Genetic and phenotypic changes in an Atlantic salmon population supplemented with non-local individuals: a longitudinal study over 21 years

Fitness consequences of targeted gene flow to counter impacts of drying climates on terrestrial-breeding frogs

Targeted gene flow (TGF) could bolster the adaptive potential of isolated populations threatened by climate change, but could also lead to outbreeding depression. Here, we explore these possibilities by creating mixed- and within-population crosses in a terrestrial-breeding frog species threatened by a drying climate. We reared embryos of the crawling frog (Pseudophryne guentheri) on wet and dry soils and quantified fitness-related traits upon hatching. TGF produced mixed outcomes in hybrids, which depended on crossing direction (origin of gametes from each sex). North-south crosses led to low embryonic survival if eggs were of a southern origin, and high malformation rates when eggs were from a northern population. Conversely, east-west crosses led to one instance of hybrid vigour, evident by increased fitness and desiccation tolerance of hybrid offspring relative to offspring produced from within-population crosses. These contrasting results highlight the need to experimentally evaluate the outcomes of TGF for focal species across generations prior to implementing management actions.

A century of genetic homogenization in Baltic salmon-evidence from archival DNA

Intra-species genetic homogenization arising from anthropogenic impacts is a major threat to biodiversity. However, few taxa have sufficient historical material to systematically quantify long-term genetic changes. Using archival DNA collected over approximately 100 years, we assessed spatio-temporal genetic change in Atlantic salmon populations across the Baltic Sea, an area heavily impacted by hydropower exploitation and associated with large-scale mitigation stocking. Analysis was carried out by screening 82 SNPs in 1680 individuals from 13 Swedish rivers. We found an overall decrease in genetic divergence and diminished isolation by distance among populations, strongly indicating genetic homogenization over the past century. We further observed an increase in genetic diversity within populations consistent with increased gene flow. The temporal genetic change was lower in larger wild populations than in smaller wild and hatchery-reared ones, indicating that larger populations have been able to support a high number of native spawners in relation to immigrants. Our results demonstrate that stocking practices of salmon in the Baltic Sea have led to the homogenization of populations over the last century, potentially compromising their ability to adapt to environmental change. Stocking of reared fish is common worldwide, and our study is a cautionary example of the potentially long-term negative effects of such activities.

Captive-bred Atlantic salmon released into the wild have fewer offspring than wild-bred fish and decrease population productivity

The release of captive-bred animals into the wild is commonly practised to restore or supplement wild populations but comes with a suite of ecological and genetic consequences. Vast numbers of hatchery-reared fish are released annually, ostensibly to restore/enhance wild populations or provide greater angling returns. While previous studies have shown that captive-bred fish perform poorly in the wild relative to wild-bred conspecifics, few have measured individual lifetime reproductive success (LRS) and how this affects population productivity. Here, we analyse data on Atlantic salmon from an intensely studied catchment into which varying numbers of captive-bred fish have escaped/been released and potentially bred over several decades. Using a molecular pedigree, we demonstrate that, on average, the LRS of captive-bred individuals was only 36% that of wild-bred individuals. A significant LRS difference remained after excluding individuals that left no surviving offspring, some of which might have simply failed to spawn, consistent with transgenerational effects on offspring survival. The annual productivity of the mixed population (wild-bred plus captive-bred) was lower in years where captive-bred fish comprised a greater fraction of potential spawners. These results bolster previous empirical and theoretical findings that intentional stocking, or non-intentional escapees, threaten, rather than enhance, recipient natural populations.

Long-term stocking practices threaten the original genetic diversity of the southernmost European populations of Atlantic salmon Salmo salar

Many Atlantic salmon Salmo salar populations in Europe are threatened by previous stocking with foreign hatchery strains. Temporal patterns of genetic characteristics of salmon from northern Spain, the southernmost European populations, were compared before and after species decline and heavy stocking with specimens from northern Europe. Eleven microsatellite loci were analysed in archival (scales from 1958-1960) and contemporary (2007-2008) samples from the River Sella. Temporal analyses revealed a similar heterozygosity between archival and contemporary samples, despite a drastic decrease in population abundance, while the contemporary sample showed a higher allelic richness due to the occurrence of foreign alleles. Considering only the alleles with at least 4% frequency in the archival sample, 2 alleles exclusive to the River Sella were absent in the contemporary sample, and 14 alleles showed a decrease of at least 4% frequency. Four alleles common in Scotland showed a high occurrence in the contemporary sample, so they are good candidates as markers of introgression of foreign genes. The heavy stocking with non-native Scottish broodstocks between 1970 and 1990 caused the introgression found in the contemporary sample when compared with the pristine population. An abrupt decrease was evident when the estimates of effective number of breeders were adjusted to take into account overlapping generations (NbAdj), effective population size (NeAdj) estimated from NbAdj, and number of breeders estimated using the sibship assignment method (NbSIB). The very low effective size values found in the contemporary sample, together with the detrimental synergy between genetic drift and high rates of introgression, represent a severe risk for the conservation of native salmon.

