ESHG 2013 abstracts

A couple of weeks before the ESHG 2013 conference, here are a few abstracts that caught my eye. Feel free to point to more interesting presentations in the comments section.

• J16.05 - Checking the hypothesis of a Balkan origin of the Armenians
• P17.5 - Y chromosome haplogroup analysis to estimate genetic origin of Balts
• J16.27 - Armenian Highland as a transition corridor for the spread of Neolithic agriculturists
• J16.14 - In Search of the Origin of Haplogroup J1-P58
• J16.03 - Y-chromosome haplogroup analysis in the Besermyan ethnic group
• P17.4 - Mitochondrial DNA Analysis of the Southeast European Genetic Variation Reveals a New, Local Subbranching in Hg X2
• P16.085 - Population diversity and history of the Indian subcontinent: Uncovering the deeper mosaic of sub-structuring and the intricate network of dispersals
• J16.43 - Ancient mtDNA diversity in Bulgaria
• P16.072 - Mitochondrial DNA diversity in medieval and modern Romanian population
• P16.012 - Frequency analysis of the CCR5-Delta32 allele in medieval and modern Romanian population
• J16.78 - The gene pool of Argyn in the context of generic structure of Kazakhs according to data on SNP-Y-Chromosome markers.

ESHG 2012 abstracts

I had posted some interesting titles in April, and it is finally time for us, mere mortals, to have access to the abstracts. A few of the abstracts:


Title: P10.39 - Analysis of mitochondrial DNA haplotypes of old human populations from the Bronze and Iron Age from Romania

Keywords: mitochondrial DNA; haplotypes; Bronze and Age populations

Authors: A. Rodewald1, G. Cardos2, C. Tesio3;

Abstract: Our genetic study was focused on old human populations from the Bronze and Iron Ages from Romania in order to analysed their genetic variation and their genetic kinship al mitochondrial DNA(mtDNA)level with today´s Romanian populations and other modern European populations. The ancient DNA(aDNA)was extracted from skeletal remains of 50 individuals from the Bronze and Iron Age by a phenol-chloroform DNA extraction method.MtDNA HVR I and HVR II regions were amplified by PCR and sequenced by the dideoxy chain terminator method.The aDNA data were analysed in comparison with corresponding mtDNA data of modern Romanian people and other 11 European populations.The ancient mtDNA haplotypes were framed into 12 haplogroups. The most frequent mtDNA haplotype identified in the old individual sample from Romania was the CRS-like, and the most frequent haplogroup was H. Significant differences in haplogroup frequencies between the old people and modern Romanians were found. Low values of internal standard genetic diversity indices suggested reduced genetic variability within old human populations from the Bronze and Iron Age from Romania, in contrast to all modern European populations and also modern Romanians, which showed higher mitochondrial haplogroup diversity values. This fact might be the result of social and cultural local organization in small tribes, partially reproductively isolated. Concerning the genetic relationships at mitochondrial level, old human populations from Romania have shown closer genetic relationship to Turks of Thracian origin,while modern Romanians were closer to modern Bulgarian, Italian, Greek and Spanish populations.

The relationship between prehistoric Romanian mtDNA and modern Thracian Turkish one is not very surprising, given that the latter are basically descended from populations of indigenous origin that converted to Islam during the Ottoman era. It will be worthwhile to see exactly which locations/communities were used to sample from. It is awesome that we are beginning to get ancient DNA data from southeastern Europe.



Title: P10.40 - Complete mitochondrial DNA diversity in Iranians
Keywords: Mitochondrial DNA; population; Iran
Authors: A. Bahmanimehr1, M. Derenko2, B. Malyarchuk2, G. Denisova2, M. Perkova2, S. Farjadian3, L. Yepiskoposyan1;

Abstract: The complete sequencing of mitochondrial DNA has contributed a great deal to the understanding of the timing and direction of human dispersals around the world. To elucidate the early stages of human colonization process outside of Africa and to investigate the demographic history of human populations from the Middle East we have completely sequenced the mtDNAs of 275 Iranians represented by Persians (N=105), Mazandaranians (N=4), Azerbaijanians (N=22), Kurds (N=5), Lurs (N=5), Armenians (N=10), Bakhtiarians (N=2), Gilakis (N=2), Indians (N=1), Turkmens (N=10), and Qashqais (N=109). Overall diversity is very high, with 252 different sequences falling into 75 major haplogroups within macrohaplogroups L, N and M. The majority of Iranian mtDNAs (90.9%) belongs to Western Eurasian component composed of haplogroups N1, N2, X, R2’JT, U, and R0, though the impact of African (L2a, L3d, L3f), Southern Asian (R8, M4, M5, M18, M42), and Eastern Eurasian (A4, B4, C4, C5, D4, F1, G2a) lineages is also perceptible being found at frequencies of 1.5%, 2.5%, and 5.1%, respectively. Results of molecular dating of Iranian mtDNA lineages show that macrohaplogroup N and its haplogroups N1, R, U, R2’JT coalesce to the time of 45-60 kya, marking the first stages of modern humans movement out of Africa. The ancient ancestry of Iranian gene pool is also confirmed by revealing of the unique N23 lineage survived both in Persians and Qashqais, albeit at low frequencies. This study was supported by Russian Foundation for Basic Research (11-04-00620) and by Far-East Branch of the Russian Academy of Sciences (12-III-A-06-101).

Title: P10.58 - A Y -chromosome portrait of modern Bulgarians as viewed from different spatiotemporal aspects
Keywords: Y chromosome; Bulgarians; haplogroup
Authors: S. Karachanak1,2, V. Grugni2, D. Nesheva1, N. Al-Zahery2, V. Battaglia2, C. Nici2, V. Carossa2, Y. Yordanov3, A. Torroni2, A. S. Galabov4, O. Semino2,5, D. Toncheva1,5;

Abstract: To address the structure and evolution of the Bulgarian paternal gene pool, we have examined the Y chromosome variation in 809 Bulgarian males. The analysis was performed by high-resolution genotyping of biallelic markers and by analyzing the STR variation within certain haplogroups. The biallelic markers were analyzed by PCR/RFLP and PCR/DHPLC assay. Seventeen fast-evolving Y-STRs were amplified using the multiplex AmpFlSTR Yfiler PCR Amplification Kit (Applied Biosystems) and were read on ABI 310 genetic analyzer with GeneMapper software.We found that the Bulgarian Y chromosome gene pool is primarily contained within haplogroups common in Europe and surrounding areas. Furthermore, when patrilineal relationships are visualized in a broader context by principal component analysis, Bulgarians are located among European populations. The analysis of molecular variance shows that the genetic variation within the country is structured among Western, Central and Eastern Bulgaria, rather than among the Black Sea coast, the Danubian Plane, Thrace and the Southwest mountainous region; which indicates that the Balkan Mountains have been permeable to human movements.
Y-STR variation ages and median joining networks of haplogroups E-V13, J-M241, R-M458, R-L23 and I-M423 were calculated together with data from other populations. For this purpose, the analyses of STR variation within haplogroups were based on 8 STR loci, with the exception of haplogroup R-M458, for which the STR profiles were further reduced to 7 loci. In general, the Y-STR data reveal that different prehistoric and historic events have left detectable traces in the Bulgarian Y chromosome gene pool.

This is quite welcome, as Bulgaria has been a bit of a "black hole" in population genetics. Finally having an authoritative sample on its Y-chromosome composition is extremely important.


