基于分子标记的油松种群遗传保护分析

利用分子标记技术分析了山西5个天然油松种群140个个体的遗传特征,比较了不同种群的多态位点显性频率、遗传多样性指数、基因流和分化系数.筛选的5个ISSR引物和5个RAPD引物共扩增到位点68个,其中多态位点50个遗传参数的统计分析显示,多态位点的显性频率、遗传多样性指数、分化系数分别介于0.000 0～1.000 0、0.0200～0.500 0和0.003 7～0.615 62:间,表明油松种群遗传多样性的主要来源是等位基因频率的不同和部分位点较大程度的遗传分化.根据油松的种群遗传学特征,认为只有加强天然油松林的生境保护,使其不产生片断化,才能使油松的遗传资源得到有效保护.图2表4参16     

河北省黄顶菊4个地理种群遗传结构分析

利用AFLP技术对河北省黄顶菊[Flaveria bidentis(L.)Kuntze]4个地理种群的遗传结构及其影响因素进行了研究.结果表明,在物种水平上黄顶菊具有较高的遗传多样性;虽然种群间存在较高水平的基因流,但在种群水平上4个种群遗传多样性差异显著,具有较高的遗传分化.分析表明,影响黄顶菊遗传结构的因素较为复杂,入侵时间、环境差异、入侵行为中遭受的奠基者效应和瓶颈效应均影响种群的遗传多样性和遗传分化.聚类分析表明,4个种群间具有明显的种源地的地源性亲缘关系.     

利用RAPD标记分析卧龙自然保护区不同海拔沙棘种群的遗传变异

从1800m到3400m五个海拔连续取样,用RAPD分子标记研究了卧龙自然保护区中国沙棘种群的遗传结构和遗传变异.用11条寡核苷酸引物,扩增得到151个重复性好的位点,其中143个多态位点,多态率达94.7%.在5个沙棘种群中,总遗传多样性值(HT)为0.289,B种群内的遗传多样性值为0.315,这完全符合沙棘这种多年生、远交的木本植物高遗传变异的特性.5个种群内遗传多样性随海拔升高呈低—高—低变异趋势,在2200m海拔处的B种群遗传多样性达最大值0.315,3400m海拔处的E种群则表现最小,仅0.098.5个种群间的遗传分化值GST=0.406,也即是说有40.6%的遗传变异存在于种群间,59.4%存在种群内.1800m海拔处的A种群与其他种群的明显分离是造成种群间遗传分化大的原因.UPGMA聚类图和PCoA散点图分别进一步确证了5个种群间关系和所有个体间的关系.最后,经过Mantel检测,遗传距离与海拔表现了明显的相关性(r=0.646,P=0.011).     

金花茶遗传多样性和遗传结构AFLP分析

利用扩增片段长度多态性(amplified fragment length polymorphism,AFLP)分子标记技术,对金花茶(Camellia nitidissima) 4个天然种群的遗传多样性和遗传结构进行研究,为金花茶资源的有效保护和高效利用提供科学依据。结果表明,8对引物共扩增出1 619个DNA位点,其中1 473个位点具多态性,多态性位点百分率为90. 98%。金花茶物种水平基因多样性指数和Shannon信息指数为0. 146和0. 246,种群水平基因多样性指数和Shannon信息指数为0. 131和0. 215; 4个金花茶种群的多态位点百分率、基因多样性指数和Shannon信息指数变化趋势一致,其中多态位点百分率介于56. 83%～72. 11%之间,基因多样性指数介于0. 122～0. 138之间,Shannon信息指数介于0. 197～0. 228之间。金花茶种群间的遗传分化系数介于0. 139～0. 289之间,遗传变异主要存在于种群内。分子变异分析(AMOVA)结果表明,金花茶种群内遗传变异为81. 52%,种群间遗传变异为18. 48%,遗传变异主要存在于种群内。非加权组平均法(UPGMA)聚类结果表明,种群间遗传变异与其地理距离无明显相关性。应加强现有金花茶种群的就地保护,促进种群自然更新,同时加强迁地保护。     

基于COI基因序列的饰纹姬蛙四川盆地种群遗传多样性

饰纹姬蛙(Microhyla fissipes)在中国广泛分布于秦岭以南地区,在四川盆地是常见的两栖动物之一,研究其种群遗传多样性可为当地两栖动物的保护与管理提供重要的遗传基础资料和理论依据.采用线粒体COI基因为分子标记,探讨四川盆地饰纹姬蛙种群遗传多样性及其分化程度、种群历史动态.共采集饰纹姬蛙28个种群354只,成功获得其COI基因618 bps片段序列.分析结果发现17种单倍型,总体单倍型多样性(H_d)为0.166,核苷酸多样性(P_i)为0.000 75,基因流(N_m)为1.60.各种群间固定系数(F_(st))和遗传分化系数(G_(st))分别为0.270、0.140.中性检验中,Tajima’s D=-2.380,P 0.001;Fu’s Fs=-22.169,P 0.02,均具有显著性差异;错配分布图呈泊松状的单峰.通过计算得出种群扩张时间约在更新世晚期0.235 Ma BP.上述结果表明,四川盆地饰纹姬蛙种群遗传多样性较低,种群间基因交流水平高,不同种群间遗传分化不明显,并且在历史上有过扩张的现象.     

