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.     

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.     

High microsatellite genetic variability of the stone loach, Barbatula barbatula, in anthropogenically disturbed watercourses

Abstract  Genetic variation within and among stone loach, Barbatula barbatula L., populations inhabiting anthropogenically degraded watercourses in Flanders (northern part of Belgium) was assessed using five microsatellite markers. High levels of genetic diversity were observed at all sampling sites, (MNA: 6.2–11.2; H _O: 0.64–0.75; H _E: 0.67–0.85). Estimates of the effective population size varied between 1535 and 3021 individuals and there were no indications of recent severe bottlenecks. Significant genetic differentiation was observed among sites belonging to different river systems and drainage basins. These results suggest human activities, such as pollution and river engineering, have not impacted significantly on genetic variability in the stone loach populations investigated. It is possible that this lack of genetic erosion may be attributed to species-specific characteristics such as pollution tolerance and ecological flexibility.     

Genetic variation and population structure of the caramote prawn Penaeus kerathurus (Forskäl) from the eastern and western Mediterranean coasts in Tunisia

Ten populations of Penaeus kerathurus (Forskäl), a prawn of high commercial value, were sampled from the eastern and western Mediterranean coastal waters of Tunisia and screened electrophoretically for genetic variation at 13 allozyme loci. Four among the six polymorphic loci were out of Hardy–Weinberg equilibrium (H–WE) in at least one population. In the same way, the multilocus test showed deviation from H–WE in six populations. These populations showed heterozygote deficiency whereas the average heterozygosity for the four remaining ones is quite similar to the expected levels. Genetic variability was low. The number of alleles per locus ranged from 1.2 to 1.5 (average=1.3), and the observed heterozygosity varied between 0.010 and 0.048 (average=0.021). Significant population differentiation (F_ST=0.076, P<0.05) in the total data set reflected the differentiation of the two populations, which were at the margins of the range sampled, from all the others (Pairwise F_ST values ranged from 0.035 to 0.208). Although there was no significant differentiation among the other populations (pairwise F_ST values ranged from ?0.006 to 0.201, P>0.05). Our data suggest a population structure consistent with separation by Mediterranean Sea basins that might reflect different local biogeographical zones.     

基于SSR-seq技术评估中间球海胆多代选育群体和普通养殖群体的遗传多样性

为明确不同选育群体中间球海胆的遗传多样性和遗传结构,利用SSR-seq技术和15个微卫星位点,对1个家系选育群体(FP)、1个群体选育群体(IP)和1个未经选育的普通养殖群体(CP)的遗传多样性及遗传结构进行了分析。结果显示,15个微卫星位点共检测出112个等位基因,FP、IP、CP 3个群体的平均观测等位基因数(N_a)分别为5.077、5.133和6.133个,平均有效等位基因(N_e)分别为2.816、2.873和3.638个,平均观测杂合度(H_o)分别为0.522、0.441和0.501,平均期望杂合度(H_e)分别为0.595、0.599和0.667,平均多态性信息含量(PIC)分别为0.546、0.543和0.623。家系选育群体(FP) H_e与H_o的差值(0.073)低于IP (0.158)和CP (0.166),平均固定指数(F)(0.115)低于IP (0.248)和CP (0.246)。3个群体间遗传分化系数(F_st)介...     

Disentangling individual movement between populations from effective dispersal in the facultative anadromous Salmo trutta L.

Gathering information on both individual movement and gene flow is rarely possible when studying dispersal among populations in fish species. It is, however, possible to assess both at a reasonable cost in Salmo trutta L. on the Atlantic coast of Europe where the facultative anadromous species is composed of discrete populations of brown trout residents occupying distinct river systems, but exchanging phenotypically distinguishable sea trout migrants. We performed two kinds of genetic analyses using individual microsatellite genotypes: the stock identification of sea trout entering each corridor and the estimates of effective dispersal through each corridor. We observed that individual movement (nonlocal individuals of each source population ranging from 4% to 35% of the sea trout run) never translates into effective dispersal except in one of four migratory corridors examined. The likely origin of this uniquely detected gene flow event is discussed in the light of well‐documented migratory fish management actions undertaken in the past in the studied area.     