Title: P10.45 - Population isolates from Greece offer potential for powerful disease gene mapping: the HELIC-Pomak and MANOLIS studies
Keywords: population isolate; genetic association; rare variants
Authors: I. Tachmazidou1, A. Farmaki2, L. Southam1, K. Palin1, N. W. Rayner1,3, E. Daoutidou2, I. Ntalla2, K. Panoutsopoulou1, G. Dedousis2, E. Zeggini1;

Abstract: The study of low-frequency and rare variants can be empowered by focusing on isolated populations, in which rare variants may have increased in frequency and linkage disequilibrium tends to be extended. Sequencing is efficient in isolates, because variants are shared in extended haplotype contexts, supporting accurate imputation. Here we assess sample sets collected from two Greek populations: the Pomak villages are a set of religiously-isolated mountainous villages in the North (population size 11,000); Anogia is a mountainous village on Crete, with high levels of longevity (population size 4,000). 747 and 1118 individuals respectively were typed on the Illumina OmniExpress platform. We calculated genome-wide IBS statistics to assess the degree of relatedness and compared it with the general Greek population (707 samples with OmniExpress data, TEENAGE study). We additionally calculated the proportion of individuals with at least one “surrogate parent” as a means for accurate long-range haplotype phasing and imputation, as proposed by Kong et al, Nature Genetics 2008. We find 1-1.4% of individual pairs with pi-hat>0.05, and ~0.4% with pi-hat>0.1 in the isolates compared to 0% in the general Greek population. We also find that ~80%-82% of subjects have at least one surrogate parent in the isolates, compared to ~1% in the outbred Greek population. We have established the HELIC-Pomak and MANOLIS cohorts as genetic isolates and are currently whole-genome sequencing 250 individuals to enable imputation and subsequent association testing. This approach has the potential to identify novel robust associations with disease-related complex traits.

It will be wonderful if some of these population samples become publicly available.

ESHG 2012 titles

The abstract text will be available only two weeks prior to the meeting in June, lest us mere mortals receive more hints about recent scientific progress than we deserve.

The presentations/posters at ESHG were probably ready -as relatively mature work- by the beginning of this year, and will find themselves in journals by its end. This is a year's delay from the time when research could have been available to when it will actually  be so.

It is worth reminding ourselves what the whole charade of pre-publication peer review and the conference circuit, a fossil of a time when there was no WWW or webcasting, amounts to little more than a way of  delaying the dissemination of new research. It is a little ironic that journals and conferences were invented to facilitate the flow of scientific information to as wide an audience as possible, and are now used to make it more difficult.

I put in bold some titles of particular interest.

• T. W. Winkler et al. C06.2. Genome-wide search for gender different genetic loci for human anthropometric traits: Methods and results from genome-wide meta-analyses across 270,000 Individuals
• O. Delaneau et al. C17.2. Haplotype phasing using next-generation sequencing reads
• L. M. Huckins et al. Using ancestry-informative markers to identify fine structure across 15 populations of European origin.
• A. Rodewald et al. Analysis of mitochondrial DNA haplotypes of old human populations from the Bronze and Iron Age from Romania
• A. Bahmanimehr et al. Complete mitochondrial DNA diversity in Iranians
• I. Uktverytė et al. mtDNA haplogroups in the population of Lithuania
• I. Tachmazidou et al. Population isolates from Greece offer potential for powerful disease gene mapping: the HELIC-Pomak and MANOLIS studies
• C. Stemper et al. Very high frequency of hereditary prosopagnosia among individuals with high intellectual ability
• S. Karachanak et al. A Y -chromosome portrait of modern Bulgarians as viewed from different spatiotemporal aspects
• A. Puzuka et al. Ethnogenetic Estimation of Baltic ancestry

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.

ESHG 2010 abstracts

Some excerpts from this year's European Society of Human Genetics meeting:

P10.31 - Pigmentation gene MC1R shows strong genetic patterning in Eurasia

We present a comprehensive analysis of allele/haplotype frequencies from five functional SNPs (rs1805005, rs2228479, rs1805007, rs1805008, and rs885479) in MC1R throughout Eurasia, including from 12,151 individuals from 141 regional populations, focussing on novel genotype data from 38 Central Asian populations.

P10.39 - Genetic variation in Bulgarians: a mitochondrial DNA perspective

The structure and diversity of the Bulgarian mitochondrial DNA (mtDNA) gene pool is still almost unknown. In the present study, we have evaluated the extent and nature of mtDNA variation in the largest Bulgarian sample to date, comprising 855 healthy unrelated subjects from across the country.

P10.41 - Mitochondrial genome diversity in Ulchi, the tungusic-speaking tribe of the Russian Far East

The present report is based on the study of mtDNA variation in Ulchi (n=74), a Tungusic-speaking tribe of hunters and fishermen dispersed along the lakes and reaches of the Lower Amur. MtDNA analysis revealed 39 distinct mtDNA haplotypes belonging to 21 Eurasian haplogroups C2-C3, D3-D8, D11, G1-G2, M7-M9, Z, B, F, N9, Y and U4, with overall N macrohaplogroup derivatives frequency 53%, M - 43%, and R - 4%.

P10.62 - Genetic structure of Western Caucasus populations on the base of uniparental polymorphisms

We have analyzed 52 markers in coding region of the mtDNA and 48 markers in the non-recombining part of the Y-chromosome in 592 individuals representing five populations from western Caucasus (Abkhazians, Adyghes, Abazins, Georgians, and Circassians). Y-chromosome haplogroups G-M201 and J2 (J-M172) account for more than 50% of all haplogroup diversity in the studied populations. Haplogroup G-M201 in the Western Caucasus populations is represented only by subclade G2a (G-P15) with the insignificantly low exception in the Adyghe population where G1a (G-P20) amounts to less than 1%. In contrast to high frequency of J2 haplogroup J1 exhibit moderate occurrence and vary from 2 to 6 %. Haplogroup R1a (R-SRY10831.2) is also present in all studied populations.

ESHG 2009 abstracts

ESHG 2009 is in two weeks, and there are some very interesting abstracts, including a tantalizing new study on Y-chromosome haplogroup R1b1b2 (R-M269).

Phylogeography of human Y chromosome haplogroup R1b1b2 (R-M269) in Europe

F. Cruciani et al.

The human Y chromosome haplogroup R1b1b2 (R-M269) displays an extremely wide geographic distribution within Europe, with a decreasing frequency cline from Iberia (frequencies up to 90%) towards the Balkans (usually less than 10%). Previous studies have proposed that the observed R1b1b2 frequency cline is due to a population expansion from an Iberian Ice-age refugium after the LGM (Malaspina et al. 1998; Semino et al. 2000).

In this study, we explored the phylogeography of the human Y chromosome haplogroup R1b1b2 by analyzing more than 2,000 males from Europe. The haplogroup-defining marker M269 (Cruciani et al. 2002), and two additional internal markers (U106 and U152, Sims et al 2007) which identify internal branches (R1b1b2g and R1b1b2h) were analyzed. The paragroup R1b1b2*(xR1b1b2g, R1b1b2h) and the haplogroups R1b1b2g and R1b1b2h showed quite different frequency distribution patterns within Europe, with frequency peaks in the Iberian Peninsula, northern Europe and northern Italy/France, respectively. The overall frequency pattern of R1b1b2 haplogroup is suggestive of multiple events of migration and expansion within Europe rather than a single and uniform spread of people from an Iberian Ice-age refugium.

