Article

Y-Chromosomal variation in the Czech Republic.

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Abstract

To analyze the contribution of the Czech population to the Y-chromosome diversity landscape of Europe and to reconstruct past demographic events, we typed 257 males from five locations for 21 UEPs. Moreover, 141 carriers of the three most common haplogroups were typed for 10 microsatellites and coalescent analyses applied. Sixteen Hg's characterized by derived alleles were identified, the most common being R1a-SRY(10831) and P-DYS257*(xR1a). The pool of haplogroups within I-M170 represented the third most common clade. Overall, the degree of population structure was low. The ages for Hg I-M170, P-DYS257*(xR1a), and R1a-SRY(10831) ap peared to be comparable and compatible with their presence during or soon after the LGM. A signal of population growth beginning in the first millennium B.C. was detected. Its similarity among the three most common Hg's indicated that growth was characteristic for a gene pool that already contained all of them. The Czech population appears to be influenced, to a very moderate extent, by genetic inputs from outside Europe in the post-Neolithic and historical times. Population growth postdated the archaeologically documented introduction of Neolithic technology and the estimated central value coincides with a period of repeated changes driven by the development of metal technologies and the associated social and trade organization.

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... However, it should be noted that Re bała et al. (2007) have observed the genetic homogeneity of Western and Eastern Slavic populations extending from Slovakia and the Ukraine to Belarus and Russia, and also involving some Southern Slavic populations (such as Slovenians and western Croatians); that research however contains no data on the Czech Y-STR variation. Meanwhile, another study has shown the existence of significant differences between Poles and Czechs as far as Y-SNP polymorphism is concerned (Luca et al., 2007). Moreover, the same study reports that Czech populations display frequencies of Y chromosome haplogroups intermediate to those of Poles and Germans, mainly due to the lower frequency of R1a characteristic among Slavs and higher Table 2). ...
... Haplotypes are labeled as follows: Cz, Czechs; Sl, Slovaks; Pl, Poles; Ru, Russians. frequency of R1b characteristic among Germans and other populations of Western Europe (Luca et al., 2007). Thus, in the case of Poles, Czechs, and Germans, our study of Y-STR polymorphism replicates the results obtained earlier for Y-SNPs. ...
... We believe that the significant differences in Y-STR haplotype frequencies between Western Slavs, observed in this and in the previous study (Luca et al., 2007), can be explained using historical and archeological records regarding the early history of Slavic settlements in Central and Eastern Europe. It is generally assumed that the spread of Slavic culture to the West between late sixth and ninth century took two alternative routes along the Carpathian Mountains, on their northern and southern sides. ...
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Analysis of Y chromosome Y-STRs has proven to be a useful tool in the field of population genetics, especially in the case of closely related populations. We collected DNA samples from 169 males of Czech origin, 80 males of Slovakian origin, and 142 males dwelling Northern Poland. We performed Y-STR analysis of 12 loci in the samples collected (PowerPlex Y system from Promega) and compared the Y chromosome haplotype frequencies between the populations investigated. Also, we used Y-STR data available from the literature for comparison purposes. We observed significant differences between Y chromosome pools of Czechs and Slovaks compared to other Slavic and European populations. At the same time we were able to point to a specific group of Y-STR haplotypes belonging to an R1a haplogroup that seems to be shared by Slavic populations dwelling in Central Europe. The observed Y chromosome diversity may be explained by taking into consideration archeological and historical data regarding early Slav migrations.
... Considering the European context, the R1a haplogroup frequency of 33% found for Slovakia is comparable to that estimated in neighbouring countries such as 34% in the Czech Republic (Luca et al., 2007) and 26% in Hungary (Volgyi et al., 2009). On the other hand, R1a frequencies of 45% or higher were detected in northern and eastern regions, namely Poland, Ukraine and Russia (Kayser et al., 2005;Malyarchuk et al., 2004;Mielnik-Sikorska et al., 2013;Roewer et al., 2008). ...
... R1b occurs at a frequency of 25% in Slovakia, which is similar to the frequency of 28% found for the Czech Republic (Luca et al., 2007), while it occurs at a somewhat lower frequency (20%) in Hungary (Volgyi et al., 2009). In Austria its frequency is higher than 42% (Niederstatter et al., 2012) and it further increases towards Iberia in the west, where the highest frequencies in Europe ($ 65%) are observed (Adams et al., 2008;Beleza et al., 2006). ...
... A frequency of $ 20% for haplogroup I in Slovakia is also observed in the Czech Republic, as well as in Hungary, Ukraine, Russia and Tyrolean Austria (Luca et al., 2007;Malyarchuk et al., 2004;Mielnik-Sikorska et al., 2013;Niederstatter et al., 2012;Roewer et al., 2008;Volgyi et al., 2009). In contrast to R1a and R1b, however, the spatial frequency distribution of this haplogroup displays two separate peaks, in the north and in the south of the continent, respectively (not shown). ...
Article
Background: Several demographic events have been postulated to explain the contemporaneous structure of European genetic diversity. First, an initial settlement of the continent by anatomically modern humans; second, the re-settlement of northern latitudes after the Last Glacial Maximum; third, the demic diffusion of Neolithic farmers from the Near East; and, fourth, several historical events such as the Slavic migration. Aim: The aim of this study was to provide a more integrated picture of male-specific genetic relationships of Slovakia within the broader pan-European genetic landscape. Subjects and methods: This study analysed a new Y-chromosome data-set (156 individuals) for both SNP and STR polymorphisms in population samples from five different Slovakian localities. Results: It was found that the male diversity of Slovakia is embedded in the clinal pattern of the major R1a and R1b clades extending over the continent and a similar pattern of population structure is found with Y-specific SNP or STR variation. Conclusion: The highly significant correlation between the results based on fast evolving STRs on one hand and slow evolving SNPs on the other hand suggests a recent timeframe for the settlement of the area.
... All samples were from collections of the authors, assembled in the 1980's, 1990's and 2000's to perform population studies in the region [39][40][41][70][71][72]. The original blood sampling was performed by colleagues and operators at a number of collaborating Institutions and included the recording of the subject's place of residence. ...
... The 40 locations comprised a group of residents in Moravia (Czech Republic) [71] as a reference for the Central European population (North-Western outgroup). In order to have an appropriate counterpart, we also included in the study (41st location) the Palestinians of the CEPH HGDP panel [73], as a South-Eastern outgroup. ...
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Human forensic STRs used for individual identification have been reported to have little power for inter-population analyses. Several methods have been developed which incorporate information on the spatial distribution of individuals to arrive at a description of the arrangement of diversity. We genotyped at 16 forensic STRs a large population sample obtained from many locations in Italy, Greece and Turkey, i.e. three countries crucial to the understanding of discontinuities at the European/Asian junction and the genetic legacy of ancient migrations, but seldom represented together in previous studies. Using spatial PCA on the full dataset, we detected patterns of population affinities in the area. Additionally, we devised objective criteria to reduce the overall complexity into reduced datasets. Independent spatially explicit methods applied to these latter datasets converged in showing that the extraction of information on long- to medium-range geographical trends and structuring from the overall diversity is possible. All analyses returned the picture of a background clinal variation, with regional discontinuities captured by each of the reduced datasets. Several aspects of our results are confirmed on external STR datasets and replicate those of genome-wide SNP typings. High levels of gene flow were inferred within the main continental areas by coalescent simulations. These results are promising from a microevolutionary perspective, in view of the fast pace at which forensic data are being accumulated for many locales. It is foreseeable that this will allow the exploitation of an invaluable genotypic resource, assembled for other (forensic) purposes, to clarify important aspects in the formation of local gene pools.
... The Czech Republic is located at a traditional crosssection of Western and Eastern Europe with concomitant historic influences from the Northern as well as Southern European populations. Until now there was only one Y chromosome population study in the Czech population performed for 257 males sampled at five locations [15]. 53 Czechs (mostly from Prague and the Central Bohemian Region) were included in the comprehensive study on Y chromosome diversity showing opposing clines for major haplogroups in Central Europe [16]. ...
... Czechs are a Slavic-speaking population, yet a substantial historical amalgamation with Germanic-speaking western populations occurred during the last centuries. While a sharp genetic border was found between Poland and Germany [11], the frequency distribution of haplotypes in the Czech Republic and its neighbours resembles far more a smooth cline than a sharp border [15]. Whereas 15% of the total Y-STR haplotypes variation between Poland and Germany is explained by inter-population differences [11], this value is only 1.9% for the Czech/Germany comparison and 2.77% for the Czech/Poland comparison (Table S4). ...