基于线粒体控制区序列的三疣梭子蟹增殖放流亲蟹遗传多样性研究

为研究山东沿海三疣梭子蟹增殖放流亲蟹群体的遗传多样性状况,实验采用536 bp的线粒体DNA控制区片段作为分子标记,对4个亲蟹群体的遗传多样性和遗传结构进行了分析。结果显示,301个三疣梭子蟹个体共检测到155个单倍型,4个群体的单倍型多样度为0.972 3~0.993 0,核苷酸多样度为0.021 2~0.023 6,表现出丰富的遗传多样性。AMOVA分析和Fst分析结果均显示,4个三疣梭子蟹亲蟹群体间遗传分化微弱,未形成明显的遗传结构,NJ系统树中未出现与各群体相对应的的谱系分支。研究表明,4个增殖放流亲蟹群体的遗传多样性丰富,且其遗传结构与放流海域的野生群体间没有明显分化,种质资源质量较好。此外,群体历史动态分析显示,渤海南部和黄海北部的三疣梭子蟹历史上曾经历过群体扩张事件。     

Genetic diversity of cultured and wild populations of the giant freshwater prawn Macrobrachium rosenbergii (de Man, 1879) based on microsatellite analysis

Freshwater prawn (Macrobrachium rosenbergii) culture in the Western Hemisphere is primarily, if not entirely, derived from 36 individual prawns originally introduced to Hawaii from Malaysia in 1965 and 1966. Little information is available regarding genetic variation within and among cultured prawn stocks worldwide. The goal of the current study was to characterize genetic diversity in various prawn populations with emphasis on those cultured in North America. Five microsatellite loci were screened to estimate genetic diversity in two wild (Myanmar and India‐wild) and seven cultured (Hawaii‐1, Hawaii‐2, India‐cultured, Israel, Kentucky, Mississippi and Texas) populations. Average allelic richness ranged from 3.96 (Israel) to 20.45 (Myanmar). Average expected heterozygosity ranged from 0.580 (Israel) to 0.935 (Myanmar). Many of the cultured populations exhibited reduced genetic diversity when compared with the Myanmar and the India‐cultured populations. Significant deficiency in heterozygotes was detected in the India‐cultured, Mississippi and Kentucky populations (overall F_is estimated of 0.053, 0.067 and 0.108 respectively) reflecting moderate levels of inbreeding. Overall estimate of fixation index (F_st = 0.1569) revealed moderately high levels of differentiation among the populations. Outcome of this study provide a baseline assessment of genetic diversity in some available strains that will be useful for the development of breeding programmes.     

Genetic variation measured by microsatellites among three strains of domesticated rainbow trout (Oncorhynchus mykiss, Walbaum)

Genetic variation fuels selective change in natural and captive populations. In establishing a broodstock for selective improvement, the level of genetic diversity is an important consideration because it provides an indication of the scope for selective progress. Three domesticated strains of rainbow trout, Oncorhynchus mykiss (Walbaum), were examined at nine polymorphic microsatellite loci to assess detectable levels of allelic diversity and heterozygosity within and differentiation among the strains. A total of 126 alleles were observed to segregate into unique multilocus genotypes for each of the 152 individuals assayed. There was an average heterozygosity of 71.5% at these nine loci, and an average of 14 alleles at a locus. Each locus was represented by alleles unique to at least two of the three strains. Deviations from Hardy–Weinberg expectations of genotype frequencies were detected in each strain. Subsequent analysis indicated sub‐structuring within strains leading to Wahlund effects that caused these deviations. Significant differences in genotype frequencies and pairwise F_ST values demonstrated that all strains were unique. The overall F_ST of 0.089 provides additional evidence of unique genetic diversity present in each strain, and agrees well with the degree of genetic variation found in rainbow trout across broad geographical ranges. The genetic diversity contributed by each population suggests that there is greater scope for selective improvement of numerous traits within a synthetic strain combining these three strains than within any individual strain.     

