Early effects of the strategies of creating a genetic refuge and direct translocation for conserving and restoring populations of native brown trout

1. The conservation of salmonid inter‐ and intra‐specific diversity is a well‐known challenge, and general management guidelines and conservation processes are available. However, research demonstrating the outcomes of practical conservation actions is largely lacking. 2. We monitored the spatiotemporal genetic and demographic evolution of a native Mediterranean brown trout population in a river in the French Alps to assess the efficacy and early effects of genetic refuge (i.e. cessation of stocking) and wild trout translocation strategies. We also studied the use of angling as a tool to limit the introgression of the wild standing population. 3. We found that the rate of non‐native alleles in wild populations was age dependent, underpinning the importance of using age profiles in the design of genetic conservation studies. 4. Genetic refuge and direct translocation of wild trout resulted in a rapid and significant decrease in the percentages of non‐native alleles. Moreover, the genetic refuge strategy resulted in a significant reduction in the number of pure non‐native individuals, without changing trout densities, whilst direct translocations resulted in the establishment of dense, self‐sustaining native trout populations. Direct translocations changed the distribution of genotype categories and increased densities up to 55‐fold in 3 years. Our results also showed that angling resulted in a selective pressure on non‐native trout introduced at fry stage, whereas non‐native trout issued from natural recruitment were not affected. 5. Our study provides insights for improving the efficacy of practical conservation policies and can be used in other native freshwater fish conservation plans. Proactive measures such as direct translocation need to be implemented together with passive approaches such as genetic refuge policies. Before implementing such actions, accurate genetic and demographic studies at small geographical scales are essential to ensure that no self‐sustaining population of non‐native fish is present. To obtain rapid colonisation, we recommend introducing fish along whole river sections rather than concentrating on a few river stretches. Angling pressure can be used as an additional tool to improve restoration.     

The Wilderness Act and Fish Stocking: An Overview of Legislation, Judicial Interpretation, and Agency Implementation

Many high-elevation lakes in designated wilderness are stocked with native and nonnative fish by state fish and game agencies to provide recreational fishing opportunities. In several areas, this practice has become controversial with state wildlife managers who support historical recreational use of wilderness, federal wilderness managers who assert that stocking compromises some of the ecological and social values of wilderness, and different public groups that support one or the other position. Herein we examine this controversy from the perspective of the 1964 Wilderness Act, its judicial interpretation, the policies of the federal agencies, and formal agreements between federal and state agencies. Although some state stocking programs restore native fish populations, other programs may compromise some of the ecological and social values of wilderness areas. Further, although current federal regulations recognize state authority for fish stocking, judicial interpretation gives federal agencies the authority for direct involvement in decisions regarding fish stocking in wilderness. Where there are differences of opinion between state and federal managers, this judicial interpretation strongly points to the need for improved cooperation, communication, and coordination between state wildlife managers and federal wilderness managers to balance recreational fishing opportunities and other wildlife management activities with wilderness values. Received 28 March 2000; Accepted 16 August 2000.     

Identification and conservation of remnant genetic resources of brown trout in relict populations from Western Mediterranean streams

Brown trout is a cold-adapted freshwater species with restricted distribution to headwater streams in rivers of the South European peninsulas, where populations are highly vulnerable because Mediterranean regions are highly sensitive to the global climatic warming. Moreover, these populations are endangered due to the introgressive hybridization with cultured stocks. Individuals from six remnant populations in Western Mediterranean rivers were sequenced for the complete mitochondrial DNA control region and genotyped for 11 nuclear markers. Three different brown trout lineages were present in the studied region. Significant genetic divergence was observed among locations and a strong effect of genetic drift was suggested. An important stocking impact (close to 25%) was detected in the zone. Significant correlations between mitochondrial-based rates of hatchery introgression and water flow variation suggested a higher impact of stocked females in unstable habitats. In spite of hatchery introgression, all populations remained highly differentiated, suggesting that native genetic resources are still abundant. However, climatic predictions indicated that suitable habitats for the species in these rivers will be reduced and hence trout populations are highly endangered and vulnerable. Thus, management policies should take into account these predictions to design upstream refuge areas to protect remnant native trout in the region.     

