Y-chromosome haplotype distribution in Han Chinese populations and modern human origin in East Asians

We investigated the distribution of Y-chromosome haplotype using 19 Y-SNPs in Han Chinese populations from 22 provinces of China. Our data indicate distinctive patterns of Y chromosome between southern and northern Han Chinese populations. The southern po

Evolution of the DRD2 gene haplotype and its association with alcoholism in Mexican Americans

The human D2 dopamine receptor gene (DRD2) plays a central role in the neuromodulation of appetitive behaviors and is implicated in having a possible role in susceptibility to alcoholism. We genotyped an SNP in DRD2 Exon 8 in 251 nonalcoholic, unrelated, healthy controls and 200 alcoholic Mexican Americans. The DRD2 haplotypes were analyzed using the Exon 8 genotype in combination with five other SNP genotypes, which were obtained from our previous study. The ancestral origins of the DRD2 polymorphisms have been determined by sequencing the homologous region in other higher primates. Twenty DRD2 haplotypes, defined as H1 to H20 based on their frequency from high to low, were obtained in this major minority population. The ancestral haplotype "I-132-G-C-G-A1" and two one-step mutation haplotypes were absent in our study population. The haplotype H1, "I-B1-T-C-A-A1", with the highest frequency in the population, is a three-step mutation from the ancestral form. The first five or eight major haplotypes make up 87% or 95% of the entire population, respectively. The prevalence of the haplotype H1+ (H1/H1 and H1/Hn genotypes) is significantly higher in alcoholics and alcoholic subgroups, including early onset drinkers and benders, than in their respective control groups. The Promoter -141C allele is in linkage disequilibrium (LD) with five other loci in the nonalcoholic group, but not in the alcoholic group. All of the other five loci are in LD in both the alcoholic and control groups. The DRD2 TaqI B allele is in complete LD with the allele located in intron 6. Five SNPs, Promoter -141C, TaqI B (or Intron 6), Exon 7, Exon 8, and TaqI A, are sufficient to define the DRD2 haplotypes in Mexican Americans. Our data indicate that the DRD2 haplotypes are associated with alcoholism in Mexican Americans. (c) 2005 Elsevier Inc. All rights reserved.

Haplotype frequency distribution and linkage disequilibrium analysis of single nucleotide polymorphisms at the human FMO3 gene locus

We analyzed flavin-containing monooxygenase 3 (FMO3) polymorphisms, haplotype structure, and linkage disequilibrium (LD) in 256 Han Chinese and 50 African-American individuals to compare their haplotype frequencies and LD with other world populations. For

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication(1,2). To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data(3). Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.

长花马先蒿的居群遗传变异与生物地理学

青藏高原地区是我国植物物种多样性和特有性最高的地区，且作为东亚植物区系的一个现代分化中心受世人瞩目。长花马先蒿是青藏高原高山草甸的广布种，其地理分布格局的形成与高原的隆升和气候变迁有着密切关系。因此，对长花马先蒿进行谱系生物地理学研究，有助于探讨青藏高原地区物种快速分化的机制和群体建立过程。 本研究对长花马先蒿11个居群、188个个体的叶绿体DNA trnT-trnF区进行了序列分析，发现该片段的长度变异范围为1441-1472bp。对位排列后的矩阵（含外类群）长1534bp，内类群中含33个碱基替换和 17 个插入/缺失,可分为20种单倍型。11个地理居群的总核苷酸多态性（π）为0.00468，单倍型多态性（Hd）为0.853，居群间的遗传变异（FST）高达88.2％，说明长花马先蒿具有很高的遗传多样性，且居群间发生了强烈遗传分化。 系统发育和遗传多样性分析发现长花马先蒿的20种叶绿体单倍型可归于四个地理单元——川西高海拔地区、川北地区、云南德钦地区及川藏地区。进一步分析发现：4个地理单元间存在着显著的遗传分化, 说明长花马先蒿具有明显的谱系地理分布格局。其中川西高海拔地区的四种主导单倍型构成了系统发育树最基部的一支，而以川西地区为中心、向南扩展至云南的两个居群所包含的几种单倍型均属于比较进化的类型。单倍型的网络关系(Network) 显示出西藏、青海、云南及四川北部的一些单倍型间遗传差异很小，亲缘关系很近。上述结果表明：长花马先蒿群体在冰期后的重新扩张过程主要表现为由南往北的递进式扩散，第四纪冰期气候的反复波动导致了该物种居群随生境变化而不断扩张或收缩,形成了现今的分布格局。初步推测川西地区很可能曾是长花马先蒿在第四纪冰期时的重要避难所，瓶颈效应和奠基者效应对其遗传多样性分布格局有重要影响。

