the opposite. Below is a table of Fst distances between components:

The close relationship between the two Caucasoid components is apparent (Fst=0.033), but note fairly large Fst divergences between the morphologically Mongoloid groups. I attribute this mostly to the very low population sizes of these groups, which have probably affected them by drift. For the less demographically constrained Altaic and East Asian components, Fst=0.044.

If you are not familiar with these ethnic groups, the Red Book of the Peoples of the Russian Empire and the Ethnologue indexes on Altaic and Uralic are invaluable, as are the portraits of ethnic groups of China. On the right a picture of a Nganasan.

UPDATE: Also, a past post from the blog, collating Y-haplogroup N frequencies with anthropological descriptions. Nganasans apparently belong to haplogroup N at a frequency of 92.1%!

ADMIXTURE across Eurasia: from Anatolia to Siberia

(Last Update: Oct 17)

Here is a result of an ADMIXTURE run of a few populations from Eurasia (left to right: Turks, Armenians, Georgians, followed by a mix of Uygur, Mongolians, Yakut, Hezhen in no order), combining the HGDP dataset with that of Behar et al. (2010).

It's more of a test, rather than a final result, as I've just finished integrating the two datasets, but it's a nice comparison of a wide assortment of linguistic families.

Notice Turks and Armenians being quite similar to each other, (green+blue), although Turks are differentiated by the presence of an east Eurasian component (5.5%). On the basis of uniparental markers, five years ago, I estimated this component as 6.2% which seems to be right on the money. In the combined Armenian/Georgian sample this admixture is only 0.14% and as can be seen is limited to a handful of Georgian individuals.

It is interesting that Georgians belong semi-uniquely to the green cluster. Turks' non-Mongoloid ancestors were Indo-European speaking like the Armenians still are. It would be tempting to see in the blue-green contrast an Indo-European/Caucasian one, especially as the Caucasoid component further east seems to be mainly blue, in agreement with the idea that it was Indo-Europeans (in particular mainly Iranic speakers) who brought Caucasoid genes to the heartland of Asia.

UPDATE I (Oct 17):

Moving to the north, we see (left-to-right) Han (red), Hungarian/Belorussian (blue), Chuvash (first red "step"), Uzbek (second red "step"). Unlike the Turks, the Hungarians, who also speak a language that came from the east, seem to lack a noticeable east Eurasian component.

Their linguistic conversion was one of elite dominance, where a handful of Mongoloid and quasi-Mongoloid upper echelons left their language but not their genes:

According to his observations, the “overlords” were characterized by Turanid, Uralian and Pamir race elements and also by certain long-headed components. The “middle layer” or “warriors’ layer”, however, showed an anthropological profile distinctly different from that of the overlords. It was essentially constituted by Mediterraneans, Nordoids (who might also have been tall robust Mediterraneans) and Pamir component while the absence of Turanid and Uralian race characteristics was remarkable. As regards the third layer, the so-called “common folk”, they were dominated, just as the middle layer was, by Mediterranean and Nordoid elements but, in addition, the Cromagnoid ones were also significant.

The Chuvash are Turkic and live in Europe, while the Uzbeks, closer to the Altaic homeland in Asia are also Turkic, and have a predictable higher percentage of east Eurasian genes.

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.

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mtDNA variation in Uzbekistan

Int J Legal Med DOI 10.1007/s00414-009-0406-z

The mtDNA composition of Uzbekistan: a microcosm of Central Asian patterns

Jodi A. Irwin et al.

Abstract

In order to better characterize and understand the mtDNA population genetics of Central Asia, the mtDNA control regions of over 1,500 individuals from Uzbekistan
have been sequenced. Although all samples were obtained from individuals residing in Uzbekistan, individuals with direct ancestry from neighboring Central Asian countries are included. Individuals of Uzbek ancestry represent five distinct geographic regions of Uzbekistan: Fergana, Karakalpakstan, Khorezm, Qashkadarya, and Tashkent. Individuals with direct ancestry in nearby countries originate from Kazakhstan, Kyrgyzstan, Russia, Afghanistan, Turkmenistan, and Tajikistan. Our data reinforce the evidence of distinct clinal patterns that have been described among Central Asian populations with classical, mtDNA, and Y-chromosomal markers. Our data also reveal hallmarks of recent demographic events. Despite their current close geographic proximity, the populations with ancestry in neighboring countries show little sign of admixture and retain the primary mtDNA patterns of their source populations. The genetic distances and haplogroup distributions among the ethnic populations are more indicative of a broad east–west cline among their source populations than of their relatively small geographic distances from one another in Uzbekistan. Given the significant mtDNA heterogeneity detected, our results emphasize the need for heightened caution in the forensic interpretation of mtDNA data in regions as historically rich and genetically diverse as Central Asia.

