Extreme genetic differentiation among the remnant populations of marble trout (Salmo marmoratus) in Slovenia

Populations of the marble trout (Salmo marmoratus) have declined critically due to introgression by brown trout (Salmo trutta) strains. In order to define strategies for long-term conservation, we examined the genetic structure of the 8 known pure populations using 15 microsatellite loci. The analyses reveal extraordinarily strong genetic differentiation among populations separated by < 15 km, and extremely low levels of intrapopulation genetic variability. As natural recolonization seems highly unlikely, appropriate management and conservation strategies should comprise the reintroduction of pure populations from mixed stocks (translocation) to avoid further loss of genetic diversity.     

内蒙古中东部草原大针茅的种群遗传分化

对内蒙古中东部草原区分布的 11个大针茅 (Stipa grandis P. Smirn)地理种群进行了 RAPD分析。从 10 0个随机引物中筛选出 18个有效引物 ,共扩增出 2 2 1条 DNA带 ,多态性 DNA带 12 1条 ,占 5 4 .75 % ,平均每个引物扩增的 DNA带数为 12 .2 8条 ;特异性 DNA带 2 5条 ,占 11.31%。基于 Jaccard遗传相似性系数对此 2 2 1条 DNA带进行 U PGMA聚类分析 ,将 11个种群分为 3类 ,白音锡勒牧场的 8个种群聚为一类 ,林西种群和克什克腾种群两个种群聚为一类 ,阿巴嘎种群单独成为第 3类。用Mantel检验作进一步分析表明 ,在相对较大的尺度上 ,大针茅的遗传分化与地理距离相关极显著 (g>g0 .0 0 5) ;而在相对较小的尺度上 (白音锡勒牧场 8个种群 ) ,相关不显著 (gg0 .0 5)。     

内蒙古中东部草原区克氏针茅种群遗传分化的RAPD研究

采用 RAPD-PCR技术对内蒙古中东部草原分布的 7个克氏针茅 (Stip a krylovii Roshev.)种群进行了分析。从 10 0个 10碱基随机引物中筛选出 2 1个有效引物 ,共扩增出 2 2 9条稳定的 DNA带 ,其中 171条带具有多态性 ,多态性百分比 (PPB)为74.67%。将每个扩增产物看作一个独立的性状 ,按其有无列出二元数据矩阵 ,计算 Jaccard、简单匹配系数 (SM)和 Dice遗传相似性系数 ,通过 UPGMA法构建分子标记聚类图 ;并通过主成分分析 (PCA)和主轴法分析 (PAF) ,将 7个种群分类 ;统计各个种群特异性 DNA带 ,计算占总扩增条带的百分数。结果表明 :(1)不同地理种群之间扩增结果差异明显 ,具有丰富的遗传多样性 ;(2 )不同地理种群间存在一定程度的分化 ,这种分化是与种群之间的实际距离相联系的 ,相距越远 ,种群相似程度越低 ,进一步分析表明种群的分化是与所处生境逐渐旱化相一致的 ;(3 )聚类图上将 7个种群分为 3类 ,PCA和 PAF分析通过 3个成分或因子也将 7个种群分为 3类 ,支持了聚类图的分类结果 ;(4)特异性位点所占百分比与种群所处生境也有一定的联系 ,它与环境干燥度的相关系数为 0 .76(P<0 .0 5)。     

Identifying mechanisms of genetic differentiation among populations in vagile species: historical factors dominate genetic differentiation in seabirds

