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.     

Mitochondrial origin of the matrilocal Mosuo people in China

The Mosuo people are currently the only matrilocal population in China. The origins of the population and their matrilocal tradition remain unknown. To address these questions, we studied the mitochondrial DNA (mtDNA) diversity of the Mosuo. Lower mtDNA diversity is expected in matrilocal populations because the women remain with their families after marriage, and there is generally less movement of mtDNA genomes in matrilocal populations. However, the haplotype diversity of this population is not lower than the neighboring patrilocal populations, indicating that the Mosuo started practicing matrilocality at least after the Paleolithic Age. A previous haplogroup frequency clustering study indicated that the Mosuo are closest to the Naxi people, but the network analysis of individual sequence haplotypes presented herein shows that most Mosuo lineages cluster with Pumi lineages. Therefore, we concluded that the Mosuo people have the closest genetic relationship with the Pumi, and that they started to practice matrilocality several thousand years ago.     

Multiple origins of Tibetan Y chromosomes

The genetic origin of Tibetans was investigated using Y chromosome markers. A total of three populations were studied, two from central Tibet speaking central Tibetan and one from Yunnan speaking Kham. Two dominant paternal lineages (>80%) were identified in all three populations with one possibly from central Asia (YAP+) and the other from east Asia (M122C). We conclude that Tibetan Y chromosomes may have been derived from two different gene pools, given the virtual absence of M122C in central Asia and YAP+ in east Asia, with drift an unlikely mechanism accounting for these observations.     

利用SSR标记分析云南、西藏和新疆小麦的遗传多样性

用185对SSR引物对52份中国西部特有小麦的遗传多样性进行了研究分析。在31份云南小麦材料中,共检测到488个等位变异,每一个SSR引物可检测到1至9个等位变异,平均为2.64个;平均PIC值为0.2764。在15份西藏小麦材料中,共检测到472个等位变异,每个引物可扩增出1到8个等位变异,平均为2.55个;平均PIC值为0.3082。在6份新疆小麦材料中,共检测到308个等位变异,每一个SSR引物可检测1到5个等位变异,平均为1.66个;平均PIC值为0.1944。185对SSR引物在云南、西藏和新疆小麦的21条染色体、7个部分同源群和3个染色体组上检测到的等位位点的多态性存在明显差异。云南、西藏和新疆小麦均以3B染色体较高,而1D染色体最低;在7个部分同源群中,均以第三部分同源群最高,第六部分同源群最低;在A、B和D染色体组上,均以B染色体组最高,D染色体组最低,A染色体组居中。利用185对SSR引物计算了云南、西藏和新疆小麦群体内及其群体间的遗传距离(GD)和平均遗传距离,结果显示,西藏小麦和云南小麦群体内的平均遗传距离要高于新疆小麦,而云南小麦和西藏小麦间的平均遗传距离低于两者与新疆小麦的平均遗传距离。聚类分析结果也表明,云南小麦和西藏小麦的亲缘关系较近,但两者与新疆小麦的亲缘关系相对较远。     

Genetic architecture of a small, recently aggregated Aleut population: Bering Island, Russia

The fishing community of Bering Island, located in the Russian Commander Islands off the Kamchatka Peninsula, was originally founded by a small number of Russian soldiers and merchants, along with Aleuts forcibly relocated from the western region of the Aleutian archipelago. The purpose of this study is to characterize the genetic variation of Bering Island inhabitants for autosomal, mitochondrial, and Y-chromosome DNA and classic genetic markers and to investigate the genetic impact of the 19th-century founding and subsequent demographic events on this heterogeneous community. Our results show a loss of diversity among maternal lineages in the Bering Aleut population, with fixation of mtDNA haplogroup D, as revealed by median-joining network analysis and mismatch differences. Conversely, paternal haplotypes exhibit an increase in diversity and the presence of a substantial number of non-Native lineages. Admixture results, based on autosomal STR data, indicate that parental contributions to the mixed Aleut population of Bering are approximately 60% Aleut and 40% Russian. Classic genetic markers show affinities between the Bering Island Aleuts and the other historically founded Aleut communities of St. Paul and St. George in the Pribilof Islands, Alaska. This study demonstrates that the opposing evolutionary forces of genetic drift and gene flow acted on the maternal and paternal lineages, respectively, to shape the genetic structure of the present-day inhabitants of Bering Island.     

