Identifying footprints of selection in stocked brown trout populations: a spatio‐temporal approach

Studies of interactions between farmed and wild salmonid fishes have suggested reduced fitness of farmed strains in the wild, but evidence for selection at the genic level is lacking. We studied three brown trout populations in Denmark which have been significantly admixed with stocked hatchery trout (19–64%), along with two hatchery strains used for stocking. The wild populations were represented by contemporary samples (2000–2006) and two of them by historical samples (1943–1956). We analysed 61 microsatellite loci, nine of which showed putative functional relationships [expressed sequence tag (EST)‐linked or quantitative trait loci]. F_ST‐based outlier tests provided support for diversifying selection at chromosome regions marked by three loci, two anonymous and one EST‐linked. Patterns of differentiation suggested that the loci were candidates for being under diversifying hitch‐hiking selection in hatchery vs. wild environments. Analysis of hatchery strain admixture proportions showed that in one wild population, two of the loci showed significantly lower admixture proportions than the putatively neutral loci, implying contemporary selection against alleles introduced by hatchery strain trout. In the most strongly admixed population, however, there was no evidence for selection, possibly because of immigration by stocked trout overcoming selection against hatchery‐derived alleles or supportive breeding practices allowing hatchery strain trout to escape natural selection. To our knowledge, this is the first study demonstrating footprints of selection in wild salmonid populations subject to spawning intrusion by farmed fish.     

Dynamic micro-geographic and temporal genetic diversity in vertebrates: the case of lake-spawning populations of brown trout (Salmo trutta)

Conservation of species should be based on knowledge of effective population sizes and understanding of how breeding tactics and selection of recruitment habitats lead to genetic structuring. In the stream‐spawning and genetically diverse brown trout, spawning and rearing areas may be restricted source habitats. Spatio–temporal genetic variability patterns were studied in brown trout occupying three lakes characterized by restricted stream habitat but high recruitment levels. This suggested non‐typical lake‐spawning, potentially representing additional spatio–temporal genetic variation in continuous habitats. Three years of sampling documented presence of young‐of‐the‐year cohorts in littoral lake areas with groundwater inflow, confirming lake‐spawning trout in all three lakes. Nine microsatellite markers assayed across 901 young‐of‐the‐year individuals indicated overall substantial genetic differentiation in space and time. Nested gene diversity analyses revealed highly significant (≤P = 0.002) differentiation on all hierarchical levels, represented by regional lakes (F_LT = 0.281), stream vs. lake habitat within regional lakes (F_HL = 0.045), sample site within habitats (F_SH = 0.010), and cohorts within sample sites (F_CS = 0.016). Genetic structuring was, however, different among lakes. It was more pronounced in a natural lake, which exhibited temporally stable structuring both between two lake‐spawning populations and between lake‐ and stream spawners. Hence, it is demonstrated that lake‐spawning brown trout form genetically distinct populations and may significantly contribute to genetic diversity. In another lake, differentiation was substantial between stream‐ and lake‐spawning populations but not within habitat. In the third lake, there was less apparent spatial or temporal genetic structuring. Calculation of effective population sizes suggested small spawning populations in general, both within streams and lakes, and indicates that the presence of lake‐spawning populations tended to reduce genetic drift in the total (meta‐) population of the lake.     

Minimal gene flow from introduced brown trout (Salmo trutta L.) after 30 years of stocking

Lake Tinnsjø, Norway, has been heavily stocked over three decades with two different brown trout stocks. A population genetic survey based on 13 allozyme coding loci was conducted to investigate the genetic composition of the present trout population and the genetic impact of the two donors. Contrary to expectations, highly significant differences in allelic frequencies between Lake Tinnsjø trout and the two donor stocks were found at several loci, suggesting minimal gene flow from stocked trout to the wild populations. Pairwise genetic distance values were several times higher between donor stocks and Lake Tinnsjø samples than between the various spawning inlets to Lake Tinnsjø. F_st increased from 0.024 to 0.090, when samples from the donor stocks were included in the material. There were no deviations from expected Hardy–Weinberg distribution of genotypes in the spawning inlets. It was concluded that the donor stocks contributed little to the trout gene pool in the lake. A possible exception is the trout population below the lake outlet.     

