不同居群红砂的遗传多样性分析

为了探究不同居群红砂(Reaumuria soogorica)的遗传多样性水平及居群遗传结构。本研究运用SSR分子标记技术对来源于内蒙古、宁夏、甘肃16个不同居群的299份红砂材料进行遗传多样性分析。结果表明11对引物共扩增出67个等位基因,扩增等位基因多态率为83.58%,多态信息含量(Polymorphism information content, PIC)为0.396;居群的等位基因数(Allele number, Na)和有效等位基因数(Effective number of alleles, Ne)为3.735,2.221;香农信息指数(Shannon information index, I)为0.763;居群间遗传分化系数(Fixation index, Fst)为0.041～0.210,平均值为0.088。AMOVA结果表明,居群间的遗传差异仅占变异总来源的5.8%。本研究得出结论红砂的基因多态性为中度,等位基因不均匀的分布在染色体上。观测杂合度和固定指数说明居群内杂合度缺失,纯合体过量。Fst指数表明居群间分化程度较低,且红砂的遗传变异主要来自源于个体内DNA序列的...     

Genetic analysis of Mexican Criollo cattle populations

The objective of this study was to evaluate the genetic structure of Mexican Criollo cattle populations using microsatellite genetic markers. DNA samples were collected from 168 animals from four Mexican Criollo cattle populations, geographically isolated in remote areas of Sierra Madre Occidental (West Highlands). Also were included samples from two breeds with Iberian origin: the fighting bull (n = 24) and the milking central American Criollo (n = 24) and one Asiatic breed: Guzerat (n = 32). Genetic analysis consisted of the estimation of the genetic diversity in each population by the allele number and the average expected heterozygosity found in nine microsatellite loci. Furthermore, genetic relationships among the populations were defined by their genetic distances. Our data shows that Mexican cattle populations have a relatively high level of genetic diversity based either on the mean number of alleles (10.2-13.6) and on the expected heterozygosity (0.71-0.85). The degree of observed homozygosity within the Criollo populations was remarkable and probably caused by inbreeding (reduced effective population size) possibly due to reproductive structure within populations. Our data shows that considerable genetic differentiation has been occurred among the Criollo cattle populations in different regions of Mexico.     

基于小尺度高原鼢鼠种群遗传结构研究

高原鼢鼠是青藏高原特有的地下啮齿动物,研究其种群遗传结构对于了解扩散、基因交流等方面具有重要意义。本研究利用微卫星分子标记技术,分析祁连山东段高寒草甸区小尺度下4个高原鼢鼠种群的遗传多样性和遗传结构特点。结果表明:1)4个种群有效等位基因(Ne)为83.6,种群平均观测杂合度(Ho)最高为0.32,平均期望杂合度(He)最高为0.50,平均多态信息含量(PIC)为0.40,遗传多态性处于中等水平。2)种群遗传结构推导分析结果为 4 个种群被分成 2 组,MYT(马营滩种群)为一组,XNG(下南泥沟种群)、MYR(马营河东边种群)、MYL(马营河西边种群)为一组。3)试验区高原鼢鼠种群间近交系数(F_ST)都大于0.05,种群间的基因流值(N_m)都小于1,特殊岛状栖息地限制了高原鼢鼠种群基因流,河流和公路可能对种群内和种群间个体交流有阻碍作用。     

Genetic diversity of Chinese domestic goat based on the mitochondrial DNA sequence variation