Elucidating the factors underlying the origin and maintenance of genetic variation among populations is crucial for our understanding of their ecology and evolution, and also to help identify conservation priorities. While intrinsic movement has been hypothesized as the major determinant of population genetic structuring in abundant vagile species, growing evidence indicates that vagility does not always predict genetic differentiation. However, identifying the determinants of genetic structuring can be challenging, and these are largely unknown for most vagile species. Although, in principle, levels of gene flow can be inferred from neutral allele frequency divergence among populations, underlying assumptions may be unrealistic. Moreover, molecular studies have suggested that contemporary gene flow has often not overridden historical influences on population genetic structure, which indicates potential inadequacies of any interpretations that fail to consider the influence of history in shaping that structure. This exhaustive review of the theoretical and empirical literature investigates the determinants of population genetic differentiation using seabirds as a model system for vagile taxa. Seabirds provide a tractable group within which to identify the determinants of genetic differentiation, given their widespread distribution in marine habitats and an abundance of ecological and genetic studies conducted on this group. Herein we evaluate mitochondrial DNA (mtDNA) variation in 73 seabird species. Lack of mutation–drift equilibrium observed in 19% of species coincided with lower estimates of genetic differentiation, suggesting that dynamic demographic histories can often lead to erroneous interpretations of contemporary gene flow, even in vagile species. Presence of land across the species sampling range, or sampling of breeding colonies representing ice‐free Pleistocene refuge zones, appear to be associated with genetic differentiation in Tropical and Southern Temperate species, respectively, indicating that long‐term barriers and persistence of populations are important for their genetic structuring. Conversely, biotic factors commonly considered to influence population genetic structure, such as spatial segregation during foraging, were inconsistently associated with population genetic differentiation. In light of these results, we recommend that genetic studies should consider potential historical events when identifying determinants of genetic differentiation among populations to avoid overestimating the role of contemporary factors, even for highly vagile taxa.     

Population structure of species: Eco-geographic units and genetic differentiation between populations

A two-step approach, based on a combined use of environmental, geographic, and genetic data, is suggested for studying population structures of species. First, populations are grouped into eco-geographic units (EGUs) according to the environmental gradients in the studied part of the species range, the types of life strategies, and other non-genetic characteristics that are presumably associated with adaptation and interpopulation gene flows. Second, the selected EGUs are tested for their congruence with genetic data by comparing the genetic differentiation between populations within EGUs to that between populations of different EGUs. Some of the issues discussed are as follows: the relationship of the EGU concept with the concepts of biogeocenosis and evolutionarily significant units (ESUs); designing EGUs in practice; the level of EGUs in a hierarchical population structure; and the weights of genetic and phenotypic markers in estimating population differentiation. The population structure of a salmonid fish, the Sakhalin taimen, in terms of eco-geographic units is considered as an example.     

Molecular and quantitative genetic differentiation in European populations of Silene latifolia (Caryophyllaceae)

BACKGROUND AND AIMS: Among-population differentiation in phenotypic traits and allelic variation is expected as a consequence of isolation, drift, founder effects and local selection. Therefore, investigating molecular and quantitative genetic divergence is a pre-requisite for studies of local adaptation in response to selection under variable environmental conditions. METHODS: Among- and within-population variation were investigated in six geographically separated European populations of the white campion, Silene latifolia, both for molecular variation at six newly developed microsatellite loci and for quantitative variation in morphological and life-history traits. To avoid confounding effects of the maternal environment, phenotypic traits were measured on greenhouse-reared F(1) offspring. Tests were made for clinal variation, and the correlations among molecular, geographic and phenotypic distances were compared with Mantel tests. KEY RESULTS: The six populations of Silene latifolia investigated showed significant molecular and quantitative genetic differentiation. Geographic and phenotypic distances were significantly associated. Age at first flowering increased significantly with latitude and exhibited a Q(st) value of 0.17 in females and 0.10 in males, consistent with adaptation to local environmental conditions. By contrast, no evidence of isolation-by-distance and no significant association between molecular and phenotypic distances were found. CONCLUSIONS: Significant molecular genetic divergence among populations of Silene latifolia, from the European native range is consistent with known limited seed and pollen flow distances, while significant quantitative genetic divergence among populations and clinal variation for age at first flowering suggest local adaptation.     