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Twelve Y-chromosomal short tandem repeats (Y-STR) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, and DYS439) included in the PowerPlex Y Kit (Promega Corporation, Madison, USA) were studied for 1750 unrelated males living in 14 regions of the Czech Republic. A total of 1148 different haplotypes were found. The overall haplotype diversity (HD) was determined as 0.998. Analysis of Molecular Variance (AMOVA) reveals non-significant distances between regions concerning their haplotype distribution, thus allowing to use the whole sample as a representative reference database of the Czech Republic. Median network analysis shows a remarkable bipartite composition of the Czech haplotypes, falling in distinct clusters with Eastern and Western European roots.
... Y-chromozóm se dědí pouze po otcovské (paternální) linii a je možné určit, do jaké rodové linie (haploskupiny) náleží určitý haplotyp Ychromozómu. Ze vzorku byl stanoven částečný haplotyp Y-chromozómu a byla predikována haploskupina G2, která není v naší geografické oblasti běžná (4 % mužů současné populace; podle Luca et al. 2007). V okolních zemích jsou četnosti výskytu srovnatelné (Banks 2008). ...
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A NEAR EASTERN HAPLOTYPE IN THE BURIAL OF A YOUNG MAN WITH A FISSURE IN THE SKULL FROM THE EARLY MEDIEVAL CEMETERY AT TETÍN In the paper, the results of the anthropological investigation of graveNo. 7 fromthe earlymedieval cemetery at Tetín are published. At the same time, the partial results of a pilot archeogenetical project are presented. According to the basic data, the individual was of the male gender, belonged to the adultus I stage (20–30 years), and was about 167 cmtall. According to the pathological finding, he suffered froma congenital cerebral herniation (cephalocele, hernia cerebri) between parietal bones, caused by a congenial limited fissure of the skull (cranioschisis). For the purpose of prediction of geographical origin, an analysis of the Y chromosome was carried out and theG2 haplogroup was predicted (defined by theM201mutation), which probably arose in the Near East or in South Asia from the F haplogroup. Its spread took place during the Neolithic agricultural revolution.
... 36; Cinnioglu et al. 2004.133–135; Peri≠i≤ et al. 2005; Luca et al. 2007; Novelletto 2007). ...
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The 14C gradient of pottery dispersal suggests that the sites in the southern Balkans are not significantly older than those in the northern and eastern Balkans. A gradual demic diffusion model from south to north and a millennium time span vector thus find no confirmation in the set of AMS 14C dates and associated contexts that mark pottery dispersal within Southeastern Europe. The first 'demic event' that was hypothesised to reshape significantly European population structure and generate a uniform process of neolithisation of southestern Europe has no confirmation in fre- quency of Y-chromosome subhaplogroups J2b and E3b1 distribution within modern population in Southeastern Europe. IZVLE! EK - 14C datumi prve keramike ka! ejo, da zgodnje neolitska najdi"# a na jugu Balkana niso starej" a od onih na severu. AMS 14C datumi ne potrjujejo modela postopne demske difuzije od juga proti severu in tiso# letni # asovni zamik pri " iritvi keramike. Prvi 'demski dogodek', ki naj bi domnev- no preoblikoval evropsko populacijsko sestavo, v jugovzhodni Evropi pa povzro# il proces enovite neo- litizacije, ni potrjen s pogostostjo pojavljanja Y-kromosomskih haploskupin J2b in E3b1 pri sedanjih populacijah v jugovzhodni Evropi.
... Obtained maps (Figures 5A and 5B) appeared to be almost identical—correlation coefficient between them is equal to 0.997. This finding shows that synthetic maps of Russian Y chromosomal data are not9,10,12,13,15161720,21,33,37,39,41–55 in the GGMAG program package as described in 56 and 57 . Because of different phylogenetic resolution levels of data from literature, not all of them were included for creating all eight maps. ...
Article
Progress in the mapping of population genetic substructure provides a core source of data for the reconstruction of the demographic history of our species and for the discovery of common signals relevant to disease research: These two aspects of enquiry overlap in their empirical data content and are especially informative at continental and subcontinental levels. In the present study of the variation of the Y chromosome pool of ethnic Russians, we show that the patrilineages within the pre-Ivan the Terrible historic borders of Russia have two main distinct sources. One of these antedates the linguistic split between West and East Slavonic-speaking people and is common for the two groups; the other is genetically highlighted by the pre-eminence of haplogroup (hg) N3 and is most parsimoniously explained by extensive assimilation of (or language change in) northeastern indigenous Finno-Ugric tribes. Although hg N3 is common for both East European and Siberian Y chromosomes, other typically Siberian or Mongolian hgs (Q and C) have negligible influence within the studied Russian Y chromosome pool. The distribution of all frequent Y chromosome haplogroups (which account for 95% of the Y chromosomal spectrum in Russians) follows a similar north-south clinal pattern among autosomal markers, apparent from synthetic maps. Multidimensional scaling (MDS) plots comparing intra ethnic and interethnic variation of Y chromosome in Europe show that although well detectable, intraethnic variation signals do not cross interethnic borders, except between Poles, Ukrainians, and central-southern Russians, thereby revealing their overwhelmingly shared patrilineal ancestry.
... Thus, the present work discloses a further level of complexity in the interpretation of the genetic landscape of southeastern Europe, this being to a large extent the consequence of a recent population increase in situ rather than the result of a mere flow of western Asian migrants in the early Neolithic. Indeed, Y-chromosomal data from regions to the north (Kasperaviči ut_ e et al. 2004), northwest (Luca et al. 2007), and west (Di Giacomo et al. 2004) to the Balkans show signatures of demographic events that match archeologically documented changes in the population size in the 1st millennia BC. ...
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Detailed population data were obtained on the distribution of novel biallelic markers that finely dissect the human Y-chromosome haplogroup E-M78. Among 6,501 Y chromosomes sampled in 81 human populations worldwide, we found 517 E-M78 chromosomes and assigned them to 10 subhaplogroups. Eleven microsatellite loci were used to further evaluate subhaplogroup internal diversification. The geographic and quantitative analyses of haplogroup and microsatellite diversity is strongly suggestive of a northeastern African origin of E-M78, with a corridor for bidirectional migrations between northeastern and eastern Africa (at least 2 episodes between 23.9–17.3 ky and 18.0–5.9 ky ago), trans-Mediterranean migrations directly from northern Africa to Europe (mainly in the last 13.0 ky), and flow from northeastern Africa to western Asia between 20.0 and 6.8 ky ago. A single clade within E-M78 (E-V13) highlights a range expansion in the Bronze Age of southeastern Europe, which is also detected by haplogroup J-M12. Phylogeography pattern of molecular radiation and coalescence estimates for both haplogroups are similar and reveal that the genetic landscape of this region is, to a large extent, the consequence of a recent population growth in situ rather than the result of a mere flow of western Asian migrants in the early Neolithic. Our results not only provide a refinement of previous evolutionary hypotheses but also well-defined time frames for past human movements both in northern/eastern Africa and western Eurasia.
... Samples from Nigeria (Dendi, coded WAF inFig. 1), Ethiopia (Amhara [AMH] and Oromo [ORO]), Egypt [EGY], Italy [ITA], Czech Republic [CZK] and Greece [GRE] were previously described57585960, whereas the remaining population samples (i.e. Mordovians [MOE], Perm Russians [PER], Khanti and Mansi [K&M], Yakut [YKL], Chukchee [CHK]) are described here for the first time. ...
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Genetic variation at NAT2 has been long recognized as the cause of differential ability to metabolize a wide variety of drugs of therapeutic use. Here, we explore the pattern of genetic variation in 12 human populations that significantly extend the geographic range and resolution of previous surveys, to test the hypothesis that different dietary regimens and lifestyles may explain inter-population differences in NAT2 variation. The entire coding region was resequenced in 98 subjects and six polymorphic positions were genotyped in 150 additional subjects. A single previously undescribed variant was found (34T>C; 12Y>H). Several aspects of the data do not fit the expectations of a neutral model, as assessed by coalescent simulations. Tajima's D is positive in all populations, indicating an excess of intermediate alleles. The level of between-population differentiation is low, and is mainly accounted for by the proportion of fast vs. slow acetylators. However, haplotype frequencies significantly differ across groups of populations with different subsistence. Data on the structure of haplotypes and their frequencies are compatible with a model in which slow-causing variants were present in widely dispersed populations before major shifts to pastoralism and/or agriculture. In this model, slow-causing mutations gained a selective advantage in populations shifting from hunting-gathering to pastoralism/agriculture. We suggest the diminished dietary availability of folates resulting from the nutritional shift, as the possible cause of the fitness increase associated to haplotypes carrying mutations that reduce enzymatic activity.
... The low percentage (<2%) of shared lineages between Treilles and current populations, and the fact that the ancestral and current G2a haplotypes do not seem related, imply that the G2a lineage of Treilles was probably lost between the end of the Neolithic and today. Few ancient data are currently available on Y-haplogroups to confirm this hypothesis, but G2a haplotypes have been found in other prehistoric remains; two ancient DNA studies revealed the presence of G2a in the Czech Republic during the seventh century (31) and in a German sample of a central European Neolithic culture (13), whereas this haplogroup is very rare in these places nowadays (32). ...