The aim of this study was to characterize the genetic diversity of domestic goat in China. For this purpose, we determined the sequence of the mitochondrial DNA (mtDNA) control region in 72 individuals of the Yangtze River delta white goat, and reanalysed 723 published samples from 31 breeds/populations across China. All goat haplotypes were classified into four haplogroups (A–D) previously described. The phylogenetic pattern that emerged from the mtDNA control region sequence was confirmed by the analysis of the entire cytochrome b sequence of eight goats representative of the four haplogroups. It appeared that in Chinese domestic goat, haplogroups A and B were dominant and distributed in nearly all breeds/populations, while haplogroups C and D were only found in seven breeds/populations. Four breeds/populations contained all four haplogroups. When grouping the breeds/populations into five geographic groups based on their geographic distributions and ecological conditions, the southern pasturing area had the highest diversity whereas the northern farming area had the lowest diversity. 84.29% and 11.37% of the genetic variation were distributed within breeds and among breeds within the ecologically geographical areas, respectively; only 4% of genetic variation was observed among the five geographic areas. We speculate that the traditional seasonal pastoralism, the annual long-distance migrations that occurred in the past, and the commercial trade would account for the observed pattern by having favoured gene flows.     

西藏光核桃自然居群遗传多样性的SRAP分析

利用SRAP标记对来自西藏境内的4个光核桃自然居群的遗传多样性和群体遗传结构进行了分析和评价。选用20对引物对4个居群的70份材料进行扩增,检测到338个多态位点。在居群水平上,多态位点百分率为63.96%,Nei’s基因多样性和Shannon’s信息指数分别为0.194 3和0.295 5。在物种水平上,多态位点百分率为89.89%,Nei’s基因多样性和Shannon’s信息指数分别为0.246 0和0.383 9。居群间的遗传分化系数为0.170 9,居群间的基因流为1.213 0。UPGMA聚类图中,70个个体未按4个居群各自聚在一起。结果表明,光核桃遗传多样性水平较高,居群间遗传分化较小,居群间的基因交流程度较高。     

蒙古冰草遗传多样性的等位酶分析

采用聚丙烯酰胺凝胶电泳技术检测了内蒙古中东部地区蒙古冰草6个天然居群和2个栽培品种的遗传多样性和居群结构，12个酶位点的多态位点百分率为67.71%，基因多样性指数（He)为0.285，显示出了较高的遗传多样性，从遗传多样性的分布格局来看，8个居群的遗传分化系数Gsr=0.129，表明在总的遗传变异中，只有12.9%的变异存在于居群间，而87.1%的变异存在于居群内，同时，6个天然居群的总基因多样度（HT=0.439)和基因分化系数（GST=0.032)也大于2个栽培品种的相应值（HT=0.423,GST=0.010)。UPGMA聚类分析的结果表明，蒙古冰草居群间的遗传分化与生态环境因子间有着密切的相关性。     

Genomic differentiation with isolation by distance along a latitudinal gradient in the spotted-leg treefrog Polypedates megacephalus

The patterns of isolation by distance (IBD) entailing increased genetic differentiation among populations have aroused extensive concerns for evolutionary biologists. Although the IBD may act on spatial processes contributing to the genetic differentiation among populations in anuran species, the factors shaping the IBD of frogs among populations in natural systems are largely unknown. Here, we studied the genetic differentiation among six populations with 24 individuals of the spotted-leg treefrog along a latitudinal gradient (1860.31 km) based on 1020 single nucleotide polymorphisms from restriction site-associated DNA sequencing. The results showed that the genetic diversity differed significantly among populations and that the insular populations had higher genetic diversity than the mainland populations. Furthermore, we also found a significant genetic differentiation among populations (F_ST = 0.277) and no sign of inbreeding (F_UNI = −0.145). The IBD was detected for all populations, and a higher degree of the IBD was indicated when controlling for the effects of the isolation between Hainan and mainland populations caused by the Qiongzhou Strait. Our findings suggest that the form of the Qiongzhou Strait plays a key role in shaping the genetic diversity and population differentiation in treefrogs.     

