塔里木裂腹鱼群体遗传结构及遗传多样性分析

塔里木裂腹鱼为塔里木河水系特有濒危裂腹鱼类。研究采集5个群体(多浪渠首、喀拉喀什河、木扎提河、塔什库尔干、玉龙喀什河)塔里木裂腹鱼,扩增线粒体控制区第一高变区,共获得长度456 bp序列95条。塔里木裂腹鱼单倍型多样度和核苷酸多样度分别为0.7118、0.0024。AMOVA分析显示,群体间遗传分化显著。FST值统计检验表明,除喀拉喀什河群体与玉龙喀什河群体之间差异不显著外,其他两两群体之间都是显著的。分子系统树和单倍型网络图分析表明,塔里木裂腹鱼单倍型间关系较近。中性检验和mismatch分析显示,塔里木裂腹鱼群体经历过近期群体扩张事件。根据核苷酸不配对分布τ值计算其群体扩张时间为20万年前。天山、昆仑山的运动以及第四纪冰期-间冰期的变化可能影响了塔里木裂腹鱼的群体历史动态。     

Genotypic and phenotypic consequences of reintroduction history in the black-footed ferret (<Emphasis Type="Italic">Mustela nigripes</Emphasis>)

Population augmentation with translocated individuals has been shown to alleviate the effects of bottlenecks and drift. The first step to determine whether restoration for genetic considerations is warranted is to genetically monitor reintroduced populations and compare results to those from the source. To assess the need for genetic restoration, we evaluated genetic diversity and structure of reintroduced (n = 3) and captive populations of the endangered black-footed ferret (Mustela nigripes). We measured genotypic changes among populations using seven microsatellite markers and compared phenotypic changes with eight morphometric characters. Results indicated that for the population which rapidly grew post-reintroduction, genetic diversity was equivalent to the captive, source population. When growth languished, only the population that was augmented yearly maintained diversity. Without augmentation, allelic diversity declined precipitously and phenotypic changes were apparent. Ferrets from the genetically depaupertate population had smaller limbs and smaller overall body size than ferrets from the two populations with greater diversity. Population divergence (F _ST = 0.10 ± 0.01) was surprisingly high given the common source of populations. Thus, it appears that 5–10 years of isolation resulted in both genotypic divergence and phenotypic changes to populations. We recommend translocation of 30–40 captive individuals per annum to reintroduction sites which have not become established quickly. This approach will maximize the retention of genetic diversity, yet maintain the beneficial effects of local adaptation without being swamped by immigration.     

Genetic structure of expanding wolf (Canis lupus) populations in Italy and Croatia,and the early steps of the recolonization of the Eastern Alps

After centuries of range contraction and demographic declines wolves are now expanding in Europe, colonizing regions from where they have been absent for centuries. Wolf colonizing the western Alps originate by the expansion of the Italian population. Vagrant wolves of Italian and Dinaric-Balkan origins have been recently observed in the Eastern Alps. In this study we compared the genetic structure of wolf populations in Italy and Croatia, aiming to identify the sources of the ongoing recolonization of the Eastern Alps. DNA samples, extracted from 282 Italian and 152 Croatian wolves, were genotyped at 12 autosomal microsatellites (STR), four Y-linked STR and at the hypervariable part of the mitochondrial DNA control-region (mtDNA CR1). Wolves in Croatia and Italy underwent recent demographic bottlenecks, but they differ in genetic diversity and population structure. Wolves in Croatia were more variable at STR loci (N_A = 7.4, H_O = 0.66, H_E = 0.72; n = 152) than wolves in Italy (N_A = 5.3, H_O = 0.57, H_E = 0.58; n = 282). We found four mitochondrial DNA (mtDNA CR1) and 11 Y-STR haplotypes in Croatian wolves, but only one mtDNA CR1 and three Y-STR haplotypes in Italy. Wolves in Croatia were subdivided into three genetically distinct subpopulations (in Dalmatia, Gorski kotar and Lika regions), while Italian wolves were not sub-structured. Assignment testing shows that the eastern and central Alps are recolonized by wolves dispersing from both the Italian and Dinaric populations. The recolonization of the Alps will predictably continue in the future and the new population will be genetically admixed and very variable with greater opportunities for local adaptations and survival.     

Comparative population structure of three snook species (Teleostei: Centropomidae) from the eastern central Pacific

Three snook species, Centropomus viridis, Centropomus medius, and Centropomus robalito, from the eastern central Pacific, representing three of the four proposed phyletic lineages in the genus, were analyzed for genetic variability by means of allozyme and RAPD to evaluate the divergence between populations at different levels of dispersal ability and to evaluate the importance of barriers to dispersal in the population subdivision and genetic diversity. Levels of genetic diversity among species estimated by allozymes were similar and consistent with the observed levels of differentiation in marine fish species. Mean heterozygosity ranged from 0.089 for C. viridis to 0.10 for C. robalito. Genetic diversity for the snook species studied was slightly higher than the mean estimation reported in allozymes for 106 marine fish (0.055) and for anadromous fish species (0.043 to 0.057). Multilocus allele frequency homogeneity tests and population-subdivision estimates for both allozyme and RAPD markers revealed the existence of population structure in C. viridis and C. medius, in coincidence with geographic separation of samples, whereas no divergence was detected in C. robalito. This finding may be attributed to the greater population size of C. robalito, which originated by a recent population range expansion, and hence the potential for dispersal is mediated by larval drift. Fluctuations in population size and population range expansion are used to explain discrepancies between levels of genetic diversity and population structure in the studied species. Supplementary material to this paper is available in electronic format at     

