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.     

Low allozyme variation in snapper, Pagrus auratus, in Victoria, Australia

The population genetic structure of snapper, Pagrus auratus (Bloch and Schneider), in Victoria was investigated using six polymorphic allozyme loci. Fish were sampled from four sites in Victoria and single locations in South Australia, Western Australia and New Zealand. Although there were distinct genetic differences between the snapper populations from each of the Australian states and New Zealand, only minor and largely insignificant differences were detected among Victorian populations. The results are consistent with previous genetic and tagging studies that indicate no mixing between snapper stocks in Victoria and Spencer Gulf in South Australia. This justifies separate management of the snapper fisheries in these regions. The low levels of polymorphism and heterozygosity in Victorian snapper suggest an isolation by distance model of population structure rather than one of discrete subpopulations.     

Genetic variation in farmed populations of the gilthead sea bream Sparus aurata in Greece using microsatellite DNA markers

Genetic variation in seven reared stocks of gilthead sea bream Sparus aurata, originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of two natural populations from the Ionian and the Adriatic Seas. The total number of alleles per marker ranged from 11 to 19 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic diversity and expected heterozygosity. The global genetic differentiation for the cultivated samples was significant as indicated by F_st analysis, which might indicate random genetic drift and inbreeding events operating in the hatcheries. On the contrary, no significant difference was found between the two wild populations. Population pairwise tests between farmed and wild stocks were also significant, with the exception of one hatchery sample, the Central Greece 1, which was not significantly different from the two wild samples perhaps due to its recent use in aquaculture from wild‐caught animals. The UPGMA tree topology grouped the wild samples together with the Central Greece 1 stock, and showed a clear division between wild and farmed sample sets for the six remaining hatchery samples. Knowledge of the genetic variation in S. aurata cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for the proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes.     

Forecasting the genetic influences of red drum stock enhancement in South Carolina

The South Carolina Department of Natural Resources (SCDNR) began stocking red drum, Sciaenops ocellatus (Linnaeus), in 1989 to augment the abundance of juveniles available for recreational harvest in South Carolina estuaries. While stock enhancement can help supplement wild populations under high fishing pressure, releasing hatchery‐raised fish into the wild also presents the risk of decreased genetic diversity. An individual‐based model (IBM) was developed to forecast the genetic influences of stocking on the wild spawning population to inform responsible stocking strategies. Model results indicated the SCDNR red drum stock enhancement programme should maintain mean contributions of stocked fish no greater than 30% per year class over a 45‐year stocking period, coupled with at least 10 effective breeders in the hatchery replaced annually, to maintain current levels of genetic diversity estimated in the wild population. The IBM is a useful tool for hatchery managers to guide responsible stock enhancement.     

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

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Genetic relatedness and differentiation of hatchery populations of Asian seabass (Lates calcarifer) (Bloch, 1790) broodstock in Thailand inferred from microsatellite genetic markers

After more than 20 years of hatchery production of Asian seabass in Thailand, genetic information is still lacking for effective genetic management and a selective breeding programme. This study aimed to evaluate genetic status of existing hatchery populations and genetic consequences of a selective breeding attempt. We examined genetic relatedness in seven hatchery samples, including a selectively bred population (RACF‐F1), compared with three wild samples using 11 microsatellite loci. Genetic diversity and relatedness values within most hatchery samples, except for RACF‐F1, did not differ from those of wild populations (P > 0.05). RACF‐F1 had the lowest allelic diversity and effective population size (A_r = 6.99; N_e = 7.8) and highest relatedness values (mean r_xy = 0.075–0.204). Pairwise Φ_ST values, principal component analysis and model‐based cluster analyses revealed three genetically distinct hatchery groups: Eastern Thailand (CHN, RACF, NSCF and SKCF), Southern Thailand (NICA) and the Andaman Sea (STCF). Results suggest that exiting domestic populations capture reasonable amount of genetic variation and can be useful for a base population for genetic improvement programmes. In addition, given the rapid increase in relatedness that we observed in one selectively bred population, we recommend using selection methods and hatchery practices that reduce variability in family contribution in the subsequent generations.     

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.     

