May 14, 2011

ESHG 2011 abstracts are online

From here. I didn't find much of interest this year, except a long-overdue look at Bulgarian Y-chromosomes but with not a very informative abstract.

Y-Chromosome genetic variation of modern Bulgarians
S. Karachanak et al.
To date, Bulgarian Y chromosomes have been studied only in macrogeographic context or in the lineage-based approach. Therefore, in order to comprehensively characterize Bulgarian Y-chromosome variation, we have performed high-resolution phylogenetic analysis of 812 healthy,unrelated Bulgarian males and compared the results with Y-chromosome data from other Eurasian populations.
The genotyping of 60 biallelic markers was performed in hierarchical order by RFLP and DHPLC analyses. The position of Bulgarians among other populations was visualized by Principal Component (PC) analysis.
About 80% of the total genetic variation in Bulgarians falls within haplogroups E-M35, I-M170, J-M172, R-M17 and R-M269. This finding shows that the Bulgarian haplogroup profile is congruent with those described for most European populations.
Among the prehistoric events marked by the observed haplogroups, the greatest contribution comes from the range expansion of local Mesolithic foragers triggered by adoption of agriculture introduced by a cadre of Near Eastern farmers. The Bulgarian Y chromosome gene pool also bears signals of the recolonization from different glacial refugia, the spread of agriculture from the Near East and the expansion of early farmers along the Central and East European river basins.
As for the interpopulation analysis, similarly to mtDNA, Bulgarians belong to the cluster of European populations, still being slightly distant from them. Bulgarians are distant from Turks (despite geographical proximity), Arabic and Caucasus populations and Indians. These trends in the PCA graph likely reflect not only prehistoric, but also more recent demographic events that have shaped the Y chromosome structure of modern Bulgarians.

An abstract on Yakuts seems to report the link between the Altaic-Turkic Yakut and the Altaic-Tungusic Evenk that I also discovered recently.

Autosomal and uniparental genetic diversity of the populations of Sakha (Yakutia): Implications for the peopling of Northeast Eurasia
S. A. Fedorov et al.
Sakha Autonomous Republic occupies a quarter of Siberian total land area in its northeastern part, is an important region for understanding the colonization of the Northern Eurasia by anatomically modern humans. To characterize the genetic variation in Sakha both the haploid mitochondrial DNA (mtDNA) and Y chromosomal as well as diploid autosomal loci (650 000 SNPs) of genome were analyzed in five native populations of Sakha (Yakuts, Evenks, Evens, Dolgans and Yukaghirs).
While striking prevalence of Y chromosome haplogroup N1c in gene pool differentiates Yakuts from other populations, the mtDNA and autosomal analyses demonstrate genetic similarity of all native populations of Sakha, in particular Yakuts and Evenks. The results also demonstrate closest genetic proximity of the populations of Sakha with southern Siberians. Both mtDNA and autosomal analyses reveal deep genetic discontinuity between Siberian and Beringian populations. MtDNA haplogroups A2 and G1b, prevalent in Beringian populations, are either minor or even absent in Sakha, where haplogroups C and D dominate. Autosomal analysis also differentiates Beringian populations from those of Sakha. Our results support the scenario that the territory of Sakha was colonized from the regions west and eastward of Lake Baikal with only minor gene flow from Lower Amur/Southern Okhotsk region and/or Kamchatka.
An abstract on Lithuanian Y-chromosomes

The place of the population of Lithuania between Northern and Eastern Europe: Y chromosome analysis
I. Uktverytė et al.

