异源四倍体鲫鲤及其原始亲本遗传变异的微卫星标记分析

采用从鲤中分离出来的32对微卫星DNA标记,对异源四倍体鲫鲤、红鲫和野鲤的基因组DNA进行了研究。在筛选出的15对微卫星引物中,随引物不同,各等位基因数为1～8个,大小在100～420bp之间。从3个不同群体内部的遗传相似系数来看,异源四倍体鲫鲤个体之间的遗传相似系数最大,说明异源四倍体鲫鲤群体内部的遗传变异程度最低,已经形成了一个遗传性状稳定的群体。从3个不同群体之间的遗传相似系数来看,异源四倍体鲫鲤和红鲫遗传相似系数为0．5625,和野鲤的遗传相似系数为0．5125,说明异源四倍体鲫鲤接受原始母本的遗传物质比原始父本野鲤要多一些。微卫星标记与以前报道的RAPD标记的检测结果是相似的,然而由微卫星标记获得的种群内和种群间的遗传距离均大于RAPD,说明微卫星标记比RAPD标记显示出更高的个体多态性。     

Environmental pressure rather than ongoing hybridization is responsible for an altitudinal cline in the morphologies of two oaks

在相关类群之间的接触区,表型变异可能源于遗传和/或环境梯度。本研究旨在阐明两种栎属植物[Quercus crispula (QCC)和 Q. mongolicoides (QCM)],在其接触区沿海拔梯度形成叶片形态表型变异的原因。对于源自接触区48个个体和QCC和QCM的每个参照 种群24个个体样本,我们测定其6种叶片形态特征,同时记录13个核微卫星位点的基因型。我们通过构建模型解释表型变异(叶片形态)与环境(海拔)和遗传(参照种群世系)梯度的关系。研究结果表明,形态和遗传标记均能较好地区分参照种群中的两个品种。我们能够确认形态和遗传标记的作用。接触区种群内的个体具有略偏向QCM分支的中间世系,其形态分布与参照种群中两个变种的形态分布重叠。海拔会显著影响叶片形态性状,而遗传对叶片形态性状无显著影响。接触区种群的世系和种间杂合性分布与F₂或后代杂交种中的分布相似。这些结果表明,在两种栎属植物QCC和QCM之间的接触区,并没有发生杂交,但环境压力通过表型可塑性和/或功能基因的变异,导致了其在形态性状上的海拔梯度效应。     

异源四倍体鲫鲤、三倍体湘云鲫和它们父母本线粒体DNA 12S rRNA基因遗传变异的分析

采用质粒克隆测序方法,获得了异源四倍体鲫鲤5个个体、异源四倍体鲫鲤雌核发育二倍体后代2个个体、三倍体湘云鲫2个个体及红鲫、湘江野鲤和日本白鲫各1个个体的线粒体DNA 12S rRNA基因的全序列。经对比发现,异源四倍体5个个体共享2种单元型,异源四倍体鲫鲤雌核发育二倍体后代2个个体、三倍体湘云鲫2个个体以及红鲫、湘江野鲤和日本白鲫各1个个体分别共享1种单元型。用MEGA 1.0 软件分析了它们的碱基组成和核苷酸序列差异,用邻接法构建系统进化树。它们间的序列同源性在95%~99%之间,异源四倍体鲫鲤、三倍体湘云鲫和它们母本（分别为红鲫和日本白鲫）之间的序列同源性大于异源四倍体鲫鲤、三倍体湘云鲫和它们父本（分别为湘江野鲤和异源四倍体鲫鲤）之间的序列同源性,结果表明：异源四倍体鲫鲤和三倍体湘云鲫在线粒体DNA 12S rRNA基因上具有母性遗传特征。本研究另一值得注意地方的是异源四倍体鲫鲤经过9代(F3-F11)繁殖后,在5个个体中发现了2种单元型,说明在四倍体基因库中存在遗传多样性,为四倍体基因库的繁殖、保护和种群复壮提供了一些有价值的信息。     

种群微卫星DNA分析中样本量对各种遗传多样性度量指标的影响

我们以中国飞蝗种群的微卫星遗传分析数据为例 ,评估了取样对种群遗传多样性指标的影响 ,结果显示 :样本大小与所观测到的每位点等位基因数、平均等位基因数及基因丰富度指数均呈显著正相关 ,而与期望杂合度无显著相关 ;微卫星位点多态性的高低直接影响所观测到的种群基因丰富度及其检测所需的样本量 ;对大多数种群遗传和分子生态学研究而言 ,30 - 5 0个个体是微卫星DNA分析所需要的最小样本量。基因丰富度经过稀疏法或多次随机抽样法校正后 ,可适用于瓶颈效应等种群历史数量变动的检测。另外 ,在研究中 ,还应避免采集时间的不同及样本的性比构成所可能造成的对种群遗传结构的影响     