Range-wide genetic differentiation of Eugenia dysenterica (Myrtaceae) populations in Brazilian Cerrado

The analysis of geographic patterns in genetic variation has been one of the most important current tools to understand ecological and evolutionary processes underlying population structure. However, inferring such processes from population data may be misleading if biased geographic samples are analyzed. Here we expand previous analyses of Eugenia dysenterica population structure in Brazilian Cerrado, analyzing a larger number of populations distributed throughout a broader geographic region covering most of species' range. We provide new estimates of genetic diversity and population structure based on SSR markers from both neutral and genic regions, using several cluster and ordination techniques. These analyzes reveal a continuous northwestern-southeastern gradient in population differentiation, and not two distinct clusters of populations as suggested in some previous studies. This more comprehensive analysis also reinforces that a simple process of stochastic differentiation do not explain the observed patterns. Moreover, we conclude that explanations for population differentiation may focus on why genetic diversity decreases toward southeastern populations and not necessarily on barriers and interruption of gene flow creating regional patterns of population differentiation.     

Extreme genetic diversity in asexual grass thrips populations

The continuous generation of genetic variation has been proposed as one of the main factors explaining the maintenance of sexual reproduction in nature. However, populations of asexual individuals may attain high levels of genetic diversity through within‐lineage diversification, replicate transitions to asexuality from sexual ancestors and migration. How these mechanisms affect genetic variation in populations of closely related sexual and asexual taxa can therefore provide insights into the role of genetic diversity for the maintenance of sexual reproduction. Here, we evaluate patterns of intra‐ and interpopulation genetic diversity in sexual and asexual populations of Aptinothrips rufus grass thrips. Asexual A. rufus populations are found throughout the world, whereas sexual populations appear to be confined to few locations in the Mediterranean region. We found that asexual A. rufus populations are characterized by extremely high levels of genetic diversity, both in comparison with their sexual relatives and in comparison with other asexual species. Migration is extensive among asexual populations over large geographic distances, whereas close sexual populations are strongly isolated from each other. The combination of extensive migration with replicate evolution of asexual lineages, and a past demographic expansion in at least one of them, generated high local clone diversities in A. rufus. These high clone diversities in asexual populations may mimic certain benefits conferred by sex via genetic diversity and could help explain the extreme success of asexual A. rufus populations.     

Genetic differentiation in Eurasian populations of the postfire ascomycete Daldinia loculata

The genetic population structure of the postfire ascomycete Daldinia loculata was studied to test for differentiation on a continental scale. Ninety-six samples of spore families, each comprising mycelia from six to 10 spores originating from single perithecia, were sampled from one Russian and six Fennoscandian forest sites. Allelic distribution was assayed for six nuclear gene loci by restriction enzyme analyses of polymerase chain reaction (PCR)-amplified gene fragments. In addition, the full sequence of the gene fragment was analysed for a subset of haploid single-ascospore isolates in a multiallelic approach. A third data set was generated by using arbitrary-primed PCR with the core sequence of the phage M13 as primer. Although there was a reduction in heterozygosity in the total population from what would have been expected at random mating, the levels of genetic differentiation among the Eurasian subpopulations of D. loculata were low. All subpopulations were found to be in Hardy-Weinberg equilibrium and gametic equilibrium was observed between all investigated nuclear gene loci. The results obtained by the different markers were consistent; we confirmed low levels of genetic differentiation among the Eurasian subpopulations of D. loculata. The differentiation did not increase with distance; the Russian subpopulation, sampled more than 7000 km from the Fennoscandian subpopulations, was only moderately differentiated from the others (FST = 0.00-0.14). In contrast, one of the Swedish populations was the most highly differentiated from the others, with FST and GST values of 0.10-0.16. The results suggest that D. loculata consists of a long-lived background Eurasian population of latent mycelia in nonburned forests, established by sexual ascospores dispersed from scattered burned forest sites. Local differentiation is probably due to founder effects of populations in areas with low fire frequency. A tentative life cycle of D. loculata is presented.     

