Phylogeography and origin of Indian domestic goats

The Indian subcontinent contains 20 well-characterized goat breeds, which vary in their genetic potential for the production of milk, meat, and fibre; disease resistance; heat tolerance; and fecundity. Indian goats make up 20% of the world's goat population, but there has been no extensive study of these economically important animals. Therefore, we have undertaken the present investigation of 363 goats belonging to 10 different breeds from different geographic regions of India using mtDNA sequence data from the HVRI region. We find evidence for population structure and novel lineages in Indian goats and cannot reconcile the genetic diversity found within the major lineage with domestication starting 10,000 years ago from a single mtDNA ancestor. Thus, we propose a more complex origin for domestic goats.     

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 introgession of mtDNA from yak to Diqing cattle.     

Mitochondrial DNA variation of modern Tuscans supports the near eastern origin of Etruscans

The origin of the Etruscan people has been a source of major controversy for the past 2,500 years, and several hypotheses have been proposed to explain their language and sophisticated culture, including an Aegean/Anatolian origin. To address this issue, we analyzed the mitochondrial DNA (mtDNA) of 322 subjects from three well-defined areas of Tuscany and compared their sequence variation with that of 55 western Eurasian populations. Interpopulation comparisons reveal that the modern population of Murlo, a small town of Etruscan origin, is characterized by an unusually high frequency (17.5%) of Near Eastern mtDNA haplogroups. Each of these haplogroups is represented by different haplotypes, thus dismissing the possibility that the genetic allocation of the Murlo people is due to drift. Other Tuscan populations do not show the same striking feature; however, overall, ~5% of mtDNA haplotypes in Tuscany are shared exclusively between Tuscans and Near Easterners and occupy terminal positions in the phylogeny. These findings support a direct and rather recent genetic input from the Near East--a scenario in agreement with the Lydian origin of Etruscans. Such a genetic contribution has been extensively diluted by admixture, but it appears that there are still locations in Tuscany, such as Murlo, where traces of its arrival are easily detectable.     

中国黄牛mtDNA D-loop遗传多样性及起源

黄牛自古以来就是我国一个重要的畜种,其经济、文化价值很高。我国是世界上黄牛品种资源最丰富的国家之一。据《中国牛品种志》介绍,把一些地区同种异名的黄牛品种合并以后,尚有28个地方黄牛品种,按照其地理分布区域分为北方黄牛、中原黄牛和南方黄牛三大类型(邱怀,1986)。如果把中国地方黄牛品种分得更细,则有49个固有品种(常洪,1995)。关于中国黄牛的起源,历来有不同的观点。一般认为,中国黄牛是多元起源的,但究竟起源于哪几个牛种,观点不一(陈宏等,1993;于汝梁等,1993;Yu et al.,1999;陈幼春,1990)。主要的观点有:(1)中国黄牛主要起源于…     

新疆塔吉克族人群线粒体DNA序列多态性研究

目的：研究中国新疆塔吉克族人群线粒体DNA D环区序列遗传多态性,并结合文史资料,对塔吉克族的起源及迁移进行了初步探讨。方法：应用PCR扩增产物直接测序法,对34名塔吉克族无关个体线粒体DNA D一环区高变区Ⅰ进行测序分析。结果：34个个体核苷酸序列与Anderson相应序列比较共发现有47处突变位点,构成22种单倍型塔吉克族线粒体DNA D环高变一区基因差异度为0.9822,偶合概率为0.0466。结论：研究表明新疆塔吉克族与高加索人种遗传关系较近。     

塔克拉玛干沙漠腹地隔离人群线粒体DNA序列多态性分析

对新疆塔克拉玛干沙漠腹地的75名克里雅人线粒体DNA的高可变I区的15996—16401的片段进行了序列分析,在所测定的75个个体中,共检测到68个位点存在变异,界定了71种不同的单倍型。克里雅人群的核昔酸变异度和平均核苷酸差异都介于所报道的东方人群和西方人群之间。根据Neighbor-joining法构建系统发育树,发现中亚的各人群均处于东方人群的亚洲谱系和西方人群的欧洲谱系之间,并且克里雅与新疆维吾尔和境外维吾尔之间的遗传距离最近,表明他们之间有很密切的亲缘关系。     

Mitochondrial DNA polymorphism in populations of aboriginal residents of the Far East

An analysis of mtDNA polymorphism in eight populations of aboriginal residents (N = 519) of the Far East has been performed. The majority of haplogroups revealed in the examined groups were of East Eurasian origin. Haplogroup D was revealed in seven populations and its frequency varied from 2.8% in Koryaks to 28.3% and 28.9% in Nanaians and Evenks, respectively. Chukchi and Koryak populations, which belong to the same language family, exhibited haplogroup G, which has the same motive and indicates the genetic kinship of both populations. The presence of East Eurasian haplogroups A and D with a strong predominance of haplogroup A in Chukchi indicates the closer relationship of this population both with Asian and Canadian Eskimos and northern Atapasks on the other side of Bering Strait. The high level of genetic variability was revealed in populations belonging to the Tungus-Manjur group. The high frequency of east Eurasian haplogroups in Nanaians could result from close historical associations with Siberian Evenks.     

