Y-chromosomal Binary Haplogroups in the Japanese Population and their Relationship to 16 Y-STR Polymorphisms

We investigated Y chromosomal binary and STR polymorphisms in 263 unrelated male individuals from the Japanese population and further examined the relationships between the two separate types of data. Using 47 biallelic markers we distinguished 20 haplogroups, four of which (D2b1/-022457, O3/-002611*, O3/-LINE1 del, and O3/-021354*) were newly defined in this study. Most haplogroups in the Japanese population are found in one of the three major clades, C, D, or O. Among these, two major lineages, D2b and O2b, account for 66% of Japanese Y chromosomes. Haplotype diversity of binary markers was calculated at 86.3%. The addition of 16 Y-STR markers increased the number of haplotypes to 225, yielding a haplotype diversity of 99.40%. A comparison of binary haplogroups and Y-STR type revealed a close association between certain binary haplogroups and Y-STR allelic or conformational differences, such as those at the DXYS156Y, DYS390m, DYS392, DYS437, DYS438 and DYS388 loci. Based on our data on the relationships between binary and STR polymorphisms, we estimated the binary haplogroups of individuals from STR haplotypes and frequencies of binary haplogroups in other Japanese, Korean and Taiwanese Han populations. The present data will enable researchers to connect data from binary haplogrouping in anthropological studies and Y-STR typing in forensic studies in East Asian populations, especially those in and around Japan.     

Mitochondrial DNA variation in Jordanians and their genetic relationship to other Middle East populations

Background: The Levant is a crucial region in understanding human migrations between Africa and Eurasia. Although some mitochondrial DNA (mtDNA) studies have been carried out in this region, they have not included the Jordan area. This paper deals with the mtDNA composition of two Jordan populations.

Aim: The main objectives of this article are: first, to report mtDNA sequences of an urban and an isolate sample from Jordan and, second, to compare them with each other and with other nearby populations.

Subjects and methods: The analyses are based on HVSI and HVSII mtDNA sequences and diagnostic RFLPs to unequivocally classify into haplogroups 101 Amman and 44 Dead Sea unrelated individuals from Jordan.

Results: Statistical analysis revealed that, whereas the sample from Amman did not significantly differ from their Levantine neighbours, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its outstanding Eurasian haplogroup U3 frequency (39%) and its south-Saharan Africa lineages (19%) are the highest in the Middle East. On the contrary, the lack ((preHV)1) or comparatively low frequency (J and T) of Neolithic lineages is also striking. Although strong drift by geographic isolation could explain the anomalous mtDNA pool of the Dead Sea sample, the fact that its mtDNA lineage composition mirrors, in geographic origin and haplogroup frequencies, its Y-chromosome pool, points to founder effect as the main cause. Ancestral M1 lineages detected in Jordan that have affinities with those recently found in Northwest but not East Africa question the African origin of the M1 haplogroup.

Conclusion: Results are in agreement with an old human settlement in the Jordan region. However, in spite of the attested migratory spreads, genetically divergent populations, such as that of the Dead Sea, still exist in the area.     

Y-chromosomal evidence of the cultural diffusion of agriculture in southeast Europe

The debate concerning the mechanisms underlying the prehistoric spread of farming to Southeast Europe is framed around the opposing roles of population movement and cultural diffusion. To investigate the possible involvement of local people during the transition of agriculture in the Balkans, we analysed patterns of Y-chromosome diversity in 1206 subjects from 17 population samples, mainly from Southeast Europe. Evidence from three Y-chromosome lineages, I-M423, E-V13 and J-M241, make it possible to distinguish between Holocene Mesolithic forager and subsequent Neolithic range expansions from the eastern Sahara and the Near East, respectively. In particular, whereas the Balkan microsatellite variation associated to J-M241 correlates with the Neolithic period, those related to E-V13 and I-M423 Balkan Y chromosomes are consistent with a late Mesolithic time frame. In addition, the low frequency and variance associated to I-M423 and E-V13 in Anatolia and the Middle East, support an European Mesolithic origin of these two clades. Thus, these Balkan Mesolithic foragers with their own autochthonous genetic signatures, were destined to become the earliest to adopt farming, when it was subsequently introduced by a cadre of migrating farmers from the Near East. These initial local converted farmers became the principal agents spreading this economy using maritime leapfrog colonization strategies in the Adriatic and transmitting the Neolithic cultural package to other adjacent Mesolithic populations. The ensuing range expansions of E-V13 and I-M423 parallel in space and time the diffusion of Neolithic Impressed Ware, thereby supporting a case of cultural diffusion using genetic evidence.     

