唐鱼养殖种群与广州附近4个野生种群的遗传关系

唐鱼(Tanichthys albonubes)是为数不多的几种原产中国的世界性观赏鱼类之一。自2003年以来, 多个唐鱼野生种群相继被发现, 其濒危状态和等级由野外灭绝降为极危。为研究唐鱼养殖种群与广州附近野生种群之间的遗传关系, 本文分析了唐鱼3个代表性养殖种群和4个野生种群, 共计186个样本的Cyt b基因、2个核基因(ENC1和RAG1)以及13个微卫星位点数据。基于K2P模型的遗传距离结果显示, 唐鱼野生种群间的遗传距离在0.005-0.015之间, 养殖种群间的遗传距离为0.001-0.009。系统发育分析表明, 唐鱼养殖种群包含4个单倍型谱系分支, 其中2个分别与广州附近2个野生种群聚在一起, 另外2个分别独立成支。单倍型网络亲缘关系分析显示, 清远种群只有1个单倍型且与芳村养殖种群共享, 芳村养殖种群拥有最多的单倍型。基于微卫星数据的STRUCTURE分析表明, 所有种群最佳分簇数为2, 清远种群与养殖种群聚为一簇, 良口和石门种群聚为另一簇。主成分分析结果显示, 养殖种群高度重叠并能与野生种群分开, 清远种群与养殖种群存在部分重叠。利用IMa3的基因流分析表明, 存在清远种群至芳村养殖种群的单向基因流。综合本文结果, 作者认为唐鱼养殖种群应起源于广州附近多个野生种群。清远种群来源于养殖种群中的芳村养殖种群。建议在未来唐鱼的保护策略中, 应禁止不规范的放流活动并且禁止将不同野生种群补充至养殖种群, 同时加强唐鱼养殖种群和野生种群的遗传资源管理和持续监测。     

唐鱼细胞色素P450 1A基因cDNA克隆及分析

鱼类细胞色素P450 1A(CYP1A)基因作为一种有效的生物标志物已被广泛应用于环境污染物的评价,唐鱼在水环境污染监测中有较好的应用优势,为建立唐鱼在水环境的检测的有效生物标志物方法,本研究对其CYP1A基因进行克隆。利用RT-PCR法扩增出一条651bp的唐鱼CYP1A基因cDNA片段,该片段与其他物种的CYP1A基因具有很高的相似性。在此基础上进行5'端扩增和3'RACE获得了唐鱼CYP1A基因的全长cDNA序列,其长度为2177bp,其中编码区长1566bp,编码521个氨基酸残基组成的蛋白质,推测该蛋白质分子量大小为58.5kDa,理论等电点为5.65。所得序列具有CYP1A分子的主要特征和功能域,包括亚铁血红素结合区、酶功能所需的精氨酸密码子和终止密码子。推导出的氨基酸序列与斑马鱼、底鳉、虹鳟、大西洋鳕、人、鼠等脊椎动物同源性分别为87.7%、70.1%、76.2%、62.2%、54.5%、55.7%。     

Population genetic structure in the endemic cyprinid fish Microphysogobio alticorpus in Taiwan: Evidence for a new phylogeographical area

The Formosa Bank is a significant zoogeographical barrier for the freshwater fish in Southern Taiwan. Here, we present population genetic structure analyses on Microphysogobio alticorpus populations in Taiwan, and biogeographic pattern to infer the relationship between historic dispersal geological dynamics. A total of 24 haplotypes were genotyped for mitochondrial CR + cyt b region in 134 specimens collected from 9 populations. Relatively high levels of haplotype diversity (h = 0.896) and low levels of nucleotide diversity (π = 0.005) were detected in M. alticorpus. Two major phylogenetic haplotype groups, Clade N1+N2 and S, were revealed and estimated to diverge about 0.121 myr (million years) ago. Haplotype network and population genetic analyses indicated significant genetic structure (F_ST = 0.876), largely concordant with the geographical location of the populations. According to SAMOVA analysis, M. alticorpus populations were divided into five units that can be explained by episodes of dispersal and population expansion followed by population fragmentation and restricted gene flow. The results of the topological pattern and network suggested that the Kaoping River was the first habitat colonized by the ancestor of M. alticorpus, before the northward dispersal.     

