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.     

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.     

Effects of stocking on the genetic structure of brown trout,Salmo trutta,in Central Europe inferred from mitochondrial and nuclear DNA markers

Abstract Stocking has had a considerable effect on wild brown trout, Salmo trutta L., populations throughout Europe. To elucidate this impact and to outline further management strategies, the genetic structure of 25 wild populations and five hatchery stocks from Czech Republic and Slovakia were analysed using mitochondrial (control region) and nuclear DNA (microsatellites, LDH‐C1*) markers. Stocking practices have caused massive hybridisation between the Atlantic and Danube brown trout strains in the central Danube basin and have lead to a loss of among‐population divergence in Slovakia and the eastern part of Czech Republic. Comparison with studies from neighbouring countries revealed substantial differences in haplotype, allele frequencies and genetic diversity across Central Europe. Differences in stocking management and origin of breeding stocks appear to be crucial factors for the spatial variability of the genetic structure of brown trout.     

Genetic effects of introduced hatchery stocks on indigenous brown trout (Salmo trutta L.) populations in Spain

Abstract– To assess the levels of gene introgression from cultured to wild brown trout populations, four officially stocked locations and four nonstocked locations were sampled for one to three consecutive years and compared to the hatchery strain used for stocking. Allozyme analysis for 25 loci included those previously described as providing allelic markers distinguishing hatchery stocks and native populations. Different levels of hybridization and introgression with hatchery índividuals were detected in stocked drainages as well as in protected locations. These findings indicate that new policies for stocking and monitoring hatchery fish are needed if gene pools of wild Spanish brown trout populations are to be preserved.     

Genetic Introgression Between Arctic Charr (Salvelinus Alpinus) and Brook Trout (Salvelinus Fontinalis) in Bavarian Hatchery Stocks Inferred from Nuclear and Mitochondrial DNA Markers

Nuclear insulin-like growth factor 2 gene (IGF-2), growth hormone 1 gene (GH-1) and internal transcribed spacer 1 (ITS-1) of the ribosomal DNA as well as the mitochondrial NADH-3 and NADH-4 dehydrogenase genes (ND-3/4) exhibited species-specific restriction fragment patterns and three microsatellite loci (Sfo18, Ssa85 and Ssa197) had non-overlapping allele size ranges in Arctic charr and brook trout and were used as diagnostic markers for testing genetic purity of hatchery stocks and wild populations of Arctic charr and brook trout in Bavaria, Germany. Screening of four wild populations (three in Arctic charr and one in brook trout) revealed only a single hybrid (back-cross to brook trout) individual in L. Starnberg. In contrast, in three (out of five) hatchery stocks of Arctic charr and in both hatchery stocks of brook trout hybrids were detected with the frequency from 3 to 100%. Three hatchery stocks (SS2, SA and BS1) represent a hybrid swarm because they contained a very high proportion of hybrids (from 83 to 100%) and most or all hybrid individuals had alien alleles at only one or a few of six unlinked diagnostic loci, indicating that post-F₁ hybrids represent the majority of individuals in these stocks and introgression has taken place. Release or escape of introgressed individuals from hatcheries into natural water bodies should be avoided in order to protect the biological diversity and genetic integrity of native fish populations.     

Summer survival and activity patterns of estuary feeding anadromous Salmo trutta

There is generally a very poor understanding of how anadromous brown trout, Salmo trutta, use marine ecosystems. In this study, we use acoustic telemetry techniques to test four alternative hypotheses for estuarine coastal habitat use by this species on a population in the Clyde, west-central Scotland. Anadromous brown trout in their second (or more) summer feeding in the marine environment did not show patterns of estuarine use predicted from studies on other populations of this species. They did not (a) use the inner Clyde Estuary as a staging post for onward migration to open coastal waters, nor did they (b) pass through the estuary rapidly nor did they (c) make multiple incursions into freshwater. In contrast, fish utilised a very geographically constrained area of the inner estuary (<8 km in length), within which fish were highly mobile, exhibiting more activity during a flooding tide and exhibited high survivorship compared with reports from other studies. The reasons why estuarine use by anadromous brown trout in the Clyde may differ from that reported elsewhere is discussed.     

