Social selection in Y-chromosome haplogroup C3 clusters

There was another recent paper on Y-chromosome haplogroup C recently. The authors of the current paper also present dates with both the evolutionary and genealogical mutation rate. They write:

The age of accumulated STR variation within hg C3, estimated using the method of Zhivotovsky et al. (2004), is about 14.9 ky or 4.1 ky depending on the mutation rate values selected for calculations (Table 3). The older time estimate is most compatible with the view that hg C3 haplotypes were present in Siberia during the Last Glacial Maximum from where the ancestors of C3b Native Americans migrated to the Beringia (Karafet et al., 2002; Zegura et al., 2004).

However, as I noted in my review of the earlier paper:

A case in point is haplogroup C3b-P39; according to the authors' date, this ought to be related to the early arrival of the ancestors of Amerindians, but haplogroup C in the Americans has a strong relationship with Na-Dene speakers such as Athapaskans, and it seems to me that a late spread of this haplogroup is more consistent with its limited geographical distribution and strong linguistic associations.

If C3 had spread into the Americas "early" (together with the other main haplogroup, Q), then we would expect to see it today all over the Americas (perhaps lost here and there due to drift in small populations), and in all language groups. However, this is not what we see. Hence, I am inclined to believe in the more recent spread of C3 into the Americas, together with Na-Dene speakers.

From the paper:

The median joining network of subcluster C3c appears to be complex, with several common haplotypes present in different populations (Fig. 2). Our analysis revealed that the age of this subcluster is about 5.9 ky or 1.6 ky, whereas the age of subcluster C3d appears to be younger – about 2.0 ky or 0.5 ky, depending on the mutation rate values selected.

Haplogroup C3c dominates Kalmyks, Evenks, Evens, i.e. Mongolic-Tungusic populations; C3d in Mongols, Buryats, Khamnigans (Mongolic-speakers).

As I noted in the Cohen Modal Haplotype paper, age estimation must harmonize with both the observed Y-STR variation and known demography. The key questions are: has there been enough time for haplogroup ? to accumulate so much variation, and to grow to such a population size?

Younger haplogroup ages often hit a stumbling block in trying to explain demography (hence my reservations on the CMH paper). Yet, it is much easier to consider massive demographic growth/social selection in Mongols and associated peoples, as the evidence for that growth and expansion is a part of history, and it also harmonizes with what we know about nomadic peoples.

In any case, the real age could be different than the point estimates, both due to the limitations of Y-STR markers, as well as the potential presence of outliers, in which the recently expanded group within a haplogroup dominates the age estimate.

The authors also deal with the Genghis Khan "star cluster" which is part of the paragroup C3*. Here is what they have to say:

It is suggested that this subcluster appears to have originated in Mongolia about 1 ky ago, taking into account the genealogical mutation rate (Zerjal et al., 2003). Our present and previous (Derenko et al., 2007b) studies have shown that the highest frequency of the “star cluster” in C3∗ is observed in Mongols (35%), whereas in Siberia it varies from 8% in Altaian Kazakhs and 6.5% in Buryats to less than 3% in Tuvinians, Altaians and Shors (Table S2). According to our data, the age of the “star cluster” in C3∗ is 2.8 ± 1.0 or 0.78 ± 0.27 ky, based on the evolutionary and genealogical mutation rates, respectively.

Genghis Khan flourished about 0.8ky. If we accept (as I do) the genealogical rate as closer to the truth, then the "star cluster" is related to Genghis and his male relatives, otherwise it is a completely unrelated phenomenon.

Annals of Human Genetics DOI: 10.1111/j.1469-1809.2010.00601.x

Phylogeography of the Y-chromosome haplogroup C in northern Eurasia

Boris Malyarchuk et al.

