Spatial genetic structure of northern pike (Esox lucius) in the Baltic Sea

The genetic relationships among 337 northern pike (Esox lucius) collected from the coastal zone of the central Baltic region and the Finnish islands of Aland were analysed using five microsatellite loci. Spatial structure was delineated using both traditional F-statistics and individually based approaches including spatial autocorrelation analysis. Our results indicate that the observed genotypic distribution is incompatible with that of a single, panmictic population. Isolation by distance appears important for shaping the genetic structure of pike in this region resulting in a largely continuous genetic change over the study area. Spatial autocorrelation analysis (Moran's I) of individual pairwise genotypic data show significant positive genetic correlation among pike collected within geographical distances of less than c. 100-150 km (genetic patch size). We suggest that the genetic patch size may be used as a preliminary basis for identifying management units for pike in the Baltic Sea.     

Microsatellite genetic variation reveals extensive introgression between wild and introduced stocks, and a new evolutionary unit in French pike Esox lucius L.

The genetic variability of 11 French pike Esox lucius populations from rivers or extensive aquaculture ponds was analysed using seven microsatellite markers. The fish stocking of eastern European pike in French rivers is widespread, so five supplementary populations from this region were also analysed. Genetic variability within the French population was small, and similar to that previously found in Europe for this species. French populations from stocked rivers and extensive farms formed a genetically homogeneous group, and did not diverge from most eastern European samples, which may reflect either ancestral polymorphism or a complete introgression of French populations by introduced stocks. Bayesian analysis of the admixture between populations enabled identification of the French populations that were likely to be affected by introduced stocks (of local or foreign origin). Three genetically distinct evolutionary branches were identified: continental Europe, Danube basin, and south‐western France. The last is a new finding in the species which needs to be further explored by comparisons with wild populations at other sites.     

Landscape variability explains spatial pattern of population structure of northern pike (Esox lucius) in a large fluvial system

A growing number of studies have been investigating the influence of contemporary environmental factors on population genetic structure, but few have addressed the issue of spatial patterns in the variable intensity of factors influencing the extent of population structure, and particularly so in aquatic ecosystems. In this study, we document the landscape genetics of northern pike (Esox lucius), based on the analysis of nearly 3000 individuals from 40 sampling sites using 22 microsatellites along the Lake Ontario – St. Lawrence River system (750 km) that locally presents diverse degrees of interannual water level variation. Genetic structure was globally very weak (F_ST = 0.0208) but spatially variable with mean level of differentiation in the upstream section of the studied area being threefold higher (F_ST = 0.0297) than observed in the downstream sector (F_ST = 0.0100). Beside interannual water level fluctuation, 19 additional variables were considered and a multiple regression on distance matrices model (R² = 0.6397, P < 0.001) revealed that water masses (b = 0.3617, P < 0.001) and man‐made dams (b = 0.4852, P < 0.005) reduced genetic connectivity. Local level of interannual water level stability was positively associated to the extent of genetic differentiation (b = 0.3499, P < 0.05). As water level variation impacts on yearly quality and localization of spawning habitats, our study illustrates how temporal variation in local habitat availability, caused by interannual water level fluctuations, may locally decrease population genetic structure by forcing fish to move over longer distances to find suitable habitat. This study thus represents one of the rare examples of how environmental fluctuations may influence spatial variation in the extent of population genetic structure within a given species.     

Genetic characterization of 18 novel microsatellite loci in northern pike (Esox lucius L.)

The northern pike (Esox lucius L.), an important predatory freshwater species, is undergoing significant population decline. In this study, 18 novel polymorphic microsatellite loci were isolated and used for assessing genetic variation in the Chinese Ulungur and Hungarian Balaton populations of the species. The number of alleles ranged from 2 to 13, observed heterozygosity from 0.154 to 0.920 and expected heterozygosity from 0.145 to 0.921, thereby indicating the specific usefulness of these suites of markers for investigating genetic variability.     

A biochemical genetic analysis of populations of the northern pike, Esox lucius L., from Europe and North America

Genetic variation as identified by starch gel electrophoresis and enzyme staining was studied in seven populations of the northern pike, Esox lucius L. Samples derived from populations in northern U.S., Canada, Swedish fresh water, Swedish Baltic, the Netherlands, England and Ireland were analysed for variation at between 10 and 26 enzyme-coding loci. Polymorphism was found to be restricted to three loci: Sod-1 (mitochondrial superoxide dismutase), Ldh-2 (heart-type lactate dehydrogenase) and Got-1 (cytoplasmic glutamateoxalate transaminase). Mean heterozygosity ( H ) over all seven population samples was estimated to be 0·019. This extremely low variability, relative to reported data for other fish species, is discussed in terms of the structure and possible origins of pike populations.     