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mtDNA of Uzbekistan

International Journal of Legal Medicine doi:10.1007/s00414-009-0406-z

The mtDNA composition of Uzbekistan: a microcosm of Central Asian patterns

Jodi A. Irwin et al.

Abstract

In order to better characterize and understand the mtDNA population genetics of Central Asia, the mtDNA control regions of over 1,500 individuals from Uzbekistan have been sequenced. Although all samples were obtained from individuals residing in Uzbekistan, individuals with direct ancestry from neighboring Central Asian countries are included. Individuals of Uzbek ancestry represent five distinct geographic regions of Uzbekistan: Fergana, Karakalpakstan, Khorezm, Qashkadarya, and Tashkent. Individuals with direct ancestry in nearby countries originate from Kazakhstan, Kyrgyzstan, Russia, Afghanistan, Turkmenistan, and Tajikistan. Our data reinforce the evidence of distinct clinal patterns that have been described among Central Asian populations with classical, mtDNA, and Y-chromosomal markers. Our data also reveal hallmarks of recent demographic events. Despite their current close geographic proximity, the populations with ancestry in neighboring countries show little sign of admixture and retain the primary mtDNA patterns of their source populations. The genetic distances and haplogroup distributions among the ethnic populations are more indicative of a broad east–west cline among their source populations than of their relatively small geographic distances from one another in Uzbekistan. Given the significant mtDNA heterogeneity detected, our results emphasize the need for heightened caution in the forensic interpretation of mtDNA data in regions as historically rich and genetically diverse as Central Asia.

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Neanderthals of the East

A new paper from Svante Paabo's team that shows that Neanderthals may have lived further to the east that can be assumed based on paleoanthropological evidence. Roughly speaking, to identify some remains as Neanderthals, anthropologists have to detect features belonging to the "constellation of features" typical of that species. However, when the material is limited in quantity, one cannot do this: most of the Neanderthal-identifying features are missing! Obviously, this is not a problem with DNA methods, since DNA can be extracted from small bone and tooth fragments.

Nature advance online publication 30 September 2007 | doi:10.1038/nature06193

Neanderthals in central Asia and Siberia

Johannes Krause et al.

Morphological traits typical of Neanderthals began to appear in European hominids at least 400,000 years ago1 and about 150,000 years ago2 in western Asia. After their initial appearance, such traits increased in frequency and the extent to which they are expressed until they disappeared shortly after 30,000 years ago. However, because most fossil hominid remains are fragmentary, it can be difficult or impossible to determine unambiguously whether a fossil is of Neanderthal origin. This limits the ability to determine when and where Neanderthals lived. To determine how far to the east Neanderthals ranged, we determined mitochondrial DNA (mtDNA) sequences from hominid remains found in Uzbekistan and in the Altai region of southern Siberia. Here we show that the DNA sequences from these fossils fall within the European Neanderthal mtDNA variation. Thus, the geographic range of Neanderthals is likely to have extended at least 2,000 km further to the east than commonly assumed.

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mtDNA of ancient Inner Mongolian tribe

From the conclusions:

The present study shows that the genetic structure of the Wanggu tribe is a complex matriline, involving the admixture of Europeans and Asians, including East
Asian and Siberian groups. Moreover, the Asian lineage probably contributes more than the European lineage to the ancient tribe. The Wanggu tribe has closer affinities with the Uzbeks and Uighurs, which to some extent reflects that the Wanggu tribe has a recent common origin with the two groups. Nevertheless, our conclusions are inevitably constrained by the small sample size of the Wanggu tribe. More samples and more studies will sufficiently reveal the origin of the ancient tribe.

American Journal of Physical Anthropology (Early View)

Molecular genetic analysis of Wanggu remains, Inner Mongolia, China

Yuqin Fu et al.