Development of Gene‐derived SNP Markers and Their Application for the Assessment of Genetic Diversity in Wild and Cultured Populations in Sea Cucumber,Apostichopus japonicus

The Apostichopus japonicus is a valuable aquaculture species in China. In this study, 51 single nucleotide polymorphisms (SNPs) were identified from expressed sequence tags of sea cucumber using high‐resolution melting. The average observed heterozygosity (Ho) and expected heterozygosity (He) were 0.2462 and 0.2897, respectively. Thirty‐two of these loci were used for estimating the genetic similarity and variation between the five hatchery stocks from China and two wild stocks from Japan. No significant differences in Ho or He were observed between the wild and hatchery populations. The pairwise Fst (which ranged from 0.0119 to 0.0236) and the genetic identity (which varied from 0.9802 to 0.9915) showed no significant differentiation between the wild and cultured stocks. The analysis of molecular variance indicated the source of variation was at the level of “within the populations.” The information on the genetic variation and differentiation in cultured and wild populations of A. japonicus obtained in this study is useful for setting up suitable guidelines for founding and maintaining of cultured stocks and for future genetic improvement by selective breeding.     

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 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.     

Genetic differentiation of wild and hatchery Oujiang color common carp: potential application to the identification of escapees

The escape or release of cultured and domesticated organisms into the wild poses a threat to the genetic integrity of natural populations. Based on data from 17 microsatellite loci, the genetic differentiation between wild and hatchery Oujiang color common carp Cyprinus carpio var. color was investigated, and its potential application for identifying the escapees of hatchery strains was assessed using Bayesian genetic assignment. No significant differences were observed between pooled hatchery and pooled wild populations in terms of allelic richness (A _R), observed heterozygosity (H _O), and inbreeding coefficient (F _IS). Analysis of molecular variance and pairwise F _ST comparisons suggested significant genetic differentiation between hatchery strains and between hatchery and wild populations, which was further confirmed by principal components analysis and Bayesian clustering analysis. Bayesian genetic alignment showed high self-assignment accuracy (ranging from 86.0 to 96.0%) in the original populations, demonstrating the ability of this technique to identify hatchery Oujiang color common carp escapees in the wild population.     

Validity of fluctuating asymmetry as a gauge of genetic stress in ayu stocks

An increasing demand for stocking of hatchery-reared ayu, Plecoglossus altivelis, has aroused concerns about their genetic status which has an effect on their post-stocking performance and the conservation of native biodiversity. Instead of costly analysis, fluctuating asymmetry (FA) was examined to test its suitability as an indirect measure of genetic diversity. Two bilateral traits, pectoral and pelvic fin rays, were targeted, and two wild and four hatchery populations of ayu were sampled for comparison. Frequency of FA in soft-rays was not similar between specimens in both pelvic and pectoral fins. The wild populations did not show FA incidences lower than the hatchery populations, suggesting a considerable degree of environmental stress operating in the wild populations. Comparison between the hatchery populations showed overall increasing FA incidence with the decrease in genetic diversity, although the correlation was not complete in detail. In conclusion, FA can be used as a convenient tool to compare genetic status, but quantified evaluation is rather limited to monitoring changes in the genetic variation within a hatchery population.     

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.     

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.     

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.     

Genetic diversity and relatedness estimates for captive barramundi (Lates calcarifer,Bloch) broodstock informs efforts to form a base population for selective breeding

Aquaculture of barramundi or Asian seabass (Lates calcarifer) is growing in both Australia and Southeast Asia and there is substantial interest to improve production efficiency through selective breeding. The establishment of a large and genetically diverse base population is a prerequisite for a sustainable and long‐term productive breeding program. Before selective breeding programs can begin for Australian barramundi it is important to assess the overall genetic diversity of current captive broodstock populations. To address this question, 407 captive barramundi broodstock from eight separate Australian broodstock populations were genotyped using 16 polymorphic microsatellite DNA markers. A Bayesian STRUCTURE analysis indicated that captive Australian broodstock are broadly divided into two genetic stocks. Multivariate analysis between broodstock individuals and pairwise F_ST between broodstock populations also supported the existence of two stocks. Comparisons with data obtained from natural stocks suggested that hatchery individuals were either sourced from the two stocks or represented an admixture between them. Genetic diversity was low within each broodstock population (allelic richness ranged from 2.67 to 3.42 and heterozygosity ranged from 0.453 to 0.537) and relatedness estimates within hatcheries were generally low (average r was equal to 0.141). We recommend sourcing captive individuals according to high levels of neutral genetic diversity and low levels of relatedness for the establishment of a base population. We also make recommendations about including genetically diverse wild individuals.     