伊洛河马口鱼遗传差异及其种群分化研究

研究利用细胞色素b(Cyt b)基因分析了采自于伊洛河的48个马口鱼(Opsariichthys bidens)个体间的遗传距离, 并构建其系统发育关系。分析结果显示, 48个个体聚为两个支持率为100%的分支, 分支间没有共享单倍型。每个分支的样本覆盖了所有的采样点, 分支内个体间的平均遗传距离为0.2%, 而分支间的遗传距离为3.1%。微卫星分析结果显示, 99.88%的遗传差异来自于种群内个体间, 种群间的差异只占了0.12%, 两个分支种群并没有发生显著的遗传分化(F_st=0.0012, P=1)。以δ13C和δ15N构建了两个分支的生态位, 结果显示, 伊洛河马口鱼的两个分支的营养生态位没有发生分离。基于线粒体Cyt b基因的遗传分歧, 伊洛河马口鱼的两个分支可能代表不同的物种。但它们在种群遗传结构上并没有发生显著的种群分化, 个体间亲缘关系树与系统发育树的分歧暗示种群间不存在生殖隔离, 营养生态位也没有分离。研究结果并不符合隐存种的解释, 伊洛河马口鱼两个分支间线粒体DNA的遗传差异可能源自于祖先种群或者种间杂交。     

四川省二化螟不同地理种群遗传多态性的差异分析

【目的】为了解四川省二化螟Chilo suppressalis (Walker)不同地理种群的遗传结构,分析各个种群间的亲缘关系,为区域治理对策提供新的依据。【方法】通过测定四川省17个市县二化螟样本的线粒体COⅡ基因和核糖体ITS基因,利用MEGA软件分析二化螟不同地理种群的基因遗传多样性,以获取样本群体遗传多样性信息。【结果】对114条幼虫线粒体COⅡ基因序列分析发现,在500 bp的区段中共有147个位点存在多态性,包含33个单倍型;川东地区和川西地区二化螟种群的单倍型多样度分别为0.703 83和0.802 26;系统发育树显示,除眉山-1-1种群之外,其他二化螟地理种群聚合为一个大分支。而对同批二化螟核糖体ITS基因序列分析结果表明,在533 bp的区段中存在299个位点多态性,有92个单倍型;川东地区和川西地区二化螟种群的单倍型多样度分别为0.967 48和0.975 71;在系统发育树中,犍为种群聚合为一支,其余种群聚合为一支。【结论】川西地区二化螟线粒体COⅡ基因和核糖体ITS基因多态性比川东地区样本丰富。地理种群之间的遗传分化与分布之间的相关性不大,这可能与种群本身差异相差不大相关。     

食蟹猴微卫星DNA标记遗传监测及多态性分析

目的研究国内食蟹猴种群的遗传背景特性,建立食蟹猴种群遗传质量监测方法。方法采用微卫星DNA遗传标记技术对50只食蟹猴种群个体进行遗传质量监测及DNA多态性分析。结果从100个微卫星DNA位点中筛选出20个多态性高的位点,其食蟹猴种群个体的等位基因数目为5-10条,个体间均呈现高度的多态性;其观察等位基因数（Na）为5.0～10.0,有效等位基因数（Ne）为4.6118～8.3404,基因多样性（H）为0.7832～0.8801和香隆信息指数（I）为1.5651～2.1592。结论本实验有效地分析了食蟹猴种群的遗传多态性,为今后筛选特异性微卫星位点来建立食蟹猴种群遗传质量监测方法提供了理论依据。     

基于粪便DNA的马鹿种群数量和性比

为分析黑龙江省完达山林区马鹿种群生存状态,制定科学有效地保护措施,从分子水平研究了种群数量和性比。2006、2007两年冬季跟踪马鹿足迹链,于五泡林场共搜集210份粪便,以成功提取DNA的167份作为分析样本。通过多态性较高的7个微卫星位点进行了基因分型分析,显示167份粪便DNA分属66只个体。基于非损伤性标志重捕法,统计出林场内马鹿数量2a平均47(39—60)只,密度0.302(0.251—0.386)只/km2,与2002年大样方法调查结果相比有减无增。SRY基因性别鉴定显示,种群雌雄性比1.00∶2.00(22♀,44♂),存在较多雄性个体,分析认为偷猎是导致性比失衡的最主要原因。数量的持续下降和性比失衡提示完达山林区马鹿种群数量的恢复需要更好地保护工作。     

