Y chromosome haplogroup Q5 in India

BMC Evol Biol. 2007 Nov 19;7:232.

A novel subgroup Q5 of human Y-chromosomal haplogroup Q in India.

Sharma S, Rai E, Bhat AK, Bhanwer AS, Bamezai RN.

BACKGROUND: Y-chromosomal haplogroup (Y-HG) Q is suggested to originate in Asia and represent recent founder paternal Native American radiation into the Americas. This group is delineated into Q1, Q2 and Q3 subgroups defined by biallelic markers M120, M25/M143 and M3, respectively. Recently, a novel subgroup Q4 has been identified which is defined by bi-allelic marker M346, representing HG Q (0.41%, 3/728) in Indian population. With scanty details of HG Q in Asia, especially India, it was pertinent to explore the status of the Y-HG Q in Indian population to gather an insight to determine the extent of diversity within this region. RESULTS: We observed 15/630 (2.38%) Y-HG Q individuals in India with an ancestral state at M120, M25, M3 and M346 markers, indicating an absence of already known Q1, Q2, Q3 and Q4 sub-haplogroups. Interestingly, we further observed a novel 4 bp deletion/insertion polymorphism (ss4 bp, rs41352448) at 72,314 position of human arylsulfatase D pseudogene, defining a novel sub-lineage Q5 (in 5/15 individuals, i.e., 33.3 % of the observed Y-HG Q) with distributions independent of the social, cultural, linguistic and geographical affiliations in India. CONCLUSION: The study adds another sublineage Q5 in the already existing arrangement of Y-HG Q in literature. It was quite interesting to observe an ancestral state Q* and a novel sub-branch Q5, not reported elsewhere, in Indian subcontinent, though in low frequency. A novel subgroup Q4 was identified recently which is also restricted to Indian subcontinent. The most plausible explanation for these observations could be an ancestral migration of individuals bearing ancestral lineage Q* to Indian subcontinent followed by an autochthonous differentiation to Q4 and Q5 sublineages later on. However, other explanations of, either the presence of both the sub haplogroups (Q4 and Q5) in ancestral migrants or recent migrations from central Asia, cannot be ruled out till the distribution and diversity of these subgroups is explored extensively in Central Asia and other regions.

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mtDNA of Altaian Kazakhs from Russia

From the paper:

In this study, we also find that all Turkic and Mongolic groups possess a common set of maternal haplogroups (C, D, G2a, H), and a minimal number of haplotypes from these lineages at appreciable frequencies. However, the overall patterns of haplotype sharing amongst these groups vary considerably. This finding is not necessarily incompatible with the cultural diffusion model per se, but implies that present day Turkic-Mongolic ethnic groups emerged from a common mtDNA pool that was widely distributed in Central and East Asia.

This suggests that the movements of Turkic-Mongolic people did not consist only of males but also had a female component to them. Also of interest from the paper:

Haplogroup N1a was also present in the Altaian Kazakhs. Seeing as how there were no occurrences of this lineage in other Kazakh populations or neighboring populations (Kolman et al., 1996; Comas et al., 1998; Yao et al., 2004), this finding was intriguing (Table 3). The haplotypic variation within the seven N1a samples was relatively high (Table 2), with these haplotypes belonging to both the European and Central Asian branches of this haplogroup, as recently defined by Haak et al. (2005). Thus, the source of N1a haplotypes in Altaian Kazakhs was unclear, although they seemed to have originated west of this part of Central Asia (Gokcumen et al., 2007).

Interestingly, mtDNA haplogroup N1a also pops up in Havik Brahmins from India, ancient high status Hungarians, as well as Iron Age Kazakhstan, and Neolithic Central Europeans.

American Journal of Physical Anthropology (early view)

Genetic variation in the enigmatic Altaian Kazakhs of South-Central Russia: Insights into Turkic population history

Omer Gokcumen et al.

