Brief communication: Y-chromosome haplotypes in Egypt

We analyzed Y-chromosome haplotypes in the Nile River Valley in Egypt in 274 unrelated males, using the p49a,f TaqI polymorphism. These individuals were born in three regions along the river: in Alexandria (the Delta and Lower Egypt), in Upper Egypt, and in Lower Nubia. Fifteen different p49a,f TaqI haplotypes are present in Egypt, the three most common being haplotype V (39.4%), haplotype XI (18.9%), and haplotype IV (13.9%). Haplotype V is a characteristic Arab haplotype, with a northern geographic distribution in Egypt in the Nile River Valley. Haplotype IV, characteristic of sub-Saharan populations, shows a southern geographic distribution in Egypt.     

The origin of Yakuts: analysis of Y-chromosome haplotypes

Gene pool structure of Sakha Republic (Yakutia) native population has been studied: we defined composition and frequencies of Y-chromosome haplogroups for Yakuts. Six haplogroups: C3 x M77, C3c, N*, N2, N3a and R1a1 have been revealed in Yakut gene pool. A greater part of Y-chromosome in Yakut population belongs to N3a haplogroup (89%). All investigated Yakut population samples have low values of gene diversity, calculated based on haplogroup frequencies. Gene differentiation of the investigated samples estimated using the analysis of molecular variance (AMOVA) by two marker systems (haplogroup frequencies and microsatellite haplotypes of Y-chromosome) revealed a portion of interpopulation differences amounting to 0.24 and 2.85%, respectively. Frequencies and molecular phylogeny of YSTR-haplotypes were revealed for N3a haplogroup of Y-chromosome. Altogether forty haplotypes were found in Yakuts. Evenks and Yakuts are characterized by overlapping and very specific spectrum of N3a haplotypes, which is not typical for other Siberian ethnic groups. Cluster analysis of populations by N3a YSTR-haplotypes shows Yakut isolation from Turkic-speaking populations in the South Siberia. Genetic diversity generation time for a specific spectrum of Yakut haplotypes was estimated as 4.45 +/- 1.96 thousand years. As opposed to the data on mtDNA, the obtained results give an evidence for significant contribution of a local palaeolithic component into Y-chromosomal Yakut gene pool. Ethnogenetic reconstruction of the present picture of genetic diversity in N3a haplogroup in the territory of Siberia is under consideration.     

Y-chromosome haplotypes in Corsica

We studied the distribution of Y-chromosome specific haplotypes (detected by the TaqI polymorphism of probes p49a,f) on a total of 328 Corsican males native of the regions of Ajaccio, Bastia and Corte. Three haplotypes are differential among regions: haplotype XV (A3 C1 D2 F1 I1), preponderant in the North of the island, haplotype V (A2 C0 D0 F1 I1) in the South, and haplotype XII (A3 C0 D1 F1 I0) in the highlands of the centre. Distribution of haplotypes can be explained by Corsican history and geography.     

Genetic diversity within a caste population of India as measured by Y-chromosome haplogroups and haplotypes: subcastes of the Golla of Andhra Pradesh

The extent of population subdivision based on 15 Y-chromosome polymorphisms was studied in seven subcastes of the Golla (Karnam, Pokanati, Erra, Doddi, Punugu, Puja, and Kurava), who inhabit the Chittoor district of southern Andhra Pradesh, India. These Golla subcastes are traditionally pastoralists, culturally homogeneous and endogamous. DNA samples from 146 Golla males were scored for seven unique event polymorphisms (UEPs) and eight microsatellites, permitting allocation of each into haplogroups and haplotypes, respectively. Genetic diversity (D) was high (range, 0.9048-0.9921), and most of the genetic variance (>91%) was explained by intrapopulation differences. Median-joining network analysis of microsatellite haplotypes demonstrated an absence of any structure according to subcaste affiliation. Superimposition of UEPs on this phylogeny, however, did create some distinct clusters, indicating congruence between haplotype and haplogroup phylogenies. Our results suggest many male ancestors for the Golla as well as for each of the subcastes. Genetic distances among the seven subcastes, based on autosomal markers (short tandem repeats and human leukocyte antigens) as well as those on the chromosome Y, indicate that the Kurava may not be a true subcaste of the Golla. Although this finding is based on a very small Kurava sample, it is in accordance with ethnohistorical accounts related by community elders. The Punugu was the first to hive off the main Golla group, and the most recently separated subcastes (Karnam, Erra, Doddi, and Pokanati) fissioned from the Puja. This phylogeny receives support from the analysis of autosomal microsatellites as well as HLA loci in the same samples. In particular, there is a significant correlation (r = 0.8569; P = 0.0097) between Y-chromosome- and autosomal STR-based distances.     