Isolation and Purification of Carp Mitochondrial DNA and Structural Analysis of Its tRNA~(Cys) Gene and the Light Strand Origin

A new method is presented with which we isolated milochondrial DNA from fresh carp liver usingdifferential centrifugation and DNase treatment that gave high yield of purified product with an easyand economical procedure. Highly distinct bands were displayed in agarose gel electrophoresls ofthe product digested with restrictlon enzymes, which were successfully used in constructingrestriction map and molecular clone of mitochondrial genes. With DNAs thus obtained, we havecloned cysteine tRNA gene (tRNA~(Cys) gene) of carp mitochondria, determined the nucleotide sequenceof it and the light strand origin, and depicted the cloverleaf secondary structure of tDNA~(Cya) and thelight strand origin. Analysis of nucleotide sequences of tRNA~(Cy) genes of 5 vertebrates has revealedunusual features of carp mitochondrial tRNA~(Cy) gene as compared with their cytoplasmic counter-parts, Altogether 36 bases were found in the light strand origin of carp mitochondriaf: 11 pairs in thestem; and 14 bases in the loop. As compared with those of other 11 vertebrate species, the sequenceof the stem is very conservative while both sequence and length of the loop are quite variable. Thestructure of the stem-loop may play an important role in light strand replication.     

Mitochondrial DNA polymorphisms in nine aboriginal groups of Taiwan: implications for the population history of aboriginal Taiwanese

Mitochondrial DNA (mtDNA) polymorphisms in the D-loop region and the intergenic COII/tRNA(Lys) 9-bp deletion were examined in 180 individuals from all nine aboriginal Taiwanese groups: Atayal, Saisiat, Bunun, Tsou, Rukai, Paiwan, Ami, Puyuma, and Yami. A comparison of 563-bp sequences showed that there were 61 different sequence types, of which 42 types were specific to respective aboriginal groups. D-loop sequence variation and phylogenetic analysis enabled the 180 aboriginal lineages to be classified into eight monophyletic clusters (designated C1-C8). Phylogeographic analysis revealed that two (C2 and C4) of the eight clusters were new characteristic clusters of aboriginal Taiwanese and accounted for 8.3% and 13.9% of the aboriginal lineages, respectively. From the estimated coalescent times for the two unique clusters, the mtDNA lineages leading to such clusters were inferred to have been introduced into Taiwan approximately 11,000-26,000 years ago, suggesting ancient immigrations of the two mtDNA lineages. Genetic distances, based on net nucleotide diversities between populations, revealed three distinct clusters that were comprised of northern mountain (Atayal and Saisiat), southern mountain (Rukai and Paiwan), and middle mountain/east coast (Bunun, Tsou, Ami, Puyuma, and Yami) groups, respectively. Furthermore, phylogenetic analysis of 16 human populations (including six other Asian populations and one African population) confirmed that the three clusters for aboriginal Taiwanese had remained largely intact. Each of the clusters (north, south, and middle-east coast) was characterized by a high frequency of a particular lineage (C4, C2, and 9-bp deletion, respectively). This may result from random genetic drift among the aboriginal groups after a single introduction of all the mtDNA lineages into Taiwan, but another plausible explanation is that at least three genetically distinct ancestral populations have contributed to the maternal gene pool of aboriginal Taiwanese.     

Vascular plant diversity in the sacred groves of Jaintia Hills in northeast India

Diversity of vascular plants was studied in three sacred groves of the Jaintia Hills, in northeast India. About 395 species, 250 genera, and 108 families comprising pteridophytes, gymnosperms and angiosperms were found in the groves. Orchidaceae, Rubiaceae, Asteraceae and Lauraceae were dominant families and Ficus was the largest genus, with nine species. About 160 tree species were distributed in canopy, subcanopy and under canopy strata of the forest. Concentration of tropical and temperate elements of the neighbouring Sino-Himalayan and Burma-Malayan regions, and endemic (54 species), rare (31 species) and primitive taxa (38 species) due to favourable climatic conditions and prolonged protection have contributed to the high species richness of the groves. Their better management and protection is important for the conservation of plant diversity in the region and also for the benefit of indigenous tribes of the state.     

