Hatchery Introgression Research Articles

Evaluation of genetic consequences of stocking on the southern-margin populations of white-spotted charr.

Coldwater-adapted freshwater fishes, especially their populations along warm-range margins, are most vulnerable to the climate oscillations associated with global warming. Stocking is a major strategy for avoiding the extinction of these species. However, while stocking can reverse the decline of isolated populations, it may also result in a loss of genetic diversity in the native local population due to the introgressive replacement of hatchery genes. To plan an adequate strategy for conserving locally adapted populations, the genetic impacts of stocking on native lineages should be evaluated from small river branches to wide-ranging drainage areas. We investigated the population genetic structure of white-spotted charr (Salvelinus leucomaenis) within its southern range (Lake Biwa basin, Japan). By applying genome-wide SNP analysis to the population's genetic structure, we assessed the extent of genetic introgression resulting from stocking. White-spotted charr in the Lake Biwa watershed constitutes a distinctive genetic group, within which apparent genetic differentiation was observed. The hatchery-reared fish line commonly used for supplementation stocking in the catchment was discernable from the native population, enabling us to analyze genetic introgression across the entire drainage area. Admixed individuals resulting from hatchery introgression were observed in most of the stocked sites that showed relatively high heterozygosity and nucleotide diversity. However, their genetic differentiation was much lower than that of native populations. The supplementation history as well as the road availability contributed substantially to the introgression of hatchery genes. Populations with the native genetic structure remained in the upstream regions of the tested rivers. However, their heterozygosity and nucleotide diversity were low when compared with that of the populations with hatchery supplementation. Our results shed light on the genetic impacts of stocking on isolated native populations and suggest that conventional supplementation methods cannot preserve a unique biodiversity in the distribution margin.

Integrating otolith and genetic tools to reveal intraspecific biodiversity in a highly impacted salmon population.

Intraspecific biodiversity is vital for species persistence in an increasingly volatile world. By embracing methods that integrate information at different spatiotemporal scales, we can directly monitor and reconstruct changes in intraspecific biodiversity. Here we combined genetics and otolith biochronologies to describe the genotypic and phenotypic diversity of Chinook salmon (Oncorhynchus tshawytscha) in the Yuba River, California, comparing cohorts that experienced a range of hydroclimatic conditions. Yuba River salmon have been heavily impacted by habitat loss and degradation, and large influxes of unmarked hatchery fish each year have led to concern about introgression and uncertainty around the viability of its wild populations, particularly the rarer spring-run salmon. Otolith strontium isotopes showed that Yuba River origin fish represented, on average, 42% (range 7%-73%) of spawners across six return years (2009-2011, 2018-2020), with large interannual variability. The remainder of adult Chinook salmon in the river were primarily strays from the nearby Feather River hatchery, and since 2018 from the Mokelumne River hatchery. Among the Yuba-origin spawners, on average, 30% (range 14%-50%) exhibited the spring-run genotype. The Yuba-origin fish also displayed a variety of outmigration phenotypes that differed in the timing and size at which they left the Yuba river. Early-migrating fry dominated the returns (mean 59%, range 33%-89%), and their contribution rates were negatively correlated with freshwater flows. It is unlikely that fry survival rates are elevated during droughts, suggesting that this trend reflects disproportionately low survival of larger later migrating parr, smolts, and yearlings along the migratory corridor in drier years. Otolith daily increments indicated generally faster growth rates in non-natal habitats, emphasizing the importance of continuing upstream restoration efforts to improve in-river growing conditions. Together, these findings show that, despite a long history of habitat degradation and hatchery introgression, the Yuba River maintains intraspecific biodiversity that should be taken into account in future management, restoration, and reintroduction plans. The finding that genotypic spring-run are reproducing, surviving, and returning to the Yuba River every year suggests that re-establishment of an independent population is possible, although hatchery-wild interactions would need to be carefully considered. Integrating methods is critical to monitor changes in key genetic, physiological, and behavioral traits to assess population viability and resilience.

Salmon hatchery strays can demographically boost wild populations at the cost of diversity: quantitative genetic modelling of Alaska pink salmon.