利用微卫星遗传标记评估5个西藏牦牛群体遗传多样性及群体结构

【目的】 评估当前西藏主要牦牛群体遗传多样性，梳理不同地区群体间遗传结构，明确西藏5个牦牛群体（阿里牦牛、斯布牦牛、娘亚牦牛、类乌齐牦牛和帕里牦牛）的保种情况和种群间系统发育关系。【方法】 利用13个微卫星标记（SSR）对5个牦牛群体共计195个个体进行基因分型，并对各群体的等位基因数量、基因杂合度、多态信息含量及群体间遗传距离等遗传参数进行评估。【结果】 阿里牦牛群体等位基因数最多（6.43），类乌齐牦牛等位基因数最少（5.00）；观测杂合度范围为0.5311（娘亚牦牛）~0.5995（类乌齐牦牛）。各群体内偏离Hardy-Weinberg平衡的位点数为5（类乌齐牦牛）~9（阿里牦牛）个；群体内近交系数最高为0.172（阿里牦牛），且4个群体（阿里牦牛、娘亚牦牛、斯布牦牛和帕里牦牛）存在显著近交风险（P<0.05）。从遗传结构来看，所有群体间均为显著遗传分歧（P<0.05），STRUCTURE分析结果显示，5个牦牛群体划分为3个簇，其中阿里牦牛较其他牦牛群体具有更为丰富的遗传背景。系统发育树结果表明，不同群体间系统发育关系相对独立，且与种群栖息地分布不一致。主坐标分析（PCoA）结果显示，不同群体间部分个体存在较近亲缘关系，表明不同群体间存在遗传物质交流。【结论】 5个西藏牦牛群体具有丰富的遗传多样性水平，且种群系统发育关系相对独立，但多数群体存在群体事件风险。本研究不仅有助于明确西藏牦牛地方种群遗传多样性水平，同时可为今后的保种策略提升提供理论参考。     

冰草属植物醇溶蛋白遗传分析与评价

利用A-PAGE酸性聚丙烯酰胺凝胶电泳技术,对采自内蒙古、河北、山西、宁夏、甘肃和吉林6省,经引种栽培筛选出的5种12个冰草属植物居群醇溶蛋白进行遗传结构分析和评价研究。结果表明,供试材料总计电泳出了37条相对迁移率不同的醇溶蛋白带纹,在α、β、γ、ω区分别有5、15、10和7条,4条谱带为稳定表达带,多态率89.19%。不同物种居群间蛋白多样性丰富程度不同,冰草醇溶蛋白遗传多样性指数最丰富。其次为蒙古冰草,遗传多样性相对最低的为细茎冰草。种间遗传分化占冰草属物种遗传多样性的78.70%;冰草地区间的遗传多样性占总体遗传多样性的73.31%。Jaccard系数为0.498时聚为4类,同种不同材料基本能够聚在一起,但有交叉现象;地理分布相近的物种聚类在一起。     

四川三个藏猪群体的微卫星遗传多样性分析

本研究利用已开发的18对微卫星引物,分析了四川境内阿坝、稻城和德格三个藏猪群体共143个个体18条常染色体上的微卫星遗传多样性。结果表明:阿坝藏猪群体多态信息含量和观测杂合度比其他两群低,群体遗传变异较小;三个群体Nei氏标准遗传距离均在0.6以上,平均基因流值大于1,表明三个群体各有特点,群内基因交流频繁。     

Genetic diversity decreases as population density declines: Implications of temporal variation in mitochondrial haplotype frequencies in a natural population of Tscherskia triton

Although the spatial genetic differentiation that occurs in animal populations has been extensively studied, information on temporal variations in genetic structure and diversity is still lacking, especially for animals with oscillating populations. In the present study, we used the mtDNA D‐loop sequence to assess the temporal genetic variation in samples from six successive years for the greater long‐tailed hamster, Tscherskia triton. Sampling was carried out between 1998 and 2003 in cropland on the North China Plain, China. A total of 108 individuals were analyzed. The temporal samples showed a high level of genetic diversity. Substantial genetic changes in haplotype frequencies over time were detected for the hamster population. Random genetic drift and migration are likely to be the major factors responsible for the observed temporal pattern. The genetic diversity of the hamster population was higher in years with higher population density, and lower in years with lower population density. The result supports our hypothesis that genetic diversity decreases when population density declines in animals whose population oscillates greatly between years. The combined effects of inbreeding and genetic drift caused by reproduction, dispersal and population size might play important roles in the observed changes in genetic structure and diversity between years.     