Combining genetics and population history in the study of ethnic diversity in the People's Republic of China

Genomic data have increasingly been used to complement linguistic, archeological, and anthropological evidence in reconstructing the origins and migratory patterns of modern humans. East Asia is a particular hotspot of human migration, especially mainland China, where a large number of human fossils have been unearthed and more than 20% of the world's population now resides. There are 56 officially recognized ethnic populations (minzu) in China. In the present study we investigated the ancestry and genetic diversity of nine populations: the majority Han of Liaoning Province; the Miao, Yao, Kucong, and Tibetan communities of Yunnan Province in southwest China; and four Muslim populations, the Hui, Bonan, Dongxiang, and Sala from central and northern China. We used both biparental and uniparental markers to determine patterns of diversity at autosomal, mitochondrial, and Y-chromosome loci. The study populations displayed several paternal origins but restricted maternal ancestries. From the Y-chromosome data in particular, major demographic changes, such as the Neolithic population expansion and more recent historical events including migration along the Silk Road, could be inferred. Specific aspects of the internal structure and organization of the study populations, including endogamy and consanguinity, were uncovered using autosomal markers. However, we encountered interpretive problems in terms of the definition of the present-day ethnic study populations in China, which appear to reflect past and present political as well as genetic influences.     

云南4个少数民族8个Y-STR位点的多态分布

对云南蒙古族、纳西族、普米族和藏族4个少数民族共183份样本进行了8个Y—STR位点的多态性分析。结果显示：4个民族都保留着较高的Y—STR遗传多态性,在测出的55个等位基因中共构建了101种单倍型,其中蒙古族有29种,纳西族有17种,普米族有26种,藏族有45种。Rst距阵表明,云南蒙古族与普米族和纳西族的遗传距离最远,分别为0．28945和0．25862;云南藏族与普米族的遗传距离较远,为0．20109;云南藏族与纳西族的遗传距离最近,比其他民族两两之间的距离小1个数量级,仅为0．09475。结合历史学和民族学对4个民族父系遗传的亲缘关系进行了初步的比较分析。     

Genealogy and palaeodrainage basins in Yunnan Province: phylogeography of the Yunnan spiny frog,Nanorana yunnanensis (Dicroglossidae)

Historical drainage patterns adjacent to the Qinghai‐Tibetan Plateau differed markedly from those of today. We examined the relationship between drainage history and geographic patterns of genetic variation in the Yunnan spiny frog, Nanorana yunnanensis, using approximately 981 base pairs of mitochondrial DNA partial sequences from protein‐coding genes ND1 and ND2, and intervening areas including complete tRNA^Ile, tRNA^Gln and tRNA^Met. Two null hypotheses were tested: (i) that genetic patterns do not correspond to the development of drainage systems and (ii) that populations had been stable and not experienced population expansion, bottlenecking and selection. Genealogical analyses identified three, major, well‐supported maternal lineages, each of which had two sublineages. These divergent lineages were completely concordant with six geographical regions. Genetic structure and divergence were strongly congruent with historical rather than contemporary drainage patterns. Most lineages and sublineages were formed via population fragmentation during the rearrangement of paleodrainage basins in the Early Pliocene and Early Pleistocene. Sympatric lineages occurred only in localities at the boundaries of major drainages, likely reflecting secondary contact of previously allopatric populations. Extensive population expansion probably occurred early in the Middle Pleistocene accompanying dramatic climatic oscillations.     

中国香菇自然种质的rDNA遗传多样性分析

测定了全国范围内的59个野生香菇菌株rDNA的ITS区域的序列。所得序列的总长度在723-727个碱基之间,G+C含量也基本稳定在57.5%左右。用Phylip3.6软件包对59个ITS序列进行DNA数据分析。结果表明59个菌株被划分到3个不同的谱系中,其中谱系Ⅰ包括11个菌株,分布较为均衡,涉及东北、西北、西南和东部沿海等地区的8个省份;谱系Ⅱ包括14菌株,以西北、西南的4个省份为主;谱系Ⅲ包括34个菌株,覆盖范围最广,除东北和西北高原地区外,其它均有涉及。地缘关系分析表明以陕、甘为主的西北高原地区的菌株涉及Ⅰ、Ⅱ两个谱系;以闽、浙、赣和台湾为主的东部沿海地区的菌株涉及Ⅰ、Ⅲ两个谱系;而以云、贵、川为主的西南地区的菌株则覆盖到了所有的3个谱系。这三个地区的香菇遗传多样性最丰富,西南地区尤为突出,是香菇种质资源保护与利用的重点区域。     