Hatcheries are vital to many salmon fisheries, with inherent risks and rewards. While hatcheries can increase the returns of adult fish, the demographic and evolutionary consequences for natural populations interacting with hatchery fish on spawning grounds remain unclear. This study examined the impacts of stray hatchery-origin pink salmon on natural population productivity and resilience. We explored temporal assortative mating dynamics using a quantitative genetic model that assumed the only difference between hatchery- and natural-origin adults was their return timing to natural spawning grounds. This model was parameterized with empirical data from an intensive multi-generational study of hatchery-wild interactions in the world's largest pink salmon fisheries enhancement program located in Prince William Sound, Alaska. Across scenarios of increasing hatchery fish presence on spawning grounds, our findings underscore a trade-off between demographic enhancement and preservation of natural population diversity. While enhancement bolstered natural population sizes towards local carrying capacities, hatchery introgression reduced variation in adult return timing by up to 20%. Results indicated that hatchery-origin alleles can rapidly assimilate into natural populations, despite the reduced fitness of hatchery fish attributable to phenotypic mismatches. These findings elucidate the potential for long-term demographic and evolutionary consequences arising from specific hatchery-wild interactions, emphasizing the need for management strategies that balance demographic enhancement with the conservation of natural diversity.

Native Population Structure beyond Hatchery Introgression in the Endemic Sicilian Trout

Brown trout populations living in the limit of the distribution of the species face challenging environmental conditions. In islands, this vulnerable situation is exacerbated by geographical isolation. Sicilian trout persist only in the south-eastern part of the island and, based on their morphological characteristics, they have been recognized as a distinct species named Salmo cettii. We present the most extensive genetic study on Sicilian trout, based on 213 individuals from nine different streams in four basins. Sequencing of the mitochondrial control region and genotyping of the LDH-C* locus and eight microsatellite markers were carried out to evaluate hatchery introgression from past stocking practices in natural populations and to estimate the gene diversity distribution in populations. Results showed that only trout from the Tellesimo River remained free of hatchery introgression. Gene diversity was low in this native population, but increased in the rest of the samples, probably because of the introduction of hatchery genes. Despite the high level of introgression, the distribution of gene diversity depicted a clear natural pattern of population structure related to the hydrographic hierarchy. Because they represent long evolutionary histories, Sicilian trout populations should be considered of high conservation priority and managed according to at least four different genetic units.

Redundancy analysis, genome-wide association studies and the pigmentation of brown trout (Salmo trutta L.).

The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.

Using genetic data to advance stream fish reintroduction science: a case study in brook trout

Widespread extirpation of native fish populations has led to a rise in species reintroduction efforts worldwide. Most efforts have relied on demographic data alone to guide project design and evaluate success. However, the genetic characteristics of many imperiled fish populations including low diversity, local adaptation, and hatchery introgression emphasize the importance of genetic data in the design and monitoring of reintroduction efforts. Focusing on a case study of brook trout (Salvelinus fontinalis) in North Carolina, we show how the combined use of genetic and demographic data can support reintroduction efforts by improving source population selection and providing opportunities to evaluate genetic viability and adaptive potential in restored populations. Using this combined approach, we reintroduced brook trout into a restored stream from two source populations and monitored changes in genetic diversity and population size in source and recipient populations. Three years after the initial translocation, the reintroduced population had comparable density, but higher genetic diversity, than either source population. This study demonstrates the utility of genetic and demographic data for reintroduction efforts, particularly when extant populations are genetically depauperate and maintaining adaptive potential is a primary restoration goal. However, we emphasize the value of continued monitoring at longer temporal and spatial scales to determine the effects of stochastic process on the long‐term adaptive capacity and persistence of reintroduced populations. Overall, inclusion of genetic data in reintroduction efforts offers increased ability to meet project goals while simultaneously conserving critical sources of adaptive variation that exist across the landscape.

Genomic Hatchery Introgression in Brown Trout (Salmo trutta L.): Development of a Diagnostic SNP Panel for Monitoring the Impacted Mediterranean Rivers