References:

Malaspina et al. (1998) Am J Hum Genet 63:847-860
Semino et al. (2000) Science 290:1155-1159
Cruciani et al. (2002) Am J Hum Genet 70:1197-1214
Sims et al. (2007) Hum Mutat 28:97

Note that in the abstract below, the authors refer to Slavopaionians, not Macedonians.

Y chromosome haplogroup R1a is associated with prostate cancer risk among Macedonian males

D. Plaseska-Karanfilska et al.

Prostate cancer (PC) is one of the most common male-specific cancers. Its incidence varies considerably between populations. Recent surveys suggest that PC is influenced by both genetic and environmental factors, although the etiology of the disease remains unknown in the majority of cases. Certain Y chromosomal lineages have been suggested to predispose individuals to prostate cancer in Japanese population, but no association has been found among Korean and Swedish patients. The aim of this study was to investigate the association between Y chromosomal haplogroups and predisposition to prostate cancer in Macedonian men. We studied 84 PC patients and 126 males from the general population of Macedonian ethnic origin. A total of 28 markers have been studied by multiplex PCR and SNaPshot analysis. Nineteen different Y haplogroups were determined; the most frequent being I1b-P37b, E3b1-M78, R1a-SRY 1532, R1b-P25 and J2b1a-M241. The frequency of R1a was significantly higher in PC patients (20.2%) in comparison with the controls (9.5%) [p=0.027; OR=2.41 (1.09-5.36)]. When stratified according to age, even stronger association was observed between haplogroup R1a and prostate cancer in patients of >65 years of age [p=0.004; OR=3.24 (1.41-7.46)]. Our results suggest that Y chromosome haplogroup R1a is associated with an increased prostate cancer risk in Macedonian men.

The genetic position of Western Brittany (Finistère, France) in the Celtic Y chromosome landscape

K. Rouault et al.

Brittany, a large peninsula located at the western part of France, is of particular interest because of its historical settlement and its relative geographic and cultural isolation. Brittany was invaded by waves of migration from Britain and Ireland between the 4th and 7th centuries and, therefore, belongs to the Brythonic branch of the Insular Celtic language. We have focused our study on the department of Finistère, the most western territorial unit of Brittany, and its administrative and historical areas. To explore the diversity of the Y-chromosome, we analyzed a total of 348 unrelated males using a combination of 23 biallelic markers and 12 microsatellite loci. The molecular analysis revealed that 82.2% of the Y chromosomes fell into haplogroup R1b, placing Finistère within the Western European landscape. Interestingly, at a microgeographical level, differences were detected by the haplogroup R1a* being confined to the south of the department, while haplogroups E3b, F, G, J2, K and R1a1 were found in the north. Nevertheless, geographical distribution of haplogroups and haplotypes suggested territorial homogeneity inside Finistère. Most of the Y-chromosomal gene pool in Finistère is shared with European, especially British, populations, thus corroborating the historical reports of ancient migrations to Brittany. Finally, the results are consistent with those obtained from classic genetic markers and support the Celtic paternal heritage of the Finistère population.

Mitochondrial Genome Diversity in Tungusic-speaking Populations (Even and Evenki) and Resettlement of Arctic Siberia After the Last Glacial Maximum

I. O. Mazunin et al.

The present study includes the Even/Evenki, hunters and reindeer-breeders, sampled from a few localities scattered across their vast geographic range encompassing low Yana-Indigirka-Kolyma in the west and the Sea of Okhotsk coast in the east. The mtDNA data show a very close affinity of the Even/Evenki with the Yukaghir, typical reindeer hunters, dominating in extreme northeastern Siberia until the middle of 18th century but now being on the brink of extinction. We found that the majority of mtDNA diversity in the Tungusic-speaking populations was accounted for by Siberian-East Eurasian lineages C2, C3, D2, D3, D4-D9 and G1. The similarity in the haplogroup C and D mtDNA intrinsic variation between the Even and Yukaghir populations is pronounced and indicates that the Even/Evenki harbor an essential portion of the ancestral Yukaghir pool. The phylogeography of the D4-D9 point to an early Neolithic phase expansion initiated northward to the northern and eastern perimeters of former Beringia. Concerning unique D2* lineage (Volodko et al. 2008), the network analysis encompassing four complete sequences, three of the Yukaghir from the low Indigirka-Kolyma region and one of the Evenk from the upper reaches of the Aldan River would suggest that the founding haplotype (1935-8683-14905) for D2* originated within western part of former Beringia. In the meanwhile, the core of the Even/Evenki mtDNA pool residing in the midst of the Yukaghir ancient territory would represent a recent amalgamation of the remnants of the Yukaghir and northern Tungusic-speakers (Even/Evenki) originated in the mid-Amur region.

X-chromosomal haplotypes in global human populations

V. A. Stepanov, I. Y. Khitrinskaya;

To reconstruct the origin and evolution of X-chromosomal lineages in global human populations we investigated the genetic diversity in 23 population samples (about 1500 individuals totally) using SNP markers in a single linkage disequilibrium region of ZFX gene. About sixty haplotypes belonging to 3 phylogenetic branches (A, B, and F) originated from the single African root were found in the total sample. Branch A includes mostly African haplotypes, whereas four major haplotypes belonging to different sub-branches of B (haplotype E8) and F (haplotypes H4, I3 and I11) were present in Eurasia. Major haplotype of the older branch B (E8) is almost evenly distributed among Eurasian populations. Haplotypes of the younger phylogenetic branches demonstrates clinal distribution with the sharp frequency changes from East to West. Haplotype H4 is presumably “Eastern-Eurasian”. It reaches the highest frequency in Eastern and South-Eastern Asians. Haplotypes I3 and I11 in the contrary show the clear frequency gradient from West to East with the highest frequency in Europeans, moderate frequency in Central Asia, and the minimal frequency in North-East and South-East Asia. The total level of genetic differentiation of global human populations estimated by the analysis of molecular variance of X-chromosomal haplotypes (Fst = 9.1%) is quite high and roughly corresponds to those measured for most other types of genetic markers except Y-chromosomal haplogroups which are characterized by the much higher level of between-population differences.

Dissecting the genetic make-up of Central Eastern Sardinia using a high density set of sex and autosomal markers

L. M. Pardo

Genetic isolates are valuable for identifying genetic variations underlying complex traits. However, prior knowledge of the genetic structure of the isolate is fundamental for carrying-out genome-wide association studies (GWAS) in these populations. The Sardinian population is currently the target of GWAS because of its ancient origin and long-standing isolation. To perform GWAS in Sardinia, we aim to characterize a subpopulation from the archaic area of Central-Eastern Sardinia at the genomic level. We used sex-specific markers (Y-chromosome and mtDNA) to assess the heterogeneity of the founder lineages and the divergence from other populations. In addition, we used a dense set of autosomal markers (SNP 5.0 array, Affymetrix) to investigate genome-wide Linkage Disequilibrium, to construct a Copy Number Variation map and to estimate pair-wise kinship and inbreeding.We first determined Y-chromosome lineages in 256 unrelated Sardinians using biallelic and microsatellite markers. Our analysis showed that the frequency of the major Y haplogroups clearly sets this population apart from other European haplogroups. The analysis of microsatellite markers revealed a high degree of gene diversity. Pairwise kinship and inbreeding were estimated in 113 subjects using 77709 autosomal SNP markers. We found that 16% of the subject pairs shared identical-by descent alleles more often than expected by chance. Furthermore, 60% of the subjects had low inbreeding coefficient values. Our preliminary results confirm that Sardinia is genetically different from other populations, as shown by Y-chromosome markers. The kinship and inbreeding estimates indicate some degree of relatedness among Sardinians, as expected for an isolated population.