国内虹鳟代表性养殖群体的高通量SNP芯片检测及遗传分析

本研究旨在对国内虹鳟(Oncorhynchus mykiss)代表性养殖群体开展全基因组水平的遗传评估。利用57K单核苷酸多态性(single nucleotide polymorphism,SNP)芯片,检测了来自不同地域的6个虹鳟养殖群体样本共计48尾,包括黑龙江虹鳟、黑龙江金鳟、四川虹鳟、四川金鳟、北京虹鳟和北京金鳟,共获得有效SNP位点50201个,在中国虹鳟中的多态比例达到97.7%,表明该芯片虽然基于美国和挪威虹鳟群体设计,但对中国群体同样具有良好的适用性。各群体最小等位基因频率均值为0.240~0.267,与国外主流养殖群体相近,黑龙江虹鳟、四川虹鳟和北京虹鳟群体内遗传多样性丰富,多态位点比例为83.6%~84.9%,与国外主流养殖群体相近,而黑龙江金鳟、四川金鳟和北京金鳟,多态位点比例相对较低,在60.2%~76.9%范围内。应用6个中国虹鳟群体和2个美国虹鳟群体数据开展系统发育分析、主成分分析和群体遗传结构STRUCTURE分析,结果显示8个群体可分为3个祖源类群,其中3个金鳟群体为遗传联系较紧密的一个类群,黑龙江虹鳟和北京虹鳟为一个类群,而四川虹鳟与2个美国虹鳟群体为一个类群,部分中国养殖群体中有显著离群个体存在,表明群体遗传背景不均一。本研究表明,高密度SNP芯片在我国虹鳟养殖群体遗传分析中具有广泛的应用前景,能够为种质资源评估、本土化良种培育、制种和引种工作提供基因组水平的参考信息。     

Electrophoretic evaluation of a supplemental stocking programme for brown trout, Salmo trutta L.

Abstract. Over a 15-year period hatchery brown trout, Salmo trutta L., have been added 10 Lower Lough Erne, Northern Ireland to supplement declining native populations. Introductions have mainly comprised eyed ova and fingerlings, stocked into a number of rivers in the Erne drainage. Utilizing a natural genetic tag an electrophoretic assessment of the stocking programme was undertaken. The percentage hatchery genetic contribution in trout populations varied widely from river to river (19%-91%). Lough-caught brown trout (3+ and older) showed a substantial (21·5%) hatchery genetic component. Introgression of native-and hatchery stocks was evident. The resultant deleterious genetic consequences for the conservation of the unique Lough Erne brown trout gene pool arc discussed and alternative management strategies are proposed.     

Population genetics of the European trout (Salmo trutta L.) migration system in the river Rhine: recolonisation by sea trout

Abstract –  Allozyme genetics (34 loci) is studied in up to 1010 European trout ( Salmo trutta ) from the Rhine, Meuse, Weser, Elbe and Danube river systems in Central Europe. Population samples from single collection sites, chiefly small streams ( G _CG = 0.2126), rather than the divergence of the trout from Atlantic and Danubian drainages ( G _SG = 0.0711), contributed to the overall gene diversity of G _ST = 0.2824. Sea trout ( n  = 164) and brown trout ( n  = 767) in Atlantic rivers adhere to the same biogeographical stock, but anadromous trout from the Rhine and the Elbe display more genetic cohesion than resident brown trout from the Rhine system alone. Strayers from the Elbe could have founded the recently re-established sea trout population of the Rhine, after a few decades of absence or precarious rarity. Migrants may even connect the Rhine and Elbe stocks by ongoing gene flow. A release–recapture study confirms that all trout in the Rhine belong to one partly migratory population network: Six of 2400 juvenile sea trout released into a tributary of the Rhine were later recorded as emigrants to the Rhine delta, against three of 1600 released brown trout. One migrant had entered the open North Sea, but the other dispersers were recorded in fresh waters of the Rhine delta (Ijsselmeer, Amstelmeer). Stocking presumably elevated both heterozygosity and fixation indices of brown trout, but this effect is subtle within the range of the Atlantic population group. Improved sea trout management in the Rhine, and modifications to brown trout stocking in the upper Danubian area are recommended.     

Investigating the genetic structure of trout from the Garden of Ninfa (central Italy): Suggestions for conservation and management

Mediterranean populations of brown trout (Salmo trutta L. complex) have lost a large part of their genetic distinctiveness, mostly due to massive restocking, and the waters of the Gardens of Ninfa (province of Latina, central Italy, Site of Community Importance since 2013) are regarded as one of a few potential reservoirs of autochthonous trout lineages in the Tyrrhenian drainage of the Italian peninsula. In this study, nuclear and mitochondrial markers were used on brown trout samples from Ninfa to estimate non‐Mediterranean influence in the population gene pool, potential changes of genetic structure over time and genetic relationships with other sites known (or suspected) to host native trout gene pools. Striking changes in both microsatellite and mtDNA allele frequencies over a 9‐year time span were found and provided evidence of unrecorded stocking from the nearby Lake Fibreno. Results are analysed in the light of potential ecological consequences of such events on a longer time scale and provide a scientific background for fisheries management and conservation programmes in the area.     