Shared and Separate Knowledge among Eight Cultural Groups Based on Ethnobotanical Uses of Rhododendron (Ericaceae) in Yunnan Province, China

Shared and Separate Knowledge among Eight Cultural Groups Based on Ethnobotanical Uses of Rhododendron (Ericaceae) in Yunnan Province, China. Yunnan, a province in southwest China, is known for its cultural diversity of 25 ethnic minorities and its vast Himalayan biodiversity, especially of Rhododendron. Previous literature has shown that some cultural groups share ethnobotanical knowledge while other cultural groups keep their knowledge separate. We investigated factors that may lead to the sharing of knowledge based on the uses of rhododendron among seven cultural minorities (the Bai, Dulong, Lisu, Naxi, Nu, Tibetan, and Yi) and the Han majority. Semistructured interviews about rhododendrons were conducted with approximately 30 individuals in each cultural group. Cluster analyses and a new analysis method were conducted to determine the within-group homogeneity of knowledge of rhododendron uses to test hypotheses related to strength of cultural traditions. The Dulong, Lisu, and Nu were compared with each other as these groups share villages and languages. The Naxi, Tibetan, and Yi live predominantly with members of their cultural group, and are often monolingual; thus, these three cultural minorities were compared. The Bai and Han compose the final comparison as the Bai are increasingly interacting with the local Han majority as tourism grows in that area. The Bai, Dulong, Han, Lisu, and Nu had variable answers within each group, while the Naxi, Tibetan, and Yi have homogeneous knowledge of uses of rhododendron within their cultural group. Among the eight cultural groups compared for this study, factors such as sharing of language, overlap of living situation, and sharing of markets leads to non-homogenous knowledge of rhododendron uses among members of the same cultural group.     

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。     

The quest for Y-chromosomal markers - methodological strategies for mammalian non-model organisms

Tracing maternal and paternal lineages independently to explore breeding systems and dispersal strategies in natural populations has been high on the wish-list of evolutionary biologists. As males are the heterogametic sex in mammals, such sex-specific patterns can be indirectly observed when Y chromosome polymorphism is combined with mitochondrial sequence information. Over the past decade, Y-chromosomal markers applied to human populations have revealed remarkable differences in the demographic history and behaviour between the sexes. However, with a few exceptions, genetic data tracing the paternal line are lacking in most other mammalian species. This deficit can be attributed to the difficulty of developing Y-specific genetic markers in non-model organisms and the general low levels of polymorphisms observed on the Y chromosome. Here, we present an overview of the currently employed strategies for developing paternal markers in mammals. Moreover, we review the practical feasibility and requirements of various methodological strategies and highlight their future prospects when combined with new molecular techniques such as next generation sequencing.     

云南纳西族HLA—DRB1基因多态性研究及其族源分析

首次在国内采用本室改进的高分辨率的基于内含子的PCR－SBT分型方法,检测云南纳西族HLA－DRB1基因多态性。在60例纳西族个体中共检出37种HLA－DRB1等位基因,其显著特点是等位基因的类型检出较多,频率分布比较平均,除12021（17.50%）外其他的等位基因频率均低于8％,其他较常见的等位基因（＞5％）还有1404（7.50%）,1504（5.83%0,04051（5.83%0,08032（5.83%）,09012（5％）,03011（5％）。这几种中频等位基因共占可检出等位基因的35％,与12021一起共占52.49%,其中DRB1＊0305、0438、1123、1132、1310、0812为首次在我国人群中检出,并且在世界各地人群中也比较罕见。以纳西族和世界各地人群的HLA－DRB1频率进行了聚类分析。比较分析的结果显示纳西族明显属于中国南方族群,未显示出其族源来自北方的痕迹。根据遗传数据,并参照民族学、历史学研究,对其民族起源做了初步的分析。     

Deep into the roots of the Libyan Tuareg: a genetic survey of their paternal heritage

