Genetic diversity and phylogenetic origin of brown trout Salmo trutta populations in eastern Balkans

The study focuses on the phylogenetic origin and genetic diversity of brown trout in the eastern part of the Balkan Peninsula. It further aims to reveal the impact of human-mediated transfers and stocking with non-indigenous trout on the populations in this area. For these purposes, mtDNA control region and microsatellite variation of 204 individuals from 16 populations were analysed. The results indicate that mtDNA haplotypes from the lower Danube basin and southern Black Sea basins differ substantially from a subclade of the Danubian lineage consisting of haplotypes found so far in the most of the Danube basin and in the Caspian and Aral Sea basins. Considering also the results of demographic analyses, this study evidences a complex evolutionary history of brown trout in the southern and western parts of the Black Sea basin. In the Aegean Sea basin, a high frequency of the central haplotype of Adriatic mtDNA lineage has been found. The other Adriatic lineage haplotypes found in this basin differ from the central haplotype by one mutational step only, indicating a recent evolution of the Adriatic lineage in the Aegean Sea basin. Substantial genetic differentiation among populations and basins was revealed. The hybridization with Atlantic brown trout was indicated in both sea basins, but especially in the Danube basin. Compared to other European regions, it can be inferred that the introgression of exogenous brown trout in the eastern Balkan populations is rather low.     

Historical demography of brown trout (Salmo trutta) in the Adriatic drainage including the putative S. letnica endemic to Lake Ohrid

We explore the historical demography of the Adriatic lineage of brown trout and more explicitly the colonization and phylogenetic placement of Ohrid trout, based on variation at 12 microsatellite loci and the mtDNA control region. All Adriatic basin haplotypes reside in derived positions in a network that represents the entire lineage. The central presumably most ancestral haplotype in this network is restricted to the Iberian Peninsula, where it is very common, supporting a Western Mediterranean origin for the lineage. The expansion statistic R2, Bayesian based estimates of demographic parameters, and star-like genealogies support expansions on several geographic scales, whereas application of pairwise mismatch analysis was somewhat ambiguous. The estimated time since expansion (155,000 years ago) for the Adriatic lineage was supported by a narrow confidence interval compared to previous studies. Based on microsatellite and mtDNA sequence variation, the endemic Ohrid trout represents a monophyletic lineage isolated from other Adriatic basin populations, but nonetheless most likely evolving from within the Adriatic lineage of brown trout. Our results do not support the existence of population structuring within Lake Ohrid, even though samples included two putative intra-lacustrine forms. In the interests of protecting the unique biodiversity of this ancient ecosystem, we recommend retaining the taxonomic epithet Salmo letnica for the endemic Ohrid trout.     

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。     

中国北鳅谱系地理学分析

北鳅(Lefua costata)为冷水性鱼类,分布于淮河以北,分析遗传结构能够反映其适应环境变迁的响应.基于线粒体D-loop区211条序列分析了我国北鳅的谱系地理学和遗传多样性,样本采自9条水系共18个样点.单倍型分析显示共计55个单倍型,呈高单倍型多样性(h=0.9304)和高核苷酸多样性(π=0.0087).单...     

Phylogenetic status of brown trout Salmo trutta populations in five rivers from the southern Caspian Sea and two inland lake basins,Iran: a morphogenetic approach

Interrelationships, origin and phylogenetic affinities of brown trout Salmo trutta populations from the southern Caspian Sea basin, Orumieh and Namak Lake basins in Iran were analysed from complete mtDNA control region sequences, 12 microsatellite loci and morphological characters. Among 129 specimens from six populations, seven haplotypes were observed. Based on mtDNA haplotype data, the Orumieh and southern Caspian populations did not differ significantly, but the Namak basin–Karaj population presented a unique haplotype closely related to the haplotypes of the other populations (0·1% Kimura two‐parameter, K2P divergence). All Iranian haplotypes clustered as a distinct group within the Danube phylogenetic grouping, with an average K2P distance of 0·41% relative to other Danubian haplotypes. The Karaj haplotype in the Namak basin was related to a haplotype (Da26) formerly identified in the Tigris basin in Turkey, to a Salmo trutta oxianus haplotype from the Aral Sea basin, and to haplotype Da1a with two mutational steps, as well as to other Iranian haplotypes with one to two mutational steps, which may indicate a centre of origin in the Caspian basin. In contrast to results of the mtDNA analysis, more pronounced differentiation was observed among the populations studied in the morphological and microsatellite DNA data, except for the two populations from the Orumieh basin, which were similar, possibly due to anthropogenic causes.     

