Y-chromosomal STR haplotypes in a population sample from continental Greece, and the islands of Crete and Chios

Y-chromosomal analysis of Greek Cypriots reveals a primarily common pre-Ottoman paternal ancestry with Turkish Cypriots

Genetics can provide invaluable information on the ancestry of the current inhabitants of Cyprus. A Y-chromosome analysis was performed to (i) determine paternal ancestry among the Greek Cypriot (GCy) community in the context of the Central and Eastern Mediterranean and the Near East; and (ii) identify genetic similarities and differences between Greek Cypriots (GCy) and Turkish Cypriots (TCy). Our haplotype-based analysis has revealed that GCy and TCy patrilineages derive primarily from a single gene pool and show very close genetic affinity (low genetic differentiation) to Calabrian Italian and Lebanese patrilineages. In terms of more recent (past millennium) ancestry, as indicated by Y-haplotype sharing, GCy and TCy share much more haplotypes between them than with any surrounding population (7-8% of total haplotypes shared), while TCy also share around 3% of haplotypes with mainland Turks, and to a lesser extent with North Africans. In terms of Y-haplogroup frequencies, again GCy and TCy show very similar distributions, with the predominant haplogroups in both being J2a-M410, E-M78, and G2-P287. Overall, GCy also have a similar Y-haplogroup distribution to non-Turkic Anatolian and Southwest Caucasian populations, as well as Cretan Greeks. TCy show a slight shift towards Turkish populations, due to the presence of Eastern Eurasian (some of which of possible Ottoman origin) Y-haplogroups. Overall, the Y-chromosome analysis performed, using both Y-STR haplotype and binary Y-haplogroup data puts Cypriot in the middle of a genetic continuum stretching from the Levant to Southeast Europe and reveals that despite some differences in haplotype sharing and haplogroup structure, Greek Cypriots and Turkish Cypriots share primarily a common pre-Ottoman paternal ancestry.

Genetic diversity and haplotype structure of 21 Y-STRs, including nine noncore loci, in South Tunisian Population: Forensic relevance

Y chromosome STRs (Y-STRs) are being used frequently in forensic laboratories. Previous studies of Y-STR polymorphisms in different groups of the Tunisian population identified low levels of diversity and discrimination capacity (DC) using various commercial marker sets. This definitely limits the use of such systems for Y-STRs genotyping in Tunisia. In our investigation on South Tunisia, 200 unrelated males were typed for the 12 conventional Y-STRs included in the PowerPlex® Y System. Additional set of nine noncore Y-STRs including DYS446, DYS456, DYS458, DYS388, DYS444, DYS445, DYS449, DYS710, and DYS464 markers were genotyped and evaluated for their potential in improving DC. Allele frequency, gene diversity, haplotype diversity (HD), and DC calculation revealed that DYS464 was the most diverse marker followed by DYS710 and DYS449 markers. The standard panel of 12 Y-STRs (DC = 80.5%) and the nine markers were combined to obtain DC of 99%. Among the 198 different haplotypes observed, 196 haplotypes were unique (HD = 99.999). Out of the nine noncore set, six Y-STRs (DYS458, DYS456, DYS449, DYS710, DYS444, and DYS464) had the greatest impact on enhancing DC. Our data provided putative Y-STRs combination to be used for genetic and forensic applications.

Exploring genomic structure differences and similarities between the Greek and European HapMap populations: implications for association studies

Studies of the genomic structure of the Greek population and Southeastern Europe are limited, despite the central position of the area as a gateway for human migrations into Europe. HapMap has provided a unique tool for the analysis of human genetic variation. Europe is represented by the CEU (Northwestern Europe) and the TSI populations (Tuscan Italians from Southern Europe), which serve as reference for the design of genetic association studies. Furthermore, genetic association findings are often transferred to unstudied populations. Although initial studies support the fact that the CEU can, in general, be used as reference for the selection of tagging SNPs in European populations, this has not been extensively studied across Europe. We set out to explore the genomic structure of the Greek population (56 individuals) and compare it to the HapMap TSI and CEU populations. We studied 1112 SNPs (27 regions, 13 chromosomes). Although the HapMap European populations are, in general, a good reference for the Greek population, regions of population differentiation do exist and results should not be light-heartedly generalized. We conclude that, perhaps due to the individual evolutionary history of each genomic region, geographic proximity is not always a perfect guide for selecting a reference population for an unstudied population.