Mitochondrial DNA analysis in Tibet: Implications for the origin of the Tibetan population and its adaptation to high altitude

Mitochondrial DNAs (mtDNAs) of 54 Tibetans residing at altitudes ranging from 3,000–4,500 m were amplified by polymerase chain reaction (PCR), examined by high-resolution restriction endonuclease analysis, and compared with those previously described in 10 other Asian and Siberian populations. This comparison revealed that more than 50% of Asian mtDNAs belong to a unique mtDNA lineage which is found only among Mongoloids, suggesting that this lineage most likely originated in Asia at an early stage of the human colonization of that continent. Within the Tibetan mtDNAs, sets of additional linked polymorphic sites defined seven minor lineages of related mtDNA haplotypes (haplogroups). The frequency and distribution of these haplogroups in modern Asian populations are supportive of previous genetic evidence that Tibetans, although located in southern Asia, share common ancestral origins with northern Mongoloid populations. This analysis of Tibetan mtDNAs also suggests that mtDNA mutations are unlikely to play a major role in the adaptation of Tibetans to high altitudes. © 1994 Wiley-Liss, Inc.     

Mitochondrial DNA polymorphisms in a sample of Albanian population (Tirana)

RFLPs of mtDNA for HpaI, BamHI, HaeII, MspI, AvaII and HincII were analysed in a sample of 100 from collected in Tirana (Albania). Eighteen mtDNA types were identified, four of which are new: two because of new morphs for Hpa/HincII (HpaI-9^Tir/HincII-17^Tir) and AvaII (AvaII-35Tir), and two because of new associations between morphs which were already known. Albanian data were compared with corresponding ones from Calabrians (Southern Italians) and Arbreshes (people of Albanian ancestry living in Calabria). Even though the examined mtDNA markers do not reveal important differences among the three groups, the analysis of both morphs and types shows a trend which places Arbreshes closer to Calabrians than to Albanians.     

Mitochondrial DNA polymorphisms in the Albanian population of Calabria (Southern Italy)

RFLPs of mtDNA for HpaI, BamHI, HaeII, MspI, AvaII and HincII were analyzed in 100 individuals from 15 Albanian villages of the Cosenza province (Calabria, Southern Italy). Thirteen mtDNA types were identified, one of which is new and is due to an AvaII morph (AvaII 27^Alb) never described before. Other two types (15-2 and 40-2) previously unfound in Italians were detected in one and two individuals respectively. The intra-group homogeneity (F=.49) resulted to be the highest found among the Italian groups examined so far. It is however very similar to that of a control sample of the Calabria population (F=.46). On the whole no important differences have emerged in the comparison between Albanians and not Albanians from Calabria. These results can indicate either that the markers we examined are not discriminative or that genetic admixture has occurred at least by immigration of Calabrian women into the Albanian group.     

广西壮族人群线粒体ＤＮＡ序列遗传多态性分析

测定了８３例广西壮族人的线粒体ＤＮＡ（mtDNA）第一高变区５１５bp的序列,并从这一母系遗传标记的角度对壮族人群的起源和群体的遗传结构进行了探讨,在所测定的８３个个体中,共检测到６６个单倍型,包括７１个多态位点,显示了高度的遗传多样性,对单倍型的系统发育分析表明：壮族人群内部存在一定的分化,不同地区的壮族人群在mtＤＮＡ遗传变异上有一定的差异,其中柳州和河池地区的个体有一半以上属于聚类簇Ⅱ,而南宁和百色地区的个体属于聚类族Ⅰ的较多,结合已相关报道的人群比较分析显示,壮族和我国北方民族群体亲缘关系较远,而与南方的少数民族及南方汉族亲缘关系较近,壮族人群中单倍型辐射型体分布,系统树中壮族人群与其他人群聚类先后次序都表明壮族是一个较为典型的南方群体。     

Mitochondrial DNA variation of Salvelinus species found in Finland

Mitochondrial DNA (mtDNA) was purified from the Arctic charr, Salvelinus alpinus , the brook charr, Salvelinus fontinalis , and the lake charr, Salvelinus namaycush , and digested with restriction enzymes Ava II, Hinf I, Eco R V, Pst I and Xba I. Two Arctic charr samples were from natural populations and they represented two different morphotypes of Arctic charr. All other studied populations were hatchery maintained. Eight additional restriction enzymes and double digestions were employed to study morphotypes of Arctic charr. We distinguished two morphotypes with restriction enzyme Nci I. Sequence divergence among mtDNA types was 2.9–3.8% between S. alpinus and S. fontinalis , 3.4–4.6% between S. alpinus and S. namaycush , and 4.7–5.3% between S. fontinalis and S. namaycush . lntraspecific variation was lowest in Arctic charr, the average of nucleon diversity for three populations being 0.179, while for brook charr and for lake charr nucleon diversity was 0.334 and 0.550, respectively. According to the number of mtDNA types, it is obvious that introduction to Finland and hatchery propagation have not greatly affected the mtDNA variation of brook charr or lake charr.     