Genetic differences between four European populations

V. Moskvina et al.

Population stratification can distort the results of genome-wide association studies (GWAS). One approach to deal with this inflation of the statistic is to estimate the inflation factor and adjust the detection statistic accordingly. However, the evolutionally forces work with different strength in some regions of the human genome, e.g. around the lactase gene (LCT) and the HLA region, making such an adjustment inappropriate.

We examined the population differences in four European populations (Scotland, Ireland, Sweden and Bulgaria) using data from GWAS performed with the Affymetrix 6.0 array at the Broad Institute. We show that there are >20,000 SNPs which are highly (p less than 10-6) significantly stratified between the four populations, after genome wide Bonferroni correction for multiple testing. We then examined the top 20 stratified regions to see what genes might have caused the top differences, using a highly conservative cut-off of p less than 10-40. Some of the loci span genes reported before: hair colour and pigmentation (HERC2, EXOC2), the LCT gene, genes involved in NAD metabolism, and genes involved in immunity (HLA and the Toll-like receptor genes TLR10, TLR 1, TLR 6). Among the top hits were several genes which have not yet been reported as stratified within European populations, indicating that they might also provide a selective advantage. Some involve other immunity genes (CD99, ILT6), but others show no obvious effect on positive selection: several zinc fingers, and most intriguingly, FOXP2, implicated in speech development. Future GWAS should take into consideration any positive associations with these genes.

Genomic runs of homozygosity: population history and disease

R. McQuillan

Runs of homozygosity (ROH), resulting from the inheritance from both parents of identical haplotypes, are abundant in the human genome. ROH length is determined partly by the number of generations since the common ancestor: offspring of cousin matings have long ROH, while the numerous shorter ROH reflect shared ancestry tens and hundreds of generations ago. In studies of European populations we show that Froh, a multipoint estimate of individual autozygosity derived from genomic ROH, distinguishes clearly between subpopulations classified in terms of demographic history and correlates strongly with pedigree-derived inbreeding coefficients. In a global population dataset, analysis of ROH allows categorisation of individuals into four major groups, inferred to have (a) parental relatedness in the last 150 years (many south and west Asians), (b) shared parental ancestry arising hundreds to thousands of years ago through population isolation and restricted effective population size (Ne), but little recent inbreeding (Oceanians, African hunter-gatherers, some European and south Asian isolates), (c) both ancient and recent parental relatedness (Native Americans), and (d) only the background level of shared ancestry relating to continental Ne (east Asians, urban Europeans; African agriculturalists). Long runs of homozygosity are therefore a widespread and underappreciated characteristic of our genomes which record past consanguinity and population isolation and provide a unique record of individual demographic history. Individual ROH measures also allow quantification of the disease risk arising from polygenic recessive effects. We present preliminary data from a survey of the effects of ROH on quantitative disease-related traits and disease risk.

European Lactase Persistence Allele is Associated With Increase in Body Mass Index

J. A. Kettunen et al.

The global prevalence of obesity, usually indexed by body mass index (BMI) cut-offs, has increased significantly in the recent decades, mainly due to positive energy balance. However, the impact of a selection for specific genes cannot be excluded. Here we have tested the association between BMI and one of the best known genetic variants showing strong selective pressure: the functional variant in the cis-regulatory element of the lactase gene. We tested this variant since it is presumed to provide nutritional advantage in specific physical and cultural environments. We found that the variant responsible for lactase persistence among Europeans was also associated with higher BMI in a Nordic population sample (p = 1.3*10-5) of 15 209 individuals, the size of the effect being close to that of FTO. We tested the effect of population stratification and concluded that the association was not due to population substructure.

ESHG 2008 abstracts

The European Society of Human Genetics conference is coming up, and there are some very interesting abstracts.

Note: The ESHG site has updated with a notice that the abstracts are embargoed until their presentation time. Therefore, I have decided to remove the body of this post until then, although I think it is a bit weird to embargo something that one places on the public web. In any case, you can find the abstracts easily by going to the site above. (June 1): post restored.

The peopling of North Asia: Y and X perspectives

V. A. Stepanov, V. Kharkov, I. Khitrinskaya, O. Medvedeva, M. Spiridonova, A. Marusin, V. Puzyrev; Institute for Medical Genetics, Tomsk, Russian Federation.

Presentation Number: P07.056

To reconstruct the origin and evolution of human populations in North Asia we investigated the genetic diversity in 50 population samples (about 2000 individuals totally) using Y and X chromosome lineages. Y-chromosomal haplotypes were constructed with unique event polymorphisms (UEP) and STR markers according to Y Chromosome consortium (YCC) classification. SNP markers in a single 60 kb linkage disequilibrium region of ZFX gene was used to trace the X chromosomal population history. The genetic diversity of Y haplogroups was quite high (0.70 - 0.95) in most populations except few very isolated groups. The proportion of inter-population differences in the total genetic variability measured by Fst statistics is 17% for binary haplogroups and 19% for YSTR. Multidimensional scaling and principal component analysis revealed four major components in North Asian Y gene pool, reflecting the presence of Paleoasiatic (Q), Proto-Uralic (N3, N2), Eastern Asian (O, C), and Western Eurasian (R1, I, J) lineages. X-chromosomal haplotypes in North Asia are less divers (gene diversity within populations 0.65 - 0.80) and less differentiated (Fst = 4%) compared to Y lineages. The population clustering by X and Y gives, to a first approximation, a similar picture, and matrixes of genetic distances between populations for X and Y haplotypes significantly correlates. The age of genetic diversity generation and time of population differentiation demonstrates the Upper Paleolithic origin of major Y and X lineages and post-glacial population expansions. This work is supported by RFBR grants ##06-04-48274 and 07-04-01629.

The following seems to be a very important study; in particular the notion that particular Y chromosome/mtDNA haplogroups may be associated with higher or lower fertility may have implications about their distribution.

UPDATE (May 21): I did a quick and dirty analysis of the Y-haplogroup and mtDNA-haplogroup data from Bosch et al. (2006) (Ann Hum Genet. 2006 Jul;70(Pt 4):459-87.), and there is a -0.43 correlation between Y-haplogroup I and mtDNA-haplogroup H and a +0.46 correlation between Y-haplogroup R1 and mtDNA-haplogroup H. While not significant (with only 10 populations), this is definitely in the right direction for a selection effect for/against specific Y-DNA/mtDNA combinations.

... on the other hand, another quick and dirty analysis of 23 populations from Rootsi's survey on Y-haplogroup I and mtDNA frequencies from AJHG Volume 80, Issue 4, April 2007, Pages 759-768 didn't turn up any correlation. Perhaps, someone can look at possible correlations between Y-chromosome and mtDNA haplogroups in Europe to see if anything interesting turns up.

