秦岭细鳞鲑群体遗传结构

秦岭细鳞鲑(Brachymystax lenok tsinlingensis)是秦岭地区特有鱼类,近年来由于环境恶化及人类活动的加剧,已对其造成严重影响,种群处于濒危状态,因此研究秦岭细鳞鲑的群体遗传结构、演化历史、分布动态等对其进行有效保护具有重要意义。本研究用线粒体D-loop区序列对秦岭地区6个群体(n=112)进行了遗传结构和群体演化分析。D-loop区扩增出的891bp序列在112个个体中,检测到42个变异位点,共26个单倍型;碱基序列总的单倍型多样度较高为0.883,核苷酸多样度为0.00799。AMOVA分析显示,60.05%的分子差异位于群体内,39.95%的分子差异位于群体间,Fst值统计检验表明,除那布大河群体与漳河群体和千河群体之间差异不显著之外,其余两两群体之间Fst值统计检验均为显著。系统树和单倍型网络图分析表明,6个地理群体的单倍型按照渭河上游和渭河中游两个河段形成两个大的类群,且5个群体共享一个单倍型H2,表明这些群体具有相同的演化历史,为同一个祖先群体演化而来。中性检验和歧点分布显示,秦岭细鳞鲑种群大小保持相对稳定,未经历明显的种群扩张。同时建议将渭河上游秦岭细鳞鲑群体作为一个整体进行重点保护。     

基于线粒体控制区和微卫星标记探讨秦岭细鳞鲑物种有效性

文章基于线粒体控制区基因序列和微卫星标记比较秦岭细鳞鲑(Brachymystax tsinlingensis Li)、黑龙江流域的尖吻细鳞鲑(Brachymystax lenok Pallas)和钝吻细鳞鲑(Brachymystax tumensis Mori)的分子遗传差异, 为澄清其分类地位争议提供分子证据。结果表明: (1)扩增217个样本的mtDNA D-loop区序列, 共获得45个单倍型, 类群间无共享单倍型; 基于单倍型构建的系统进化树显示三个细鳞鲑类群呈独立的支系; (2)基于14个呈多态性位点的遗传分化结果表明, 秦岭细鳞鲑与尖吻或钝吻细鳞鲑之间的遗传距离均大于尖吻细鳞鲑和钝吻细鳞鲑之间的遗传距离; (3)基于线粒体D-loop和多态性微卫星位点计算出的遗传分化系数(F_ST)都远高于0.25, 表明三个类群间的遗传分化程度极高。这些结果表明, 秦岭细鳞鲑与黑龙江流域细鳞鲑之间遗传分化程度高, 结合前期发现秦岭细鳞鲑与黑龙江细鳞鲑类群有明显形态分化的研究结果及它们之间地理隔离已久的现状, 研究初步判定秦岭细鳞鲑为独立物种, 并建议以Brachymystax tsinlingensis Li为拉丁名。同时, 建议将秦岭细鳞鲑作为独立单元进行保护, 避免人为引种或杂交等因素造成种质资源破坏。     

中国胭脂鱼线粒体控制区遗传多样性分析

利用PCR技术扩增了采自长江宜昌江段和清江的8尾中国胭脂鱼线粒体DNA控制区全序列,研究发现该种具有脊椎动物线粒体控制区的一般结构,在获得的958bp的碱基序列中,共检测出32个多态性核苷酸变异位点,多态位点比例为0.033。核苷酸的变异位点除一个为缺失外,其余全部为碱基转换。变异位点主要集中在55-365bp高变异区,而其他区域突变稀少,个体的变异在0-1.36%之间,表现出较大的个体多态性差异。中国胭脂鱼的线粒体控制区的变异远大于美国胭脂鱼（Moxostoma robustum)的0.016。     