塔里木裂腹鱼群体遗传多样性的AFLP分析

采用AFLP技术对喀拉喀什河、塔什库尔干河、阿克苏河多浪渠首、木扎提河4个群体共80尾塔里木裂腹鱼(Schizothorax biddulphi Günther)个体进行了遗传多样性分析。6对选择性扩增引物共扩增得到212个位点,其中多态性位点141个,多态位点比例为66.51%。4个群体的Shannon多样性指数(I)为0.316 9-0.544 3,Nei’s遗传多样性指数(H)为0.213 9-0.376 2,群体间的遗传距离为0.078 1-0.250 2。塔什库尔干河群体的多态位点比例、Shannon多样性指数和Nei’s遗传多样性指数均高于其它三个群体。AMOVA分析结果显示,群体总遗传变异85.17%来自群体内差异,而14.83%来自群体间差异,表明塔里木裂腹鱼遗传变异主要来源于群体内个体间,但群体间已存在一定程度的遗传分化。用UPGMA方法构建的群体系统进化树显示,多浪渠首群体和木扎提河群体首先聚类,然后依次与塔什库尔干河群体、喀拉喀什河群体聚类,这一方面与地理位置有关,另一方面与河流的自然环境有关。     

Impact of human‐induced environmental changes on genetic structure and variability in Atlantic salmon,Salmo salar

The genetic effects on Atlantic salmon, Salmo salar L., populations from potential bottleneck situations caused by human activities in two Norwegian rivers, Lærdalselva and Batnfjordelva, were studied by analysing DNA from fish scales collected before and after the populations had been exposed to human‐induced changes: river regulation, Gyrodactylus salaris infection and rotenone treatment. Using 15 microsatellites, no significant changes were found in the genetic structure and diversity of four population samples from Lærdalselva collected over 34 years. However, salmon from Lærdalselva were significantly differentiated from nearby (Årøyelva) and more distant (Batnfjordelva and Suldalslågen) populations, testifying to the power of the marker system to detect small genetic differences. Furthermore, two population samples from Batnfjordelva, collected 20 years apart, showed low but significant differentiation. The lack of effects on neutral genetic composition in Lærdalselva, despite several potentially severe bottleneck events, indicates that stocking and sea cohorts maintain the status quo of this population.     

基于线粒体Cyt b分析入侵云南四大水系的麦穗鱼群体遗传结构

为揭示麦穗鱼入侵云南后群体的遗传多样性和遗传分化差异现状,实验采集了云南澜沧江、怒江、红河、伊洛瓦底江水系13个样点,及黄河、长江、珠江原产地水系6个样点的麦穗鱼群体共计220尾样本,利用线粒体细胞色素b基因(Cyt b)全序列作为分子标记,初步分析了麦穗鱼群体的遗传多样性、遗传结构和遗传分化情况。结果显示,共检测到72个变异位点,定义25个Cyt b单倍型。云南四大水系麦穗鱼单倍型多样性和核苷酸多样性分别为0.828±0.014和0.005 44±0.001 18。云南四大水系和黄河、长江、珠江水系相比,具有较高的遗传多样性。单倍型系统发育树与单倍型网络图显示,黄河群体单倍型独立,云南各水系单倍型与珠江、长江单倍型混杂,推测云南麦穗鱼主要来源于珠江和长江,这与云南省引种经济鱼类历史一致。分子变异分析(AMOVA)显示,云南四大水系麦穗鱼群体间具有程度较高的遗传分化,其中大多数遗传变异存在于群体内(72.60%),群体间的遗传变异为28.62%,水系间为1.22%。结果发现麦穗鱼遗传分化与当前水系的分布格局不吻合。Fu’s Fs中性检验结果和核苷酸不配对分析结果均表明,云南四大水系麦穗鱼群体未发生扩张。麦穗鱼进入云南各水系后,单倍型多样性较高,可能来源于多个地区。在后续对麦穗鱼的管理过程中,需要注意避免单倍型特殊的群体与其他地区群体的交流,减少水系间相互引种。此外,通过开发麦穗鱼资源利用方式来提高麦穗鱼利用率,以控制其群体数量,从而减小其对当地土著物种和渔业养殖的危害。     

Genetic characterization of naturalized populations of brown trout Salmo trutta L. in southern Chile using allozyme and microsatellite markers