Role of environmental factors in the spread of domestic trout in Mediterranean streams

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Genetic introgression between wild and stocked brown trout in the Douro River basin, Spain

The genetic diversity of Spanish brown trout is currently threatened by stocking with exogenous brown trout from Central and Northern Europe. In the Douro River basin 25% of the analysed populations in the present study showed introgression by genes of hatchery origin. The mean introgression estimated by the single locus approach ( S ) varied from 0 to 22% among populations, with a mean value of 3%. The hatchery allele markers were absent in populations where stocking ceased in 1993. However, the introgression effect was observed in all populations stocked until 1998. It seems that cessation of stocking is a good measure for restoring native populations. A thorough review of published and present data of genetic interactions between wild and stocked brown trout in Spanish rivers indicates different levels of introgression between basins. The absence of a clear geographical pattern in the introgression level suggests that ecological interactions and local stocking programmes may play an important role in stocking success. Finally, several guidelines are provided for conservation and management of native brown trout populations in Spanish rivers.     

Multiple electrofishing as a mitigate tool for removing nonnative Atlantic brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis> L.) threatening a native Mediterranean brown trout population

In the native range of the brown trout (Salmo trutta L.) in Europe, the hybridization of native populations by nonnative domesticated strains introduced by stocking is one of the most serious threats to the long-term conservation of diversity within this species. With the objective of conserving and restoring the native gene pool, fishery managers are beginning to implement various management strategies at the local scale. Nevertheless, few case studies have been published that investigate the effectiveness of the various different conservation strategies for native brown trout populations. In the Chevenne Creek, a small French mountain stream, we tested the strategy of removing nonnative individuals by multiple electrofishing carried out by fishery managers in order to evaluate its feasibility and effectiveness for eliminating a nonnative population threatening a native population. Electrofishing produced major reductions in the nonnative population between 2006 and 2009, with 82–100% of nonnative individuals being removed over a period of 4 years. Nevertheless, despite multiple-electrofishing campaigns, this nonnative population was not entirely eradicated, and some natural recruitment persisted. The young of the year and subadults were less effectively removed than the adults. The results suggest that repeated electrofishing campaigns can be used by managers to reduce the nonnative brown trout population with the objective of conserving the native gene pool, but the removal operation must be continued for at least 4 consecutive years. This strategy, which is feasible in small streams, has to be followed by complementary operations to allow the restoration of a new, native, self-sustainable brown trout population.     

Loss of genetic integrity correlates with stocking intensity in brook charr (Salvelinus fontinalis)

Supportive breeding and stocking performed with non‐native or domesticated fish to support sport fishery industry is a common practice throughout the world. Such practices are likely to modify the genetic integrity of natural populations depending on the extent of genetic differences between domesticated and wild fish and on the intensity of stocking. The purpose of this study is to assess the effects of variable stocking intensities on patterns of genetic diversity and population differentiation among nearly 2000 brook charr (Salvelinus fontinalis) from 24 lakes located in two wildlife reserves in Québec, Canada. Our results indicated that the level of genetic diversity was increased in more intensively stocked lakes, mainly due to the introduction of new alleles of domestic origin. As a consequence, the population genetic structure was strongly homogenized by intense stocking. Heavily stocked lakes presented higher admixture levels and lower levels of among lakes genetic differentiation than moderately and un‐stocked lakes. Moreover, the number of stocking events explained the observed pattern of population genetic structure as much as hydrographical connections among lakes in each reserve. We discuss the implications for the conservation of exploited fish populations and the management of stocking practices.     

Dynamics of introgressive hybridization assessed by SNP population genomics of coding genes in stocked brook charr (Salvelinus fontinalis)

