Alternative reproductive tactics increase effective population size and decrease inbreeding in wild Atlantic salmon

Alternative life-history strategy contributions to effective population size in a naturally spawning salmon population

Alternative life-history tactics are predicted to affect within-population genetic processes but have received little attention. For example, the impact of precocious males on effective population size (N e) has not been quantified directly in Pacific salmon Oncorhynchus spp., even though they can make up a large percentage of the total male spawners. We investigated the contribution of precocial males ("jacks") to N e in a naturally spawning population of Coho Salmon O. kisutch from the Auke Creek watershed in Juneau, Alaska. Mature adults that returned from 2009 to 2019 (~8000 individuals) were genotyped at 259 single-nucleotide polymorphism (SNP) loci for parentage analysis. We used demographic and genetic methods to estimate the effective number of breeders per year (N b). Jack contribution to N b was assessed by comparing values of N b calculated with and without jacks and their offspring. Over a range of N b values (108-406), the average jack contribution to N b from 2009 to 2015 was 12.9% (SE = 3.8%). Jacks consistently made up over 20% of the total male spawners. The presence of jacks did not seem to influence N b/N. The linkage disequilibrium N e estimate was lower than the demographic estimate, possibly due to immigration effects on population genetic processes: based on external marks and parentage data, we estimated that immigrant spawners produced 4.5% of all returning offspring. Our results demonstrate that jacks can influence N b and N e and can make a substantial contribution to population dynamics and conservation of threatened stocks.

Evaluating the evolutionary mechanisms maintaining alternative mating strategies in a simulated bull trout (Salvelinus confluentus) population

The coexistence of distinct alternative mating strategies (AMS) is often explained by mechanisms involving trade-offs between reproductive traits and lifetime fitness; yet their relative importance remains poorly understood. Here, we used an established individual-based, spatially explicit model to simulate bull trout (Salvelinus confluentus) in the Skagit River (Washington, USA) and investigated the influence of female mating preference, sneaker-specific mortality, and variation in age-at-maturity on AMS persistence using global sensitivity analyses and boosted regression trees. We assumed that two genetically fixed AMS coexisted within the population: sneaker males (characterized by younger age-at-maturity, greater AMS-specific mortality, and lower reproductive fitness) and territorial males. After 300 years, variation in relative sneaker success in the system was explained by sneaker males' reproductive fitness (72%) and, to a lesser extent, the length of their reproductive lifespan (21%) and their proportion in the initial population (8%). However, under a wide range of parameter values, our simulated scenarios predicted the extinction of territorial males or their persistence in small, declining populations. Although these results do not resolve the coexistence of AMS in salmonids, they reinforce the importance of mechanisms reducing sneaker's lifetime reproductive success in favoring AMS coexistence within salmonid populations but also limit the prediction that, without any other selective mechanisms at play, strong female preference for mating with territorial males and differences in reproductive lifespan allow the stable coexistence of distinct AMS.

Effects of stocking at the parr stage on the reproductive fitness and genetic diversity of a wild population of Atlantic salmon (Salmo salar L.)

Captive-breeding programs are among the most adopted conservation practices to mitigate the loss of biodiversity, including genetic diversity. However, both genetic and nongenetic changes occurring in captivity can reduce the fitness of supplemented individuals, which complicate rehabilitation efforts. In the case of Atlantic salmon, the intensity of changes that occur in captivity and their impact on fitness will vary with the stocking practice adopted. In this study, we test whether salmon stocked at the parr stage have reduced reproductive success compared with their wild conspecifics and whether they contribute to increase genetic diversity in the targeted population. To do so, we use high-throughput microsatellite sequencing of 38 loci to accurately assign 2381 offspring to a comprehensive set of possible parents from a supplemented Atlantic salmon population in Québec, Canada. Captive-bred salmon stocked at the parr stage had fewer mates than their wild conspecifics, as well as a reduced relative reproductive success (RSS) compared with their wild counterparts. Nonetheless, in comparison with previous studies, stocking at the parr stage significantly improved RSS compared with salmon stocked as smolts and they displayed a reduction in reproductive success similar to salmon stocked as fry, which spend less time in captivity than parr. Moreover, supplementation of captive-bred salmon significantly contributed to increasing genetic diversity. These results should contribute to informing resource managers in determining the best stocking practice to enhance Atlantic salmon populations.