Evolution and migration history of the Chinese population inferred from Chinese Y-chromosome evidence

Y-chromosomes from 76 Chinese men covering 33 ethnical minorities throughout China as well as the Han majority were collected as genetic material for the study of Chinese nonrecombinant Y-chromosome (NRY) phylogeny. Of the accepted worldwide NRY haplogroups, three (haplogroups D, C, O) were significant in this sample, extending previous assessments of Chinese genetic diversity. Based on geographic, linguistic, and ethnohistorical information, the 33 Chinese ethnical minorities in our survey were divided into the following four subgroups: North, Tibet, West, and South. Inferred from the distribution of the newfound immediate ancestor lineage haplogroup O^*, which has M214 but not M175, we argue that the southern origin scenario of this most common Chinese Y haplogroup is not very likely. We tentatively propose a West/North-origin hypothesis, suggesting that haplogroup O originated in West/North China and mainly evolved in China and thence spread further throughout eastern Eurasia. The nested cladistic analysis revealed in detail a multilayered, multidirectional, and continuous history of ethnic admixture that has shaped the contemporary Chinese population. Our results give some new clues to the evolution and migration of the Chinese population and its subsequence moving about in this land, which are in accordance with the historical records.The first two authors contributed equally to this study.     

A Perspective on the History of the Iberian Gypsies Provided by Phylogeographic Analysis of Y-Chromosome Lineages

The European Gypsies, commonly referred to as Roma, are represented by a vast number of groups spread across many countries. Although sharing a common origin, the Gypsy groups are highly heterogeneous as a consequence of genetic drift and different levels of admixture with surrounding populations. With this study we aimed at contributing to the knowledge of the Roma history by studying 17 Y-STR and 34 Y-SNP loci in a sample of 126 Portuguese Gypsies. Distinct genetic hallmarks of their past and migration route were detected, namely: an ancestral component, shared by all Roma groups, that reflects their origin in India (H1a-M82; ∼17%); an influence from their long permanence in the Balkans/Middle-East region (J2a1b-M67, J2a1b1-M92, I-M170, Q-M242; ∼31%); traces of contacts with European populations preceding the entrance in the Iberian Peninsula (R1b1c-M269, J2b1a-M241; ∼10%); and a high proportion of admixture with the non-Gypsy population from Iberia (R1b1c-M269, R1-M173/del.M269, J2a-M410, I1b1b-M26, E3b1b-M81; ∼37%). Among the Portuguese Gypsies the proportion of introgression from host populations is higher than observed in other groups, a fact which is somewhat unexpected since the arrival of the Roma to Portugal is documented to be more recent than in Central or East Europe.     

Drawing the history of the Hutterite population on a genetic landscape: inference from Y-chromosome and mtDNA genotypes

Although the North American Hutterites trace their origins to South Tyrol, no attempts have been made to examine the genetic migration history of the Hutterites before emigrating to the United States in the 1870s. To investigate this, we studied 9 microsatellite loci and 11 unique event polymorphism (UEP) markers on the Y-chromosome, the hypervariable region I (HVRI) of the mitochondrial DNA (mtDNA), as well as the complete mtDNA genome of Hutterite and South Tyrolean samples. Only 6 out of 14 Y-chromosome UEP+microsatellite haplotypes and 3 out of 11 mitochondrial haplotypes that were present in the Hutterites were also present in the South Tyrolean population. The phylogenetic relationships inferred from Y-chromosome and mtDNA databases show that the Hutterites have a unique genetic background related to a similar extent to central and eastern European populations. An admixture analysis indicates, however, a relatively high genetic contribution of central European populations to the Hutterite gene pool. These results are consistent with historical records on Hutterite migrations and demographic history. In addition, our data reveal similar numbers of Y and mitochondrial haplotypes in Hutterite male and female founders, respectively. The Hutterite male and female gene pools are similar with respect to genetic diversity and genetic distance measures and comparable with respect to their origins, suggesting a similar evolutionary history.     

The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups

The Philippines exhibits a rich diversity of people, languages, and culture, including so-called ‘Negrito'' groups that have for long fascinated anthropologists, yet little is known about their genetic diversity. We report here, a survey of Y-chromosome variation in 390 individuals from 16 Filipino ethnolinguistic groups, including six Negrito groups, from across the archipelago. We find extreme diversity in the Y-chromosome lineages of Filipino groups with heterogeneity seen in both Negrito and non-Negrito groups, which does not support a simple dichotomy of Filipino groups as Negrito vs non-Negrito. Filipino non-recombining region of the human Y chromosome lineages reflect a chronology that extends from after the initial colonization of the Asia-Pacific region, to the time frame of the Austronesian expansion. Filipino groups appear to have diverse genetic affinities with different populations in the Asia-Pacific region. In particular, some Negrito groups are associated with indigenous Australians, with a potential time for the association ranging from the initial colonization of the region to more recent (after colonization) times. Overall, our results indicate extensive heterogeneity contributing to a complex genetic history for Filipino groups, with varying roles for migrations from outside the Philippines, genetic drift, and admixture among neighboring groups.     