Brown trout (Salmo trutta L.) populations have been restocked during recent decades to satisfy angling demand and counterbalance the decline of wild populations. Millions of fertile brown trout individuals were released into Mediterranean and Atlantic rivers from hatcheries with homogeneous central European stocks. Consequently, many native gene pools have become endangered by introgressive hybridization with those hatchery stocks. Different genetic tools have been used to identify and evaluate the degree of introgression starting from pure native and restocking reference populations (e.g., LDH-C* locus, microsatellites). However, due to the high genetic structuring of brown trout, the definition of the "native pool" is hard to achieve. Additionally, although the LDH-C* locus is useful for determining the introgression degree at the population level, its consistency at individual level is far from being accurate, especially after several generations were since releases. Accordingly, the development of a more powerful and cost-effective tool is essential for an appropriate monitoring to recover brown-trout-native gene pools. Here, we used the 2b restriction site-associated DNA sequencing (2b-RADseq) and Stacks 2 with a reference genome to identify single-nucleotide polymorphisms (SNPs) diagnostic for hatchery-native fish discrimination in the Atlantic and Mediterranean drainages of the Iberian Peninsula. A final set of 20 SNPs was validated in a MassARRAY® System genotyping by contrasting data with the whole SNP dataset using samples with different degree of introgression from those previously recorded. Heterogeneous introgression impact was confirmed among and within river basins, and was the highest in the Mediterranean Slope. The SNP tool reported here should be assessed in a broader sample scenario in Southern Europe considering its potential for monitoring recovery plans.

Broadscale Population Structure and Hatchery Introgression of Midwestern Brook Trout

AbstractBrook Trout Salvelinus fontinalis have faced significant declines throughout their native range and have been stocked in Midwestern waters since the late 1800s to offset such losses. Several studies have investigated the genetic effects of these stockings, but these efforts have been confined to relatively small spatial scales. In this study, we compiled 8,454 Brook Trout microsatellite genotypes from 188 wild Midwestern populations and 26 hatchery strains to provide novel insights of broadscale population structure, regional patterns of genetic diversity, and estimates of hatchery introgression for inland Wisconsin populations. Our results indicate high levels of differentiation among our study populations, a lack of hydrological population structuring, lower estimates of genetic diversity in the Driftless Area, and that hatchery introgression has been largely confined to regions of inland Wisconsin that have been heavily affected by anthropogenic disturbances (i.e., the Driftless Area). We also provide evidence that populations may be able to purge hatchery‐derived alleles, discuss possible mechanisms behind this phenomenon, and consider their relevance to accurate estimation of hatchery introgression. Collectively, these results summarize the genetic effects of over a century of anthropogenic disturbance on native Brook Trout populations and emphasize the importance of integrating historical data into contemporary genetic research of intensively managed species.

Genetic Structure of Maryland Brook Trout Populations: Management Implications for a Threatened Species

AbstractBrook Trout Salvelinus fontinalis have declined across their native range due to multiple anthropogenic factors, including landscape alteration and climate change. Although coldwater streams in Maryland (eastern United States) historically supported significant Brook Trout populations, only fragmented remnant populations remain, with the exception of the upper Savage River watershed in western Maryland. Using microsatellite data from 38 collections, we defined genetic relationships of Brook Trout populations in Maryland drainages. Microsatellite analyses of Brook Trout indicated the presence of five major discrete units defined as the Youghiogheny (Ohio), Susquehanna, Patapsco/Gunpowder, Catoctin, and Upper Potomac, with a distinct genetic subunit present in the Savage River (upper Potomac). We did not observe evidence for widespread hatchery introgression with native Brook Trout. However, genetic effects due to fragmentation were evident in several Maryland Brook Trout populations, resulting in erosion of diversity that may have negative implications for their future persistence. Our current study supplements an increasing body of evidence that Brook Trout populations in Maryland are highly susceptible to multiple anthropogenic stresses, and many populations may be extirpated in the near future. Future management efforts focused on habitat protection and potential stream restoration, coupled with a comprehensive assessment framework that includes genetic considerations, may provide the best outlook for Brook Trout populations in Maryland.

Development of Genetic Baseline Information to Support the Conservation and Management of Wild Brook Trout in North Carolina

