Genetic variation and the relationship between stream and lake ecotypes of a threatened desert Catostomid,the Warner sucker (Catostomus warnerensis)

Many fish species exhibit diverse life history strategies that help maintain population viability. An understanding of the relationships among these strategies is crucial for prioritising conservation actions. The Warner sucker, endemic to the Warner Lakes Basin in southern Oregon, USA, is one example of a taxon where a lack of information regarding relationships among life history strategies has hampered conservation efforts. Warner suckers have two distinct life history types: stream‐type fish that have a fluvial life history and lake‐type fish that have an adfluvial life history. There are advantages and disadvantages associated with each life history, and presently the relationship between life history types is not well understood. Our objectives were to determine the amount of genetic variation within and among tributary populations of Warner suckers and to determine the origins of suckers collected in the Warner Lakes. We collected individuals from four tributary populations, a refugial population, and Hart and Crump lakes and genotyped them at 16 microsatellite loci. Estimates of genetic variation among populations suggested low levels of gene flow (F_ST = 0.153) and genetic variation among populations seemed to be influenced by population and habitat characteristics. Nearly all of the individuals collected in Hart and Crump lakes originated in a single tributary, Deep Creek, which likely reflects reduced habitat connectivity between most other tributaries and the Warner Lakes. Data presented in this study are useful for evaluating the status of Warner sucker populations and for prioritising conservation actions such as the removal and modification of barriers.     

A review of ecological models for brown trout: towards a new demogenetic model

Abstract – Ecological models for stream fish range in scale from individual fish to entire populations. They have been used to assess habitat quality and to predict the demographic and genetic responses to management or disturbance. In this paper, we conduct the first comprehensive review and synthesis of the vast body of modelling literature on the brown trout, Salmo trutta L., with the aim of developing the framework for a demogenetic model, i.e., a model integrating both population dynamics and genetics. We use a bibliometric literature review to identify two main categories of models: population ecology (including population dynamics and population genetics) and population distribution (including habitat–hydraulic and spatial distribution). We assess how these models have previously been applied to stream fish, particularly brown trout, and how recent models have begun to integrate them to address two key management and conservation questions: (i) How can we predict fish population responses to management intervention? and (ii) How is the genetic structure of fish populations influenced by landscape characteristics? Because salmonid populations tend to show watershed scale variation in both demographic and genetic traits, we propose that models combining demographic, genetic and spatial data are promising tools for improving their management and conservation. We conclude with a framework for an individual‐based, spatially explicit demogenetic model that we will apply to stream‐dwelling brown trout populations in the near future.     

Census and effective population sizes of white‐spotted charr (Salvelinus leucomaenis) in a fragmented landscape

Several habitat models have been proposed to predict population size for stream fishes and to guide habitat assessment and monitoring techniques. However, most models do not incorporate the potential advantage of molecular genetic markers. We conducted a field survey and microsatellite DNA analyses to quantify the relationships among genetic diversity, census/effective population size and habitat variables in fragmented populations of white‐spotted charr (Salvelinus leucomaenis). The census population size significantly increased with the stream length, the number of pools and a pool‐riffle sequence index, a proxy for channel‐unit habitat type complexity within reaches. Population density was correlated with the pool‐riffle sequence index only. Genetic diversity and effective population size were not correlated with the habitat variables or census population size. There was a lack of isolation‐by‐distance population structure in the studied populations. Our results suggest that stream length and the number of pools within reaches associated with habitat complexity are the habitat variables that explain the majority of variation in population size of white‐spotted charr. Our findings provide further evidence that census population size per se is a poor indicator of the inclusive genetic diversity within populations in a fragmented landscape.     

Microsatellite diversity assessment of brown trout (Salmo trutta) population structure indicate limited genetic impact of stocking in a Norwegian alpine lake

Abstract – Releases of non-native trout often result in introgression into natural populations and negative genetic effects. The causal ecological mechanisms for a wide range of reported outcomes are poorly understood. Brown trout population structure in an alpine lake with three major recruitment streams was assessed by analysis for eight DNA microsatellite markers and compared with the non-native population. The lake is subject to a 40-year recorded history of stocking with exogenous trout. No certain deviations from Hardy–Weinberg equilibrium were found. Tests for population differentiation and genetic distance indicated separate populations for all the sampled areas, and with the exogenous population as a cluster quite different from the others. Assignment tests indicated that only a small fraction of the fish sampled from the lake originated from the introduced trout strain (<3%). Wild discriminate, naturally reproducing populations characterize this alpine lake ecosystem, in spite of 40 years of stocking, which appears to have had a limited impact. It is unlikely that this population structure can ultimately be explained by trout movement patterns. Genetic analysis needs to be supplemented by studies of local life history strategies, to evaluate the relative importance of local adaptation versus random genetic differentiation, because implications for conservation and management are different.     