Mitochondrial DNA and Y-chromosome variation in five eastern Aleut communities: Evidence for genetic substructure in the Aleut population

Since Russian contact in 1741, the Aleut communities of southwestern Alaska have undergone a series of demographic upheavals stemming from forced relocations, disease epidemics, population bottlenecks, and pervasive admixture with European populations. This study investigates the impact of key historical events on the genetic structure of the Aleut population through analysis of mitochondrial and Y-chromosome DNA variation in five eastern Aleut communities. Results from HVS-I sequencing and Y-chromosome typing reveal patterns of variability that exhibit east–west geographic differentiation for the major Aleut haplogroups. This finding is underscored by SAMOVA and Monmonier analyses that identify genetic discontinuities between eastern and western Aleut populations. The majority of Aleut Y-chromosomes were characterized to haplogroups of mostly Russian, Scandinavian and Western European origin (approximately 85%), which is in stark contrast to the 3.6% of Aleut mtDNA lineages identified as non-Native American, and thus indicating a large degree of asymmetrical gene flow between European men and Aleut women. Overall, this study identifies a significant relationship between geography and genetic variation in the Aleut population, with a distinct substructure along an east–west axis that reflects the combined effects of founder events in aggregate island communities, male-biased gene flow from European populations, and the original peopling of the Aleutian Archipelago.     

Y-Chromosome Analysis of Ancient Hungarian and Two Modern Hungarian-Speaking Populations from the Carpathian Basin

The Hungarian population belongs linguistically to the Finno-Ugric branch of the Uralic family. The Tat C allele is an interesting marker in the Finno-Ugric context, distributed in all the Finno-Ugric-speaking populations, except for Hungarians. This question arises whether the ancestral Hungarians, who settled in the Carpathian Basin, harbored this polymorphism or not. 100 men from modern Hungary, 97 Szeklers (a Hungarian-speaking population from Transylvania), and 4 archaeologically Hungarian bone samples from the 10^th century were studied for this polymorphism. Among the modern individuals, only one Szekler carries the Tat C allele, whereas out of the four skeletal remains, two possess the allele. The latter finding, even allowing for the low sample number, appears to indicate a Siberian lineage of the invading Hungarians, which later has largely disappeared.
The two modern Hungarian-speaking populations, based on 22 Y-chromosomal binary markers, share similar components described for other Europeans, except for the presence of the haplogroup P*(xM173) in Szekler samples, which may reflect a Central Asian connection, and high frequency of haplogroup J in both Szeklers and Hungarians. MDS analysis based on haplogroup frequency values, confirms that modern Hungarian and Szekler populations are genetically closely related, and similar to populations from Central Europe and the Balkans.     

The Peopling of Modern Bosnia-Herzegovina: Y-chromosome Haplogroups in the Three Main Ethnic Groups

The variation at 28 Y‐chromosome biallelic markers was analysed in 256 males (90 Croats, 81 Serbs and 85 Bosniacs) from Bosnia‐Herzegovina. An important shared feature between the three ethnic groups is the high frequency of the “Palaeolithic” European‐specific haplogroup (Hg) I, a likely signature of a Balkan population re‐expansion after the Last Glacial Maximum. This haplogroup is almost completely represented by the sub‐haplogroup I‐P37 whose frequency is, however, higher in the Croats (～71%) than in Bosniacs (～44%) and Serbs (～31%). Other rather frequent haplogroups are E (～15%) and J (～7%), which are considered to have arrived from the Middle East in Neolithic and post‐Neolithic times, and R‐M17 (～14%), which probably marked several arrivals, at different times, from eastern Eurasia. Hg E, almost exclusively represented by its subclade E‐M78, is more common in the Serbs (～20%) than in Bosniacs (～13%) and Croats (～9%), and Hg J, observed in only one Croat, encompasses ～9% of the Serbs and ～12% of the Bosniacs, where it shows its highest diversification. By contrast, Hg R‐M17 displays similar frequencies in all three groups. On the whole, the three main groups of Bosnia‐Herzegovina, in spite of some quantitative differences, share a large fraction of the same ancient gene pool distinctive for the Balkan area.     