Population structure in the endangered cyprinid fish Pararasbora moltrechti in Taiwan, based on mitochondrial and microsatellite DNAs

The genetic structure of four populations of Pararasbora moltrechti, an endemic species of the Cyprinidae in Taiwan, was investigated based on the genetic variation of mtDNA Cyt b gene and five microsatellite loci. High haplotype diversity (h = 0.92) but low nucleotide diversity (0.004) in mtDNA was detected in this endangered species. In total, 33 haplotypes and four clusters were identified in its mtDNA. Nevertheless, low correspondence was found between geographical division and mtDNA clusters. In contrast, Bayesian cluster analysis of the microsatellite data identified four genetic groups and revealed highly structured populations. Significantly negative Tajima's D statistics and mismatch distribution analyses suggest that P. moltrechti populations may have experienced a demographic expansion. In light of the results of a nested clade analysis of mtDNA haplotypes, we conclude that recent population fluctuations and restricted gene flow played major roles in shaping the spatial genetic structure of P. moltrechti populations.     

中国家驴的非洲起源研究

对我国13个家驴品种367条序列(其中引用文献资料241条)的mtDNA D-loop 区399 bp进行分析, 共检测到96种单倍型57个多态位点, 其单倍型多样度为0.767~0.967, 核苷酸多样度为0.014~0.032, 表明我国家驴的遗传多态性丰富。与3个努比亚野驴、3个索马里野驴和6个亚洲野驴的序列构建 NJ系统发育树, 证明我国家驴的母系起源为非洲野驴中的索马里驴和努比亚驴, 亚洲野驴不是中国家驴的母系祖先。     

尾斑瘰螈种群的D-loop区遗传多样性分析

以线粒体DNA D-loop序列为分子标记,研究了采自雷公山和武陵山的尾斑瘰螈(Paramesotriton caudopunclatus)5个种群的遗传多样性.获得42个个体mtDNA D-loop区序列,长度为690 bp,其中有30个变异位点,由此定义了13个单倍型.5个种群中未出现共享单倍型的现象.尾斑瘰螈种群...     

秦岭细鳞鲑人工繁育群体与野生群体遗传变异分析

研究利用线粒体DNA（细胞色素b基因序列和D-loop区序列）序列对秦岭细鳞鲑（Brachymystax lenok tsinlingensis）野生群体和人工繁育群体的种群遗传结构进行了分析。结果表明, 在86个个体扩增出的线粒体D-loop区730 bp片段中, A+T含量（63.5%）明显高于G+C含量（36.5%）。Cyt b基因序列扩增1141 bp, A+T含量（52.8%）明显高于G+C含量（47.2%）。野生群体43个个体共检测到18个单倍型, 繁育群体43个个体中共检测到24个单倍型, 两个群体共享8个单倍型; 秦岭细鳞鲑野生群体的单倍型多样性和核苷酸多样性（h=0.9070.026; =0.002870.00074）低于繁育群体（h=0.9170.035; =0.003490.00083）, AMOVA分析显示, 98.37%的分子差异位于群体内, 1.63%的分子差异位于群体间, 两群体之间的遗传分化水平较低（Fst=0.01631, P=0.1075; Nm=30.16）。采用邻接法构建的系统发育树和单倍型网络图分析表明, 各群体内的个体不形成单系群, 两者之间互有交叉。总之, 秦岭细鳞鲑野生群体与繁育群体之间基因交流充分, 未出现遗传分化。       

Application of mtDNA d-loop region for the study of Russian sturgeon population structure from Iranian coastline of the Caspian Sea

The population structure of the Russian sturgeon ( Acipenser gueldenstaedtii ) was investigated using PCR amplification of the mtDNA D-loop region. Seven composite haplotypes were detected and average nucleotide and haplotype diversity over all samples were found to be 0.05 ± 0.00 and 0.75 ± 0.00 (mean ± SE) respectively. Restriction digest of the mtDNA D-loop region detected two genotypes A and B with a relative high frequencies of 0.5 and 0.36 respectively. These two genotypes (A and B) can be considered as potential genetic markers for different biological groups, stocks or seasonal races of Russian sturgeon. A maximum of 10.8% nucleotide diversity was found between haplotypes AAAAB and BBBBF. 100% heteroplasmy was found in Russian sturgeon and restriction digest of the mtDNA D-loop region also exhibited site heteroplasmy.     

