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.     

缢蛏种群遗传多样性的周年变异分析

利用线粒体COI标记分析了福建省宁德市漳湾镇横屿村滩涂5个月份缢蛏群体(S3,S5,S7,S9,S11)的遗传结构,以期评估不同月份时期种群的遗传多样性差异。基于线粒体COI基因的结果表明,5个缢蛏群体的平均核苷酸差异数位于2.7836-3.6894之间,核苷酸多样性指数位于0.0050-0.0066之间,遗传多样性水平大致表现为S3和S5群体较高于S7和S9群体,明显高于S11群体。AMOVA分析结果显示,群体间遗传变异量占总变异的7.18%,而群体内变异达到了92.82%,说明遗传差异主要来自于群体内部。由此可见,从3月份到11月份,缢蛏群体的遗传多样性水平呈现出下降趋势,尤其是在11月份,差异最为明显。     

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。     

牦牛分子遗传多样性研究进展

遗传多样性研究可有效地揭示牦牛的遗传变异, 是牦牛群体遗传学研究的主要内容之一。自20世纪70年代以来, 人们已对牦牛的体形外貌特征、染色体核型(带型)、生理生化特性和DNA序列变异等进行了较为深入地研究。随着分子遗传学和DNA测序技术的迅猛发展, 近年来的研究主要集中在牦牛的分子遗传多样性。文章对近15年来牦牛mtDNA和核基因组分子标记及侯选基因多样性的研究现状进行了综述, 对前景进行展望, 以期为牦牛群体基因组学等研究提供依据。     

东北地区狍种群的遗传多样性研究

狍为我国重要的经济动物,并且是国家一级保护动物东北虎的主要猎物之一。因此,深入了解狍各地理单元内种群的遗传变异,可以为我们制定保护管理策略提供依据,进而使珍稀濒危物种得到有效的保护和管理。本文对88个不同狍个体(来自8个不同地点)的线粒体DNA控制区的部分序列进行了测定和群体分析,获得了463bp的片断,并检测到59个变异位点,占分析长度的7.84%,且这59个变异位点皆为碱基置换,未出现碱基插入或缺失的现象,定义了30种单倍型,核苷酸多样性平均值为0.02641,种群总体遗传多样性较高。从Tajima’sD和FuandLi’sD值的估算结果来看,这8个狍种群相对于中性进化的歧异度并没有明显的偏离(P0.1),没有明显的证据显示这8个狍种群间存在很强的平衡选择。30个单倍型整体上将东北狍种群分为3个亚群,分子变异分析表明3个亚群间基因流Nm均大于1,说明这3个狍亚群间存在着基因流。     

江苏连云港与盐城海域口虾蛄种群的遗传多样性

为了解口虾蛄野生种群的遗传多样性水平,采集了4个不同地理种群的口虾蛄44个样品,利用线粒体细胞色素c氧化酶Ⅰ亚基序列为分子标记,初步分析了口虾蛄野生群体的遗传多样性及遗传结构。研究共获得627bp的COⅠ序列,检测到27个单倍型,30个变异位点。在4个种群中,燕尾港与射阳种群、赣榆与连岛镇种群、赣榆与燕尾港种群之间存在明显的遗传分化,但在贝叶斯系统树中未形成明显的地理分化格局;4个野生种群都有高的单倍型多样性水平和相对低的核苷酸多样性水平;歧点分布及中性检验均支持口虾蛄野生种群在历史上发生快速扩张事件。     

基于粪便DNA的雪豹种群调查和遗传多样性

雪豹 (Panthera uncia) 是仅分布于亚洲高海拔山区的珍稀濒危猫科动物.本研究在印度西南部(Ladakh)、中国青海和蒙古国的南部(南Gobi)3个独立的雪豹分布区共采集109份粪便样品.应用线粒体DNA(mtDNA) cyt b基因特异性引物对109份粪便样品进行鉴定,发现有31份粪便来自雪豹,其中印度Ladakh、我国青海和蒙古国南Gobi的雪豹样品分别为17份、3份和11份.利用重新筛选设计的7对家猫(Felis catus)微卫星引物,对雪豹粪便样品进行了基因分型分析,结果发现在Ladakh和南Gobi检测到的雪豹粪便样品分别来自4只和5只不同的雪豹个体,而青海的样品则来自同一只雪豹;遗传多样性统计分析表明,蒙古国南Gobi的雪豹微卫星遗传多样性水平低于印度的Ladakh.研究结果表明了粪便DNA在雪豹种群监测和遗传多样性研究中的可行性.     

