大石鸡边缘种群的遗传结构

大石鸡（Alectoris magna）分布于青海西部、东部,甘肃中部和宁夏西部的干部和半干旱区,由于环境变化,其种群向甘肃南部森林被砍伐的地区扩散,形成涟缘种群。本研究采用聚合酶链式反应（PCR）和直接测序的方法获得了采自甘肃的大石鸡一个边缘种群和两个中心地理种群共39个个体的线粒体DNA（mtDNA）控制区基因（D－loop）456－457个核苷酸的基因序列,16个变异位点（占整个序列的3.5%）有15个单倍型。边缘扩散种群有3种单倍型,M6与另两个种群共有,单倍型频率为0.108,而M4和M5为其特有,单倍型频率分别为0.081和0.027。边缘种群的单倍型比率和遗传多样性分别为37.5%和0.549。中心地理种群1和种群2各有7个单倍型,除M6炳种群共有,其余为自所特有,单倍型比率分别为46.7%和50.0%,遗传多样性分别是0.729和0.786。边缘种群的单倍型比率和遗传多样性均低于中心地理种群。     

基于线粒体Cyt b基因的雉鸡甘肃亚种的种群遗传结构

采用聚合酶链式反应(PCR)和直接测序法分析雉鸡甘肃亚种的种群遗传结构。测序获得了8个种群79个样本的长819bp的线粒体细胞色素b(Cytb)基因序列,发现7个变异位点,界定了6种单倍型(Haplotype),其中Hap-1是共享单倍型,占79.75%。在8个种群中,除ZJC和CHX种群外,其它种群的核苷酸多样性和单倍型多样性都很低,种群间遗传分化小,基因流大。ZJC种群由于亚种间的基因渗透,导致其遗传多样性最高。CHX种群受徽成盆地周边山地的森林隔离作用,单倍型最多。分子方差分析(AMOVA)表明,遗传变异主要发生在种群内,占86.44%。种群间和地理种群组间差异不显著。地理种群组的核苷酸多样性(π)同形态上的变异规律一致。FS值检测表明,雉鸡甘肃亚种曾发生过快速扩张。     

基于线粒体DNA的大石鸡种群遗传变异

大石鸡(Alectoris magna)是我国的特有鸟类,其种群数量由于受到栖息地片断化和人类狩猎的影响而日益减少。本文以mtDNA的控制区部分序列(1,127bp)和细胞色素b部分序列(807bp)为分子标记,研究了大石鸡分布区内12个种群234个样本的遗传变异。173个样本的控制区序列中共发现了34个多态位点,定义了44种单倍型,平均单倍型多样性和核苷酸多样性分别为0.916±0.011和0.00449±0.00242,所有种群中单倍型多样性最高的是靖远和民和种群(0.894±0.063),最低的是海原种群(0.476±0.155)。230个样本的细胞色素b序列中共发现了13个多态位点,定义了14种单倍型。平均单倍型多样性为0.738±0.024,平均核苷酸多样性为0.00216±0.00009,所有种群中单倍型多样性最高的是共和种群(0.763±0.059),最低的为德令哈种群(0.000±0.000)。所有遗传多样性参数与样本量均无显著相关性。控制区和细胞色素b的单倍型邻接树均显示大石鸡在系统发生树上没有互为单系发生的种群存在,因此应该将大石鸡作为一个独立的进化显著单元(ESU)来对待。AMOVA结果显示大部分遗传变异分布于种群内,但种群间和群组间也存在显著的遗传变异,所以应该把各个种群作为独立的管理单元(MU)来实现短期内的管理和保护。对德令哈、都兰、礼县、张家川、海原等遗传多样性较低的边缘种群应重点保护,另外,对共和、贵德和靖远3个遗传多样性较高的种群也应重点加以保护。     