Male infertility induced by mtDNA/Y unfavorable combination? An association study on human mitochondrial DNA

S. C. Gomes1, S. Fernandes2, R. Gonçalves1, A. T. Fernandes1, A. Barros3, H. Geada4, A. Brehm1; 1Human Genetics Laboratory, University of Madeira, Funchal, Portugal, 2Genetics Department, Faculty of Medicine, University of Porto, Porto, Portugal, 3Centre of Reproductive Genetics A Barros, Porto, Portugal, 4Faculty of Medicine, University of Lisbon, Lisboa, Portugal.

Presentation Number: P07.084

There is growing evidence that certain mtDNA haplogroups determine a genetic susceptibility to various disorders bringing out the interest in the possible role of mtDNA background on the phenotype expression of mitochondrial genetic disorders. An association between haplogroup T and asthenospermia has been reported and several sublineages of haplogroup U were associated with differences in sperm motility and vitality. The deletion of some DAZ copies gene in 10-15% of azoospermic and oligospermic patients has been reported but also present in fertile men belonging to certain Y-haplogroups. The findings of one study have rarely been replicated by studies in other populations and conflicting associations have been reported. Our focus in this case-control study is to investigate the existence of other influences, besides a weak mtDNA background, promoting male infertility. The occurrence of a specific mtDNA variant associated to a certain Y-chromosome haplogroup could represent a vital link that will compromise the sperm function and be responsible for male infertility. A group of 99 infertile men and other one composed by 90 subjects with proven fertility were selected and analysed. The frequency of the combination mtDNA-haplogroup H (especially with the CRS sequence) and Y-haplogroup R was higher in fertile than in infertile men seemingly to be favorable to fertility. On the other hand, a considerable number of infertile men belonging to mtDNA-haplogroup H (CRS) and to Y-haplogroup I, associated to a specific DAZ gene deletion pattern- 2+4d, suggests a non favorable combination to male fertility.

The Bayash Roma: phylogenetic dissection of Eurasian paternal genetic elements

I. Martinovic Klaric, M. Pericic Salihovic, L. Barac Lauc, B. Janicijevic; Institute for Anthropological Research, Zagreb, Croatia.

Presentation Number: P07.110

The Bayash consist of numerous and small Romani groups speaking different dialects of the Romanian language and living dispersedly in Croatia, Hungary, Bosnia and Herzegovina, Serbia, Romania, Bulgaria, and to the lesser extent in Macedonia, Greece, Ukraine, Slovakia and Slovenia. Larger Bayash groups migrated to Croatia most likely during the 19th century, after abolition of slavery in Romania. Molecular architecture and the origin of the Croatian Bayash paternal gene pool was addressed by analysing 151 Bayash Y chromosomes from two Croatian regions, 332 Y chromosomes from Romani populations across Europe, 814 Y-chromosomes from non-Romani host populations living in Southeastern, Southern and Eastern Europe as well as with 1680 Y-chromosomes from South Asian populations. The Bayash in Croatia represent one population of largely shared paternal genetic history characterized by substantial percentage (44%) of common H1-M82 and E3b1-M78 lineages. Relatively ancient expansion signals and limited diversity of Indian specific H1-M82 lineages imply descent from closely related paternal ancestors who could have been settled in the Indian subcontinent between 7th and 9th centuries AD. Minimal time divergence of the Bayash subpopulations is consistent with their putative migratory split within Romania towards Wallachia and Transilvania. Substantial percentage of E3b1 lineages and high associated microsatellite variance in the Bayash men is a reflection of significant admixture with majority populations from the Vardar-Morava-Danube catchment basin - possibly a common paternal signature of Romani populations in Southeastern Europe. Additional traces of admixture are evident in the modest presence of typical European haplogroups.

Are the Moravian Valachs of Czech Republic the Aromuns of Central Europe? Model population for isolation and admixture

E. Ehler1,2, V. Vančata2; 1Department of Anthropology and Human Genetics, Charles University in Prague, Faculty of Science, Prague, Czech Republic, 2Department of Biology and Ecological Education, Charles University in Prague, Faculty of Education, Prague, Czech Republic.

Presentation Number: P07.129

Moravian Valachs of Czech Republic are one of the most distinct ethnic groups from Central Europe. Related to similar populations in Poland and Slovakia, they emerge at the end of 15th century, as the north-westernmost prominence of migration that started 250 years earlier in northern Romania. Being predominately highland sheep herders and of putative Romanian origin, they represent a Central European analogue of Balkan Aromanian populations. We have gathered Y-chromosomal, linguistic, ethnographic and historical data for this population and compared them with surrounding as well as with east European populations. Linguistic data show specific parts of shared vocabulary of Romanian origin between several pastoral groups in Central and Eastern Europe. Comparing genetic and linguistic pairwise distance matrices (Mantel test) in these populations did not revealed any significant correlation. Thus we confirmed that plain geographical distance still plays the major role in genetic distances between populations in Europe. From our further analysis it is clear, that the Moravian Valachs, after at least five centuries of admixture, are not overly genetically different from surrounding populations. On the other hand, from the point of view of intra-population diversity, they are much more similar to isolated Balkan populations (e.g. Aromuns) than to Central European populations.

Phylogeography of the human Y chromosome haplogroup E3a

F. Cruciani1, B. Trombetta1, D. Sellitto2, C. Nodale1, R. Scozzari1; 1Sapienza Università di Roma, Rome, Italy, 2Consiglio Nazionale delle Ricerche, Rome, Italy.

Presentation Number: P07.134

The Y chromosome specific biallelic marker DYS271 defines the most common haplogroup (E3a) currently found in sub-Saharan Africa. A sister clade, E3b (E-M215), is rare in sub-Saharan Africa, but very common in northern and eastern Africa. On the whole, these two clades represent more than 70% of the Y chromosomes of the African continent. A third clade belonging to E3 (E3c or E-M329) has been recently reported to be present only in eastern Africa, at low frequencies. In this study we analyzed more than 1,600 Y chromosomes from 55 African populations, using both new and previously described biallelic markers, in order to refine the phylogeny and the geographic distribution of the E3a haplogroup. The most common E-DYS271 sub-clades (E-DYS271*, E-M191, E-U209) showed a non uniform distribution across sub-Saharan Africa. Most of the E-DYS271 chromosomes found in northern and western Africa belong to the paragroup E-DYS271*, which is rare in central and southern Africa. In these latter regions, haplogroups E-M191 and E-U209 show similar frequency distributions and coalescence ages (13 and 11 kyr, respectively), suggesting their involvement in the same migratory event/s. By the use of two new phylogenetically equivalent markers (V38 and V89), the earlier tripartite structure of E3 haplogroup was resolved in favor of a common ancestor for haplogroups E-DYS271 (formerly E3a) and E-M329 (formerly E3c). The new topology of the E3 haplogroup is suggestive of a relatively recent eastern African origin for the majority of the chromosomes presently found in sub-Saharan Africa.