气候因素对狍种群遗传多样性的影响

采用聚合酶链式反应(PCR)技术分析测定了6个狍(Capreolus Pygargus)种群的分子遗传特征.遗传分析表明:狍迎春种群具有较低的单倍型多样性(H=0.622±0.138)和核苷酸多样性(π=0.386±0.00383),图强种群具有较高的单倍型多样性(H=0.857±0.044)和核苷酸多样(π=2.580±0.01914),Tajima'sD和Fu and Li'sD值检测结果表明这6个狍种群相对于中性进化的歧异度并没有明显的偏离(P>0.1);相关性分析表明:狍遗传多样性与纬度(r=0.770)和海拔(r=0.719)呈显著正相关,与年平均气温(r=-0.519)和无霜期(r=-0.652)呈显著负相关,与经度(r=-0.258)和年平均降水量(r=-0.205)呈显著的不相关.     

东海海域口虾蛄种群遗传多样性

为准确掌握中国沿海口虾蛄(Oratosquilla oratoria)种群遗传结构、合理开发利用其资源,采用线粒体DNA(mt DNA)细胞色素氧化酶Ⅰ(COⅠ)序列分析方法检测东海海域(庙子湖岛、南韭山、大陈岛、南麂岛)口虾蛄种群遗传多样性,并与黄渤海群体和南海群体进行比较分析(基因序列来源于Gen Bank)。经PCR扩增与测序获得100条658 bp的东海海域口虾蛄COⅠ基因序列,基于这些序列分析得到的变异位点数、单倍型数、单倍型多样性指数与核苷酸多样性指数分别为60、60、0.963±0.011和0.005 94±0.000 44,分析认为东海海域口虾蛄具有较高的单倍型多样性和较高的核苷酸多样性。单倍型分子系统树、分子方差分析及两两群体间的遗传分化系数(Fst)分析结果表明,东海海域口虾蛄遗传变异主要来自于群体内(Fst=﹣0.007 78,P0.05),各地理群体间遗传分化不显著,Fst值范围为﹣0.016 53~﹣0.009 08(P0.05),它们可能进行了一定程度的基因交流;通过与黄渤海群体及南海群体基因序列比较分析,口虾蛄东海群体、黄渤海群体与南海群体遗传变异主要来自于群体间(Fst=0.849 71,P0.01),且单倍型分子系统树存在2个显著分化的单倍型类群。东海群体与黄渤海群体间存在显著的遗传分化(Fst=0.884 58,P0.01),而与南海群体间不存在显著的遗传分化(Fst=0.020 44,P0.05),这种遗传结构模式可能与历史上的气候变化及所处海域海洋环境条件相关。建议今后对中国沿海口虾蛄资源进行开发利用时,将黄渤海群体看作一个管理单元,东海群体与南海群体看作一个管理单元。     

Allelic and genotypic diversity in long-term asexual populations of the pea aphid, Acyrthosiphon pisum in comparison with sexual populations

Many aphid species exhibit geographical variation in the mode of reproduction that ranges from cyclical parthenogenesis with a sexual phase to obligate parthenogenesis (asexual reproduction). Theoretical studies predict that organisms reproducing asexually should maintain higher allelic diversity per locus but lower genotypic diversity than organisms reproducing sexually. To corroborate this hypothesis, we evaluated genotypic and allelic diversities in the sexual and asexual populations of the pea aphid, Acyrthosiphon pisum (Harris). Microsatellite analysis revealed that populations in central Japan are asexual, whereas populations in northern Japan are obligatorily sexual. No mixed populations were detected in our study sites. Phylogenetic analysis using microsatellite data and mitochondrial cytochrome oxidase subunit I (COI) gene sequences revealed a long history of asexuality in central Japan and negated the possibility of the recent origin of the asexual populations from the sexual populations. Asexual populations exhibited much lower genotypic diversity but higher allelic richness per locus than did sexual populations. Asexual populations consisted of a few predominant clones that were considerably differentiated from one another. Sexual populations on alfalfa, an exotic plant in Japan, were most closely related to asexual populations associated with Vicia sativa L. The alfalfa-associated sexual populations harboured one COI haplotype that was included in the haplotype clade of the asexual populations. Available evidence suggests that the sexuality of the alfalfa-associated populations has recently been restored through the northward migration and colonization of alfalfa by V. sativa- associated lineages. Therefore, our results support the theoretical predictions and provide a new perspective on the origin of sexual populations.     