Y-STR genetic diversity in autochthonous Andalusians from Huelva and Granada provinces (Spain)

Seventeen Y-chromosomal short tandem repeats (STRs) were analyzed in 347 healthy, unrelated, autochthonous males from the Andalusian provinces of Huelva (N=167) and Granada (N=180). AmpFlSTR Y-filer PCR Amplification kit (Applied Biosystems) was used to type the Y-STR markers. A total of 156 and 166 different haplotypes for the 17 Y-STR set were detected in Huelva, and Granada, respectively. The same haplotype diversity was found for both samples (0.998±0.001), and the overall discrimination capacity was 0.904. The most common minimal haplotype (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393) in both subpopulations was 14-13-16-24-11-13-13, which is also the most frequent haplotype among Atlantic European populations. Comparison analysis using pairwise R(ST) values and Analysis of Molecular Variance (AMOVA) revealed a significant genetic distance between our Andalusian samples and other ones from the northern Iberian fringe (including Basque and Pyrenean populations). However, results from the multi-dimensional scaling analysis (MDS) yielded a well-defined group of Iberian populations separated from the other Mediterranean clusters observed.

Genetic polymorphisms for 17 Y-chromosomal STR haplotypes in Jammu and Kashmir Saraswat Brahmin population

In this study 17 Y-chromosomal STRs (including DYS19, DYS389I, DS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y GATA H4) were analysed using blood samples of 122 unrelated male individuals belonging to Saraswat Brahmin community from Jammu (ID YP000599) and Kashmir (ID YP000600) region of J&K state of India. The allelic frequency distribution and haplotype diversity of 17 Y-chromosomal STR for both the populations were calculated. In the Kashmiri Saraswat group, a total of 109 haplotypes were identified in 122 individuals, of these haplotypes, 101 were found only once. The gene diversity values of STR loci ranged from 0.4813 (DYS391) to 0.8645 (DYS385a/b) for Jammu & Kashmiri Saraswat Brahmins.

Linking Italy and the Balkans. A Y-chromosome perspective from the Arbereshe of Calabria

BACKGROUND

The Arbereshe are an Albanian-speaking ethno-linguistic minority who settled in Calabria (southern Italy) about five centuries ago.

AIM

This study aims to clarify the genetic relationships between Italy and the Balkans through analysis of Y-chromosome variability in a peculiar case study, the Arbereshe.

SUBJECT AND METHODS

Founder surnames were used as a means to identify a sample of individuals that might trace back to the Albanians at the time of their establishment in Italy. These results were compared with data of more than 1000 individuals from Italy and the Balkans.

RESULTS

The distributions of haplogroups (defined using 31 UEPs) and haplotypes (12 STRs) show that the Italian and Balkan populations are clearly divergent from each other. Within this genetic landscape, the Arbereshe are characterized by two peculiarities: (a) they are a clear outlier in the Italian genetic background, showing a strong genetic affinity with southern Balkans populations; and (b) they retain a high degree of genetic diversity.

CONCLUSION

These results support the hypothesis that the surname-chosen Arbereshe are representative of the Y-chromosome genetic variability of the Albanian founder population. Accordingly, the Arbereshe genetic structure can contribute to the interpretation of the recent biological history of the southern Balkans. Intra-haplogroup analyses suggest that this area may have experienced important changes in the last five centuries, resulting in a marked increase in the frequency of haplogroups I2a and J2.

