The origin of Mosuo people as revealed by mtDNA and Y chromosome variation

The Mosuo, living in the Lugu Lake area in northwest Yunnan Province, China, is the only matriarchal population in China. The Mosuo was officially identified as Naxi nationality although its relationship with Naxi remains controversial. We studied the genetic relationship between the Mosuo and five other ethnic groups currently residing in northwest Yunnan, i.e. Naxi, Tibetan, Bai, Yi and Pumi, by typing the genetic variations in mtDNA HVS1 and 21 Y chromosome markers (13 SNPs & 8 STR markers). We showed that the maternal lineages of the Mosuo bear the strongest resemblance with those found in Naxi while its paternal lineages are more similar to those that are prevalent in Yunnan Tibetan. The marked difference between paternal and maternal lineages may be attributable to the genetic history, matriarchal structure, and visiting marriage.     

The origin of Mosuo people as revealed by mtDNA and Y chromosome variation

The Mosuo, living in the Lugu Lake area in northwest Yunnan Province, China, is the only matriarchal population in China. The Mosuo was officially identified as Naxi nationality although its relationship with Naxi remains controversial. We studied the genetic relationship between the Mosuo and five other ethnic groups currently residing in northwest Yunnan, i.e. Naxi, Tibetan, Bai, Yi and Pumi, by typing the genetic variations in mtDNA HVS1 and 21 Y chromosome markers (13 SNPs & 8 STR markers). We showed that the maternal lineages of the Mosuo bear the strongest resemblance with those found in Naxi while its paternal lineages are more similar to those that are prevalent in Yunnan Tibetan. The marked difference between paternal and maternal lineages may be attributable to the genetic history, matriarchal structure, and visiting marriage.     

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.     

Early population differentiation in extinct aborigines from Tierra del Fuego-Patagonia: ancient mtDNA sequences and Y-chromosome STR characterization

Ancient mtDNA was successfully recovered from 24 skeletal samples of a total of 60 ancient individuals from Patagonia-Tierra del Fuego, dated to 100-400 years BP, for which consistent amplifications and two-strand sequences were obtained. Y-chromosome STRs (DYS434, DYS437, DYS439, DYS393, DYS391, DYS390, DYS19, DYS389I, DYS389II, and DYS388) and the biallelic system DYS199 were also amplified, Y-STR alleles could be characterized in nine cases, with an average of 4.1 loci per sample correctly typed. In two samples of the same ethnic group (Aonikenk), an identical and complete eight-loci haplotype was recovered. The DYS199 biallelic system was used as a control of contamination by modern DNA and, along with DYS19, as a marker of American origin. The analysis of both mtDNA and Y-STRs revealed DNA from Amerindian ancestry. The observed polymorphisms are consistent with the hypothesis that the ancient Fuegians are close to populations from south-central Chile and Argentina, but their high nucleotide diversity and the frequency of single lineages strongly support early genetic differentiation of the Fuegians through combined processes of population bottleneck, isolation, and/or migration, followed by strong genetic drift. This suggests an early genetic diversification of the Fuegians right after their arrival at the southernmost extreme of South America.     

Y-chromosome variation among Sudanese: restricted gene flow, concordance with language, geography, and history

We study the major levels of Y-chromosome haplogroup variation in 15 Sudanese populations by typing major Y-haplogroups in 445 unrelated males representing the three linguistic families in Sudan. Our analysis shows Sudanese populations fall into haplogroups A, B, E, F, I, J, K, and R in frequencies of 16.9, 7.9, 34.4, 3.1, 1.3, 22.5, 0.9, and 13% respectively. Haplogroups A, B, and E occur mainly in Nilo-Saharan speaking groups including Nilotics, Fur, Borgu, and Masalit; whereas haplogroups F, I, J, K, and R are more frequent among Afro-Asiatic speaking groups including Arabs, Beja, Copts, and Hausa, and Niger-Congo speakers from the Fulani ethnic group. Mantel tests reveal a strong correlation between genetic and linguistic structures (r = 0.31, P = 0.007), and a similar correlation between genetic and geographic distances (r = 0.29, P = 0.025) that appears after removing nomadic pastoralists of no known geographic locality from the analysis. The bulk of genetic diversity appears to be a consequence of recent migrations and demographic events mainly from Asia and Europe, evident in a higher migration rate for speakers of Afro-Asiatic as compared with the Nilo-Saharan family of languages, and a generally higher effective population size for the former. The data provide insights not only into the history of the Nile Valley, but also in part to the history of Africa and the area of the Sahel.     