基于线粒体D-loop区和Cyt b基因分析广西禾花鲤三个群体遗传结构

研究基于线粒体D-loop区和Cyt b基因部分序列, 分析了广西全州、融水、环江三地禾花鲤(Cyprinus carpio)的遗传结构。在3个群体中共鉴定到19种D-loop与Cyt b序列的组合单倍型, 总的单倍型多样性(H_d)和核苷酸多样性(π)分别为0.916±0.010和0.008±0.004, 禾花鲤线粒体DNA具有单倍型多样性高和核苷酸多样性低的特点。环江群体单倍型多样性最低, 但是核苷酸多样性却最高, 反映了环江群体存在最明显的谱系混杂。分子方差分析(AMOVA)显示遗传变异主要来源于群体内部(71.54%), 禾花鲤三个群体间有显著的遗传分化(F_st=0.285; P<0.01)。系统发育分析表明, 多数样本的线粒体单倍型属于华南鲤(C. carpio rubrefusus)类型, 同时三地禾花鲤中均检测到一定频率的西鲤(C. carpio carpio)或远东鲤(C. carpio haematopterus)类型的线粒体单倍型, 提示禾花鲤可能受到鲤养殖品种的杂交渐渗。研究初步揭示了广西禾花鲤的种质资源现状, 为禾花鲤这一地方特色“稻鱼共作”品种的选育和苗种管理提供了必要的依据。     

Phylogeography, intraspecific structure and sex-biased dispersal of Dall's porpoise, Phocoenoides dalli, revealed by mitochondrial and microsatellite DNA analyses

Mitochondrial DNA (mtDNA) control-region sequences and microsatellite loci length polymorphisms were used to estimate phylogeographical patterns (historical patterns underlying contemporary distribution), intraspecific population structure and gender-biased dispersal of Phocoenoides dalli dalli across its entire range. One-hundred and thirteen animals from several geographical strata were sequenced over 379 bp of mtDNA, resulting in 58 mtDNA haplotypes. Analysis using F(ST) values (based on haplotype frequencies) and phi(ST) values (based on frequencies and genetic distances between haplotypes) yielded statistically significant separation (bootstrap values P < 0.05) among most of the stocks currently used for management purposes. A minimum spanning network of haplotypes showed two very distinctive clusters, differentially occupied by western and eastern populations, with some common widespread haplotypes. This suggests some degree of phyletic radiation from west to east, superimposed on gene flow. Highly male-biased migration was detected for several population comparisons. Nuclear microsatellite DNA markers (119 individuals and six loci) provided additional support for population subdivision and gender-biased dispersal detected in the mtDNA sequences. Analysis using F(ST) values (based on allelic frequencies) yielded statistically significant separation between some, but not all, populations distinguished by mtDNA analysis. R(ST) values (based on frequencies of and genetic distance between alleles) showed no statistically significant subdivision. Again, highly male-biased dispersal was detected for all population comparisons, suggesting, together with morphological and reproductive data, the existence of sexual selection. Our molecular results argue for nine distinct dalli-type populations that should be treated as separate units for management purposes.     

基于线粒体COI基因序列的黄胫小车蝗不同地理种群的遗传分化及基因流分析

黄胫小车蝗Oedaleus infernalis Saussure是一种在我国分布广泛、 对农牧业生产危害严重的经济害虫。本文对黄胫小车蝗10个地理种群的线粒体COI基因序列进行测序和分析, 利用DnaSP 5.0和Arlequin 3.5.1.2软件对该蝗虫种群间的遗传多样性、 遗传分化程度、 基因流水平及分子变异进行了分析, 建立了单倍型贝叶斯系统发育进化树和单倍型网络图。结果表明： 在所分析的144个序列样本中, 共检测到21种单倍型, 其中1种单倍型为10个地理种群所共享。总群体的单倍型多样性指数为0.653, 各地理种群单倍型多样度范围在0.423~0.790之间。总群体和各种群的Tajima’s D检验结果皆不显著, 说明该种害虫在较近的历史上未经历群体扩张。总群体的遗传分化系数Gst为0.04436, 固定系数Fst为0.05255, 基因流Nm为9.01。AMOVA分子方差分析结果表明, 黄胫小车蝗的遗传分化主要来自种群内部, 种群间的遗传变异水平较低。各地理种群的遗传距离的大小与其地理距离间没有显著的相关性。贝叶斯系统发育进化树与单倍型网络图显示, 黄胫小车蝗各地理种群中的单倍型散布在不同的分布群中, 分布格局较为混杂, 未形成明显的系统地理结构。研究结果揭示, 黄胫小车蝗各种群间的基因交流并未受到地理距离的影响。     