Recent genetic studies of the Tuareg have begun to uncover the origin of this semi-nomadic northwest African people and their relationship with African populations. For centuries they were caravan traders plying the trade routes between the Mediterranean coast and south-Saharan Africa. Their origin most likely coincides with the fall of the Garamantes who inhabited the Fezzan (Libya) between the 1st millennium BC and the 5th century AD. In this study we report novel data on the Y-chromosome variation in the Libyan Tuareg from Al Awaynat and Tahala, two villages in Fezzan, whose maternal genetic pool was previously characterized. High-resolution investigation of 37 Y-chromosome STR loci and analysis of 35 bi-allelic markers in 47 individuals revealed a predominant northwest African component (E-M81, haplogroup E1b1b1b) which likely originated in the second half of the Holocene in the same ancestral population that contributed to the maternal pool of the Libyan Tuareg. A significant paternal contribution from south-Saharan Africa (E-U175, haplogroup E1b1a8) was also detected, which may likely be due to recent secondary introduction, possibly through slavery practices or fusion between different tribal groups. The difference in haplogroup composition between the villages of Al Awaynat and Tahala suggests that founder effects and drift played a significant role in shaping the genetic pool of the Libyan Tuareg.     

Genetic variation and population structure of “Zangli” pear landraces in Tibet revealed by SSR markers

Pear (Pyrus L.) is one of the most important fruits in temperate regions. Even in the mountainous border region of Tibet, Sichuan, and Yunnan Provinces (China), a variety of highly adapted pear landraces were discovered in Tibetan Autonomous Prefecture and were named “Zangli pears.” Here, we analyzed genetic diversity of 29 genotypes of Zangli distributed in Tibetan Region, together with 30 genotypes of sand pear (P. pyrifolia) in border regions, and 8 genotypes of P. ussuriensis as out groups, using simple sequence repeats (SSR) markers. Twenty-eight SSR markers displayed high polymorphism with a total of 202 alleles. Cluster analysis revealed a close genetic relationship between Zangli and sand pears, while population structure analysis revealed that gene flow between the western and eastern side of the Jin-sha River was restricted by geographic isolation. Diversity statistics for five geographic groups implied a migration event from Sichuan and Yunnan Provinces to the border region of western Sichuan, eastern Tibet, and northwestern Yunnan Provinces. Six specific genetic alleles in Zangli pear landraces might be related to their adaption to severe environmental conditions.     

Genetic structure analysis of three Hispanic populations from Costa Rica, Mexico, and the southwestern United States using Y-chromosome STR markers and mtDNA sequences

Two hundred seventeen male subjects from Costa Rica, Mexico, and the Hispanic population of the southwestern United States were studied. Twelve Y-chromosome STRs and the HVSI sequence of the mtDNA were analyzed to describe their genetic structure and to compare maternal and paternal lineages. All subjects are part of two NIMH-funded studies to localize schizophrenia susceptibility genes in Hispanic populations of Mexican and Central American ancestry. We showed that these three populations are similar in their internal genetic characteristics, as revealed by analyses of mtDNA and Y-chromosome STR diversity. These populations are related through their maternal lineage in a stronger way than through their paternal lineage, because a higher number of shared haplotypes and polymorphisms are seen in the mtDNA (compared to Y-chromosome STRs). These results provide evidence of previous contact between the three populations and shared histories. An analysis of molecular variance revealed no genetic differentiation for the mtDNA for the three populations, but differentiation was detected in the Y-chromosome STRs. Genetic distance analysis showed that the three populations are closely related, probably as a result of migration between close neighbors, as indicated by shared haplotypes and their demographic histories. This relationship could be an important common feature for genetic studies in Latin American and Hispanic populations.     

Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions

Kazakh populations have traditionally lived as nomadic pastoralists that seasonally migrate across the steppe and surrounding mountain ranges in Kazakhstan and southern Siberia. To clarify their population history from a paternal perspective, we analyzed the non-recombining portion of the Y-chromosome from Kazakh populations living in southern Altai Republic, Russia, using a high-resolution analysis of 60 biallelic markers and 17 STRs. We noted distinct differences in the patterns of genetic variation between maternal and paternal genetic systems in the Altaian Kazakhs. While they possess a variety of East and West Eurasian mtDNA haplogroups, only three East Eurasian paternal haplogroups appear at significant frequencies (C3*, C3c and O3a3c*). In addition, the Y-STR data revealed low genetic diversity within these lineages. Analysis of the combined biallelic and STR data also demonstrated genetic differences among Kazakh populations from across Central Asia. The observed differences between Altaian Kazakhs and indigenous Kazakhs were not the result of admixture between Altaian Kazakhs and indigenous Altaians. Overall, the shared paternal ancestry of Kazakhs differentiates them from other Central Asian populations. In addition, all of them showed evidence of genetic influence by the 13(th) century CE Mongol Empire. Ultimately, the social and cultural traditions of the Kazakhs shaped their current pattern of genetic variation.     