Y-chromosome lineages in Xhosa and Zulu Bantu speaking populations

R. P. A. Gonçalves, H. Spínola, A. Brehm; Human Genetics Laboratory, Funchal, Portugal.

Presentation Number: P07.137

Y-chromosome Single Nucleotide Polymorphisms have been analysed in Zulu and Xhosa, two southern Africa Bantu speaking populations. These two ethnic groups have their origin on the farmer’s Bantu expansion from Niger-Congo border towards sub-Sahel regions on the southern tip of the continent, during the past 3000 years. Seven different Y-chromosome haplogroups were found in Zulu contrasting with only two in Xhosa. E3a, a common haplogroup among West sub-Saharans associated to Bantu migration was the most prevalent in both populations (56.9% in Zulu and 90% in Xhosa). The second most common haplogroup was E2 (29.3% in Zulu and 10% in Xhosa), present both in West and East African populations. The present-day Zulu and Xhosa paternal legacy is essentially of West sub-Saharan origin. Zulu population shows a most diverse genetic influence comparing to Xhosa, revealing some pre-Bantu expansion markers and East African influences. Zulu presents 8.6% Y-chromosome haplogroups (A, B, J1) of non-Bantu influence that could indicate gene flow from other populations, particularly Khoisan.

Human genetic population structure: Patterns and underlying processes

Presentation Time: Tuesday, 9:15 a.m. - 9:45 a.m.

G. Barbujani; University of Ferrara, Department of Biology and Evolution, Ferrara, Italy.

Presentation Number: S15.2

Classical studies of genetic diversity in humans consistently showed that the largest proportion of human diversity occurs among members of the same population. On average, differences among different populations in the same continent represent 5% of the global human variance, and differences among continents another 10%. Genetic variation is largely discordant across the genome, meaning that different loci show different spatial patterns, and implying that a good description of population structure can only be based on the analysis of multiple loci. Studies of single loci are also unlikely to reasonably identify an individual’s place of origin. A general decline of genetic of genetic diversity with distance from Africa, and a parallel increase in linkage disequilibrium, can be accounted for by the effects of a series of founder effects accompanying the spread of anatomically-modern humans from Africa. Recent DNA analyses at the global level show that most allelic variants are cosmopolitan and only a small percentage are continent-specific, whereas a clearer continental structure emerges when considering composite haplotypes. This suggests that, at the global level, gene flow has had a strong impact on genetic diversity, through both directional dispersal and successive short-range migratory exchanges. At the local level, several factors have contributed to genetic differentiation, and, in particular, language barriers have been shown to be associated with small but non-negligible increases of the genetic differences between neighboring populations.

Hierarchical analysis of 28 Y-chromosome SNP’s in the population of the Republic of Macedonia

P. Noveski, S. Trivodalieva, G. D. Efremov, D. Plaseska-Karanfilska;
Macedonian Academy of Sciences and Arts, Research Centre for Genetic Engineering and Biotechnology, Skopje, Macedonia, The Former Yugoslav Republic of.

Presentation Number: P05.211

Analysis of Y-chromosome haplogroups, defined by single nucleotide polymorphisms (SNP’s), has become a standard approach for studying the origin of human populations and measuring the variability among them. Furthermore, Y-SNP’s represent a new forensic tool, because their population specificity may allow to determine the origin of any male sample of interest for forensic purposes. The aim of this study was to develop a strategy for rapid, simple and inexpensive Y-chromosome SNP’s typing in the population of R. Macedonia. We have studied a total of 343 DNA male samples; 211 Macedonians, 111 Albanians and 21 of other ethnic origin (Roma, Serbs and Turks). Methodology included multiplex PCR and single nucleotide extension reaction by SNaPshot multiplex kit. The set of 28 markers has been grouped in 5 multiplexes in order to determine the most frequent haplogroups using only 1 or 2 multiplexes. Twenty different Y haplogroups were determined among 343 male DNA samples. The finding that five haplogroups (E3b1, I1b1, J2b1a, R1a and R1b) comprise more than 70% of the Y chromosomes is consistent with the typical European Y chromosome gene pool. The distribution of the Y-haplogroups differs between Macedonians and Albanians. The most common Y haplogroup among Macedonians is I1b1 (27.5%), followed by three haplogroups present with similar frequencies E3b1 (15.6%), R1a (14.2%) and R1b (11.4%). Among Albanians the most frequent Y haplogroup is E3b1 (28.8%), followed by R1b (18.0%), J2b1a (13.5%) and R1a (12.6%).

The following paper (probably) refers to a recent study, according to which:

One of the most elevated values of 35delG prevalence corresponds to Greece (1/28); the pattern of various 35delG prevalences is interpretated in the present meta-analysis as the result of Ancient Greek colonizations of the "Magna Grecia" in historical times.

Strong linkage disequilibrium for the frequent GJB2 35delG mutation in the Greek population
H. Kokotas¹, L. Van Laer², M. Grigoriadou¹, V. Iliadou³, J. Economides⁴, S. Pomoni¹, A. Pampanos¹, N. Eleftheriades⁵, E. Ferekidou⁶, S. Korres⁶, A. Giannoulia-Karantana⁷, G. Van Camp², M. B. Petersen¹;
¹Institute of Child Health, Athens, Greece, ²University of Antwerp, Antwerp, Belgium, ³AHEPA Hospital, Thessaloniki, Greece, ⁴‘Aghia Sophia’ Children’s Hospital, Athens, Greece, ⁵St. Loukas Hospital, Thessaloniki, Greece, ⁶Athens University, Athens, Greece, ⁷Athens University Medical School, Athens, Greece.

Presentation Number: P06.080

Approximately one in 1,000 children is affected by severe or profound hearing loss at birth or during early childhood (prelingual deafness). Up to forty percent of autosomal recessive, congenital, severe to profound hearing impairment cases result from mutations in a single gene, GJB2. The 35delG mutation accounts for the majority of GJB2 mutations detected in Caucasian populations and represents one of the most frequent disease mutations identified so far. Some previous studies have assumed that the high frequency of the 35delG mutation reflects the presence of a mutational hot spot, whilst other studies support the theory of a common founder. Greece is amongst the countries presenting high frequency of the 35delG mutation (3.5%), and a recent study raised the hypothesis of the origin of this mutation in ancient Greece. We genotyped 60 Greek deafness patients homozygous for the 35delG mutation for six single nucleotide polymorphisms (SNPs) and two microsatellite markers, mapping within or flanking the GJB2 gene, as compared to 60 Greek hearing controls. A strong linkage disequilibrium was found between the 35delG mutation and markers inside or flanking the GJB2 gene, at distances of 34 kb on the centromeric and 90 kb on the telomeric side of the gene, respectively. Our study supports the hypothesis of a founder effect and we further propose that ethnic groups of Greek ancestry could have propagated the 35delG mutation, as evidenced by historical data beginning from the 15^th century BC.

ESHG 2007 abstracts

I had previously posted about a presentation in this year's ESHG conference about the Y chromosomes of Etruscans. At that time, there was no abstract online, but I noticed that the book of abstracts is available (pdf). The conference took place last June and there will be probably publications coming out of the presentations there.

Some interesting abstracts; you will probably find many more in the volume's 396 pages.

Related to the abstract below about ACTN in Finnish athletes.

P1206. ACTN and ACE genotypes in Greek elite athletes

I. D. Papadimitriou et al.

Only a few attempts have been made to shed light upon the influence of genes in making an Olympic champion. The aim of our study is to elucidate the genetic differences among a group of 101 elite Greek power-oriented track and field athletes and a random representative sample (181) of the Greek population by analyzing ACTN3 and ACE genotypes. Athletes were defined as elite and included to the sample if they had represented Greece at the international level. Standard molecular genetic methodologies were followed. Genotype and allele frequencies were compared between elite athletes and controls by the Chi-squared test using the statistical package GENEPOP V. 3.4. Preliminary results for ACE locus indicated that the gene frequencies in the Greek elite athletes are similar to other northern European populations. Furthermore, concerning the ACTN3 locus, it was showed that ACTN3 genotype and allele frequencies in the top power-oriented athletes were statistically significantly different from those in the random
sample of the Greek population: the frequency of the RR ACTN3 genotype in power-oriented athletes vs. the general population was 47.94% vs. 25.97%. The difference was even more prominent for comparison of the subgroup of sprinters to controls. The results suggest an overall
strong association between the presence of the RR genotype and elite power performance. Therefore, the ACTN3 gene might be used as a molecular genetic marker to at least partially predict an athlete’s ability to achieve peak power and sprinting performance.


