Meta‐analysis of growth rates for a circumpolar fish,the northern pike ( Esox lucius), with emphasis on effects of continent,climate and latitude

For circumpolar species, little is known on how somatic growth rates can vary at large, transcontinental spatial scales. In this study, a meta‐analysis of growth rates was conducted for northern pike ( Esox lucius) across North America and Eurasia. Growth rates of northern pike did not differ between North American and ‘coastal Eurasian’ pike (e.g., UK, Ireland, Sweden), while growth rates for both of these groups were significantly higher compared to ‘inland Eurasian’ pike (mainly in Russia). There was no difference in growth between lentic and lotic habitats on either continent. In North America, pike growth was positively correlated with temperature, but in Eurasia, pike growth correlated poorly with most climatic variables. Similarly, maximum longevity in pike populations was significantly predicted by latitude in North America, but not in Eurasia. After standardising annual pike growth by the thermal opportunity for growth, a highly significant countergradient growth relationship was found for North American pike, while a significant, but considerably less predictive countergradient growth relationship was found for Eurasian pike. This study provides novel insights into the ecology of a circumpolar species and how populations function at extraordinarily large spatial scales. First, pike appear to be cosmopolitan across hydrologic habitats having fast or slow growth in either lentic or lotic environments. Secondly, continental‐scale differences in pike growth rates are suggestive of major genetic and life‐history differences. Finally, variable climate–growth relationships and countergradient growth patterns indicate that global climate change is likely to affect circumpolar fishes like pike in complex, nonlinear ways.     

Colonization history and human translocations explain the population genetic structure of the noble crayfish (Astacus astacus) in Fennoscandia: Implications for the management of a critically endangered species

1. The noble crayfish (Astacus astacus) is an endangered freshwater species in Europe. The main threat is from lethal crayfish plague, caused by the oomycete Aphanomyces astaci that has been spread over Europe by introduced North American crayfish species, acting as chronic carriers of the disease.
2. Most of the remaining noble crayfish populations are found in the Baltic Sea area, and there is an urgent need to implement conservation actions to slow down or halt the extinction rate in this region. However, limited knowledge about the genetic structure of populations in this area has so far precluded the development of conservation strategies that take genetic aspects into consideration.
3. Key objectives of this large-scale genetic study, covering 77 locations mainly from northern Europe, were to describe the contemporary population genetic structure of the noble crayfish in the Fennoscandian peninsula (Sweden, Norway, and Finland), taking postglacial colonization history into account, and to evaluate how human activities such as stocking have affected the genetic structure of the populations.
4. Analyses of 15 microsatellite markers revealed three main genetic clusters corresponding to populations in northern, middle, and southern Fennoscandia, with measures of genetic diversity being markedly higher within populations in the southern cluster. The observed genetic structure probably mirrors two main colonizations of the Baltic Sea basin after the last glaciation period. At the same time, several deviations from this pattern were observed, reflecting past human translocations of noble crayfish.
5. The results are discussed in relation to the conservation and management of this critically endangered species. In particular, we recommend increased efforts to protect the few remaining noble crayfish populations in southern Fennoscandia and the use of genetic information when planning stocking activities, such as reintroductions following local extinctions.

     

Conservation genetics and management implications for European grayling, Thymallus thymallus: synthesis of phylogeography and population genetics

Abstract  European grayling, Thymallus thymallus (L.), populations have steadily declined since the mid-1980s, mostly because of habitat degradation and increased predation pressure. To provide guidelines for conservation strategies and future management programmes, delineation of conservation and management units is warranted. Over the last decade, several studies have investigated the phylogeography and population genetic structure of T. thymallus using mitochondrial and nuclear microsatellite DNA markers. However, no study has covered the distribution range of T. thymallus across Europe; thus, a comprehensive survey of the evolutionary history of the species is lacking. This paper synthesises the major findings of the molecular studies and provides guidelines for the conservation and management of genetic resources of T. thymallus . At least five major mtDNA lineages have evolved in geographical isolation during the Pleistocene and these lineages should be recognised as the basic evolutionary significant units for T. thymallus in northern, central and southern Europe. There is also evidence for a high level of admixture among major lineages and sublineages, especially in the contact zones of drainages (e.g. in mainland Sweden and Norway and in central Germany), most probably resulting from a complex process of post-glacial and inter-glacial colonisation and re-colonisation events from different refugia during the Pleistocene ice ages. Based on the microsatellite data, T. thymallus shows a substantial level of inter-population genetic differentiation and, compared with other freshwater fish species, a relatively low level of within-population genetic diversity. The species develops discrete population structure, both within hydrologically connected rivers or lakes on comparatively small scales as well as in large river systems.     