AbstractAfter centuries of declines, there is growing interest in conserving extant wild populations of Brook Trout Salvelinus fontinalis and reintroducing Brook Trout populations of native ancestry. A population genetic baseline can enhance conservation outcomes and promote restoration success. Consequently, it is important to document existing patterns of genetic variation across the landscape and translate these data into an approachable format for fisheries managers. We genotyped 9,507 Brook Trout representing 467 wild collections at 12 microsatellite loci to establish a genetic baseline for North Carolina, USA. Rarefied allelic richness (mean = 3.12) and observed heterozygosity (mean = 0.42), which reflect within‐population diversity, were low to moderate relative to levels typically observed at higher latitudes. Effective population sizes (Ne) varied widely but were often very low (151 collections had an estimated Ne < 10). Despite decades of intensive stocking across the state, we found little to no evidence of hatchery introgression in most populations. Although genetic variation was significant at a variety of spatial scales (mean pairwise = 0.73), substantial genetic variation occurred between patches within individual watersheds. Analysis of molecular variance indicated that a substantial portion (28.5%) of the observed genetic variation was attributable to differences among populations, with additional genetic variation among hydrologic unit codes (HUCs; 16.0, 16.6, 12.1, and 9.4% of the overall variation among 12‐, 10‐, 8‐, and 6‐digit HUCs, respectively). We discuss a suite of potential applications for this type of genetic data to enhance management outcomes, such as conservation prioritization and selection of source stocks for reintroductions or genetic rescue.

Multiple decades of stocking has resulted in limited hatchery introgression in wild brook trout (Salvelinus fontinalis) populations of Nova Scotia.

Many populations of freshwater fishes are threatened with losses, and increasingly, the release of hatchery individuals is one strategy being implemented to support wild populations. However, stocking of hatchery individuals may pose long‐term threats to wild populations, particularly if genetic interactions occur between wild and hatchery individuals. One highly prized sport fish that has been heavily stocked throughout its range is the brook trout (Salvelinus fontinalis). In Nova Scotia, Canada, hatchery brook trout have been stocked since the early 1900s, and despite continued stocking efforts, populations have suffered declines in recent decades. Before this study, the genetic structure of brook trout populations in the province was unknown; however, given the potential negative consequences associated with hatchery stocking, it is possible that hatchery programs have adversely affected the genetic integrity of wild populations. To assess the influence of hatchery supplementation on wild populations, we genotyped wild brook trout from 12 river systems and hatchery brook trout from two major hatcheries using 100 microsatellite loci. Genetic analyses of wild trout revealed extensive population genetic structure among and within river systems and significant isolation‐by‐distance. Hatchery stocks were genetically distinct from wild populations, and most populations showed limited to no evidence of hatchery introgression (<5% hatchery ancestry). Only a single location had a substantial number of hatchery‐derived trout and was located in the only river where a local strain is used for supplementation. The amount of hatchery stocking within a watershed did not influence the level of hatchery introgression. Neutral genetic structure of wild populations was influenced by geography with some influence of climate and stocking indices. Overall, our study suggests that long‐term stocking has not significantly affected the genetic integrity of wild trout populations, highlighting the variable outcomes of stocking and the need to evaluate the consequences on a case‐by‐case basis.

Genetic diversity, admixture, and hatchery influence in Brook Trout (Salvelinus fontinalis) throughout western New York State.

Although Brook Trout are distributed across most of eastern North America, population numbers have declined in many regions due to habitat loss, climate change, and competition with non‐native species. In New York State, Brook Trout habitat has been substantially reduced, with many areas showing complete extirpation of Brook Trout populations, predominantly in the western portion of the state. Small, fragmented populations are at risk of genetic diversity loss, inbreeding depression, and reduced fitness, leading to a greater potential for local extirpation. Genetic monitoring is a practical tool that can facilitate further conservation‐decision making regarding small populations. In this study, we used 12 microsatellite loci to examine 3,436 sampled Brook Trout, representing 75 sites from the Allegheny, Erie/Niagara, Genesee, Oswego, Lake Ontario, and Susquehanna drainage basins throughout western New York State. Three Brook Trout hatchery strains were also genetically characterized to evaluate the degree of hatchery introgression between wild populations and hatchery strains stocked in the region. Overall, estimates of genetic diversity varied widely: Allelic richness ranged from 2.23 to 7.485, and expected heterozygosity ranged from 0.402 to 0.766. As observed for Brook Trout in other regions, we found a high degree of genetic differentiation among populations, with all comparisons except one showing significant F ST values. Hatchery introgression was found to be minimal, with estimates ranging from 1.96% to 3.10% of wild individuals exhibiting membership proportions to a hatchery strain cluster exceeding 10% (q ≥ 0.10). Results from this investigation can be used to prioritize management efforts for Brook Trout in western New York State and act as a baseline to monitor future population trends.

Limited hatchery introgression into wild brook trout (Salvelinus fontinalis) populations despite reoccurring stocking.