长江流域■种群遗传多样性和遗传结构分析

鱼类群体遗传学研究主要集中在经济鱼类或濒危物种,然而一些经济价值较低的物种的遗传结构却甚少关注。因此,研究选择了经济价值较低的■(Hemiculter leucisculus),共计323尾个体分别来自13个长江流域及其附属湖泊的自然群体。通过扩增线粒体DNA Cytb基因序列片段(1100 bp),以探讨■种群遗传结构和遗传多样性。遗传多样性分析呈现出高单倍型多样性和高核苷酸多样性的模式,表明该种群在长江流域较为稳定。另外,基于线粒体细胞色素b基因的系统发育分析,显示■有5个线粒体谱系(谱系A-F)组成。中性检验和核苷酸错配分布分析均显示谱系A、B、E、F曾经历过种群扩张,并且呈现从上游向中游扩张的规律。谱系间较高且显著的遗传分化指数和显著的系统进化关系,均表明谱系A-F之间存在明显的遗传分化,暗示长江流域可能至少存在4个不同线粒体DNA水平上的种。■种群的遗传结构和多样性可能受到了长江流域特定格局的影响。     

东北梅花鹿野生种群分布与 遗传变异的分子鉴定

梅花鹿东北亚种(Cervus nippon hortulorum)曾被认为已野外灭绝,近年来在黑龙江东南部和吉林东部临近边境地区发现少量分布,其生境隔离、面积狭小,破碎化严重。亟需对其种群的遗传变化,特别是遗传多样性和近交衰退等种群遗传信息开展进一步评价,增强保护与管理的针对性。本研究在大、小兴安岭和长白山设计9个重点研究区域,共收集673份疑似梅花鹿粪样样本。首先基于线粒体DNA Cyt b基因测序技术开展物种鉴定,并对鉴定为梅花鹿的阳性样本利用微卫星技术进行个体识别。结果证实,东北梅花鹿仅在老爷岭东部山脉有分布,106份梅花鹿粪便DNA中识别出33只个体(穆棱保护区20只,老爷岭保护区13只)。33个Cyt b基因序列共检测出6个变异位点和5个单倍型,单倍型多样性指数(Hd)为0.621,核苷酸多样性指数(Pi)为0.006 7;微卫星检出种群平均等位基因数(Na)7.1个,观测杂合度(Ho)0.604,期望杂合度(He)0.712,固定系数(Fis)0.152。结果表明,东北梅花鹿种群遗传多样性丰富,但也存在一定程度的杂合度不足和近亲繁殖;种群近期经历了瓶颈效应,未发生种群扩张;群体间无遗传分化,可作为一个管理单元加以保护。建议,对东北梅花鹿稀有单倍型个体重点监测和保护,恰当时期考虑圈养种群野外放归,以提高野外个体间基因交流和快速种群恢复。     

Gene flow from multiple sources maintains high genetic diversity and stable population history of Common Moorhen Gallinula chloropus in China

In this study, we used mitochondrial control sequences and microsatellite data from 231 Common Moorhen Gallinula chloropus individuals sampled from 19 sites in China to analyse their genetic structure and evolutionary history. High genetic diversity was found for all populations, although microsatellite analysis showed that the genetic diversity in non‐migratory populations was significantly higher than in migratory populations. High gene flow occurred between neighbouring populations, although long‐distance gene flow also occurred. The Huazhong population was the single greatest genetic source for other populations. High gene flow probably led to the shallow genetic structure that we observed. Demographic expansion was found in migratory populations, non‐migratory populations and with all individuals combined. The expansion time for all populations combined was estimated to be 221 000 years ago. The Common Moorhen population grew rapidly during the interglacial before the last glacial maximum (LGM), then remained generally stable from the LGM to the present.     

应用SRAP标记分析福瑞鲤及其原始亲本的遗传结构

摘要：应用SRAP分子标记对建鲤（Cyprinus carpio var. jian）、黄河鲤（C.c.haematopterus）和福瑞鲤（FFRC Strain Common Carp,C.carpio）进行遗传结构分析。结果显示,筛选出的10个多态性较好的引物组合共扩增出110个位点,其中多态性位点92个,平均多...     