马鹿阿拉善亚种遗传多样性和群体结构

马鹿阿拉善亚种（Cervus elaphus alashanicus）又称阿拉善马鹿,目前仅分布于贺兰山地区,是我国马鹿亚种分布范围最狭窄的一个隔离种群。为了解阿拉善马鹿的种群遗传多样性及遗传变异情况,以对该种群的保护提供科学参考,对在贺兰山采集的93个野生个体新鲜粪便样本的线粒体控制区部分序列（991 bp）进行扩增和分析,共检测到68个变异位点,定义16种单倍型,平均单倍型多样性为0.405,平均核苷酸多样性为0.00232,说明种群遗传多样性水平较低。中性检验和错配分布分析表明阿拉善马鹿曾出现过种群扩张,贝叶斯天际线分析（BSP）显示扩张时间约在末次冰盛期（0.028—0.010 Ma）。FST检验表明阿拉善马鹿种群内存在显著遗传分化,系统发育树和单倍型网络图分析表明群体间没有明显的系统地理格局。本研究表明阿拉善马鹿目前种群遗传多样性较低,建议加大对该亚种的关注和保护力度。       

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。     

四川地区猕猴线粒体DNA 控制区遗传多样性及其种群遗传结构

猕猴是最理想的医学实验灵长类动物,并且是国家二级保护动物。四川地区的猕猴数量多、分布广,全面了解其遗传背景对于该地区猕猴资源的保护与合理利用具有重要的意义。本研究对来自四川8 个地理种群的231个不同猕猴个体的线粒体DNA 控制区部分序列进行了测定和群体分析,发现了110 个变异位点(22. 49% ),定义了56 种单倍型,其单倍型多样性(h)平均值为0. 686、核苷酸多样性(π)平均值为0. 01483,种群总体遗传多样性较高;进一步分析表明,8 个地理种群间存在着明显的遗传分化(F_st = 0. 70412,P < 0. 05),种群间基因交流较低(N_m < 1);系统发育树显示,四川猕猴8 个地理种群的单倍型基本上成簇分布在系统树上,与地理位置呈现一定的对应关系,说明四川猕猴具有明显的系统地理分布格局。地理隔离和人类活动可能是促使四川猕猴种群分化的主要因素。     

高原鼢鼠线粒体谱系地理学和遗传多样性

高原鼢鼠是一类地下独居啮齿动物,为青藏高原特有种之一。为研究该物种的谱系地理学和遗传多样性,本文测定了采自青藏高原东部3个地理种群8个小种群共37个个体的线粒体D-loop区序列变异。在长度为627bp的序列中,共发现50个变异位点,定义了26种单倍型。该物种的单倍型多样性（Haplotype diversity,H）较高和核苷酸多样性（Nucleotide diversity,πn）较低。谱系分析得到3个稳定的分支,分别与采集的地理种群相吻合：同一地理种群内单倍型之间遗传差异小,而不同地理来源的单倍型之间存在较大区别。距离隔离分析表明高原鼢鼠的遗传分化与地理距离呈正相关。AMOVA分析同样表明地理种群之间存在显著差异：地理种群间变异占遗传变异的80.45%。高原鼢鼠的这种遗传结构特点可能主要是由于第四纪气候变迁、该物种稳定的地下生活环境和有限的迁移能力造成的。     

基于线粒体DNA的中国亚洲象种群遗传多样性及种群遗传结构

亚洲象是我国国家一级保护动物.本文利用非损伤性取样法,以亚洲象粪便中脱落的肠道上皮细胞为DNA来源,选用线粒体DNA作为分子标记,对分布于我国境内的亚洲象种群的遗传结构和种群遗传多样性进行研究.本研究得到mtDNA序列片段长度为556 bp,经对178个个体进行扩增结果分析,共得到24个单倍型.在5个地理种群中,除南滚河种群外,其他4个种群中的114个个体共享同一单倍型,南滚河种群与其他种群间未观察到共享单倍型.系统发生分析,观察到中国境内现有亚洲象种群在进化上分为两大分支,α和β.其中分支α中包含除南滚河种群外的4个地理种群,分支β仅含有南滚河种群,表明南滚河种群与其他4个地理种群间存在明显分化.遗传多样性分析结果表明,中国境内的亚洲象种群的遗传多样性水平较低,分析原因认为是栖息地破碎化阻断了种群间有效的基因交流.     

