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Migration in animals and associated adaptations to contrasting environments are underpinned by complex genetic architecture. Here, we explore the genomic basis of facultative anadromy in brown trout (Salmo trutta), wherein some individuals migrate to sea while others remain resident in natal rivers, to better understand how alternative migratory tactics (AMTs) are maintained evolutionarily. To identify genomic variants associated with AMTs, we sequenced whole genomes for 194 individual trout from five anadromous–resident population pairs, situated above and below waterfalls, in five different Irish rivers. These waterfalls act as natural barriers to upstream migration and hence we predicted that loci underpinning AMTs should be under similar divergent selection across these replicate pairs. A sliding windows based analysis revealed a highly polygenic adaptive divergence between anadromous and resident populations, encompassing 329 differentiated genomic regions. These regions were associated with 292 genes involved in various processes crucial for AMTs, including energy homeostasis, reproduction, osmoregulation, immunity, circadian rhythm and neural function. Furthermore, examining patterns of diversity we were able to link specific genes and biological processes to putative AMT trait classes: migratory‐propensity, migratory‐lifestyle and residency. Importantly, AMT outlier regions possessed higher genetic diversity than the background genome, particularly in the anadromous group, suggesting balancing selection may play a role in maintaining genetic variation. Overall, the results from this study provide important insights into the genetic architecture of migration and the evolutionary mechanisms shaping genomic diversity within and across populations. [ABSTRACT FROM AUTHOR]

Although historical records of introductions that trigger successful biological invasions are common, subsequent patterns of dispersal and colonisation routes are unclear. We use microsatellites to examine genetic population structuring of established invasive brown trout (Salmo trutta) populations in Newfoundland, Canada, for evidence of 'natural' dispersal, humanmediated introductions, and colonisation routes. We also explored ancestry of contemporary populations relative to presumed progenitors. Results analysed using STRUCTURE, DAPC, a NJ tree and [F.sub.ST] comparisons support records of historical introductions; current Newfoundland populations are largely descended from Scottish stock, with St. John's the primary introduction site. Subsequent dispersal of these trout was facilitated principally by anadromy, largely consistent with a classic stepping-stone model, with significant isolation-by-distance. With one exception, dispersal along the north and south coasts of the Avalon peninsula appears to be natural and independent, involving stochastic processes resulting in unique outcomes for population composition. This study is a good example of dispersal patterns during a contemporary invasion underscoring the potential for non- anadromous founders to re-express anadromy, facilitating colonization of distant sites. Bien que les cas documentes d'introductions qui declenchent des envahissements biologiques durables soient repandus, les motifs de dispersion et les voies de colonisation subsequents ne sont pas bien etablis. Nous utilisons les microsatellites pour examiner la structure genetique de populations de truites brunes (Salmo trutta) envahissantes etablies a Terre-Neuve (Canada) afin de chercher des indices de dispersion << naturelle >> et d'introductions mediees par l'humain et de l'information sur d'eventuelles voies de colonisation. Nous explorons egalement l'ascendance de populations actuelles par rapport a des progeniteurs presumes. Les resultats analyses avec STRUCTURE, DAPC, un arbre phylogenetique et la comparaison de [F.sub.ST] appuient les cas documentes passes d'introductions; les populations actuelles a Terre-Neuve descendent en bonne partie du stock ecossais, St. John's en constituant le principal lieu d'introduction. La dispersion subsequente de ces truites a principalement ete facilitee par l'anadromie, ce qui concorde assez bien avec un modele classique d'etapes intermediates, l'isolement par la distance etant aussi importante. A une exception pres, les dispersions le long des cotes nord et sud de la peninsule d'Avalon semblent etre naturelles et independantes, mues par des processus stochastiques qui ont produit des resultats uniques sur le plan de la composition des populations. L'etude fournit un bon exemple de motifs de dispersion durant un envahissement moderne, soulignant la possibilite pour des fondateurs non anadromes de reexprimer une anadromie, facilitant ainsi la colonisation de sites distaux. [Traduit par la Redaction], Introduction The distribution of species through time and space is the result of the complex interplay between evolutionary history and everchanging ecological factors. Identifying the colonisation pathways and mechanisms involved [...]