蕨属的系统发育及谱系地理学研究

蕨属（Pteridium Gled. ex Scop）分布范围极广，几乎遍布于全世界。关于此属的属下分类一直争论不休，主要是因为此属的分布广，形态变异比较大，变异类型之间形态差异不显著，缺乏明确的鉴别性状，或者变异类型之间存在过渡。 本研究利用叶绿体rps4-trnS DNA序列和trnS-G DNA序列构建了世界不同地区蕨属植物的系统关系及中国区域蕨属植物的系统关系，同时构建了世界不同地区蕨属植物的单倍型关系。我们发现，（1）南美洲和澳洲的蕨属植物分化最早;（2）北美洲的蕨属植物遗传变异最丰富，有多条相互独立的进化线（evolutionary lineages）;（3）欧亚大陆和非洲的蕨属植物都与北美洲具有密切关系;（4）大洋洲的蕨属植物同时受南美洲和亚洲蕨属植物的影响;（5）东亚的蕨属植物直接受北美洲蕨属植物的影响，与欧洲和非洲没有直接的关系;（6）非洲和欧洲的蕨属植物关系密切，有着相同的起源。 根据不同地点的蕨属植物的系统关系和单倍型Network关系，我们认为，蕨属植物起源于南美洲，而后向北美洲和澳洲扩散。在北美洲东部和东南部蕨属植物得到繁荣并分别向三个方向扩散与分化。第一个方向是朝北美西部扩散，第二个方向是两次独立扩散到亚洲，第三个方向是扩散到非洲，进而由非洲向欧洲扩散。 根据叶绿体基因所揭示的世界不同地区蕨属植物的发生和发展规律结合前人的研究，我们认为蕨属包含四个物种。Pteridium aquilinum (L.) Kuhn，分布于北美洲、亚洲、非洲和欧洲。该种分布广泛，存在一定的地理分化，可进一步划分8个亚种。Pteridium esculentum (G. Forst.) Cokayne，分布于南美洲，并扩散到澳大利亚，甚至东南亚国家。Pteridium caudatum (L.) Maxon，分布于中美洲和南美洲，是个异源四倍体。Pteridium semihastatum (Wall. ex Ag.) S.B.Andrews，分布于澳洲和东南亚，是个异源四倍体。 通过分子数据和形态分析相结合，作者认为中国蕨属包括两个亚种，即蕨[Pteridium aquilinum (L.) Kuhn subsp.japonicum (Nakai) Á.Löve & D.Löve]和毛轴蕨[Pteridium aquilinum (L.) Kuhn subsp. revolutum (Bl.) X. Q. Chen, stat. nov.]。作者认为，《中国植物志》中记载的食蕨，特有种云南蕨、糙轴蕨、镰羽蕨和长羽蕨并不存在或只是蕨或毛轴蕨的变形，或者毛轴蕨与蕨的杂交个体。 为了今后更进一步研究蕨属植物的系统与进化关系、居群的遗传结构等问题，作者还分离了8个具有多态性的微卫星位点，探讨了微卫星引物开发设计过程中如何提高效率等问题。

云南僰人源流的父系和母系遗传研究

对云南僰人32份男性DNA样本进行Y染色体单倍型以及mitochondrial DNA (mtDNA)单倍型分析,结果发现云南僰人的父系和母系遗传组分都表现出典型的南方人群的遗传特征.由僰人的数据结合已经发表的东亚人群的Y染色体和mtDNA单倍型(haplotype)数据进行Multidimensional Scaling(MDS)分析,结果表明,在MDS分布图中僰人群体的Y染色体单倍型和mtDNA单倍型都与南方人群聚在一起.这一结果支持僰人的遗传族源为东亚南方人群后裔,与考古学的推论相一致.结合历史和考古学证据来探讨僰人的起源和史前迁移,为揭开"僰人悬棺"这种独特的考古文化的起源和史前传播提供遗传学的研究证据.