An evaluation of the potential factors affecting lifetime reproductive success in salmonids

Lifetime reproductive success (LRS), the number of offspring produced over an organism's lifetime, is a fundamental component of Darwinian fitness. For taxa such as salmonids with multiple species of conservation concern, understanding the factors affecting LRS is critical for the development and implementation of successful conservation management practices. Here, we reviewed the published literature to synthesize factors affecting LRS in salmonids including significant effects of hatchery rearing, life history, and phenotypic variation, and behavioral and spawning interactions. Additionally, we found that LRS is affected by competitive behavior on the spawning grounds, genetic compatibility, local adaptation, and hybridization. Our review of existing literature revealed limitations of LRS studies, and we emphasize the following areas that warrant further attention in future research: (1) expanding the range of studies assessing LRS across different life-history strategies, specifically accounting for distinct reproductive and migratory phenotypes; (2) broadening the variety of species represented in salmonid fitness studies; (3) constructing multigenerational pedigrees to track long-term fitness effects; (4) conducting LRS studies that investigate the effects of aquatic stressors, such as anthropogenic effects, pathogens, environmental factors in both freshwater and marine environments, and assessing overall body condition, and (5) utilizing appropriate statistical approaches to determine the factors that explain the greatest variation in fitness and providing information regarding biological significance, power limitations, and potential sources of error in salmonid parentage studies. Overall, this review emphasizes that studies of LRS have profoundly advanced scientific understanding of salmonid fitness, but substantial challenges need to be overcome to assist with long-term recovery of these keystone species in aquatic ecosystems.

Considering sampling bias in close-kin mark-recapture abundance estimates of Atlantic salmon

Genetic methods for the estimation of population size can be powerful alternatives to conventional methods. Close-kin mark-recapture (CKMR) is based on the principles of conventional mark-recapture, but instead of being physically marked, individuals are marked through their close kin. The aim of this study was to evaluate the potential of CKMR for the estimation of spawner abundance in Atlantic salmon and how age, sex, spatial, and temporal sampling bias may affect CKMR estimates. Spawner abundance in a wild population was estimated from genetic samples of adults returning in 2018 and of their potential offspring collected in 2019. Adult samples were obtained in two ways. First, adults were sampled and released alive in the breeding habitat during spawning surveys. Second, genetic samples were collected from out-migrating smolts PIT-tagged in 2017 and registered when returning as adults in 2018. CKMR estimates based on adult samples collected during spawning surveys were somewhat higher than conventional counts. Uncertainty was small (CV < 0.15), due to the detection of a high number of parent-offspring pairs. Sampling of adults was age- and size-biased and correction for those biases resulted in moderate changes in the CKMR estimate. Juvenile dispersal was limited, but spatially balanced sampling of adults rendered CKMR estimates robust to spatially biased sampling of juveniles. CKMR estimates based on returning PIT-tagged adults were approximately twice as high as estimates based on samples collected during spawning surveys. We suggest that estimates based on PIT-tagged fish reflect the total abundance of adults entering the river, while estimates based on samples collected during spawning surveys reflect the abundance of adults present in the breeding habitat at the time of spawning. Our study showed that CKMR can be used to estimate spawner abundance in Atlantic salmon, with a moderate sampling effort, but a carefully designed sampling regime is required.

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.

Interbreeding between local and translocated populations of a cleaner fish in an experimental mesocosm predicts risk of disrupted local adaptation

Translocation of organisms within or outside its native range carries the risk of modifying the community of the recipient ecosystems and induces gene flow between locally adapted populations or closely related species. In this study, we evaluated the genetic consequences of large-scale translocation of cleaner wrasses that has become a common practice within the salmon aquaculture industry in northern Europe to combat sea lice infestation. A major concern with this practice is the potential for hybridization of escaped organisms with the local, recipient wrasse population, and thus potentially introduce exogenous alleles and breaking down coadapted gene complexes in local populations. We investigated the potential threat for such genetic introgressions in a large seminatural mesocosm basin. The experimental setting represented a simulated translocation of corkwing wrasse (Symphodus melops) that occurs on a large scale in the Norwegian salmon industry. Parentage assignment analysis of mesocosm's offspring revealed 30% (195 out of 651 offspring) interbreeding between the two populations, despite their being genetically (F ST = 0.094, p < 0.05) and phenotypically differentiated. Moreover, our results suggest that reproductive fitness of the translocated western population doubled that of the local southern population. Our results confirm that human translocations may overcome the impediments imposed by natural habitat discontinuities and urge for immediate action to manage the genetic resources of these small benthic wrasses.