Isolation and characterization of microsatellite markers for the White Cloud Mountain minnow (Tanichthys albonubes) in wild and cultured populations

We developed 12 microsatellite loci for the endangered minnow species, Tanichthys albonubes, using PCR-based isolation of microsatellite arrays. These new markers were tested in 26 individuals from a wild population collected from Guangzhou in China and 26 individuals from a cultured strain. The number of alleles ranged from two to nine and the expected heterozygosity from 0.177 to 0.853. The wild population had significantly higher allelic richness than the cultured strain, with a mean allelic richness of 5.52 (range = 3.69-8.64) and 3.13 (range = 1.99-5.73) for the wild population and the cultured strain, respectively. No evidence of a recent bottleneck was detected in the wild population, but it was found in the cultured strain based on the BOTTLENECK test. These primers can be used to understand the demography and to examine genetic differences between the cultured T. albonubes strains and wild populations to help determine conservation and reintroduction strategies.     

Mitochondrial DNA reveals a mosaic pattern of phylogeographical structure in Atlantic and Mediterranean populations of anchovy (Engraulis encrasicolus)

This study extends the geographic coverage of a previous study of mitochondrial DNA restriction fragment length polymorphism in European anchovy. Both studies together include 24 samples representing 17 localities extending from the Black Sea, through the Mediterranean Sea to the eastern Atlantic as far south as Dakar, Senegal. Eighty-eight haplotypes define two clades (A and B) separated by 3.2% sequence divergence. Clade A has a star-like genealogy indicative of a recent population expansion. Clade B has a more complex genealogy, consisting of several haplotypes at intermediate frequencies. The distributions of these clades consist of a mosaic with abrupt changes between some areas and gradients between other areas. Clade A predominates the Black and Aegean seas, but is present throughout the Mediterranean. Unexpectedly, new data show that clade A is also at a high frequency in the Atlantic, from Portugal to at least Senegal. Overall, the level of genetic differentiation among populations is high (F(ST)=0.148, p<0.0001), with the greatest differences between basins. AMOVA reveals four main geographical groups: Atlantic, central Mediterranean, Aegean Sea, and Black Sea. Mismatch distribution clearly indicates historical bottleneck and population expansion for clade A, while for clade B such evidence is equivocal. This difference may reflect a range expansion for both clades, but with higher gene flow (Nm values) between demes for clade A. Both contemporary and historical processes are important in shaping the complex genetic population structure of European anchovy.     

Phylogeography and genetic structure of the endemic cyprinid fish Microphysogobio brevirostris in northern Taiwan

This study used the mitochondrial DNA cytochrome b and control region sequences to examine the population genetic structure of Microphysogobio brevirostris, an endemic cyprinid species in northern Taiwan. In total, 90 specimens were collected from six populations belonging to four major rivers. All haplotypes were identified as two major clades (Clades N and S), exhibiting a southern and a northern distribution. The results of statistical dispersal-vicariance analysis (S-DIVA) revealed that two vicariance events and one dispersal event shaped the phylogeographic pattern of M. brevirostris. These results suggest that the ancestral populations of M. brevirostris are widely distributed throughout northern Taiwan, north of the Miaoli Plateau. The ancestral populations then diverged into two clades (N and S) by the raising of the Taoyuan Plateau. Finally, two major rivers of the S clade diverged and dispersed into adjacent rivers. Besides, our results revealed that Microphysogobio alticorpus and M. brevirostris colonized Taiwan during the same ice age through different colonization routes.     

Phylogeography, genetic diversity and conservation of the large copper butterfly Lycaena dispar in Europe

We argue that insect species conservation at large scales should take account of the distribution of genetic diversity among populations. Maintenance of genetic diversity may be vital in retaining a species' adaptive capacity and evolutionary potential. We illustrate the concept using the example of the large copper butterfly Lycaena dispar in Europe. This species has become extinct in parts of its range and is declining rapidly in others, whilst conversely, increasing in many areas. The latter has recently reduced its conservation status. Mitochondrial DNA analysis is used to construct a phylogeography from a preliminary sample set obtained from across Europe. A cytochrome b fragment of 402 base pairs was sequenced and 10 haplotypes were found. Relatedness among populations suggest that those from northern and central Europe are closely related and probably form one evolutionary significant unit (ESU) reflecting post-glacial colonization from southeast Europe. In contrast, the sample from Italy is divergent and should be considered a separate ESU. Our results, combined with ecological data, suggest that conservation action for this species should be targeted on specific regions and populations.     