This study describes the genetic structure of five naturalized populations of brown trout in southern Chile using allozyme and microsatellite markers to establish levels of intra‐ and interpopulation genetic variability and divergence. Fourteen enzymatic systems were used comprising 20 loci and three microsatellite loci specific to brown trout. The genetic variability values (allozymes, P=20–35%, average=27%, H_O=0.118–0.160, average=0.141; microsatellites, P=33.3–100%, average=66.66%, H_O=0.202–0.274, average=0.229) are similar to values described in other naturalized populations of brown trout present in Chile, but higher than those observed in European populations of this species. Values of total genetic diversity (H_T) (allozymes=0.1216 and microsatellites=0.3504) and relative genetic divergence (G_ST) (allozymes=9.5% and microsatellites=15%) were also similar to the results obtained in previous studies of Chilean populations of brown trout. These values, when compared with those obtained in Europe, proved to be similar for H_T but lower for G_ST. The low interpopulational genetic differentiation was in accordance with the small genetic distance observed between the populations analysed (D Nei=0.004–0.025). On the other hand, the high frequency of one of the two alternative alleles of the phylogeographic marker locus LDH‐5* in the populations analysed (LDH‐5*90>0.84) would indicate a European origin, in particular Atlantic as opposed to Mediterranean, for the brown trout introduced into Chile. The high levels of genetic variability suggest a mixed origin for the naturalized brown trout in Chile, which could have originated either before or during the introduction process. Nevertheless, the low level of genetic differentiation between populations could reflect the short lapse of time in evolutionary terms, during which populations introduced into Chile have been exposed to different evolutionary forces, and which has not been sufficiently long to produce greater genetic differentiation between populations.     

基于微卫星评估草鱼放流亲本对野生群体遗传多样性的影响

利用筛选的13对草鱼多态性微卫星标记,开展了2011至2015年长江中游草鱼亲本增殖放流对野生群体遗传多样性的影响评估。通过对各位点的遗传多样性分析,13个微卫星位点的多态信息含量为0.8622(0.657~0.950),基因多样度为0.8555(0.675~0.936)。15个群体的有效等位基因数为7.4503~10.1536,等位基因丰度为11.483~15.204,说明15个草鱼群体的遗传多样性水平总体较高。遗传分化指数分析表明,群体间不存在显著遗传分化(FST5%)。通过贝叶斯聚类分析和主成分分析可将草鱼群体分为4个组群,根据分组结果以及来源划分分别对草鱼群体进行AMOVA分析,发现遗传变异大部分来自于群体内个体间,组间及组内群体间的分化水平较低(FCT5%,FSC5%),与FST分析结果一致。研究表明,当前草鱼亲本增殖放流模式对野生群体遗传结构影响不明显。     

Genetic diversity within sea trout population from an intensively stocked southern Baltic river,based on microsatellite DNA analysis

Sea trout, Salmo trutta L., populations in the Slupia River basin have been affected by mass stocking with smolts and fry. This work is focused on a small‐scale differentiation in sea trout populations from one basin with a strong emphasis on the relationship between wild and hatchery origin fish. A total of 216 sea trout were genotyped at 10 microsatellite loci. Global F_ST obtained by amova was low at 0.0165. Pairwise F_ST were significant for all tests except wild and stocked adults. The highest pairwise difference was found between the hatchery sample and Kwacza (F_ST = 0.038). Analysis of the genetic structure revealed micro‐geographical differentiation with four subpopulations. The quality of the artificial spawning was found not to be adequate with a high risk of adverse effects to the whole population. All future stocking actions in the basin should consider the existing population structures.     

Current status of the brown trout (Salmo trutta) populations within eastern Pyrenees genetic refuges

Since the end of the 20th century, some headwaters of rivers in the eastern Pyrenees have been designated as genetic refuges to protect remaining native brown trout (Salmo trutta) diversity. The declaration was based on limited or no evidence of genetic impact from released non‐native Atlantic hatchery fish. Hatchery releases were completely banned into the genetic refuges, but pre‐existing fishing activities were maintained. Specific locations in each refuge have been monitored every 2–3 trout generations to update genetic information to accurately assess the contribution of these reservoirs to the preservation of native brown trout gene pools. This work updates genetic information to year 2014 in three of these locations (in Ter, Freser and Flamisell rivers). Previous studies identified hatchery introgressed populations within refuges and suggested discrepancies between the underlying intention of the genetic refuges and the gene pools detected. Therefore, we also examined genetic divergences among locations inside refuge river segments. Combined information at five microsatellite and the lactate dehydrogenase C (LDH‐C*) loci showed reduced but significant temporal native allele frequency fluctuations in some of the above specific locations that did not modify overall levels of local diversity and river divergences. Bayesian clustering analyses confirmed the presence of differentiated native units within each genetic refuge. Some locations of the Freser River within the genetic refuge area showed high hatchery impact of non‐native fish (over 20%). We discuss additional local actions (releases of native fish, selective removals and fishery reinforcement with sterile individuals) to improve the conservation objective of genetic refuges.     