Estimating the effective number of breeders from single parr samples for conservation monitoring of wild populations of Atlantic salmon Salmo salar

This study assesses whether the effective number of breeders (N_b ) can be estimated using a time and cost-effective protocol using genetic sibship reconstruction from a single sample of young-of-the-year (YOY) for the purposes of Atlantic salmon Salmo salar population monitoring. N_b was estimated for 10 consecutive reproductive seasons for S. salar in the River Nivelle, a small population located at the rear-edge of the species distribution area in France, chronically under its conservation limit and subjected to anthropogenic and environmental changes. Subsampling of real and simulated data showed that accurate estimates of N_b can be obtained from YOY genotypes, collected at moderate random sampling intensity, achievable using routine juvenile electrofishing protocols. Spatial bias and time elapsed since spawning were found to affect estimates, which must be accounted for in sampling designs. N_b estimated in autumn for S. salar in the River Nivelle was low and variable across years from 23 (95% C.I. 14-41) to 75 (53-101) and was not statistically correlated with the estimated number of returning adults, but it was positively correlated with the estimated number of YOY at age 9 months. N_b was found to be lower for intermediate levels of redd aggregation, suggesting that the strength of the competition between males to access females affects reproductive success variance depending on redd spatial configuration. Thus, environmental factors such as habitat availability and quality for spawning and YOY development predominate over demographic ones (number of returning adults) in driving long-term population viability for S. salar in the River Nivelle. This study showcases N_b as an integrated parameter, encompassing demographic and ecological information about a reproductive event, relevant to the assessment of both short-term effects of management practices and long-term population conservation status.

A critical assessment of estimating census population size from genetic population size (or vice versa) in three fishes

Technological and methodological advances have facilitated the use of genetic data to infer census population size (Nc) in natural populations, particularly where traditional mark-and-recapture is challenging. The effective number of breeders (Nb) describes how many adults effectively contribute to a cohort and is often correlated with Nc. Predicting Nc from Nb or vice versa in species with overlapping generations has important implications for conservation by permitting (i) estimation of the more difficult to quantify variable and (ii) inferences of Nb/Nc relationships in related species lacking data. We quantitatively synthesized Nb/Nc relationships in three salmonid fishes where sufficient data have recently accumulated. Mixed-effects models were analysed in which each variable was included as a dependent variable or predictor term (Nb from Nc and vice versa). Species-dependent Nb/Nc slope estimates were significantly positive in two of three species. Variation in species slopes was likely due to varying life histories and reinforce caution when inferring Nb/Nc from taxonomically related species. Models provided maximum probable estimates for Nb and Nc for two species. However, study, population and year effects explained substantial amounts of variation (39%-57%). Consequently, prediction intervals were wide and included or were close to zero for all population sizes and species; model predictive utility was limited. Cost-benefit trade-offs when estimating Nb and/or Nc were also discussed using a real-world system example. Our findings based on salmonids suggest that no short cuts currently exist when estimating population size and researchers should focus on quantifying the variable of interest or be aware of caveats when inferring the desired variable because of cost or logistics. We caution that the salmonid species examined share life-history traits that may obscure relationships between Nb and Nc. Sufficient data on other taxa were unavailable; additional research examining Nb/Nc relationships in species with potentially relevant life-history trait differences (e.g., differing survival curves) is needed.

Effective number of breeders from sibship reconstruction: empirical evaluations using hatchery steelhead

Effective population size (N_e) is among the most important metrics in evolutionary biology. In natural populations, it is often difficult to collect adequate demographic data to calculate N_e directly. Consequently, genetic methods to estimate N_e have been developed. Two N_e estimators based on sibship reconstruction using multilocus genotype data have been developed in recent years: sibship assignment and parentage analysis without parents. In this study, we evaluated the accuracy of sibship reconstruction using a large empirical dataset from five hatchery steelhead populations with known pedigrees and using 95 single nucleotide polymorphism (SNP) markers. We challenged the software COLONY with 2,599,961 known relationships and demonstrated that reconstruction of full‐sib and unrelated pairs was greater than 95% and 99% accurate, respectively. However, reconstruction of half‐sib pairs was poor (<5% accurate). Despite poor half‐sib reconstruction, both estimators provided accurate estimates of the effective number of breeders (N_b) when sample sizes were near or greater than the true N_b and when assuming a monogamous mating system. We further demonstrated that both methods provide roughly equivalent estimates of N_b. Our results indicate that sibship reconstruction and current SNP panels provide promise for estimating N_b in steelhead populations in the region.