Assessment of DNA fingerprinting for determining genetic diversity in sheep populations

Genomic DNA, prepared from 12 animals from four sheep flocks, was digested with either HaeIII or Hin fI and probed with three DNA fingerprinting probes. Mean DNA fingerprint band sharing and band frequency calculated for each flock were used to estimate genetic diversity. Each of the DNA fingerprinting systems showed the same trend in diversity within the sampled flocks, and greater diversity between the flocks than within the flocks. DNA fingerprinting therefore provides a useful measure of genetic diversity in sheep.     

Methods for minimizing the loss of genetic diversity in conserved populations with overlapping generations

Minimization of the average coancestry in a population has been theoretically proven to be the most efficient method to preserve genetic diversity. In the present study, based on a population genetic model, two methods to minimize the average coancestry in populations with overlapping generations were developed. For a given parental coancestry structure, the first method (OG) minimizes the average coancestry in the next generation, and the second method (LT) is designed to minimize the long-term accumulation of coancestry. The efficiencies of the two methods were examined by stochastic simulation. Compared to random choice of parents, the annual effective population sizes under the two proposed methods increased 2–3 folds. The difference among the two methods was small in a population with short generation interval. For populations with long generation intervals, the OG method showed a slightly larger annual effective size in an initial few years. However, in the subsequent years, the LT method gave a 5–15% larger annual effective size than the OG method. From these results, it is suggested that the LT method would be preferred to the OG method in most practical situations.     

Variation in mitochondrial DNA and maternal genetic ancestry of Ethiopian cattle populations

This study describes complete control region sequences of mitochondrial DNA (mtDNA) from 117 Ethiopian cattle from 10 representative populations, in conjunction with the available cattle sequences in GenBank. In total, 79 polymorphic sites were detected, and these defined 81 different haplotypes. The haplotype and nucleotide diversity of Ethiopian cattle did not vary among the populations studied. All mtDNA sequences from Ethiopian cattle converged into one main maternal lineage (T1) that corresponds to African Bos taurus cattle. According to the results of this study, no zebu mtDNA haplotypes have been found in Ethiopia, where the most extensive hybridization took place on the African continent.     

蜜蜂遗传多态性的影响因素及主要研究方法

蜜蜂遗传多态性与蜜蜂种质资源保存、优良品种繁育和科学引种等问题密切相关,具有重要的研究价值。文章综述蜜蜂遗传多态性的影响因素和研究方法,影响因素包括自然因素和人为因素,自然因素主要有环境因子和种群竞争等,人为因素主要有品种引进和农药毒害作用等;研究方法包括形态学检测和DNA分析检测等。通过比较各研究方法的优缺点,认为宜采用多种方法相结合的手段进行全方位、多角度地综合评价蜜蜂的遗传多态性。     

Patterns of genetic diversity in outcrossing and selfing populations of Arabidopsis lyrata

Arabidopsis lyrata is normally considered an obligately outcrossing species with a strong self-incompatibility system, but a shift in mating system towards inbreeding has been found in some North American populations (subspecies A. lyrata ssp. lyrata). This study provides a survey of the Great Lakes region of Canada to determine the extent of this mating system variation and how outcrossing rates are related to current population density, geographical distribution, and genetic diversity. Based on variation at microsatellite markers (progeny arrays to estimate multilocus outcrossing rates and population samples to estimate diversity measures) and controlled greenhouse pollinations, populations can be divided into two groups: (i) group A, consisting of individuals capable of setting selfed seed (including autogamous fruit set in the absence of pollinators), showing depressed outcrossing rates (T(m) = 0.2-0.6), heterozygosity (H(O) = 0.02-0.06) and genetic diversity (H(E) = 0.08-0.10); and (ii) group B, consisting of individuals that are predominantly self-incompatible (T(m) > 0.8), require pollinators for seeds set, and showing higher levels of heterozygosity (H(O) = 0.13-0.31) and diversity (H(E) = 0.19-0.410). Current population density is not related to the shift in mating system but does vary with latitude. Restricted gene flow among populations was evident among all but two populations (F(ST) = 0.11-0.8). Group A populations were more differentiated from one another (F(ST) = 0.78) than they were from group B populations (F(ST) = 0.59), with 41% of the variation partitioned within populations, 47% between populations, and 12% between groups. No significant relationship was found between genetic and geographical distance. Results are discussed in the context of possible postglacial expansion scenarios in relation to loss of self-incompatibility.     