Y chromosome haplotypes reveal prehistorical migrations to the Himalayas

By using 19 Y chromosome biallelic markers and 3 Y chromosome microsatellite markers, we analyzed the genetic structure of 31 indigenous Sino-Tibetan speaking populations (607 individuals) currently residing in East, Southeast, and South Asia. Our results showed that a T to C mutation at locus M122 is highly prevalent in almost all of the Sino-Tibetan populations, implying a strong genetic affinity among populations in the same language family. Furthermore, the extremely high frequency of H8, a haplotype derived from M122C, in the Sino-Tibetan speaking populations in the Himalayas including Tibet and northeast India indicated a strong bottleneck effect that occurred during a westward and then southward migration of the founding population of Tibeto-Burmans. We, therefore, postulate that the ancient people, who lived in the upper-middle Yellow River basin about 10,000 years ago and developed one of the earliest Neolithic cultures in East Asia, were the ancestors of modem Sino-Tibetan populations.

Pseudomonas duriflava sp nov., isolated from a desert soil

A Gram-negative, rod-shaped, non-motile, non-spore-forming bacterium, designated strain HR2(T) was isolated from a soil sample from the Talklimaken Desert in Xinjiang Province, China. Strain HR2(T) grew optimally at pH 7.0-8.0 and 30-37 degrees C in the presence of 0-1% (w/v) NaCl. An analysis of 16S rRNA gene sequences revealed that strain HR2(T) fell within the radiation of the genus Pseudomonas, the highest level of similarity being found with respect to Pseudomonas luteola IAM 13000(T) (97.5%); the levels of sequence similarity with respect to other recognized Pseudomonas species were < 96.4%. DNA-DNA hybridization showed that the genetic relatedness between strain HR2(T) and P. luteola IAM 13000(T) was 53.2%. The G + C content of the genomic DNA of strain HR2(T) was 55.2 mol%. The major fatty acids were 18: 1, summed feature 3 and 16:0. The hydroxylated fatty acids 10:0 3-OH, 12:0 3-OH and 12:0 2-OH were also present. The data obtained in this polyphasic study indicated that this isolate represents a novel species of the genus Pseudomonas, for which the name Pseudomonas duriflava sp. nov. is proposed, The type strain is HR2(T) (=KCTC 221129(T) =CGMCC 1.6858(T)).

Mitochondrial DNA variation in cattle of South China: origin and introgression

Ten restriction endonucleases were used to investigate the mitochondrial DNA restriction fragment length polymorphism (mtDNA RFLP) of 11 native cattle breeds and one cultivated cattle breed in South China. Twenty-three restriction morphs were detected, which can be sorted into five haplotypes, A phylogenetic tree of the haplotypes was constructed by using the 'upgma' method. Our study showed that haplotype I and II are identical to the zebu (Bos indicus) and taurine (Bos taurus) haplotypes, respectively. Zebu and taurine were the two major origins of cattle populations in South China, and the zebu probably had more influence on the native cattle population than taurine did. Haplotype III is identical to haplotype I of yak (Bos grunniens), which was only detected in the Diqing cattle breed. Haplotype IV was detected for the first time. This haplotype, found only in Dehong cattle, might be from an independent domestication event, probably from another Bos indicus population. Divergence of haplotypes I and IV occurred about 268,000-535 000 years ago, much earlier than the 10,000-year history of cattle husbandry. Our results also suggest a secondary introgression of mtDNA from yak to Diqing cattle.

Evolutionary history of the mtDNA 9-bp deletion in Chinese populations and its relevance to the peopling of east and southeast Asia

In total, 1218 Chinese from twelve ethnic groups and nine Han geographic groups were screened for the mtDNA 9-bp deletion motif. The frequency of the 9-bp deletion in all samples was 14.7% but ranged from 0% to 32% in the various ethnic groups. Three individuals had a triplication of the 9-bp segment. Phylogenetic and demographic analyses of the mtDNA hypervariable segment 1 (HVS1) sequences suggest that the 9-bp deletion occurred more than once in China. The majority of the Chinese deletion:haplotypes (about 90%) have a common origin as a mutational event following an initial expansion of modem humans in eastern Asia. Other deletion haplotypes and the three haplotypes with a 9-bp triplication may have arisen independently in the Chinese, presumably by replication error. HVS1 haplotype analysis suggests two possible migration routes of the 9-bp deletion in east and southeast Asia. Both migrations originated in China with one route leading to the Pacific Islands via Taiwan, the other to southeast Asia and possibly the Nicobar Islands. Along both routes of peopling, a decrease in HVS1 diversity of the mtDNA haplotypes is observed. The "Polynesian motif (16217T/C, 16247A/G, and 16261C/T)" and the 16140T/C, 16266C/A, or C/G polymorphisms appear specific to each migration route.