泛希姬蝽不同地理种群的遗传多样性和遗传分化

泛希姬蝽Himacerus apterus(Fabricius)是半翅目姬蝽科中重要的天敌种类,本文旨在分析泛希姬蝽不同地理种群的遗传多样性和遗传分化情况。利用COI作为标记基因,使用DnaSP、Arlequin、MEGA等软件分析了中国4个省12个种群33个体的单倍型多样性、遗传结构分化、系统发育等。共发现19个单倍型,所有单倍型中仅H1为共享单倍型,为宁夏和陕西共有,且出现频率最高。总体单倍型多样性指数Hd=0.913,核苷酸多样性指数π=0.006,平均核苷酸差异数k=4.083。Tajima's D=-0.853,P>0.100,表明泛希姬蝽未经过种群扩张。AMOVA分析表明种群内的分子变异大于种群间分子变异,变异比例分别为45.393%和36.594%,遗传分化指数均大于0.250,差异水平极显著。泛希姬蝽不同地理种群遗传多样性较高,宁夏与内蒙古、山西、陕西省分组间存在极度的遗传分化。种群间遗传距离和地理距离无相关性,表明地理距离不是影响种群间遗传距离的重要因素。通过比较4个省采集点的环境特点,认为地区间基因流受限和气温、猎物的差异可能是影响遗传分化的重要因素。     

中国北方球孢白僵菌的遗传多样性和种群遗传结构

将在中国北方13省采集分离的622株球孢白僵菌按省份划分成13个亚种群,其中寄主可以鉴定到目的8目昆虫和蜘蛛目的568株按目划分成9个亚种群,用ISSR(简单重复序列区间)分子标记技术进行遗传多样性和种群遗传结构分析.结果表明:各多样性指数皆显示我国北方地区球孢白僵菌的遗传多样性水平较高,种群的异质性较强.其中内蒙古亚种群的遗传多样性和种群异质性最高,河南亚种群最低;鳞翅目亚种群的遗传多样性和种群异质性最高,蜘蛛目亚种群最低.河南与辽宁亚种群间以及蜘蛛目与螳螂目亚种群间的遗传分化系数以及遗传距离最大,宁夏与陕西亚种群间以及鞘翅目与膜翅目亚种群间最小.按寄主目划分的亚种群间的平均遗传分化系数和平均遗传距离均低于按省份划分的亚种群.这些结果以及基于遗传距离的亚种群聚类分析都证明我国北方球孢白僵菌的遗传谱系与寄主来源和地理来源均无关系.我国北方球孢白僵菌的变异主要是由各不同寄主目内科间及属间的变异造成的,也是由各省不同采集地以及采集地内部不同微生境间的差异造成的.     

陇东黄土高原石鸡的遗传多样性与保护

石鸡 (Alectorischukar)是我国北方重要的猎鸟 ,由于栖息地片断化和人类狩猎 ,陇东黄土高原上的石鸡数量正日益减少。本文用PCR直接测序的方法 ,测定了陇东黄土高原 8个石鸡种群mtDNA控制区I区和部分II区的4 91个碱基 ,探讨其遗传多样性。 78个样本共发现 2 4个变异位点 (占所测序列的 4 .89% )和 2 5种单倍型 (占所测样本的 32 .0 5 % )。 8个种群中 ,铜川种群的序列变异率、单倍型多样性和核苷酸多样性都最高 ,分别是 0 .4 7、0 .82和 0 .0 0 2 9;而红回种群的最低 ,仅分别为 0 .10、0 .2 8和 0 .0 0 0 8,这与红回种群受奠基者效应、遗传隔离和自然选择的作用有关。 8个种群共享 1种单倍型C1,说明它们来自共同祖先 ,是 1个单系群 ,属于 1个进化显著单元 ,但它们聚成两个集群。两集群间单倍型相似性指数仅 0 .15 ,遗传距离达 0 .4 3% ,单因素方差分析显示遗传变异差异显著 (F =5 .0 2 >F0 .0 5(14 ,1) =4 .0 6 ) ,分别有 13种和 10种单倍型为两个集群所特有。基于遗传差异性 ,陇东黄土高原的石鸡应分为两个管理单元进行保护 ,尤其对遗传变异和遗传多样性最高的铜川种群应进行重点保护。     

