ESHG abstracts

I had previously posted some titles from this year's European Society of Human Genetics conference. There is now a pdf volume on the ESHG which contains all the abstracts of the conference. Some of them have already been published, and doubtlessly more of them will be published next year. I will discuss below some of the more intriguing entries:

F. Cruciani et al., Molecular dissection of the Y chromosome haplogroups A, E and R1b

The male-specific region of the human Y chromosome (MSY) is characterized by a low amount of sequence diversity compared to the mtDNA, the autosomes and the X chromosome. Recently, the use of DHPLC and direct sequencing of DNA has permitted to identify more than 300 new single nucleotide polymorphisms (SNPs) on the MSY. The analysis of the geographic distribution of the haplogroups identified by these markers has provided new insights in the history of human populations, at the same time, it came out that undetected Y chromosome SNPs still contain useful information. In this study we have analyzed the sequence variation of 60 kb of the TBL1Y gene. While previous studies have analyzed the sequence variation of the Y chromosome in a random sample of individuals, we here focus on 22 chromosomes belonging to three specific haplogroups (A, R1b and E), whose geographic distribution is relevant for the human evolutionary history of Africa and/or western Eurasia. We discovered 32 new SNPs, and placed them in the known Y chromosome phylogenetic tree: about half of the new mutations identify new branches of the tree. The geographic distribution of five new E-M78 sub-haplogroups, analyzed in more than 6,000 subjects from Eurasia and Africa, has led to the identification of interesting evolutionary patterns.

The discovery of new subclades, especially for E-M78 and R1b will be especially welcome for those interested in finer distinctions in these widely prevalent haplogroups. R1b for example occurs throughout the Caucasoid world, and so far very few meaningful sub-haplogroups of it were known. E-M78 is the main sublineage of haplogroup E3b and until now there was evidence fo haplotype clusters that differentiated E-M78 chromosomes; the discovery of new sub-haplogroups will probably reflect to some degree these previously known haplotype clusters.

People interested in their own personal anthropology may be advised to wait until the publication of the R1b and E-M78 sub-haplogroups and their incorporation into commercial "fine-resolution" SNP tests, if they are considering undertaking such a test.

I. Kutuev et al., Phylogeographic analysis of mtDNA and Y chromosome lineages in Caucasus populations

The Greater Caucasus marks a traditional boundary between Europe and Asia. Linguistically, it is one of the most diverse areas of the continental Eurasia, while genetics of the people living there is poorly understood. Mitochondrial DNA and NRY variability was studied in 23 Caucasus populations speaking Caucasus, Turkic, andIndo-European languages. Total sample comprised more than 1700 individuals on Y chromosome and more than 2100 individuals on mtDNA. Genetic outliers among the studied populations are relatively recently arrived Turkic speaking Nogays. The indigenous Caucasus populations possess generally less than 5% of eastern Eurasian mtDNA and Y-chromosomal haplotypes - in a profound contrast to the Turkic-speaking people at the other side of the Caspian, but not so dissimilar compared to the Volga-Turkic Tatars and Chuvashis or to the Anatolian Turks. Haplogroup frequency variation within the Caucasus populations, in some instances significant, appears to be caused primarily by specific aspects of the demographic history of populations. Phylogeographically, a particularly intriguing finding is the presence, though at low frequencies, of a predominantly northeastern African haplogroup M1 in many North Caucasus populations, though they lack sub-Saharan L lineages, relatively frequent in the Arab-speaking Levant. Results obtained help to place the Caucasus populations into the scenario of the peopling of Eurasia with anatomically modern humans. Possible migration routs, peopling of steppe and mountain parts of the Caucasus and causes of high linguistic diversity presence in this region is analyzed in this study.

The finding of M1 lineages in the Caucasus not associated with Sub-Saharan L lineages is important, because it can be explained in only one of two ways:

1. M1 originated in Asia, so its presence in east Africa can be explained by back-migration from Asia. We know that macrohaplogroup M originated in Asia, but it is not clear whether M1 itself originated in Asia or Africa; the "trail" of M lineages between South Asia and Eastern Africa is still flimsy, so we cannot draw any conclusions on this matter yet.
   
2. M1 originated in eastern Africa, but during a time when there was a much small level of penetration of sub-Saharan L lineages into the region.

V. Stepanov et al., Genetic diversity and differentiation of Y-chromosomal lineages in North Eurasia

Composition and frequency of Y-chromosomal haplogroups, defined by the genotyping of 36 biallelic loci in non-recombining part of Ychromosome, was revealed for native population of Siberia, Central Asia and Eastern Europe. Slavonic ethnic groups, which geographically represent Eastern Europe, are characterized by the high frequency of R1a1, I*, I1b, and N3a clades and by the presence of R1b3, J2, E, and G. Most frequent haplorgoup is R1a1, which comprises 44-51% of Y-chromosomes. The distinguishing peculiarity of Central Asian Caucasoids is the high frequency of Caucasoid clades R1a1, J*, J2, and the presence of R1b3 and G. Twenty-five haplogroups were found in gene pool of native Siberian populations. Only 7 of them have the frequency higher than 3%. In sum these 7 clades comprise 86% of Siberian samples. In populations of Southern Siberia the most frequent haplogroup is R1a1. The high frequency of N3a is characteristic for Eastern Siberians, and in Yakuts its frequency is almost 90%. Koryaks, Buryats and Nivkhs have the highest frequency of C3* lineage among investigated populations. Haplogroup O* revealed with variable frequency in most of Siberian. Highest frequency of Q* was found in Ketsand Northern Altayans (85% and 32%, respectively).The high level of genetic differentiation of North Eurasian population on Y-chromosomal lineages was revealed. The proportion of inter-population differences in the total genetic variability of region’s population according to the analysis of molecular variance is 19.04%. Genetic differences between territorial groups took 6.9% of total genetic variability, whereas 12.8% is the inter-population differences within groups.