陕西省林麝mtDNA D-loop区序列结构和种群遗传多样性

林麝(Moschus berezovskii)曾广泛分布于中国,由于盗猎和栖息地缩小,秦岭地区野生种群数量迅速下降,圈养繁殖种群已成立了几十年,但大多数圈养种群的遗传背景不清,种群规模增长非常缓慢。为了给这一物种的保护和管理提供有用的信息,调查了陕西省林麝1个圈养种群3个野生种群线粒体DNA(mt DNA)D-Loop 632 bp片段的遗传多样性和种群结构。在69个个体中其碱基组成为A+T的平均含量63.2%高于G+C含量36.8%,共检测到变异位点171个(约占总位点数的27.05%)。核苷酸多样性(Pi)为0.04424,平均核苷酸差异数(K)为19.908。69个个体分属32个单倍型,单倍型间的平均遗传距离(P)为0.070。32个单倍型构建的NJ系统树聚为3个分支,4个林麝群体中的单倍型是随机分布的。4个群体的平均遗传距离为0.043(标准误SE为0.005),凤县养殖场群体与留坝和陇县群体的亲缘关系较远。单倍型间的平均遗传距离为0.043,可见其遗传分化尚未达到种群分化的水平。结果表明,陕西省林麝群体mt DNA D-loop区序列存在着较丰富的变异和遗传多样性,凤县野生群体和凤县养殖场群体的核苷酸多样性和单倍型多样较高,养殖场种群没有出现近亲繁殖及遗传多样性下降的情况。凤县野生群体和凤县养殖场群体两者遗传分化较小,存在着较高的基因流水平。     

Genetic Structure of Brown Trout (Salmo trutta) Populations from Turkey Based on Microsatellite Data

This present study investigated micro- and macro-geographic microsatellite DNA variations using five polymorphic microsatellite loci from 27 brown trout populations in Turkey. Average number of alleles and average observed heterozygosity were 7.4 and 0.254, respectively. Even populations from the same sea basin and river system (the so called micro-geographic regions) had unique alleles. Genetic variation among the populations from macro-geographic regions (different sea basins and river systems) was 45.78%. The mtDNA lineages of brown trout that have previously been identified by mtDNA analyses were supported by the analysis of the microsatellite DNA data in general. The Çatak population, which belongs to the Tigris lineage, was clustered together with the Euphrates populations within the Adriatic mtDNA lineage, based on microsatellite data. Both mitochondrial and microsatellite DNA analyses have made it possible to determine a secondary contact between Adriatic and Tigris lineages.     

Variation of the mitochondrial DNA control region in the populations of southern form of Dolly Varden (<Emphasis Type="Italic">Salvelinus malma krascheninnikovi</Emphasis>) from Sakhalin

Analysis of a 551-bp segment of the mitochondrial DNA control region in 23 individuals from nine populations of Dolly Varden from Sakhalin and three individuals from the Shikaribetsu Lake (Hokkaido) revealed the presence of seven haplotypes of southern form, along with one haplotype of northern form of Dolly Varden. All seven haplotypes of southern Dolly Varden were earlier described in the populations from Hokkaido. Hierarchical analysis of molecular variance (AMOVA) based on the haplotype frequencies, performed using literature data, suggested that, during the glacial epoch, there were three regional population groups of Dolly Varden (from eastern and western coasts of Sakhalin, and from Southern Primorye). Population groups from Sakhalin and Primorye were clearly separated. The differences between two Sakhalin population groups in the mtDNA haplotype frequencies were not statistically significant. However, relative to the earlier obtained data on microsatellite loci, these differences were statistically significant. For the populations of Sakhalin Dolly Varden, the data on mitochondrial and microsatellite DNA variation supplement each other.     

Genetic variation and population structure of the Japanese sika deer (Cervus nippon) in the Tohoku District based on mitochondrial D-loop sequences

The sika deer (Cervus nippon) once inhabited the entire Tohoku District, the northeastern part of the main island of Japan. Currently, they are isolated as three discontinuous populations on Mt. Goyo, the Oshika Peninsula, and Kinkazan Island. To assess the genetic diversity and relationships among the sika deer populations in the Tohoku District, we analyzed the mitochondrial DNA D-loop sequences from 177 individuals. We detected a total of five haplotypes. Three haplotypes were present in the population from Mt. Goyo at a haplotype diversity of 0.235 ± 0.061, two haplotypes in the population from the Oshika Peninsula at 0.171 ± 0.064, and only one haplotype was detected in the population from the Kinkazan Island. A significant genetic differentiation was observed among all population pairs. Collectively, our data supports the observed population bottlenecks in the past. Four of the five haplotypes were specific to one of the three populations, whereas only one haplotype was shared between the Mt. Goyo and the Oshika Peninsula populations. This common haplotype may indicate a common ancestral population in the Tohoku District. Conversely, the D-loop haplotypes were completely different among the Kinkazan Island and Oshika Peninsula populations. The lack of a shared haplotype indicates that female gene flow between the two populations is very limited and that the 0.6 km strait acts as a strong barrier.     