Reliance on lakes by salmon,trout and charr (Oncorhynchus,Salmo and Salvelinus): An evaluation of spawning habitats,rearing strategies and trophic polymorphisms

Salmonid fishes may reside within or migrate between stream and lake habitats, or undergo anadromous migrations between freshwater and the ocean. While the degree of anadromy of salmonids has been thoroughly compared, no analogous review has examined the degree of lake use. To assess the extent of reliance on lake habitat in this family, we considered 16 species of salmon, trout and charr from the genera Oncorhynchus, Salmo and Salvelinus, comparing their (a) use of lakes as spawning habitat, (b) rearing strategies in lakes, and (c) occurrence and diversity of lacustrine trophic polymorphism. In identifying the primary life‐history patterns of each species and exploring the lesser‐known lacustrine behaviours, we found that the extent of reliance on lakes exhibits a negative association with the degree of anadromy. Oncorhynchus rely least on lakes, Salmo to an intermediate level and Salvelinus the most, opposite of the general prevalence of anadromy among these genera. Lakes are critical to adfluvial and lake‐resident salmonids, but they also support anadromous and fluvial life histories by providing spawning, rearing, overwintering and/or summer refuge habitat. Adfluviality, although a non‐anadromous life history, consists of similar migration‐related traits and behaviours as anadromy, including the parr–smolt transformation, sex‐biased patterns of migration and residency, and the presence of precocious males. Lakes support life‐history variants, reproductive ecotypes and trophic morphs unique to lacustrine habitat. Therefore, conservation of salmonids is dependent on maintaining the diversity and quality of their habitats, including lakes.     

A genetic comparison of sympatric anadromous and resident Atlantic salmon

Many studies have identified the importance of local adaptation in Atlantic salmon (Salmo salar) and the strong genetic differences that exist between allopatric or parapatric resident and anadromous populations. However, as truly sympatric migratory phenotypes of Atlantic salmon have not been studied, it remains unclear whether distinct genotypes previously associated with life history differences are maintained through reproductive isolation and subsequent genetic drift or through natural selection induced by different life history requirements. In this study, sympatric anadromous and resident Atlantic salmon were sampled from three Newfoundland (Canada) watersheds to evaluate the genetic divergence of these life history forms. Eight microsatellite loci were used to quantify genetic variation within and among populations. Metrics of genetic differentiation (exact tests for population differentiation, pairwise θ values) provide no evidence of genetic differentiation between some sympatric anadromous and resident phenotypes within a system with no history of segregation. In the remaining two watersheds, the observed differentiation appears to be a consequence of historical segregation rather than life history form. Nonetheless, these differences have been maintained in contemporary times for several generations. At broader spatial scales, resident salmon were more genetically divergent from one another than anadromous life history forms and were more closely related to anadromous salmon from within their watershed than to resident salmon from other watersheds. The study indicates that both life history forms can be maintained within a single population, but that sympatric populations of different life histories can maintain genetic differences for at least several generations after being reconnected.     

基于线粒体控制区的江苏湖鲚群体遗传多样性和遗传结构分析#br#

为掌握江苏省重要湖泊湖鲚(Coilia nasus taihuensis)群体的遗传多样性和遗传结构,利用线粒体控制区(D-loop)全序列分析了6个湖泊(太湖、滆湖、高邮湖、白马湖、洪泽湖和骆马湖)湖鲚野生群体的遗传多样性水平和群体分化情况。结果表明,6个群体共214尾样本的D-loop序列中,共发现103个变异位点,92种单倍型。6个群体的单倍型多样性为0.726~0.951,核苷酸多样性为0.00552~0.01036,6个群体整体的单倍型和核苷酸多样性分别为0.857和0.00729,表明湖鲚群体的遗传多样性较高,且符合高单倍型多样性和低核苷酸多样性特点。分子方差分析(AMOVA)结果表明,群体间变异百分比为6.20%,群体内变异百分比为93.80%,说明遗传变异主要来自群体内部。群体总的遗传分化系数(F_st)为0.06199(P<0.01),两两群体间的F_st显示,滆湖群体与其他群体间存在极显著的遗传分化(P<0.001),而其他群体间无显著分化(P>0.05)。单倍型分子系统进化树和网络进化图显示,6个群体的单倍型形成了2个谱系,但谱系组成与群体地理分布无相关性。中性检验分析结果显示,湖鲚群体进化过程中经历过种群扩张,扩张时间大约发生在0.089~0.160百万年前。研究结果表明,湖鲚群体具有较高的遗传多样性,滆湖群体与其他群体具有极显著的遗传分化,且拥有多个独享单倍型,应将滆湖群体单独作为一个管理单位,其他5个群体作为一个整体进行管理和利用。     