Importance of life‐history and landscape characteristics for genetic structure and genetic diversity of brown trout (Salmo trutta L.)

Abstract – Investigating the influence of evolutionary forces on the genetic structure and genetic diversity remains a major challenge. Yet, it is of considerable interest for conservation and management of a species. This study investigates the influence of life‐history and landscape features, such as altitude, connectivity and habitat size, on genetic diversity and genetic structure of brown trout (Salmo trutta L.) with stream‐resident, lake‐dwelling and sea‐migrating life‐history in two river systems in northern Sweden. Using regression tree analysis including ecological and landscape characteristics, we show that life history is the most important variable explaining genetic diversity and population differentiation. Sea‐migrating populations show high diversity and low differentiation, and lake‐ and stream‐resident populations show low diversity and high population differentiation, among all samples. No overall genetic correlation with geographical distance was noted; however, among sea‐migrating populations within the River Vindelälven drainage, this pattern was observed. This study illustrates that life‐history and landscape features help to explain genetic structure and genetic variation. The information is important for conservation and management actions, such as fisheries regulations, habitat restorations, stocking of hatchery fish, defining management units and introducing genetic monitoring programmes.     

Genetic diversity and population structure of the veined rapa whelk <Emphasis Type="Italic">Rapana venosa</Emphasis> along the coast of China based on microsatellites

Knowledge of the genetic diversity and population structure of marine species across their distribution range is essential for the formulation of effective management and conservation strategies. The veined rapa whelk Rapana venosa is a commercially important fisheries resource in East Asia. To provide basic information for fisheries management and artificial breeding, research on the genetic diversity and population structure of R. venosa across the species’ range in China was carried out using 11 microsatellite loci. All of the 11 populations showed high levels of genetic diversity. Shallow, but significant genetic divergences were detected among these populations, suggesting two geographic subdivision groups of R. venosa along the Chinese coast, with nine populations in northern China forming one group and the other two populations (Rizhao and Zhoushan) forming another. A significant isolation by distance pattern was observed in this species (r = 0.412, P = 0.012), indicating that isolation by geographic distance may play an important role in population differentiation. These results could provide valuable genetic information for the fishery management of R. venosa.     

白斑狗鱼家系亲本遗传结构的微卫星分析

近年来,新疆土著鱼类白斑狗鱼（Esox lucius）已成为重要的养殖对象。本研究用8对微卫星标记扩增了190-360bp的2-7条带,分析构建了白斑狗鱼家系亲本的遗传结构。白斑狗鱼雌、雄亲鱼的观测杂合度和预期杂合度分别为0.6438、0.7066和0.6500、0.7076,表明白斑狗鱼亲本杂合度较高。雌、雄亲鱼平均多态信息含量分别为0.6464和0.6486。总体上8个微卫星位点具有较高的多态性,雌雄亲本间遗传距离为0.0426,适于分析白斑狗鱼亲本的遗传结构。F统计显示,白斑狗鱼近亲交配不严重,适合作为家系选育亲本。     

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.     

Population structure,genetic diversity,and colonization history of the eastern pondmussel,Sagittunio nasutus,in the Great Lakes drainage

1. The eastern pondmussel, Sagittunio nasutus (Bivalvia: Unionida), has declined in abundance and distribution in eastern North America over the last few decades. The declines are predominantly the result of infestation by invasive dreissenid mussels and changes in habitat. The species is now considered imperilled across large portions of its distribution, especially in the Laurentian Great Lakes region.
2. The genetic diversity and structure of the remnant populations in the Great Lakes region were assessed using 10 newly developed microsatellite DNA loci for S. nasutus. Understanding the remaining populations can inform future management projects and determine whether the remnant populations have experienced a genetic bottleneck or a founder effect. We hope that this will inform the conservation of other species in regions founded by, and isolated from, a more genetically diverse source population or with disjointed geographical distributions.
3. Focusing on the Great Lakes region, samples (n = 428) from 62 collection sites in 28 water bodies were collected. Across the locations sampled for S. nasutus 11 genetic populations were identified, with significant genetic differentiation among them. The genetic structure of the species was assessed, with genetic similarities among populations compared and with geographical routes of colonization and gene flow evaluated.
4. Initial colonization from the Atlantic coast into Lake Erie and Lake Ontario is evident, followed by colonization events into nearby inland rivers and lakes. Analyses found evidence of inbreeding in all but one population and evidence of past genetic bottlenecks or strong founder effects in all but four populations. This study deepens our understanding of the genetic past and present of this imperilled species, providing conservation suggestions for the future management of the species.