Genetic refuges for a self‐sustained fishery: experience in wild brown trout populations in the eastern Pyrenees

Abstract – Management policies balancing harvest and conservation of natural populations of fish are difficult to establish, both scientifically and politically. This issue is particularly difficult when those populations represent native genetic resources. Since 1997, several brown trout populations in the eastern Pyrenees Mountains (Spain) were designated as ‘genetic refuges’ under varying fishing regulations, where releases of hatchery‐origin fish are not permitted. We analysed genetic variation in samples of brown trout from six of those refuge populations and four non‐refuge populations within the same region. Each population was sampled in four separate years: 1993, 1999, 2004 and 2006. Our analyses were based on a diagnostic allele (LDH‐C*90) that distinguishes native and exogenous hatchery populations. Comparisons were based on stocking histories before and after refuge designations and on three management strategies: fished, unfished and catch‐and‐release. Overall, we detected significant genetic introgression resulting from past stocking practices despite the current restriction of hatchery releases imposed by the recent genetic refuge policy. However, this new policy has prevented detectable introgression from increasing throughout the region and together with additional measures on length and number of captured fish is contributing to self‐sustained fisheries that are achieving conservation goals. Quick acceptance of ‘genetic refuges’ by anglers in one particular river, the Ter River basin, has been a key factor in protecting native gene pools compared with the Segre River basins where refuges were not readily accepted.     

Genetic structure of brown trout,Salmo trutta,populations from differently sized tributaries of Lake Mjøsa in south‐east Norway

This study was based on genotyping eight microsatellite loci of 463 brown trout, Salmo trutta L., sampled in nine differently sized tributaries in three areas on the eastern shore of Lake Mjøsa, south‐eastern Norway. The populations were genetically structured, and Mantel's test showed that genetic distance correlated positively with geographical distance. Temporal differentiation F_ST over a 2‐year period was estimated in five streams and was non‐significant after Bonferroni correction. Effective population size N_e was positively correlated with the habitat length available from the lake (0.3–22 km) and negatively with the number of full sib pairs in the sample. There was no correlation between N_e and genetic diversity, and private alleles were recorded in three medium‐sized streams, but not in the largest two. The importance of small spawning and nursery streams for the maintenance of genetic diversity of brown trout was demonstrated.     

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.     

Genetic diversity status of Pacific white shrimp (<Emphasis Type="Italic">Litopenaeus vannamei</Emphasis>) using SSR markers in Iran

Genetic diversity is vital for the maintenance of genetic pool in cultured shrimps. In order to estimate the current status of genetic diversity in Litopenaeus vannamei shrimp in Iran, as an exotic species, a total of 45 individuals from Amiri and Gorgeaj farms in Jask port of Hormozgan province and one hatchery in Gomishan city of Golestan province, were detected using four microsatellite loci. The number of alleles per locus was 5–10, and the mean effective number of alleles (N _e) across populations and loci ranged from 4.834 to 5.148. The overall mean observed heterozygosity (H _o) ranged from 0.450 to 0.479, which was lower than the expected one (0.789–0.794). There was nothing remarkable about any of the allele frequencies across populations or loci. The mean inbreeding coefficient (F _IS) and pairwise genetic differentiation (F _ST) among populations were 41.6 % and 0.133, respectively. The three studied populations departed from Hardy–Weinberg equilibrium (HWE). Analysis of molecular variance revealed 14 % variability among and 86 % within populations. However, considering departing from HWE and the high F _IS and F, the moderate pairwise F _ST values, importance of introducing genetically diverse broodstock and monitoring to control inbreeding is discussed.