Genetic structure of chukar partridge ( Alectoris chukar) populations in the Longdong Loess Plateau, China

This study used polymerase chain reaction (PCR) and dideoxy direct sequencing methods to analyze the genetic structure of the chukar partridge (Alectoris chukar) in the Longdong Loess Plateau, northwestern China. A total of 491 nucleotides of mitochondrial DNA from the control region gene were sequenced for 78 chukar partridges from eight different populations. The 24 variable positions defined 25 haplotypes. The high gene flow (Nm=3.75) implied little genetic differentiation between the eight populations. All the populations shared the haplotype C_1, which suggested that they all came from a common ancestor. The 25 haplotypes were spread through the populations, but could be clustered into two groups. The haplotype similar index between the two groups was only 0.15, with a genetic distance of 0.43%. The genetic variation was significantly different between the two groups, which had been isolated for all of recorded history. The genetic structure of chukar partridge populations in the Plateau appears to be the result of the synergistic effect of a glacier, along with debris flow and human activities since the middle of the Pleistocene.Communicated by F. Bairlein     

Mitochondrial DNA sequence variability in red-legged partridge, <Emphasis Type="Italic">Alectoris rufa</Emphasis>, Spanish populations and the origins of genetic contamination from <Emphasis Type="Italic">A. chukar</Emphasis>

The analysis of 135 mitochondrial D-loop sequences of the Iberian autochthonous red-legged partridge (Alectoris rufa) from wild population hunting bags from various locations and fowl runs in Spain yielded 37 different haplotypes. Among these, three haplotypes correspond to chukar partridges (Alectoris chukar), indicating genetic introgression from birds illegally introduced for restocking: three individuals carrying such haplotypes where found in natural populations, one appeared among those sampled on a mass reproduction farm and the remaining 10 in another fowl-run. The geographical origin of the contaminating chukar haplotypes could be assigned to the most easterly area of the chukar partridge geographical distribution in China. Molecular diversity parameters in the A. rufa samples indicate a considerable amount of genetic variation. Φ_ST showed significant differences among populations that are not explained by geographical distance alone. Particularly, one northern population (Palencia) shows a certain degree of genetic differentiation that could reflect a previously suggested subspecies division. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic indications of translocated and stocked grey partridges (Perdix perdix): does the indigenous Danish grey partridge still exist?

Non‐local population stocking can have adverse genetic effects on wild populations through loss of genetic diversity and introgressive hybridization. The grey partridge (Perdix perdix) has been an important European game species for centuries, widely subject to translocation and stocking. After c. 80 years of releasing reared grey partridges in Denmark, this study investigated whether an indigenous Danish grey partridge still existed. If so, they would (1) belong to the western European clade (W1) and (2) be more closely related to the historical, indigenous grey partridges than to farm‐bred partridges. These predictions were tested by analysing the variation in both the mitochondrial control region (CR1) and microsatellite markers in museum samples representing the ancestral indigenous Danish grey partridge, contemporary wild grey partridges and farmed grey partridges from the five largest farms in Denmark. Phylogeography and population structure analyses showed traces of the indigenous Danish grey partridges amongst recent wild partridges in certain areas and significant genetic differences between farmed partridges and historical and recent partridges. The results also showed that the indigenous Danish grey partridges belonged to the western European clade (W1 haplotype). A foreign stocking effect was detected on the remote island of Bornholm, where the current population originated from introduced Danish and Bohemian grey partridges. The loss of haplotype diversity over time in certain geographical areas probably results from serious declines in wild Danish grey partridge numbers in recent decades. This, combined with the observation that hybridization between released stocked and wild partridges can occur, may complicate recovery of partridge populations. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 694–710.     