Population genetic structure and demographic history of the endemic Formosan lesser horseshoe bat (Rhinolophus monoceros)

Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. Taiwan formed around 5 million years ago from tectonic uplift, and has been connected to mainland Asia several times since its emergence. A central mountain range runs north to south, bisecting the island, and potentially impedes gene flow along an east-west axis. The Formosan lesser horseshoe bat (Rhinolophus monoceros) is endemic to Taiwan, where it is found mainly at low altitude. To determine the population structure and the demographic and colonization history of this species, we examined variation in the mitochondrial DNA control region in 203 bats sampled at 26 sites. We found very high haplotype and nucleotide diversity, which decreased from the centre to the south and north. Population differentiation followed a pattern of isolation by distance, though most regional genetic variance was attributable to differences between the relatively isolated southern population and those from other regions. A haplotype network was consistent with these findings and also suggested a southward colonization, followed by subsequent secondary contact between the south and other regions. Mismatch distributions were used to infer a past population expansion predating the last glacial maximum, and a neighbour-joining tree showed that R. monoceros formed a monophyletic grouping with respect to its sister taxa. Taken together, our results suggest that this taxon arose from a single period of colonization, and that demographic growth followed in the late Pleistocene. Current genetic structure reflects limited gene flow, probably coupled with stepwise colonization in the past. We consider explanations for the persistence of the species through multiple glacial maxima.     

Seasonal dynamics of fatty acid composition in female northern pike (Esox lucius L.)

Seasonal changes in the fatty acid composition of neutral and polar lipids were measured in the ovary, liver, white muscle, and adipopancreatic tissue of northern pike. The role of environmental and physiological factors underlying these changes was evaluated. From late summer (August–September) to winter (January–March), the weight percentage of n-3 polyunsaturated fatty acids (especially 22:6n3) declined significantly in the neutral lipids of all somatic tissues examined. However, large quantities of n-3 polyunsaturated fatty acids accumulated in the recrude cing ovaries during fall and the weight percentage of n-3 polyunsaturated fatty acids in ovary polar lipids also increased significantly. Additionally, the n-3 polyunsaturated fatty acid content of somatic polar lipids increased significantly during fall due to increases in the total polar lipid content of the somatic tissues. This suggests that during fall n-3 polyunsaturated fatty acid are diverted away from somatic neutral lipids and thereby conserved for use in ovary construction and for incorporation into tissue polar lipids. The percentage of n-3 polyunsaturated fatty acid in ovary neutral lipids also declined during fall and early winter, perhaps as an adaptation to conserve these fatty acids for storage in oocyte polar lipids and later incorporation into cellular membranes of the developing embryo. Reductions in the n-3 polyunsaturated fatty acids content of somatic and ovarian neutral lipids during fall were compensated for specifically by increases in the percentage of monounsaturated fatty acids rather than saturated fatty acids. This suggests that the ratio of saturated to unsaturated fatty acids in pike neutral lipid, is regulated physiologically, and hence may influence the physiological functioning of these lipids. During fall and early winter the percentage of saturated fatty acids declined significantly in the polar lipids of all tissues examined. This change was consistent with the known effects of cold acclimation on the fatty acid composition of cellular membranes. As the ovaries were recrudescing from September to January, liver polar lipids exhibited significant decreases in the percentage of total polyunsaturated fatty acids and n-3 polyunsaturated fatty acids and increases in monounsaturated fatty acids, and acquired a fatty acid composition very similar to that of ovary polar lipids. Therefore, seasonal changes in the percentage of polyunsaturated and monounsaturated fatty acids in liver polar lipids probably reflect the liver's role in vitellogenesis rather than the effects of temperature on membrane fatty acid composition. At all times of year, the fatty acid compositions of white muscle and adipopancreatic tissue neutral lipids were very similar, which may indicate a close metabolic relationship between these lipid compartments.Abbreviations AP adipopancreatic - BHT butylated hydroxytoluene - CI confidence interval - EFA essential fatty acids - MUFA monounsaturated fatty acids - NL neutral lipids - PL polar lipids - PUFA polyunsaturated fatty acids - SFA saturated fatty acids     