生境破碎化对动植物遗传多样性的影响研究进展

生境破碎化是生物多样性降低的主要原因之一,此前研究多集中在生境破碎化对物种和生态系统多样性的影响.综述了生境破碎化的成因、度量和理论基础,以及对动植物遗传多样性的影响机理和生态学效应.生境破碎化主要通过增加种群间隔离程度和降低有效种群大小等途径限制种群间基因交流,提高遗传漂变频率,从而影响动植物遗传多样性;但是影响效应取决于植物繁殖策略和动物迁移能力,以及传粉方式、种群大小、生命周期、生境的景观特性等因素;而且生境破碎化对动植物遗传多样性的影响大多存在滞后效应.由此可见,生境破碎化对动植物遗传多样性的影响因素多且复杂,而且不易及时发现,从而忽略生境破碎化对遗传多样性的负面影响;未来应加强生境破碎化对动植物遗传多样性的影响研究,特别是在更长时间尺度上的生境破碎化研究.(表1参73)     

基于线粒体控制区(D-loop)序列的珠江赤眼鳟遗传多样性与遗传分化

为了解珠江流域重要野生经济鱼类赤眼鳟的遗传多样性和遗传分化现状,对柳江、西江、北江、郁江、南盘江和红水河6个自然种群共170尾个体的线粒体控制区(D-loop)序列进行测定与分析.结果显示,共获得长978 bp的序列,检测出106个单倍型,单倍型多样性平均为0.982 0,核苷酸多样性平均为0.013 53,表明珠江流域赤眼鳟具有较高的遗传多样性.遗传距离和遗传分化结果均显示珠江流域赤眼鳟未出现明显分化,各种群亲缘关系较近.基于D-loop序列构建的NJ树显示,106个单倍型分为两大支系(A支和B支).A支包含6个种群中的大部分单倍型,未形成明显单系群;B支由西江种群的两个特有单倍型组成.单倍型网络亲缘关系分析结果也表明其未出现明显分化.AMOVA分析结果表明,绝大部分变异出现在种群内(99.36%),而地理区间和地理区内种群间的变异很小.中性检验显示,珠江流域赤眼鳟历史上曾发生过种群扩张.综合上述研究结果,认为西江为珠江流域赤眼鳟的扩散中心.     

麻疯树种质资源遗传多样性的ISSR分析

采用ISSR分子标记技术对大戟科属麻疯树9个自然居群的遗传多样性水平和遗传结构进行了研究.用10个引物对9个居群共135个样品进行了扩增,共获得169条清晰的扩增位点,其中多态性位点164个.POPGENE分析结果表明,麻疯树居群具有丰富的遗传多样水平(多态百分率PPB=97.04%,Neis遗传多样性H=0.2357,Shannon信息指数I=0.3760).AMOVA分析表明,9个自然居群间遗传多样性出现了较大的遗传分化(Gst=0.5398)可能与其有限的基因流(Nm=0.4667)和遗传漂变有关;而居群内有限的遗传分化可能是由于麻疯树自交、近交占主导方式的繁育方式有关.并进行了麻疯树居群的聚类分析.图3表4参19     

大贵寺国家森林公园野生青檀居群的遗传多样性

利用ISSR分子标记技术对湖北省大贵寺国家森林公园野生青檀（Pteroceltis tatarinowii Maxim．）居群进行遗传多样性分析。用11条ISSR引物对6个青檀居群64个样品进行扩增,扩增片段长度在200bp至3000bp之间,检测到179个位点,其中多态位点165个,多态位点百分率（P）为92．14％。青檀在物种水平上的Nei基因多样性指数（胁）和Shannon信息指数∽分别为0．273和0．423,在居群水平上分别为0．225和0．343,显示出青檀有着较高的遗传多样性。居群间的遗传分化系数（Gsr）为0．192,表明青檀居群间存在着较大的遗传分化;UPGMA聚类分析表明遗传距离与海拔差距有一定的相关性,相邻海拔的青檀居群间遗传距离较近。不同海拔导致的异质生境可能是影响青檀居群遗传分化的主要原因。     