基于线粒体Cytb基因全序列的松江鲈群体遗传结构分析

对松江鲈(Trachidermus fasciatus Heckel)中国沿海7个群体和日本有明海群体的线粒体Cytb基因全序列进行了测定、分析。结果显示: 47个个体共检测到31个单倍型, 8个群体均呈现出较高的单倍型多样性(0.60-1.00)和较低的核苷酸多样性(0.0005-0.0041)的特点。AMOVA分析结果及单倍型邻接关系树和单倍型网络关系图均显示松江鲈分为中国和日本两个世系, 而中国世系的7个群体未呈现出明显的地理遗传结构。基于核苷酸Kimura双参数替代模型计算得出的中国和日本两个世系的净遗传距离, 再参照其他硬骨鱼类线粒体Cytb基因2%/Ma(百万年)的分歧速率, 推测松江鲈中日两个世系间分化时间约为41万年前。对中国世系进行群体历史动态分析, 中性检验结果均为负值且显著, 核苷酸不配对分布呈单峰型, 表明松江鲈中国世系曾发生过群体扩张, 其扩张时间大约为12万年前。     

濒危植物矮沙冬青的等位酶多样性及居群分化

采用超薄平板微型聚丙烯酰胺等电聚焦技术,对珍稀濒危植物矮沙冬青(Ammopiptanthus nanus)6个自然居群的等位酶遗传多样性进行了初步研究。8个酶系统、l9个酶位点的检测结果表明,矮沙冬青具有较低的遗传变异水平。物种水平上的遗传多样性参数为：P=21．05％,A=1．21,Ht=0．040;居群水平上的平均遗传多样性为：P=14．04％,A=1．14(0．04),Ht=0．036(0．018),比长寿命多年生木本的狭域分布种和特有种的多样性水平都低。F-统计量分析显示,矮沙冬青在居群水平(F15=0．129)和总居群水平(FIT=0．202)上都表现为杂合子缺乏;Fsr=0．085表明居群问遗传分化较小,这与居群间较高的遗传一致度(I=0．997)的结果一致。据研究结果推测矮沙冬青进化历史上经历过遗传瓶颈,是造成遗传多样性水平偏低的重要原因。基于研究结果,提出应当重点保护遗传变异相对丰富的何依儿佣克尔(KE)居群,并且可将其作为引种的种源地。     

Limits to genetic bottlenecks and founder events imposed by the Allee effect

The Allee effect can result in a negative population growth rate at low population density. Consequently, populations below a minimum (critical) density are unlikely to persist. A lower limit on population size should constrain the loss of genetic variability due to genetic drift during population bottlenecks or founder events. We explored this phenomenon by modeling changes in genetic variability and differentiation during simulated bottlenecks of the alpine copepod, Hesperodiaptomus shoshone. Lake surveys, whole-lake re-introduction experiments and model calculations all indicate that H. shoshone should be unlikely to establish or persist at densities less than 0.5–5 individuals m⁻³. We estimated the corresponding range in minimum effective population size using the distribution of habitat (lake) sizes in nature and used these values to model the expected heterozygosity, allelic richness and genetic differentiation resulting from population bottlenecks. We found that during realistic bottlenecks or founder events, >90% of H. shoshone populations in the Sierra Nevada may be resistant to significant changes in heterozygosity or genetic distance, and 70–75% of populations may lose <10% of allelic richness. We suggest that ecological constraints on minimum population size be considered when using genetic markers to estimate historical population dynamics.     

Comparing the genetic diversity and structure of indigenous Korean and Chinese populations of Laodelphax striatellus Fallén using mitochondrial haplotypes

The small brown planthopper, Laodelphax striatellus Fallén, is a major migratory pest from China to Korea and transmits viral diseases of rice plants. In this study, we compared the genetic structures of overwintered indigenous Korean and Chinese populations. The eight Korean populations consisted of 33 haplotypes, and 16 of these were newly identified. The genetic diversity of the Korean population revealed high haplotype diversity (Hd) and low nucleotide diversity (π) of 0.86 ± 0.017 and 0.0024 ± 0.0001 on average, respectively. These values for the Chinese population were Hd = 0.92 ± 0.016 and π = 0.0026 ± 0.0002. Overall, genetic distances by pairwise F_ST were generally low, ranging from ? 0.022 to 0.089. Moreover, the Korean population revealed its ongoing population expansion by showing negative values in the neutrality test (Tajima's D = ? 1.4, Fu's Fs = ? 15.8) and a unimodal pattern in the mismatch distribution analysis. The genetic structures and population relationships were determined using 8 indigenous Korean and 30 Chinese populations by Bayesian approaches and population tree construction, respectively. The genetic structure was inferred as five (K = 5), and all indigenous Korean populations as well as 10 Chinese populations from the Shanghai city, Anhui, Henan, Jiangsu, Liaoning, Shandong, and Zhejiang provinces were grouped into ‘G3’. These results provide partial support for unidirectional gene flow by migratory Chinese populations into Korea. Further analysis conducted using specimens from China and Korea collected in similar periods is necessary to clarify the migration population's origin and its effect on the genetic structure of the indigenous populations.     