The Altaian Kazakhs, a Turkic speaking group, now reside in the southern part of the Altai Republic in south-central Russia. According to historical accounts, they are one of several ethnic and geographical subdivisions of the Kazakh nomadic group that migrated from China and Western Mongolia into the Altai region during the 19th Century. However, their population history of the Altaian Kazakhs and the genetic relationships with other Kazakh groups and neighboring Turkic-speaking populations is not well understood. To begin elucidating their genetic history, we analyzed the mtDNAs from 237 Altaian Kazakhs through a combination of SNP analysis and HVS1 sequencing. This analysis revealed that their mtDNA gene pool was comprised of roughly equal proportions of East (A-G, M7, M13, Y and Z) and West (H, HV, pre-HV, R, IK, JT, X, U) Eurasian haplogroups, with the haplotypic diversity within haplogroups C, D, H, and U being particularly high. This pattern of diversity likely reflects the complex interactions of the Kazakhs with other Turkic groups, Mongolians, and indigenous Altaians. Overall, these data have important implications for Kazakh population history, the genetic prehistory of the Altai-Sayan region, and the phylogeography of major mitochondrial lineages in Eurasia.

Link

Huge paper on human genetic relationships based on 650K SNPs

If you thought that this week's Nature paper on human variation was nice, another new paper in Science will be another pleasant surprise. It seems that every time I turn my head geneticists are raising the number of SNPs they study. Lots of populations, 650K SNPs, and a treasure trove of new insight into where humans come from and how we differ from each other.

Before I get into the details of the paper, I want to reiterate my conviction that the problem of human origins is not really a hard one. It just requires a lot of data, a lot of populations, individuals sampled, a lot of genetic markers. Our history, our race, and now it seems even our ethnicity can be read off our genes. We just need to invest the money and effort to find out. With that said, it is sad that the same-old roster of populations from the CEPH panel makes yet another appearance.

There is really a lot on the paper that might interest you, but I will note a few points. First, look at the following PC plot from the paper.



No, your eyes aren't deceiving you. This paper is proof positive that European ethnicities can be distinguished from each other genetically. Even close-by populations (in this case the French and the Italians) are neatly separated. When geographic distance increases there isn't even a hint of confusion: e.g., Russians, Orcadians, and Basque are neatly and clearly separated from other groups. Doubtlessly there would be some more overlap if more individuals/population were used, but the thrust of the discovery is intact: it seems that several European ethnicities and local populations make sense not only culturally but also biologically.

Now, take a look at the standard STRUCTURE analysis which provides meaningful results up to K=7. The standard Sub-Saharan, Native American, East Asian, and Oceanian clusters are there, but now there is meaningful structure within the Caucasoids as well; they are broken into "Middle Eastern", "European", and "Central South Asian" groups.



I would guess that the "brown" Middle-Eastern cluster is largely an Arab/Semitic phenomenon, although the inclusion of the Berber Mozabites is interesting. If it reflected a pre-historic phenomenon, then it would be difficult to explain its apparent total lack of influence in Europe, except for a barely perceptible spillage into Tuscany, which once again reiterates the idiosyncratic "Middle Eastern" trace of that Italian population of likely Etruscan descendants.

The "Central South Asian" group is also extremely interesting, for several reasons. First, it reinforces the previous claim that the Kalash, rather than Greek descendants, as some romantics would have them, are simply a non-European native population, with no evidence of European ancestry. Second, it shows that there is minimal, yet evident European influence in Central Asia, which I would relate to the eastern Indo-Iranians. Third, Central Asian influence in Europe is non-evident, except for a trace among the Russians (and substantially more among the Adygei a people of the Caucasus). Fourth the minority Mongoloid and "Boreal" (Purple) influence in Russians is affirmed. Note that we are dealing with ethnic Russians from the north (Vologda oblast), and Russians are a heterogeneous people in terms of their origin.

We can only wish for inclusion of further populations in future studies of the kind. In particular, eastern and southeastern Europe and non-Arab West Asia, Siberia would be invaluable in further understanding Caucasoid origins, and perhaps uncovering additional structure.