威海荣成鹿角菜野生种群遗传多样性及资源保护策略

利用随机扩增多态性DNA（RAPD）方法对威海荣成地区鹿角菜（Silvetiasiliquosa）野生种群共30个个体的遗传多样性水平及遗传结构进行研究。结果表明,利用21条随机引物共检测到112个多态性位点,多态性位点百分率为93．75％,Nei基因多样性指数为0．3515±0．1352,Shannon多样性指数为0．5046±0．1126。通过聚类分析而划为一类的3个亚种群间的遗传分化指数为0．1349～0．2189,基因流为1．7793。研究结果表明威海荣成地区的鹿角菜种群遗传多样性较高,种群内存在较为明显的遗传分化,种群遗传资源不受遗传漂变的影响。针对当地鹿角菜遗传资源的现状,应加强现存种群的就地保护,恢复种群规模;进行取样养殖保护时则需避免因近交而造成种群资源退化。     

Human Impacts on Drainages of the Mesa Central, Mexico, and Its Genetic Effects on an Endangered Fish, Zoogoneticus quitzeoensis

Abstract:  The Mesa Central of Mexico is of special conservation interest due to its high richness of freshwater fish species, of which the goodeines are one of the most representative groups. Through an integrated approach, we determined conservation priorities for goodeine populations. We based our recommendations on the genetic diversity (variation in five microsatellite DNA loci) in 10 populations of Zoogoneticus quitzeoensis and on an analysis of ecological (e.g., presence of exotic species), social (e.g., political situation), and environmental (e.g., pollution) information for 52 historical occurrence points for species in the genus Zoogoneticus . Patterns of genetic erosion and genetic diversity indices were closely associated with human impact. Recent bottleneck events were most evident in the populations from remnants of the lakes drained at the beginning of the twentieth century. We identified seven operational conservation units (OCUs), all of which should be conserved because they contain unique portions of the total variation of the species. Special attention needs to be given to increase genetic variability, recover population sizes, and reestablish contact among populations within OCUs. It is imperative to create an integrative and effective approach for the recovery and conservation of the freshwater fish diversity of Central Mexico that is based on social and natural sciences.     

Genetic structure in lagoons: the effects of habitat discontinuity and low dispersal ability on populations of <Emphasis Type="Italic">Atherina boyeri</Emphasis>

Atherina boyeri is a common inhabitant of the Mediterranean brackish and coastal waters. Several recent studies proposed the recognition of three distinct forms/species (one lagoon/freshwater and two marine) within an A. boyeri complex. In this study, we used 10 newly available microsatellite loci to better define the genetic structure of the lagoon form. A total of 428 fishes from 11 lagoons along the Italian and Albanian coasts and three Italian lakes were analyzed. A pronounced genetic spatial structure was confirmed for all considered geographic scales (near, medium and broad). A restricted gene flow was detected, suggesting reduced population connectivity. The comparison of present data and previous studies, based on mtDNA and RAPD markers, allowed a preliminary identification of the roles of recent factors (gene flow, habitat discontinuity and water currents) and past events (e.g., Pleistocene glaciations) in shaping the pattern of genetic differentiation.     

Microsatellite variation and significant population genetic structure of endangered finless porpoises (Neophocaena phocaenoides) in Chinese coastal waters and the Yangtze River

The finless porpoise (Neophocaena phocaenoides) inhabits a wide range of tropical and temperate waters of the Indo-Pacific region. Genetic structure of finless porpoises in Chinese waters in three regions (Yangtze River, Yellow Sea, and South China Sea) was analyzed, including the Yangtze finless porpoise which is widely known because of its highly endangered status and unusual adaptation to freshwater. To assist in conservation and management of this species, ten microsatellite loci were used to genotype 125 individuals from the three regions. Contrary to the low genetic diversity revealed in previous mtDNA control region sequence analyses, relatively high levels of genetic variation in microsatellite profiles (H _E = 0.732–0.795) were found. Bayesian clustering analysis suggested that finless porpoises in Chinese waters could be described as three distinct genetic groups, which corresponded well to population “units” (populations, subspecies, or species) delimited in earlier studies, based on morphological variation, distribution, and genetic analyses. Genetic differentiation between regions was significant, with F _ST values ranging from 0.07 to 0.137. Immigration rates estimated using a Bayesian method and population ancestry analyses suggested no or very limited gene flow among regional types, even in the area of overlap between types. These results strongly support the classification of porpoises in these regions into distinct evolutionarily significant units, including at least two separate species, and therefore they should be treated as different management units in the design and implementation of conservation programmes.     