Phylogeography of the rock partridge (Alectoris graeca)

We used mitochondrial DNA control-region and microsatellite data to infer the evolutionary history and past demographic changes in 332 rock partridges (Alectoris graeca) sampled from throughout the species' distribution range, with the exception of the central Balkans region. Maternal and biparental DNA markers indicated concordantly that rock partridge populations are structured geographically (mtDNA phiST = 0.86, microsatellite FST = 0.35; RST = 0.31; P < 0.001). Phylogenetic analyses of 22 mtDNA haplotypes identified two major phylogroups (supported by bootstrap values = 93%), splitting partridges from Sicily vs. all the other sampled populations at an average Tamura-Nei genetic distance of 0.035, which corresponds to 65% of the average distance between closely related species of Alectoris. Coalescent estimates of divergence times suggested that rock partridges in Sicily were isolated for more than 200000 years. This deep subdivision was confirmed by multivariate, Bayesian clustering and population assignment analyses of microsatellite genotypes, which supported also a subdivision of partridges from the Alps vs. populations in the Apennines, Albania and Greece. Partridges in the Apennines and Albania-Greece were probably connected by gene flow since recently through a late Pleistocene Adriatic landbridge. Deglaciated Alps were probably colonized by distinct and, perhaps, not yet sampled source populations. Bottleneck and mismatch analyses indicate that rock partridges have lost variability through past population declines, and did not expand recently. Deglaciated areas could have been recolonized without any strong demographic expansion. Genetic data partially supported subspecies subdivisions, and allowed delimiting distinct conservation units. Rock partridges in Sicily, formally recognized as A. g. whitakeri, met the criteria for a distinct evolutionary significant unit.     

陇东黄土高原石鸡的分子系统地理结构

本文运用聚合链式反应和直接测序的方法测定陇东黄土高原 8个石鸡 (Alectorischukar)地理种群 78个样本的mtDNA控制区 4 91bp ,建立其分子系统地理结构。 78个样本共发现 2 4个变异位点 ,2 5种单倍型。 8个地理种群共享单倍型C1 ,6个种群共享单倍型C2 ,种群间有一定的基因交流。 8个地理种群的 2 5种单倍型在NJ树中相互混杂 ,没有形成独立的地理结构 ,但聚成两个分支。单倍型网络图显示 2 5种单倍型聚成两个星状的集群 ,分别以单倍型C1和C2为中心。这两个群间的遗传差异显著。陇东黄土高原石鸡的系统地理结构属于“系统发生连续 ,具有部分空间隔离”的地理格局。这种地理格局是更新世冰川、泥石流和人类活动共同作用的结果     

基于线粒体DNA控制区的石鸡华北亚种的种群历史动态研究

隶属于鸟纲鸡形目雉科的石鸡是一个多型种,在我国已有7个亚种被报道,其中石鸡华北亚种是我国的特有鸟。用石鸡华北亚种(Alectoris chukar pubescens)12个地理种群112个样本的线粒体DNA控制区(mt DNA CR)1154 bp序列的信息研究了石鸡华北亚种的种群历史动态。112个样本中共发现28个变异位点,定义了29种单倍型,其中12个地理种群的50个样本共享单倍型H1,8个地理种群的16个样本共享单倍型H4。地理种群间存在较大的基因流,且种群间没有由于地理距离产生隔离的证据。负的Tajima(D=-1.336,P0.05)和Fu(Fs=-1.720,P0.05)统计检验值及错配分布的单峰模式都支持石鸡华北亚种经历了种群扩张。石鸡华北亚种大部分种群的错配分布与种群过去的扩张相一致,扩张发生在晚更新世中期的第五寒冷期(0.027—0.06 Ma)。推测其扩张的原因可能为:1)更新世期间我国北方地区没有发生大规模的冰川,2)青藏高原的隆升使我国北方干旱化和荒漠化加剧利于石鸡种群的扩散。武都(WD)位于东洋界,而石鸡是典型的古北界的鸟种,表明WD种群可能是石鸡在东洋界的一个建群种,因此需要给予充分的关注。     