Analysis of Mitochondrial DNA Lineages in Yakuts

To study the mitochondrial gene pool structure in Yakuts, polymorphism of mtDNA hypervariable segment I (16,024–16,390) was analyzed in 191 people sampled from the indigenous population of the Sakha Republic. In total, 67 haplotypes of 14 haplogroups were detected. Most (91.6%) haplotypes belonged to haplogroups A, B, C, D, F, G, M*, and Y, which are specific for East Eurasian ethnic groups; 8.4% haplotypes represented Caucasian haplogroups H, HV1, J, T, U, and W. A high frequency of mtDNA types belonging to Asian supercluster M was peculiar for Yakuts: mtDNA types belonging to haplogroup C, D, or G and undifferentiated mtDNA types of haplogroup M (M*) accounted for 81% of all haplotypes. The highest diversity was observed for haplogroups C and D, which comprised respectively 22 (44%) and 18 (30%) haplotypes. Yakuts showed the lowest genetic diversity (H = 0.964) among all Turkic ethnic groups. Phylogenetic analysis testified to common genetic substrate of Yakuts, Mongols, and Central Asian (Kazakh, Kyrgyz, Uighur) populations. Yakuts proved to share 21 (55.5%) mtDNA haplotypes with the Central Asian ethnic groups and Mongols. Comparisons with modern Paleoasian populations (Chukcha, Itelmen, Koryaks) revealed three (8.9%) haplotypes common for Yakuts and Koryaks. The results of mtDNA analysis disagree with the hypothesis of an appreciable Paleoasian contribution to the modern Yakut gene pool.     

壮族Y染色体分型及其内部遗传结构

壮族是中国最大的少数民族,与东南亚的泰老族群关系密切,在东亚人群的遗传结构研究中地位非常特殊。本研究调查了壮族各个支系的Y染色体多样性,通过主成分分析、聚类分析和分子方差分析,揭示壮族的内部父系遗传结构。结果发现,壮族的主要Y染色体单倍群为O%＊,O2a,O1。传统的对壮族按方言分为南北二组的分类方法在遗传上并没有依据,壮族支系体现出从东往西的梯度变化过程。这说明壮族的结构中有几个层次,最早的成分普遍出现在各个支系中,第二层是由东部来的百越核心成分,第三层是北方来的汉族成分。壮族内部遗传结构的分析将有助于对东亚人群的南来起源的研究。     

Y-chromosome Genotyping and Genetic Structure of Zhuang Populations

Zhuang, the largest ethnic minority population in China, is one of the descendant groups of the ancient Bai-Yue. Linguistically, Zhuang languages are grouped into northern and southern dialects. To characterize its genetic structure, 13 East Asian-specific Y-chromosome biallelic markers and 7 Y-chromosome short tandem repeat (STR) markers were used to infer the haplogroups of Zhuang populations. Our results showed that O*, O2a, and O1 are the predominant haplogroups in Zhuang. Frequency distribution and principal component analysis showed that Zhuang was closely related to groups of Bai-Yue origin and therefore was likely to be the descendant of Bai-Yue. The results of principal component analysis and hierarchical clustering analysis contradicted the linguistically derived north-south division. Interestingly, a west-east clinal trend of haplotype frequency changes was observed, which was supported by AMOVA analysis that showed that between-population variance of east-west division was larger than that of north-south division. O* network suggested that the Hongshuihe branch was the center of Zhuang. Our study suggests that there are three major components in Zhuang. The O* and O2a constituted the original component; later, O1 was brought into Zhuang, especially eastern Zhuang; and finally, northern Han population brought O3 into the Zhuang populations.     