Abstract

The Wanggu tribe, which contributed significantly to the foundation of the Yuan Dynasty, was one of the groups living on the Mongolian steppes during the Jin-Yuan period (AD 1127-1368) of Chinese history. However, there has been both archaeological and historical dispute regarding the origin of the ancient tribe. Recently, we discovered human remains of the Wanggu tribe in the Chengbozi cemetery in the Siziwang Banner of Inner Mongolia, China. To investigate the genetic structure of the Wanggu tribe and to trace the origins of the tribe at a molecular level, we analyzed the control-region sequences and coding regions of mitochondrial DNA (mtDNA) from the remains by direct sequencing and restriction-fragment length polymorphism analysis. In combination with mtDNA data of 15 extant Eurasian populations, we performed phylogenetic analysis and multidimensional scaling analysis. Our results show that the genetic structure of the Wanggu tribe in the Jin-Yuan period is a complex matriline, containing admixture from both Asian and European populations. In addition, we reveal that on the basis of mtDNA data, the ancient tribe may share a recent common ancestor with the Turkic-speaking Uzbeks and Uighurs.

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Population genetics of Indus Valley populations

A new article confirms that the genetic composition of the population of the Indo-Gangetic plain (Pakistan and NW India) consists of West Eurasian (Caucasoid) and indigenous South Asian elements. The contribution of other elements such as Sub-Saharan African in the Makrani "Negroids", the significant contribution of indigenous female South Asian elements to the Parsis (who are of Iranian origin, but live in India), and the contribution of Mongoloid elements in groups such as the Hunza, and the Hazara is also confirmed. The mtDNA distribution is shown below:



In terms of their Y-chromosome, the population of the region is of western Eurasian (Caucasoid) origin, also including a variant which has developed in the region and is found at lesser frequency elsewhere:

In striking contrast to the mtDNA data, there is no strong evidence in Pakistani populations of Y-chromosome signatures of the early inhabitants of the region following the African exodus (Qamar et al. 2002, Zerjal et al. 2002), with their Y-chromosomes largely replaced by subsequent migrations or gene flow. The Y-chromosome gene pool of Pakistani populations is mainly attributable to western Eurasian lineages, particularly from the Middle East (Qamar et al. 2002). Conversely, few traces of East Asian haplogroups are observed in the Indus Valley populations. One Y-chromosome haplogroup (L-M20) has a high mean frequency of 14% in Pakistan and so differs from all other haplogroups in its frequency distribution. L-M20 is also observed, although at lower frequencies, in neighbouring countries, such as India, Tajikistan, Uzbekistan and Russia. Both the frequency distribution and estimated expansion time (~7,000 YBP) of this lineage suggest that its spread in the Indus Valley may be associated with the expansion of local farming groups during the Neolithic period (Qamar et al. 2002).

Update

For easier access, here is a break-down of Indian Y-chromosomal distribution taken from a recent comprehensive study (pdf).



And, a similar study on Y-chromosomal distribution from Pakistan (pdf):



Annals of Human Biology Mar-Apr 32(2):154-62.

A population genetics perspective of the Indus Valley through uniparentally-inherited markers.

McElreavey K and Quintana-Murci L.

Analysis of mtDNA and Y-chromosome variation in the Indo-Gangetic plains shows that it was a region where genetic components of different geographical origins (from west, east and south) met. The genetic architecture of the populations now living in the area comprise genetic components dating back to different time-periods during the Palaeolithic and the Neolithic. mtDNA data analysis has demonstrated a number of deep-rooting lineages of Pleistocene origin that may be witness to the arrival of the first settlers of South and Southwest Asia after humans left Africa around 60,000 YBP. In addition, comparisons of Y-chromosome and mtDNA data have indicated a number of recent and sexually asymmetrical demographic events, such as the migrations of the Parsis from Iran to India, and the maternal traces of the East African slave trade.

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How Turkish are the Anatolians?

The Anatolians are the ethnic descendants of both the indigenous populations of Asia Minor who converted to Islam (and were thus spared from the genocidal campaign of the Ottomans and Kemalists during the early 20th century), and also of non-indigenous populations from the Balkans, the Middle East, and Central Asia. From Central Asia came the Turks, who were the main agent for the Islamization and during the last century Turkification of Asia Minor.

To what extent are the Anatolians descended from Central Asian Turks? The study of Cinnioglu et al. (2004) discovered an occurrence of 3.4% of Mongoloid Y-chromosomal haplogroups in Anatolia (haplogroups Q, O, and C).