Long-term captive breeding does not necessarily prevent reestablishment: lessons learned from Eagle Lake rainbow trout

Captive breeding of animals is often cited as an important tool in conservation, especially for fishes, but there are few reports of long-term (<50 years) success of captive breeding programs, even in salmonid fishes. Here we describe the captive breeding program for Eagle Lake rainbow trout, Oncorhynchus mykiss aquilarum, which is endemic to the Eagle Lake watershed of northeastern California. The population in Eagle Lake has been dependent on captive breeding for more than 60 years and supports a trophy fishery in the lake. Nevertheless, the basic life history, ecological, and genetic traits of the subspecies still seem to be mostly intact. Although management has apparently minimized negative effects of hatchery rearing, reestablishing a wild population would ensure maintenance of its distinctive life history and its value for future use as a hatchery fish. An important factor that makes reestablishment possible is that the habitat in Eagle Lake is still intact and that Pine Creek, its major spawning stream, is recovering as habitat. With the exception of an abundant alien brook trout (Salvelinus fontinalis) population in Pine Creek, the habitat factors that led to the presumed near-extinction of Eagle Lake rainbow trout in the early twentieth century have been ameliorated, although the final stages of reestablishment (eradication of brook trout, unequivocal demonstration of successful spawning migration) have still not been completed. The Eagle Lake rainbow trout story shows that long-term captive breeding of migratory salmonid fishes does not necessarily prevent reestablishment of wild populations, provided effort is made to counter the effects of hatchery selection and that natural habitats are restored for reintroduction. Long-term success, however, ultimately depends upon eliminating hatchery influences on wild-spawning populations. Extinction of Eagle Lake rainbow trout as a wild species becomes increasingly likely if we fail to act boldly to protect it and the Eagle Lake watershed.     

A genetically distinct wild redband trout (<Emphasis Type="Italic">Oncorhynchus mykiss gairdneri</Emphasis>) population in Crane Prairie Reservoir,Oregon, persists despite extensive stocking of hatchery rainbow trout (<Emphasis Type="Italic">O. m. irideus</Emphasis>)

Crane Prairie Reservoir in the upper Deschutes River Basin has historically supported a wild population of migratory Deschutes River redband trout. Owing to its status as a premier destination for recreational angling in Oregon, the reservoir has been stocked with domesticated hatchery rainbow trout since 1955. In recent years the wild redband trout population has experienced a substantial decline. Effects on productivity related to genetic interaction with naturally spawning hatchery-origin fish (fitness risks) have not been determined. The species Oncorhynchus mykiss has been characterized with substantial genetic diversity throughout the Deschutes River Basin that further heightens the challenge of identifying specific conservation needs of wild populations. A conservation plan for Crane Prairie wild redband trout requires a better understanding of the natural reproductive success of out-of-basin hatchery trout in the reservoir tributaries, and the similarity between Crane Prairie redband trout with other extant redband trout populations in the basin. Using a suite of 17 microsatellite nuclear DNA markers, we evaluated the genetic structure among Crane Prairie Reservoir redband trout, hatchery rainbow trout, and two adjacent populations of redband trout from within the Upper Deschutes River Basin. We observed significant heterogeneity between the hatchery and wild Crane Prairie populations that may reflect differences in life histories, differential productivity and assortative mating. The genetic distinctions observed among the three redband trout populations suggest restricted gene flow and genetic drift within the upper basin. Temporally stratified sampling and larger numbers of samples will be necessary to confirm these conclusions.     