Y-chromosome specific alleles and haplotypes in European and Asian populations: Linkage disequilibrium and geographic diversity

Variation on the Y chromosome may permit our understanding the evolution of the human paternal lineage and male gene flow. This study reports upon the distribution and non random association of alleles at four Y-chromosome specific loci in four populations, three Caucasoid (Italian, Greek and Slav) and one Asian. The markers include insertion/deletion (p12f), point mutation (92R7 and pYαI), and repeat sequence (p21A1) polymorphisms. Our data confirm that the p12f/TaqI 8 kb allele is a Caucasoid marker and that Asians are monomorphic at three of the loci (p12f, 92R7, and pYαI). The alleles at 92R7 and pYαI were found to be in complete disequilibrium in Europeans. Y-haplotype diversity was highly significant between Asians and all three European groups (P < 0.001), but the Greeks and Italians were also significantly different with respect to some alleles and haplotypes (P < 0.02). We find strong evidence that the p12f/TaqI 8 kb allele may have arisen only once, as a deletion event, and, additionally, that the present-day frequency distribution of Y chromosomes carrying the p12f/8 kb allele suggests that it may have been spread by colonising sea-faring peoples from the Near East, possibly the Phoenicians, rather than by expansion of Neolithic farmers into continental Europe. The p12f deletion is the key marker of a unique Y chromosome, found only in Caucasians to date, labelled ‘Mediterranean’ and this further increases the level of Y-chromosome diversity seen among Caucasoids when compared to the other major population groups. Am J Phys Anthropol 104:167–176, 1997. © 1997 Wiley-Liss, Inc.     

Y-chromosome diversity in Native Mexicans reveals continental transition of genetic structure in the Americas

The genetic characterization of Native Mexicans is important to understand multiethnic based features influencing the medical genetics of present Mexican populations, as well as to the reconstruct the peopling of the Americas. We describe the Y-chromosome genetic diversity of 197 Native Mexicans from 11 populations and 1,044 individuals from 44 Native American populations after combining with publicly available data. We found extensive heterogeneity among Native Mexican populations and ample segregation of Q-M242* (46%) and Q-M3 (54%) haplogroups within Mexico. The northernmost sampled populations falling outside Mesoamerica (Pima and Tarahumara) showed a clear differentiation with respect to the other populations, which is in agreement with previous results from mtDNA lineages. However, our results point toward a complex genetic makeup of Native Mexicans whose maternal and paternal lineages reveal different narratives of their population history, with sex-biased continental contributions and different admixture proportions. At a continental scale, we found that Arctic populations and the northernmost groups from North America cluster together, but we did not find a clear differentiation within Mesoamerica and the rest of the continent, which coupled with the fact that the majority of individuals from Central and South American samples are restricted to the Q-M3 branch, supports the notion that most Native Americans from Mesoamerica southwards are descendants from a single wave of migration. This observation is compatible with the idea that present day Mexico might have constituted an area of transition in the diversification of paternal lineages during the colonization of the Americas.     

汉族群体23个Y染色体双等位基因标记遗传多态性研究

为了筛选在汉族群体中具有多态性的Y染色体双等位基因标记并获取其群体遗传学数据。采用片段长度差异等位基因特异性PCR和PAGE技术对武汉地区160名男性汉族无关个体的23个Y染色体双等位基因标记（M7,M9,M50,M88,M89,M95,M111,M117,M119,M121,M122,M134,M159,M164,M175,M214,LINE1,MSY2,RPS4Y711,SRY＋465,IMS-JST164520,IMS-JST021354和IMS-JST003305）进行分型。除M50、M159和M164外,其余20个标记在武汉汉族群体中均具有遗传多态性,其基因多样性（GD）范围为0.0126～0.4855,共检出35种不同单体群组合（Hg1～35）,单体群多样性（HD）为0.9471。表明20个Y染色体双等位基因标记组成的单体群具有较高的遗传多样性,在法医学应用和群体进化研究中具有较高的实用价值。     