     

Genetic comparison of Iranian and Azeri populations of the oriental bream Abramis brama orientalis (Berg) using microsatellites

The aim of this study was to compare, levels of genetic polymorphism between Iranian and Azeri bream (Abramis brama orientalis) populations using five microsatellite loci. The reduced number of alleles in the Iranian populations compared with the Azeri population led us to infer that the genetic variability of the Iranian stocks has been reduced due to inbreeding and genetic drift. Significant population differentiation (F_st) was observed between the Azeri and the Iranian populations, which could be explained by the higher number of alleles in the Azeri population. Significant deviations from Hardy–Weinberg equilibrium were found at more loci in the Iranian populations than the Azeri population. Beyond the hypothesis of null alleles, the heterozygote deficiency may have arisen due to breeding between related individuals in the Iranian populations. This investigation represents the first approach to the knowledge of the genetic variability of Iranian and Azeri bream populations using microsatellite markers, and the reported results could be of interest for management and conservation programmes of this species in Iran.     

Population structure of long tailed hake Macruronus magellanicus in the Pacific and Atlantic oceans: Implications for fisheries management

Pre-spawning adult samples of long tailed hake, Macruronus magellanicus, were obtained from fisheries vessels in one location in the southeast Pacific Ocean and three in the southwest Atlantic Ocean, at different latitudes. Population structure was determined based on six nuclear hypervariable microsatellite loci and on mitochondrial DNA sequence variation at the locus COI. Paired tests of genic differentiation for microsatellite loci indicate the existence of genetic population structure for this species, where significant differences exist between some southern and northern samples. Multivariate analysis (factorial correspondence analysis) of microsatellite variation showed differentiation between the Pacific and the Atlantic populations. Analysis of the mitochondrial variation confirmed the microsatellite analysis of population structure, and revealed some additional differentiation between northern and southern Atlantic samples and exclusive haplotypes in each region. These findings suggest that the species should be managed as north–south separate stocks in the Atlantic Ocean.     

Population genetic divergence of bonnethead sharks Sphyrna tiburo in the western North Atlantic: Implications for conservation

1. Sharks are a priority for conservation because numerous species, including small-sized coastal species, are being heavily exploited by commercial and recreational fisheries. Understanding the genetic population structure of sharks is key to effective management, maximizing their evolutionary potential in a rapidly changing environment and preventing population declines.
2. Limited dispersal is an important factor promoting population divergence for several coastal shark species. The genetic variation in 14 microsatellite loci and 21,006 single nucleotide polymorphisms genotyped using restriction-site-associated DNA sequencing was analysed to assess the genetic structure of the bonnethead shark, Sphyrna tiburo, in the western North Atlantic.
3. Genetic differences were identified among three well-defined regions: the western Florida coast, the south-eastern US Atlantic coast, and the southern Gulf of Mexico. Results support previous studies based on mitochondrial DNA sequences in defining differences among these regions and suggest limitations of bonnethead sharks in routinely performing long-distance migrations.
4. The limited connectivity among regions explains the pattern of genetic divergence but also reported divergence at the species/subspecies level. These genetically discrete bonnethead populations have independent evolutionary histories that may include local adaptations to specific areas.
5. Bonnethead sharks are currently managed as two stocks in the USA owing to recent genetic, tagging, and life history studies; however, no stock assessments or management plans exist for Mexico. These results not only serve to reinforce US management strategies and provide critical data about the extent of gene flow and sex dispersal among populations, but also begin the process of effective management in the waters of Mexico to ensure the long-term productivity and resilience of this species. With an absence of gene flow between populations from US waters and the southern Gulf of Mexico, there is a need for management plans based upon independent biological and population dynamics data since limited or no opportunities for populations to interchange individuals may occur to re-establish population viability.