Due to increased anthropogenic pressures on many fish populations, supplementing wild populations with captive‐raised individuals has become an increasingly common management practice. Stocking programs can be controversial due to uncertainty about the long‐term fitness effects of genetic introgression on wild populations. In particular, introgression between hatchery and wild individuals can cause declines in wild population fitness, resiliency, and adaptive potential and contribute to local population extirpation. However, low survival and fitness of captive‐raised individuals can minimize the long‐term genetic consequences of stocking in wild populations, and to date the prevalence of introgression in actively stocked ecosystems has not been rigorously evaluated. We quantified the extent of introgression in 30 populations of wild brook trout (Salvelinus fontinalis) in a Pennsylvania watershed and examined the correlation between introgression and 11 environmental covariates. Genetic assignment tests were used to determine the origin (wild vs. captive‐raised) for 1,742 wild‐caught and 300 hatchery brook trout. To avoid assignment biases, individuals were assigned to two simulated populations that represented the average allele frequencies in wild and hatchery groups. Fish with intermediate probabilities of wild ancestry were classified as introgressed, with threshold values determined through simulation. Even with reoccurring stocking at most sites, over 93% of wild‐caught individuals probabilistically assigned to wild origin, and only 5.6% of wild‐caught fish assigned to introgressed. Models examining environmental drivers of introgression explained <3% of the among‐population variability, and all estimated effects were highly uncertain. This was not surprising given overall low introgression observed in this study. Our results suggest that introgression of hatchery‐derived genotypes can occur at low rates, even in actively stocked ecosystems and across a range of habitats. However, a cautious approach to stocking may still be warranted, as the potential effects of stocking on wild population fitness and the mechanisms limiting introgression are not known.

Assessing the impact of stocking northern-origin hatchery brook trout on the genetics of wild populations in North Carolina

The release of hatchery-origin fish into streams with endemics can degrade the genetics of wild populations if interbreeding occurs. Starting in the 1800s, brook trout descendent from wild populations in the northeastern United States were stocked from hatcheries into streams across broad areas of North America to create and enhance fishery resources. Across the southeastern United States, many millions of hatchery-origin brook trout have been released into hundreds of streams, but the extent of introgression with native populations is not well resolved despite large phylogeographic distances between these groups. We used three assessment approaches based on 12 microsatellite loci to examine the extent of hatchery introgression in 406 wild brook trout populations in North Carolina. We found high levels of differentiation among most collections (mean F′ST = 0.718), and among most wild collections and hatchery strains (mean F′ST = 0.732). Our assessment of hatchery introgression was consistent across the three metrics, and indicated that most wild populations have not been strongly influenced by supplemental stocking. However, a small proportion of wild populations in North Carolina appear to have been strongly influenced by stocked conspecifics, or in some cases, may have been founded entirely by hatchery lineages. In addition, we found significant differences in the apparent extent of hatchery introgression among major watersheds, with the Savannah River being the most strongly impacted. Conversely, populations in the Pee Dee River watershed showed little to no evidence of hatchery introgression. Our study represents the first large-scale effort to quantify the extent of hatchery introgression across brook trout populations in the southern Appalachians using highly polymorphic microsatellite markers.

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

Abstract1. 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 (FST = 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.

Restricted gene flow between resident Oncorhynchus mykiss and an admixed population of anadromous steelhead.

The species Oncorhynchus mykiss is characterized by a complex life history that presents a significant challenge for population monitoring and conservation management. Many factors contribute to genetic variation in O. mykiss populations, including sympatry among migratory phenotypes, habitat heterogeneity, hatchery introgression, and immigration (stray) rates. The relative influences of these and other factors are contingent on characteristics of the local environment. The Rock Creek subbasin in the middle Columbia River has no history of hatchery supplementation and no dams or artificial barriers. Limited intervention and minimal management have led to a dearth of information regarding the genetic distinctiveness of the extant O. mykiss population in Rock Creek and its tributaries. We used 192 SNP markers and collections sampled over a 5‐year period to evaluate the temporal and spatial genetic structures of O. mykiss between upper and lower watersheds of the Rock Creek subbasin. We investigated potential limits to gene flow within the lower watershed where the stream is fragmented by seasonally dry stretches of streambed, and between upper and lower watershed regions. We found minor genetic differentiation within the lower watershed occupied by anadromous steelhead (FST = 0.004), and evidence that immigrant influences were prevalent and ubiquitous. Populations in the upper watershed above partial natural barriers were highly distinct (FST = 0.093) and minimally impacted by apparent introgression. Genetic structure between watersheds paralleled differences in local demographics (e.g., variation in size), migratory restrictions, and habitat discontinuity. The evidence of restricted gene flow between putative remnant resident populations in the upper watershed and the admixed anadromous population in the lower watershed has implications for local steelhead productivity and regional conservation.