Substitution of Hainan indigenous genetic lineage in the Utsat people,exiles of the Champa kingdom

The Utsat people do not belong to one of the recognized ethnic groups in Hainan, China. Some historical literature and linguistic classification confirm a close cultural relationship between the Utsat and Cham people; however, the genetic relationship between these two populations is not known. In the present study, we typed paternal Y chromosome and maternal mitochondrial (mt) DNA markers in 102 Utsat people to gain a better understanding of the genetic history of this population. High frequencies of the Y chromosome haplogroup O1a*-M119 and mtDNA lineages D4, F2a, F1b, F1a1, B5a, M8a, M*, D5, and B4a exhibit a pattern similar to that seen in neighboring indigenous populations. Cluster analyses (principal component analyses and networks) of the Utsat, Cham, and other ethnic groups in East Asia indicate that the Utsat are much closer to the Hainan indigenous ethnic groups than to the Cham and other mainland southeast Asian populations. These findings suggest that the origins of the Utsat likely involved massive assimilation of indigenous ethnic groups. During the assimilation process, the language of Utsat has been structurally changed to a tonal language; however, their Islamic beliefs may have helped to keep their culture and self-identification.     

Asymmetry in Family History Implicates Nonstandard Genetic Mechanisms: Application to the Genetics of Breast Cancer

Genome-wide association studies typically target inherited autosomal variants, but less studied genetic mechanisms can play a role in complex disease. Sex-linked variants aside, three genetic phenomena can induce differential risk in maternal versus paternal lineages of affected individuals: 1. maternal effects, reflecting the maternal genome''s influence on prenatal development; 2. mitochondrial variants, which are inherited maternally; 3. autosomal genes, whose effects depend on parent of origin. We algebraically show that small asymmetries in family histories of affected individuals may reflect much larger genetic risks acting via those mechanisms. We apply these ideas to a study of sisters of women with breast cancer. Among 5,091 distinct families of women reporting that exactly one grandmother had breast cancer, risk was skewed toward maternal grandmothers (p<0.0001), especially if the granddaughter was diagnosed between age 45 and 54. Maternal genetic effects, mitochondrial variants, or variant genes with parent-of-origin effects may influence risk of perimenopausal breast cancer.     

Effects of seed- and pollen-mediated gene dispersal on genetic structure among Quercus salicina saplings

We evaluated the effects of seed- and pollen-mediated gene dispersal on genetic structure among Quercus salicina saplings. Parentage analysis using 10 microsatellite markers indicated that the 111 adult trees located within a 11.56 ha plot in the Tatera Forest Reserve, Japan, included only one parent of 44.2% and both parents of 40.7% of the 226 saplings located in a 1-ha core plot at its center. Coancestry (F(ij)) estimates indicated that there was strong genetic structure among the saplings. The numbers of pairs of full- and half-siblings were high among neighboring saplings, suggesting that there was strong maternal half-sibling family structure among the saplings around their seed parents, probably generated by the spatially limited seed dispersal and the small extent of overlapping seed shadows owing to the low density of adults. The frequencies also suggest that the maternal half-sibling families are interspersed with full-siblings, produced by correlated mating, probably because pollination frequency depends on the distance between parents. The frequencies of pairs of half-siblings decreased as the distance between saplings increased, but did not fall to zero even at distances up to the 90-95 m class, suggesting that paternal half-siblings originating from correlated paternity were widely distributed owing to extensive pollen flow. We separately examined the genetic structure for maternal and paternal alleles in the saplings. Unsurprisingly, very strong genetic structure was detected for maternal alleles. However, weak (but significant) genetic structure was also detected for paternal alleles. Therefore, pollen dispersal may affect the extent of genetic structure as well as seed dispersal.