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The Neolithic is a key period in the history of the European settlement. Although archaeological and present-day genetic data suggest several hypotheses regarding the human migration patterns at this period, validation of these hypotheses with the use of ancient genetic data has been limited. In this context, we studied DNA extracted from 53 individuals buried in a necropolis used by a French local community 5,000 y ago. The relatively good DNA preservation of the samples allowed us to obtain autosomal, Y-chromosomal, and/or mtDNA data for 29 of the 53 samples studied. From these datasets, we established close parental relationships within the necropolis and determined maternal and paternal lineages as well as the absence of an allele associated with lactase persistence, probably carried by Neolithic cultures of central Europe. Our study provides an integrative view of the genetic past in southern France at the end of the Neolithic period. Furthermore, the Y-haplotype lineages characterized and the study of their current repartition in European populations confirm a greater influence of the Mediterranean than the Central European route in the peopling of southern Europe during the Neolithic transition.
... Y-chromosomal data for the population of the Czech Republic is still fractional. Kráčmarová et al published a short report on paleolithic and neolithic Y chromosomal haplogroups in the Czech population (1) and Luca et al performed a refined study of the same data (2). Zastera et al published a major study on Czech Y-chromosomal data (3). ...
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To evaluate Y-chromosomal diversity of the Moravian Valachs of the Czech Republic and compare them with a Czech population sample and other samples from Central and South-Eastern Europe, and to evaluate the effects of genetic isolation and sampling. The first sample set of the Valachs consisted of 94 unrelated male donors from the Valach region in northeastern Czech Republic border-area. The second sample set of the Valachs consisted of 79 men who originated from 7 paternal lineages defined by surname. No close relatives were sampled. The third sample set consisted of 273 unrelated men from the whole of the Czech Republic and was used for comparison, as well as published data for other 27 populations. The total number of samples was 3244. Y-short tandem repeat (STR) markers were typed by standard methods using PowerPlex® Y System (Promega) and Yfiler® Amplification Kit (Applied Biosystems) kits. Y-chromosomal haplogroups were estimated from the haplotype information. Haplotype diversity and other intra- and inter-population statistics were computed. The Moravian Valachs showed a lower genetic variability of Y-STR markers than other Central European populations, resembling more to the isolated Balkan populations (Aromuns, Csango, Bulgarian, and Macedonian Roma) than the surrounding populations (Czechs, Slovaks, Poles, Saxons). We illustrated the effect of sampling on Valach paternal lineages, which includes reduction of discrimination capacity and variability inside Y-chromosomal haplogroups. Valach modal haplotype belongs to R1a haplogroup and it was not detected in the Czech population. The Moravian Valachs display strong substructure and isolation in their Y chromosomal markers. They represent a unique Central European population model for population genetics.
... The proband (see above) together with his brother and father belong to the R1A haplogroup, which represents approximately 40% of the Czech Republic population. One of the proband's 1 sons is a R1B haplogroup carrier (in the Czech Republic approximately 35%), while the second son is in the H haplogroup, which is very rare in the Czech Republic [27]. ...
Article
The article describes the clinical, biochemical, enzymological and molecular genetics findings in two patients from two families with xanthinuria type I. Biochemical analysis using high performance liquid chromatography, allopurinol loading test and analysis of xanthine oxidase activity in plasma and of uromodulin excretion in urine were performed. Sequencing analysis of the xanthine dehydrogenase gene and the haplotype and statistical analyses of consanguinity were performed. Probands showed extremely low concentrations of uric acid, on seven occasions under the limit of detection. The concentration of uric acid in 38-year-old female was 15 μmol/L in serum and 0.04 mmol/L in urine. Excretion of xanthine in urine was 170 mmol/mol creatinine. The concentration of uric acid in 25-year-old male was 0.03 mmol/L in urine. Excretion of xanthine in urine was 141 mmol/mol creatinine. The allopurinol loading test confirmed xanthinuria type I. The xanthine oxidase activities in patients were 0 and 0.4 pmol/h/mL of plasma. We found three nonsense changes: p.P214QfsX4 and unpublished p.R825X and p.R881X. We found two nonconsanguineous compound heterozygotes with xanthinuria type I caused by three nonsense changes. The methods used did not confirm consanguinity in the probands, thus there might be an unconfirmed biological relationship or mutational hotspot.
... In all runs but one we modeled a simple binary split, with a gamma (1,1) distribution as a prior for splitting time expressed in coalescent units. We also used a model of exponential growth in an initially constant-sized population with settings and priors similar to the relaxed conditions described previously by Luca et al. (2007). In particular the priors for the growth rate and ancestral chromosome pool size fluctuated between 0.00 and 0.04 (Ammerman and Cavalli-Sforza, 1984) and around 1000, respectively. ...
Article
The African Sahel is conducive to studies of divergence/admixture genetic events as a result of its population history being so closely related with past climatic changes. Today, it is a place of the co-existence of two differing food-producing subsistence systems, i.e., that of sedentary farmers and nomadic pastoralists, whose populations have likely been formed from several dispersed indigenous hunter-gatherer groups. Using new methodology, we show here that the male gene pool of the extant populations of the African Sahel harbors signatures of multiple and differentiated contributions from different genetic sources. We also show that even if the Fulani pastoralists and their neighboring farmers share high frequencies of four Y chromosome subhaplogroups of E, they have drawn on molecularly differentiated subgroups at different times. These findings, based on combinations of SNP and STR polymorphisms, add to our previous knowledge and highlight the role of differences in the demographic history and displacements of the Sahelian populations as a major factor in the segregation of the Y chromosome lineages in Africa. Interestingly, within the Fulani pastoralist population as a whole, a differentiation of the groups from Niger is characterized by their high presence of R1b-M343 and E1b1b1-M35. Moreover, the R1b-M343 is represented in our dataset exclusively in the Fulani group and our analyses infer a north-to-south African migration route during a recent past. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.
... The sub-clade R1a1a-M17 is derived from R1a1-M240 (SRY10831.2) and shows a marked population structure across the European continent. It is highly represented (> 35%) in eastern Europe (Luca et al. 2007;Balanovsky et al. 2008;Fechner et al. 2008;Rootsi et al. 2012;Underhill et al. 2015). Likewise, in Mediterranean Europe, the frequencies of R1a-M17 increase towards the East. ...
Article
Background: The geography of southern Iberia, and an abundant archaeological record of human occupation, are ideal conditions for a full understanding of scenarios of genetic history in the area. Recent advances in the phylogeography of Y-chromosome lineages offer the opportunity to set upper bounds for the appearance of different genetic components. Aim: To provide a global knowledge on the Y haplogroups observed in Andalusia with their Y microsatellite variation. Preferential attention is given to the vehement debate about the age, origin and expansion of R1b-M269 clade and sub-lineages. Subject and methods: 414 male DNA samples from western and eastern autochthonous Andalusians were genotyped for a set of Y-SNPs and Y-STRs. Gene diversity, potential population genetic structures and coalescent times were assessed. Results: Most of the analysed samples belong to the European haplogroup R1b1a1a2-M269 whereas haplogroups E, J, I, G, and T show lower frequencies. A phylogenetic dissection of the R1b-M269 was performed and younger time frames than those previously reported in the literature were obtained for its sub-lineages. Conclusion: The particular Andalusian R1b-M269 assemblage confirms the shallow topology of the clade. Moreover, the sharing of lineages with the rest of Europe indicates the impact in Iberia of an amount of pre-existing diversity, with the possible exception of R1b-DF27. Lineages such as J2-M172 and G-M201, highlight the importance of maritime travels of early farmers who reached the Iberian Peninsula.
... We review and discuss here three studies (Di Giacomo et al. 2004;Cruciani et al. 2007;Luca et al. 2007) that found genetic evidence of demographic events which occurred after the spread of the Neolithic culture from the Levant and involved Central and South-Eastern Europe. ...
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The phylogeny of the human Y chromosome as defined by unique event polymorphisms is being worked out in fine detail. The emerging picture of the geographic distribution of different branches of the evolutionary tree (haplogroups), and the possibility of genetically dating their antiquity, are important tools in the reconstruction of major peopling, population resettlement and demographic expansion events. In the last 10 000 years many such events took place, but they are so close together in time that the populations that experienced them carry Y chromosomal types which can hardly be distinguished genetically. Nevertheless, under some circumstances, one can detect departures from the model of a major dispersal of people over much of the territory, as classically claimed for the European Neolithic. The results of three studies of haplogroups relevant for Southern European populations are discussed. These analyses seem to resolve the signal of recent post-Neolithic events from the noise of the main East-to-West Palaeolithic/early Neolithic migrations. They also confirm that, provided an appropriate level of resolution is used, patterns of diversity among chromosomes which originated outside Europe may often be recognized as the result of discontinuous processes which occurred within Europe.