Some characteristics of a pike Esox lucius L. population in an Irish reservoir

A study of a stocked upland reservoir trout fishery, using gill nets, revealed the presence of a large stock of pike and poor trout numbers. The overall growth rate of pike was slow. Two year-classes of pike dominated, but the broad age and length frequency ranges, and the high average weight of individuals were indicative of an unexploited stock. Higher than normal water levels during the spawning period and into the summer period in both 1985 and 1986, coincided with the dominant pike year-classes recorded several years later. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genomic inbreeding and population structure of northern pike (Esox lucius) in Xinjiang,China

Northern pike (Esox lucius) was widely distributed in the high latitudes of the northern hemisphere. In China, northern pike was originally distributed only in the upper reaches of the Irtysh River in Xinjiang and has appeared in many water bodies outside the Irtysh River Basin in Northern Xinjiang. A total of four populations were collected from north to south in Xinjiang, including Irtysh River (RIR), Ulungu Lake (LUL), a small lake nearby Ulungu River (LJD), and Bosten Lake (LBO). We estimated population genomic parameters, performed gene flow analysis, and estimated the effective population size of each population. The proportion of individuals with high inbreeding coefficient (F ≥ 0.0625) accounted for 36.4% (44/121) of all sequenced individuals, approximately 4.5% (1/22) in LUL, 25.9% (7/27) in LBO, 42.9% (18/42) in RIR, and 60% (18/30) in LJD. RIR had the highest mean of genomic relatedness (coancestry coefficient = 0.025 ± 0.040, IBD = 0.036 ± 0.078). Gene flow results showed that the population spreading was from RIR into two branches, one was LBO, and the other continued to split into LUL and LJD, and migration signal from LBO to LUL was detected. Our results suggested that the extinction risk of northern pike was very low in Xinjiang of China, and the controlled capture fishery of northern pike could be developed reasonably.     

The influence of angling-induced exercise on the carbohydrate metabolism of northern pike (Esox lucius L.)

Summary Capture by angling was used to induce burst exercise in northern pike. By 3 h after exercise blood lactate had risen to levels of 15.2 mmol l⁻¹ (Fig. 2), which greatly exceeded the maximum post-exercise levels (4.0 mmol l⁻¹) previously reported for muskellunge, a close relative of pike. White muscle lactate level was high, 41.8 mmol kg⁻¹, immediately after capture but declined to 23.2 mmol kg⁻¹ by 6 h (Fig. 2). Blood glucose level more than doubled after exercise and remained elevated even after 96 h of recovery (Fig. 2). During the first 6 h after angling, pike disposed of 9.57 mmol (861 mg) of lactate per kg body weight. A whole body metabolic rate of 153 mg O₂ kg⁻¹ h⁻¹ is sufficient to account for this rate of lactate removal through oxidation (Table 3). However, the metabolic rate of the highly oxidative organs and tissues (red muscle, gills, liver, kidney, heart, and spleen) must be very high (>1,000 mg O₂ kg⁻¹ h⁻¹) to oxidize even 60% of the lactate that disappeared from pike after exercise (Fig. 5). Mortality of pike from angling stress was less than 3%.     

Microsatellite analysis of demographic genetic structure in fragmented populations of the tropical tree Symphonia globulifera

We developed genetic markers for three microsatellite loci in the tropical tree Symphonia globulifera and used them to examine the demographic genetic consequences of forest fragmentation. High levels of genetic variation were revealed in samples of adults, saplings, and seedlings. The more-variable loci exhibited less stability in allelic composition across sites and stages. The number of alleles per hectare (ha) of forest was similar when continuous forest plots were compared to plots from fragmented forest for all three stages. This pattern also held for the number of unique multilocus adult and sapling genotypes, but the number of unique seedling genotypes per ha of fragmented forest greatly exceeded expectations based on continuous forest data, probably due to the concentration of seeds into remnant forest patches by foraging bats. Significant inbreeding and genetic differentiation were most often associated with the fragmented forest and the seedlings. Finally, principal component analysis reaffirmed that a bottleneck, acting in concert with pre-existing genetic structure in the adults, had led to enhanced and rapid divergence in the seedlings following deforestation, a result that is of central interest for landscape management.     