Competition between hatchery‐raised and wild brown trout Salmo trutta in enclosures – do hatchery releases have negative effects on wild populations?

Abstract –  We compared the growth and prey consumption of juvenile hatchery and wild brown trout of similar genetic origin in 12 wire mesh cages in a natural river in North-Eastern Finland. Wild trout started feeding shortly after the start of the experiment, and clearly earlier than novel hatchery trout, but ate less in the presence of hatchery trout. When accompanied with wild trout, novel hatchery trout started to feed earlier, consumed more live prey, and lost less weight than when in allopatry. Hatchery trout grew more slowly than wild trout. To our knowledge, this is the first study to show that hatchery trout benefit from the presence of wild, experienced trout in a complex semi-natural environment. However, our results also indicate that the benefits to hatchery fish are not transferred to wild fish, and ultimately that care should be exercised in management actions when using hatchery trout to supplement wild populations. On the other hand survival potential of the novel hatchery brown trout could be better in the wild when also undomesticated trout are present.     

Failure of predator conditioning: an experimental study of predator avoidance in brown trout (Salmo trutta)

Many studies have documented that hatchery‐reared salmonids generally have inferior survival after being stocked compared with wild conspecifics, hatchery and wild salmonids have been observed to differ in their antipredator responses. The response of brown trout (Salmo trutta) juveniles (0+) of differing backgrounds to a live predator was compared in two experiments. First, the antipredator behaviour of predator‐naïve hatchery‐reared brown trout and wild‐exposed brown trout were assessed in behavioural trials which lasted for eight days. Second, predator‐naïve and predator‐conditioned hatchery‐reared brown trout were assessed in identical behavioural trials. Brown trout were ‘predator‐conditioned’ by being held in a stream‐water aquarium with adult Atlantic salmon (Salmo salar) and adult brown trout for two days prior to behavioural trials. Predator‐conditioned hatchery‐reared brown trout spent more time in shelters in the trial aquaria than predator‐naïve hatchery‐reared fish, but did not differ in time spent in the predator‐free area. Predator conditioning may account for the increased time spent in the shelter, but does not appear to have affected time spent in the predator‐free area. However, even if significant alteration in behaviour can be noted in the laboratory, the response might not be appropriate in the wild.     

Assessment of three strategies practiced by fishery managers for restoring native brown trout (Salmo trutta) populations in Northern French Alpine Streams

Abstract – The efficiency of three strategies carried out by fisheries managers to restore native Mediterranean brown trout populations threatened by non‐native Atlantic populations were assessed. The strategies tested were (i) genetic refuge area where stocking is banned, (ii) stocking with Mediterranean fry and (iii) translocation of wild Mediterranean spawners. Using two discriminatory microsatellite loci between Atlantic and Mediterranean alleles, we compared the genetic composition of samples before and after the changes of practices. The three strategies had several detectable effects in the standing populations causing strong temporal changes in departures from Hardy–Weinberg equilibrium and linkage equilibrium between loci and the apparition of new Mediterranean alleles. The significant reductions in the proportions of Atlantic alleles observed over time can mostly be explained by the disappearing of the pure non‐native Atlantic trout after the stopping of hatchery releases. The results, however, also suggest that the active strategies carried out by managers led to intraspecific introgression between both non‐native Atlantic and native Mediterranean strains.     

Electrophoretic characterization of three hatchery-reared strains of rainbow trout, Oncorhynchus mykiss (Walbaum)

Abstract. Significant differences were found in allelic frequency distribution among three strains of rainbow trout, Oncorhynchus mykiss (Walbaum). The isocitrate dehydrogenase ( IDH-3, 4 * 1.1.1.42) locus was fixed in two of the strains while the superoxide dismutase ( SOD-I * 1.15.1.1) locus was absent in one of the strains.
Similarity indices ranged from 0·973 to 0·988 on the scale of 1·000 among pairwise comparisons of the strains while Nei's genetic distance was 0·012 between Mount Lassen and Manx, 0·025 between Mount Lassen and Tagwerker and 0·027 between Manx and Tagwerker. Gene diversity was highest in the Mount Lassen strain, followed by Manx, with Tagwerker having the least. These differences in gene diversity were attributed to breeding and management practices used at the hatchery. The need for characterization of strains of rainbow trout, especially in crossbreeding programmes that aim to increase genetic variation, was emphasized by these results.