... Most West and East Slavs of Central-East Europe form genetically a compact group of populations that, as a general rule, differ from their western (Germanic-speaking) and eastern (Finno-Ugric-speaking) neighbors (Fig 2A and 2B; Fig 4A and 4B). However, so-called 'contact' zones of this group with non-Slavic peoples are characterized by various patterns of genetic clines or sharp genetic borders [27,32,[56][57][58]. For example, there is a pronounced genetic proximity between Czechs and their immediate Germanic neighbors in the west (Fig 2A and 2B, Fig 3) [27,58] that could be attributed to the pre-Slavic gene pool formation of Central-East Europeans. ...
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The Slavic branch of the Balto-Slavic sub-family of Indo-European languages underwent rapid divergence as a result of the spatial expansion of its speakers from Central-East Europe, in early medieval times. This expansion-mainly to East Europe and the northern Balkans-resulted in the incorporation of genetic components from numerous autochthonous populations into the Slavic gene pools. Here, we characterize genetic variation in all extant ethnic groups speaking Balto-Slavic languages by analyzing mitochondrial DNA (n = 6,876), Y-chromosomes (n = 6,079) and genome-wide SNP profiles (n = 296), within the context of other European populations. We also reassess the phylogeny of Slavic languages within the Balto-Slavic branch of Indo-European. We find that genetic distances among Balto-Slavic populations, based on autosomal and Y-chromosomal loci, show a high correlation (0.9) both with each other and with geography, but a slightly lower correlation (0.7) with mitochondrial DNA and linguistic affiliation. The data suggest that genetic diversity of the present-day Slavs was predominantly shaped in situ, and we detect two different substrata: 'central-east European' for West and East Slavs, and 'south-east European' for South Slavs. A pattern of distribution of segments identical by descent between groups of East-West and South Slavs suggests shared ancestry or a modest gene flow between those two groups, which might derive from the historic spread of Slavic people.
... The WHO standard criteria have given a lower reference limit of pH 7. In our study conducted on 150 sub fertile men attending an infertility centre in south India, we noticed that the pH range of maximum number of samples vary from pH 8-pH 9. Similar findings were also observed in the Norwegian population in a study conducted by Haugen et al. It was also noticed that similar Y chromosome haplotype existed between Norwegians and Dravidians and North Indians [26,27,28]. ...
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Purpose: To determine the clinical relevance of determining the semen pH during semen analysis as per WHO (World Health Organisation) standard criteria among the infertile couple attending a tertiary ART (Assisted Reproductive Technology) Centre in South India. Methods: Regular Semen analysis as per WHO standards (2010) Results: The Semen pH value showed no major correlation with other Semen parameters and also varied greatly from the given WHO standard. Conclusion: The semen pH determined during semen analysis is found to have not much relevance for clinical practice. The clinical relevance of semen pH for Azoospermia patient needs to be revised.
... Genetic studies of ancient mt-DNA of individuals from the early Neolithic in Central Europe have shown that only 25% of mt-DNA haplotypes of Neolithic farmers originate from the Near East (Haak et al., 2005). This corresponds to the results of recent work on molecular genetics, which shows that around 80% of the genetic make-up of the current population in the Czech territory has its roots in the Upper Palaeolithic (Kra´cˇmarova´et al., 2006;Luca et al., 2007). The continuity of settlement of Central Europe from the Upper Palaeolithic period until today was also presumed by Vlcˇek (1991Vlcˇek ( , 1996 on the basis of morphology, especially that of the cranial skeleton. ...
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One of the largest skeletal series of the Upper Palaeolithic period from Predmostí was destroyed during the Second World War, but the study of this material continues up to the present. The discovery of Matiegka's original photographic documentation on glass plates [Velemínská et al., 2004. The use of recently re-discovered glass plate photo-documentation of those human fossil finds from Predmostí u Prerova destroyed during World War II. J. Nat. Mus. Nat. Hist. Ser. 173, 129-132] gives an opportunity to perform a new and detailed craniometric analysis of five adult skulls in their lateral projection. The craniometric data were analysed using specialised Craniometrics software, and the analysis included morphological and dimensional comparisons with current Central European norms. The aim of the study was not only to monitor the skull shape as a whole, but predominantly, to evaluate the size and shape of various parts of the splanchnocranium. The Upper Palaeolithic skulls are significantly longer, and male skulls are also higher than the current norms. The crania of anatomically modern humans are characterised by two general structural features: mid-lower facial retraction and neurocranial globularity. The height of the face of the Palaeolithic skulls corresponds to that of the current Central European population. The face has a markedly longer mandibular body (3-4 SD), while female mandibular rami are shorter. The skulls are further characterised by a smaller gonial angle, the increased steepness of the mandibular ramus, and the greater angle of the chin. These changes in the size and shape associated with anterior rotation of the face produce a strong protrusion of both jaws, but the sagittal inter-maxillary relationships remain unchanged. The observed facial morphology is similar to the Czech Upper Palaeolithic skulls from Dolní Vestonice. This study confirms the main diachronic changes between skulls of Upper Palaeolithic and present-day human populations.
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Historic and linguistic records indicate that Slovaks belong to the Slavic population. We performed a population genetic study on 250 unrelated Slovak males, who were typed for 12 Y-short tandem repeats (STRs) (b). The corresponding Y-haplogroups were deduced using Whit Athey's Haplogroup Predictor. The most common haplogroup R1a is presented by 38% of individuals. The next two haplogroups (I2a and R1b) are presented at frequencies higher than 10%, 9 haplogroups range from 1 to 10% and 3 haplogroups are presented at frequencies lower than 1%. The obtained re-sults show that a significant majority of the Slovak paternal gene pool belongs to Eastern European Y-lineages and indicate the Slavic origin. Pairwise analysis confirmed that our population is more similar to the surrounding populations, and less similar to those of Bosnia and Herzegovina and Croatia.
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Historic and linguistic records indicate that Slovaks belong to the Slavic population. We performed a population genetic study on 250 unrelated Slovak males, who were typed for 12 Y-short tandem repeats (STRs) (b). The corresponding Y-haplogroups were deduced using Whit Athey's Haplogroup Predictor. The most common haplogroup R1a is presented by 38% of individuals. The next two haplogroups (I2a and R1b) are presented at frequencies higher than 10%, 9 haplogroups range from 1 to 10% and 3 haplogroups are presented at frequencies lower than 1%. The obtained re-sults show that a significant majority of the Slovak paternal gene pool belongs to Eastern European Y-lineages and indicate the Slavic origin. Pairwise analysis confirmed that our population is more similar to the surrounding populations, and less similar to those of Bosnia and Herzegovina and Croatia.
Article
Human Y-chromosome haplogroups are important markers used mainly in population genetic studies. The haplogroups are defined by several SNPs according to the phylogeny and international nomenclature. The alternative method to estimate the Y-chromosome haplogroups is to predict Y-chromosome haplotypes from a set of Y-STR markers using software for Y-haplogroup prediction. The purpose of this study was to compare the accuracy of three types of Y-haplogroup prediction software and to determine the structure of Slovak population revealed by the Y-chromosome haplogroups. We used a sample of 166 Slovak males in which 12 Y-STR markers were genotyped in our previous study. These results were analyzed by three different software products that predict Y-haplogroups. To estimate the accuracy of these prediction software, Y-haplogroups were determined in the same sample by genotyping Y-chromosome SNPs. Haplogroups were correctly predicted in 98.80 % (Whit Athey's Haplogroup Predictor), 97.59 % (Jim Cullen's Haplogroup Predictor) and 98.19 % (YPredictor by Vadim Urasin 1.5.0) of individuals. The occurrence of errors in Y-chromosome haplogroup prediction suggests that the validation using SNP analysis is appropriate when high accuracy is required. The results of SNP based haplotype determination indicate that 39.15 % of the Slovak population belongs to R1a-M198 lineage, which is one of the main European lineages.
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The polymorphism of the male-specific portion of the Y chromosome has been increasingly used to describe the composition of the European gene pool and to reconstruct its formation. Here the theoretical grounds and the limitations of this approach are presented, together with the different views on debated issues. The emerging picture for the composition of the male gene pool of the continent is illustrated, but local peculiarities that represent departures from the main trends are also highlighted, in order to illustrate the main unifying feature, i.e. the overlay of recent patterns onto more ancient ones. A synopsis of the main findings and conclusions obtained in regional studies has also been compiled.
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An official journal of the Genetics Society, Heredity publishes high-quality articles describing original research and theoretical insights in all areas of genetics. Research papers are complimented by News & Commentary articles and reviews, keeping researchers and students abreast of hot topics in the field.