Diverse juvenile life‐history behaviours contribute to the spawning stock of an anadromous fish population

Habitat quality often varies substantially across space and time, producing a shifting mosaic of growth and mortality trade‐offs across watersheds. Traditional studies of juvenile habitat use have emphasised the evolution of single optimal strategies that maximise recruitment to adulthood and eventual fitness. However, linking the distribution of individual behaviours that contribute to recruitment at the population level has been elusive, particularly for highly fecund aquatic organisms. We examined juvenile habitat use within a population of sockeye salmon (Oncorhynchus nerka) that spawn in a watershed consisting of two interconnected lakes and a marine lagoon. Otolith microchemical analysis revealed that the productive headwater lake accounted for about half of juvenile growth for those individuals surviving to spawn in a single river in the upper watershed. However, 47% of adults had achieved more than half of their juvenile growth in the downstream less productive lake, and 3% of individuals migrated to the estuarine environment during their first summer and returned to freshwater to overwinter before migrating back to sea. These results describe a diversity of viable habitat‐use strategies by juvenile sockeye salmon that may buffer the population against poor conditions in any single rearing environment, reduce density‐dependent mortality and have implications for the designation of critical habitat for conservation purposes. A network of accessible alternative habitats providing trade‐offs in growth and survival may be important for long‐term viability of populations.     

Explaining spatial variability in stream habitats using both natural and management‐influenced landscape predictors

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Genetic diversity of two Philippine native freshwater goby species (Perciformes: Gobiidae): implications for conservation

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Genetic diversity and population history of Tanichthys albonubes (Teleostei: Cyprinidae): Implications for conservation

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Genetic differentiation of the bronze featherback Notopterus notopterus between Mekong River and Tonle Sap Lake populations by mitochondrial DNA analysis

ABSTRACT:   Although the bronze featherback Notopterus notopterus is an important fish in South-East Asia, the population structure has not been investigated. In this study, genetic diversity and population structure of the bronze featherback were examined using nucleotide sequence analysis of the mitochondrial DNA control region for 332 fish collected from Tonle Sap Lake and the Mekong River in Cambodia. The average nucleotide diversity (π) of all samples was 0.033, and the Mekong River samples had higher nucleotide diversity (0.034) than Tonle Sap Lake samples (0.028). The nucleotide diversity between the lake and river samples varied from 0.029 to 0.037. The genetic differentiation between the river and lake populations was also supported by the pairwise F -statistic values and hierarchical analysis of molecular variance, indicating that the Tonle Sap Lake population is genetically isolated from the population in main stream of the Mekong River.     

Do dams increase genetic diversity in brown trout (Salmo trutta)? Microgeographic differentiation in a fragmented river

Abstract – Local genetic differentiation may potentially arise in recently fragmented populations. Brown trout is a polytypic species exhibiting substantial genetic differentiation, which may evolve in few generations. Movement (semi‐)barriers in rivers may cause fragmentation, isolation and genetic differentiation in fish. In the Måna River (28 km) flowing from the alpine Lake Møsvatn to the boreal Lake Tinnsjø, construction of four hydropower dams during the period 1906–1957 have fragmented the previously (since last Ice Age) continuous wild resident brown trout population. Samples from the two lakes (N = 40) and six sites in the river (N = 30) isolated at different times were analysed at nine microsatellite loci. All populations showed substantial genetic variation (mean number of alleles per locus 5.3–8.9, observed heterozygosity 0.57–0.65 per population, overall F_st = 0.032). Pairwise multilocus F_st estimates indicated no significant differentiation between populations in the two lakes, and no or little differentiation in the lower river (F_st = 0.0035–0.0091). The microgeographic differentiation among wild resident trout at these sites was less than expected based on similar previous studies. However, results from the upper river, in particular the site immediately below the Lake Møsvatn outlet and dam, indicated isolation (F_st > 0.035). Calculation of genetic distances and assignment tests corroborated these results, as did a significant correlation between years of isolation (since dam construction) and F_st. The population structuring is most likely a result of fragmentation by dams, which has increased overall genetic diversity. This increased local differentiation may be caused by natural selection, but more likely by genetic drift in small, recently fragmented populations. Increased local genetic diversity by genetic drift does not justify conservation measures aiming at preserving genetic diversity.     