Admixture analysis of stocked brown trout populations using mapped microsatellite DNA markers: indigenous trout persist in introgressed populations

Admixture between wild and captive populations is an increasing concern in conservation biology. Understanding the extent of admixture and the processes involved requires identification of admixed and non-admixed individuals. This can be achieved by statistical methods employing Bayesian clustering, but resolution is low if genetic differentiation is weak. Here, we analyse stocked brown trout populations represented by historical (1943–1956) and contemporary (2000s) samples, where genetic differentiation between wild populations and stocked trout is weak (pairwise F_ST of 0.047 and 0.053). By analysing a high number of microsatellite DNA markers (50) and making use of linkage map information, we achieve clear identification of admixed and non-admixed trout. Moreover, despite strong population-level admixture by hatchery strain trout in one of the populations (70.8%), non-admixed individuals nevertheless persist (7 out of 53 individuals). These remnants of the indigenous population are characterized by later spawning time than the majority of the admixed individuals. We hypothesize that isolation by time mediated by spawning time differences between wild and hatchery strain trout is a major factor rescuing a part of the indigenous population from introgression.     

Determinants of hierarchical genetic structure in Atlantic salmon populations: environmental factors vs. anthropogenic influences

Disentangling the effects of natural environmental features and anthropogenic factors on the genetic structure of endangered populations is an important challenge for conservation biology. Here, we investigated the combined influences of major environmental features and stocking with non‐native fish on the genetic structure and local adaptation of Atlantic salmon (Salmo salar) populations. We used 17 microsatellite loci to genotype 975 individuals originating from 34 French rivers. Bayesian analyses revealed a hierarchical genetic structure into five geographically distinct clusters. Coastal distance, geological substrate and river length were strong predictors of population structure. Gene flow was higher among rivers with similar geologies, suggesting local adaptation to geological substrate. The effect of river length was mainly owing to one highly differentiated population that has the farthest spawning grounds off the river mouth (up to 900 km) and the largest fish, suggesting local adaptation to river length. We detected high levels of admixture in stocked populations but also in neighbouring ones, implying large‐scale impacts of stocking through dispersal of non‐native individuals. However, we found relatively few admixed individuals suggesting a lower fitness of stocked fish and/or some reproductive isolation between wild and stocked individuals. When excluding stocked populations, genetic structure increased as did its correlation with environmental factors. This study overall indicates that geological substrate and river length are major environmental factors influencing gene flow and potential local adaptation among Atlantic salmon populations but that stocking with non‐native individuals may ultimately disrupt these natural patterns of gene flow among locally adapted populations.     

Stocking activities for the Arctic charr in Lake Geneva: Genetic effects in space and time

Artificial stocking practices are widely used by resource managers worldwide, in order to sustain fish populations exploited by both recreational and commercial activities, but their benefits are controversial. Former practices involved exotic strains, although current programs rather consider artificial breeding of local fishes (supportive breeding). Understanding the complex genetic effects of these management strategies is an important challenge with economic and conservation implications, especially in the context of population declines. In this study, we focus on the declining Arctic charr (Salvelinus alpinus) population from Lake Geneva (Switzerland and France), which has initially been restocked with allochtonous fishes in the early eighties, followed by supportive breeding. In this context, we conducted a genetic survey to document the evolution of the genetic diversity and structure throughout the last 50 years, before and after the initiation of hatchery supplementation, using contemporary and historical samples. We show that the introduction of exotic fishes was associated with a genetic bottleneck in the 1980–1990s, a break of Hardy–Weinberg Equilibrium (HWE), a reduction in genetic diversity, an increase in genetic structure among spawning sites, and a change in their genetic composition. Together with better environmental conditions, three decades of subsequent supportive breeding using local fishes allowed to re‐establish HWE and the initial levels of genetic variation. However, current spawning sites have not fully recovered their original genetic composition and were extensively homogenized across the lake. Our study demonstrates the drastic genetic consequences of different restocking tactics in a comprehensive spatiotemporal framework and suggests that genetic alteration by nonlocal stocking may be partly reversible through supportive breeding. We recommend that conservation‐based programs consider local diversity and implement adequate protocols to limit the genetic homogenization of this Arctic charr population.     

Population structure and impact of supportive breeding inferred from mitochondrial and microsatellite DNA analyses in land-locked Atlantic salmon Salmo salar L.