     

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。     

The genetic structure of Mytilus chilensis (Hupé 1854) populations along the Chilean coast based on RAPDs analysis

The Chilean blue mussel Mytilus chilensis is an important commercial species. However, little has been published on the population genetics of this species, despite the need to implement management and conservation policies. Randomly amplified polymorphic DNA‐polymerase chain reaction analysis was used to estimate genetic variation within and between eight natural populations along the whole range of its Chilean natural distribution (ca. 1900 km from Arauco (VIII Region) to Punta Arenas (XII Region)). The values of Nei's unbiased genetic distance, D (0.030–0.107), among populations were small, despite the large geographic separation. A mantel test using 50 000 randomizations showed evidence for a significant correlation (r=0.74, P<0.05) between genetic and geographic (coastal) distance. Punta Arenas population was the most genetically differentiated from the others, although the scale of differentiation was not large (D=0.076–0.107). The levels of gene flow (Nm=1.55) found in this study prevent differentiation among populations by genetic drift. This is the result of the long‐lived planktotrophic larvae of M. chilensis, which provides this species with considerable dispersal ability throughout its range, which is favoured by the ocean currents along the Chilean coast. A restricted larval dispersal towards the north due to the Cape Horn Current derived from the West Wind Drift could be the cause of the higher genetic differentiation of Punta Arenas population from the northern populations. For management purposes of the M. chilensis fishery, the results provide no evidence for discrete stocks, with the possible exception of the Punta Arenas population. The present study provides the baseline data in order to continue further characterization of these mussel populations, considering the great increase in aquaculture of this species.     

Genetic divergence in Indian populations of M. rosenbergii using microsatellite markers

Macrobrachium rosenbergii, known as the giant freshwater prawn or Malaysian prawn, is the sixth largest aquaculture species in Asia. Knowledge of genetic diversity of M. rosenbergii is important to support management and conservation programmes, which will subsequently help in sustainable production of this economically important species. This study aimed to analyse the genetic diversity and population structure of five M. rosenbergii populations using 11 microsatellite loci. In analysing 240 samples, the number of alleles, observed heterozygosity (H_O) and expected heterozygosity (H_E) ranged from 3 to 20, from 0.250 to 0.978 and from 0.556 to 0.944 respectively. The five stocks of M. rosenbergii displayed high level of genetic diversity. Both the F_ST and amova analyses showed that there was significant genetic differentiation among all populations. The UPGMA dendrogram based on Nei's genetic distance matrix revealed that the Narmada and Mahi populations were in one cluster and Mahanadi and Subarnarekha populations in another single major branch, whereas the Kerala population clearly showed a separate cluster. This information on genetic variation will be useful for genetic improvement and conservation of Indian populations of giant freshwater prawn M. rosenbergii.     

Microsatellite analysis of the genetic population structure of native and translocated Aristotle's catfish (Silurus aristotelis)

The genetic structure of two native Silurus aristotelis (one of Europe's oldest surviving freshwater fish species) populations was investigated using eight microsatellite loci. Average values of population heterozygosity were very high, even approaching values reported for marine fishes, possibly due to stable population sizes and the prolonged undisturbed conditions prevailing in the lakes that represent the native distribution of S. aristotelis. The success of an attempt to introduce the species into a new environment was also evaluated. No loss of genetic variability in the introduced population was detected. Additionally, assignment tests and trees based on genetic distances among individuals indicated the low differentiation of the translocated population from its donor population, and, differentiated the two autochthonous populations successfully. Comparisons with previous allozyme and mitochondrial RFLP studies were also made and showed that results on relative levels of genetic variability among populations were in good agreement among all methods. However, microsatellite analysis exhibited higher power of statistical tests for differentiation among population samples compared to allozymes.     

Genetic differentiation between Zhe oyster Crassostrea plicatula and pacific oyster Crassostrea gigas populations in China assessed by microsatellite analysis

ABSTRACT:   Genetic differentiation and relationships between Crassostrea plicatula and Crassostrea gigas populations from China were studied by means of the microsatellite technique. Seven loci were used to screen five populations each collected from C. plicatula and C. gigas . All loci showed high polymorphism for all populations, as observed in average number of alleles per locus (19.1–28.1), and average expected heterozygosity (0.891–0.954). Significant departures from Hardy–Weinberg equilibrium due to heterozygote deficiency were observed over most populations at each locus and were best explained by null alleles. F _ST values showed significant genetic differentiation between C. plicatula and C. gigas populations. According to the neighbor-joining tree constructed on the basis of the genetic distance ( D _A), the ten populations fell into two distinct groups ( C. plicatula and C. gigas groups), and the results of principal coordinate analysis and assignment tests also supported the neighbor-joining clustering. The outcomes presented here suggested that the microsatellite markers have great potential for differentiating C. plicatula from C. gigas populations. The information obtained in this study has important implications for the suitable management and conservation of these genetic resources in China.     