This study seems to confirm what we already knew about the distribution of haplogroups in northern Eurasia, but it seems like a comprehensive survey of the area, which will be very useful when it appears in print.

S. Sengupta et al., Genescape of India, as Reconstructed from Polymorphic DNA Variation in the Y chromosome

The contemporary male gene pool of ethnic India largely comprises haplogroups that originated indigenously, in southeast Asia, and in west and central Asia. The indigenous haplogroup is predominant among the tribal group . The southeast Asian influence is largely on the male gene pools of Tibeto-Burman speaking tribals and Austro-Asiatic and Dravidian. The west and central Asian influence is primarily on caste groups - both Indo-European and Dravidian. The haplogroup diversity within the various tribal groups is lower than that within the caste groups. Analyses of molecular variance showed higher genetic variability among populations within linguistic clusters of tribals compared to castes. Moreover, the between group variability in the Indo-European caste cluster is higher than that in the Dravidian
caste cluster. This may be a reflection of diverse ancestries, antiquities and isolation of the tribals, coupled with subsequent cultural (linguistic) homogenization. Lesser between group genetic variability in caste groups may be a reflection of their recent founding history. The complete congruence of the patterns of Y-chromosomal and mitochondrial DNA differentiation may be indicative of inflow of both male and female genes from similar source populations. The rank order of FST values showed that tribes and castes are most differentiated, followed by upper and middle caste, upper and lower caste and middle and lower caste.

Again, this study seems to confirm the indigenous component in Indians, and the higher prevalence of western and central Asian Caucasoid haplogroups in castes compared to tribals. Also of interest is the finding that the main difference in the Indian population is between castes and tribals: within the castes, differentiation decreases towards the lower castes, the most differentiated ones being the upper castes.

E. Bogácsi-Szabó et al., Maternal and paternal lineages in ancient and modern Hungarians

Hungarian language represents the westernmost group of the Finno-Ugric language phylum, surrounded entirely by Indo-European speaking populations. Their linguistic isolation in the Carpathian basin suggests the possibility that they might also show a significant genetic isolation. According to historical data at the end of the 9th century Hungarian conquerors from the west side of the Ural Mountains settled down into the Carpathian Basin and took the hegemony. To determine the genetic background of Hungarians we examined mitochondrial and Y chromosomal DNA from ancient `conquerors` from Hungary, originated from the 10th century and from modern Hungarian-speaking adults from today's Hungary and Transylvanian Seklers (Romania). DNA was extracted from 35 excavated ancient bones and hair samples of 125 and 80 modern Hungarians and Seklers, respectively. Mitochondrial haplogroups were determined with HVS I sequencing and RFLP typing. The mtDNA HVS I sequences were compared with 2615 samples from 34 Eurasian populations retrieved from published data. ARLEQUIN 2.001 Software was used to estimate genetic distances between populations. The resulting matrix was summarized in two dimensions by use of Multidimensional Scaling. The M46 biallelic Y chromosomal marker (TAT, often called Uralic migration marker) was also investigated from 2 ancient, 34 modern Hungarian and 60 Sekler samples. Our results suggest that the modern Hungarian gene pool is very similar to other central European ones concerning the mitochondrial and Y chromosomal markers, while the ancient population contains more Asian type elements.

This is a very exciting study comparing ancient Magyar mtDNA and Y chromosomes (at least the Tat-C marker) with those of modern Hungarian speakers. Physical anthropologists have long identified a Mongoloid and mixed Mongoloid component in the Magyars, and this is now confirmed with the finding of Tat-C and Mongoloid mtDNA in the ancient Magyars at a higher frequency than in the modern population. Today, Hungarians are predominantly Caucasoid, and this is supported by the molecular data and reflects the assimilation of the indigenous Caucasoid population by the more "Asian" original Magyar population.

F. di Giacomo et al., Y chromosomal variation in the Czech Republic

In order to analyse the contribution of the Czech Republic to the genetic landscape of Europe, we typed 257 male subjects from 5 locations for 17 Unique Event Polymorphisms of the Y chromosome. Sixteen haplogroups or sub-haplogroups were identified, with only 5 chromosomes uncharacterized. Overall, the degree of population structuring was low. The three commonest haplogroups were R1a
(0.344), P*(xR1a) (0.281) and I (0.184). M157, M56 and M87 showed no variation within haplogroup R1a. Haplogroup I was mostly represented as I1b* and I1b2 was also detected in this population. Thus, the majority of the Czech male gene pool is accounted for by the three main haplogroups found in western and central Europe, the Balkans and the Carpathians. Haplogroup J was found at low frequency, in agreement with a low gene flow with the Mediterranean. In order to draw inferences on the dynamics of the Czech population, we typed 141 carriers of the 3 most common haplogroups for 10 microsatellites, and applied coalescent analyses. While the age of the I clade agreed with that reported in the vast study of Rootsi et al (2004), the ages of its sub-haplogroups differed considerably, showing that the I chromosomes sampled in the Czech Republic are a subset of those found throughout Europe. Haplogroup R1a turned out to be the youngest with an estimated age well after the Last Glacial Maximum. For all three major haplogroups the results indicate a fast population growth, beginning at approximately 60-80 generations ago.

The young age of R1a1 in Czechs, combined with its high frequency make it a likely candidate as reflecting historical or recent prehistorical events, and less likely to reflect the post-LGM recolonization of Europe.