Four tributaries of Lake St-Jean (Québec, Canada) are used for spawning and juvenile habitat by land-locked Atlantic salmon. Spawning runs have drastically declined since the mid-1980s, and consequently, a supportive-breeding programme was undertaken in 1990. In this study, we analysed seven microsatellite loci and mtDNA, and empirically estimated effective population sizes to test the hypotheses that (i) fish spawning in different tributaries form genetically distinct populations and (ii) the supportive breeding programme causes genetic perturbations on wild populations. Allele frequency distribution, molecular variance and genetic distance estimates all supported the hypothesis of genetic differentiation among salmon from different tributaries. Gene flow among some populations was much more restricted than previously reported for anadromous populations despite the small geographical scale (40 km) involved. Both mtDNA and microsatellites revealed a more pronounced differentiation between populations from two tributaries of a single river compared with their differentiation with a population from a neighbouring river. The comparison of wild and F₁-hatchery fish (produced from breeders originating from the same river) indicated significant changes in allele frequencies and losses of low-frequency alleles but no reduction in heterozygosity. Estimates of variance and inbreeding population size indicated that susceptibility to genetic drift and inbreeding in one population increased by twofold after only one generation of supplementation.     

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.     

Temporal constraints on the potential role of fry odors as cues of past reproductive success for spawning lake trout

Deciding where to reproduce is a major challenge for most animals. Many select habitats based upon cues of successful reproduction by conspecifics, such as the presence of offspring from past reproductive events. For example, some fishes select spawning habitat following odors released by juveniles whose rearing habitat overlaps with spawning habitat. However, juveniles may emigrate before adults begin to search for spawning habitat; hence, the efficacy of juvenile cues could be constrained by degradation or dissipation rates. In lake trout (Salvelinus namaycush), odors deposited by the previous year's offspring have been hypothesized to guide adults to spawning reefs. However, in most extant populations, lake trout fry emigrate from spawning reefs during the spring and adults spawn during the fall. Therefore, we postulated that the role of fry odors in guiding habitat selection might be constrained by the time between fry emigration and adult spawning. Time course chemical, physiological, and behavioral assays indicated that the odors deposited by fry likely degrade or dissipate before adults select spawning habitats. Furthermore, fry feces did not attract wild lake trout to constructed spawning reefs in Lake Huron. Taken together, our results indicate fry odors are unlikely to act as cues for lake trout searching for spawning reefs in populations whose juveniles emigrate before the spawning season, and underscore the importance of environmental constraints on social cues.     

Simple signals indicate which period of the annual cycle drives declines in seasonal populations

For declining wild populations, a critical aspect of effective conservation is understanding when and where the causes of decline occur. The primary drivers of decline in migratory and seasonal populations can often be attributed to a specific period of the year. However, generic, broadly applicable indicators of these season‐specific drivers of population decline remain elusive. We used a multi‐generation experiment to investigate whether habitat loss in either the breeding or non‐breeding period generated distinct signatures of population decline. When breeding habitat was reduced, population size remained relatively stable for several generations, before declining precipitously. When non‐breeding habitat was reduced, between‐season variation in population counts increased relative to control populations, and non‐breeding population size declined steadily. Changes in seasonal vital rates and other indicators were predicted by the season in which habitat loss treatment occurred. Per capita reproductive output increased when non‐breeding habitat was reduced and decreased with breeding habitat reduction, whereas per capita non‐breeding survival showed the opposite trends. Our results reveal how simple signals inherent in counts and demographics of declining populations can indicate which period of the annual cycle is driving declines.     

Life history and ecological characteristics of humper and lean ecotypes of lake trout stocked in Lake Erie

Through combined effects of over-exploitation and predation by invasive non-native sea lamprey Petromyzon marinus (Linneaus 1958), the lake trout Salvelinus namaycush (Walbaum 1972) population in Lake Erie collapsed and was considered extirpated by 1950; annual stocking occurred in 1969 to bolster and maintain this population as natural recruitment ceased. While various hatchery strains of lean ecotype lake trout remain the focus of Lake Erie’s stocking, between 2004 and 2011 a humper-like ecotype was stocked to aid re-establishment efforts. We assessed ecotype performance via adult fish collected during the summer-stratified period (2004–2017) and evaluated if life history and ecological characteristics varied between stocked ecotypes. Ecotype-specific differences in survival, length-at-age, accumulation of weight with length, and diet were observed. Lean lake trout grew faster (length-at-age) and matured at larger sizes than the humper ecotype. Humper lake trout exhibited higher sea lamprey wounding and lower survival rates than lean lake trout. Humpers also consumed more benthic prey fish than lean lake trout, suggesting this ecotype may exhibit a more benthic orientation than leans. Our study represents the first evaluation of how a non-lean ecotype lake trout performs outside their native ecosystem and provides fishery managers with valuable information relevant to re-establishing lake trout populations in the Great Lakes.