Salmonid fishes rank among species being most severely affected by introgressive hybridization as a result of a long tradition of stocking with hatchery-reared conspecifics. The objectives of this study were (i) to evaluate the genetic consequences of stocking and resulting introgression rates on the genetic integrity of natural populations of brook charr, (ii) to identify genomic regions potentially associated with adaptation to natural and artificial rearing environments, and (iii) to test the null hypothesis that introgression from domesticated brook charr into wild populations is homogeneous among loci. A total of 336 individuals were sampled from nine lakes, which were stocked at different intensities with domestic fish. Individuals were genotyped at 280 SNPs located in transcribed regions and developed by means of next-generation sequencing. As previously reported with microsatellites, we observed a positive relationship between stocking intensity and genetic diversity among stocking groups, and a decrease in population differentiation. Individual admixture proportions also increased with stocking intensity. Moreover, genomic cline analysis revealed 27 SNPs, seven of which were also identified as outliers in a genome scan, which showed an introgression rate either more restricted or enhanced relative to neutral expectations. This indicated that selection, mainly for growth-related biological processes, has favored or hampered the introgression of genomic blocks into the introgressed wild populations. Overall, this study highlights the usefulness of investigating the impact of stocking on the dynamics of introgression of potentially adaptive genetic variation to better understand the consequences of such practice on the genomic integrity of wild populations.     

Estimating the long-term effects of stocking domesticated trout into wild brown trout (Salmo trutta) populations: an approach using microsatellite DNA analysis of historical and contemporary samples

Indigenous salmonid fish gene pools are affected by domesticated conspecifics, derived from aquaculture escapes and deliberate releases. Variability was examined at nine microsatellite loci in order to assess the long-term impact of stocking domesticated trout in two brown trout populations. The study was based on analysis of two historical samples (1945-56), represented by old scale collections, and seven contemporary samples (1986-2000). In one population historical and contemporary samples were remarkably genetically similar despite more than a decade of intense stocking. Estimation of admixture proportions showed a small genetic contribution from domesticated trout (approximately 6%), and individual admixture analysis demonstrated a majority of nonadmixed individuals. The expected genetic contribution by domesticated trout was 64%, assessed from the number of stocked trout and assuming equal survival and reproductive performance of wild and domesticated trout. This demonstrates poor performance and low fitness of domesticated trout in the wild. In another population there was a strong genetic contribution from domesticated trout (between 57% and 88% in different samples), both in samples from a broodstock thought to represent the indigenous population and in a sample of wild spawners. Survival of domesticated trout and admixture with indigenous fish in the broodstock and subsequent stocking into the river, combined with a low population size of native trout relative to the number of stocked trout, could explain the observed introgression. Few nonadmixed individuals remained in the introgressed population, and I discuss how individual admixture analysis can be used to identify and conserve nonintrogressed remains of the population.     

Outbreeding Depression in Hybrids Between Spatially Separated Pink Salmon, Oncorhynchus gorbuscha, Populations: Marine Survival, Homing ability, and Variability in Family Size

Hybridization between distinct populations and introgression of nonnative genes can erode fitness of native populations through outbreeding depression, either by producing a phenotype intermediate to that of both contributing genomes (and maladapted in either population's environment) or by disrupting distinct coadapted complexes of epistatic genes. In salmon, fitness-related traits such as homing ability or family-size distribution may be eroded. We investigated geographically separated pink salmon populations in repeated trials in independent broodyears (odd and even). Hybrids were made between female Auke Creek (Southeast Alaska) pink salmon and Pillar Creek (Kodiak Island, ～1 000 km away) males; hybrids and their offspring were compared to offspring of control crosses of the same females with Auke Creek males. Parentage assignment from microsatellite analysis was used to improve estimates of survival and straying and to examine variation of family size. Hybridization reduced return rates of adults (a proxy for survival at sea) in the F₁ generation in the odd-year broodline (p < 0.0001) but not in the even-year broodline (p = 0.678). Hybridization reduced survival in both the odd- and even-broodyear F₂ (p < 0.005 and p < 0.0001). Hybridization did not appear to impair homing ability; weekly surveys revealed similar straying rates (～2%) by both hybrid and control fish into nearby (～1 km) Waydelich Creek in both generations in both trials. Hybridization did not increase the index of variability (σ²/μ) in family size. Decreased survival in the hybrid F₂ generation supports an epistatic model of outbreeding depression; nonepistatic effects may have contributed to reduced survival in the odd-broodyear F₁ hybrid fish. Outbreeding depression in hybrids of geographically separated populations demonstrates that introgression of nonnative fish can erode fitness, and should be recognized as a potential detriment of both aquaculture and management practices.     