To reconstruct the phylogenetic structure of Y-chromosome haplogroup (hg) C in populations of northern Eurasia, we have analyzed the diversity of microsatellite (STR) loci in a total sample of 413 males from 18 ethnic groups of Siberia, Eastern Asia and Eastern Europe. Analysis of SNP markers revealed that all Y-chromosomes studied belong to hg C3 and its subhaplogroups C3c and C3d, although some populations (such as Mongols and Koryaks) demonstrate a relatively high input (more than 30%) of yet unidentified C3* haplotypes. Median joining network analysis of STR haplotypes demonstrates that Y-chromosome gene pools of populations studied are characterized by the presence of DNA clusters originating from a limited number of frequent founder haplotypes. These are subhaplogroup C3d characteristic for Mongolic-speaking populations, “star cluster” in C3* paragroup, and a set of DYS19 duplicated C3c Y-chromosomes. All these DNA clusters show relatively recent coalescent times (less than 3000 years), so it is probable that founder effects, including social selection resulting in high male fertility associated with a limited number of paternal lineages, may explain the observed distribution of hg C3 lineages.

Link

Y chromosomes of Kalmyks

Forensic Sci Int. 2007 Feb 19; [Epub ahead of print]

Y-chromosomal STR haplotypes in Kalmyk population samples.

Roewer L, Kruger C, Willuweit S, Nagy M, Rodig H, Kokshunova L, Rothamel T, Kravchenko S, Jobling MA, Stoneking M, Nasidze I.

Seventeen Y-chromosomal short tandem repeats (STRs), DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, GATA-H4, DYS448, DYS456, DYS458, DYS635 were typed in DNA samples from the Kalmyk population (n=99). The population is characterized by a high proportion of duplicated DYS19 alleles and deletions of the locus DYS448 on the background of the Central Asian haplogroup C*. AMOVA analysis reveals a close vicinity to Mongolian and Kazakh populations and large genetic distance to geographical neighbours from Russia, Ukraine and the Caucasus.

Link

The Gagauz of Moldova

Annals of Human Genetics (Online Early)

The Gagauz, a Linguistic Enclave, are not a Genetic Isolate

Ivan Nasidze et al.

Summary

The Gagauz are a Turkic-speaking group that migrated from Turkey to their present location in the southern part of the Republic of Moldova about 150 years ago. Surrounded by Indo-European-speaking populations, they thus form a linguistic enclave, which raises the following question: to what extent have they remained in genetic isolation from their geographic neighbours? Analyses of mtDNA and Y chromosome variation indicate that despite their linguistic differences, the Gagauz have admixed extensively with neighbouring groups. Our data suggest that there has been more mtDNA than Y chromosome admixture, in keeping with the patrilocal nature of these groups. Moreover, when compared with another linguistic enclave, the Kalmyks there appears to be a correlation between the amount of genetic admixture and the amount of linguistic influence that these two linguistic enclaves have experienced from neighbouring groups.

Link

Mongoloid components in Eastern Europe

Slavs and other eastern Europeans are typically Caucasoid although one does not seldom find among them individuals with certain attenuated Mongoloid influences. The extent of Mongoloid admixture in eastern Europe will eventually be determined by autosomal admixture studies which sample the relevant source populations of the Mongoloid component in Europe, namely the Uralic and Altaic speakers of Siberia and Central Asia.

At present, the only study which studied the genomic study of a Slavic sample of Russians (Science 20 December 2002: Vol. 298. no. 5602, pp. 2381 - 2385) determined a 93% membership coefficient in the main Caucasoid cluster, with a 3% membership in the main (East Asian) Mongoloid cluster. Unfortunately Central Asian Turkic and Finno-Ugrian populations from Europe and Asia were not sampled.

The presence of Mongoloid mtDNA types in East Europe is well established, but it should be remembered that movements from the east did not usually involve large numbers of women (*). Therefore, one expects that inference from mtDNA will underestimate the total number of immigrants.

Moreover, as I have pointed out before, Turkic speakers of Central Asia were likely to possess majority components of Caucasoid Y chromosomes associated with Mongoloid mtDNA components. Today, haplogroup C chromosomes make up a large component of Y-chromosome variation in Central Asia (including the famous "Genghis Khan" line), but these were probably added (from the east), late in history, since the Mongol expansion is at the end of the great period of Altaic migrations to the west (Huns, Seljuks, Ottomans, Bulgars, etc.)