Frequency and Pattern of Heteroplasmy in the Control Region of Human Mitochondrial DNA

In this work, we present the results of the screening of human mitochondrial DNA (mtDNA) heteroplasmy in the control region of mtDNA from 210 unrelated Spanish individuals. Both hypervariable regions of mtDNA were amplified and sequenced in order to identify and quantify point and length heteroplasmy. Of the 210 individuals analyzed, 30% were fully homoplasmic and the remaining presented point and/or length heteroplasmy. The prevalent form of heteroplasmy was length heteroplasmy in the poly(C) tract of the hypervariable region II (HVRII), followed by length heteroplasmy in the poly(C) tract of hypervariable region I (HVRI) and, finally, point heteroplasmy, which was found in 3.81% of the individuals analyzed. Moreover, no significant differences were found in the proportions of the different kinds of heteroplasmy in the population when blood and buccal cell samples were compared. The pattern of heteroplasmy in HVRI and HVRII presents important differences. Moreover, the mutational profile in heteroplasmy seems to be different from the mutational pattern detected in population. The results suggest that a considerable number of mutations and, particularly, transitions that appear in heteroplasmy are probably eliminated by drift and/or by selection acting at different mtDNA levels of organization. Taking as a whole the results reported in this work, it is mandatory to perform a broad-scale screening of heteroplasmy to better establish the heteroplasmy profile which would be important for medical, evolutionary, and forensic proposes.     

Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer

The mitochondrial genome of grape (Vitis vinifera), the largestorganelle genome sequenced so far, is presented. The genomeis 773,279 nt long and has the highest coding capacity amongknown angiosperm mitochondrial DNAs (mtDNAs). The proportionof promiscuous DNA of plastid origin in the genome is also thelargest ever reported for an angiosperm mtDNA, both in absoluteand relative terms. In all, 42.4% of chloroplast genome of Vitishas been incorporated into its mitochondrial genome. In orderto test if horizontal gene transfer (HGT) has also contributedto the gene content of the grape mtDNA, we built phylogenetictrees with the coding sequences of mitochondrial genes of grapeand their homologs from plant mitochondrial genomes. Many incongruentgene tree topologies were obtained. However, the extent of incongruencebetween these gene trees is not significantly greater than thatobserved among optimal trees for chloroplast genes, the commonancestry of which has never been in doubt. In both cases, weattribute this incongruence to artifacts of tree reconstruction,insufficient numbers of characters, and gene paralogy. Thisfinding leads us to question the recent phylogenetic interpretationof Bergthorsson et al. (2003, 2004) and Richardson and Palmer(2007) that rampant HGT into the mtDNA of Amborella best explainsphylogenetic incongruence between mitochondrial gene trees forangiosperms. The only evidence for HGT into the Vitis mtDNAfound involves fragments of two coding sequences stemming fromtwo closteroviruses that cause the leaf roll disease of thisplant. We also report that analysis of sequences shared by bothchloroplast and mitochondrial genomes provides evidence fora previously unknown gene transfer route from the mitochondrionto the chloroplast.     

Mitochondrial DNA analyses of Indian water buffalo support a distinct genetic origin of river and swamp buffalo

Water buffalo (Bubalus bubalis) is broadly classified into river and swamp categories, but it remains disputed whether these two types were independently domesticated, or if they are the result of a single domestication event. In this study, we sequenced the mitochondrial D-loop region and cytochrome b gene of 217 and 80 buffalo respectively from eight breeds/locations in northern, north-western, central and southern India and compared our results with published Mediterranean and swamp buffalo sequences. Using these data, river and swamp buffalo were distinguished into two distinct clades. Based upon the existing knowledge of cytogenetic, ecological and phenotypic parameters, molecular data and present-day distribution of the river and swamp buffalo, we suggest that these two types were domesticated independently, and that classification of the river and swamp buffalo as two related subspecies is more appropriate.     

云南地区恒河猴线粒体DNA控制区遗传多态性研究

目的从分子水平探讨云南地区恒河猴遗传多样性,为今后开展恒河猴遗传资源的保护及合理利用提供借鉴和背景资料。方法采用PCR直接测序法测定云南地区恒河猴96份样品的线粒体DNA控制区全序列,用Mege 4.0和DNA SP软件对变异位点数、简约信息位点数、单倍型、单倍型多样度、核苷酸多样度等遗传信息进行分析,基于邻接法（neighbor-joining,NJ）和最小进化法（minimum-evolution,ME）构建系统发生树。结果在96份样品中,共检测出了149个多态性位点,定义了46种单倍型,单倍型多样度（Hd）为0.968±0.007,核苷酸多样度（Pi）为0.020。结论云南地区恒河猴存在着较丰富的遗传多态性。