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The ancestry of modern Europeans is a subject of debate among geneticists, archaeologists, and anthropologists. A crucial question is the extent to which Europeans are descended from the first European farmers in the Neolithic Age 7500 years ago or from Paleolithic hunter-gatherers who were present in Europe since 40,000 years ago. Here we present an analysis of ancient DNA from early European farmers. We successfully extracted and sequenced intact stretches of maternally inherited mitochondrial DNA (mtDNA) from 24 out of 57 Neolithic skeletons from various locations in Germany, Austria, and Hungary. We found that 25% of the Neolithic farmers had one characteristic mtDNA type and that this type formerly was widespread among Neolithic farmers in Central Europe. Europeans today have a 150-times lower frequency (0.2%) of this mtDNA type, revealing that these first Neolithic farmers did not have a strong genetic influence on modern European female lineages. Our finding lends weight to a proposed Paleolithic ancestry for modern Europeans.
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We surveyed nine diallelic polymorphic sites on the Y chromosomes of 1,544 individuals from Africa, Asia, Europe, Oceania, and the New World. Phylogenetic analyses of these nine sites resulted in a tree for 10 distinct Y haplotypes with a coalescence time of approximately 150,000 years. The 10 haplotypes were unevenly distributed among human populations: 5 were restricted to a particular continent, 2 were shared between Africa and Europe, 1 was present only in the Old World, and 2 were found in all geographic regions surveyed. The ancestral haplotype was limited to African populations. Random permutation procedures revealed statistically significant patterns of geographical structuring of this paternal genetic variation. The results of a nested cladistic analysis indicated that these geographical associations arose through a combination of processes, including restricted, recurrent gene flow (isolation by distance) and range expansions. We inferred that one of the oldest events in the nested cladistic analysis was a range expansion out of Africa which resulted in the complete replacement of Y chromosomes throughout the Old World, a finding consistent with many versions of the Out of Africa Replacement Model. A second and more recent range expansion brought Asian Y chromosomes back to Africa without replacing the indigenous African male gene pool. Thus, the previously observed high levels of Y chromosomal genetic diversity in Africa may be due in part to bidirectional population movements. Finally, a comparison of our results with those from nested cladistic analyses of human mtDNA and beta-globin data revealed different patterns of inferences for males and females concerning the relative roles of population history (range expansions) and population structure (recurrent gene flow), thereby adding a new sex-specific component to models of human evolution.
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The haplotypes at four polymorphic loci of the Y chromosome were determined in 245 Caucasian males from 12 subpopulations. The data show that haplotype radiation occurred among Caucasians. Haplotype radiation was accompanied by recurrent mutations at STR loci that caused partial randomization of haplotype structure. The present distribution of alleles at short tandem repeats (STRs) can be explained by a mutation pattern similar to those described for autosomal STRs. The degree of variation among groups of subpopulations was assayed by using the Analysis of Molecular Variance. The results confirm a faster divergence of the Y chromosome as compared to the rest of the genome.
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Mutations in the Y linked testis determining gene SRY cause 46,XY sex reversal. However, only about 15% of cases of 46,XY sex reversal are accounted for by mutations in SRY. In this study we have investigated the possibility that mutations affecting the expression of SRY might cause some of the cases of sex reversal in which the coding sequence of SRY is normal. We have screened 2 kb of DNA immediately 5' to the SRY coding sequence in 49 subjects with varying degrees of 46,XY sex reversal. Two variant bases were identified, one of which was determined to be a polymorphism and the other is unique, but familial.
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Y chromosome haplotypes are particularly useful in deciphering human evolutionary history because they accentuate the effects of drift, migration, and range expansion. Significant acceleration of Y biallelic marker discovery and subsequent typing involving heteroduplex detection has been achieved by implementing an innovative and cost-efficient method called denaturing high-performance liquid chromatography (DHPLC). The power of the method resides in its sensitivity and ability to rapidly compare amplified sequences in an automated manner. We have determined the allelic states of 22 Y polymorphisms; 19 of which are unreported, in 718 diverse extant chromosomes; established haplotype frequencies; and deduced a phylogeny. All major geographic regions, including Eurasia, are characterized by mutations reflecting episodes of genetic drift and expansion. Most biallelic markers are localized regionally. However, some show wider dispersal and designate older, core haplotypes. One transversion defines a major haplogroup that distinguishes a previously unknown deep, apparently non-African branch. It provides evidence of an ancient bottleneck event. It is now possible to anticipate the inevitable detailed reconstruction of human Y chromosome genealogy based on several tens to even hundreds of these important polymorphisms.
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Ease and accuracy of typing, together with high levels of polymorphism and widespread distribution in the genome, make microsatellite (or short tandem repeat) loci an attractive potential source of information about both population histories and evolutionary processes. However, microsatellite data are difficult to interpret, in particular because of the frequency of back-mutations. Stochastic models for the underlying genetic processes can be specified, but in the past they have been too complicated for direct analysis. Recent developments in stochastic simulation methodology now allow direct inference about both historical events, such as genealogical coalescence times, and evolutionary parameters, such as mutation rates. A feature of the Markov chain Monte Carlo (MCMC) algorithm that we propose here is that the likelihood computations are simplified by treating the (unknown) ancestral allelic states as auxiliary parameters. We illustrate the algorithm by analyzing microsatellite samples simulated under the model. Our results suggest that a single microsatellite usually does not provide enough information for useful inferences, but that several completely linked microsatellites can be informative about some aspects of genealogical history and evolutionary processes. We also reanalyze data from a previously published human Y chromosome microsatellite study, finding evidence for an effective population size for human Y chromosomes in the low thousands and a recent time since their most recent common ancestor: the 95% interval runs from approximately 15, 000 to 130,000 years, with most likely values around 30,000 years.
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In 1995, much to the delight of mitochondrial Eve (Cann et al. 1987), the search for a suitable partner resulted in the discovery of Y-chromosomal Adam (Dorit et al. 1995; Paabo 1995). Like Eve, he was traced back to sub-Saharan Africa, although with a date of 270,000 years ago, he seems a bit older than she. On the basis of the absence of sequence variation in a part of the ZFY gene in 38 globally dispersed male subjects, this date was not undisputed (Donnelly et al. 1996; Fu and Li 1996; Rogers et al. 1996; Weiss and von Haeseler 1996). Later in the same year, two additional studies did reveal a limited number of sequence variants on other parts of the Y chromosome. Because of these variants, estimates were obtained of the times back to our most recent common (male) ancestor of 37,000–49,000 years ago (Whitfield et al. 1995) and of 51,000–411,000 years ago (Hammer 1994). Now, just 5 years later, with simple PCR strategies, ⩾250 polymorphic loci scattered over the entire nonrecombining part of the human Y chromosome can be identified. Among these polymorphisms are (1) biallelic markers with a low mutation rate representing unique (or near-unique) mutation events (UMEs) in human evolution, such as single base-pair substitutions (Underhill et al. 1997), an ALU insertion/deletion polymorphism (Hammer 1994), or a LINE insertion (Santos et al. 2000); (2) moderately fast-evolving microsatellites or simple-tandem repeats (STRs), with an average mutation frequency of ∼.2% per generation (Heyer et al. 1997; Jobling et al. 1999; Kayser et al. 2000); and (3) fast-evolving loci, such as the minisatellite locus MSY1 (Jobling et al. 1998) with a mutation frequency of 6%–11% per generation. With the exception of the two pseudoautosomal regions, the almost 60–Mb nonrecombining part of the Y chromosome is transmitted strictly from father to son without recombination (Jobling and Tyler-Smith 1995). This renders the Y chromosome probably the most versatile haplotypic genotyping system of the human genome. It is thus not surprising that chromosome-Y polymorphisms have been used to follow the migration patterns of our male ancestors from the recent past (Heyer et al. 1997; Foster et al. 1998) through historical times (Skorecki et al. 1997; Hammer et al. 2000), to the origins of modern humans (Hammer et al. 1998). Recently, two excellent review articles featuring the Y chromosome were published. The first (Bertranpetit 2000) addresses the difficulties of reliably tracing back human origins solely on the basis of Y-chromosomal UMEs. The second (Jobling and Tyler-Smith 2000) gives a detailed discussion of many genetic aspects of the Y chromosome in the context of disease and selection. This editorial will be restricted to the combined use of UMEs and STRs on the Y chromosome to reconstruct our genetic history. This application has received considerable attention in recent articles published in this journal and elsewhere (see, e.g., Zerjal et al. 1997; Bianchi et al. 1998; Hurles et al. 1998, 1999; Kittles et al. 1998; Bosch et al. 1999; Karafet et al. 1999; Lahermo et al. 1999; Ruiz-Linares et al. 1999; Helgason et al. 2000b; Hill et al. 2000; Santos et al. 2000). That the combined use of Y-chromosomal UMEs and STRs is not without any caveats will be explained below.