Combining population genomics and forward simulations to investigate stocking impacts: A case study of Muskellunge (Esox masquinongy) from the St. Lawrence River basin

Understanding the genetic and evolutionary impacts of stocking on wild fish populations has long been of interest as negative consequences such as reduced fitness and loss of genetic diversity are commonly reported outcomes. In an attempt to sustain a fishery, managers implemented nearly five decades of extensive stocking of over a million Muskellunge (Esox masquinongy), a native species in the Lower St. Lawrence River (Québec, Canada). We investigated the effect of this stocking on population genetic structure and allelic diversity in the St. Lawrence River in addition to tributaries and several stocked inland lakes. Using genotype by sequencing, we genotyped 643 individuals representing 22 locations and combined this information with forward simulations to investigate the genetic consequences of long-term stocking. Individuals native to the St. Lawrence watershed were genetically differentiated from stocking sources and tributaries, and inland lakes were naturally differentiated from the main river. Empirical data and simulations within the St. Lawrence River revealed weak stocking effects on admixture patterns. Our data suggest that the genetic structure associated with stocked fish was diluted into its relatively large effective population size. This interpretation is also consistent with a hypothesis that selection against introgression was in operation and relatively efficient within the large St. Lawrence River system. In contrast, smaller populations from adjacent tributaries and lakes displayed greater stocking-related admixture that resulted in comparatively higher heterozygosity than the St. Lawrence. Finally, individuals from inland lakes that were established by stocking maintained a close affinity with their source populations. This study illustrated a benefit of combining extensive genomic data with forward simulations for improved inference regarding population-level genetic effects of long-term stocking, and its relevance for fishery management decision making.

Estimating the relative fitness of escaped farmed salmon offspring in the wild and modelling the consequences of invasion for wild populations

Throughout their native range, wild Atlantic salmon populations are threatened by hybridization and introgression with escapees from net-pen salmon aquaculture. Although domestic-wild hybrid offspring have shown reduced fitness in laboratory and field experiments, consequential impacts on population abundance and genetic integrity remain difficult to predict in the field, in part because the strength of selection against domestic offspring is often unknown and context-dependent. Here, we follow a single large escape event of farmed Atlantic salmon in southern Newfoundland and monitor changes in the in-river proportions of hybrids and feral individuals over time using genetically based hybrid identification. Over a three-year period following the escape, the overall proportion of wild parr increased consistently (total wild proportion of 71.6%, 75.1% and 87.5% each year, respectively), with subsequent declines in feral (genetically pure farmed individuals originating from escaped, farmed adults) and hybrid parr. We quantify the strength of selection against parr of aquaculture ancestry and explore the genetic and demographic consequences for populations in the region. Within-cohort changes in the relative proportions of feral and F1 parr suggest reduced relative survival compared to wild individuals over the first (0.15 and 0.81 for feral and F1, respectively) and second years of life (0.26, 0.83). These relative survivorship estimates were used to inform an individual-based salmon eco-genetic model to project changes in adult abundance and overall allele frequency across three invasion scenarios ranging from short-term to long-term invasion and three relative survival scenarios. Modelling results indicate that total population abundance and time to recovery were greatly affected by relative survivorship and predict significant declines in wild population abundance under continued large escape events and calculated survivorship. Overall, this work demonstrates the importance of estimating the strength of selection against domestic offspring in the wild to predict the long-term impact of farmed salmon escape events on wild populations.

Does variation in egg structure among five populations of Atlantic salmon (Salmo salar) influence their survival in low oxygen conditions?