Microsatellite polymorphism and genetic differentiation in three Norwegian populations of Elymus alaskanus (Poaceae)

 Variation at seven microsatellite loci was investigated in three local E. alaskanus populations from Norway and microsatellite variation was compared with allozyme variation. The percentage of polymorphic loci was 81%, the mean number of alleles per polymorphic locus was 5.7 and expected heterozygosity was 0.37. An F-statistic analysis revealed an overall 48% deficit of heterozygotes over Hardy-Weinberg expectations. Gene diversity is mainly explained by the within population component. The averaged between population differentiation coefficient, F _st , over 7 loci is only 0.13, which accounts for only 13% of the whole diversity and was contrary to allozyme analysis. The mean genetic distance between populations was 0.12. However, a χ² -test showed that allele frequencies were different (p < 0.05) among the populations at 5 of the 7 loci. In comparison with the genetic variation detected by allozymes, microsatellite loci showed higher levels of genetic variation. Microsatellite analysis revealed that population H10576 possesses the lowest genetic variation among the tested three populations, which concur with allozyme analysis. The dendrogram generated by microsatellites agreed very well with allozymic data. Our results suggest that natural selection may be an important factor in shaping the genetic diversity in these three local E. alaskanus populations. Possible explanations for deficit heterozygosity and incongruence between microsatellites and allozymes are discussed. Received November 6, 2001; accepted April 24, 2002 Published online: November 14, 2002 Addresses of the authors: Genlou Sun (e-mail: Genlou.sun@STMARYS.CA), Biology Department, Saint Mary's University, Halifax. Nova Scotia, B3H 3C3, Canada. B. Salomon, R. von Bothmer, Department of Crop Science, The Swedish University of Agricultural Sciences, P.O. Box 44, SE-230 53, Alnarp, Sweden.     

Low genetic variability and strong differentiation among isolated populations of the rare steppe grass Stipa capillata L. in Central Europe

Stipa capillata L. (Poaceae) is a rare grassland species in Central Europe that is thought to have once been widespread in post‐glacial times. Such relict species are expected to show low genetic diversity within populations and high genetic differentiation between populations due to bottlenecks, long‐term isolation and ongoing habitat fragmentation. These patterns should be particularly pronounced in selfing species. We analysed patterns of random amplified polymorphic DNA (RAPD) variation in the facultatively cleistogamous S. capillata to examine whether genetic diversity is associated with population size, and to draw initial conclusions on the migration history of this species in Central Europe. We analysed 31 S. capillata populations distributed in northeastern, central and western Germany, Switzerland and Slovakia. Estimates of genetic diversity at the population level were low and not related to population size. Among all populations, extraordinarily high levels of genetic differentiation (amova : φ_ST = 0.86; Bayesian analysis: θ^B = 0.758) and isolation‐by‐distance were detected. Hierarchical amova indicated that most of the variability was partitioned among geographic regions (59%), or among populations between regions when the genetically distinct Slovakian populations were excluded. These findings are supported by results of a multivariate ordination analysis. We also found two different groups in an UPGMA cluster analysis: one that contained the populations from Slovakia, and the other that combined the populations from Germany and Switzerland. Our findings imply that S. capillata is indeed a relict species that experienced strong bottlenecks in Central Europe, enhanced by isolation and selfing. Most likely, populations in Slovakia were not the main genetic source for the post‐glacial colonization of Central Europe.     

Bioclimatic regions influence genetic structure of four Jordanian Stipa species

Strong environmental gradients can affect the genetic structure of plant populations, but little is known as to whether closely related species respond similarly or idiosyncratically to ecogeographic variation. We analysed the extent to which gradients in temperature and rainfall shape the genetic structure of four Stipa species in four bioclimatic regions in Jordan. Genetic diversity, differentiation and structure of Stipa species were investigated using amplified fragment length polymorphism (AFLP) molecular markers. For each of the four study species, we sampled 120 individuals from ten populations situated in distinct bioclimatic regions and assessed the degree of genetic diversity and genetic differentiation within and among populations. The widespread ruderals Stipa capensis and S. parviflora had higher genetic diversity than the geographically restricted semi‐desert species S. arabica and S. lagascae. In three of the four species, genetic diversity strongly decreased with precipitation, while genetic diversity increased with temperature in S. capensis. Most genetic diversity resided among populations in the semi‐desert species (Φ_ST = 0.572/0.595 in S. arabica/lagascae) but within populations in the ruderal species (Φ_ST = 0.355/0.387 S. capensis/parviflora). Principal coordinate analysis ( PCoA) and STRUCTURE analysis showed that Stipa populations of all species clustered ecogeographically. A genome scan revealed that divergent selection at particular AFLP loci contributed to genetic differentiation. Irrespective of their different life histories, Stipa species responded similarly to the bioclimatic gradient in Jordan. We conclude that, in addition to predominant random processes, steep climatic gradients might shape the genetic structure of plant populations.     