Phylogeography of European grayling, <Emphasis Type="Italic">Thymallus thymallus</Emphasis> (Actinopterygii,Salmonidae), within the Northern Adriatic basin: evidence for native and exotic mitochondrial DNA lineages

Phylogeographic information on European grayling, Thymallus thymallus, is still fragmentary for the Northern Adriatic basin. In this article, we provide complete mitochondrial DNA control region sequence data of 456 grayling specimens from 21 sampling sites across distinct river drainages. Thirty-seven haplotypes were resolved and clustered into Danubian, Atlantic and Adriatic lineages. The latter clade, composed of 16 new haplotypes, was identified in 12 out of 17 Adriatic sampling sites and reached frequencies of 0.97 within single water courses of the Adige and the Po drainages. However, native Adriatic haplotypes were accompanied by Danubian and/or Atlantic variants in all cases. A positive correlation between hatchery haplotype frequency and annual stocking input pointed to a direct effect of stocking intensity on the genetic architecture of wild populations, although natural trans-basin colonisation may have additionally complicated the situation. However, both the extent and patterns of introgression between native and foreign strains, as well as microgeographic population structure within the Adriatic lineage will be clarified by future molecular surveys, based on nuclear genetic markers. Until then, conservation management must include an immediate cessation of stocking of commercial grayling stocks, as well as the prohibition of grayling translocation, even at the intra-drainage level.     

Evidence for selective angling of introduced trout and their hybrids in a stocked brown trout population

Comparisons of the genetic composition of brown trout Salmo trutta captured by anglers and by electrofishing based on three diagnostic microsatellite loci provided strong evidence that angling is selective in a stocked brown trout population. At two sites, anglers caught significantly younger trout and proportionally more introduced hatchery trout and hybrids than were observed in electrofishing surveys. Selective angling, in combination with a small legal catch size, may have considerably eliminated introduced trout and hybrids before spawning at the study sites, and thus may have reduced the introgression of alien genes into the local gene pool. Angling can be an important factor influencing the genetic structure of fish populations and should be taken into account in studies of introgressive hybridization in stocked fish populations and their management. In this study, demographic consequences of stocking were not assessed. Thus, even though the genetic consequences of stocking may be minimal or largely reversible through angling, resource competition between native and introduced trout, until they reach legal catch size, is expected to have a negative effect on the productivity of the indigenous trout population.     

Extreme genetic differentiation among the remnant populations of marble trout (Salmo marmoratus) in Slovenia

Populations of the marble trout (Salmo marmoratus) have declined critically due to introgression by brown trout (Salmo trutta) strains. In order to define strategies for long-term conservation, we examined the genetic structure of the 8 known pure populations using 15 microsatellite loci. The analyses reveal extraordinarily strong genetic differentiation among populations separated by < 15 km, and extremely low levels of intrapopulation genetic variability. As natural recolonization seems highly unlikely, appropriate management and conservation strategies should comprise the reintroduction of pure populations from mixed stocks (translocation) to avoid further loss of genetic diversity.     

Effects of nonnative species on the stability of riverine fish communities

Despite the increasing ubiquity of biological invasions worldwide, little is known about the scale-dependent effects of nonnative species on real-world ecological dynamics. Here, using an extensive time series dataset of riverine fish communities across different biogeographic regions of the world, we assessed the effects of nonnative species on the temporal variability and synchrony in abundance at different organizational levels (population, metapopulation, community and metacommunity) and spatial scales (stream reach and river basin). At the reach scale, we found that populations of nonnative species were more variable over time than native species, and that this effect scaled up to the community level – significantly destabilizing the dynamics of riverine fish communities. Nonnative species not only contributed to reduced community stability, but also increased variability of native populations. By contrast, we found no effect of nonnative species dominance on local interspecific synchrony among native species. At the basin scale, nonnative metapopulations were again more variable than the native ones. However, neither native metapopulations nor metacommunities showed differences in temporal variability or synchrony as nonnative species dominance increased basin-wide. This suggests a ‘dilution effect’ where the contribution to regional stability of local native populations from sites displaying low levels of invasion reduced the destabilizing effects of nonnative species. Overall, our results indicate that accounting for the destabilizing effect of nonnative species is critical to understanding native species persistence and community stability.     