Oxygen supply to the salmonid egg surface can be limited by external factors such as sedimentation and groundwater upwelling, while the egg membrane itself can impede diffusion from the egg surface to the embryo. Therefore, the structure of egg membranes could affect the rate at which embryos obtain oxygen from their surroundings. Published field data indicate that oxygen stress experienced by salmonid eggs can vary widely among populations. Therefore, if membrane architecture influences diffusion rate to the embryo, selection for more permeable membranes could occur in oxygen-stressed environments. Using electron microscopy, the membrane structure of eggs obtained from five UK Atlantic salmon (Salmo salar) populations is described. Membrane thickness, porosity and permeability to dissolved oxygen varied among populations. Furthermore, comparison of membranes of eggs that survived laboratory controlled low-oxygen conditions compared to those that died suggested that ova with less permeable membranes were more susceptible to hypoxia-induced mortality. In addition, membrane porosity was lower than previously reported indicating that oxygen requirements during incubation have been underestimated, so models such as the mass transfer theory that predict incubation success could currently overestimate ova survival. Variation in egg membrane structure influences low oxygen tolerance of Atlantic salmon embryos and could represent adaptation to low oxygen stress. Consequently, stock enhancement techniques such as supportive breeding that relieve incubation stress could erode structural adaptations.

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.

A question of scale: Replication and the effective evaluation of conservation interventions

Conservation interventions can keep critically endangered species from going extinct and stabilize threatened populations. The species-specific, case-by-case approaches and small sample sizes inherent to applied conservation measures are not well suited to scientific evaluations of outcomes. Debates about whether a method “works” become entrenched in a vote-counting framework. Furthermore, population-level replication is rare but necessary for disentangling the effects of an intervention from other drivers of population change. Turtle headstarting is a conservation tool that has attracted strong opinions but little robust data. Logistical limitations, such as those imposed by the long lives of turtles, have slowed experimental evaluation and constrained the use of replication or experimental controls. Headstarting project goals vary among projects and stakeholders, and success is not always explicitly defined. To facilitate robust evaluations, we provide direction for data collection and reporting to guide the application of conservation interventions in logistically challenging systems. We offer recommendations for standardized data collection that allow their valuable results to contribute to the development of best practices, regardless of the magnitude of the project. An evidence-based and collaborative approach will lead to improved program design and reporting, and will facilitate constructive evaluation of interventions both within and among conservation programs.

Severe consequences of habitat fragmentation on genetic diversity of an endangered Australian freshwater fish: A call for assisted gene flow

Genetic diversity underpins the ability of populations to persist and adapt to environmental changes. Substantial empirical data show that genetic diversity rapidly deteriorates in small and isolated populations due to genetic drift, leading to reduction in adaptive potential and fitness and increase in inbreeding. Assisted gene flow (e.g. via translocations) can reverse these trends, but lack of data on fitness loss and fear of impairing population "uniqueness" often prevents managers from acting. Here, we use population genetic and riverscape genetic analyses and simulations to explore the consequences of extensive habitat loss and fragmentation on population genetic diversity and future population trajectories of an endangered Australian freshwater fish, Macquarie perch Macquaria australasica. Using guidelines to assess the risk of outbreeding depression under admixture, we develop recommendations for population management, identify populations requiring genetic rescue and/or genetic restoration and potential donor sources. We found that most remaining populations of Macquarie perch have low genetic diversity, and effective population sizes below the threshold required to retain adaptive potential. Our simulations showed that under management inaction, smaller populations of Macquarie perch will face inbreeding depression within a few decades, but regular small-scale translocations will rapidly rescue populations from inbreeding depression and increase adaptive potential through genetic restoration. Despite the lack of data on fitness loss, based on our genetic data for Macquarie perch populations, simulations and empirical results from other systems, we recommend regular and frequent translocations among remnant populations within catchments. These translocations will emulate the effect of historical gene flow and improve population persistence through decrease in demographic and genetic stochasticity. Increasing population genetic connectivity within each catchment will help to maintain large effective population sizes and maximize species adaptive potential. The approach proposed here could be readily applicable to genetic management of other threatened species to improve their adaptive potential.

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.