Mating system and individual reproductive success of sympatric anadromous and resident brook charr, <Emphasis Type="Italic">Salvelinus fontinalis</Emphasis>, under natural conditions

Salmonids are known for the occurrence in sympatry of two life-history forms, one that undergoes migration to sea before returning to freshwater to reproduce (anadromous) and one that inhabits freshwater without a migration phase (resident). Whereas one breeding population is often suggested by population genetic studies, mating patterns have rarely been directly assessed, especially when both sexes are found within each life-history form. By using highly polymorphic microsatellite loci and parentage analysis in a natural population of sympatric anadromous and resident brook charr (Salvelinus fontinalis), we found that gene flow occurred between the two forms and was mediated by resident males mating with both resident and anadromous females. Determinants of reproductive success, estimated by the number of surviving juveniles (ages 1 and 2 years), differed between the sexes. No strong evidence of the influence of size on individual reproductive success was found for males, whereas larger females (and hence most likely to be anadromous) were more successful. The higher individual reproductive success of anadromous fish compared to residents was mainly explained by this higher reproductive success of anadromous females. We suggest that resident males adopt a “sneaking” reproductive tactic as a way of increasing their reproductive success by mating with females of all sizes in all habitats. The persistence of the resident tactic among females may be linked to their advantage in accessing spatially constrained spawning areas in small tributary streams unavailable to larger females.     

Contrasting population structures in two sympatric fishes in the Baltic Sea basin

Detailed multispecies studies on the patterns of genetic variability and differentiation in marine environments are still rare. Using mitochondrial and nuclear genetic markers, we compared genetic variability and population structuring of threespine (Gasterosteus aculeatus) and ninespine (Pungitius pungitius) sticklebacks from the same eleven marine and six freshwater locations within the Baltic Sea basin. Analyses of both marker types revealed a significantly lower degree of genetic structuring in both marine and freshwater populations of threespine than those ninespine sticklebacks. Isolation-by-distance (IBD) was detected across the marine populations in both species, suggesting spatially limited gene flow. However, the levels of genetic diversity and differentiation across the localities were uncorrelated between the two species in both marine and freshwater environments. Accordingly, estimates of effective population sizes were larger and migration rates were higher for three- than for ninespine sticklebacks. Hence, ninespine stickleback populations from the Baltic Sea basin appear to be subject to stronger genetic drift than sympatric threespine sticklebacks, and the proximate reason for this difference is likely to be found from autecological differences between the two species. In accordance with the earlier studies, genetic variability was higher and the degree of genetic differentiation was lower in marine than in freshwater populations in both species.     

Genetic diversity and population structure of the Chinese mitten crab <Emphasis Type="Italic">Eriocheir sinensis</Emphasis> in its native range

The Chinese mitten crab Eriocheir sinensis is an indigenous and economically important species in China, but can also be found as invasive species in Europe and America. Mitten crabs have been exploited extensively as a food resource since the 1990s. Despite its ecological and economic importance, the genetic structure of native mitten crab populations is not well understood. In this paper, we investigated the genetic structure of mitten crab populations in China by screening samples from ten locations covering six river systems at six microsatellite loci. Our results provide further evidence that mitten crabs from the River Nanliujiang in Southern China are a genetically differentiated population within the native range of Eriocheir, and should be recognized as a separate taxonomic unit. In contrast, extremely low levels of genetic differentiation and no significant geographic population structure were found among the samples located north of the River Nanliujiang. Based on the reproductive biology of mitten crabs and the geography of their habitat we argue that both natural and human-mediated gene flow are unlikely to fully account for the similar allele frequency distributions at microsatellite loci. Large population sizes of mitten crabs suggest instead that a virtual absence of genetic drift and significant homoplasy of microsatellite alleles have contributed to the observed pattern. Furthermore, a coalescent-based maximum likelihood method indicated a more than two-fold lower effective population size of the Southern population compared to the Northern Group and low but significant levels of gene flow between both areas.     