Origin of rabbit (Oryctolagus cuniculus) in China: evidence from mitochondrial DNA control region sequence analysis

A fragment of mitochondrial DNA (mtDNA) control region (similar to700 bp) was sequenced in 104 individuals from 20 breeds (three Chinese domestic breeds, five recently derived breeds and 12 introduced breeds) of domestic rabbits, Oryctolagus cuniculus . Nineteen sites were polymorphic, with 18 transitions and one insertion/deletion, and eight haplotypes (A1, A2, A3, A4, A5, A6, A7 and A8) were identified. Haplotype A1 was the most common and occurred in 89 individuals. In the 25 Chinese rabbits, only haplotype A1 was observed, while four haplotypes (A1, A3, A5 and A6) were found in 26 recently derived individuals. Haplotype A2 was shared by seven individuals among three introduced strains. The other six haplotypes accounted for 0. 96-1. 92% of the animals. Combined with the published sequences of European rabbits, a reduced median-joining network was constructed. The Chinese rabbit mtDNAs were scattered into two clusters of European rabbits. These results suggest that the (so-called) Chinese rabbits were introduced from Europe. Genetic diversity in Chinese rabbits was very low.

Origin and dispersal of atypical aldehyde dehydrogenase ALDH2*487Lys

The East Asian respond with a marked facial flushing and mild to moderate symptoms of intoxication after drinking the amounts of alcohol that has no detectable effect on European. The alcohol sensitivity in Orientals is due to a delayed oxidation of aceta

Evidence for Positive Selection on the Osteogenin (BMP3) Gene in Human Populations

Background: Human skeletal system has evolved rapidly since the dispersal of modern humans from Africa, potentially driven by selection and adaptation. Osteogenin (BMP3) plays an important role in skeletal development and bone osteogenesis as an antagonist of the osteogenic bone morphogenetic proteins, and negatively regulates bone mineral density. Methodology/Principal Findings: Here, we resequenced the BMP3 gene from individuals in four geographically separated modern human populations. Features supportive of positive selection in the BMP3 gene were found including the presence of an excess of nonsynonymous mutations in modern humans, and a significantly lower genetic diversity that deviates from neutrality. The prevalent haplotypes of the first exon region in Europeans demonstrated features of long-range haplotype homogeneity. In contrast with findings in European, the derived allele SNP Arg192Gln shows higher extended haplotype homozygosity in East Asian. The worldwide allele frequency distribution of SNP shows not only a high-derived allele frequency in Asians, but also in Americans, which is suggestive of functional adaptation. Conclusions/Significance: In conclusion, we provide evidence for recent positive selection operating upon a crucial gene in skeletal development, which may provide new insight into the evolution of the skeletal system and bone development.

Prion protein gene (PRNP) polymorphisms in native Chinese cattle

Le polymorphisme au sein de quatre regions du gene codant pour la proteine prion bovine (PRNP) confere la susceptibilite a l'encephalopathie bovine spongiforme (BSE). Ceux-ci comprennent un polymorphisme d'insertion/deletion (indel) de 23 pb dans le promoteur, un indel de 12 pb dans l'intron 1, un octapeptide repete ou un indel de 24 pb au sein du cadre de lecture, et un polymorphisme mononucleotidique (SNP) dans la region codante. Dans ce travail, les auteurs ont examine la frequence des genotypes, des alleles et des haplotypes pour ces indel au sein de 349 bovins d'origine chinoise, de meme que la sequence nucleotidique de ce gene chez 50 de ces animaux. Leurs resultats montrent que l'allele ayant la deletion de 12 pb et l'haplotype combinant la deletion de 23 pb et la deletion de 12 pb, lesquels ont ete suggeres comme etant importants pour la susceptibilite a la BSE, sont rares au sein des bovins du sud de la Chine. Une difference significative a ete observee entre les bovins affectes par la BSE et les bovins chinois sains pour ce qui est de l'indel de 12 pb. Au total, 14 SNP ont ete observes dans la region codante du gene PRNP chez les bovins chinois. Trois de ces SNP etaient associes a des changements d'acides amines (K3T, P54S et S154N). La substitution E211K qui a ete rapportee recemment chez un cas atypique de la BSE chez un bovin americain n'a pas ete detectee dans ce travail.