The evolutionary history of grey wolf Y chromosomes

Analyses of Y chromosome haplotypes uniquely provide a paternal picture of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA (mtDNA). Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf (Canis lupis) Y chromosome, probably representing most of the male‐specific, nonampliconic sequence from the euchromatic part of the chromosome. We characterized this sequence and then identified ≈1,500 Y‐linked single nucleotide polymorphisms in a sample of 145 resequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in 24 dogs and eight other canids. We found 53 Y chromosome haplotypes, of which 26 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated because individual haplotypes were never shared between geographically distant areas, and genetically similar haplotypes were only found within the same geographical region. The deepest split between grey wolf haplogroups was estimated to have occurred 125,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as most recent immigrant haplotypes were present in the neighbouring Finnish population, but not in sequenced wolves from elsewhere in the world, or in dogs.     

Haplotype analysis of the mitochondrial DNA d‐loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democratic Republic of Congo

This study aimed at assessing haplotype diversity and population dynamics of three Congolese indigenous goat populations that included Kasai goat (KG), small goat (SG), and dwarf goat (DG) of the Democratic Republic of Congo (DRC). The 1169 bp d‐loop region of mitochondrial DNA (mtDNA) was sequenced for 339 Congolese indigenous goats. The total length of sequences was used to generate the haplotypes and evaluate their diversities, whereas the hypervariable region (HVI, 453 bp) was analyzed to define the maternal variation and the demographic dynamic. A total of 568 segregating sites that generated 192 haplotypes were observed from the entire d‐loop region (1169 bp d‐loop). Phylogenetic analyses using reference haplotypes from the six globally defined goat mtDNA haplogroups showed that all the three Congolese indigenous goat populations studied clustered into the dominant haplogroup A, as revealed by the neighbor‐joining (NJ) tree and median‐joining (MJ) network. Nine haplotypes were shared between the studied goats and goat populations from Pakistan (1 haplotype), Kenya, Ethiopia and Algeria (1 haplotype), Zimbabwe (1 haplotype), Cameroon (3 haplotypes), and Mozambique (3 haplotypes). The population pairwise analysis (F_ST ) indicated a weak differentiation between the Congolese indigenous goat populations. Negative and significant (p‐value <.05) values for Fu''s Fs (−20.418) and Tajima''s (−2.189) tests showed the expansion in the history of the three Congolese indigenous goat populations. These results suggest a weak differentiation and a single maternal origin for the studied goats. This information will contribute to the improvement of the management strategies and long‐term conservation of indigenous goats in DRC.     

Peopling of three Mediterranean islands (Corsica,Sardinia, and Sicily) inferred by Y-chromosome biallelic variability

An informative set of biallelic polymorphisms was used to study the structure of Y-chromosome variability in a sample from the Mediterranean islands of Corsica and Sicily, and compared with data on Sardinia to gain insights into the ethnogenesis of these island populations. The results were interpreted in a broader Mediterranean context by including in the analysis neighboring populations previously studied with the same methodology. All samples studied were enclosed in the comparable spectrum of European Y-chromosome variability. Pronounced differences were observed between the islands as well as in the percentages of haplotypes previously shown to have distinctive patterns of continental phylogeography. Approximately 60% of the Sicilian haplotypes are also prevalent in Southern Italy and Greece. Conversely, the Corsican sample had elevated levels of alternative haplotypes common in Northern Italy. Sardinia showed a haplotype ratio similar to that observed in Corsica, but with a remarkable difference in the presence of a lineage defined by marker M26, which approaches 35% in Sardinia but seems absent in Corsica. Although geographically adjacent, the data suggest different colonization histories and a minimal amount of recent gene flow between them. Our results identify possible ancestral continental sources of the various island populations and underscore the influence of founder effect and genetic drift. The Y-chromosome data are consistent with comparable mtDNA data at the RFLP haplogroup level of resolution, as well as linguistic and historic knowledge.     