Effects of stocking on the genetic diversity of brown trout populations of the Adriatic and Danubian drainages in Switzerland

This study focuses on genetic variation of brown trout Salmo trutta populations of the Adriatic and Danubian drainages in Switzerland. The allozyme and other protein loci data show a major replacement of native stocks from the Adriatic drainages by introduced hatchery trout of Atlantic basin origin. In most samples, diagnostic alleles for the Adriatic form of Salmo trutta f. fario and for the marbled trout Salmo trutta marmoratus are found at very low frequencies (f<0.15). Taking into account previous genetic studies on brown trout of this basin, the Danubian samples are not heavily contaminated with foreign alleles. The results are consistent with records of local stocking activities which account in part for the high introgression rates of Atlantic alleles into local populations of the Adriatic drainages. In addition, introgression is enhanced by a decrease of natural reproduction which is caused by a deterioration of trout habitats through human activities. Furthermore, a third mechanism is proposed that may contribute to the high introgression rates observed: if Atlantic trout are introduced, the reproductive barriers between the two native forms, marbled trout and Adriatic fario respectively, break down. Atlantic trout apparently hybridize with both native forms and generate gene flow between them. In some parts of Adriatic drainages in Switzerland, the patterns of introgression and hybridization are further complicated by introduction of trout from the Danubian system. Alleles of the marbled trout are also found in the samples of the Danubian drainage system. These are due to stocking activities across the watershed.     

A sturgeon view on conservation genetics

The order of Acipenseriformes (sturgeon and paddlefishes) contains the economic most valuable species in world trade: the producers of black caviar. Mainly because of their high economic value, sturgeon and paddlefishes were and are the goal of many conservation programs worldwide. In this review, I present some of the main conclusions that can be drawn from previous conservation efforts. My review is divided into two parts. The first part deals with species identification methods, which are necessary for international trade control (Convention on International Trade in Endangered Species of Wild Fauna and Flora). Considering the outcome of all previous forensic studies, I conclude, firstly, it is necessary to use large sample sizes to avoid misinterpretation of possible diagnostic substitutions, and, secondly, the combination of both DNA types (mitochondrial and nuclear markers) is recommended for correct species identification. The second part deals with the influence of restocking/release programs on native populations. The outcome of previous stocking efforts indicates that, in most cases, stocking with nonnative specimens is economically nonsense because most translocation efforts failed. In addition, in cases where such efforts were successful, they influenced negatively the genotypic structure (inbreeding and outbreeding depressions) of native populations. In fact, nonnative stocking does jeopardize adaptation and blurs the genetic differences used to discriminate populations. Furthermore, if it is necessary to release individuals to avoid extinction, released specimens should be as young as possible (homing fidelity).     

Detecting and quantifying introgression in hybridized populations: simplifying assumptions yield overconfidence and uncertainty

A growing threat to the conservation of many native species worldwide is genetic introgression from non‐native species. Although improved molecular genetic techniques are increasing the availability of species‐diagnostic markers for many species, efficient field sampling design and reliable data interpretation require accurate estimates of uncertainty associated with the detection of non‐native alleles and the quantification of introgression in native populations. Using fish populations as examples, we developed a simulation model of an age‐structured population that tracks the introduction and inheritance of non‐native alleles across generations by simulating stochastic mating and survival of individual fish and the resulting transmission of diagnostic markers. To simulate detection and quantification of introgression, we sampled varying combinations of n fish and m diagnostic markers to detect and quantify introgression from thousands of virtual, independent fish populations for a wide range of hybridization scenarios. Using the results of simulated sampling, we quantified the extent to which common simplifying assumptions regarding population structure and inheritance mechanisms can lead to the following: (i) overconfidence in our ability to detect non‐native alleles and (ii) unrealistically narrow confidence intervals for estimates of the proportion of non‐native alleles present. Under many circumstances, commonly used simplifying assumptions underestimate the probability of failing to detect ongoing introgression and the uncertainty associated with estimates of introgression by orders of magnitude. Such overconfidence in our ability to detect and quantify introgression can affect critical conservation and management decisions regarding native species undergoing or at risk of introgression from non‐native species.     