Paleolithic spread of Y-chromosomal lineage of tribes in eastern and northeastern India

Background: The Indian peninsula provides a suitable region for examination of the demographic impact of migrations and invasions in historical times, because its complex recent history has involved the long-term residence of different populations with distinct geographical origins and their own particular cultural characteristics.

Aim: The aim of the present study was to analyse Y chromosome haplotypes in tribes from eastern and north-eastern India, which provided the necessary phylogeographic resolution.

Subjects and methods: A total of 32 Y-chromosome SNPs and 17 Y-STRs were genotyped in 607 males from nine populations (Munda, Birhor, Oraon, Paharia, Santhal, Ho, Lachung, Mech and Rajbanshi) residing in East and Northeastern India.

Results: Y-chromosomal analysis revealed high frequency of the O2a haplogroup in Austroasiatic tribes and high haplotype diversity within specific haplogroups demonstrating a lesser degree of admixture of these populations with neighbouring populations in eastern India. In addition, the presence of O3a haplogroups in Sino-Tibetan populations reflects the influx from Southeast Asia during the demographic expansion through the Northeastern corridor.

Conclusion: The study suggested that the majority of the male gene flow of Austroasiatic tribes occurred during the late Pleistocene period. The results suggest gene flow from Southeast Asia to Northeast India, albeit more significantly among Tibeto-Burman than Austroasiatic-speaking populations.     

Y-chromosome Lineages from Portugal, Madeira and Açores Record Elements of Sephardim and Berber Ancestry

A total of 553 Y‐chromosomes were analyzed from mainland Portugal and the North Atlantic Archipelagos of Açores and Madeira, in order to characterize the genetic composition of their male gene pool. A large majority (78–83% of each population) of the male lineages could be classified as belonging to three basic Y chromosomal haplogroups, R1b, J, and E3b. While R1b, accounting for more than half of the lineages in any of the Portuguese sub‐populations, is a characteristic marker of many different West European populations, haplogroups J and E3b consist of lineages that are typical of the circum‐Mediterranean region or even East Africa. The highly diverse haplogroup E3b in Portuguese likely combines sub‐clades of distinct origins. The present composition of the Y chromosomes in Portugal in this haplogroup likely reflects a pre‐Arab component shared with North African populations or testifies, at least in part, to the influence of Sephardic Jews. In contrast to the marginally low sub‐Saharan African Y chromosome component in Portuguese, such lineages have been detected at a moderately high frequency in our previous survey of mtDNA from the same samples, indicating the presence of sex‐related gene flow, most likely mediated by the Atlantic slave trade.     

Unusual in vivo rearrangements of the Y-chromosome in two males

In the present paper two male patients with dic Y-chromosomes are reported with special attention to the identical and peculiar Y-chromosome rearrangements. Different cell types with variable morphology of the rearranged Y-chromosomes were found in both patients.     

Phylogeography of Y-chromosome haplogroup Q1a1a-M120, a paternal lineage connecting populations in Siberia and East Asia

Background: Previous studies have suggested that the human Y-chromosome haplogroup Q1a1a-M120, a widespread paternal lineage in East Asian populations, originated in South Siberia. However, much uncertainty remains regarding the origin, diversification, and expansion of this paternal lineage.

Aim: To explore the origin and diffusion of paternal Q-M120 lineages in East Asia.

Subjects and methods: The authors generated 26 new Y chromosome sequences of Q-M120 males and co-analysed 45 Y chromosome sequences of this haplogroup. A highly-revised phylogenetic tree of haplogroup Q-M120 with age estimates was reconstructed. Additionally, a comprehensive phylogeographic analysis of this lineage was performed including 15,007 samples from 440 populations in eastern Eurasia.

Results: An ancient connection of this lineage with populations in Siberia was revealed. However, this paternal lineage experienced an in-situ expansion between 5000 and 3000?years ago in northwestern China. Ancient populations with high frequencies of Q-M120 were involved in the formation of ancient Huaxia populations before 2000?years ago; this haplogroup eventually became one of the founding paternal lineages of modern Han populations.

Conclusion: This study provides a clear pattern of the origin and diffusion process of haplogroup Q1a1a-M120, as well as the role of this paternal lineage during the formation of ancient Huaxia populations and modern Han populations.     

Paternal lineages in southern Iberia provide time frames for gene flow from mainland Europe and the Mediterranean world

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: Four hundred and fourteen 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.     