Seasonal patterns of downstream movement in partially migratory stream‐dwelling Dolly Varden

Migration is a common behaviour among salmonids, but not all individuals within a population migrate, instead becoming residents and remaining in their natal streams. This phenomenon, known as “partial migration,” is well studied among sea‐run and lake‐run populations; however, the lower migratory benefits and costs for mainstem‐run individuals question whether the same mechanisms can be applied for stream‐dwelling salmonids. In this study, we investigated main stem‐run timing and body condition of partially migratory stream‐dwelling Dolly Varden charr (Salvelinus malma) in the Shiisorapuchi River in central Hokkaido, Japan. Based on commonly observed patterns in sea‐run and lake‐run salmonids, we predicted that migration would occur during spring and consist predominantly of age 1 +  females with some small subordinate males. Traps were placed at the mouths of two small tributaries along the Shiisorapuchi River periodically from May to December 2015. Adipose fin samples were taken for DNA to sex the individuals. Consistent to initial predictions, downstream movement occurs only once in the spring, dominated by age‐1 +  females. Trapped fishes (presumed migrants) were slightly longer but slimmer compared to the fish caught in the tributaries (presumed resident), which may be equivalent to smolts in anadromous populations. Regardless of migratory habitat, mechanisms driving partial migration in salmonids may be the same as long as production between natal stream and feeding habitats is significantly different.     

基于线粒体Cyt b基因序列的绿鳍马面鲀6个野生群体的遗传结构分析

利用线粒体细胞色素b(cytochrome b,Cyt b)基因分析了我国沿海绿鳍马面鲀(Thamnaconus septentrionalis)6个野生群体(大连、秦皇岛、蓬莱、日照、舟山和汕头)的遗传多样性和群体遗传结构。结果显示,在176个个体915 bp的Cyt b部分序列中共检测到32个变异位点和30个单倍型;6个群体的单倍型多样性为0.883~0.953,核苷酸多样性0.0032~0.0039;群体间固定指数较小,呈中低度分化;AMOVA分析表明,遗传变异主要来源于群体内,群体间遗传分化未达到显著水平。群体历史动态分析表明,绿鳍马面鲀在16.9万~42.2万年前经历种群扩张。总体上,各群体间的遗传分化较小,并未形成相应的地理支系,推测黑潮的输送作用以及绿鳍马面鲀的洄游习性维持了各群体间高强度的基因交流;中更新世中晚期的气候波动对绿鳍马面鲀的种群扩张以及地理分布格局可能具有重要影响。本研究结果加深了人们对于绿鳍马面鲀资源情况的认识,为绿鳍马面鲀资源的保护和合理利用提供了理论依据。     

Conservation of freshwater wildlife in Hong Kong: A genetic perspective

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Population genetic structure of Atlantic salmon,Salmo salar L., in the River Tamar,southwest England

Abstract Population genetic studies can be useful for informing conservation and management. In Atlantic salmon, Salmo salar L., population structuring frequently occurs between river systems, but contrasting patterns occur within rivers, highlighting the need for catchment‐specific studies to inform management. Here, population structure of Atlantic salmon was examined in the River Tamar, United Kingdom, using 12 microsatellite loci. Gene diversity and allelic richness ranged from 0.80 to 0.84 and from 8.96 to 10.24, respectively. Some evidence of genetic structure was found, including significant genetic differentiation between samples in different subcatchments (pairwise θ and tests of genic differentiation), results from assignment tests and a pattern of isolation by distance. Conversely, structure revealed only one population cluster, and an analysis of molecular variance showed no significant variation between subcatchments. Evidence of population bottlenecks depended on the mutation model assumed and is discussed with reference to catchment‐specific studies of stock abundance. Implications for implementing management actions are considered.     