羊草叶绿体非编码区多态性标记筛选及群体遗传多样性

为筛选多态性丰富的羊草叶绿体非编码区片段,本研究以9个不同地理位置的羊草居群为材料,通过对12个叶绿体非编码区DNA片段测序及其序列间变异分析试图从中找出有遗传差异的叶绿体DNA(cpDNA)片段,并利用有多态性的cpDNA片段进行遗传多样性分析。结果表明,序列ndhF-rpl32、trnL-trnF、trnC-ycf6、aptI-aptH具有比较丰富的变异,可作为下一步研究野生羊草群体遗传学和谱系地理学较为理想的分子标记。在37个羊草个体4条非编码区片段的合并序列中,共检测到15种单倍型,单倍型多态性(Hd)为0.928,核苷酸多态性(Pi)为0.00101;遗传分化指数(Fst)为0.58884,基因流(Nm)为0.17,基因流较小;中性检验Tajima’s D(-1.08542)和Fu’s Fs(-5.301)均为负值,且差异不显著(P>0.10),推测羊草遵循中性进化理论,可能经历过种群扩张;AMOVA结果显示,65%的分子变异出现在居群间,35%出现在居群内;Mantel检验得到,遗传距离与地理距离具有显著相关性(r=0.449,P<0.05);居群分化值Nst 0.386(0.1865)大于Gst 0.234(0.1506),差异显著(P<0.05),表明羊草居群存在分子谱系地理结构。通过系统发育树分析得到,羊草15个单倍型分为两大分支,H2和H10聚为一支,它们与别的居群个体亲缘关系较远,其余单倍型聚为另一支;单倍型网络图显示,H2和H12、H10和H12亲缘关系较远,与系统发育树分析结果基本一致。本研究为羊草的种质资源保护、谱系地理学研究等工作奠定了基础。     

PCR-based coprodiagnostic tools reveal dogs as reservoirs of zoonotic ancylostomiasis caused by Ancylostoma ceylanicum in temple communities in Bangkok

A survey of gastrointestinal parasites of dogs and humans from temple communities in Bangkok revealed that 58% of dogs and 3.4% of humans, among those sampled, were infected with hookworms utilising faecal flotation techniques and microscopy. A previously established polymerase chain reaction (PCR)-RFLP approach was utilised to determine the species of hookworms infecting dogs found positive for hookworm eggs. Single infections with Ancylostoma ceylanicum and Ancylostoma caninum were recorded in 77% and 9% of hookworm positive dogs, respectively and mixed infections with both species of Ancylostoma were recorded in 14% of dogs. A single-step PCR for the multiplex detection of Ancylostoma species and Necator americanus DNA in human faeces was developed and applied to characterise the species of hookworms in microscopy positive individuals. Single infection with N. americanus was recorded in five and A.ceylanicum infection in two, out of seven individuals positive for hookworm. This study demonstrates that humans are at risk of acquiring infection with A. ceylanicum in communities where this species of hookworm is endemic in dogs.     