Genetic analysis of Rutilus rutilus caspicus (Jakowlew 1870) populations in Iran by microsatellite markers

The Caspian roach (Rutilus rutilus caspicus) is regarded as one of the most important commercial species in the Caspian Sea. Despite the commercial and conservation importance of the species, information on genetic relationships and diversities at the molecular level in Rutilus rutilus caspicus is scarce. Six microsatellite loci were analysed to study the genetic variation in two major populations of Caspian roach in the Iranian waters of the Caspian Sea: the Anzali Wetland and Gorgan Bay. The F_st value between populations was 0.07, suggesting that the genetic differentiation was significant (P<0.01). Both the studied populations deviated from Hardy–Weinberg equilibrium proportions at a number of loci, mostly due to the deficiency of heterozygosities. The genetic distance between populations was 0.29, which indicates that the genetic difference among the studied populations is pronounced. The differences between both populations were not statistically significant (P>0.05), neither for average number of alleles per locus nor for observed heterozygosities. The data generated in this study provide useful information on the genetic variation and differentiation in populations of Caspian roach.     

Patterns of phenotypic and genetic variability show hidden diversity in Scottish Arctic charr

Abstract –  This study examined the degree and pattern of variability in trophic morphology in Arctic charr ( Salvelinus alpinus L. ) at three spatial scales: across 22 populations from Scotland and between and within two adjacent catchments (Laxford and Shin) in northern Scotland. In addition, the variability at six microsatellite loci between and within the Laxford and Shin systems was determined. Habitat use by charr differed significantly between populations. The pattern of variability in trophic morphology, known to influence foraging ability in charr, showed a very high degree of between-population variation with at least 52% of population pairs showing significant differences in head shape. Trophic morphology and genetic variation was also high over small geographical scales; variation being as high between charr from lakes within the same catchment, as between adjacent catchments. The pattern of both phenotypic and genotypic variation suggests a mosaic of variation across populations with geographically close populations often as distinct from each other as populations with much greater separation. Very low levels of effective migrants between populations, even within the same catchment, suggest that this variation is being maintained by very low straying rates between phenotypically and genetically distinct populations, even when there is no apparent barrier to movement. We conclude that the genetic and phenotypic integrity of charr populations across Scotland is high and that this adaptive radiation constitutes a 'hidden' element of diversity in northern freshwater systems. Two consequences of this are that the population (rather than the species) makes a more rational unit for the consideration of conservation strategies and that the habitat requirements and therefore management needs may differ significantly between populations.     

Global population genetic structure of the sequential hermaphrodite,dusky grouper (Epinephelus marginatus)

1. The dusky grouper Epinephelus marginatus is a large epinephelid species that occurs in the eastern and south-western Atlantic and western Indian Oceans. Late maturity, protogynous hermaphroditism, site fidelity, and overfishing have all contributed to its demographic decline.
2. Connectivity and demography within a broad sampling of dusky grouper populations throughout its distribution were assessed. To do so, genetic variation at 11 polymorphic microsatellite loci and a partial sequence of the mitochondrial control region (mtCR) were evaluated.
3. Two major mtCR lineages with a sequence divergence of 1.6% were found. The magnitude of genetic differentiation for mtCR among north and south Atlantic and Indian Ocean populations was high, with Φ_ST = 0.528.
4. D_EST and results of discriminant analysis of principal component revealed significant microsatellite genetic differentiation between all collection areas. Significant pairwise D_EST showed moderate (0.084) to very great (0.603) differentiation. The effective population size was low for all localities, ranging between 25 (Azores Archipelago) and 311 (Rio Grande do Sul). The overall effective population size was estimated as 299 (confidence interval = 215–412), and there was no evidence of strong or recent bottleneck effects.
5. Local and regional genetic structuring among dusky grouper populations is the consequence of the species' site fidelity, distribution across multiple oceanographic boundaries, and probably also of sequential hermaphroditism that contributes to the intensity of random genetic drift.
6. The spatial pattern of genetic structuring of dusky groupers is such that fisheries management and conservation of population genetic integrity will have to be pursued at the local and regional scales.