Implications of isolation and low genetic diversity in peripheral populations of an amphi-Atlantic coral

Limited dispersal and connectivity in marine organisms can have negative fitness effects in populations that are small and isolated, but reduced genetic exchange may also promote the potential for local adaptation. Here, we compare the levels of genetic diversity and connectivity in the coral Montastraea cavernosa among both central and peripheral populations throughout its range in the Atlantic. Genetic data from one mitochondrial and two nuclear loci in 191 individuals show that M. cavernosa is subdivided into three genetically distinct regions in the Atlantic: Caribbean-North Atlantic, Western South Atlantic (Brazil) and Eastern Tropical Atlantic (West Africa). Within each region, populations have similar allele frequencies and levels of genetic diversity; indeed, no significant differentiation was found between populations separated by as much as 3000 km, suggesting that this coral species has the ability to disperse over large distances. Gene flow within regions does not, however, translate into connectivity across the entire Atlantic. Instead, substantial differences in allele frequencies across regions suggest that genetic exchange is infrequent between the Caribbean, Brazil and West Africa. Furthermore, markedly lower levels of genetic diversity are observed in the Brazilian and West African populations. Genetic diversity and connectivity may contribute to the resilience of a coral population to disturbance. Isolated peripheral populations may be more vulnerable to human impacts, disease or climate change relative to those in the genetically diverse Caribbean-North Atlantic region.     

Genetic diversity and genetic structure of populations of Ranunculus japonicus Thunb. (Ranunculaceae)

Abstract In order to clarify the genetic diversity and population structure of Ranunculus japonicus , allozymic analysis was conducted on 60 populations in southwestern Japan. Considerable genetic variati ons were detected among the populations of R. japonicus . The genetic diversities within species ( H _es = 0.215) and within populations ( H _ep = 0.172) were slightly higher than those of other perennial herbs with widespread distribution and outcrossing plants. Significantly higher values of fixation index were detected in some populations, which might have arisen from restricted mating partners. The majority of genetic variation (approx. 80%) resided within a population and a moderate level of genetic differentiation ( G _ST = 0.203) was observed among populations. The F _ST value (0.203) suggests the existence of a substantial population structure in this species. The highly significant correlation between geographic distance and F _ST values indicates that isolation by distance has played an important role in the construction of the genetic structure of this species.     

The nature and reality of the aphid clone: genetic variation, adaptation and evolution

1 When aphid clones and clonality are discussed, it is still often said that they are ‘genetically identical’, a statement for which there is no direct evidence, and certainly not for the entire genome. By contrast, there is a growing body of empirical data from the application of high resolution molecular (DNA) markers that aphid asexual lineages rapidly mutate and that, in some documented cases, this variation is selectable, either positively or negatively. 2 Although it is true that, in enclosed conditions (e.g. laboratory or field cage), a so‐called clone as defined as the asexual progeny of a single foundress may be traceable, this is rarely if ever possible in the field without the use of genetic markers, and even then, usually only at a relatively few loci (multilocus genotypes, ‘MLGs’). 3 The continued use of the term clone without qualification of its true nature and the reality of its interesting biology is likely to hamper a proper understanding of the ecology and evolution of these insects (which are interesting in their own right because of their complex life histories, but also because they are important as major pests globally, both by causing direct feeding damage and by transmitting pathogenic plant viruses and thereby leading to huge economic losses in the agricultural, horticultural and forestry industries). 4 In this short review, I provide evidence of what is now known about aphid clonality after the widespread use of molecular markers, comprising information mainly gained within the last 15 years or so. 5 The data demonstrate widespread adaptation and evolution, sometimes involving introgression and hybridization. Because of this new knowledge, our ideas of what constitutes a clone are in need of serious re‐evaluation.     

基于SSR标记的8个山荆子居群遗传多样性和遗传关系分析

采用10对SSR引物对8个山荆子[Malus baccata (L.) Borkh.]居群140个单株的基因组总DNA进行PCR扩增,并据此对8个居群的遗传多样性和遗传关系进行了分析.结果表明:用10对SSR引物共扩增出91条带,多态性条带百分率达100.00％.8个居群的遗传多样性参数差异较大,有效等位基因数为1.437 9～1.535 0,Nei's基因多样性指数为0.256 0～0.309 2,Shannon信息指数为0.376 7～0.459 2,多态性条带百分率为64.84％～85.71％.居群间的有效等位基因数为1.616 9,Nei's基因多样性指数为0.355 1,Shannon信息指数为0.528 5,均明显高于居群内;8个居群间的基因流为1.739 5,基因分化系数为0.223 3,显示居群间的基因交换较多.UPGMA聚类分析结果表明:在Nei's遗传距离0.148 6处,8个居群被分为3组,河北塞罕坝居群单独为一组,山西五台山居群和北京东灵山居群为一组,其余5个居群为一组.据此推测:山荆子起源于中国华北和东北地区,山西灵空山、黑龙江小兴安岭、吉林长白山和山西中条山居群可能是其遗传多样性的核心居群.