Evidence for long-term change in length, mass and migration phenology of anadromous spawners in French Atlantic salmon Salmo salar

This study provides new data on Atlantic salmon Salmo salar life-history traits across France. Using a long-term recreational angling database (1987-2013) covering 34 rivers in three regions (genetic units), a decline in individual length, mass and a delayed adult return to French rivers was reported. Temporal similarities in trait variations between regions may be attributed to common change in environmental conditions at sea. The relative rate of change in phenotypic traits was more pronounced in early maturing fish [1 sea-winter (1SW) fish] than in late maturing fish (2SW fish). Such contrasted response within populations highlights the need to account for the diversity in life histories when exploring mechanisms of phenotypic change in S. salar. Such detailed life-history data on returning S. salar have not previously been reported from France. This study on French populations also contributes to reducing the gap in knowledge by providing further empirical evidence of a global pattern in S. salar across its distribution range. Results are consistent with the hypothesis that the observed changes in life-history traits are primarily associated with environmental changes in the North Atlantic Ocean. They also emphasize the presence of less important, but still significant contrasts between region and life history.

StrAuto: automation and parallelization of STRUCTURE analysis

Background

Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data sets poses computational challenges for this analysis. Although at least one tool currently implements parallel computing to reduce computational overload of this analysis, it does not fully automate the use of replicate STRUCTURE analysis runs required for downstream inference of optimal K. There is pressing need for a tool that can deploy population structure analysis on high performance computing clusters.

Results

We present an updated version of the popular Python program StrAuto, to streamline population structure analysis using parallel computing. StrAuto implements a pipeline that combines STRUCTURE analysis with the Evanno ΔK analysis and visualization of results using STRUCTURE HARVESTER. Using benchmarking tests, we demonstrate that StrAuto significantly reduces the computational time needed to perform iterative STRUCTURE analysis by distributing runs over two or more processors.

Conclusion

StrAuto is the first tool to integrate STRUCTURE analysis with post-processing using a pipeline approach in addition to implementing parallel computation – a set up ideal for deployment on computing clusters. StrAuto is distributed under the GNU GPL (General Public License) and available to download from http://strauto.popgen.org.

Characterizing the trophic niches of stocked and resident cyprinid fishes: consistency in partitioning over time, space and body sizes

Hatchery‐reared fish are commonly stocked into freshwaters to enhance recreational angling. As these fishes are often of high trophic position and attain relatively large sizes, they potentially interact with functionally similar resident fishes and modify food‐web structure. Hatchery‐reared barbel Barbus barbus are frequently stocked to enhance riverine cyprinid fish communities in Europe; these fish can survive for over 20 years and exceed 8 kg. Here, their trophic consequences for resident fish communities were tested using cohabitation studies, mainly involving chub Squalius cephalus, a similarly large‐bodied, omnivorous and long‐lived species. These studies were completed over three spatial scales: pond mesocosms, two streams and three lowland rivers, and used stable isotope analysis. Experiments in mesocosms over 100 days revealed rapid formation of dietary specializations and discrete trophic niches in juvenile B. barbus and S. cephalus. This niche partitioning between the species was also apparent in the streams over 2 years. In the lowland rivers, where fish were mature individuals within established populations, this pattern was also generally apparent in fishes of much larger body sizes. Thus, the stocking of these hatchery‐reared fish only incurred minor consequences for the trophic ecology of resident fish, with strong patterns of trophic niche partitioning and diet specialization. Application of these results to decision‐making frameworks should enable managers to make objective decisions on whether cyprinid fish should be stocked into lowland rivers according to ecological risk.

Assessing early fitness consequences of exotic gene flow in the wild: a field study with Iberian pine relicts

Gene flow from plantations of nonlocal (genetically exotic) tree provenances into natural stands of the same species is probably a widespread phenomenon, but its effects remain largely unexamined. We investigated early fitness consequences of intraspecific exotic gene flow in the wild by assessing differences in survival among native, nonlocal, and F1 intraspecific hybrid seedlings naturally established within two native pine relicts (one of Pinus pinaster and the other of P. sylvestris) surrounded by nonlocal plantations. We obtained broad‐scale temporally sequential genotypic samples of a cohort of recruits in each pine relict, from seeds before dispersal to established seedlings months after emergence, tracking temporal changes in the estimated proportion of each parental cross‐type. Results show significant proportions of exotic male gametes before seed dispersal in the two pine relicts. Subsequently to seedling establishment, the frequency of exotic male gametes became nonsignificant in P. pinaster, and dropped by half in P. sylvestris. Exotic zygotic gene flow was significantly different from zero among early recruits for P. sylvestris, decreasing throughout seedling establishment. Seedling mortality resulted in small late sample sizes, and temporal differences in exotic gene flow estimates were not significant, so we could not reject the null hypothesis of invariant early viability across parental cross types in the wild.