As a result a proportion of the eastern immigrants into Europe would be undetectable with Y-chromosome markers, namely the substantial fraction with Caucasoid Y chromosomes and Mongoloid mtDNA. The male immigrants of this type would impart their Y chromosomes in the regions they invaded, but not their maternal mtDNA. In the Altai-Kizhi group, for example, 71% Caucasoid Y chromosomes are associated with 76% non-Caucasoid mtDNA.

Consider a population with 3/4 Caucasoid Y chromosomes and 3/4 Mongoloid mtDNA. Consider that the migrant group consists of 3/4 men and 1/4 women. Under such circumstances we would expect approximately the same rate of Mongoloid mtDNA and Y chromosomes in the recipient population. Moreover, the inferred admixture proportion from the frequencies of Mongoloid mtDNA and Y chromosomes would underestimate the true rate of Mongoloid admixture by a factor of 2.

Unfortunately, the presence of Mongoloid Y chromosomes has not been properly studied until now. In the recent Y chromosome study of the Czech Republic for example, the main Mongoloid Y-haplogroups (C, Q, O) likely to have accompanied the women bearing the 3% Mongoloid mtDNA were not examined and could be part of the Y*, P*, and K* paragroups. Similarly, none of these haplogroups were studied in a recent study on Poland and Germany.

In conclusion:

• The mtDNA evidence suggests a very low-level introgression of Mongoloid components into Eastern Europe.
• The extent of this admixture is likely to be underestimated by the genetic profile of the source population and the excess of male migrants.
• The best estimate of the admixture rate will be determined by autosomal studies that sample relevant Uralic-Altaic source populations, but is probably unlikely to amount to more than a few percentage points.
  

(*) Except in folk migrations such as those of the Kalmyks.

August 1 update of YHRD

YHRD, the Y Chromosome Haplotype Reference Database has been updated on August 1:

The following populations were added today: Iceland, Elista (Russia, Kalmyks), Ecuador (Mestizo, Afroamerican, Quichua, Huaorani), Bama (China, Yao), Chengdu (China, Han), Zhenning (China, Buyi), Molidawa (China, Daur and Ewenki), Yuanjiang (China, Hani), Tongjiang (China, Hezhen), Tongxin (China, Hui), Yanji (China, Korean), Tongshi (China, Li), Xiuyan (China, Manchu), Alihe (China, Oroqen), Maowen (China, Qiang), Luoyuan (China, Fujian), Lhasa (China, Tibet), Yili (China, Xibe, Uigur and Han), Harbin (China, Han), Hailar (China, Mongolian), Lanzhou (China, Han), Liannan (China, Yao), Meixian (China, Han), Urumqi (China, Uigur), Mongolia, Japan, Korea, Gdansk (Poland), Nepal, Sao Paulo State (Brazil, European, African, Oriental and Pardo), Buenos Aires (Argentina), Santa Fe (Argentina), Mendoza (Argentina), Rio Negro (Argentina), Chubut (Argentina), Misiones (Argentina), Corrientes (Argentina), Formosa (Argentina), Chaco (Argentina), Salta (Argentina). We would like to thank the following colleagues for submitting these population samples: Daniel Corach and his group (Buenos Aires), Rune Andreassen and his group (Oslo, Norway), Ivan Nasidze and his group (Leipzig, Germany), Fabricio Gonzalez and his group (Quito, Ecuador), Chris Tyler-Smith, Yali Xue and their group (Cambridge, UK), Richard Pawlowski and his group (Gdansk, Poland), Rogerio Nogueira Oliveira and his group (Sao Paulo, Brazil), Gustavo Penacino and his group (Buenos Aires, Argentina), Emma Parkin, Mark Jobling and their group (Leicester, UK).

So, head on there to see if you get any new matches for your Y-chromosome samples.