基于线粒体控制区的序列变异分析青海东部甘肃鼢鼠遗传多样性

甘肃鼢鼠(Myospalax cansus)是一种终年营地下独居生活的小型掘土类动物。本文通过测定mt DNA的控制区部分序列(530 bp)变异,分析青海东部地区8个甘肃鼢鼠地理种群遗传多样性与遗传结构。158个样本共发现26个变异位点,定义了39种单倍型,整体的平均单倍型多样性高(h=0.953 2)、核苷酸多样性低(π=0.006 36)。歧点分布和中性检验均说明青海东部甘肃鼢鼠种群在历史上存在着快速扩张的事件。基于邻接法构建的网络关系图中,单倍型呈星状分布,没有按地理位置形成对应类群。基因流(Nm)数据显示多数地理种群间基因交流贫乏,AMOVA结果显示种群内与种群间遗传变异分别为48.82%和51.18%,遗传分化明显。IBD分析表明,甘肃鼢鼠的遗传分化与地理距离呈正相关,说明距离隔离对甘肃鼢鼠种群分化具有重要作用。甘肃鼢鼠的这种遗传多样性与种群遗传结构特点,可能是地下生活方式靠挖掘迁移带来的较小扩散能力的结果。     

基于线粒体控制区和微卫星标记探讨秦岭细鳞鲑物种有效性

为了从全基因组InDel角度进行全国地理尺度细鳞鲑属遗传分化与适应性研究, 文章对采自陕西、甘肃、新疆、河北和黑龙江的6个细鳞鲑群体(共90尾样本)进行建库测序及InDel检测分析。结果表明: 6个细鳞鲑群体共检测到3056034个高质量InDel突变位点, 缺失位点数大于插入位点数, 将各基因区域标准化后观察到内含子区富集到相对更多的InDel位点。所有系统发育树分支中共统计到1715464个固定的InDel, 占总数的56.08%, 且主要位于每个谱系的基部。群体结构分析结果显示每个细鳞鲑地理群体均具有相对独立的遗传结构。适应性分析方面: 利用群体分支统计方法检测到秦岭地区细鳞鲑适应性相关的621个候选受选择基因, 并筛选到两个影响外显子序列的缺失位点, 分别导致insr和dnhd1缺失了两个和一个氨基酸密码子。对所有候选受选择基因的富集分析结果显示主要在神经发育和代谢等途径发挥作用。研究可为秦岭细鳞鲑山区溪流生境适应性候选基因的深入挖掘及人工增殖和保护中分子标记的开发提供基础资料, 也为进一步厘清细鳞鲑属物种分化提供参考。

     

基于线粒体DNA控制区序列变异探讨黑龙江和图们江细鳞鲑属鱼类的分类地位

基于细鳞鲑属Brachymystas鱼类的线粒体DNA控制区基因序列变异,对分布于黑龙江水系中国境内的尖吻细鳞鲑(sharp-snouted lenok)和钝吻细鳞鲑(blunt-snouted lenok),及分布于图们江的图们江细鳞鲑B.tumensis进行分子系统关系研究,为进一步确定黑龙江水系2种细鳞鲑的分类学地位、有效命名及图们江细鳞鲑物种地位性提供分子生物学依据.分布于黑龙江水系的细鳞鲑种群在系统发育树中明显构成2个独立的进化分支,分别对应可经形态鉴别而差异显著的尖吻细鳞鲑和钝吻细鳞鲑,平均序列分歧为1.9%,在属内已达到种间分化水平;图们江细鳞鲑与尖吻细鳞鲑的呼玛河、乌苏里江、奎勒河等种群共同构为1个进化分支,与尖吻细鳞鲑的序列分歧(平均为1.2%)远低于与钝吻细鳞鲑的序列分歧(平均为2.2%).结合形态学的初步研究结果(图们江细鳞鲑的主要形态特征偏向于尖吻细鳞鲑),不支持图们江细鳞鲑独立种的分类地位,建议为尖吻细鳞鲑B.lenok的同物异名,也不支持普遍认为的钝吻细鳞鲑的有效学名为B.tumensis,其有效命名还待商榷,暂属未定名种.综上所述,基于基因序列分析的遗传学结果进一步验证了形态学的分类结论,即在黑龙江水系细鳞鲑属有2个独立的种,分别为尖吻细鳞鲑B.lenok和钝吻细鳞鲑B.sp.,而图们江细鳞鲑B.tumensis应归为尖吻细鳞鲑B.lenok的同物异名.     