Differential Greek and northern African migrations to Sicily are supported by genetic evidence from the Y chromosome

The presence or absence of genetic heterogeneity in Sicily has long been debated. Through the analysis of the variation of Y-chromosome lineages, using the combination of haplogroups and short tandem repeats from several areas of Sicily, we show that traces of genetic flows occurred in the island, due to ancient Greek colonization and to northern African contributions, are still visible on the basis of the distribution of some lineages. The genetic contribution of Greek chromosomes to the Sicilian gene pool is estimated to be about 37% whereas the contribution of North African populations is estimated to be around 6%.In particular, the presence of a modal haplotype coming from the southern Balkan Peninsula and of its one-step derivates associated to E3b1a2-V13, supports a common genetic heritage between Sicilians and Greeks. The estimate of Time to Most Recent Common Ancestor is about 2380 years before present, which broadly agrees with the archaeological traces of the Greek classic era. The Eastern and Western part of Sicily appear to be significantly different by the chi(2)-analysis, although the extent of such differentiation is not very high according to an analysis of molecular variance. The presence of a high number of different haplogroups in the island makes its gene diversity to reach about 0.9. The general heterogeneous composition of haplogroups in our Sicilian data is similar to the patterns observed in other major islands of the Mediterranean, reflecting the complex histories of settlements in Sicily.     

男性不育患者ICSI治疗后子代Y染色体微缺失基因的研究

目的 探讨亲代胞浆内单精子注射技术(intracytoplasmic sperm injection,ICSI)治疗时精液情况与子代AZF基因缺失率的相关性.方法 应用多重PCR技术,检测81例ICSI妊娠、42例体外受精(in vitro fertilization,IVF)妊娠及50例自然妊娠的男性及其子代外周血中AZF基因缺失情况.结果 自然妊娠组亲代、IVF组、ICSI组亲代AZF缺失率比较差异无统计学意义(0,0,6.2％,P=0.05),自然妊娠组子代与IVF组、ICSI组子代AZF缺失率比较差异有统计学意义(2％,0,10.3％,P=0.02).ICSI组中亲代精液正常者、少精症、严重少精症、梗阻性无精症者AZF缺失率比较差异无统计学意义(0,4.8％,10.5％,12.5％,P=0.33),ICSI组中四组子代AZF缺失率比较差异有统计学意义(0,4.5％,13.6％,27.8％,P=0.02).结论 IVF、ICSI的操作过程不会增加Y染色体微缺失的发生率及扩大AZF缺失片段,子代Y染色体AZF缺失的新生突变可能与亲代精液情况存在关联.     

Isolates in a corridor of migrations: a high-resolution analysis of Y-chromosome variation in Jordan

A high-resolution, Y-chromosome analysis using 46 binary markers has been carried out in two Jordan populations, one from the metropolitan area of Amman and the other from the Dead Sea, an area geographically isolated. Comparisons with neighboring populations showed that whereas the sample from Amman did not significantly differ from their Levantine neighbors, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its high R1*-M173 frequency (40%) has until now only been found in northern Cameroonian samples. This contrasts with the comparatively low presence of J representatives (9%), which is the modal clade in Middle Eastern populations, including Amman. The Dead Sea sample also showed a high presence of E3b3a-M34 lineages (31%), which is only comparable to that found in Ethiopians. Although ancient and recent ties with sub-Saharan and eastern Africans cannot be discarded, it seems that isolation, strong drift, and/or founder effects are responsible for the anomalous Y-chromosome pool of this population. These results demonstrate that, at a fine scale, the smooth, continental clines detected for several Y-chromosome markers are often disrupted by genetically divergent populations.     

Mitochondrial characterisation of two Spanish populations from the Vera and Bejar valleys (Central Spain)

This survey reports the mitochondrial data of two Spanish populations living in the Vera and Bejar valleys, on the opposite slopes of the Sierra de Gredos (Central Spain), which crosses Spain east to west. The aim of the study was to characterise the mitochondrial genetic pool of the Vera and Bejar populations to investigate a putative mitogenetic differentiation between them, evidence that would support the role of the Sierra de Gredos as a genetic barrier in their micro-evolutionary histories. Blood samples of 137 people (66 from Vera and 71 from Bejar) were collected and mtDNA hypervariable regions I and II (HVR-I and HVR-II) were dissected along with several mtDNA-coding region SNPs. The main European mitochondrial lineages have been found both in Vera and in Bejar, together with the typical African haplogroups L (in Vera) and U6 (in Bejar). F_ST value and the 95% credible regions calculated for haplogroup frequencies do not reveal genetic differentiation among the populations. Vera and Bejar contain an expected mitochondrial variability within them, but they do not seem to be genetically different from each other, leading us to conclude that the Sierra de Gredos is not a significant genetic barrier in their maternal genetic history.