Note that the CEPH panel has revealed that ethnic groups can be distinguished genetically, there is little more than it can offer in terms of understanding origins. The next milestone would be either to include previously unsampled populations, or to dig into ethnic groups themselves, and see if sub-ethnic entities are also discernible in our genomes. Genetic genealogists are in for a good time in the coming years...

Science 22 February 2008: Vol. 319. no. 5866, pp. 1100 - 1104

Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation

Jun Z. Li,1,2*{dagger} Devin M. Absher,1,2* Hua Tang,1 Audrey M. Southwick,1,2 Amanda M. Casto,1 Sohini Ramachandran,4 Howard M. Cann,5 Gregory S. Barsh,1,3 Marcus Feldman,4{ddagger} Luigi L. Cavalli-Sforza,1{ddagger} Richard M. Myers1,2{ddagger}

Human genetic diversity is shaped by both demographic and biological factors and has fundamental implications for understanding the genetic basis of diseases. We studied 938 unrelated individuals from 51 populations of the Human Genome Diversity Panel at 650,000 common single-nucleotide polymorphism loci. Individual ancestry and population substructure were detectable with very high resolution. The relationship between haplotype heterozygosity and geography was consistent with the hypothesis of a serial founder effect with a single origin in sub-Saharan Africa. In addition, we observed a pattern of ancestral allele frequency distributions that reflects variation in population dynamics among geographic regions. This data set allows the most comprehensive characterization to date of human genetic variation.

Link

How Turkish are the Anatolians? (new Alu insertion polymorphism study)

In my 2005 blog post How Turkish are the Anatolians, I estimated, based on Y chromosome frequencies the Central Asian Turkic contribution to the modern-day Anatolians.

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.

In a subsequent post on Non-Caucasoid admixture in Turks I estimated that the combined (bi-parental) contribution of Mongoloids in Turks:

Based on these numbers, the non-Caucasoid admixture in Turks can be quantified as 1.87% Negroid, and 6.18% Mongoloid, total 8.05%.

Given that Central Asians, including the likely Turkic ancestors of modern-day Turkish-speaking Anatolians are partly Mongoloid, this later estimate is compatible with a genetic contribution similar to that quoted above.

So, I was pleased to see a new study based on a different set of autosomal Alu insertion polymorphisms from a group of Turkish scientists that arrived at a similar estimate of the Central Asian admixture in Anatolians. So, it appears that about 1/8 of ancestry of Anatolians (equivalent to one great grandparent) came from a Central Asian Turk.

It is very refreshing to see a paper by Turkish scientists who acknowledge what exactly that other 7/8 of the Anatolians' ancestry actually consists of:

Before Seljuks, Anatolia was under the rule of Eastern Romans but was mainly inhabited by people of Greek origin for nearly two millennia (Toynbee, 1970). The process of change of language and religion by the Seljuks that is assimilation of the residents but not the invaders in Anatolia, was one of the puzzles of history (Toynbee, 1970). As the part of puzzle, estimation of the relative size of arriving nomads was the concern of many studies.

American Journal of Physical Anthropology (online early) 10.1002/ajpa.20772

Alu insertion polymorphisms and an assessment of the genetic contribution of Central Asia to Anatolia with respect to the Balkans

Ceren Caner Berkman et al.