铜鱼线粒体控制区的序列变异和遗传多样性

采用PCR和DNA测序技术研究长江中上游野生铜鱼的遗传多样性和群体遗传学特征,从9个采样点共获得100尾铜鱼,用于分析的线粒体DNA控制区的片段序列为946bp。在100个序列中,共检测出变异位点47个(其中增添/缺失位点8个),单倍型41种。9个地理群体的平均单倍型多样性(Hd)和平均核苷酸多样性(Pi)分别为0.9257±0.0162和0.004178±0.002337,表现出较贫乏的遗传多样性。群体间的分化指数(FST值)、平均基因流(Nm)、分子方差分析(AMOVA)和平均K2-P遗传距离均表明9个铜鱼地理群体间存在广泛的基因交流,未明显发生群体遗传分化。另外,共享单倍型比例较高,约为34%(14/41)。单倍型的UPGMA分子系统树和简约网络图显示单倍型的聚类与地理分群没有相关性。上述结果表明9个铜鱼地理群体属于同一种群。     

黑龙江黑斑狗鱼线粒体控制区的遗传变异

测定了黑龙江抚远江段和虎林江段黑斑狗鱼(Esoxreicherti)线粒体控制区5'端的560bp序列,在12尾黑斑狗鱼序列中未检测到任何变异位点,即所有个体的序列均完全一致,共享同一种单倍型,群体内和群体间的核苷酸多样性均为0.黑龙江黑斑狗鱼线粒体DNA如此贫乏的遗传多样性,一方面可能是黑龙江水系黑斑狗鱼在更新世冰期可能曾遭受过严重的瓶颈效应;另一方面则可能因目前是国内黑斑狗鱼种群数量锐减,种质资源急剧衰退,导致种群遗传多样性的丧失.建议广泛取样调查不同地理种群,并采用AFLP和微卫星等分子标记检测遗传多样性,以确定遗传变异丰富的黑斑狗鱼种群加以保护,促进黑龙江流域黑斑狗鱼资源的有效保护和可持续利用.     

红腹锦鸡线粒体DNA控制区结构和遗传变异研究

红腹锦鸡(Chrysolophus pictus)是中国特有珍稀鸟类,仅见于中国中部和西部的山地,为国家二级重点保护动物.采用聚合酶链式反应和直接测序的方法测定了采自湖南新宁县和龙山县的28只红腹锦鸡线粒体DNA控制区序列.在获得的1 123 bp的碱基序列中,碱基含量为T 32.79%、C 26.07%、A 26.62%和G14.52%,共检测出20个多态性核苷酸变异位点,其中简约信息位点11个.对比其它已报导的雉类控制区结构,对红腹锦鸡控制区结构进行了分析,识别了其高变Ⅰ区、中间保守Ⅱ区和保守Ⅲ区,找到了与终止相关的序列TAS以及保守序列(F、E、D、C).28个样本共发现11种单倍型,其中单倍型hap1和hap2的比例很高.新宁种群的遗传多样性比龙山种群的高,两个种群存在基因流较频繁,未出现明显遗传分化.     