Low genotyping error rates in non-invasively collected samples from roe deer of the Bavarian Forest National Park

Genetic wildlife monitoring is increasingly carried out on the basis of non-invasively collected samples, whereby the most commonly used DNA sources are skin appendages (hairs, feathers) and faeces. In order to guide decisions regarding future adequate ways to monitor the roe deer (Capreolus capreolus) population of the Bavarian Forest National Park in Germany, we tested these two different types of DNA source materials to compare their suitability for genetic monitoring. We determined the haplotypes (d-loop) of 19 roe deer and genotyped each individual (tissue, hairs, faeces) across 12 microsatellite loci. The amount of missing and erroneous microsatellite alleles obtained from hair and faeces samples, respectively, was estimated based on comparisons with the corresponding tissue sample control. We observed no missing alleles in hair samples, but in fecal samples PCR failed in 30 out of 228 instances (19 individuals x 12 loci), corresponding to a frequency of missing alleles of 13.2% across all loci and individuals. In genotypes generated from hairs erroneous alleles were detected in 2 out of 228 instances (0.9%), while genotypes retrieved from fecal samples displayed erroneous alleles in 6 out of 198 remaining instances (3%). We conclude that both hair and fecal samples are generally well suited for genetic roe deer monitoring, but that fecal sample based analyses require a larger sample size to account for higher PCR failure rates.     

Sampling for Microsatellite-Based Population Genetic Studies: 25 to 30 Individuals per Population Is Enough to Accurately Estimate Allele Frequencies

One of the most common questions asked before starting a new population genetic study using microsatellite allele frequencies is “how many individuals do I need to sample from each population?” This question has previously been answered by addressing how many individuals are needed to detect all of the alleles present in a population (i.e. rarefaction based analyses). However, we argue that obtaining accurate allele frequencies and accurate estimates of diversity are much more important than detecting all of the alleles, given that very rare alleles (i.e. new mutations) are not very informative for assessing genetic diversity within a population or genetic structure among populations. Here we present a comparison of allele frequencies, expected heterozygosities and genetic distances between real and simulated populations by randomly subsampling 5–100 individuals from four empirical microsatellite genotype datasets (Formica lugubris, Sciurus vulgaris, Thalassarche melanophris, and Himantopus novaezelandia) to create 100 replicate datasets at each sample size. Despite differences in taxon (two birds, one mammal, one insect), population size, number of loci and polymorphism across loci, the degree of differences between simulated and empirical dataset allele frequencies, expected heterozygosities and pairwise F_ST values were almost identical among the four datasets at each sample size. Variability in allele frequency and expected heterozygosity among replicates decreased with increasing sample size, but these decreases were minimal above sample sizes of 25 to 30. Therefore, there appears to be little benefit in sampling more than 25 to 30 individuals per population for population genetic studies based on microsatellite allele frequencies.     

Detecting population structure in a high gene-flow species,Atlantic herring (Clupea harengus): direct,simultaneous evaluation of neutral vs putatively selected loci

In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species.     

Unique and isolated: population structure has implications for management of the endangered New Zealand sea lion

Female otariids (eared seals) frequently display strong levels of philopatry, a behaviour that has the potential to influence population structure, particularly at the mitochondrial level. Conversely, male otariids often move between breeding colonies, likely facilitating nuclear gene flow between colonies. Such gender-specific movements have the potential to influence species population structure. Here we investigate the genetic population structure of the endangered New Zealand (NZ) sea lion, using nuclear (microsatellite) and mitochondrial molecular markers, with the intention to better inform conservation through identification of management units for the species. The strong levels of female philopatry in this species have potential to lead to population structure at the mitochondrial loci. In contrast, weak or no population structure is expected across nuclear loci. NZ sea lions were sampled from the main breeding areas across the species’ current distribution (three Auckland Islands sites, two Campbell Island sites, one Stewart Island site and one Otago Peninsula site). Individuals were screened for microsatellite (n?=?271; 16 loci) and mitochondrial (n?=?56; 1027 bp D-loop and 1189 bp cytb). Despite a small (c. 9880 individuals) population size, moderate levels of microsatellite variation are observed in the NZ sea lions, in contrast to low levels of mitochondrial genetic variation. Results from mitochondrial DNA analyses revealed no population structure, suggesting that the strong level of female philopatry in NZ sea lions alone is not sufficient to maintain genetic population structure. Due to the frequent male movements between breeding colonies, no population structure was detected across the nuclear loci either. The absence of genetic structure suggests that, from a genetic perspective, NZ sea lions can be considered to be a single population. Despite this, the differing impacts of threats (e.g. fisheries by-catch) to each individual breeding colony must also be taken into consideration when defining management units for this endangered species.     

Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans)

Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within approximately 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single-copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter-ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neu varied by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions of FST are expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex-biased dispersal. Furthermore, divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci.     

Population differentiation in the Pacific white-sided dolphin Lagenorhynchus obliquidens inferred from mitochondrial DNA and microsatellite analyses

We investigated genetic diversity and differentiation of the Pacific white-sided dolphin (Lagenorhynchus obliquidens) in Japanese coastal waters and offshore North Pacific by analyzing mitochondrial DNA and nuclear microsatellite variation. A total of 519 bp of the mitochondrial control region was sequenced and five microsatellite locus were genotyped for 59 individuals. A high level of haplotypic diversity (h=96.1%), moderate level of nucleotide diversity (pi=1.65%) and average expected heterozygosity (HE=0.66-0.76) were within an extent of those reported for other odontocetes. Consistent genetic difference between the samples from Japanese coastal Pacific-Sea of Japan and offshore North Pacific was indicated by analyses of molecular variance (AMOVAs) based on mtDNA and microsatellite variations, comparison of genetic variabilities, and geographical distributions of mtDNA haplotypes and microsatellite alleles. This result suggests that Pacific white-sided dolphins in each of the above two areas belong to different populations between which gene flow has been severely restricted. The low genetic diversity and mtDNA genealogy of the population in Japanese coastal waters suggest that it originated from a small population that colonized the Sea of Japan or that experienced population reduction when this Sea was isolated from the North Pacific during a glacial period in the Late Pleistocene.     

Genetic analysis of southern African gemsbok (Oryx gazella) reveals high variability, distinct lineages and strong divergence from the East African Oryx beisa

We carried out a population genetic analysis of five southern African gemsbok (Oryx gazella) populations based on 530 bp of the mitochondrial control region and ten microsatellites in 75 individuals. Both markers show the high variability often observed in African bovids. Three of the populations which can be traced back to very small founding or current sizes do not show any signs of reduced variability compared to the remaining populations. The mitochondrial haplotypes form three distinct lineages which most likely originated in the Pleistocene when climate fluctuations led to periodical reduction and spreading of gemsbok habitat and which, today, are found throughout the distribution range. Bayesian microsatellite analyses yielded two groups, suggesting a more recent geographical differentiation following the admixture of the mtDNA lineages. Combining our sequences with available published data of the remaining oryx species allowed for a direct molecular comparison of O. gazella and O. beisa which have sometimes been considered a single species. The average genetic divergence between haplotypes from the two taxa was very high (39.9%), supporting their classification into two different species.     

Genetic Diversity in Endangered Guizhou Snub-Nosed Monkeys (Rhinopithecus brelichi): Contrasting Results from Microsatellite and Mitochondrial DNA Data

To evaluate the conservation status of a species or population it is necessary to gain insight into its ecological requirements, reproduction, genetic population structure, and overall genetic diversity. In our study we examined the genetic diversity of Rhinopithecus brelichi by analyzing microsatellite data and compared them with already existing data derived from mitochondrial DNA, which revealed that R. brelichi exhibits the lowest mitochondrial diversity of all so far studied Rhinopithecus species. In contrast, the genetic diversity of nuclear DNA is high and comparable to other Rhinopithecus species, i.e. the examined microsatellite loci are similarly highly polymorphic as in other species of the genus. An explanation for these differences in mitochondrial and nuclear genetic diversity could be a male biased dispersal. Females most likely stay within their natal band and males migrate between bands, thus mitochondrial DNA will not be exchanged between bands but nuclear DNA via males. A Bayesian Skyline Plot based on mitochondrial DNA sequences shows a strong decrease of the female effective population size (N_ef) starting about 3,500 to 4,000 years ago, which concurs with the increasing human population in the area and respective expansion of agriculture. Given that we found no indication for a loss of nuclear DNA diversity in R. brelichi it seems that this factor does not represent the most prominent conservation threat for the long-term survival of the species. Conservation efforts should therefore focus more on immediate threats such as development of tourism and habitat destruction.