C17. Origin of the Etruscans: novel clues from the Y chromosome lineages

A. Piazza et al.

Three hypotheses have been proposed on the origin of the distinctive Etruscan civilization and language that flourished ca. 3,000 years before present (BP) in Central Italy: 1) an external Anatolian source (Lydia and Lemnos) as claimed by Herodotus, 2) an autochthonous
process of formation from the preceding Villanovan society as firstly proposed by Dionysius of Halicarnassus and 3) an influence from Northern Europe. A synthetic geographical map summarizing 34 classical genetic markers in Italy differentiates a genetically homogeneous
Central Italian region between the Arno and Tiber rivers (ancient Etruria) from the rest of Italy. While this fact was tentatively interpreted as a genetic footprint of the Etruscans, its verification remained a challenge due to lack of data on differentiation of such markers and its calibration
with time. Here we show the genetic relationships of modern Etrurians, who mostly settled in Tuscany, with other Italian, Near Eastern and Aegean peoples by comparing the Y-chromosome DNA variation in 1,264 unrelated healthy males from: Tuscany-Italy (n=263), North Italy (n=306), South Balkans (n=359), Lemnos island (n=60), Sicily and Sardinia (n=276). The Tuscany samples were collected in Volterra (n=116), Murlo (n=86) and Casentino Valley (n=61).
We found traces of recent Near Eastern gene flow still present in Tuscany, especially in the archaeologically important village of Murlo. The samples from Tuscany show eastern haplogroups E3b1-M78, G2*-P15, J2a1b*-M67 and K2-M70 with frequencies very similar to those observed in Turkey and surrounding areas, but significantly different from those of neighbouring Italian regions. The microsatellite haplotypes associated to these haplogroups allow inference of ancestor lineages for Etruria and Near East whose time to the most recent common ancestors is relatively recent (about 3,500 years BP) and supports a possible non autochthonous post-Neolithic signal associated with the Etruscans.

P1135. Y chromosome analysis in subpopulations of Bashkirs from Russia

A. S. Lobov et al.

The Volga-Ural region which is located between Europe and Asia has been the arena of permanent genetic exchanges among Siberian, Central Asian, Eastern European populations. We have sampled seven Bashkir subpopulations from different parts of the Volga-Ural region and neighboring areas of Russia: Orenburg (N=79), Perm (N=72), Samara and Saratov (N=51), and from Bashkortostan Republic: Abzelilovskiy (N=152), Sterlibashevskiy (N=54), Baimakskiy (N=95), and Burzaynskiy area (N=82). These samples are currently being analyzed using 24 diallelic markers of Y-chromosome (M89, M9, M20, M48, M73, M130, M170, M172, M175, M201, M207, M214, M217, M231, M253, M269, M306(M173), P15, P37, P43, SRY1532, Tat, 92R7(M74), 12f2). According to our preliminary findings Turkic speaking Bashkirs are characterized by prevalence of R1b3 and R1a lineages. Among all subpopulations, Perm and Baimakskiy area represent with hight frequency (0.748 0.769,).It indicate there closeness with West European populations. Haplogroup R1a have frequency value 0.486 in Samara and Saratov’s Bashkirs and frequency value 0.370 Bashkirs from Sterlibashevskiy area. The N3 characterize for subpopulation Bashkirs from Sterlibashevskiy area (0.537), Orenburg (0.342). Bashkirs from Abzelilovskiy area have main frequency (0.474). These differences possibly indicate that different subpopulations of Bashkirs have different origin. We found that Bashkirs from Perm district were characterized by relatively low genetic diversity, which could be explained by founder effect. Bashkirs from Orenburg region which are anthropologically closer to Ugro-Finnic populations are characterized by high frequency of N3 haplogroup. We will try to compare our results with archeologycal, historycal and anthropological data in discussed about of origin of different groups Bashkir

P1191. Analysis of mitochondrial DNA polymorphism in four Siberian ethnic groups

M. V. Golubenko et al.

Mitochondrial DNA polymorphism was studied in 1130 individuals from 12 populations of the most numerous Siberian peoples - Altaians (4 populations), Tivinians (3 populations), Yakuts (2 populations) and Buryats (3 populations). 308 different HVS1 haplotypes were revealed
in total which belong to 34 different mtDNA haplogroups, mainly of East-Eurasian origin. Portion of “West-Eurasian” mtDNA haplogroups was the highest in Altaians (up to 46%) and Buryats (up to 20%). AMOVA analysis has shown that 95,78% of HVSI variation was within populations, 2.09% could be explained by inter-population differentiation and 2.09% was variability between ethnic groups. Test on differentiation of polymorphism in population pairs has shown that in all cases except the pair of Yakut samples the differentiation was significant. AMOVA analysis for separate ethnic groups revealed the highest degree of intraethnic differentiation for Altaians (3.78%), followed by Tuvinians (2.61%) and then Buryats (0.43%). Comparison of spectrum of
haplogroups and individual haplotypes in the populations under investigation also shows significant differentiation of native Siberian populations. Only two haplotypes from haplogroup C and one haplotype from D could be considered as common for all four ethnicities. One more
haplotype from C was abundant in Tuvinians, Yakuts and Buryats but rare in Altaians. Substantial number of haplotypes was population-specific. Analysis of migrations and interethnic marriages revealed various effects of these factors depending both on ethnicity and particular
population. The results suggest considerable ethnic differentiation in the studied Siberian peoples, as well as geographic differentiation.


P1192. Paleomolecular genetic analyses (mitochondrial and nuclear DNA polymorphisms) on some Thracian populations from Romania, dating from the Bronze and Iron Age

G. M. Cardos et al.

We have performed this study on the skeletal remains of some old Thracian populations from Romania, dating from the Bronze and Iron Age. Therefore, within our research we analysed mtDNA (HVR I and HVR II regions) and nuclear DNA (vWA31A Microsatellite) polymorphisms
in order to show the degree of their genetic kinship with other old and modern European populations, especially with nowadays Romanian population. We also amplified the Amelogenin gene to identify the genetic sex of old individuals. We have used three methods for DNA-extraction from human fossils and adapted them on the degradation
state of the biological material: the phenol-chloroform DNA extraction method, the DNA extraction method with guanidine-tiocianate and silica-particles, and the DNA-extraction method with Invisorb Forensic After amplifying by PCR, the mtDNA sequences were sequenced
by the Sanger method. The nuclear vWA31A Microsatellite polymorphisms and the Amelogenin gene sequences were demonstrated on PAA gel, Ag-stained.
We have compared the mtDNA sequences of 50 old Thracian individuals with mtDNA sequences of the present-day Romanian population and other European, Asian and African modern and old populations. The frequencies of vWA31A Microsatellite were compared with similar genetic data of other modern populations from all over the world. Our results suggest that the old Thracian populations might have made an important contribution to the foundation of the modern genetic Romanian pool and also reflect an evident genetic similarity between the old Thracian populations and other modern populations from South-East Europe.