Fine-scale genetic structure of brook trout in a dendritic stream network

Conservation management of threatened species requires identifying the landscape features that shape population structure. Within river ecosystems, the dendritic nature of river networks and physical barriers, such as waterfalls, can strongly shape population structure. We examined population structure of native brook trout in a river network in northern New Hampshire, USA, including above and below waterfalls. We genotyped fish at 12 microsatellite loci including samples from six tributaries, mobile adults from three mainstem rivers, and fish from the hatchery broodstock that had been earlier stocked in the study region. We found that two subpopulations in tributaries above waterfalls were distinguished as unique genetic clusters with high levels of among population genetic diversity (average pairwise FST = 0.20) and low levels of within population genetic diversity (average allelic richness AR = 3.55), including one sub-population above a waterfall. With only one exception, subpopulations below waterfalls exhibited patterns of genetic diversity within and among populations consistent with contemporary gene flow among these subpopulations (average FST = 0.03; AR = 5.83). Most mobile adult fish caught in the mainstem rivers were genetically similar to those found in tributaries without waterfalls, suggesting that mobile individuals are likely connecting below-barrier subpopulations. Despite recent hatchery stocking in this system, we did not observe evidence of hatchery introgression with wild-caught fish. The complex metapopulation of naturally isolated and connected subpopulations of brook trout described in this study highlights the importance of considering fine scale genetic structure in conservation management.

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.

Dispersal and demography of brown trout, Salmo trutta, inferred from population and family structure in unstable Mediterranean streams

The spatial distribution of closely related individuals can be inferred from genetic data and provides valuable information about dispersal patterns and gene flow contributing to the population genetic structure of organisms. Here, we analyzed family distribution of brown trout Salmo trutta in the uppermost reaches of the Mediterranean Son River basin by genotyping nine microsatellite loci. Population structure suggested a model of two units heavily affected by hatchery introgression superimposed on a hydrographic pattern. We observed kin-biased spatial distribution, implying limited dispersal of related fish, probably favored by severe climate conditions in this system. However, downstream dispersal was observed for some large adult fish. Variance in family size defined small estimates of effective population sizes (Ne) in all streams. Comparison of estimates by several methods indicated that factors other than variation of family size are responsible for such low values. The population structure in the Son River basin is, then, represented by interconnected locations in which dispersion of the fish is probably conditioned by oscillations in water discharge, particularly the extremely low water flow during summer. Stream discharge variation could also be related to the flexibility of the mating system. Such characteristics make populations especially vulnerable to stocking and to any other potential effects.

Genetic versus Rearing-Environment Effects on Phenotype: Hatchery and Natural Rearing Effects on Hatchery- and Wild-Born Coho Salmon

With the current trends in climate and fisheries, well-designed mitigative strategies for conserving fish stocks may become increasingly necessary. The poor post-release survival of hatchery-reared Pacific salmon indicates that salmon enhancement programs require assessment. The objective of this study was to determine the relative roles that genotype and rearing environment play in the phenotypic expression of young salmon, including their survival, growth, physiology, swimming endurance, predator avoidance and migratory behaviour. Wild- and hatchery-born coho salmon adults (Oncorhynchus kisutch) returning to the Chehalis River in British Columbia, Canada, were crossed to create pure hatchery, pure wild, and hybrid offspring. A proportion of the progeny from each cross was reared in a traditional hatchery environment, whereas the remaining fry were reared naturally in a contained side channel. The resulting phenotypic differences between replicates, between rearing environments, and between cross types were compared. While there were few phenotypic differences noted between genetic groups reared in the same habitat, rearing environment played a significant role in smolt size, survival, swimming endurance, predator avoidance and migratory behaviour. The lack of any observed genetic differences between wild- and hatchery-born salmon may be due to the long-term mixing of these genotypes from hatchery introgression into wild populations, or conversely, due to strong selection in nature—capable of maintaining highly fit genotypes whether or not fish have experienced part of their life history under cultured conditions.