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Binary polymorphisms associated with the non-recombining region of the human Y chromosome (NRY) preserve the paternal genetic legacy of our species that has persisted to the present, permitting inference of human evolution, population affinity and demographic history. We used denaturing high-performance liquid chromatography (DHPLC; ref. 2) to identify 160 of the 166 bi-allelic and 1 tri-allelic site that formed a parsimonious genealogy of 116 haplotypes, several of which display distinct population affinities based on the analysis of 1062 globally representative individuals. A minority of contemporary East Africans and Khoisan represent the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa between 35,000 and 89,000 years ago.
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A genetic perspective of human history in Europe was derived from 22 binary markers of the nonrecombining Y chromosome (NRY). Ten lineages account for >95% of the 1007 European Y chromosomes studied. Geographic distribution and age estimates of alleles are compatible with two Paleolithic and one Neolithic migratory episode that have contributed to the modern European gene pool. A significant correlation between the NRY haplotype data and principal components based on 95 protein markers was observed, indicating the effectiveness of NRY binary polymorphisms in the characterization of human population composition and history.
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Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant clines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. Principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low, nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift.
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In a previous study, we showed that the observation of high frequencies of certain inherited disorders in the population of Saguenay Lac Saint Jean (SLSJ) in Quebec can be explained in terms of the variance and the auto-correlation of effective family size (EFS) across generations. Correlated EFS, across generations, allows alleles introduced as a single copy to reach very high frequencies in about 12 generations. Here, we investigate the impact of this same demographic process on allelic association between a disease locus and closely linked neutral markers. We model the fate of a disease allele, introduced as a single copy, and of its surrounding haplotype. We show that the auto-correlation of EFS across generations increases the expected proportion of individuals who carry the ancestral haplotype in the present generation. Thus, the length of a shared haplotype is longer, making this population useful for coarse mapping. But this autocorrelation decreases the estimated value; thus ignoring the auto-correlation in EFS leads to an underestimate of the recombination rate. This result is of importance, since socio-demographic processes such as auto-correlation of EFS across generations have been described in other human populations.
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Although molecular genetic evidence continues to accumulate that is consistent with a recent common African ancestry of modern humans, its ability to illuminate regional histories remains incomplete. A set of unique event polymorphisms associated with the non-recombining portion of the Y-chromosome (NRY) addresses this issue by providing evidence concerning successful migrations originating from Africa, which can be interpreted as subsequent colonizations, differentiations and migrations overlaid upon previous population ranges. A total of 205 markers identified by denaturing high performance liquid chromatography (DHPLC), together with 13 taken from the literature, were used to construct a parsimonious genealogy. Ancestral allelic states were deduced from orthologous great ape sequences. A total of 131 unique haplotypes were defined which trace the microevolutionary trajectory of global modern human genetic diversification. The genealogy provides a detailed phylogeographic portrait of contemporary global population structure that is emblematic of human origins, divergence and population history that is consistent with climatic, paleoanthropological and other genetic knowledge.
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We examined 43 biallelic polymorphisms on the nonrecombining portion of the Y chromosome (NRY) in 50 human populations encompassing a total of 2,858 males to study the geographic structure of Y-chromosome variation. Patterns of NRY diversity varied according to geographic region and method/level of comparison. For example, populations from Central Asia had the highest levels of heterozygosity, while African populations exhibited a higher level of mean pairwise differences among haplotypes. At the global level, 36% of the total variance of NRY haplotypes was attributable to differences among populations (i.e., Phi(ST) = 0.36). When a series of AMOVA analyses was performed on different groupings of the 50 populations, high levels of among-groups variance (Phi(CT)) were found between Africans, Native Americans, and a single group containing all 36 remaining populations. The same three population groupings formed distinct clusters in multidimensional scaling plots. A nested cladistic analysis (NCA) demonstrated that both population structure processes (recurrent gene flow restricted by isolation by distance and long-distance dispersals) and population history events (contiguous range expansions and long-distance colonizations) were instrumental in explaining this tripartite division of global NRY diversity. As in our previous analyses of smaller NRY data sets, the NCA detected a global contiguous range expansion out of Africa at the level of the total cladogram. Our new results support a general scenario in which, after an early out-of-Africa range expansion, global-scale patterns of NRY variation were mainly influenced by migrations out of Asia. Two other notable findings of the NCA were (1) Europe as a "receiver" of intercontinental signals primarily from Asia, and (2) the large number of intracontinental signals within Africa. Our AMOVA analyses also supported the hypothesis that patrilocality effects are evident at local and regional scales, rather than at intercontinental and global levels. Finally, our results underscore the importance of subdivision of the human paternal gene pool and imply that caution should be exercised when using models and experimental strategies based on the assumption of panmixia.
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British history contains several periods of major cultural change. It remains controversial as to how much these periods coincided with substantial immigration from continental Europe, even for those that occurred most recently. In this study, we examine genetic data for evidence of male immigration at particular times into Central England and North Wales. To do this, we used 12 biallelic polymorphisms and six microsatellite markers to define high-resolution Y chromosome haplotypes in a sample of 313 males from seven towns located along an east-west transect from East Anglia to North Wales. The Central English towns were genetically very similar, whereas the two North Welsh towns differed significantly both from each other and from the Central English towns. When we compared our data with an additional 177 samples collected in Friesland and Norway, we found that the Central English and Frisian samples were statistically indistinguishable. Using novel population genetic models that incorporate both mass migration and continuous gene flow, we conclude that these striking patterns are best explained by a substantial migration of Anglo-Saxon Y chromosomes into Central England (contributing 50%–100% to the gene pool at that time) but not into North Wales.
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We have identified a Y-chromosomal lineage with several unusual features. It was found in 16 populations throughout a large region of Asia, stretching from the Pacific to the Caspian Sea, and was present at high frequency: approximately 8% of the men in this region carry it, and it thus makes up approximately 0.5% of the world total. The pattern of variation within the lineage suggested that it originated in Mongolia approximately 1,000 years ago. Such a rapid spread cannot have occurred by chance; it must have been a result of selection. The lineage is carried by likely male-line descendants of Genghis Khan, and we therefore propose that it has spread by a novel form of social selection resulting from their behavior.
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Until recently, the Y chromosome seemed to fulfil the role of juvenile delinquent among human chromosomes--rich in junk, poor in useful attributes, reluctant to socialize with its neighbours and with an inescapable tendency to degenerate. The availability of the near-complete chromosome sequence, plus many new polymorphisms, a highly resolved phylogeny and insights into its mutation processes, now provide new avenues for investigating human evolution. Y-chromosome research is growing up.
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Analysis of 89 biallelic polymorphisms in 523 Turkish Y chromosomes revealed 52 distinct haplotypes with considerable haplogroup substructure, as exemplified by their respective levels of accumulated diversity at ten short tandem repeat (STR) loci. The major components (haplogroups E3b, G, J, I, L, N, K2, and R1; 94.1%) are shared with European and neighboring Near Eastern populations and contrast with only a minor share of haplogroups related to Central Asian (C, Q and O; 3.4%), Indian (H, R2; 1.5%) and African (A, E3*, E3a; 1%) affinity. The expansion times for 20 haplogroup assemblages was estimated from associated STR diversity. This comprehensive characterization of Y-chromosome heritage addresses many multifaceted aspects of Anatolian prehistory, including: (1) the most frequent haplogroup, J, splits into two sub-clades, one of which (J2) shows decreasing variances with increasing latitude, compatible with a northward expansion; (2) haplogroups G1 and L show affinities with south Caucasus populations in their geographic distribution as well as STR motifs; (3) frequency of haplogroup I, which originated in Europe, declines with increasing longitude, indicating gene flow arriving from Europe; (4) conversely, haplogroup G2 radiates towards Europe; (5) haplogroup E3b3 displays a latitudinal correlation with decreasing frequency northward; (6) haplogroup R1b3 emanates from Turkey towards Southeast Europe and Caucasia and; (7) high resolution SNP analysis provides evidence of a detectable yet weak signal (<9%) of recent paternal gene flow from Central Asia. The variety of Turkish haplotypes is witness to Turkey being both an important source and recipient of gene flow.
Article
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We estimate an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9x10-4 per 25 years, with a standard deviation across loci of 5.7x10-4, using data on microsatellite variation within Y chromosome haplogroups defined by unique-event polymorphisms in populations with documented short-term histories, as well as comparative data on worldwide populations at both the Y chromosome and various autosomal loci. This value is used to estimate the times of the African Bantu expansion, the divergence of Polynesian populations (the Maoris, Cook Islanders, and Samoans), and the origin of Gypsy populations from Bulgaria.