Herbivory and local genetic differentiation in natural populations of Arabidopsis thaliana (Brassicaceae)

To explore genetic variation in defence against the natural herbivores of Arabidopsis thaliana, we transplanted genotypes between a dune habitat and inland habitat in both of which A. thaliana occurred naturally. In previous years we had observed that the specialist weevils Ceutorhynchus atomus and C. contractus (Curculionidae) fed conspicuously on flowers and fruits of A. thaliana in the dunes, while these weevils were always rare in inland habitats. Taking all plants together, total fruit damage was indeed much higher in our experimental plots in the dune habitat (59.7%) relative to the inland garden habitat (18.9%). Within a habitat, additional differences existed between plants of different origins, pointing to genetic differences in ecologically relevant characters; plants of inland origin flowered a week earlier, grew better and produced more fruits than plants of dune origin. However, plants of inland origin experienced more total fruit damage by the specialist weevils (75.4%) than plants of dune origin (44.0%) when the two types grew side by side in the dune habitat. Escape from herbivory gives dune genotypes an advantage in their native habitat, whereas stronger growth and higher survival gives inland genotypes an edge under garden conditions.     

Low genetic diversity but local genetic differentiation in endemic Minasia (Asteraceae) species from Brazil

Espinhaço Range is a Brazilian chain of mountains, extremely rich in endemic species. Minasia has six species, all perennial herbs endemic to this range. Twenty-two populations were sampled from all Minasia species and assayed for allozyme variation. The species showed low genetic variation, compatible with the expectation for endemics. Genetic identities in Serra do Cipó and Diamantina were high, even between populations of different species. On the other hand M. cabralensis, from Serra do Cabral, was more differentiated from the other species. We also observed a marked genetic differentiation within M. cabralensis. Most strikingly, two close populations of this species showed very different allele frequencies. Our findings highlight the importance of local differentiation in campos rupestres. The observed genetic structure indicates that substantial portions of genetic diversity could be lost with the extinction of only one population, which is especially threatening considering the already low genetic diversity.     

Locus-specific genetic differentiation at Rw among warfarin-resistant rat (Rattus norvegicus) populations

Populations may diverge at fitness-related genes as a result of adaptation to local conditions. The ability to detect this divergence by marker-based genomic scans depends on the relative magnitudes of selection, recombination, and migration. We survey rat (Rattus norvegicus) populations to assess the effect that local selection with anticoagulant rodenticides has had on microsatellite marker variation and differentiation at the warfarin resistance gene (Rw) relative to the effect on the genomic background. Initially, using a small sample of 16 rats, we demonstrate tight linkage of microsatellite D1Rat219 to Rw by association mapping of genotypes expressing an anticoagulant-rodenticide-insensitive vitamin K 2,3-epoxide reductase (VKOR). Then, using allele frequencies at D1Rat219, we show that predicted and observed resistance levels in 27 populations correspond, suggesting intense and recent selection for resistance. A contrast of F(ST) values between D1Rat219 and the genomic background revealed that rodenticide selection has overwhelmed drift-mediated population structure only at Rw. A case-controlled design distinguished these locus-specific effects of selection at Rw from background levels of differentiation more effectively than a population-controlled approach. Our results support the notion that an analysis of locus-specific population genetic structure may assist the discovery and mapping of novel candidate loci that are the object of selection or may provide supporting evidence for previously identified loci.     