华木莲居群遗传结构与保护单元

华木莲(Sinomanglietia glauca)仅分布于江西宜春和湖南永顺, 是我国一级重点保护植物。前人采用RAPD、ISSR以及叶绿体SSCP(single-stranded conformation polymorphism)标记对华木莲进行了居群遗传学研究, 但未包括后发现的湖南居群或未检出居群内遗传变异。为了全面检测华木莲遗传多样性及其空间分布格局, 并据此确定保护单元, 本研究采用细胞核微卫星标记对华木莲所有4个居群共77个个体进行了居群遗传学分析。结果表明, 华木莲具有较低的遗传多样性(平均等位基因数A = 2.604, 平均期望杂合度H_E = 0.423)和较高的遗传分化(F_ST = 0.425)。STRUCTURE和主成分分析(Principal Coordinated Analysis, PCA)将4个居群首先分为江西、湖南两组, 江西的2个居群实际上是同一个自然繁育居群, 而湖南的2个居群则为2个分化明显的自然繁育居群。研究还发现湖南居群存在明显的杂合子过剩现象, 可能是小居群内随机因素造成的。研究结果表明华木莲可能在近期历史上遭受过强烈的瓶颈效应, 导致种群缩小、遗传多样性丧失和居群分化加剧, 需要加强对其进化潜力的保护。在制定保护措施时, 需要考虑其较高的遗传分化水平, 根据遗传结构可以将其划分为3个保护单元, 即湖南居群和江西居群分别为2个进化显著单元, 湖南居群进一步划分为2个管理单元(分别为朗溪乡云盘村和小溪乡鲁家村居群)。     

Population genetic structure of the endangered crayfish Austropotamobius pallipes in France based on microsatellite variation: biogeographical inferences and conservation implications

1. One important goal in conservation biology is to characterise evolutionary lineages within endangered species before management decisions are taken. Here, we assess population differentiation in the freshwater crayfish Austropotamobius pallipes, an endangered species endemic to western Europe and provide valuable information for the conservation of French populations. 2. Analysis of five microsatellite loci in 44 populations revealed very different within population levels of genetic diversity (0.000 < H₀ < 0.564). Two groups, corresponding to northern and southern French populations, showed a high degree of genetic differentiation in both allele frequencies and allele sizes. Comparison of these results with previous studies of A. pallipes strongly suggests that the divergence between northern and southern populations could have occurred during the last glaciation period of the Pleistocene from one Atlantic and one Mediterranean refuge. 3. Evidence for genetic admixture between these two lineages was revealed by correspondence analyses in southern populations, probably as the result of artificial translocations. 4. French populations appeared significantly differentiated among the different river drainages and were highly structured within rivers. The impact of population size, population bottlenecks and founder events on the population genetic differentiation are discussed. 5. Based on these results, we propose the designation of two evolutionarily significant units for A. pallipes in France. Our data also support the maintenance of separate demographic management strategies for crayfish inhabiting different river systems. However, genetic analyses will have to be combined with demographic and ecological data for sustainable conservation programmes.     

黑嘴鸥种群的遗传分化与迁徙模式

用分子生物学方法研究了黑嘴鸥(Larus saundersi)种群的遗传结构和分化.对我国黑嘴鸥现存的3个地方种群50个样本的线粒体DNA控制区部分片段进行了序列测定,结合已公布的的两个韩国样本的序列,比对后所获得的550 bp的序列中,共发现49个变异位点,定义了37种线粒体单元型,其中仅1种为我国3个地方种群间共享单元型,多数为各地方种群内特有.我国3个地方种群内的单元型多样性和核苷酸多态性都很高;4个地方种群合并成一个大种群时, 其线粒体单元型多样性与核苷酸多样性仍很高,分别为0.974%±0.012%和0.510%±0.042%.进一步分析表明,4个地方种群间核苷酸歧异度在0.433%-0.585%之间,种群分化程度FST在-0.03176-0.48063之间,基因流Nm在1.03-33.79之间,平均遗传距离为0.0051±0.0011.UPGMA系统发生树及最大简约网络图表明, 黑嘴鸥的演化关系呈现星状辐射,单元型之间呈现一种混杂的分布格局,地方种群没有形成明显的系统地理结构.同时运用彩色旗标技术,初步掌握了4个地方种群迁徙规律.对比分子研究结果,验证了不同地方种群间的遗传分化与其迁徙模式基本一致,同时认为黑嘴鸥不同地方繁殖种群从越冬地返回繁殖地的过程中会发生交叉.最后,鉴于黑嘴鸥不同地方种群间的遗传分化不显著,其迁徙行为具有差异性,建议在保护和遗传管理中应分别对待.     