Have Native Coho Salmon (Oncorhynchus Kisutch) Persisted in the Nooksack and Samish rivers Despite Continuous Hatchery Production Throughout the Past Century?

For over a century, Washington State Department of Fish and Wildlife has implemented hatchery programs as a means to boost salmon abundance. Concerns have developed that native populations may be replaced by hatchery strains, decreasing the genetic diversity required to respond to environmental changes. We report a comparison of microsatellite DNA variation in wild-spawning and hatchery-strain coho salmon from the Nooksack and Samish rivers in northern Puget Sound. Significant heterogeneity in genotype frequencies was detected between wild-spawning coho salmon from the upper North Fork (NF) Nooksack River and hatchery-strain coho salmon from the Nooksack River (descendants of primarily Nooksack River broodstock). Little difference in genotype frequencies was detected between wild-spawning coho salmon from the Samish River and hatchery-strain coho salmon from the Nooksack River. The 13-locus suite provided high resolution: in assignment tests over 85% of wild-spawning coho salmon from the upper NF Nooksack River were assigned to source. Wild-spawning coho salmon collected below hatcheries in the Nooksack River and 50% of wild-spawning Samish River coho salmon were assigned to hatchery collections. The genetic divergence of wild-spawning coho salmon in the upper NF Nooksack River is remarkable given the extensive stocking history and proximity of a hatchery. We suggest that these upper river fish are native coho salmon and that wild spawners in the lower Nooksack and Samish River are descendants of hatchery productions. We attribute divergence to earlier run timing in upper NF Nooksack River wild spawners, availability of extensive spawning and rearing habitat upstream of a hatchery in the upper NF Nooksack River, and a longer stocking history in the Samish River.     

Insights into Fisheries Management Practices: Using the Theory of Planned Behavior to Explain Fish Stocking among a Sample of Swiss Anglers

Using inadequate management tools often threatens the natural environment. This study focuses on the example of Swiss recreational fishermen (hereafter called “anglers”) as recreational fisheries management stakeholders. In recreational fisheries, fish stocking conducted by anglers has been identified as one important factor associated with declining fish catches. We therefore aimed to a) gain insights into why anglers want to maintain fish stocking and b) identify entry points for interventions to promote more pro-ecological management practices. Results (N = 349) showed that the majority of anglers think very uncritically about stocking and that they frequently engage in it. We conclude that outcome expectancies and beliefs about risks, in combination with a lack of stocking success controls are the main reasons that anglers retain stocking measures. We suggest that providing anglers with direct experience and feedback about stocking success is suitable to change their intentions regarding stocking and their actual stocking behavior, and thus, to promote more pro-ecological management methods. From a more general perspective, the results of this study are likely to help improve pro-ecological ecosystem management in other domains where problems similar to those in recreational fisheries management might exist.     

Alpine headwater streams as reservoirs of remnant populations of the Danubian clade of brown trout

1. The watercourses of Austria are mainly part of the Danube drainage system. Nonetheless, only few brown trout (Salmo trutta) populations of the Danubian phylogenetic lineage have been found in this region, not being introgressed by hatchery‐reared fish of the allochthonous Atlantic lineage. The present study was aimed at identifying further waterbodies that might harbour the non‐admixed gene pool of the Danubian clade trout. 2. In a first step, the complete mitochondrial DNA control region of 447 specimens from 20 sampling sites was sequenced to screen for the presence of specific haplotypes. In a second step, 332 individuals from 15 populations were analysed at 10 microsatellite DNA loci. 3. Although sampling concentrated on remote Alpine headwater streams, introgression of hatchery strains was more common than expected from existing stocking records. For seven populations, however, no evidence of recent hatchery trout introgression was found and it is suggested that they might represent the indigenous gene pool. 4. Populations showing no evidence of hatchery introgression displayed lower levels of intrapopulation variability and higher degrees of differentiation compared to purported admixed populations. 5. Our study demonstrates the necessity of combining different molecular markers to reveal the impact of introgression into wild populations, since at some sampling sites admixture would have remained undetected if only a single molecular technique was applied. 6. The identification and characterisation of non‐introgressed populations provides important information for setting conservation priorities and preventing further loss of genetic integrity of a unique element of the native fish fauna.