白鱼线粒体DNA控制区结构和种群遗传多样性分析

用特异性引物对白鱼（Anabarilius grahami）DNA进行PCR扩增,获得了白鱼线粒体DNA控制区基因全序列（930 bp）。控制区T、C、A和G碱基组成为29.8%、22.5%、33.0%和14.7%。对照其他已报道的鱼类控制区结构,对白鱼控制区结构进行了分析,识别了其终止序列区、中央保守区和保守序列区,找到了终止相关的序列TAS以及保守序列（CSB-F、CSB-D、CSB-1、CSB-2、CSB-3）。同时运用DNA分析软件对白鱼一个驯养种群（中国科学院昆明动物研究所珍稀鱼类繁育中心）及两个自然地理种群（江川县明星鱼洞、江川县牛摩村）进行了遗传多样性分析。结果显示：两个自然种群存在较强基因交流,未出现遗传分化;人工驯养种群遗传多样性最高,种群复壮程度较好。     

云南中华按蚊的遗传变异和种群结构

为了掌握云南省各地中华按蚊种群间的遗传变异和种群结构特征,测序并分析了采自云南9个样本点5个种群组的89头中华按蚊的线粒体COII基因。结果表明这些中华按蚊种群的COII基因序列平均单倍型多样性指数和核苷酸多样性指数分别为h=0.933,π=0.00406,共有51个变异位点,占分析的739个碱基总数的6.9%;定义了39个单倍型,有2个频率最高的单倍型H1和H9,分别占个体序列数的20.2%和12.4%;系统发育分析表明单倍型与地理位置没有明显的对应关系,单倍型网络图显示大部分单倍型分布没有明显的亲缘地理格局,主要以单倍型H1、H9、H4、H33和H2为中心呈星状分布,但元江和元阳构成的种群组(YU)单倍型存在明显地域分布特征;AMOVA结果表明种群组间遗传变异为12.58%,达到显著水平(P=0.04888),地理种群组间具有明显种群遗传结构。不同地区两两种群组间的Fst值和Nm值显示大部分种群组间存在基因交流,没有形成明显的遗传分化,但YU种群组和其他种群组间缺乏明显的基因交流,这主要是因为哀牢山的阻隔,使云南东西部形成两种不同的气候,产生了明显的遗传分化;歧点分布图显示为明显单峰分布,中性检测结果均为显著负值,说明云南省的中华按蚊种群在近期经历过复杂的种群扩张事件。掌握中华按蚊遗传多样性及分化特征,对中华按蚊及疟疾控制具有重要的作用。     

Population Structure and Variation in Red Snapper (<Emphasis Type="Italic">Lutjanus campechanus</Emphasis>) from the Gulf of Mexico and Atlantic Coast of Florida as Determined from Mitochondrial DNA Control Region Sequence

The mitochondrial DNA control regions of red snapper (Lutjanus campechanus) from the Gulf of Mexico (n = 140) and Atlantic coast of Florida (n = 35) were sequenced to generate a prestocking genetic baseline for planned stock enhancement. Intrasample haplotype and nucleotide diversities ranged from 0.94 to 1.00 and 1.8% to 2.5%, respectively. All population analyses were consistent with the hypothesis that red snapper constitute a single, panmictic population over the sampled range. A ubiquitous, predominant haplotype, shared by 23% of the specimens, appeared to be evolutionarily recent, in contrast to previous findings based on restriction fragment length polymorphism data. Tajimas D values were suggestive of a recent bottleneck. Mismatch distributions from Gulf samples were smooth and unimodal, characteristic of recent population expansion. However, the Atlantic sample exhibited a comparatively broader, possibly multimodal distribution, suggestive of a more stable population history. Additional control-region data may clarify potentially disparate demographic histories of Gulf and Atlantic snapper.     

The hypervariable domain of the mitochondrial control region in Atlantic spiny lobsters and its potential as a marker for investigating phylogeographic structuring

Atlantic spiny lobsters support major fisheries in northeastern Brazilian waters and in the Caribbean Sea. To avoid reduction in diversity and elimination of distinct stocks, understanding their population dynamics, including structuring of populations and genetic diversity, is critical. We here explore the potential of using the hypervariable domain in the control region of the mitochondrial DNA as a genetic marker to characterize population subdivision in spiny lobsters, using Panulirus argus as the species model. The primers designed on the neighboring conserved genes have amplified the entire control region (approx. 780 bases) of P. argus and other closely related species. Average nucleotide and haplotype diversity within P. argus were found to be high, and population structuring was hypothesized. The data suggest a division of P. argus into genetically different phylogeographic groups. The hypervariable domain seems to be useful for determining genetic differentiation of geographically distinct stocks of P. argus and other Atlantic spiny lobsters.     