A tool for tracking genetic contributions of wild Penaeus (Melicertus) plebejus broodstock to hatchery populations

Stock enhancement, restocking and sea ranching are being increasingly applied in both fisheries and conservation. The contribution of hatchery stock to fishery harvest and the maintenance of the genetic structure of stocked populations are both important considerations when releasing captive‐bred organisms into natural systems. Use of wild‐caught broodstock generally overcomes some of the genetic problems associated with domesticated hatchery populations, but there is still a need to ensure that a sufficient proportion of the natural population contribute to production of the stocked cohort to realise the genetic benefits of using wild‐caught broodstock. Releases of Penaeus (Melicertus) plebejus are under investigation as a means of increasing prawn production in recruitment‐limited areas. We used the highly variable mitochondrial control region (mtCR) to assign post‐larvae to maternal lineages in the hatchery and also to investigate the reproductive performance of female broodstock in terms of contribution to the production of the cohorts of post‐larvae in the hatchery. Our data showed that mtCR can be a useful tool for tracking lineages and provided genetic evidence that unequal contribution and underproducing females can occur even in wild‐caught broodstock. This work therefore highlights the importance of monitoring the genetic composition of pre‐release hatchery stocks.     

Population genetic structure and connectivity in the endangered Ethiopian mountain Nyala (Tragelaphus buxtoni): recommending dispersal corridors for future conservation

Habitat fragmentation is an increasing threat to wildlife species across the globe and it has been predicted that future biodiversity will decrease rapidly without the intervention of scientifically-based management. In this study we have applied a landscape genetics approach to suggest a network design that will maintain connectivity among populations of the endangered mountain Nyala (Tragelaphus buxtoni) in the fragmented highlands of Ethiopia. DNA was obtained non-invasively from 328 individuals and genetic population structure and gene flow were estimated using 12 microsatellite markers. In addition, a 475-bp segment of the mitochondrial control region was sequenced for 132 individuals. Potential dispersal corridors were determined from least-cost path analysis based on a habitat suitability map. The genetic data indicated limited gene flow between the sampled mountain Nyala populations of the Bale Massif and the Arsi Massif. The genetic differentiation observed among five sampling areas of the Bale Massif followed a pattern of isolation by distance. We detected no impact of habitat resistance on the gene flow. In the future, however, the current expanding human population in the highlands of Ethiopia may reduce the current mountain Nyala habitat and further limit migration. Hence, maintaining habitat connectivity and facilitating survival of stepping-stone populations will be important for the future conservation of the species. The approach used here may also be useful for the study and conservation of other wildlife species inhabiting areas of increasing human encroachment.     

Population genetic structure of the melon fly, <Emphasis Type="Italic">Bactrocera cucurbitae</Emphasis> (Diptera: Tephritidae), from China and Southeast Asia

The melon fly, Bactrocera cucurbitae Coquillett, is a species of fruit flies of significant agricultural interest. Of supposed Indian origin, the melon fly is now widely distributed throughout South East Asia up to China, while it has been recently eradicated from Japan. The population structure of seven geographic populations from coastal China, as well as samples from other regions of South East Asia and Japan, including lab colonies, have been studied using a 782 bp fragment of mitochondrial cytochrome oxidase I (COI) gene sequence. The observed genetic diversity was exceedingly low, considering the geographic scale of the sampling, and one single haplotype was found to be predominant from Sri Lanka to China. We confirm that Bactrocera cucurbitae exists in South East Asia as a single phyletic lineage, that Chinese populations are genetically uniform, and that no apparent genetic differentiation exists between these and three available Japanese melon fly sequences.     