Searching for the origin of Gagauzes: inferences from Y-chromosome analysis

The Gagauzes are a small Turkish-speaking ethnic group living mostly in southern Moldova and northeastern Bulgaria. The origin of the Gagauzes is obscure. They may be descendants of the Turkic nomadic tribes from the Eurasian steppes, as suggested by the "Steppe" hypothesis, or have a complex Anatolian-steppe origin, as postulated by the "Seljuk" or "Anatolian" hypothesis. To distinguish these hypotheses, a sample of 89 Y-chromosomes representing two Gagauz populations from the Republic of Moldova was analyzed for 28 binary and seven STR polymorphisms. In the gene pool of the Gagauzes a total of 15 Y-haplogroups were identified, the most common being I-P37 (20.2%), R-M17 (19.1%), G-M201 (13.5%), R-M269 (12.4%), and E-M78 (11.1%). The present Gagauz populations were compared with other Balkan, Anatolian, and Central Asian populations by means of genetic distances, nonmetric multidimentional scaling and analyses of molecular variance. The analyses showed that Gagauzes belong to the Balkan populations, suggesting that the Gagauz language represents a case of language replacement in southeastern Europe. Interestingly, the detailed study of microsatellite haplotypes revealed some sharing between the Gagauz and Turkish lineages, providing some support of the hypothesis of the "Seljuk origin" of the Gagauzes. The faster evolving microsatellite loci showed that the two Gagauz samples investigated do not represent a homogeneous group. This finding matches the cultural and linguistic heterogeneity of the Gagauzes well, suggesting a crucial role of social factors in shaping the Gagauz Y-chromosome pool and possibly also of effects of genetic drift.

Evaluation of miniY-STR multiplex PCR systems for extended 16 Y-STR loci

We developed three short amplicon Y-chromosomal short tandem repeat (miniY-STR) polymerase chain reaction multiplex systems for 16 Y-STR loci (DYS441, DYS446, DYS462, DYS481, DYS485, DYS495, DYS505, DYS510, DYS511, DYS549, DYS 575, DYS578, DYS593, DYS618, DYS638, and DYS643), using newly designed primer sets. In an assay of 238 Japanese males using the three miniY-STR systems, amplification product lengths ranged from 91 to 151 bp for all 16 Y-STR loci. We identified 212 different haplotypes among the 238 individuals, finding haplotype diversity and discrimination capacity of 0.9974 and 0.8908, respectively. An assay of degraded DNA samples using the three miniY-STR multiplex systems, including artificially degraded samples and degraded forensic casework samples, proved remarkably effective. In conclusion, analyses of miniY-STR multiplex systems will play an important role in forensic applications involving degraded DNA samples for which genotyping using only commercial kits is ill-suited.

Testing the hypothesis of an ancient Roman soldier origin of the Liqian people in northwest China: a Y-chromosome perspective

The Liqian people in north China are well known because of the controversial hypothesis of an ancient Roman mercenary origin. To test this hypothesis, 227 male individuals representing four Chinese populations were analyzed at 12 short tandem repeat (STR) loci and 12 single nucleotide polymorphisms (SNP). At the haplogroup levels, 77% Liqian Y chromosomes were restricted to East Asia. Principal component (PC) and multidimensional scaling (MDS) analysis suggests that the Liqians are closely related to Chinese populations, especially Han Chinese populations, whereas they greatly deviate from Central Asian and Western Eurasian populations. Further phylogenetic and admixture analysis confirmed that the Han Chinese contributed greatly to the Liqian gene pool. The Liqian and the Yugur people, regarded as kindred populations with common origins, present an underlying genetic difference in a median-joining network. Overall, a Roman mercenary origin could not be accepted as true according to paternal genetic variation, and the current Liqian population is more likely to be a subgroup of the Chinese majority Han.

Data for Y-chromosome haplotypes in Fang and Bubi populations from Bioko (Equatorial Guinea)

Haplotype frequencies for 16 Y-chromosomal short tandem repeat (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438 and DYS448) loci, included in the AmpFLSTR Yfiler PCR Amplification Kit, were analysed in 110 Fang and 133 Bubi individuals from Bioko Island, Equatorial Guinea. The diversity was higher in Fang population, probably since they were originally from the mainland, with which they maintain tribal village and family links, and to which they travel frequently. Comparisons were made with previously published haplotype data on European and African populations, and significant differences were found between them.

Y chromosome genetic variation in the Italian peninsula is clinal and supports an admixture model for the Mesolithic-Neolithic encounter

The Italian peninsula, given its geographical location in the middle of the Mediterranean basin, was involved in the process of the peopling of Europe since the very beginning, with first settlements dating to the Upper Paleolithic. Later on, the Neolithic revolution left clear evidence in the archeological record, with findings going back to 7000 B.C. We have investigated the demographic consequences of the agriculture revolution in this area by genotyping Y chromosome markers for almost 700 individuals from 12 different regions. Data analysis showed a non-random distribution of the observed genetic variation, with more than 70% of the Y chromosome diversity distributed along a North-South axis. While the Greek colonisation during classical time appears to have left no significant contribution, the results support a male demic diffusion model, even if population replacement was not complete and the degree of Neolithic admixture with Mesolithic inhabitants was different in different areas of Italy.