Making sense of the relationships between Ne, Nb and Nc towards defining conservation thresholds in Atlantic salmon (Salmo salar)

Effective population size over a generation (Ne) or over a reproductive cycle (Nb) and the adult census size (Nc) are important parameters in both conservation and evolutionary biology. Ne provides information regarding the rate of loss of genetic diversity and can be tracked back in time to infer demographic history of populations, whereas Nb may often be more easily quantified than Nc for short-term abundance monitoring. In this study, we propose (1) an empirical context to Waples et al. (2014) who introduced a correction to bias due to overlapping generations, and (2) a mathematical relationship between Ne and Nb for direct application in Atlantic salmon populations in Québec, Canada. To achieve this, we investigate the relationships between Ne, Nb and Nc in 10 Atlantic salmon populations, Canada, for which we genotyped 100 randomly sampled young-of-the year individuals for 5 consecutive years. The results show a positive correlation between Ne, Nb and Nc, suggesting that Nb is an indicative parameter for tracking effective population size and abundance of Atlantic salmon. However, our model allows predicting Nc from Nb values at 27% that can be partly explained by high variance in Nb/Nc both among populations (37%) and among years (19%). This result illustrates the need for thorough calibration of Nb/Nc before using Nb in monitoring programs, as well as a full understanding of the limits of such an approach. Finally, we discuss the importance of these results for the management of wild populations.

Sexual selection leads to a tenfold difference in reproductive success of alternative reproductive tactics in male Atlantic salmon

The precocious maturation of some male Atlantic salmon (Salmo salar L.) has become a textbook example of alternative mating tactics, but the only estimates of reproductive success available so far are either the collective contribution of precocious males to reproduction in the wild or individual reproductive success in oversimplified experimental conditions. Using genetic parentage analysis on anadromous and precocious potential spawners and their offspring, we quantified components of individual reproductive success of both tactics in a natural population. On average, precocious males produced 2.24 (variance 67.62) offspring, against 27.17 (3080) for anadromous males. For both tactics, most of the variance in reproductive success was due to mating success, with 83% of precocious males having no mate, against 50% for anadromous males. Body size increased reproductive success of anadromous males and tended to decrease precocious males' reproductive success. Although these results do not solve the coexistence of alternative reproductive tactics (ARTs) in Atlantic salmon, their inclusion in comprehensive models of lifetime reproductive success should shed light on the evolution of precocious maturation in Atlantic salmon and its effect on the selection of phenotypic traits.

Venturing in coral larval chimerism: a compact functional domain with fostered genotypic diversity

The globally distributed coral species Pocillopora damicornis is known to release either sexual or asexual derived planula-larvae in various reef locations. Using microsatellite loci as markers, we documented the release of asexually derived chimeric larvae (CL), originating from mosaicked maternal colonies that were also chimeras, at Thai and Philippines reefs. The CL, each presenting different combinations of maternal genotypic constituents, create genetically-complex sets of asexual propagules. This novel mode of inheritance in corals challenges classical postulations of sexual/asexual reproduction traits, as asexual derived CL represent an alliance between genotypes that significantly sways the recruits' absolute fitness. This type of inherited chimerism, while enhancing intra-entity genetic heterogeneity, is an evolutionary tactic used to increase genetic-heterogeneity, primarily in new areas colonized by a limited number of larvae. Chimerism may also facilitate combat global change impacts by exhibiting adjustable genomic combinations of within-chimera traits that could withstand alterable environmental pressures, helping Pocillopora become a successful cosmopolitan species.

Determinants of male floating behaviour and floater reproduction in a threatened population of the hihi (Notiomystis cincta)

Floating males are usually thought of as nonbreeders. However, some floating individuals are able to reproduce through extra-pair copulations. Floater reproductive success can impact breeders' sex ratio, reproductive variance, multiple paternity and inbreeding, particularly in small populations. Changes in reproductive variance alter the rate of genetic drift and loss of genetic diversity. Therefore, genetic management of threatened species requires an understanding of floater reproduction and determinants of floating behaviour to effectively conserve species. Here, we used a pedigreed, free-living population of the endangered New Zealand hihi (Notiomystis cincta) to assess variance in male reproductive success and test the genetic (inbreeding and heritability) and conditional (age and size) factors that influence floater behaviour and reproduction. Floater reproduction is common in this species. However, floater individuals have lower reproductive success and variance in reproductive success than territorial males (total and extra-pair fledglings), so their relative impact on the population's reproductive performance is low. Whether an individual becomes a floater, and if so then how successful they are, is determined mainly by individual age (young and old) and to lesser extents male size (small) and inbreeding level (inbred). Floating males have a small, but important role in population reproduction and persistence of threatened populations.

Evolutionary conservation-evaluating the adaptive potential of species

Despite intense efforts, biodiversity around the globe continues to decrease. To cease this phenomenon, we urgently need a better knowledge not only of the true extent of biodiversity, but also of the evolutionary potential of species to respond to environmental change. These aims are the heart of the developing field of Evolutionary conservation. Here, after describing problems associated with implementing evolutionary perspectives into management, we outline how evolutionary principles can contribute to efficient conservation programmes. We then introduce articles from this special issue on Evolutionary conservation, outlining how each study or review provides tools and concepts to contribute to efficient management of species or populations. Ultimately, we highlight what we believe can be future research avenues for evolutionary conservation.