Genetic characterization of game bird island populations: The conservation of the black francolin (Francolinus francolinus) of Cyprus

The release of exotic genotypes into the wild can lead to the extinction of local demes through the hybridization among distinct gene pools. This may occur between wild specimens and their domesticated relatives. Escaped pets represent a well-known pathway for the introduction of allochtonous resources, and island environments require major attention as they include small-sized and naïve populations that may be prone to extinction. We characterized the genetic make-up of the black francolin (Francolinus francolinus, Phasianidae) resident to Cyprus using microsatellite and mitochondrial DNA for the purpose of sustainable use and long-term protection of this game species. We collected 59 samples of specimens hunted in the districts of Nicosia and Paphos, while others (n = 18) were obtained from birds of unknown origin. These had been imported to a pet-centre in Nicosia, the largest in the capital offering animals either for production or leisure purposes. Both genetic systems pointed to the occurrence of distinct wild district populations that could be treated as separate management units. The non-significant value of the inbreeding coefficient (F_IS) computed for Nicosia and Paphos populations (−0.039 and −0.189, respectively: P > 0.05) and the lack of evidence for recent genetic bottlenecks did not indicate a serious risk of over-hunting. The microsatellites revealed the birds in the pet-centre as highly genetically divergent with respect to the wild ones, the mtDNA pointed to their assignment to alien Asian subspecies once they were compared to141 sequences of allopatric francolins. We advised the Game & Fauna Service to consider law enforcement to ban the import, detention and sale of these subspecies to protect the black francolin population native to Cyprus. The results are discussed in the context of a bibliographic frame including the partridges of the genus Alectoris (Phasianidae) as a model group with reference to genetic characterization and conservation of game bird island populations.     

Phylogenetic relationships and genetic diversity of badgers from the Korean Peninsula: Implications for the taxonomic status of the Korean badger

Accurate taxonomic classification of wildlife species is crucial for guiding biological research and for developing effective management and conservation programs. The taxonomic status of Eurasian badgers from South Korea remains poorly resolved. Here we assessed the phylogenetic relationships and genetic variation of Eurasia badgers using partial mitochondrial fragments to elucidate the evolutionary history and taxonomic status of badgers from the Korean Peninsula. Forty-eight unique haplotypes from 125 individuals were observed. Phylogenetic reconstructions and reduced median networks indicate that Eurasian badgers consisted of four geographic clades (Japan, Eastern Eurasia, Western Eurasia, and Caucasus) with a relatively weak split observed within Eastern Eurasia. Estimated divergence time between the Japanese and Eastern Eurasian clades, including the Korean population, was 467,100 years (69,200–1,085,500 years). The results of this study support the hypothesis that the Japanese badger migrated from the Eurasian continent over the Korea-Japan land bridge and that the Korean Peninsula was an important refugia during the Pleistocene. Our study confirmed that the South Korean badger, Meles meles, belongs to the Eastern Eurasian clade. Based on these results and those of previous studies, we recommend that the scientific name of the Korean badger be changed from M. meles to Meles leucurus (Asian badger).     

Origin of, and conservation units in, the Irish red squirrel (Sciurus vulgaris) population

Knowledge of genetic relationships among wildlife populations is fundamental to their conservation, particularly where translocations are concerned. This study involved a survey of mitochondrial DNA variation in the Irish red squirrel population. Our main aims were: (1) to determine whether the Irish red squirrel population is distinct from that found in Britain, given known translocations that took place from Britain in the 1800’s; and (2) whether inclusion of Irish data into a reanalysis of European red squirrel data could reveal patterns of postglacial spread in Ireland. We found evidence that the current Irish red squirrel population may be a mixture of native and translocated stock, and relationships between Irish and European haplotypes supported a number of colonisation events of the island. Although only one haplotype was common to both Ireland and Britain, it is probable that the most common haplotypes in Ireland are British introductions that have since become extinct in Britain. There was a significant regional genetic structure in Ireland (P < 0.001), as well as between all Irish and British regions. Although it is likely that the red squirrel will not be fundamental in tracing the colonisation of Ireland by mammals, the data demonstrated that individual regions within Ireland, as well as the Irish population as a whole, are distinct both from the British population and from each other and, therefore, these populations should be treated as separate Management Units (MU) in conservation strategies.     

Determination of genetic diversity of wild and cultured topmouth culter (Culter alburnus) inhabiting China using mitochondrial DNA and microsatellites

The topmouth culter (Culter alburnus) is one of the most commercially important freshwater fish species inhabiting China. However, very limited information is available regarding its genetic diversity and population structure, thus hindering the effective management of this fish stock. Understanding the genetic diversity of wild and cultured topmouth culter populations is highly relevant for successful hatchery management. This study evaluated the genetic diversity and structure of five wild and two cultured populations of topmouth culter in China by using microsatellites and mitochondrial DNA. The genetic diversity of wild populations was found to be lower than that of cultured populations. This finding indicates that wild topmouth culter resources should be protected to prevent further degeneration and extinction. Moreover, it demonstrated that cultured populations have greater breeding potential than wild ones. Subdivisions among wild populations were observed, which should be considered as different units for conservation and hatchery management.     