New insights into the origin and the genetic status of the Balkan donkey from Serbia

The Balkan donkey (Equus asinus L.) is commonly regarded as a large‐sized, unselected, unstructured and traditionally managed donkey breed. We assessed the current genetic status of the three largest E. asinus populations in the central Balkans (Serbia) by analysing the variability of nuclear microsatellites and the mitochondrial (mtDNA) control region of 77 and 49 individuals respectively. We further analysed our mtDNA dataset along with 209 published mtDNA sequences of ancient and modern individuals from 19 European and African populations to provide new insights into the origin and the history of the Balkan donkey. Serbian donkey populations are highly genetically diverse at both the nuclear and mtDNA levels despite severe population decline. Traditional Balkan donkeys in Serbia are rather heterogeneous; we found two groups of individuals with similar phenotypic features, somewhat distinct nuclear backgrounds and different proportions of mtDNA haplotypes belonging to matrilineal Clades 1 and 2. Another group, characterized by larger body size, different coat colour, distinct nuclear gene pool and predominantly Clade 2 haplotypes, was delineated as the Banat donkey breed. The maternal landscape of the large Balkan donkey population is highly heterogeneous and more complex than previously thought. Given the two independent domestication events in donkeys, multiple waves of introductions into the Balkans from Greece are hypothesized. Clade 2 donkeys probably appeared in Greece prior to those belonging to Clade 1, whereas expansion and diversification of Clade 1 donkeys within the Balkans predated that of Clade 2 donkeys.     

中国湛江市和哈尔滨市褐家鼠种群遗传结构及其年度变化特征

为探索褐家鼠Rattus norvegicus地理种群的遗传结构及其年度变化特点,本研究以广东省湛江市的褐家鼠指名亚种和黑龙江省哈尔滨市的褐家鼠东北亚种为主要研究对象,结合我国及世界其他褐家鼠种群的D-loop序列分析这2个褐家鼠地理种群间D-loop序列的遗传分化情况及系统进化关系,重点分析2008—2015年褐家鼠湛江种群和哈尔滨种群D-loop单倍型的年度频率变化特点。结果表明,褐家鼠湛江种群和哈尔滨种群共有32种不同的单倍型,其中有11种单倍型是2个种群共有的,有4种单倍型仅在湛江种群中出现,有17种单倍型仅在哈尔滨种群中出现。褐家鼠湛江种群D-loop区的核苷酸多态性为0.005,有27个变异位点,单倍型多态性为0.695,褐家鼠哈尔滨种群D-loop区的核苷酸多态性比湛江种群略高,为0.008,有35个变异位点,单倍型多态性为 0.793。褐家鼠湛江种群和哈尔滨种群没有经历过暴发性的扩增。褐家鼠湛江、哈尔滨和湖北3个地理种群的D-loop序列之间发生了明显的遗传分化,其中湛江种群和哈尔滨种群之间的分化程度最高,遗传分化系数F_st为0.245。褐家鼠湛江种群和哈尔滨种群的单倍型数目和主单倍型频率都发生明显波动,推测主要原因可能是由于灭鼠剂的大量使用或其他灭鼠活动导致种群出现瓶颈或更替的现象。     

长江中下游湖泊短颌鲚线粒体控制区遗传多样性分析

为探明长江中下游不同湖泊中短颌鲚(Coilia brachygnathus)遗传多样性水平和遗传分化程度,以洞庭湖、长湖、巢湖3个地理群体作为研究对象,采用线粒体控制区序列为分子标记,分别应用软件Dna SP 5.0、Arlequin3.1.1、MEGA5.0和Network 5.1进行了遗传参数统计和单倍型间分子变异分析(AMOVA),构建邻接系统树及单倍型网络图。对长江中下游短颌鲚野生群体的遗传多样性和遗传结构进行分析。结果显示,用来分析的1 236 bp D-loop区序列中共90个变异位点,54个简约信息位点。长江中下游3个地理群体中共发现58个单倍型,单倍型多样性(h)范围0.949~0.982,核苷酸多样性范围0.004 99~0.006 21,说明长江中下游3个湖泊短颌鲚地理群体具有较高的遗传多样性水平。3个短颌鲚地理群体遗传分化指数(Fst)为0.265 95,呈现出中等程度的分化水平,主要表现在巢湖群体与其他群体之间处于中等程度分化水平。依据遗传距离构建系统发育树及单倍型网络图也出现相类似结果。