白族群体间的Y染色体和线粒体DNA多态性的分析

从父系和母系基因库水平上,研究不同分布地区白族群体之间的遗传结构的异同,并对其族源以及本民族群体之间的微进化关系进行初步的探讨。利用PCR-RFLP方法对云南白族和湖南白族及云南的傣族、布依族、独龙族、怒族、阿昌族和湖南土家族共8个群体进行14个线粒体多态位点和Y染色体上的13个双等位基因位点进行基因分型。统计单倍型,在SPSS软件上进行主成分分析。结果显示,两个白族群体在Y染色体双等位基因单倍型分布上差异不大,以H6、H8为主要单倍型分布;在线粒体单倍群分布上,两个白族群体则差异显著,单倍群D、B、M8在湖南白族中的分布频率比云南白族高的多,而在云南白族中M^*、G、F的频率则比湖南白族高。对Y染色体单倍型分布频率进行主成分分析表明两个白族群体聚在一起,整体上和其他北方起源的群体聚成一组;而对线粒体的单倍群分布频率分析显示湖南白族接近湖南汉族和土家族,而云南白族则接近云南怒族和阿昌族。两个白族群体在父系遗传结构上相近,表明他们具有共同的父系族源;而母系遗传结构上的差异,可能与历史上迁到湖南的白族先民主要为男性军士,流寓到当地后与汉、土家等民族女子通婚所致。     

A multi‐perspective view of genetic variation in Cameroon

In this study, we report the genetic variation of autosomal and Y‐chromosomal microsatellites in a large Cameroon population dataset (a total of 11 populations) and jointly analyze novel and previous genetic data (mitochondrial DNA and protein coding loci) taking geographic and cultural factors into consideration. The complex pattern of genetic variation of Cameroon can in part be described by contrasting two geographic areas (corresponding to the northern and southern part of the country), which differ substantially in environmental, biological, and cultural aspects. Northern Cameroon populations show a greater within‐ and among‐group diversity, a finding that reflects the complex migratory patterns and the linguistic heterogeneity of this area. A striking reduction of Y‐chromosomal genetic diversity was observed in some populations of the northern part of the country (Podokwo and Uldeme), a result that seems to be related to their demographic history rather than to sampling issues. By exploring patterns of genetic, geographic, and linguistic variation, we detect a preferential correlation between genetics and geography for mtDNA. This finding could reflect a female matrimonial mobility that is less constrained by linguistic factors than in males. Finally, we apply the island model to mitochondrial and Y‐chromosomal data and obtain a female‐to‐male migration Nν ratio that was more than double in the northern part of the country. The combined effect of the propensity to inter‐populational admixture of females, favored by cultural contacts, and of genetic drift acting on Y‐chromosomal diversity could account for the peculiar genetic pattern observed in northern Cameroon. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

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.     

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.     

Genetic structure of Mediterranean populations revealed by Y-chromosome haplotype analysis

The allelic variability at six Y-chromosome-specific polymorphisms (YAP, DYS19, DYS389-I, DYS390, DYS391, and DYS392) was used to generate male-specific haplotypes in 333 males representing 12 population samples from the region around the Mediterranean sea. Extreme interindividual variation was observed, as more than 160 distinct Y-chromosome variants could be defined as six-locus haplotypes. Concomitant with this high variability, low levels of population genetic structure were observed. In particular, a "core" of populations directly facing the north and the east of the Mediterranean basin, from the Middle East to the Italian Peninsula, was found to be genetically undifferentiated. This observation, supported by a reanalysis of Y-specific binary polymorphisms in the same populations, suggests that at least part of the male-specific gene pools of these populations has either a very recent common origin (that could be related with the Neolithic demic diffusion hypothesis), and/or that gene flow has played a significant role in shaping the patterns of genetic variability in this region. In agreement with both hypotheses, we found that the spatial distribution of DYS392 alleles revealed a marked differentiation between the East and the West of the Mediterranean area. Through the analysis of microsatellite variation, the time to the most recent common ancestor (TMRCA) of the YAP(+) sublineage 4 has been estimated. The estimations, based on two different data sets, turn out to be quite recent (7,000-11,000 YBP), suggesting that this lineage may have been first introduced into Southern Europe through Neolithic migrations from the Middle East.     

Embryo outcome in Y-chromosome microdeleted infertile males after ICSI

A prospective study involving 118 infertile Japanese couples to assess the embryo outcomes in both azoospermic and oligoasthenoteratoazoospermic (OAT) patients with Y-chromosome microdeletion. The men were divided into two groups; azoospermia (n = 27), and OAT, sperm concentration <5 x 10(6)/ml (n = 91). They were investigated for Y-chromosome microdeletions by a polymerase chain reaction (PCR) amplification of the Y-chromosome-specific sequence tag site (STS). The embryo outcomes of patients found to have Y-microdeletion were determined. The frequency of microdeletion was 8.8% (9) and two had microdeletions distal to DAZ. The mean fertilization rate and the cleavage rate in the eight cycles of both azoospermic and oligospermic patients were 59.3 and 87.5%, respectively. The percentages of grade 1 & 2 embryos, > or =6 cells embryos, and blastocyts were 51.7, 65.6, and 45.3%, respectively. Three pregnancies resulted from the eight cycles (37.5%). CONCLUSION: in Y-chromosome microdeletion cycles in which sperm cells were available for intracytoplasmic sperm injection (ICSI), embryo outcome was comparable to conventional IVF.     

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.     

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.     