Balancing genetic uniqueness and genetic variation in determining conservation and translocation strategies: a comprehensive case study of threatened dwarf galaxias,Galaxiella pusilla (Mack) (Pisces: Galaxiidae)

Genetic markers are widely used to define and manage populations of threatened species based on the notion that populations with unique lineages of mtDNA and well‐differentiated nuclear marker frequencies should be treated separately. However, a danger of this approach is that genetic uniqueness might be emphasized at the cost of genetic diversity, which is essential for adaptation and is potentially boosted by mixing geographically separate populations. Here, we re‐explore the issue of defining management units, focussing on a detailed study of Galaxiella pusilla, a small freshwater fish of national conservation significance in Australia. Using a combination of microsatellite and mitochondrial markers, 51 populations across the species range were surveyed for genetic structure and diversity. We found an inverse relationship between genetic differentiation and genetic diversity, highlighting a long‐term risk of deliberate isolation of G. pusilla populations based on protection of unique lineages. Instead, we adopt a method for identifying genetic management units that takes into consideration both uniqueness and genetic variation. This produced a management framework to guide future translocation and re‐introduction efforts for G. pusilla, which contrasted to the framework based on a more traditional approach that may overlook important genetic variation in populations.     

Assessing genetic diversity and structure of fragmented populations of eastern white pine (Pinus strobus) and western white pine (P. monticola) for conservation management

Aims Many pine populations in Canada have fragmented distributions resulting from the effects of glaciations, overharvesting and white pine blister rust infections. Forest fragmentation can modify gene flow and reduce genetic diversity. Selective logging can reduce the density of trees, thereby altering mating patterns and increasing inbreeding. The hypothesis of the present study is that forest fragmentation will not increase inbreeding and will have no effect on genetic diversity parameters in the Canadian Pinus moniticola and P. strobus populations targeted because of (i) the long life span of the pine species, (ii) outbreeding and self-incompatibility of P. monticola and P. strobus and (iii) wind pollination resulting in high gene flow among populations. We studied the genetic diversity of P. strobus across its range in Canada, and we completed a detailed analysis of the genetic structure of P. monticola populations from western Canada using microsatellites genetic markers.Methods Seed samples from 10 P. monticola populations and 10 P. strobus populations were collected from western and eastern Canada, respectively. The mother trees included in seed lots were representative of each stand. Genomic DNA extracted from each sample was amplified with microsatellite primers. The intra- and interpopulation genetic diversity parameters were assessed using Popgene and Genepop softwares and the genetic distances among populations within each species using the PowerMarker software.Important findings Pinus monticola and P. strobus exhibited moderate to high genetic diversity. Also, both species showed low levels of inbreeding despite the geographic isolation and small stand size. Gene flow estimates were high and population differentiation values were relatively low for these fragmented forest sites.     

Mitochondrial DNA diversity and origins of domestic goats in Southwest China (excluding Tibet)

Southwest China contains about one third Chinese indigenous goat breeds representing special economic and ecological characteristics. Mitochondrial DNA (mtDNA) D-loop sequences of 312 individuals (including 109 new individuals, 203 individuals retrieved from GenBank) from 18 Chinese domestic goat breeds were used to investigate breed genetic diversity, origin and phylogeography. All goat breeds in this study proved to be extremely diverse, average haplotype diversity and nucleotide diversity being 0.9829 ± 0.0027 and 0.03615 ± 0.03257, respectively. The 312 sequences gave 148 different haplotypes. Phylogenetic analyses revealed that there were two mtDNA haplogroups identified in domestic goats in Southwest China, in which haplogroup A was predominant. Mismatch analysis showed haplogroup A had experienced population expansion events, whereas haplogroup B did not. Amova analysis showed there was no significant geographical structuring. Almost 86.23% of genetic variation was included in the within-breed variance component and only 3.5% was observed among the four geographic provinces. The results of this study contribute to the knowledge of the genetic structure and origin of domestic goats in Southwest China.