Low genetic diversity and significant structuring of the common hamster populations <Emphasis Type="Italic">Cricetus cricetus</Emphasis> in Poland revealed by the mtDNA control region sequence variation

The genetic diversity of 12 populations in the present range of the common hamster Cricetus cricetus (Linnaeus, 1758) in Poland was established. The 366 bp of the mtDNA control region was sequenced for 195 individuals. As few as seven haplotypes were found and their distribution was geographically structured. The large geographic areas were fixed or almost fixed for a single haplotype and three groups of populations, that do not share any haplotypes, have been defined. Proportions of genetic diversity attributable to variation between groups of populations, between populations within groups and within populations were 93.64, 1.92 and 4.45% (SAMOVA: p < 0.001 for all estimates), respectively. Such pattern of variation is most probably the result of historical, postglacial bottlenecks and present genetic drift after the population decline in the last few decades.     

Subspecific identity and a comparison of genetic diversity between wild and ex situ wildebeest

The original North American ex situ wildebeest population was believed to originate from the white-bearded wildebeest (Connochaetes taurinus albojubatus), which is both morphologically distinct and geographically separated from the brindled wildebeest (C. t. taurinus). However, after an import of wildebeest into North America in 2001, managers have suspected that white-bearded and brindled wildebeest were mixed in herds at multiple institutions. We sequenced the mitochondrial control region (d-loop) from a portion of the managed North American population and compared our sequences with previously published sequences from wild individuals to determine the subspecific identity and genetic diversity of our ex situ population. We were able to confidently identify C. t. albojubatus as the subspecies identity of the sampled portion of our population. Within our population, haplotype and nucleotide diversity were low (0.169 and 0.001, respectively) with a single common haplotype (H1) containing 41 of the 45 individuals sequenced, while two rare haplotypes (H2 and H3) were derived from three individuals and a single individual, respectively. Nucleotide and haplotype diversity were greater overall in the wild populations compared with our managed population. However, C. t. albojubatus was found to exhibit lower nucleotide diversity in both wild and ex situ populations when compared to other wild subspecies. Though the overall goal of the North American wildebeest population is for public education and not reintroduction, maintaining genetic diversity is vital for the long-term viability of this managed population, which may benefit from periodic supplementation of wild animals.     

Phylogeography of Japanese water crowfoot based on chloroplast DNA haplotypes

Water crowfoot, Ranunculus subgenus Batrachium, are submerged macrophytes in the Ranunculaceae. We aimed to infer the Quaternary history of these aquatic macrophytes in the Japanese archipelago. We studied 212 individuals of three perennial and one annual species from 46 populations covering the entire geographic range and found eight haplotypes based on approximately 1800 bp of four spacers in chloroplast DNA. The relationships among haplotypes were resolved using maximum parsimony and parsimony network analyses. To identify the zones of clear genetic boundaries, Monmonier's algorithm was used. The eight haplotypes were distinguished from adjacent haplotypes by one substitution or indel. Each of the 46 populations was fixed for a single haplotype. Inconsistency between cpDNA haplotypes and Batrachium taxa was found, except in one annual species. The distribution of the haplotypes in perennial species was highly geographically structured. An abrupt genetic change was detected between the Tohoku region and more southerly regions. Since the perennial Batrachium are cold-adapted, this genetic differentiation may be due to historical changes in their distributions caused by Quaternary climatic oscillations: interglacial retreats in colder refugia and glacial range expansions. The single haplotype composition of each population may have been shaped by founder effects during colonization and/or by genetic drift. The interglacial refugial populations must have been small enough to deplete haplotype diversity. Inconsistency between cpDNA haplotypes and Batrachium taxa may be due to incomplete lineage sorting of ancestral polymorphic haplotypes.