乌鳢群体遗传多样性和遗传结构分析

为了解乌鳢群体遗传变异规律,本研究对8个群体共212个个体的mtDNA控制区全序列进行群体遗传多样性、遗传结构和群体历史动态分析。结果显示,乌鳢控制区全序列长度为907 bp,乌鳢群体单倍型多样性水平变化较大,中国黄河及以北的乌鳢群体单倍型多样性水平比淮河和长江等南方群体相对较低,所有群体表现出较低的核苷酸多样性水平(h0.5%)。基于单倍型构建的系统发育树和群体聚类树结果均未显示出与地理位置相对应的谱系结构。单倍型网络图显示存在多个主单倍型。遗传结构分析显示,不同水系间存在显著的遗传差异,相同水系间遗传差异较小。群体历史动态分析显示,中国乌鳢所有群体有效种群数量在中更新世晚期到晚更新世0.222—0.050百万年出现了一次较明显的快速增长,之后在晚更新世末次冰期0.050—0.010百万年出现了有效种群下降,伴随着全新世到来,在0.010百万年之后,乌鳢群体又发生了一次较小的有效种群增长。洞庭湖群体则发生一次有效种群的快速增长,增长时间大约在0.160百万年。研究表明,青藏高原隆起后,东亚季风在中国南北方气候的差异和秦岭山脉屏障对季风的阻断作用加大了这一差异,可能对乌鳢群体的遗传多样度差异造成一定影响。乌鳢群体不存在显著的谱系结构可能与乌鳢遗传分化时间较短有关,但是地理隔离等因素导致了不同水系间确切的遗传差异。第四纪更新世气候的波动,尤其是中更新世间冰期气候的转暖、末次盛冰期的降温和冰后期全新世的到来可能对乌鳢群体的数量和栖息地的扩缩起着重要影响。     

From regionally predictable to locally complex population structure in a freshwater top predator: river systems are not always the unit of connectivity in Northern Pike Esox lucius

Contemporary genetic diversity is the product of both historical and contemporary forces, such as climatic and geological processes affecting range distribution and continuously moulded by evolutionary forces selection, gene flow and genetic drift. Predatory freshwater fishes, such as Northern Pike Esox lucius, commonly exhibit small population sizes, and several local populations are considered endangered. Pike inhabit diverse habitat types, including lakes, rivers and brackish marine waters, thus spanning from small isolated patches to large open marine systems. However, pike population structure from local to regional scales is relatively poorly described, in spite of its significance to developing conservation measures. We analysed microsatellite variation in a total of 1185 North European pike from 46 samples collected across both local and regional scales, as well as over time, to address two overarching questions: Is pike population structure associated with local and/or regional connectivity patterns, and which factors likely have the main influence on the contemporary distribution of genetic diversity? To answer this, we combined estimators of population diversity and structure to assess evidence of whether populations within (i) habitats, (ii) drainage systems and (iii) geographical regions are closer related than among these ranges, and whether patterns are temporally stable. Contrasting previous predictions that genetic drift obscures signals of postglacial colonisation history, we identified clear regional differences in population genetic signatures, suggesting a major effect of drainage divides on colonisation history and connectivity. However, several populations deviated from the general pattern, showing that local processes may be complex and need to be examined case‐by‐case.     

魁蚶4个地理群体遗传结构的RAPD分析

应用RAPD标记技术对魁蚶Scapharca broughtonii1个韩国群体与3个中国群体的遗传多样性进行RAPD分析。对4个群体的133个个体进行扩增,共检测到171个位点。其中,多态性位点为167个,4个群体的多态性位点比例:韩国群体为86.55%、黄岛群体为90.06%、蓬莱群体为85.96%和前三岛群体为89.47%;4个群体的Shannon’s多样性指数为(0.460±0.232)~(0.491±0.214),Nei’s多样性指数为(0.308±0.171)~(0.331±0.199),表明4个群体遗传多态性较高;4个群体遗传分化指数在0.006~0.121之间。其中,韩国与中国的3个群体分化明显,说明韩国与中国3个群体的遗传结构差异较大,黄岛群体与前三岛群体间的遗传分化最小。基于4个群体Nei’s遗传距离的UPGMA方法进行聚类分析显示,黄岛群体与前三岛群体最先聚类,两群体间距离最短,再与蓬莱群体聚类,最后与韩国群体聚类。这些数据可为魁蚶种质资源的合理开发和保护及遗传改良提供科学依据。