Microsatellite analysis of natterjack toad Bufo calamita Laurenti populations: consequences of dispersal from a Pleistocene refugium

Populations of the amphibian Bufo calamita were sampled for genetic analysis in eleven areas distributed across its biogeographical range in Europe. Genetic diversity estimates across eight microsatellite loci showed a decline in polymorphism, numbers of alleles and heterozygosity as a function of distance from the presumed ice-age refugium in Iberia. Trials with a selection of tree-building algorithms indicated mat UPGMA of Cavalli-Sforza chord distances (D_c) generated the tree topology most easily reconciled with other biogeographical information. Genetic distance measures were also calibrated against a postglacial event from which the separation of extant populations could be estimated in real time. D_c again outperformed two other measures (Nei's standard distance, D_s , and δμ²) in producing realistic correlations with minimal variance. The genetic analysis was consistent wim die hypodiesis that B. calamita survived in a single refugium (Iberia) during the Pleistocene glaciation and indicated that it spread north and east from there during the last interstadial which commenced about 14 000 years before present (BP). Microsatellites should provide useful tools for biogeographical investigations of other species, especially with respect to patterns of population dispersal.     

Microsatellite analysis of genetic structure in the mangrove species Avicennia marina (Forsk.) Vierh. (Avicenniaceae)

The level of genetic variation throughout the entire worldwide range of the mangrove species Avicennia marina (Forsk.) Vierh. was examined using microsatellite markers. Three microsatellite loci detected high levels of allelic diversity (70 alleles in total), essential for an accurate estimation of population genetic parameters. The informativeness of the microsatellite loci tended to increase with increasing average number of repeats. The levels of heterozygosity detected for each population, over all loci, ranged from 0.0 to 0.8, with an average of 0.407, indicating that some populations had little or no genetic variation, whereas others had a large amount. Populations at the extremes of the distribution range showed reduced levels of heterozygosity, and significant levels of inbreeding. This is not unexpected as these populations may be subject to founder effects and environmental constraints. The presence of genetic structure was tested in A. marina populations using three models: (i) a single panmictic model; (ii) the discrete subpopulation model; and (iii) the isolation by distance model. The discrete subpopulations model was supported by the overall measures of population differentiation based on the infinite alleles model (F-statistics), and the stepwise mutation model (R statistics). In addition, an analysis of molecular variance (AMOVA), using both theoretical models, found that most of the variation was between populations (41-71%), and within individuals in the total population (31-49%). There was little variation among individuals within populations (0-10%). There was no significant isolation by distance. The high levels of genetic differentiation observed among populations of A. marina may be due to environmental and ecological factors, particularly past sea level and climatic changes.     

Population structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variation

Atlantic salmon (n = 1682) from 27 anadromous river populations and two nonanadromous strains ranging from south-central Maine, USA to northern Spain were genotyped at 12 microsatellite DNA loci. This suite of moderate to highly polymorphic loci revealed 266 alleles (5-37/locus) range-wide. Statistically significant allelic and genotypic heterogeneity was observed across loci between all but one pairwise comparison. Significant isolation by distance was found within and between North American and European populations, indicating reduced gene flow at all geographical scales examined. North American Atlantic salmon populations had fewer alleles, fewer unique alleles (though at a higher frequency) and a shallower phylogenetic structure than European Atlantic salmon populations. We believe these characteristics result from the differing glacial histories of the two continents, as the North American range of Atlantic salmon was glaciated more recently and more uniformly than the European range. Genotypic assignment tests based on maximum-likelihood provided 100% correct classification to continent of origin and averaged nearly 83% correct classification to province of origin across continents. This multilocus method, which may be enhanced with additional polymorphic loci, provides fishery managers the highest degree of correct assignment to management unit of any technique currently available.     

间颅鼠兔的种群遗传结构和历史演化动态

本研究基于多个线粒体基因（包括COI、Cyt b、tRNA-Thr、tRNA-Pro、D-loop控制区部分序列共计2417bp）对间颅鼠兔（Ochotona cansus）的种群遗传结构和历史演化动态进行了研究。基于线粒体基因联合数据构建的贝叶斯树显示,间颅鼠兔分为两大支系：来自岷山山系东部的甘肃白水江和四川唐家河的种群组成了支系一;其余采样点的种群组成了支系二。基于以上基因所构建的单倍型网络图显示的遗传结构与贝叶斯树一致。贝叶斯聚类分析（BAPS）将间颅鼠兔分为4个地理种群。A种群包括甘肃白水江（BSJ）和四川唐家河（TJH）的样本;B种群仅包括四川卧龙（WL）的样本;C种群包括青海北部种群（GC、MY、QL）、青海南部-四川北部种群（JW、JZ、ZK、RE）、四川康定（KD）和陕西太白山（TB）的样本;D种群包括山西娄烦（LF）以及陕西吴起（WQ）的样本。基于线粒体基因构建的物种树进行支系分化时间的推测,结果显示4个地理种群的分化时间约为0.72 Ma、0.32 Ma、0.12 Ma, 这与造成青藏高原剧烈隆起的昆黄运动（1.10-0.60Ma）和共和运动（0.15Ma）发生时间基本吻合。采用中性检验、错配分布、扩展贝叶斯天际线（EBSPs）3种方法对间颅鼠兔的种群历史动态进行预测,分析结果显示间颅鼠兔在历史上并没有经历过显著的种群扩张,而且在末次盛冰期后开始衰减。生态位模型（ENM）预测结果表明：末次盛冰期时间颅鼠兔的潜在分布区比其现今分布区小,末次盛冰期比末次间冰期潜在分布区略大,表明间颅鼠兔受末次盛冰期影响较大。气候因子分析显示降水比温度对间颅鼠兔种群影响更大,推测降水对植被的演化影响显著,从而影响间颅鼠兔的食物来源和栖息环境。     