The genetic structure of finland.

The Finnish gene pool derives primarily from a relatively homogeneous Finno-Ugric population established during the Iron Age (100 B.C.-800 A.D.) in the southwest and southeast of Finland. Gene flow from Sweden to the southwest coastal areas, dating from prehistoric times, as well as the patterns of settlement and migration throughout Finland during the past 1000 years, appear to have been the major biosocial factors underlying the genetic structure of the contemporary population. Analysis of genetic variation and covariation at nine polymorphic loci in a large random sample of rural Finns, partitioned into either 8 countries or 27 geographic districts, showed that all of the essential features of the genetic structure suggested by the archaeological and historical data could be distinguished. Procedures for obtaining inference on the genetic structure of such a population are reviewed, including coefficients of similarity and (genetic) distance among subpopulations, the relation between linear or planar geographic structure and genetic covariation, and the methods for describing allelic differentiation. Bias resulting from the inappropriate assumption of a simple phylogenetic model can be substantial, expecially for the analysis of isolation by distance; procedures for avoiding misleading inference on the genetic structure are demonstrated.     

Risso’s dolphins (<Emphasis Type="Italic">Grampus griseus</Emphasis>) in UK waters are differentiated from a population in the Mediterranean Sea and genetically less diverse

The Risso’s dolphin (Grampus griseus) has a worldwide distribution, but little is known about their population genetic structure. Local coastal populations are never known to be abundant, and are sometimes under anthropogenic impact. Therefore the question of regional differentiation by genetic drift and overall diversity levels is of conservation interest. Here we present preliminary data that clearly indicate genetic differentiation and lower genetic diversity of a population sampled in UK waters (primarily from the Western Isles, Scotland) compared to a Mediterranean sample. Significant differentiation was found in comparison with a sample from the Mediterranean for both microsatellite DNA markers (F _ST = 0.0296) and mtDNA sequence data (F _ST = 0.260; ϕ _ST = 0.542). Allelic diversity was lower in the UK for nearly all loci.     

Amplified fragment length polymorphism analysis of the population structure and genetic diversity of Phoebe zhennan (Lauraceae), a native species to China

Phoebe zhennan S. Lee et F. N. Wei (Lauraceae), is the main source of Gold Phoebe, a rare and extremely valuable wood in China. However it has undergone a dramatic decline. In this study, we used 12 amplified fragment length polymorphism primer combinations to assay 92 accessions, which were highly representative of the entire P. zhennan germplasm. It revealed that P. zhennan consisted of three genetic populations, named as SCZ (central Sichuan), CQH (eastern Sichuan, Chongqin, Hubei and Hunan) and YG (Yunnan and Guizhou), probably owing to natural selection caused by topography differences. The CQH population further diverged into two geographical sub-populations: CD-CQ (SCD and west region of Chongqin) and HB-HN (eastern side of Chongqin, Hubei and Hunan). The loci were moderately polymorphic (40.4%). The genetic distance between SCZ and YG was the highest, between CD-CQ and HB-HN the lowest. Pairwise fixation indices (Ф_PT) between any inferred populations were significant. This rare species exhibited low genetic diversity; therefore, the results provided significant data related to the conservation and management of P. zhennan. That is, with this genetic information, land managers are equipped with better tools allowing them to more effectively protect this species and its limited genetic diversity.     

Isozyme analysis of genetic variability and population structure of Lactuca L. germplasm

Isozymes were used to investigate the genetic variability, population structure, and relationships of Lactuca germplasm. The isozyme systems revealed 16 putative loci of a total of 31 alleles. Out of these 16 loci, 11 were polymorphic. The average values of expected heterozygosity (H_e), observed heterozygosity (H_o), mean number of alleles per locus (A) and effective number of alleles per locus (A_e) were 0.2227, 0.266, 1.3005 and 1.369, respectively. The average fixation indices were lower than zero for most of the accessions studied, indicating an excess of heterozygotes. Genetic differentiation among accessions (F_ST) exhibited that 51.3% of the isozyme variation was recorded among accessions, and 48.7% of the genetic variation resided within accessions. The average values of total heterozygosity (H_T) and intra-accessional genetic diversity (H_S) were 0.352 and 0.171, respectively. Moreover, the inter-accessional genetic diversity (D_ST) ranged from 0 to 0.424 with an average of 0.18. Cluster analysis revealed that L. sativa cultivars were distributed throughout different Lactuca species. Thereby, isozymes results confirms the hypothesis of the polyphyletic origin of L. sativa. This high level of genetic variation proved that isozymes are efficient for polymorphism analysis of Lactuca germplasm.