Plant species diversity and composition of experimental grasslands affect genetic differentiation of Lolium perenne populations

Contrasting hypotheses exist about the relationship between plant species diversity and genetic diversity. However, experimental data of species diversity effects on genetic differentiation among populations are lacking. To address this, Lolium perenne was sown with an equal number of seeds in 78 experimental grasslands (Jena Experiment) varying in species richness (1, 2, 4, 8 to 16) and functional group richness and composition (1-4; grasses, legumes, small herbs, tall herbs). Population sizes were determined 4years after sowing, and single-nucleotide polymorphism (SNP) DNA markers based on bulk samples of up to 100 individuals per population were applied. Genetic distances between the field populations and the initially sown seed population increased with sown species richness. The degree of genetic differentiation from the original seed population was largely explained by actual population sizes, which suggests that genetic drift was the main driver of differentiation. Weak relationships among relative allele frequencies and species diversity or actual population sizes, and a positive correlation between actual population sizes and expected heterozygosity also supported the role of genetic drift. Functional composition had additional effects on genetic differentiation of L. perenne populations, indicating a selection because of genotype-specific interactions with other species. Our study supports that genetic diversity is likely to be lower in plant communities with a higher number of interspecific competitors. Negative effects of species richness on population sizes may increase the probability of genetic drift, and selection because of genotype-specific interactions depending on species and genotypic community composition may modulate this relationship.     

Low levels of genetic differentiation characterize Australian humpback whale (Megaptera novaeangliae) populations

Humpback whales undertake long‐distance seasonal migrations between low latitude winter breeding grounds and high latitude summer feeding grounds. We report the first in‐depth population genetic study of the humpback whales that migrate to separate winter breeding grounds along the northwestern and northeastern coasts of Australia, but overlap on summer feeding grounds around Antarctica. Weak but significant differentiation between eastern and western Australia was detected across ten microsatellite loci (F_ST = 0.005, P = 0.001; D_EST = 0.031, P = 0.001, n = 364) and mitochondrial control region sequences (F_ST = 0.017 and Φ_ST = 0.069, P = 0.001, n = 364). Bayesian clustering analyses using microsatellite data could not resolve any population structure unless sampling location was provided as a prior. This study supports the emerging evidence that weak genetic differentiation is characteristic among neighboring Southern Hemisphere humpback whale breeding populations. This may be a consequence of relatively high gene flow facilitated by overlapping summer feeding areas in Antarctic waters.     

Evidence for genetic differentiation among Caspian tern (Hydroprogne caspia) populations in North America

The Caspian tern (Hydroprogne caspia) is a globally distributed seabird that breeds throughout North America, generally in low numbers. Many colonies are threatened by habitat loss and pollution. Additionally, adult terns compete directly with salmonid stocking programs on the west coast, where a large proportion of the fish they feed their young are stocked salmon smolts. North America colonies have been classified into five ‘breeding groups’ based on banding data and geography. To help delineate effective management units, we characterized variation in mitochondrial DNA (488 base pair fragment of cytochrome b) and five microsatellite loci among 111 terns from six sites representing three of the North American breeding areas. We found significant range-wide population differentiation (cytochrome b: global Φ_ST = 0.12, P < 0.01; microsatellites: global F_ST = 0.094, P < 0.001). Pacific Coast sites differed genetically from sites east of the Rocky Mountains, and sites in Central Canada differed from those in the Great Lakes region. Gene flow among these three regions appears to be restricted. Thus, our results indicate that at least three of the breeding regions delineated using banding data and geography should be treated as separate management units.     

内蒙古中东部草原区克氏针茅形态特征和RAPD遗传分化的相关性研究

以分布在内蒙古锡林郭勒盟东部草甸草原、中部典型草原和中西部荒漠化草原的4个克氏针茅种群为研究对象,采用形态学标记和RAPD分子标记相结合的方法进行遗传分化研究。结果表明：（1）无论是用形态学数据所得欧氏遗传距离矩阵还是用RAPD所得无偏差的Nei’s遗传距离矩阵,与种群分布的地理距离之间均不存在显著的相关关系,说明克氏针茅种群遗传分化受自然选择的影响。（2）种群之间存在显著的形态分化和遗传分化（p<0.05）。（3）对形态学数据所得欧氏遗传距离矩阵和RAPD所得Nei’s无偏差遗传距离矩阵进行Mantel检验所得结果不显著,表明对克氏针茅形态分化和遗传分化起主要作用的选择力是不完全相同的。