Genetic diversity and differentiation of sea trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>) populations in Lithuanian rivers assessed by microsatellite DNA variation

The genetic diversity and differentiation of sea trout were studied in three river basins in Lithuania: Akmena-Dane, Bartuva, and Nemunas. A total of 282 individuals were genotyped at eight microsatellite loci. A similar level of genetic diversity was found in all of the populations studied: mean allelic richness ranged from 3.64 to 5.03, and average expected heterozygosity ranged from 0.588 to 0.721. Significant genetic divergence was observed among the different river basins as well as between populations within the drainages. All pairwise F _ST values were highly significant, ranging from 0.027 to 0.197. The analysis of molecular variance showed rather weak hierarchical population structuring within the Nemunas basin, which may be explained by extensive gene flow among different river basins or, alternatively, reflect the influence of artificial breeding. Information on genetic diversity and differentiation of the Lithuanian sea trout populations will be useful for future management decisions.     

基于ITS1基因分析亚东鲑(♂)、虹鳟(♀)及其F_1代遗传关系

虹鳟、棕鳟均为优质水产养殖品种,亚东鲑为棕鳟的同物异名,是19世纪西藏由欧洲引进。为探索杂种优势,对亚东鲑和虹鳟进行杂交试验,对其子一代幼鱼与虹鳟、棕鳟进行了体长和体质量测定。采用ITS1基因分析其遗传关系,并与巴基斯坦引进的棕鳟对比研究。结果发现F_1代体长、体质量增长快于虹鳟、棕鳟,其遗传多样性高于亚东鲑和虹鳟,略低于棕鳟,表明F1代具有一定杂种优势。此外,棕鳟较高的遗传多样性也反映出从巴基斯坦引进的发眼卵遗传背景较好,具有进一步养殖选育的潜力。     

Genetic characterization of Portuguese brown trout (Salmo trutta L.) and comparison with other European populations

Abstract– Allozyme and other protein loci were examined to study the genetic structure of Portuguese brown trout ( Salmo trutta ) populations. A total of 247 individuals from three tributaries of the Lima hydrological basin and a hatchery, all located in northern Portugal, were analyzed. Four of 22 protein coding loci were found to be polymorphic: CK-A1^*, GPI-A2^*, MPI-2^* and TF^*. A new allelc at the latter locus was found in Atlantic populations. The data obtained for Portuguese brown trout were compared with published data for 14 European populations and three hatchery stocks. Six polymorphic loci (CK-A1^*, GPI-A2^*, GPI-B2^*, LDH-C^*, ME^* and MPI-2^*) were used in a cluster analysis. This showed the similarity of Portuguese natural populations and northern Iberian populations and that Portuguese hatchery fish have an autochthonous origin, distinct from that of other Atlantic hatchery stocks.     

An electrophoretically-detectable genetic tag for hatchery-reared brown trout (Salmo trutta L.)

The feasibility of incorporating a unique genetic marker into a hatchery strain of brown trout is investigated. The allele Pgi-3(110) is shown to have a very limited distribution among native trout populations in Great Britain and Ireland yet is present, at low frequency, in all three hatchery stocks examined. The potential therefore exists to breed a strain of hatchery brown trout homozygous for the Pgi-3(110) allele. Individuals of such a strain could be unambiguously distinguished from virtually all native stocks. The usefulness of the genetic tag is enhanced by the strong expression of Pgi-3 in adipose fin, permitting simple biopsying. Data from population surveys and the monitoring of experimental progeny suggest selective equivalence among Pgi-3 genotypes.     

两种壳色虾夷扇贝的RAPD分析

采用RAPD技术对两种壳色虾夷扇贝Patinopecten yessoensis的遗传多样性和遗传结构及其分化进行研究。用筛选出的22个随机引物对白色贝和褐色贝各40个个体进行RAPD扩增,进行群体内及群体间的遗传学分析。白色贝共检测出128个多态位点,多态位点的比例为79．5％,Shannon遗传多样性指数为0．424;褐色贝共检测出127个多态位点,多态位点的比例为78．9％,Shannon遗传多样性指数为0．423。白色贝和褐色贝之间的遗传相似性指数和遗传距离为0．961和0．039,二者之间的遗传分化指数Gst为0．052,遗传分化的程度较低。结果表明,白色贝和褐色贝之间的等位基因频率、多态位点的比例和遗传多样性等的差别不明显,遗传变异主要来自于群体内。S285—1在褐色贝大部分个体中都能获得扩增片段,但在白色贝所有个体中均未见这个位点的扩增片段,推断S285—1为白色贝的特异阴性片段。     