Article
Four loci mapping to the nonrecombining portion of the Y chromosome were genotyped in three Japanese populations (Okinawa, Shizuoka and Aomori ) and Taiwanese. The Y Alu polymorphic (YAP) element is present in 42% of the Japanese and absent in the Taiwanese, confirming the irregular distribution of this polymorphism in Asia. Data from the four loci were used to determine genetic distances among populations, construct Y chromosome haplotypes, and estimate the degree of genetic diversity in each population. Evolutionary analysis of Y haplotypes suggests that polymorphisms at the YAP (DYS287) and DXYS5Y loci originated a single time, whereas restriction patterns at the DYS1 locus and microsatellite alleles at the DYS19 locus arose more than once. Genetic distance analysis indicated that the Okinawans are differentiated from Japanese living on Honshu. The data support the hypotheses that modern Japanese populations have resulted from distinctive genetic contributions involving the ancient Jomon people and Yayoi immigrants from Korea or mainland China, with Okinawans experiencing the least amount of admixture with the Yayoi. It is suggested that YAP(+) chromosomes migrated to Japan with the Jomon people >10,000 years ago and that a large infusion of YAP(-) chromosomes entered Japan with the Yayoi migration starting 2,300 years ago. Different degrees of genetic diversity carried by these two ancient lineages may be explained by the different lifestyles of the migrant groups, the size of the founding populations, and the antiquities of the founding events.
Article
Spatial autocorrelation analysis tests whether the observed value of a nominal, ordinal, or interval variable at one locality is independent of values of the variable at neighbouring localities. The computation of autocorrelation coefficients for nominal, ordinal, and for interval data is illustrated, together with appropriate significance tests. The method is extended to include the computation of correlograms for spatial autocorrelation. These show the autocorrelation coefficient as a function of distance between pairs of localities being considered, and summarize the patterns of geographic variation exhibited by the response surface of any given variable. Autocorrelation analysis is applied to microgeographic variation of allozyme frequencies in the snail Helix aspersa. Differences in variational patterns in two city blocks are interpreted. The inferences that can be drawn from correlograms are discussed and illustrated with the aid of some artificially generated patterns. Computational formulae, expected values and standard errors are furnished in two appendices.
Article
mtDNA sequence variation was studied in 419 individuals from nine Eurasian populations, by high-resolution RFLP analysis, and it was followed by sequencing of the control region of a subset of these mtDNAs and a detailed survey of previously published data from numerous other European populations. This analysis revealed that a major Paleolithic population expansion from the "Atlantic zone" (southwestern Europe) occurred 10,000-15,000 years ago, after the Last Glacial Maximum. As an mtDNA marker for this expansion we identified haplogroup V, an autochthonous European haplogroup, which most likely originated in the northern Iberian peninsula or southwestern France at about the time of the Younger Dryas. Its sister haplogroup, H, which is distributed throughout the entire range of Caucasoid populations and which originated in the Near East approximately 25,000-30,000 years ago, also took part in this expansion, thus rendering it by far the most frequent (40%-60%) haplogroup in western Europe. Subsequent migrations after the Younger Dryas eventually carried those "Atlantic" mtDNAs into central and northern Europe. This scenario, already implied by archaeological records, is given overwhelming support from both the distribution of the autochthonous European Y chromosome type 15, as detected by the probes 49a/f, and the synthetic maps of nuclear data.
Article
Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant clines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. Principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low, nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift.
Article
This is the version as published in the American Journal of Human Genetics by the University Of Chicago Press. Their website is http://www.journals.uchicago.edu/AJHG.home.html We have examined the worldwide distribution of a Y-chromosomal base-substitution polymorphism, the T/C transition at SRY-2627, where the T allele defines haplogroup 22; sequencing of primate homologues shows that the ancestral state cannot be determined unambiguously but is probably the C allele. Of 1,191 human Y chromosomes analyzed, 33 belong to haplogroup 22. Twenty-nine come from Iberia, and the highest frequencies are in Basques (11%; n=117) and Catalans (22%; n=32). Microsatellite and minisatellite (MSY1) diversity analysis shows that non-Iberian haplogroup-22 chromosomes are not significantly different from Iberian ones. The simplest interpretation of these data is that haplogroup 22 arose in Iberia and that non-Iberian cases reflect Iberian emigrants. Several different methods were used to date the origin of the polymorphism: microsatellite data gave ages of 1,650, 2,700, 3,100, or 3,450 years, and MSY1 gave ages of 1,000, 2,300, or 2,650 years, although 95% confidence intervals on all of these figures are wide. The age of the split between Basque and Catalan haplogroup-22 chromosomes was calculated as only 20% of the age of the lineage as a whole. This study thus provides evidence for direct or indirect gene flow over the substantial linguistic barrier between the Indo-European and non-Indo-European-speaking populations of the Catalans and the Basques, during the past few thousand years.
Article
We explored the phylogeography of human Y-chromosomal haplogroup E3b by analyzing 3,401 individuals from five continents. Our data refine the phylogeny of the entire haplogroup, which appears as a collection of lineages with very different evolutionary histories, and reveal signatures of several distinct processes of migrations and/or recurrent gene flow that occurred in Africa and western Eurasia over the past 25,000 years. In Europe, the overall frequency pattern of haplogroup E-M78 does not support the hypothesis of a uniform spread of people from a single parental Near Eastern population. The distribution of E-M81 chromosomes in Africa closely matches the present area of distribution of Berber-speaking populations on the continent, suggesting a close haplogroup–ethnic group parallelism. E-M34 chromosomes were more likely introduced in Ethiopia from the Near East. In conclusion, the present study shows that earlier work based on fewer Y-chromosome markers led to rather simple historical interpretations and highlights the fact that many population-genetic analyses are not robust to a poorly resolved phylogeny.
Article
The Y chromosome contains the largest nonrecombining block in the human genome. By virtue of its many polymorphisms, it is now the most informative haplotyping system, with applications in evolutionary studies, forensics, medical genetics, and genealogical reconstruction. However, the emergence of several unrelated and nonsystematic nomenclatures for Y-chromosomal binary haplogroups is an increasing source of confusion. To resolve this issue, 245 markers were genotyped in a globally representative set of samples, 74 of which were males from the Y Chromosome Consortium cell line repository. A single most parsimonious phylogeny was constructed for the 153 binary haplogroups observed. A simple set of rules was developed to unambiguously label the different clades nested within this tree. This hierarchical nomenclature system supersedes and unifies past nomenclatures and allows the inclusion of additional mutations and haplogroups yet to be discovered. [Supplementary Table 1, available as an online supplement at www.genome.org , lists all published markers included in this survey and primer information.]
Article
The ancestry of modern Europeans is a subject of debate among geneticists, archaeologists, and anthropologists. A crucial question is the extent to which Europeans are descended from the first European farmers in the Neolithic Age 7500 years ago or from Paleolithic hunter-gatherers who were present in Europe since 40,000 years ago. Here we present an analysis of ancient DNA from early European farmers. We successfully extracted and sequenced intact stretches of maternally inherited mitochondrial DNA (mtDNA) from 24 out of 57 Neolithic skeletons from various locations in Germany, Austria, and Hungary. We found that 25% of the Neolithic farmers had one characteristic mtDNA type and that this type formerly was widespread among Neolithic farmers in Central Europe. Europeans today have a 150-times lower frequency (0.2%) of this mtDNA type, revealing that these first Neolithic farmers did not have a strong genetic influence on modern European female lineages. Our finding lends weight to a proposed Paleolithic ancestry for modern Europeans.
Article
Four loci mapping to the nonrecombining portion of the Y chromosome were genotyped in Japanese populations from Okinawa, the southernmost island of Japan; Shizuoka and Aomori on the main island of Honshu; and a small sample of Taiwanese. The Y Alu polymorphic (YAP) element is present in 42% of the Japanese and absent in the Taiwanese, confirming the irregular distribution of this polymorphism in Asia. Data from the four loci were used to determine genetic distances among populations, construct Y chromosome haplotypes, and estimate the degree of genetic diversity in each population and on different Y chromosome haplotypes. Evolutionary analysis of Y haplotypes suggests that polymorphisms at the YAP (DYS287) and DXYS5Y loci originated a single time, whereas restriction patterns at the DYS1 locus and microsatellite alleles at the DYS19 locus arose more than once. Genetic distance analysis indicated that the Okinawans are differentiated from Japanese living on Honshu. The data support the hypotheses that modern Japanese populations have resulted from distinctive genetic contributions involving the ancient Jomon people and Yayoi immigrants from Korea or mainland China, with Okinawans experiencing the least amount of admixture with the Yayoi. It is suggested that YAP+ chromosomes migrated to Japan with the Jomon people > 10,000 years ago and that a large infusion of YAP- chromosomes entered Japan with the Yayoi migration starting 2,300 years ago. Different degrees of genetic diversity carried by these two ancient chromosomal lineages may be explained by the different life-styles (hunter-gatherer versus agriculturalist). of the migrant groups, the size of the founding populations, and the antiquities of the founding events.