In the evolutionary history of modern humans, Anatolia acted as a bridge between the Caucasus, the Near East, and Europe. Because of its geographical location, Anatolia was subject to migrations from multiple different regions throughout time. The last, well-known migration was the movement of Turkic speaking, nomadic groups from Central Asia. They invaded Anatolia and then the language of the region was gradually replaced by the Turkic language. In the present study, insertion frequencies of 10 Alu loci (A25 = 0.07, APO = 0.96, TPA25 = 0.44, ACE = 0.37, B65 = 0.57, PV92 = 0.18, FXIIIB = 0.52, D1 = 0.40, HS4.32 = 0.66, and HS4.69 = 0.30) have been determined in the Anatolian population. Together with the data compiled from other databases, the similarity of the Anatolian population to that of the Balkans and Central Asia has been visualized by multidimensional scaling method. Analysis suggested that, genetically, Anatolia is more closely related with the Balkan populations than to the Central Asian populations. Central Asian contribution to Anatolia with respect to the Balkans was quantified with an admixture analysis. Furthermore, the association between the Central Asian contribution and the language replacement episode was examined by comparative analysis of the Central Asian contribution to Anatolia, Azerbaijan (another Turkic speaking country) and their neighbors. In the present study, the Central Asian contribution to Anatolia was estimated as 13%. This was the lowest value among the populations analyzed. This observation may be explained by Anatolia having the lowest migrant/resident ratio at the time of migrations.

Link

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.

Link

Y chromosome differences between southern and northern Altaians

Genetika. 2007 May;43(5):675-87.

[Gene pool differences between northern and southern Altaians inferred from the data on Y-chromosomal haplogroups]

[Article in Russian]

[No authors listed]

Y-chromosomal haplogroups composition and frequencies were analyzed in Northern and Southern Altaians. In the gene pool of Altaians a total of 18 Y-chromosomal haplogroups were identified, including C3xM77, C3c, DxM15, E, F*, J2, I1a, I1b, K*, N*, N2, N3a, O3, P*, Q*, R1*, R1a1, and R1b3. The structured nature of the Altaic gene pool is determined by the presence of the Caucasoid and Mongoloid components, along with the ancient genetic substratum, marked by the corresponding Western and Eastern Eurasian haplogroups. Haplogroup R1a1 prevailed in both ethnic groups, accounting for about 53 and 38% of paternal lineages in Southern and Northern Altaians, respectively. This haplogroup is thought to be associated with the eastward expansion of early Indo-Europeans, and marks Caucasoid element in the gene pools of South Siberian populations. Similarly to haplogroup K*, the second frequent haplogroup Q* represents paleo-Asiatic marker, probably associated with the Ket and Samoyedic contributions to the Altaic gene pool. The presence of lineages N2 and N3a can be explained as the contribution of Finno--Ugric tribes, assimilated by ancient Turks. The presence of haplogroups C3xM77, C3c, N*, and 03 reflects the contribution of Central Asian Mongoloid groups. These haplogroups, probably, mark the latest movements of Mongolian migrants from the territory of contemporary Tuva and Mongolia. The data of factor analysis, variance analysis, cluster analysis, and phylogenetic analysis point to substantial genetic differentiation of Northern and Southern Altaians. The differences between Northern and Southern Altaians in the haplogroup composition, as well as in the internal haplotype structure were demonstrated.

Link

Reduced Y chromosome diversity of Central Asian pastoral populations

Curr Biol. 2007 Jan 9;17(1):43-8.

From social to genetic structures in central Asia.

Chaix R. et al.

Pastoral and farmer populations, who have coexisted in Central Asia since the fourth millennium B.C. , present not only different lifestyles and means of subsistence but also various types of social organization. Pastoral populations are organized into so-called descent groups (tribes, clans, and lineages) and practice exogamous marriages (a man chooses a bride in a different lineage or clan). In Central Asia, these descent groups are patrilineal: The children are systematically affiliated with the descent groups of the father. By contrast, farmer populations are organized into families (extended or nuclear) and often establish endogamous marriages with cousins . This study aims at better understanding the impact of these differences in lifestyle and social organization on the shaping of genetic diversity. We show that pastoral populations exhibit a substantial loss of Y chromosome diversity in comparison to farmers but that no such a difference is observed at the mitochondrial-DNA level. Our analyses indicate that the dynamics of patrilineal descent groups, which implies different male and female sociodemographic histories, is responsible for these sexually-asymmetric genetic patterns. This molecular signature of the pastoral social organization disappears over a few centuries only after conversion to an agricultural way of life.

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