The population of Lithuania is constituted of 6 dialectal groups which form two major ethno-linguistic groups known as Aukštaitish and Žemaitish, both speaking Baltic languages of Indo-European family. Neighbouring Finno-Ugric (Northern and Eastern Europe), Slavonic (Eastern Europe) and Germanic (Northern Europe) populations surrounding the Baltic sea region influenced historical formation of Lithuanian ethno-linguistic groups. Analysis of the Lithuanian population genetic composition helps to understand the origin, history and place among other populations.
Y chromosome analysis was performed for 301 individuals from 6 dialectal groups. 25 SNPs were genotyped (TaqMan) to determine Y haplogroup and 17 STR were analysed to determine haplotype for each individual. Most frequent haplogroups in the population of Lithuania are R1a1a (42.2%, R1a1a1g compose 8.97% in studied population) and N1c1 (40.5%) and less frequent haplogroups are R1b1b1, I1, I2a, E1b1b1 (<5% each). AMOVA showed no statistically significant differences between two major ethno-linguistic groups Aukštaitish and Žemaitish (among groups p-value=0.897, among population within groups p-value=0.194, within populations p-value=0.282 based on 10100 permutations). MDS of genetic distances based on Y-biallelic markers showed that Lithuanians are closer to Latvian and Estonian populations than to Slavic populations (European part of Russia, Poland, Ukraine, Belorussia, stress=0.029). According to the frequencies of haplogroups, no statistically significant differences between ethno-linguistic groups were detected (p>0.05), moreover, MDS analysis sets the population of Lithuania between Northern and Eastern European populations.

An abstract on Sardinian population structure.

A genome-wide analysis of Sardinian population structure
M. Steri et al.

Sardinia is particular attractive for human genetic studies, being one of the larger isolated populations and thus suitable for large-scale studies. Several attempts have been made to explore its genetic structure, but they either analyzed a large set of markers in very few samples or thousands of individuals at specific loci. Here we genotyped 2,615 individuals with the Affymetrix 6.0 array. Samples were recruited from the north, south and central east areas of the Island, and initially considered as 3 distinct populations. Genotype calling was performed with Birdseed-v2, considering all samples as a unique cluster to avoid batch effects. Subsequently, we applied standard filters for samples and SNP quality, and used IBD sharing to detect, and discard, hidden relatives. Using principal component analysis, we identified outliers and reassigned each individual accordingly. An analysis of molecular variance indicated that only 0.21% of the variability could be attributable to inter-population variation (Fst=0.002), confirming a lack of large-scale substructure. We thus considered the Sardinians as a unique sample. Compared to HapMap3 populations, as expected, higher similarity was observed with Tuscany and CEPH samples (Fst=0.005 and 0.010, respectively). A genome-wide search for SNPs highly differentiated between Sardinians and these European populations confirmed the specialness of HLA and LCT regions, and also showed elevated Fst values (>0.27) at the CR1 gene, known to be related to malaria severity. We are now integrating sequencing data of many individuals to provide a more comprehensive analysis of variants in addition to the common SNPs in current genotyping platforms.

A major new study on Arabian mtDNA

Phylogeographic analyses; mitochondrial DNA; Arabian Peninsula
V. Fernandes et al.

Phylogeographic analyses of mitochondrial DNA (mtDNA) provide insights into modern human evolution. In recent years, worldwide studies of contemporary mtDNAs have indicated that modern humans left Africa ~60,000-70,000 years ago along the “southern coastal route”, across the Red Sea and via the Arabian Peninsula. Yet no obvious signs of the passage though Arabia have been found in genetics and archaeology fields. The aims of this work are to seek for possible mtDNA relicts of the initial dispersal from Africa in Arabia and to investigate the origins of lineages that arrived later. We are doing this by sequencing the complete mtDNA molecule (~16,568 bp) from unclassified lineages (referred to as the paraphyletic clusters L3*, N* and R*) and poorly studied haplogroups within the Eurasian macrohaplogroup N, which is predominant in Arabian populations today (86% in Saudi Arabia, 66% in Yemen and 79% in Dubai), in 90 samples from Dubai, Yemen, North/East Africa, the Near East and Europe. Our results will allow to test hypotheses about the settlement of the Arabian Peninsula.

No comments: