圈养及野生藏酋猴子代遗传多样性差异分析

为评价圈养及野生藏酋猴Macaca thibetana子代遗传多样性的差异,本研究利用藏酋猴线粒体控制区(mt DNA D-loop)全长序列,对四川省金阳地区野生亲本及子一代、马边地区野生亲本及圈养繁殖子一代共102只个体开展了遗传结构变异分析。结果显示,藏酋猴mt DNA D-loop的序列长度为1 091 bp,包括115个变异位点,66个单倍型,其中,马边种群亲本与子一代共享2个单倍型,金阳种群亲本与子一代共享1个单倍型。马边种群2个世代个体的核苷酸多态性分别为0.004 77和0.004 09;而金阳种群2个世代个体的核苷酸多态性分别为0.002 30和0.002 78,子一代与亲本的遗传多样性差异无统计学意义,均处于较低水平。马边和金阳地区子一代与亲本之间的遗传距离分别为0.024 09和0.002 55,表明圈养和野生条件下的子一代与亲本间均未出现明显的遗传分化。根据D-loop全长序列所构建的邻接(NJ)树显示,金阳或马边地区的不同世代个体在NJ树上互相交叉,未形成独有的进化支,说明无论自然条件下的随机交配还是圈养繁育的人为选择压力均没有对藏酋猴种群的遗传结构造成大的影响。本研究首次利用mt DNA D-loop全长序列分析藏酋猴野外与圈养繁殖的亲本与子一代间的遗传差异,为藏酋猴实验动物遗传控制标准化提供数据支持。     

长江中游鳊群体的遗传多样性

采用线粒体DNA(mt DNA)细胞色素b基因(cytb)和控制区序列,分析长江中游宜都、沙市、燕窝、团风等4个产卵场鳊种群的遗传多样性和遗传结构。结果表明:长江中游鳊群体cytb序列共检出82个多态位点,86种单倍型,平均单倍型多样性指数(Hd)和核苷酸多样性指数(Pi)分别为0.930和0.00244;控制区序列共检出变异位点46个,单倍型76种,Hd指数和Pi指数分别为0.972和0.00505;构建的单倍型网络结构和分子方差分析(AMOVA)显示,4个群体的遗传变异绝大部分来自群体内部,群体间无显著遗传分化;群体间的分化指数(FST)、平均基因流(Nm)和平均K2-P遗传距离均表明,4个鳊地理群体间存在广泛的基因交流,未发生明显群体遗传分化;中性检验表明,鳊历史上发生了群体扩张,扩张时间在第四纪冰期后期。     

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。       

基于mtDNA COI基因的甘肃截形叶螨不同地理种群遗传分化分析

【目的】探讨甘肃截形叶螨Tetranychus truncatus种群遗传多样性、遗传分化及种群系统发育关系。【方法】本研究以2016年6-9月采自甘肃省8个不同生境的34个截形叶螨种群的518头螨样品进行mt DNA COI基因PCR扩增、测序,并利用MEGA7.0和Dna SP5.0等软件分析截形叶螨不同种群的mt DNA COI基因序列变异和遗传分化情况。【结果】在34个截形叶螨地理种群中共获得518条mt DNA COI基因片段,测定片段长度为402 bp,T,C,A和G碱基平均含量分别为43.2%,10.5%,32.2%和14.0%,A+T含量(75.4%)明显高于C+G含量(24.6%),有明显的A/T偏倚性;核酸多样性性指数为0.0328。共检出12个单倍型,单倍型指数为0.8004,其中,H2出现了14次,分布于5个生态区域,为主体单倍型,占个体样本的41%。单倍型网络中介图表明各单倍型明显聚为5个聚类簇;12个单倍型的NJ系统发育树明显地分为4支,该结果与单倍型中介网络图的结果基本一致。各种群间的遗传距离在0.001~0.08955之间。UPGMA聚类图结果表明JQ(酒泉)种群和HS(合水)种群与其他种群相比分化明显。Mantel检测结果表明,种群间的遗传距离与地理距离无显著的相关性(r=0.043,P0.05)。34个种群间的遗传分化指数Fst为0.11995,种群间变异比例为1.20%。【结论】甘肃省8个生态区的34个截形叶螨种群间的遗传距离与地理距离无显著相关性;截形叶螨的遗传变异主要来自于种群内部,种群间还未发生明显的遗传分化现象。     

草鱼野生与选育群体线粒体DNA控制区D-loop遗传变异分析

为探究经过2个选育世代后选育群体遗传多样性和遗传结构的变化, 研究对4个野生群体(邗江、九江、石首和吴江)和2个选育世代(F1和F2)进行了线粒体DNA控制区(D-loop)序列的遗传变异分析。实验结果表明, 4个野生群体在单倍型数目(H)、单倍型多样性(H_d)、核苷酸多样性(π)、平均核苷酸差异数(K)水平上均高于2个选育世代, 在2个选育世代内表现为F1代群体的核苷酸多样性(π)和平均核苷酸差异数(K)大于F2代群体, 但单倍型多样性(H_d)小于F2代群体; 单倍型分析结果表明, 6个群体间无共享单倍型, 4个野生群体间共发现2种共享单倍型(Hap1和Hap3), 石首群体和2个选育世代共享1种单倍型(Hap15); 遗传分化指数(F_st)分析结果表明, 邗江、九江、吴江3个野生群体和2个选育世代间存在较大的遗传分化(F_st范围为0.41475—0.55128), 石首群体与F1代群体之间存在较小的遗传分化, 与F2代群体之间存在中等水平的遗传分化, 同时F1代群体与F2代群体之间存在较小的遗传分化; 基于6个群体276个个体构建的邻接(Neighbor-Joining, NJ)进化树和基于27种单倍型构建的单倍型网络图也得到了相似的结论, 即邗江、九江、吴江3个野生群体和2个选育世代间的亲缘关系较远, 石首群体和2个选育世代两两之间的亲缘关系较近。以上结果表明, 经过2个世代的选择育种, 选育群体的遗传结构已发生了变化, 并且随着选育的进行, 选育世代的遗传多样性下降的较为明显, 这警示着我们在今后的育种工作中应适当改变现有的选育方案, 并实时监测选育群体的遗传多样性, 以便为今后进一步的选育工作打下坚实的基础。     

淮河水系日本沼虾群体遗传结构和系统演化的线粒体COI序列分析

测定了淮河水系17个日本沼虾(Macrobrachium nipponense)野生群体共248个个体的线粒体细胞色素氧化酶亚基I(COI)部分序列,获得623 bp核苷酸片段,包括48个变异位点,定义了31个单倍型,共享单倍型有12个,整体单倍型多样性和平均核苷酸多样性均处于中间水平。AMOVA分析表明,17个群体间的遗传分化系数Fst=0.041 3(P0.05),群体间遗传分化较小。Kimura 2-paramter遗传距离在五河与焦岗湖、花家湖及瓦埠湖群体间最大,为0.014,在高邮和邵伯湖群体之间最小,为0.003。MP系统树与单倍型进化网络关系图具有较高的一致性,31个单倍型被分为3个进化枝,其中一个进化枝主要以下游群体为主,另外2个进化枝主要以中游群体为主。群体中性检验、错配分析表明,淮河日本沼虾近期曾经历过种群扩张。     

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Cytb 和COⅠ基因对珠江、海南和红河长臀鮠群体遗传结构分析

为了解3 个种群的野生资源状况, 并对3 个种群的物种有效性进行分析, 采用Cytb 和COⅠ基因序列测定技术, 分析了珠江水系、海南水系和越南红河水系长臀鮠种群的群体遗传结构及其变异, 结果发现, 三个群体平均遗传距离分别为0.003(cytb)和0.002(coⅠ); 94 尾个体分别存在35(Cytb)和13(COⅠ)个变异位点, 分别检测出24 (Cytb)和13 (COⅠ)个单倍型, 总群体单倍型多样性(Hd)分别为0.875 (Cytb)和0.787 (COⅠ), 平均核苷酸差异数(K)分别为3.194(Cytb)和1.328(COⅠ), 核苷酸多样性指数(Pi)分别为0.00295 (Cytb)和0.00213 (COⅠ)。珠江长臀鮠单倍型多样性(Hd)和核苷酸多样性(Pi)最高, 海南最低; 对长臀鮠群体进行历史动态分析,三个种群各自无明显扩张趋于稳定, 但将三个种群作为一个群体时发现长臀鮠可能在某一个时期产生了扩张。研究结果表明, 三个种群遗传距离显著小于临界值2%,应为同一个种; 长臀鮠野生资源较为贫乏, 且海南群体最为严重。     

基于线粒体COⅡ基因序列的中华蜜蜂地理种群的遗传多样性研究

通过分析我国20个不同地理种群中蜂线粒体COⅡ序列的变异,对中华蜜蜂群体遗传分化程度遗传多样性进行全面研究。结果表明:COⅡ基因部分序列中共发现16个变异位点和18个单倍型,核苷酸差异数的平均值为0.939,核苷酸分歧度(Dxy)在0.1%~0.965%之间变化,核苷酸遗传距离为-0.007%~1.489%。总种群的Fst为0.4978,差异均极显著(P0.001)。研究结果显示种群总体单倍型多样性较为丰富,种群间核苷酸分歧度差异很大。20个东方蜜蜂不同地理种群间存在显著的遗传分化。     

长江中上游银鮈线粒体DNA遗传多样性分析

银鮈(Squalidus argentatus)是长江常见小型鱼类,分布广泛于干支流,资源量较大。本研究采用线粒体DNA(mt DNA)细胞色素b基因序列对长江中上游干流江津、荆州、监利、洪湖、黄石江段及支流赤水河、湘江等7个江段共217尾银鮈样品的遗传结构和遗传多样性进行了分析。结果显示,银鮈群体Cyt b基因序列分别检出了81个变异位点和97个单倍型,平均单倍型多样性(Hd)和核苷酸多样性(Pi)分别为0.966和0.008 6。分子方差分析(AMOVA)显示,长江中上游银鮈群体存在显著遗传分化。群体间两两比较分析发现,赤水河群体与其他群体基因交流程度低,遗传分化显著,其他群体间没有显著遗传分化。中性检验结果不支持银鮈历史上发生过群体扩张。     

Genetic diversity of captive forest musk deer (Moschus berezovskii) inferred from the mitochondrial DNA control region

Forest musk deer ( Moschus berezovskii ) were once distributed widely in China. However, wild populations have declined dramatically because of poaching and habitat loss. Captive breeding populations have been established for several decades, but the genetic backgrounds of most captive populations were unclear and the population sizes increased very slowly. To provide useful information for conservation and management of this species, we investigated the genetic diversity and population structure of forest musk deer by analysing a 582-bp fragment of the mitochondrial DNA (mtDNA) control region (CR) in three captive breeding populations in Sichuan Province, China. Ninety-four variable sites and 27 haplotypes were observed in 109 individuals, and the nucleotide and haplotype diversities were relatively high compared with those of other endangered mammals. Of the three investigated populations, the Maerkang population had the highest nucleotide diversity ( π  = 0.0568), haplotype diversity ( h  =   0.836) and average intra-population genetic distance (0.062). The analysis of molecular variance demonstrated that most variation occurred within samples and that there was significant differentiation of the three populations. Estimates of gene flow indicated that there were few genetic exchanges among the three populations. Building pedigree records and increasing gene flow between populations will be helpful for conserving these populations and this species.     

陕西凤县驯养林麝的种群动态、性比和年龄结构

林麝是濒危资源动物,林麝驯养是保育濒危林麝资源及可持续利用麝香的有效方式。基于对2001至2012年间的陕西凤县林麝驯养的监测和调查,分析了其种群动态、性比和年龄结构。结果表明,陕西凤县的林麝驯养在近10余年获得了快速发展,全县共有150余个麝场,麝场数呈指数式增长,增长率达27.33%,但其平均驯养规模无明显增长,平均存栏种群仅为16.38头。凤县的驯养麝种群总体增长近似指数式增长,增长率达27.22%,目前存栏种群已达3712头。区分性别和年龄,各亚群的增长均呈指数式增长,幼年麝的增长率(30.30%)高于成年麝(27.16%),雄麝的增长率(28.30%)高于雌麝(27.78%)。在2001至2012年间,幼麝种群的雌雄性比((102.64±3.15)%,n=12)和成年麝种群的雌雄性比((100.85±2.585)%,n=10)均显著偏雌(P0.01),但幼麝、成年麝种群间的性比差异不显著(P0.05)。在2005年及2010—2012年间,幼麝(0.5岁龄)占种群的比例为31.91%,亚成体麝(1.5岁龄)占种群的比例为21.11%,成麝(2.5—12.5岁龄)比例为42.72%,老年麝(13.5岁龄及以上)仅占种群的4.26%。合并年龄分析,育龄前个体(幼麝和亚成体麝)的平均比例为53.02%,表明凤县驯养林麝属快速增长种群,其增长潜力较大。在林麝驯养实践中,管理部门可制定准入制度或适当重组现有麝场,促进较大的驯养种群构建,并建立通畅的麝香交易渠道,控制林麝种源的过热交易,以利于林麝驯养种群的性比平衡及可持续的繁育、增长。     

The Genetic Integrity of the Ex Situ Population of the European Wildcat (Felis silvestris silvestris) Is Seriously Threatened by Introgression from Domestic Cats (Felis silvestris catus)

Studies on the genetic diversity and relatedness of zoo populations are crucial for implementing successful breeding programmes. The European wildcat, Felis s. silvestris, is subject to intensive conservation measures, including captive breeding and reintroduction. We here present the first systematic genetic analysis of the captive population of Felis s. silvestris in comparison with a natural wild population. We used microsatellites and mtDNA sequencing to assess genetic diversity, structure and integrity of the ex situ population. Our results show that the ex situ population of the European wildcat is highly structured and that it has a higher genetic diversity than the studied wild population. Some genetic clusters matched the breeding lines of certain zoos or groups of zoos that often exchanged individuals. Two mitochondrial haplotype groups were detected in the in situ populations, one of which was closely related to the most common haplotype found in domestic cats, suggesting past introgression in the wild. Although native haplotypes were also found in the captive population, the majority (68%) of captive individuals shared a common mtDNA haplotype with the domestic cat (Felis s. catus). Only six captive individuals (7.7%) were assigned as wildcats in the STRUCTURE analysis (at K = 2), two of which had domestic cat mtDNA haplotypes and only two captive individuals were assigned as purebred wildcats by NewHybrids. These results suggest that the high genetic diversity of the captive population has been caused by admixture with domestic cats. Therefore, the captive population cannot be recommended for further breeding and reintroduction.     

Molecular polymorphism of MHC-DRB gene and genetic diversity analysis of captive forest musk deer (Moschus berezovskii)

The major histocompatibility complex (MHC) is one of the most important elements in immune system for nearly all vertebrates, and is thought to be essential for an organism to recognize foreign molecules. In this study, we investigated the MHC variation in 51 forest musk deer (Moschus berezovskii) collected from three captive populations in Sichuan Province, China. Seventeen haplotypes were isolated from the 51 samples. A total of 51 mutation sites were identified and yielded a nucleotide diversity of 0.056. These haplotype sequences possessed 83 putative amino acid sites, including 24 PBR sites (peptide binding region) and 59 non-PBR sites. Out of 24 PBR sites, 15 codons showed variation (0.625), while 12 codons showed variation (0.203) in 59 non-PBR sites. Non-synonymous substitutions primarily occurred in PBR, with analyses suggesting that the Mobe-DRB gene had undergone strong positive selection during their evolution. Compared with that of some other endangered species, the forest musk deer had relatively high level of MHC diversity. Our results suggested that the MHC diversity characteristic of captive forest musk deer populations might be not responsible for their high morbidity of abscess disease.     

Microsatellite analysis of the genetic structure of captive forest musk deer populations and its implication for conservation

Forest musk deer (Moschus berezovskii) are rare as a result of poaching for musk and habitat loss. Some captive populations of forest musk deer have been established for decades in China. However, little genetic information is available for conservation management. In this paper, genetic variations, population structures, and the genetic bottleneck hypothesis were examined using 11 microsatellite loci from captive populations in Miyalo, Jinfeng and Maerkang in Sichuan Province, China. Estimates of genetic variability revealed substantial genetic variation in the three populations. A total of 142 different alleles were observed in 121 forest musk deer and the effective number of alleles per locus varied from 6.76 to 12.95. The average values of observed heterozygosity, expected heterozygosity, and Nei's expected heterozygosity were 0.552, 0.899 and 0.894 respectively. The overall significant (P < 0.001) deficit of heterozygotes because of inbreeding within breeds amounted to 34.5%. The mean F_ST (P < 0.001) showed that approximately 90.2% of the genetic variation was within populations and 9.8% was across populations. The UPGMA diagram, based on Nei's unbiased genetic distance, indicated that the three populations were differentiated into two different groups and it agreed with their origin and history. Bottleneck tests indicated that all three populations have undergone a population bottleneck, suggesting a small effective population size. Acknowledging that the genetic structure of populations has crucial conservation implications, the present genetic information should be taken into account in management plans for the conservation of captive forest musk deer.     

Phylogeography and conservation genetics of Eld's deer (Cervus eldi)

Eld's deer (Cervus eldi) is a highly endangered cervid, distributed historically throughout much of South Asia and Indochina. We analysed variation in the mitochondrial DNA (mtDNA) control region for representatives of all three Eld's deer subspecies to gain a better understanding of the genetic population structure and evolutionary history of this species. A phylogeny of mtDNA haplotypes indicates that the critically endangered and ecologically divergent C. eldi eldi is related more closely to C. e. thamin than to C. e. siamensis, a result that is consistent with biogeographic considerations. The results also suggest a strong degree of phylogeographic structure both between subspecies and among populations within subspecies, suggesting that dispersal of individuals between populations has been very limited historically. Haplotype diversity was relatively high for two of the three subspecies (thamin and siamensis), indicating that recent population declines have not yet substantially eroded genetic diversity. In contrast, we found no haplotype variation within C. eldi eldi or the Hainan Island population of C. eldi siamensis, two populations which are known to have suffered severe population bottlenecks. We also compared levels of haplotype and nucleotide diversity in an unmanaged captive population, a managed captive population and a relatively healthy wild population. Diversity indices were higher in the latter two, suggesting the efficacy of well-designed breeding programmes for maintaining genetic diversity in captivity. Based on significant genetic differentiation among Eld's deer subspecies, we recommend the continued management of this species in three distinct evolutionarily significant units (ESUs). Where possible, it may be advisable to translocate individuals between isolated populations within a subspecies to maintain levels of genetic variation in remaining Eld's deer populations.     