Brief communication: Y-chromosome haplogroup analysis indicates that Chinese Tuvans share distinctive affinity with Siberian Tuvans

Tuvans are mainly distributed in Siberia (the Republic of Tuva), Mongolia, and China. The genetic origin of Chinese Tuvans remains controversial. The Tuvans in China were classified as Mongolians in the early 1950s by the National Ethnic Affairs Commission of China, but they defined themselves as a separate group. To resolve this dispute and determine their genetic relationships with the peoples in Central Asia, we randomly selected 150 male subjects from the Tuvans in the Altai region of Xinjiang Uygur Autonomous Region in China. Fourteen Y chromosomal markers were genotyped using the RFLP method or direct sequencing. These haplogroup data were combined with public data for 15 populations in South Siberia and Central Asia. Tuvans in both China and the Republic of Tuva had the highest frequencies of haplogroups K-M9 and Q-M242. Principal component analysis demonstrated that the Tuvans in China were of a distinct cluster, separated from their neighbors, the Mongolians and Kazakhs, which finding was consistent with the Analysis of Molecular Variances. Further population tree analysis revealed that Tuvans were on a far-separated cluster from their neighbors. Based on these results, we propose that the Tuvans (in both China and the Republic of Tuva) constitute a group distinct from Mongolians and from other Central Asia populations. However, the genetic results might be the consequence of some evolutionary forces like genetic drift and founder effect, and do not necessarily reflect their ultimate origin.     

Mitochondrial DNA patterns in the Macaronesia islands: Variation within and among archipelagos

Macaronesia covers four Atlantic archipelagos: the Azores, Madeira, the Canary Islands, and the Cape Verde islands. When discovered by Europeans in the 15th century, only the Canaries were inhabited. Historical reports highlight the impact of Iberians on settlement in Macaronesia. Although important differences in their settlement are documented, its influence on their genetic structures and relationships has yet to be ascertained. In this study, the hypervariable region I (HVRI) sequence and coding region polymorphisms of mitochondrial DNA (mtDNA) in 623 individuals from the Azores (120) and Canary Islands (503) were analyzed. Combined with published data, these give a total of 1,542 haplotypes from Macaronesia and 1,067 from the Iberian Peninsula. The results obtained indicate that Cape Verde is the most distinctive archipelago, with an mtDNA pool composed almost exclusively of African lineages. However, the other archipelagos present an mtDNA profile dominated by the presence of West‐Eurasian mtDNA haplogroups with African lineages present in varying proportions. Moreover, no signs of integration of typical Canarian U6 lineages in the other archipelagos were detected. The four Macaronesia archipelagos currently have differentiated genetic profiles, and the Azores present the highest intra‐archipelago differentiation and the lowest values of diversity. The analyses performed show that the present‐day genetic profile of the Macaronesian archipelagos was mainly determined by the initial process of settlement and further microdifferentiation probably as a consequence of the small population size of some islands. Moreover, contacts between archipelagos seem to have had a low impact on the mtDNA genetic pool of each archipelago. Am J Phys Anthropol, 2010. © 2009 Wiley‐Liss, Inc.     

Insights into Iberian population origins through the construction of highly informative Y-chromosome haplotypes using biallelic markers,STRs, and the MSY1 minisatellite

To investigate the diversity of Y chromosomes in the Iberian Peninsula and the North African population of Maghreb, we constructed superhaplotypes on the basis of 10 biallelic markers, 7 microsatellites, and 1 minisatellite located in the nonrecombining portion of the human Y chromosome. The analysis of extremely high MSY1 variability was performed by reducing the MVR-codes to modular structures. Y-STRs and MSY1 data provide information about the relationship between closely related populations such as those of Iberia. Analysis of biallelic markers allowed us to identify 7 of 12 haplogroups defined by those polymorphisms. The haplogroup background showed clear differences between Iberian populations and the North African one. The use of differently mutating Y-chromosome markers allowed us to infer different population events at different time scales: the Paleolithic background of the Iberian Peninsula, the Neolithic fingerprint on Y-chromosome lineages, and the Iron Age influence in the populations of Iberia. Implications of our results for the highly debated origin of Basques are also discussed.     