Genetic structure of wild and domesticated grasscutters (Thryonomys swinderianus) from south-western Nigeria

Grasscutter (Thryonomys swinderianus) is a large rodent distributed across sub-Saharan Africa that is highly valued as a source of protein. There has been little effort to evaluate the genetic structure of grasscutters despite long-term harvesting pressure and over 40 years of grasscutter domestication in West Africa. Our objectives were to quantify the genetic structure of wild grasscutters, and to compare genetic variation from wild samples to those from various farmed samples within south-western Nigeria. We genotyped 145 wild and 88 domesticated individuals at 11 microsatellite loci and present results quantifying regional genetic structuring and the relative patterns of diversity among wild and domesticated grasscutter populations. Our data reflect high differentiation between wild and domesticated grasscutters, and significantly greater allelic richness and gene diversity in the former. Despite this, domesticated populations appear to have similar levels of observed heterozygosity and comparable levels of differentiation among domesticated samples relative to wild samples. This may be the result of high turnover within captive colonies, or frequent infusion of new animals. More detailed molecular and quantitative genetic studies are recommended on this species to be able to understand their natural variation, degree of connectivity and to improve strategies for domestication.     

Seroprevalence and risk factors associated with Neospora caninum infection in different dog populations in Spain

In this study, Neospora caninum seroprevalence and some associated risk factors were investigated in four different dog populations in Spain. N. caninum seropositivity was significantly higher in farm dogs (51%, 51/100) (P<0.001) and lower in household dogs (2.9%, 3/102) (P<0.0001). The seroprevalence in hunting (23%, 23/100) and stray (24.5%, 23/94) dogs was moderate, and no significant differences were observed between these two populations (P>0.05). A significantly higher number of dogs showed titres of 1:50-1:100 (68%, 68/100) than >or=1:200 (33%, 33/100) titres (P<0.0001). N. caninum antibodies were more often detected in mixed breed than pure breed dogs (P<0.01), but when data were stratified by dog type a significant association was not found (P>0.05). A significantly higher prevalence of N. caninum was observed in dogs over 1 year old (P<0.01), indicating that horizontal transmission may be the most important route of infection. The presence of N. caninum antibodies was significantly more frequent in Leishmania infantum-seropositive hunting (P<0.05) and stray dogs (P<0.00001). This study confirms that farm, stray and hunting dogs can be considered at-risk dog populations for N. caninum infection in Spain.     

Can low densities of carnivores result in genetic depletion? An investigation within French polecat populations

Carnivores as top predators are commonly found in relatively low densities even in optimal habitats. Despite a lack of empirical studies, it could be suspected that long‐term low density could result in genetic depletion. The genetic structure of European polecat Mustela putorius natural populations was investigated by allozyme electrophoresis in five distinct areas. Density estimates significantly differed among sites from 0.17 to 0.83 individuals/km² with an average of 0.56 individuals per km², resulting in a scattered distribution. Genetic structure varied among distinct populations both in number of polymorphic loci and heterozygosity. Polecats from Brittany revealed a very low observed heterozygosity (H_O = 0.028) whereas mean heterozygosity reached H_O = 0.072 in Brière. That the lowest heterozygosity levels and highest inbreeding coefficient F_IS were significantly associated with the lowest densities suggests that low densities may affect populations of carnivores. Both the loss of polymorphic loci and the reduction in heterozygosity rates suggest a density‐dependent effect and population density can be arguably regarded as a factor affecting genetic diversity in top carnivores.     