P1193. Analyses of mitochondrial and Y-chromosomal lineages in modern Hungarian, Szekler and ancient Hungarian populations

B. Csányi et al.

Hungarian population belongs linguistically to the Finno-Ugric branch of the Uralic language family. High-resolution mtDNA analysis of 27 ancient samples (10th-11th centuries), 101 modern Hungarian, and 76 modern Hungarian-speaking Szekler samples was performed. Only two of 27 ancient Hungarian samples are unambiguously Asian: the rest belong to one of the western Eurasian haplogroups. Statistical analyses, including 57 European and Asian populations, revealed that some Asian affinities and the genetic effect of populations who came into contact with ancient Hungarians during their migrations are seen. Though strong differences appear when the ancient Hungarian samples are analyzed according to apparent social status, as judged by grave goods. mtDNA results demonstrate that significant genetic differences exist between the ancient and recent Hungarian-speaking populations. The Y-chromosomal base substitution ”Tat”, proved to be a valuable marker in the Finno-Ugric context. The Tat C allele is widespread in many Uralic-speaking populations, while it is virtually absent in recent Hungarians. To further elucidate this finding we studied this polymorphism on 100 modern Hungarian, 97 Szekler and 4 ancient Hungarian samples. Our data revealed that only one Szekler men carries the C allele among the modern individuals, whereas out of the four skeletal remains two possess the mutation. Furthermore we examined 22 Y-chromosomal binary markers to analyze the paternal genetic diversity of the two recent populations.
Our results show that Hungarians and Szeklers share basically the same genetic components found in other European populations, genetically closely related and close to other populations from Central Europe and the Balkan.

P1219. Possible common origin for the Tibeto-Burman and Austro-Asiatic speaking populations of India: a Y-chromosome study

ESHG 2007

In this summer's European Society of Human Genetics conference one of the presentations will be on "Origin of the Etruscans: novel clues from the Y chromosome lineages". I wonder if my prediction of a high representation of Y haplogroup J1 (almost equivalent to J*(xJ2)) among the ancient Etruscans will be supported by this research. Unfortunately, I did not see an abstract posted yet. Another interesting title is "Epidemics of viral haemorrhagic fever in Medieval times as a possible selection pressure for CCR5del32 in Europe: new insights from Croatian island isolates". This involves an allele which confers resistance to the HIV virus and which is found frequently particularly in Northern Europeans, so perhaps its presence may be the result of some past selection effect against a different disease.

New paper on haplogroup E-M78

I had written about this research about a year ago, and now the relevant paper has appeared in Human Mutation. The new phylogeny within haplogroup E-M78 is shown below:



The newly discovered binary markers correspond roughly to the previously known microsatellite networks, although the correspondence is not perfect (see below):


From the paper:

Genetic differentiation among UEP defined groups of microsatellite-haplotypes is quite high (Rst = 0.59; P<10-3),> We also explored the correspondence between the two types of markers at a geographical level. There is a high and significant correlation observed between pairwise binary-haplogroup-based and microsatellite-haplotype-based distances among nine geographic regions (r = 0.91; P< 10-3). The two-dimensional plots from MDS show similar clusters of populations (Fig. 3), with slight differences possibly due to differential sensitivity of Φst and Rst to different mutational processes. North-western Africa, eastern Africa and the Balkans are well separated from each other and also from the central cluster in both diagrams. The differences are explained to a large extent by: the haplotypes associated with paragroup E-M78* (predominantly observed in north-western Africa), haplogroup E-V32 (found almost exclusively in eastern Africa) and haplogroup E-V13 (the only subset of E-M78 observed in the Balkans). E-V13 is also commonly found in the populations of the central cluster, where, however, other E-M78 sub-haplogroups are also present.

...

Taking into account the above data, the previously described European cluster α and the northern African cluster β are indeed confirmed as monophyletic groups of chromosomes, that, very likely, have their own defining binary marker yet to be discovered. Cluster α chromosomes constitute a major branch of the binary haplogroup V13, which, in turn, includes also a few, highly differentiated chromosomes - previously classified either in cluster δ or unclassified. All 29 chromosomes within cluster β belong to the paragroup E-M78*, which is relatively rare and almost exclusively restricted to a single geographic region (i.e. northern Africa), thus a common origin for at least a large part of these is likely.

Different scenarios characterize clusters δ and γ . The presence of three E-V13 chromosomes within cluster δ and the exclusion of some E-V12 and E-V22 chromosomes demonstrate that cluster δ cannot be regarded as a monophyletic unit. As for cluster γ, we have established close phylogenetic relationships of its members - now classified as E-V32 chromosomes - with those belonging to E-V12* within the E-V12 clade (Fig. 2). These relationships go undetected through the microsatellite network (red and pink chromosomes in Fig. 1B), most likely due to recurrent mutations at microsatellite loci. An alternative explanation would be that V12 has mutated twice independently in the E-M78 lineage. The latter possibility is less likely, given that V12 is within a terminal branch of the Y chromosome tree; moreover, it was never found by sequencing 18 Y*(xM78) chromosomes representing deep branches of the Y chromosome phylogeny (data not shown). Thus, the new markers we have detected now
offer the opportunity to explore in a better defined phylogenetic context the origin and distribution of the chromosomes belonging to haplogroup E-M78. Also, it is worth noting that twelve chromosomes that we were unable to assign to any cluster in the previous network analysis are now classified within four different haplogroups/paragroups (see Table 2 and Fig. 1B) as highly divergent microsatellite haplotypes. Thus, even though they represent only 5% of the total E-M78 chromosomes analyzed, their inclusion into the respective haplogroups/paragroups heavily affects inferences about time and place of origin of these haplogroups/paragroups.

Finally, although there is a strong correspondence between cluster γ − defined by the rare DYS19 11-repeat allele - and haplogroup E-V32, the presence, in cluster γ, of haplotypes belonging to the binary paragroups E M78* and E-V12* can only be explained by admitting either a paraphyletic or a polyphyletic origin for the chromosomes in the cluster.

Hum Mutat. 2006 Jul 11;27(8):831-832 [Epub ahead of print]

Molecular dissection of the Y chromosome haplogroup E-M78 (E3b1a): a posteriori evaluation of a microsatellite-network-based approach through six new biallelic markers.

Cruciani F, La Fratta R, Torroni A, Underhill PA, Scozzari R.

The human Y chromosome haplogroup E-M78 (E3b1a) occurs commonly and is distributed in northern and eastern Africa, western Asia, and all of Europe. Previously, only two rarely observed internal biallelic markers (UEPs) were known within the E-M78 clade. Here we report the identification of six novel UEPs that significantly refine the phylogeny of this haplogroup. Then, we evaluate the correspondence between the newly defined sub-haplogroups and the E-M78 haplotype clusters previously identified by an 11-microsatellite loci-based network encompassing 232 chromosomes (Cruciani et al., 2004). We observed considerable correspondence between the trees generated by the two types of markers, but also noted important discrepancies between microsatellite and UEP findings. Overall, this analysis reveals that the currently visible terminal branches of the Y tree still contain a large amount of information, in terms of undiscovered biallelic markers, and that caution is needed when using the microsatellite alleles as surrogates of unique event polymorphisms.

Link

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.