MiniY-STR quadruplex systems with short amplicon lengths for analysis of degraded DNA samples

Two short amplicon Y-chromosomal short tandem repeat (miniY-STR) quadruplex systems for the eight Y-STR loci DYS522, DYS508, DYS632, DYS556, DYS570, DYS576, DYS504 and DYS540 were devised using newly designed primer sets. Among 224 samples from Japanese population, amplification product lengths detected in these Y-STR loci ranged from 95 to 147bp, while 170 different haplotype were identified (discrimination capacity=0.7589 and haplotype diversity=0.9949). As a result of test on degraded DNA samples using the miniY-STR quadruplex systems, the systems proved to be an quite effective tools for analyzing degraded DNAs. We conclude that analyses of the miniY-STR quadruplex systems in addition to the commercial available Y-STR multiplex kits are highly useful for forensic practices of degraded DNA samples.

Paternal and maternal lineages in the Balkans show a homogeneous landscape over linguistic barriers, except for the isolated Aromuns

The Balkan Peninsula is a complex cultural mosaic comprising populations speaking languages from several branches of the Indo-European family and Altaic, as well as culturally-defined minorities such as the Aromuns who speak a Romance language. The current cultural and linguistic landscape is a palimpsest in which different peoples have contributed their cultures in a historical succession. We have sought to find any evidence of genetic stratification related to those cultural layers by typing both mtDNA and Y chromosomes, in Albanians, Romanians, Macedonians, Greeks, and five Aromun populations. We have paid special attention to the Aromuns, and sought to test genetically various hypotheses on their origins. MtDNA and Y-chromosome haplogroup frequencies in the Balkans were found to be similar to those elsewhere in Europe. MtDNA sequences and Y-chromosome STR haplotypes revealed decreased variation in some Aromun populations. Variation within Aromun populations was the primary source of genetic differentiation. Y-chromosome haplotypes tended to be shared across Aromuns, but not across non-Aromun populations. These results point to a possible common origin of the Aromuns, with drift acting to differentiate the separate Aromun communities. The homogeneity of Balkan populations prevented testing for the origin of the Aromuns, although a significant Roman contribution can be ruled out.

Y-chromosomal STR haplotypes in Sicily

Eight Y-chromosomal short tandem repeats (STRs)-DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393 and DYS385-were typed in a population sample (n=255) of unrelated Sicilian males from nine different towns on the main island and from the island of Pantelleria.

Haplotypes for 13 Y-chromosomal STR loci in South Tunisian population (Sfax region)

Nine Y-STR loci from the "minimal haplotype" (DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393) included in Y-STR Haplotype Reference Databases (YHRD) with 4 additional Y-STRs (DYS436, DYS437, DYS438, DYS439) were analyzed by PCR using duplex and Y-PLEX 12 kit, followed by automatic genotyping in a sample of 105 Tunisian males originating from Sfax region (south Tunisia). Allelic frequencies and gene diversities for each Y-STR locus were determined. The high haplotype diversity (0.9932) and discrimination capacity (0.7714) show the usefulness of these loci for human identification in forensic studies and paternity tests in Tunisia. The most common haplotype was shared by 4.7% (5 individuals) of the sample was only found in samples from the Tunisian population reported in YHRD. One private allele for DYS392 (allele 17) was discovered and duplications were observed for five loci (DYS19, DYS389I, DYS393, DYS437 and DYS439).

Y-chromosomal STR haplotypes in a Belgian population sample and identification of a micro-variant with a flanking site mutation at DYS19

Allele frequencies and haplotypes for 12 Y-chromosomal STR loci included in the Powerplex System (Promega, Madison, USA) were determined in a sample of 113 unrelated males of Belgian origin. Ninety-nine different haplotypes were observed with an overall haplotype diversity of 0.997.