叉尾斗鱼种群遗传变异与亲缘地理

通过分析采自珠江、鉴江、漠阳江、赣江、韩江、黄冈河、九龙江和闽江8个流域23个采样点121尾叉尾斗鱼mtDNA控制区3'端和临近序列共400bp,研究其种群遗传变异和亲缘地理格局。所分析序列只有13个变异位点,共有11个单倍型,碱基序列总的单倍型多样性为0.576,核苷酸多样性为0.00818,均较低。珠江流域存在群体内独有单倍型,有两个广布单倍型H1和H2,分别占所有样品的19%和62%。最小进化网络图显示单倍型没有明显的亲缘地理格局,呈星状发散,H1和H2处于中心。AMOVA分析显示变异主要来自地理区内群体间,歧点分布和中性检测显示叉尾斗鱼并未经历种群扩张。结果表明叉尾斗鱼种群遗传多样性很低且存在地理差异;各流域个体呈混杂分布格局,现有群体可能在珠江流域有东西两个起源;推测种群最近经历严重瓶颈效应。     

中国大陆黑斑侧褶蛙基于mtDNA控制区序列的种群遗传结构

用分子遗传数据研究了黑斑侧褶蛙 (Pelophylaxnigromaculata)种群的遗传结构和分化。标本采自中国大陆的 12个地点 ,每个种群测定 10只或少于 10只蛙的mtDNA控制区 5′端 6 85bp的序列。 112只蛙的序列经比对后 ,共发现 111个变异位点 ,定义了 6 7种单元型 ,其中 7种单元型为地方种群间共享单元型 ,多数单元型为地方种群内特有。 12个地方种群合并成一个大种群分析时表明 ,中国大陆黑斑侧褶蛙的线粒体单元型多样性相当高 (h=0 98± 0 0 0 5 ) ,总体核苷酸多样性也较高 (π =0 0 30 3± 0 0 0 2 9)。这样高的单元型多样性和核苷酸多样性与黑斑侧褶蛙作为古北界和东洋界的广布种、种群大是相应的。基于最大简约法的单元型系统发生树和基于邻接法的地方种群系统发生分析中 ,吉林通化和辽宁辽阳种群与中国大陆其他地方种群构成姐妹群。分子变异分析表明 ,吉林和辽宁种群代表的吉辽组和其余 10个地方种群代表的综合组间出现了显著的种群分化 (Φ CT=0 80 9,P <0 0 0 1) ,各地方种群间成对的FST及种群间的核苷酸歧异度也均表明两者之间出现了显著的遗传分化。吉辽组与综合组间的遗传分化最可能的原因就是受第四纪冰川的影响     

Genetic differentiation in the mud crab Scylla serrata (Decapoda: Portunidae) within the Indian Ocean