利用微卫星分析康西草原马匹种群的遗传多样性和群体结构

旨在揭示康西草原马匹的品种来源以及群体遗传结构。本研究采集了当地60匹健康状况良好、体重适中、3～6岁之间不区分公母马的血液样品,试验分为6个种群并以纯血马等4个国外马品种、1个我国地方马品种作为对照， 通过设计引物并提取基因组DNA结合微卫星扩增法对染色体上12个微卫星位点的等位基因进行检测，并对各种群遗传多样性参数、群体分化指数、瓶颈效应以及群体结构进行分析。试验按照群体个数为依据分为6组，每组1个重复，每个重复以该组样本量为标准。分析6个种群马的遗传参数结果表明，其中共检测到221个等位基因,平均Shannon指数为1.691；有效等位基因数(Ne)为3.649～5.397；期望杂合度(He)为0.681～0.798；观测杂合度(Ho)为0.632～0.780；平均多态信息含量(PIC)为0.643～0.772。这些结果表明，6个群体都具有很高的遗传多样性。通过微卫星DNA位点的连锁不平衡及哈迪-温伯格平衡分析发现， 大多数位点的P值都大于校正值(P=0.006 5)，表示较多位点都处于哈迪-温伯格及连锁平衡状态。各群体间群体分化系数(Fst)表明，群体间分化程度较低(Fst<0.15)。基于Nei’s遗传距离与地理距离之间Mantel相关性检验显示二者之间呈现正相关性(R=0.502)，但未达到显著水平(P=0.310)；各马匹种群瓶颈效应分析表明，P值极显著(P_(IAM)<0.01)说明该地区的马群体受到过瓶颈效应的影响且该马群体历史上数量有大规模的减少。通过 FCA因子分析、基于Nei’s标准遗传距离UPGMA树状图以及Structure贝叶斯聚类分析发现，该地区马种群与纯血马和温血马聚为一类，说明该种群最有可能主要来源于温血马和纯血马。这些结果揭示，康西草原地区马匹具有较高的遗传多样性，该地马群体的血统与纯血马和温血马相近，这为当地马遗传资源评估以及开发利用打下了坚实的基础。     

Evaluation of the genetic structure of sika deer (Cervus nippon) in Japan's Kanto and Tanzawa mountain areas,based on microsatellite markers

The browsing habits of sika deer (Cervus nippon) in Japan have caused serious ecological problems. Appropriate management of sika deer populations requires understanding the different genetic structures of local populations. In the present study, we used 10 microsatellite polymorphisms to explore the genetic structures of sika deer populations (162 individuals) living in the Kanto region. The expected heterozygosity of the Tanzawa mountain range population (Group I) was lower than that of the populations in the Kanto mountain areas (Group II). Our results suggest that moderate gene flow has occurred between the sika deer populations in the Kanto mountain areas (Group II), but not to or from the Tanzawa mountain range population (Group I). Also, genetic structure analysis showed that the Tanzawa population was separated from the other populations. This is probably attributable to a genetic bottleneck that developed in the Tanzawa sika deer population in the 1950s. However, we found that the Tanzawa population has since recovered from the bottleneck situation and now exhibits good genetic diversity. Our results show that it is essential to periodically evaluate the genetic structures of deer populations to develop conservation strategies appropriate to the specific structures of individual populations at any given time.     

退化梯度对克氏针茅种群遗传分化的影响

对重度退化、轻度退化和正常样地的克氏针茅种群进行RAPD研究。结果表明,3个种群扩增条带总数、多态位点比率、种群内稀有位点数、遗传多样性和基因多样性均是正常种群>轻度退化种群>重度退化种群。用Shannon指数估算3个种群的遗传多样性,其中72.39%的遗传变异存在于种群内,26.89%存在于种群间。重度退化与轻度退化种群,重度退化与正常种群间的遗传相似系数分别为0.8993和0.8159。在重度退化情况下克氏针茅种群遗传结构发生了一定的遗传分化。     

陕西省本氏针茅自然种群遗传多样性的ISSR分析

利用ISSR分子标记,对采自陕西省不同地区的5个本氏针茅(Stipa bungeana)自然种群进行遗传变异及群体遗传结构分析,旨在探讨本氏针茅遗传变异产生的分子生态机理,为其资源保护提供理论依据。在100个供试单株中,采用15条ISSR引物共扩增出223条可统计条带,其中多态性带182条,多态性位点比率为81.61%,Nei’s基因多样性(H)为0.1887,Shannon 信息指数(I)为0.2975,各种群之间存在较高的多态性。种群间的遗传变异为63.01%,种群内的遗传变异为36.99%,遗传分化系数φ_st 为0.6300,种群间的基因流(N_m)为0.1468,表明本氏针茅遗传分化程度较高,遗传变异主要分布在种群间,而种群内变异相对较小,且各种群间的基因交流非常有限。