Stocking impact,population structure and conservation of wild brown trout populations in inner Galicia (NW Spain), an unstable hydrologic region

1. Brown trout (Salmo trutta) is an important conservation resource in the Iberian Peninsula. The Atlantic is considered the most hydrologically stable region for the species, although inner Galicia (NW Spain) shows Mediterranean (unstable) climatic conditions. The Galician region, threatened by past releases of brown trout individuals from central European origin, harbours two native lineages, one of them endemic to the Iberian Peninsula. These populations are thus highly valuable for conservation, as well as being important for recreational fisheries. 2. In total, 546 individuals from 16 sampling sites (15 natural locations from inner Galicia and one from a central European hatchery stock) were genotyped for 11 nuclear markers (10 microsatellite loci and the LDH‐C* locus) to analyse genetic variability, population structure and introgression impact from stocking in order to assess the conservation status of brown trout in the region. Moreover, correlation among hatchery introgression and environmental variables relevant for species population dynamics was also investigated. 3. Genetic variability was within the range of Iberian brown trout (He = 0.500–0.600). Stocking impact was higher than previously reported values for the Atlantic region and was related to environmental instability. Highly significant native population differentiation was observed in the whole region (F_ST = 0.283), at least four main genetic groups being detected across the geographic distribution studied. 4. Conservation strategies at local level (including the creation of genetic refuges and temporal monitoring of genetic composition) are suggested to agencies and administrations for the sustainable management of brown trout.     

Genetic identification of trout strains

Ten strains of rainbow trout were examined for evidence of genetic diversity and inbreeding by an electrophoretic analysis of polymorphisms at enzyme loci. Variations between strains indicate either differences in ancestral origins or diversity created during husbandry. With one exception little evidence was found of allele fixation indicative of historical genetic bottlenecks. The heterozygosity levels observed were higher in the majority of strains than those reported for wild populations. The electrophoretically identified differences between strains support the differences observed in other inherited traits, such as spawning time, growth rate, shape and behaviour.     

Spatial and temporal variation in prey selection of brown trout in a cold Arkansas tailwater

Abstract –  We examined prey utilisation patterns of brown trout ( Salmo trutta Linnaeus) as related to available benthos in a cold tailwater (Little Red River, Arkansas) having low biodiversity of benthic macroinvertebrates and low availability of fish as prey. Benthic macroinvertebrates were sampled monthly in upstream and downstream sites over a 1-year period. Stomach content analysis was also performed on 30 brown trout (10 each of three size classes) collected monthly from each site. Benthic and diet diversities were low at both sites, as isopods ( Lirceus ) accounted for 67% and 51% of the numerical abundance upstream and downstream, respectively, and 80% and 70% of all prey consumed by upstream and downstream brown trout. Physid snails (upstream) and chironomid larvae (downstream) accounted for most of the remaining prey taxa consumed. Piscivory and consumption of terrestrial invertebrates were rare. There was no clear relation between diet diversity and trout size. Densities of benthic macroinvertebrates and prey consumption were significantly greater upstream than downstream. Benthic macroinvertebrate assemblages and prey consumption were seasonally constant at both sites. Generally, prey consumption was consistent with availability of each prey in the benthos; the lack of benthic diversity and overwhelming abundance of one taxon ( Lirceus) most likely contributed to food selection patterns. Although isopods are abundant within this tailwater to serve as a forage base, the displacement of native fish fauna because of the thermal regime of hypolimnetic release from Greers Ferry Reservoir probably serves as a major limitation to brown trout growth.     

High genetic introgression in alpine brown trout (Salmo trutta L.) populations from Hardangervidda, Norway

Abstract –  We studied the effect of stocking brown trout in three alpine lakes (Skavatn, Midtre Grøndalsvatn and Nordmannslågen) of the Hardangervidda mountain plateau by comparing microsatellite data from historical (1933 and 1967) and contemporary (2003) population samples. Historical and contemporary samples from a control lake (Krokavatn) and a contemporary sample from Gjuvsjå (suspected donor lake) were included as well. A total of 331 brown trout were genotyped with 11 microsatellites. Very low level of genetic diversity is observed in the historical samples from Nordmannslågen and Midtre Grøndalsvatn but not in the contemporary samples. In Skavatn historical and contemporary samples show similar genetic diversity as in the other contemporary samples. Admixture analyses with the structure program indicate high levels of introgression by nonnative brown trout in all three lakes. The stocking source for two lakes (i.e. from Gjuvsjå) is partially verifiable via our analyses. The high introgression in these lakes is discussed and the management issues are briefly addressed.     

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.