Scylla serrata (Decapoda: Portunidae) is a swimming crab that is widespread in the Indo-Pacific region and commonly found in estuarine and mangrove waters. An extended planktonic larval phase suggests high dispersal potential and the possibility of extensive gene flow between conspecific populations at least on a geographic mesoscale (tens to hundreds of kilometres).Intraspecific variation of the mitochondrial DNA cytochrome oxidase subunit I (mtDNA COI) gene was investigated in 77 individuals from four representative mangrove swamps of the African tropics (Kenya and Zanzibar) by means of DNA sequencing. We examined 535 base pairs (bp) and identified 24 different haplotypes. Each population sample is characterised by a single most frequent haplotype, shared among all four populations, and a small number of rare ones, typically present in only one or two individuals and representative of a specific population.Analysis of molecular variance (AMOVA), F_ST statistics and χ² contingency analysis of spatial distribution of mtDNA haplotype frequencies revealed in toto a significant genetic differentiation among populations. These results could indicate that gene flow might be reduced, even between geographically close sites, despite the high potential for dispersal; anyway, at the recorded level of divergence and owing to the abundance of rare haplotypes and singletons in our data set, repeated sampling over time is necessary to establish whether the recorded pattern of genetic differentiation is stable and biologically significant.Finally, integration of our data with those reported by Gopurenko et al. [Mar. Biol. 134 (1999) 227] on S. serrata from South Africa, Red Sea and Mauritius Islands allowed to infer S. serrata population structure within a larger area of the Indian Ocean region.     

Genetic variation in the midcontinental population of sandhill cranes,Grus canadensis

Three subspecies of sandhill crane (Grus canadensis) are recognized in the Midcontinental population, the lesser (Grus c. canadensis), Canadian (G. c. rowani), and greater (G. c. tabida). Blood samples collected on the population's primary spring staging area in Nebraska, U.S.A., were used to resolve the genetic relationship among these subspecies. Phylogenetic analysis of 27 G. canadensis, by DNA sequencing of a 675 bp region of the mtDNA, supports the subspecies designations of G. c. canadensis and G. c. tabida. G. c. rowani individuals were intermediate with each of the other two subspecies. Genetic divergence ranged from 6.5 to 14.5% between G. c. canadensis and G. c. tabida, 0.5 to 6.6% within G. c. canadensis, and 0.1 to 6.0% within G. c. tabida. Sufficient DNA for analysis was obtained from shed feathers indicating a source of genetic material that does not require the capture or sacrifice of the birds. Other genetic markers and methods, including satellite telemetry, are required for obtaining detailed information on crane distributions as needed to establish effective management units for the MCP.     

Phylogenetic analysis of mtCR-1 sequences of Tunisian and Egyptian hares (Lepus sp. or spp., Lagomorpha) with different coat colours

North African hares are currently considered belonging to cape hares (Lepus capensis), except for an isolated occurrence of L. victoriae in NW Algeria. However, the few existing molecular data are not unequivocal. Here, we study sequence variation (415 bp) in the hypervariable domain-1 of the mitochondrial (mt) control region, of hares with different coat colour from north-central Tunisia and NW Egypt, to test Petter's [(1959): Eléments d’une révision des Lièvres africains du sous-genre Lepus. Mammalia 23, 41–67] hypothesis that North African hares belong to L. capensis. Seven Tunisian and one Egyptian haplotypes were revealed from 28 hares and compared phylogenetically to 245 haplotypes of various Lepus species downloaded from GenBank. Neighbour joining (NJ) and principal coordinate (PCO) analyses based on a Tamura-Nei 93 distance matrix, as well as maximum parsimony (MP) analysis concordantly grouped all currently obtained haplotypes together into one monophyletic clade, and revealed relatively close relationships to the clades of African scrub hares (L. saxatilis) and brown hares (L. europaeus). The three distinguished coat colour types of Tunisian hares were paralleled only to a small extent by sequence differentiation. Haplotypes of L. capensis from the nominal Cape province of South Africa, North Africa, and China clustered into different major clades, respectively, with Chinese L. capensis haplotypes forming only a subclade within a major clade that encompassed predominantly “mountain/arctic hare-type sequences” in addition to sequences of several other palaearctic and nearctic species. One further Chinese L. capensis haplotype clustered into the L. comus clade. These results indicated occurrence of introgression and/or shared ancestral polymorphism. Such an evolutionary scenario implies using nucelar markers in addition to mtDNA for phylogenetic inferences in the genus Lepus; nevertheless, mtDNA is still useful for inferring phylogenetic history and biogeography of hares.