Brief communication: New Y‐chromosome binary markers improve phylogenetic resolution within haplogroup R1a1

Haplogroup R1a1‐M198 is a major clade of Y chromosomal haplogroups which is distributed all across Eurasia. To this date, many efforts have been made to identify large SNP‐based subgroups and migration patterns of this haplogroup. The origin and spread of R1a1 chromosomes in Eurasia has, however, remained unknown due to the lack of downstream SNPs within the R1a1 haplogroup. Since the discovery of R1a1‐M458, this is the first scientific attempt to divide haplogroup R1a1‐M198 into multiple SNP‐based sub‐haplogroups. We have genotyped 217 R1a1‐M198 samples from seven different population groups at M458, as well as the Z280 and Z93 SNPs recently identified from the “1000 Genomes Project”. The two additional binary markers present an effective tool because now more than 98% of the samples analyzed assign to one of the three sub‐haplogroups. R1a1‐M458 and R1a1‐Z280 were typical for the Hungarian population groups, whereas R1a1‐Z93 was typical for Malaysian Indians and the Hungarian Roma. Inner and Central Asia is an overlap zone for the R1a1‐Z280 and R1a1‐Z93 lineages. This pattern implies that an early differentiation zone of R1a1‐M198 conceivably occurred somewhere within the Eurasian Steppes or the Middle East and Caucasus region as they lie between South Asia and Eastern Europe. The detection of the Z93 paternal genetic imprint in the Hungarian Roma gene pool is consistent with South Asian ancestry and amends the view that H1a‐M82 is their only discernible paternal lineage of Indian heritage. © 2012 Wiley Periodicals, Inc.     

Population genetic structure of skipjack tuna Katsuwonus pelamis from the Indian coast using sequence analysis of the mitochondrial DNA D-loop region

Genetic structure of skipjack tuna Katsuwonus pelamis from the Indian region was investigated using sequence data of mitochondrial DNA (mtDNA) D-loop region. A total of 315 individuals were sampled from six major fishing grounds around the east and west coasts of India including the Andaman (Port Blair) and Lakshadweep (Minicoy) Islands. Nucleotide and gene diversities were high in all the sample collections. Significant genetic heterogeneity was observed for the mtDNA sequence data among sites (φ(ST) = 0·0273, P < 0·001). Analysis of molecular variance (AMOVA) showed significant genetic variation among four groups (φ(CT) = 0·0261, P < 0·05) which was also supported by spatial AMOVA results. The null hypothesis of single panmictic population of K. pelamis along the Indian coast can thus be rejected. Phylogenetic analysis of the mtDNA sequence data showed the presence of four clades of K. pelamis in the Indian waters. There was no clear pattern, however, of haplotypes and geographic location among samples. The results of this study suggest the occurrence of four genetically differentiated groups of K. pelamis across the coastal waters of India.     

Brief communication: mtDNA variation in North Cameroon: lack of Asian lineages and implications for back migration from Asia to sub-Saharan Africa

The hypervariable region-1 and four nucleotide positions (10400, 10873, 12308, and 12705) of the coding region of mitochondrial DNA (mtDNA) were analyzed in 441 individuals belonging to eight populations (Daba, Fali, Fulbe, Mandara, Uldeme, Podokwo, Tali, and Tupuri) from North Cameroon and four populations (Bakaka, Bassa, Bamileke, and Ewondo) from South Cameroon. All mtDNAs were assigned to five haplogroups: three sub-Saharan (L1, L2, and L3), one northern African (U6), and one European (U5). Our results contrast with the observed high frequencies of a Y-chromosome haplogroup of probable Asian origin (R1*-M173) in North Cameroon. As a first step toward a better understanding of the evident discrepancy between mtDNA and Y-chromosome data, we propose two contrasting scenarios. The first one, here termed "migration and asymmetric admixture," implies a back migration from Asia to North Cameroon of a population group carrying the haplotype R1*-M173 at high frequency, and an admixture process restricted to migrant males. The second scenario, on the other hand, temed "divergent drift," implies that modern populations of North Cameroon originated from a small population group which migrated from Asia to Africa and in which, through genetic drift, Y-chromosome haplotype R1*-M173 became predominant, whereas the Asian mtDNA haplogroups were lost.