Y chromosomes of South Siberians

A very interesting paper about South Siberia, a contact region between Caucasoids and Mongoloids right in the middle of Asia. First, the anthropological picture, which has been established for quite some time:

Unfortunately, archaeological records alone with the lack of human skeletal remains are inconclusive about the anthropological traits, which were characteristic for the Upper Paleolithic Siberian population. East Asian features thought to have been derived from early modern East Asians exist in the tooth from the Denisova Cave in the Altai region and in human remains from the Afontova Gora II site and indicate that the East Asians had moved into southwestern Siberia by 21,000 B.P. or even earlier (Alekseev 1998). Yet, the Upper Paleolithic artifacts from the 23,000-year-old Mal’ta site near Lake Baikal in south-central Siberia (Medvedev et al. 1996) have been found in association with skeletal remains that bear similar morphology with contemporary anatomically modern humans teeth from Europe thus providing the evidence for links between Siberia and the West during the Upper Paleolithic. Thus, on assuming that during the Upper Paleolithic the population of South Siberia was closely related to other East Asian populations, then during the Neolithic, admixture with populations from Eastern Europe probably occurred. The prevalence of European features among steppe zone inhabitants of Tuva, Altai, Khakassia, and West Mongolia became the most significant since the Bronze Age or even earlier (Alexeev and Gohman 1984; Alexeev 1989). The boundary of the Eastern European influence is clearly fixed at Lake Baikal. To the east of Baikal no palaeoanthropological find bears any traces of European admixture (Alekseev 1998).

Of importance is the discovery that R1a1 chromosomes in Siberians and Eastern Europeans are differentiated, and are both quite old, predating the spread of the Kurgan culture.

Divergency estimates based on Y-chromosome microsatellite variation indicate that, despite the haplotype diversity value of Eastern European R1a1-lineages exceeds that in South Siberia, the estimated ages for this haplogroup are almost equal in both regional groups—11,270±4,070 years in South Siberia and 11,380±3,200 years in Eastern Europe. These values are very close to the divergence time between the two regional groups studied (10,310±3,140 years). These results suggest that an isolation of the regional groups occurred soon after the origin of the R1a1 haplogroup.

Finally, here are the haplogroup frequencies in the various populations tested.



Update: The most frequent haplotype (#40) in Siberians, defined over (DYS19, DYS385a, DYS385b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439) is: 16 11 14 14 18 25 11 11 13 14 11 10. This was not found in the extensive Russian sample, so it may represent a quite distinctive Central Asian haplotype.

Interestingly, a search in YHRD with this haplotype revealed only a single match in the Hungarian-speaking sample Lunca de Sus, Romania [Csángó]. This may serve to illustrate the paucity of relevant samples in YHRD. If we exclude DYS438 and DYS439 which are not typed in all samples in YHRD, then additional matches are found in Central Anatolian Turks, Szekely (also Hungarian-speaking) from Romania and in Ljubljana, Slovenia. If we further remove the fast-mutating DYS385 markers, then the following matches are found.



Let's hope that more Central Asian and Siberian samples are added to YHRD soon!

Human Genetics (Early view)

Contrasting patterns of Y-chromosome variation in South Siberian populations from Baikal and Altai-Sayan regions

Miroslava Derenko et al.

Abstract In order to investigate the genetic history of autochthonous South Siberian populations and to estimate the contribution of distinct patrilineages to their gene pools, we have analyzed 17 Y-chromosomal binary markers (YAP, RPS4Y711, SRY-8299, M89, M201, M52, M170, 12f2, M9, M20, 92R7, SRY-1532, DYS199, M173, M17, Tat, and LLY22 g) in a total sample of 1,358 males from 14 ethnic groups of Siberia (Altaians-Kizhi, Teleuts, Shors, Tuvinians, Todjins, Tofalars, Sojots, Khakassians, Buryats, Evenks), Central/Eastern Asia (Mongolians and Koreans) and Eastern Europe (Kalmyks and Russians). Based on both, the distribution pattern of Y-chromosomal haplogroups and results on AMOVA analysis we observed the statistically significant genetic differentiation between the populations of Baikal and Altai–Sayan regions. We suggest that these regional differences can be best explained by different contribution of Central/Eastern Asian and Eastern European paternal lineages into gene pools of modern South Siberians. The population of the Baikal region demonstrates the prevalence of Central/Eastern Asian lineages, whereas in the populations of Altai and Sayan regions the highest paternal contribution resulted from Eastern European descent is revealed. Yet, our data on Y-chromosome STRs variation demonstrate the clear differences between the South Siberian and Eastern European R1a1-lineages with the evolutionary ages compatible with divergence time between these two regional groups.

Link