Genetic evidence for the Mongolian ancestry of Kalmyks

The Kalmyks are an ethnic group along the lower Volga River in Russia who are thought to have migrated there from Mongolia about 300 years ago. To investigate their origins, we studied mtDNA and Y-chromosome variation in 99 Kalmyks. Both mtDNA HV1 sequences and Y-chromosome SNP haplogroups indicate a close relationship of Kalmyks with Mongolians. In addition, genetic diversity for both mtDNA and the Y chromosome are comparable in Kalmyks, Mongolians, and other Central Asian groups, indicating that the Kalmyk migration was not associated with a substantial bottleneck. The so-called "Genghis Khan" Y-chromosome short tandem repeat (STR) haplotype was found in high frequency (31.3%) among Kalmyks, further supporting a strong genetic connection between Kalmyks and Mongolians. Genetic analyses of even recent, relatively well-documented migrations such as of the Kalmyks can therefore lead to new insights concerning such migrations.     

Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies

Puerto Rico and the surrounding islands rest on the eastern fringe of the Caribbean's Greater Antilles, located less than 100 miles northwest of the Lesser Antilles. Puerto Ricans are genetic descendants of pre‐Columbian peoples, as well as peoples of European and African descent through 500 years of migration to the island. To infer these patterns of pre‐Columbian and historic peopling of the Caribbean, we characterized genetic diversity in 326 individuals from the southeastern region of Puerto Rico and the island municipality of Vieques. We sequenced the mitochondrial DNA (mtDNA) control region of all of the samples and the complete mitogenomes of 12 of them to infer their putative place of origin. In addition, we genotyped 121 male samples for 25 Y‐chromosome single nucleotide polymorphism and 17 STR loci. Approximately 60% of the participants had indigenous mtDNA haplotypes (mostly from haplogroups A2 and C1), while 25% had African and 15% European haplotypes. Three A2 sublineages were unique to the Greater Antilles, one of which was similar to Mesoamerican types, while C1b haplogroups showed links to South America, suggesting that people reached the island from the two distinct continental source areas. However, none of the male participants had indigenous Y‐chromosomes, with 85% of them instead being European/Mediterranean and 15% sub‐Saharan African in origin. West Eurasian Y‐chromosome short tandem repeat haplotypes were quite diverse and showed similarities to those observed in southern Europe, North Africa and the Middle East. These results attest to the distinct, yet equally complex, pasts for the male and female ancestors of modern day Puerto Ricans. Am J Phys Anthropol 155:352–368, 2014. © 2014 Wiley Periodicals, Inc.     

Demographic and evolutionary trajectories of the Guarani and Kaingang natives of Brazil

A total of 278 individuals from two Brazilian Indian tribes (Guarani and Kaingang) living in five different localities had their mitochondrial DNA sequenced for the first hypervariable segment (HVS-I), and a fraction of them was also studied for seven biallelic Y-chromosome polymorphisms. Nineteen HVS-I lineages were detected, which showed distinct distributions in the two tribes. The G(ST) value obtained with the mtDNA data is about 5 times higher for the Guarani as compared to the Kaingang, suggesting a higher level of differentiation between the three Guarani partialities than between the two Kaingang villages. Non-Amerindian admixture varied with sex and in the Guarani was only observed through the paternal line. Using these data and those of other Tupian and Jêan tribes, it was possible to make inferences about past migratory movements and the genetic differentiation of these populations.     

Genetic perspectives on forager‐farmer interaction in the Luangwa Valley of Zambia

The transformation from a foraging way of life to a reliance on domesticated plants and animals often led to the expansion of agropastoralist populations at the expense of hunter‐gatherers (HGs). In Africa, one of these expansions involved the Niger‐Congo Bantu‐speaking populations that started to spread southwards from Cameroon/Nigeria ～4,000 years ago, bringing agricultural technologies. Genetic studies have shown different degrees of gene flow (sometimes involving sex‐biased migrations) between Bantu agriculturalists and HGs. Although these studies have covered many parts of sub‐Saharan Africa, the central part (e.g. Zambia) was not yet studied, and the interactions between immigrating food‐producers and local HGs are still unclear. Archeological evidence from the Luangwa Valley of Zambia suggests a long period of coexistence (～1,700 years) of early food‐producers and HGs. To investigate if this apparent coexistence was accompanied by genetic admixture, we analyzed the mtDNA control region, Y chromosomal unique event polymorphisms, and 12 associated Y‐ short tandem repeats in two food‐producing groups (Bisa and Kunda) that live today in the Luangwa Valley, and compared these data with available published data on African HGs. Our results suggest that both the Bisa and Kunda experienced at most low levels of admixture with HGs, and these levels do not differ between the maternal and paternal lineages. Coalescent simulations indicate that the genetic data best fit a demographic scenario with a long divergence (62,500 years) and little or no gene flow between the ancestors of the Bisa/Kunda and existing HGs. This scenario contrasts with the archaeological evidence for a long period of coexistence between the two different communities in the Luangwa Valley, and suggests a process of sociocultural boundary maintenance may have characterized their interaction. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.