乔氏新银鱼基于细胞色素b序列的种群遗传结构和种群历史

为促进乔氏新银鱼(Neosalanx jordani)种质资源的保护, 采集了长江流域和淮河流域5个乔氏新银鱼地理种群计129个样本, 利用线粒体细胞色素b基因(Cyt b)全序列作为分子标记, 初步分析了乔氏新银鱼种群的遗传多样性、遗传结构及种群历史动态。研究结果共检测到18个Cyt b单倍型, 发现和其他鱼类相比, 乔氏新银鱼具有较高的单倍型多样性(h, 0.590±0.047), 但核苷酸多样性较低(π, 0.00088±0.00011)。分子变异分析(AMOVA)表明, 乔氏新银鱼5个地理种群内个体间和流域内种群间均存在显著的遗传差异, 而长江流域与淮河流域之间遗传分化不明显, 显示乔氏新银鱼遗传分化与当前水系的分布格局不吻合。结果表明乔氏新银鱼目前的遗传格局主要是由于长距离独立的建群事件、基因流限制以及种群的持续扩张的共同作用而形成的。种群历史动态分析结果显示乔氏新银鱼种群为近期扩张种群, 其大部分变异发生在1.897万年之内, 与最后一次冰期全面消退、海平面上升、长江流域及淮河流域中下游大量湖泊(适宜生境)形成的时间相吻合。建议对现存的乔氏新银鱼种群, 特别是遗传多样性较高的那些种群(如鄱阳湖、太湖及洪泽湖种群)分别保护。     

Phylogeography and genetic structure of northern populations of the yellow warbler (Dendroica petechia)

Phylogeographic patterns of intraspecific variation can provide insights into the population-level processes responsible for speciation and yield information useful for conservation purposes. To examine phylogeography and population structure in a migratory passerine bird at both continental and regional geographical scales, we analysed 344 bp of mitochondrial DNA (mtDNA) control region sequence from 155 yellow warblers (Dendroica petechia) collected from seven locations across Canada and from Alaska. There is a major subdivision between eastern (Manitoba to Newfoundland) and western (Alaska and British Columbia) populations which appears to have developed during the recent Pleistocene. Some localities within these two regions also differ significantly in their genetic composition, suggesting further subdivision on a regional geographical scale. Eastern and western birds form distinct phylogeographic entities and the clustering of all western haplotypes with two eastern haplotypes suggests that the western haplotypes may be derived from an eastern lineage. Analyses based on coalescent models support this explanation for the origin of western haplotypes. These results are consistent with important features of Mengel's model of warbler diversification. From a conservation perspective they also suggest that individual populations of migrant birds may form demographically isolated management units on a smaller scale than previously appreciated.     

Microsatellite variation and assessment of genetic structure in tea tree (Melaleuca alternifolia– Myrtaceae)

Analysis of five microsatellite loci in 500 Melaleuca alternifolia individuals produced 98 alleles that were useful for population genetic studies. Considerable levels of observed heterozygosity were recorded (HO = 0.724), with approximately 90% of the variability being detected within populations. A low level of selfing (14%) was suggested to be the principal cause of excess homozygosity in a number of populations (overall FIS = 0.073). This study showed low levels of inbreeding in certain populations as well as a significant isolation-by-distance model. Only two groups of populations (Queensland and New South Wales) constituted different genetic provenances as a result of geographical isolation. The M. alternifolia data suggest that microsatellite loci did not always arise by a stepwise mutation process but that larger jumps in allele size may be involved in their evolution.