Article
We have identified a new T-->C transition on the human Y chromosome. C-allele chromosomes have been found only in a subset of the populations from Asia and northern Europe and reach their highest frequencies in Yakut, Buryats, and Finns. Examination of the microsatellite haplotypes of the C-allele chromosomes suggests that the mutation occurred recently in Asia. The Y chromosome thus provides both information about population relationships in Asia and evidence for a substantial paternal genetic contribution of Asians to northern European populations such as the Finns.
Article
Two hypervariable Y-specific markers, the YCAII and DYS19 STRs, and the more stable Y Alu Polymorphism (YAP) have been analysed in about 1400 individuals of 21 different populations, mainly from Europe but also from the Middle East, Africa and Asia. On the basis of the frequency distributions of these three Y-markers we compare, using different statistical analyses, their power in detecting population genetic structure and in distinguishing closely related groups. The pattern of populations' genetic affinities inferred from the three markers considered altogether suggests a strong genetic structure that, with a few exceptions, broadly corresponds to the linguistic relatedness and/or geographic location of the sampled populations.
Article
Nine single nucleotide (SNP) or indel binary polymorphisms were used to determine the frequencies and phylogenetic relationships of 12 Y chromosomal haplogroups in 289 males from Romania and the Republic of Moldova. Our data indicated a low but not null rate of the homoplasic appearance of the DYZ3 (-) allelic state. All other markers confirmed the previously proposed phylogeny. Based on the affinities between populations in terms of haplogroup frequencies, this work identified the geographical region of the Carpathians as a break point in the gene geography of Eastern Central Europe, providing a finer definition of one of the possible sharp genetic changes between Western and Eastern Europe.
Article
Population genetics has emerged as a powerful tool for unraveling human history. In addition to the study of mitochondrial and autosomal DNA, attention has recently focused on Y-chromosome variation. Ambiguities and inaccuracies in data analysis, however, pose an important obstacle to further development of the field. Here we review the methods available for genealogical inference using Y-chromosome data. Approaches can be divided into those that do and those that do not use an explicit population model in genealogical inference. We describe the strengths and weaknesses of these model-based and model-free approaches, as well as difficulties associated with the mutation process that affect both methods. In the case of genealogical inference using microsatellite loci, we use coalescent simulations to show that relatively simple generalizations of the mutation process can greatly increase the accuracy of genealogical inference. Because model-free and model-based approaches have different biases and limitations, we conclude that there is considerable benefit in the continued use of both types of approaches.
Article
We typed 1801 males from 55 locations for the Y-specific binary markers YAP, DYZ3, SRY10831 and the (CA)n microsatellites YCAII and DYS413. Phylogenetic relationships of chromosomes with the same binary haplotype were condensed in seven large one-step networks, which accounted for 95% of all chromosomes. Their coalescence ages were estimated based on microsatellite diversity. The three largest and oldest networks undergo sharp frequency changes in three areas. The more recent network 3.1A clearly discriminates between Western and Eastern European populations. Pairwise Fst showed an overall increment with increasing geographic distance but with a slope greatly reduced when compared to previous reports. By sectioning the entire data set according to geographic and linguistic criteria, we found higher Fst-on-distance slopes within Europe than in West Asia or across the two continents.
Article
In this work we focus on a microsatellite-defined Y-chromosomal lineage (network 1.2) identified by us and reported in previous studies, whose geographic distribution and antiquity appear to be compatible with the Neolithic spread of farmers. Here, we set network 1.2 in the Y-chromosomal phylogenetic tree, date it with respect to other lineages associated with the same movements by other authors, examine its diversity by means of tri- and tetranucleotide loci and discuss the implications in reconstructing the spread of this group of chromosomes in the Mediterranean area. Our results define a tripartite phylogeny within HG 9 (Rosser et al. 2000), with the deepest branching defined by alleles T (Haplogroup Eu10) or G (Haplogroup Eu9) at M172 (Semino et al. 2000), and a subsequent branching within Eu9 defined by network 1.2. Population distributions of HG 9 and network 1.2 show that their occurrence in the surveyed area is not due to the spread of people from a single parental population but, rather, to a process punctuated by at least two phases. Our data identify the wide area of the Balkans, Aegean and Anatolia as the possible homeland harbouring the largest variation within network 1.2. The use of recently proposed tests based on the stepwise mutation model suggests that its spread was associated to a population expansion, with a high rate of male gene flow in the Turkish-Greek area.
Article
We have established the use of a primer extension/mass spectrometry method (the PinPoint assay) for high-throughput SNP genotyping of the human Y chromosome. 118 markers were used to define 116 haplogroups and typing was organised in a hierarchical fashion. Twenty multiplex PCR/primer extension reactions were set up and each sample could be assigned to a haplogroup with only two to five of these multiplex analyses. A single aliquot of one enzyme was found to be sufficient for both PCR and primer extension. We observed 100% accuracy in blind validation tests. The technique thus provides a reliable, cost-effective and automated method for Y genotyping, and the advantages of using a hierarchical strategy can be applied to any DNA segment lacking recombination.
Article
A multiplex polymerase chain reaction (PCR) assay capable of simultaneously amplifying 20 Y chromosome short tandem repeat (STR) markers has been developed to aid human identity testing and male population studies. These markers include all of the Y STRs that make up the "extended haplotype" used in Europe (DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, and YCAII) plus additional polymorphic Y STRs (DYS437, DYS438, DYS439, DYS447, DYS448, DYS388, DYS426, GATA A7.1, and GATA H4). Primers for the markers DYS385, DYS389, and YCAII target duplicated regions of the Y chromosome and thus can provide two polymorphic peaks for each respective primer set. This Y STR 20plex, which utilizes 34 different PCR primers, is the first to include a simultaneous amplification of all the markers within the European "minimal" and "extended" haplotypes. Relative primer positions are compared between the newly developed primers described here and previously published ones. Efforts were made to avoid X chromosome homology in the primer design as well as close packing of PCR product size ranges in order to keep all alleles less than 350 bp through careful examination of known allele ranges. Haplotype comparisons between the 20plex and a commercially available kit found excellent agreement across the 76 samples in the Y chromosome consortium panel.
Article
The degree of population replacement in the British Isles associated with cultural changes has been extensively debated. Recent work has demonstrated that comparisons of genetic variation in the British Isles and on the European Continent can illuminate specific demographic processes in the history of the British Isles. For example, Wilson et al. used the similarity of Basque and Celtic Y chromosomes to argue for genetic continuity from the Upper Palaeolithic to the present in the paternal history of these populations (see also ). Differences in the Y chromosome composition of these groups also suggested genetic signatures of Norwegian influence in the Orkney Islands north of the Scottish mainland, an important center of Viking activities between 800 and 1300 A.D. More recently, Weale et al. argued for substantial Anglo-Saxon male migration into central England based on the analysis of eight British sample sets collected on an east-west transect across England and Wales. To provide a more complete assessment of the paternal genetic history of the British Isles, we have compared the Y chromosome composition of multiple geographically distant British sample sets with collections from Norway (two sites), Denmark, and Germany and with collections from central Ireland, representing, respectively, the putative invading and the indigenous populations. By analyzing 1772 Y chromosomes from 25 predominantly small urban locations, we found that different parts of the British Isles have sharply different paternal histories; the degree of population replacement and genetic continuity shows systematic variation across the sampled areas.
Article
We explored the spatial distribution of human Y chromosomal diversity on a microgeographic scale, by typing 30 population samples from closely spaced locations in Italy and Greece for 9 haplogroups and their internal microsatellite variation. We confirm a significant difference in the composition of the Y chromosomal gene pools of the two countries. However, within each country, heterogeneity is not organized along the lines of clinal variation deduced from studies on larger spatial scales. Microsatellite data indicate that local increases of haplogroup frequencies can be often explained by a limited number of founders. We conclude that local founder or drift effects are the main determinants in shaping the microgeographic Y chromosomal diversity.
Article
Y-chromosome diversity has been analyzed at a micro-geographical level, examining 10 binary polymorphisms and 7 short tandem repeats (STRs) in 443 samples belonging to 11 populations from two regions of Northern Spain, Galicia and Cantabria. Both regions, as a whole, cluster with other Iberian populations. However, some individual populations, particularly that from the Pas Valley in Cantabria, depart markedly from this general pattern, with higher genetic distances and reduced diversity. This unusual population is even more distinct than the Basques from their Iberian neighbors. Genetic drift in a small isolated population could explain this special behavior, and in addition to its anthropological interest, this finding has important forensic implications.