According to Tambets et al. (2004) the occurrence of Mongoloid haplogroups in present-day Central Asian Turkic Altaic speakers (Altaians) is at least 40%, with an additional 10% which might belong to haplogroup O which was not tested in this study. According to Zerjal et al. (2002) this percentage is for various Turkic speakers: Kyrgyz (22%), Dungans (32%), Uyghurs (33%), Kazaks (86%), Uzbeks (18%).

It is clear that the percentage of Mongoloid ancestry among the Turkic speakers is very variable, yet it is clear that the Proto-Turks must have been partially Mongoloid in lieu of the fact that all current Turkic speakers possess some Mongoloid admixture. The average of the six Central Asian population samples listed above is 38.5% and may serve as a first-order estimate of the paternal contribution of early Turks, who (judging by their modern descendants in Central Asia) were more Caucasoid paternally and more Mongoloid maternally.

Using the figure of 38.5%, the paternal contribution of Turks to the Anatolian population is estimated to about 11%. In lieu of the approximation, allowing for 33% relative error in either direction for both the true frequency of Mongoloid lineages in Anatolia and in early Turks, we obtain a range of 6-22%. It would thus appear that the Turkish element is a minority one in the composition of the Anatolians, but it is by no means negligible.

Genetic vs. Mythical Origins

Many peoples around the world have origin stories regarding their common ancestors. It is now possible to determine whether these stories have a basis in reality, or whether they are simply common myths. A new study tries to answer this question for several ethnic groups from Uzbekistan. As the authors point out, these are very conservative, previously nomadic, patrilineal groups with elaborate genealogies going up to 60 generations. By studying their Y-chromosomes the authors examine whether or not they share an ancestor at the various kinship levels recognized by them: lineage, clan and tribe. It is shown that lineages do in fact have common ancestors, whereas tribal ancestors are largely mythological. Thus, tribes may be formed by the coming together of various clans who invent a mythological ancestor to justify their union.

Am. J. Hum. Genet., 75:000, 2004

The Genetic or Mythical Ancestry of Descent Groups: Lessons from the Y Chromosome

Raphaëlle Chaix et al.

Traditional societies are often organized into descent groups called "lineages," "clans," and "tribes." Each of these descent groups claims to have a common ancestor, and this ancestry distinguishes the group's members from the rest of the population. To test the hypothesis of common ancestry within these groups, we compared ethnological and genetic data from five Central Asian populations. We show that, although people from the same lineage and clan share generally a recent common ancestor, no such common ancestry is observed at the tribal level. Thus, a tribe might be a conglomerate of clans who subsequently invented a mythical ancestor to strengthen group unity.

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mtDNA from Xinjiang

A new study quantifies the level of Caucasoid admixture in various populations of the Xinjiang province of China, which ranges from 0% in the Han Chinese to 43% in the Uygur.

Mol Biol Evol. 2004 Aug 18 [Epub ahead of print]

Different Matrilineal Contributions to Genetic Structure of Ethnic Groups in the Silk Road Region in China.

Yao YG

Previous studies have shown that there were extensive genetic admixtures in the Silk Road region. In the present study, we analyzed 252 mtDNAs of five ethnic groups (Uygur, Uzbek, Kazak, Mongolian, and Hui) from Xinjiang Province, China (where once was the via route of the Silk Road), together with some reported data from the adjacent regions in Central Asia. In a simple way, we classified the mtDNAs into different haplogroups (monophyletic clades in the rooted mtDNA tree) according to the available phylogenetic information and compared their frequencies to show the differences among the matrilineal genetic structures of these populations with different demographic histories. With the exception of 8 unassigned M(*), N(*) and R(*) mtDNAs, all the mtDNA types identified here belonged to defined subhaplogroups of haplogroups M and N (including R) and consisted of subsets of both the eastern and western Eurasian pools, thus providing direct evidence in supporting the suggestion that Central Asia be the place of the genetic admixture of the East and the West. Although our samples were from the same geographic location, a decreasing tendency of the western Eurasian-specific haplogroup frequency was observed, with the highest frequency present in Uygur (42.6%) and Uzbek (41.4%), followed by Kazak (30.2%), Mongolian (14.3%), and Hui (6.7%). No western Eurasian type was found in Han Chinese samples from the same place. The frequencies of the eastern Eurasian-specific haplogroups also varied in these samples. Combined with the historical records, ethno-origin, migratory history, and marriage custom might play different roles in shaping the matrilineal genetic structure of different ethnic populations resided in this region.

Link (pdf)