     

Allozyme diversity in brown trout (Salmo trutta) from Central Spain: Genetic consequences of restocking

1.  The brown trout ( Salmo trutta ) represents one of the main freshwater resources in Spain, but habitat alterations and overharvesting have contributed to the decline or disappearance of numerous natural populations. In addition, reinforcement programs of wild populations based on releases of hatchery reared fish of exogenous origin compromise the conservation of remnant native trout resources.
2.  We present allozymic data from Central Spain trout populations including stocked and unstocked populations. Although the levels of genetic variation observed were low and affected by hatchery releases (p = 18.23%, Ho= 3.39%), they were within the range observed in other European areas.
3.  The effective introduction of hatchery reared fish is genetically homogenising the populations in the studied area and disturbing the ancestral pattern of genetic variation that distinguishes the Tajo and Duero basins. Within the eight natural populations analysed, seven had alleles assigned to the foreign trout. The introgression in these populations, following the LDH-5 * 90 allele frequency, ranged between 2% and 29.4%, but those values are not in concordance with the respective stocking effort undertaken in each population. Moreover, the release of hatchery-reared fish does not solve the problems related to the reduced size of wild populations and their recruitment instability.     

Introgression variability among Iberian brown trout Evolutionary Significant Units: the influence of local management and environmental features

1. A comprehensive analysis was carried out on the effects of stocking on the genetic structure of Iberian brown trout evolutionary lineages. Introgression and genetic diversity were estimated from allozyme results of 307 populations based on own data (180) and available literature (127). Stocking records, angling regulations and environmental features related to hatchery trout performance were also analysed to determine the underlying mechanisms of the introgression effects. 2. Fifty per cent of analysed populations showed introgression by genes of hatchery origin. The mean introgression estimated by the single locus approach was 0.134. An increment of both heterozygosity and polymorphism was observed when introgression increased in stream‐dwelling populations, which could finally produce a homogenisation of the genetic structure of populations and a decrease of the species’ genetic diversity. 3. Introgression rate varied among Iberian evolutionary lineages (Evolutionary Significant Units), and was correlated with the stocking effort, except for the North Atlantic basins. The lack of adaptations for migratory behaviour in hatchery trout could explain the low impact of stocking in North Atlantic rivers where anadromous populations occur. 4. Angling regulation did not seem to influence the survival of hatchery trout. Introgression tends to be higher in heavily stocked localities with fertile waters and stable discharge, which may favour the performance of hatchery trout. 5. Trout management must be based on increasing population size by means of habitat improvement and sustainability of naturally reproducing wild stocks through appropriate angling regulations.     

Asynchrony in population dynamics of sockeye salmon in southwest Alaska

Ecologists have examined the synchronization of population dynamics across space as a means to understand how populations respond to climate variation. However, response diversity may reflect important variation among local population dynamics driven by population‐specific responses to regional environmental change. We used long‐term data on sockeye salmon Oncorhynchus nerka from pristine watersheds of southwestern Alaska to show that populations spawning in close proximity (<40 km) to one another have a limited degree of synchrony in their dynamics, even after accounting for density‐dependent processes. In fact, the dynamics of local populations of stream‐spawning sockeye salmon were no more coherent than those of stocks at a much coarser resolution across this region of Alaska. We examined four hypotheses to explain the observed patterns of asynchrony among stream‐spawning populations, and found that populations spawning in dissimilar habitats, and using different nursery lakes were less synchronized in their productivity. Similarity in the age structure of spawning adults was less correlated with synchrony in productivity. These results emphasize the importance of maintaining diverse spawning and rearing habitat for the conservation of Pacific salmon, and should guide conservation planning for Pacific salmon populations in regions where natural dynamics have been altered by habitat loss, hatchery practices, and over‐fishing.     

Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines

Analyses of historical samples can provide invaluable information on changes to the genetic composition of natural populations resulting from human activities. Here, we analyse 21 microsatellite loci in historical (archived scales from 1927 to 1956) and contemporary samples of brown trout ( Salmo trutta ) from six neighbouring rivers in Denmark, to compare the genetic structure of wild populations before and after population declines and stocking with nonlocal strains of hatchery trout. We show that all populations have been strongly affected by stocking, with admixture proportions ranging from 14 to 64%. Historical population genetic structure was characterized by isolation by distance and by positive correlations between historical effective population sizes and habitat area within river systems. Contemporary population genetic structure still showed isolation by distance, but also reflected differences among populations in hatchery trout admixture proportions. Despite significant changes to the genetic composition within populations over time, dispersal rates among populations were roughly similar before and after stocking. We also assessed whether population declines or introgression by hatchery strain trout should be the most significant conservation concern in this system. Based on theoretical considerations, we argue that population declines have had limited negative effects for the persistence of adaptive variation, but admixture with hatchery trout may have resulted in reduced local adaptation. Collectively, our study demonstrates the usefulness of analysing historical samples for identifying the most important consequences of human activities on the genetic structure of wild populations.     

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.     

Genomic consequences of a recent three‐way admixture in supplemented wild brown trout populations revealed by local ancestry tracts

Understanding the evolutionary consequences of human‐mediated introductions of domesticated strains into the wild and their subsequent admixture with natural populations is of major concern in conservation biology. However, the genomic impacts of stocking from distinct sources (locally derived vs. divergent) on the genetic integrity of wild populations remain poorly understood. We designed an approach based on estimating local ancestry along individual chromosomes to provide a detailed picture of genomic admixture in supplemented populations. We used this approach to document admixture consequences in the brown trout Salmo trutta, for which decades of stocking practices have profoundly impacted the genetic make‐up of wild populations. In southern France, small local Mediterranean populations have been subject to successive introductions of domestic strains derived from the Atlantic and Mediterranean lineages. To address the impact of stocking, we evaluate the extent of admixture from both domestic strains within populations, using 75,684 mapped SNPs obtained from double‐digested restriction site‐associated DNA sequencing. Then, the chromosomal ancestry profiles of admixed individuals reveal a wider diversity of hybrid and introgressed genotypes than estimated using classical methods for inferring ancestry and hybrid pedigrees. In addition, the length distribution of introgressed tracts retained different timings of introgression between the two domestic strains. We finally reveal opposite consequences of admixture on the level of polymorphism of the recipient populations between domestic strains. Our study illustrates the potential of using the information contained in the genomic mosaic of ancestry tracts in combination with classical methods based on allele frequencies for analysing multiple‐way admixture with population genomic data.     

Recapture rate and growth of hatchery‐reared brown trout (Salmo trutta v. fario,L.) in Blanice River and the effect of stocking on wild brown trout and grayling (Thymallus thymallus,L.)

Hatchery‐reared adult brown trout, Salmo trutta v. fario L., [215–335 mm standard length (L_S), n = 82] were individually tagged and released into three sections of the Blanice River in May 2007. Wild populations of brown trout and grayling, Thymallus thymallus, L., in these sections and three non‐stocked control sections were also tagged. The recapture rate of hatchery‐reared adult brown trout after 6 months (18%, n = 15) was comparable to that of wild adult brown trout in stocked (15%, n = 14) and control (14%, n = 11) sections. The recapture rates of wild brown trout and grayling after 6 months were higher in control sections than in stocked sections, but the differences were not significant. The movement of recaptured large juvenile wild brown trout from stocked sections was significantly higher (36%) than from control sections (9%). Wild brown trout growth and grayling growth were unaffected by stocking with adult hatchery‐reared brown trout.