Patterns of Genetic Diversity and Its Loss in Mammalian Populations

Abstract:  Policy aimed at conserving biodiversity has focused on species diversity. Loss of genetic diversity, however, can affect population persistence, evolutionary potential, and individual fitness. Although mammals are a well-studied taxonomic group, a comprehensive assessment of mammalian genetic diversity based on modern molecular markers is lacking. We examined published microsatellite data from populations of 108 mammalian species to evaluate background patterns of genetic variability across taxa and body masses. We tested for loss of genetic diversity at the population level by asking whether populations that experienced demographic threats exhibited lower levels of genetic diversity. We also evaluated the effect of ascertainment bias (a reduction in variability when microsatellite primers are transferred across species) on our assessment of genetic diversity. Heterozygosity did not vary with body mass across species ranging in size from shrews to whales. Differences across taxonomic groupings were noted at the highest level, between populations of marsupial and placental mammals. We documented consistently lower heterozygosity, however, in populations that had experienced demographic threats across a wide range of mammalian species. We also documented a significant ( p = 0.01) reduction in heterozygosity as a result of ascertainment bias. Our results suggest that populations of both rare and common mammals are currently losing genetic diversity and that conservation efforts focused above the population level may fail to protect the breadth of persisting genetic diversity. Conservation policy makers may need to focus their efforts below the species level to stem further losses of genetic resources.     

Multi-marker estimate of genetic connectivity of sole (Solea solea) in the North-East Atlantic Ocean

A thorough knowledge on the genetic connectivity of marine populations is important for fisheries management and conservation. Using a dense population sampling design and two types of neutral molecular markers (10 nuclear microsatellite loci and a mtDNA cytochrome b fragment), we inferred the genetic connectivity among the main known spawning grounds of sole (Solea solea L.) in the North-East Atlantic Ocean. The results revealed a clear genetic structure for sole in the North-East Atlantic Ocean with at least three different populations, namely the Kattegat/Skagerrak region, the North Sea and the Bay of Biscay, and with indications for a fourth population, namely the Irish/Celtic Sea. The lack of genetically meaningful differences between biological populations within the southern North Sea is likely due to a large effective population size and sufficient connection (gene flow) between populations. Nevertheless, an isolation-by-distance pattern was found based on microsatellite genotyping, while no such pattern was observed with the cytochrome b marker, indicating an historical pattern prevailing in the latter marker. Our results demonstrate the importance of a combined multi-marker approach to understand the connectivity among marine populations at region scales.     

Evidence for restricted gene flow over small spatial scales in a marine snapping shrimp <Emphasis Type="Italic">Alpheus angulosus</Emphasis>

Despite the apparent absence of geographic barriers, connectivity among marine populations may be restricted by, for example, ecological or behavioral mechanisms. In such cases, populations may show genetic differentiation even over relatively small spatial scales. Here, mitochondrial sequence data from the cytochrome oxidase I (COI) gene and seven polymorphic microsatellite markers were used to investigate fine geographic scale population genetic structure in the snapping shrimp Alpheus angulosus, a member of the A. armillatus species complex, from collections in Florida, Jamaica, and Puerto Rico carried out from 1999 to 2005. The COI data showed a deep divergence that separated these samples into two mitochondrial clades, but this divergence was not supported by the microsatellite data. The COI data reflect past population divergence not reflected in extant population structure on the whole genome level. The microsatellite data also revealed evidence for moderate population structure between populations as close as ∼10 km, and no evidence for isolation by distance, as divergences between near populations were at least as strong as those between more broadly separated populations. Overall, these data suggest a role for restricted gene flow between populations, though the mechanisms that reduce gene flow in this taxon remain unknown.     

Genetic and demographic consequences of importing animals into a small population: a simulation model of the Texas State Bison Herd (USA)

The extant 40 bison (Bison bison) constituting the Texas State Bison Herd (TSBH; USA) are directly and exclusively descended from a bison herd assembled by Charles Goodnight in the 1880s, representing a historically and genetically valuable resource. The population currently suffers from low genetic variation, low heterozygosity, high calf mortality, and low natality rates compared with other closed bison populations. Population viability analysis using the VORTEX program previously indicated a 99% chance of population extinction within the next 41 years [J. Mamm. 85 (2004) in press]. We developed a stochastic simulation model to evaluate the genetic and demographic consequences of various management scenarios for the TSBH using genotypic data from 51 microsatellite loci and demographic information recorded over a 6-year period. Our results reveal that without the introduction of new genetic variation, approximately 37% of the representative microsatellite loci will become fixed as the TSBH continues to lose genetic variation at a staggering rate of 30–40% within the next 50 years. Furthermore, if the current trends in natality and mortality rates continue, our model indicates the TSBH faces a 99% chance of extinction in the next 51 years. With the importation of unrelated male bison into the TSBH, and under the assumption of increased fitness, the probability of population survival in the next 100 years increases to 100%, and the population will reach the approximate carrying capacity of 200 bison in 15–16 years. Furthermore, our model predicts increases in genetic diversity and heterozygosity of 24.7–48.4% and 17.5–36.5%, respectively, in the next 100 years following the addition of new genetic variation. We conclude that the importation of bison into the TSBH is necessary to prevent extinction and ensure long-term population survival.