Molecular genetic diversity of musk deer Moschus moschiferus L., 1758 (Ruminantia, Artiodactyla) from the northern subspecies group

Genetic diversity within the northern subspecies group of musk deer Moschus moschiferus L., 1758 was examined based on the mtDNA control region hypervariable fragment (300-bp) sequence polymorphism. Nucleotide diversity, constituting 2.6% for the whole sample (n = 34), varied in the range from 0.6 to 1.9% for individual subspecies. Maximum values of this index were observed for Siberian subspecies (M. m. moschiferus), which had the widest range. Genetic similarity between the haplotypes of the musk deer from the Far East (Russia) and Sakhalin Island, which grouped in one cluster in a phylogenetic tree, was demonstrated. The data obtained indicate that the distribution of musk deer along the territory of Russia occurred from Eastern Siberia to the Far East, and from there to the Sakhalin Island. A currently observed decrease of the musk deer population number along with the increased habitat fragmentation can result in a decrease of the total genetic diversity and in inbreeding depression in the local isolated groups.     

Genetic quality of the Miyaluo captive forest musk deer (Moschus berezovskii) population as assessed by microsatellite loci

The Miyaluo captive forest musk deer population (Sichuan Province, China) is one of the largest captive breeding populations in the world. In order to evaluate the genetic quality and provide available genetic management strategy, seven polymorphism microsatellite loci were applied to assess the genetic variation of the Miyaluo forest musk deer. The results indicated that a total of 168 alleles were detected from these seven microsatellite loci in 361 individuals, and the number of the alleles per locus ranged from 12 to 41 with a mean of 24. The average observed heterozygosity, expected heterozygosity, and PIC were 0.782, 0.854, and 0.837, respectively. Considering the results of the loci Hardy–Weinberg equilibrium test, the comparison of the common allele frequency as well as the private allele between the adults and juveniles, we concluded that the heterozygosity and the genetic diversity of the Miyaluo captive breeding population are increasing due to the input of new individuals from other populations. However, the frequency of some alleles declined sharply, and some were even lost indicating that there is a risk for diversity loss. Thus, we proposed an improved management and breeding strategy for the captive breeding population of the forest musk deer.     

Major histocompatibility complex class II genetic variation in forest musk deer (Moschus berezovskii) in China

The major histocompatibility complex (MHC) plays an important role in the immune system of vertebrates. We used the second exon of four MHC class II genes (DRA, DQA1, DQA2 and DRB3) to assess the overall MHC variation in forest musk deer (Moschus berezovskii). We also compared the MHC variation in captive and wild populations. We observed 22 alleles at four loci (four at DRA, four at DQA1, four at DQA2 and 10 at DRB3), 15 of which were newly identified alleles. Results suggest that forest musk deer maintain relatively high MHC variation, which may result from balancing selection. Moreover, considerable diversity was observed at the DRA locus. We found a high frequency of Mobe‐DRA*02, Mobe‐DQA1*01 and Mobe‐DQA2*05 alleles, which may be important for pathogen resistance. A Ewens–Watterson test showed that the DRB3 locus in the wild population had experienced recent balancing selection. We detected a small divergence at the DRA locus, suggesting the effect of weak positive selection on the DRA gene. Alternatively, this locus may be young and not yet adapted a wide spectrum of alleles for pathogen resistance. The significant heterozygosity deficit observed at the DQA1 and DRB3 loci in the captive population and at all four loci in the wild population may be the result of a population bottleneck. Additionally, MHC genetic diversity was higher in the wild population than in the captive, suggesting that the wild population may have the ability to respond to a wider range of pathogens.     

Development and characterization of 15 novel microsatellite markers from forest musk deer (<Emphasis Type="Italic">Moschus berezovskii</Emphasis>)

A total of 15 polymorphic microsatellite loci were isolated from forest musk deer (Moschus berezovskii). These loci showed high levels of allelic diversity, presenting 6–14 alleles per locus in a group with 31 individuals. The mean observed and expected heterozygosities were 0.82 and 0.68, respectively. The average polymorphic information content value, cumulative discrimination power, overall probability of exclusion with both unknown parents or with only unknown sire for these markers were 0.78, 1.0, 0.9999 and 1.0, respectively, indicating that this suit of microsatellite loci would be a powerful tool for the genetic determination of the forest musk deer.