The deliberate release of captive‐bred individuals, the accidental escape of domesticated strains, or the invasion of closely related conspecifics into wild populations can all lead to introgressive hybridization, which poses a challenge for conservation and wildlife management. Rates of introgression and the magnitude of associated demographic impacts vary widely across ecological contexts. However, the reasons for this variation remain poorly understood. One rarely considered phenomenon in this context is soft selection, wherein relative trait values determine success in intraspecific competition for a limiting resource. Here we develop an eco‐genetic model explicitly focussed on understanding the influence of such competitive interactions on the eco‐evolutionary dynamics of wild populations experiencing an influx of foreign/domesticated individuals. The model is applicable to any taxon that experiences natural or human‐mediated inputs of locally maladapted genotypes ('intrusion'), in addition to phenotype‐dependent competition for a limiting resource (e.g. breeding sites, feeding territories). The effects of both acute and chronic intrusion depended strongly on the relative competitiveness of intruders versus locals. When intruders were competitively inferior, density‐dependent regulation limited their reproductive success (ability to compete for limited spawning sites), which prevented strong introgression or population declines from occurring. In contrast, when intruders were competitively superior, this amplified introgression and led to increased maladaptation of the admixed population. This had negative consequences for population size and population viability. The results were sensitive to the intrusion level, the magnitude of reproductive excess, trait heritability and the extent to which intruders were maladapted relative to locals. Our findings draw attention to under‐appreciated interactions between phenotype‐dependent competitive interactions and maladaptive hybridization, which may be critical to determining the impact captive breeding programmes and domesticated escapees can have on otherwise self‐sustaining wild populations. [ABSTRACT FROM AUTHOR]

While evolutionary responses require heritable variation, estimates of heritability ([h.sup.2]) from wild fish populations remain rare. A 20-year molecular pedigree for a wild Scottish population of Atlantic salmon (Salmo salar) was used to investigate genetic contributions to (co)variation in two important, correlated, phenotypic traits: 'sea age' (number of winters spent at sea prior to spawning) and size-at-maturity (body length just prior to spawning). Sea age was strongly heritable ([h.sup.2] = 0.51) and size exhibited moderate heritability ([h.sup.2] = 0.27). A very strong genetic correlation ([r.sub.G] = 0.96) between these traits implied the same functional loci must underpin variation in each. Indeed, body size within sea ages had much lower heritability that did not differ significantly from zero. Thus, within wild S. salar populations, temporal changes in sea age composition could reflect evolutionary responses, whereas rapid changes of body size within sea ages are more likely due to phenotypic plasticity. These inheritance patterns will influence the scope of evolutionary responses to factors such as harvest or climate change and, hence, have management implications for salmonid populations comprising a mix of sea ages. Si une variation heritable est necessaire pour permettre des reactions evolutives, les estimations de l'heritabilite ([h.sup.2]) obtenues pour des populations sauvages demeurent rares. Un pedigree moleculaire de 20 ans pour une population sauvage ecossaise de saumons atlantiques (Salmo salar) a ete utilise pour etudier les contributions genetiques a la (co)variation de deux caracteres phenotypiques correles importants, a savoir <> (le nombre d'hivers passes en mer avant le frai) et la taille a la maturite (la longueur du corps juste avant le frai). L'age marin est fortement heritable ([h.sup.2] = 0,51) et la taille presente une heritabilite moderee ([h.sup.2] = 0,27). Une correlation genetique tres forte ([r.sub.G] = 0,96) entre ces caracteres indique que les memes sites fonctionnels doivent sous-tendre la variation des deux caracteres. En effet, la taille du corps pour des ages marins donnes presente une heritabilite beaucoup plus faible qui n'est pas significativement differente de zero. Ainsi, dans les populations sauvages de S. salar, les changements dans le temps de la composition des ages marins pourraient refleter des reactions evolutives, alors que des changements rapides de la taille du corps au sein de classes d'age marin sont plus probablement le fait d'une plasticite phenotypique. Ces motifs d'heredite influenceront la portee des reactions evolutives a des facteurs comme l'exploitation ou les changements climatiques, ce qui a des consequences pour la gestion de populations de salmonides composees d'un melange d'ages marins. [Traduit par la Redaction], Introduction Life-history traits such as age and size at first reproduction are typically expected to be under strong selection, given their close links with Darwinian fitness (Stearns 1992; Roff 2002). [...]

Global warming has been implicated in widespread demographic changes in Atlantic salmon Salmo salar populations, but projections of life‐history responses to future climate change are lacking. Here, we first exploit multiple decades of climate and biological data from the Burrishoole catchment in the west of Ireland to model statistical relationships between atmospheric variables, water temperature, and freshwater growth of juvenile Atlantic salmon. We then use this information to project potential changes in juvenile growth and life‐history scheduling under three shared socioeconomic pathway and representative concentration pathway scenarios from 1961 to 2100, based on an ensemble of five climate models. Historical water temperatures were well predicted with a recurrent neural network, using observation‐based atmospheric forcing data. Length‐at‐age was in turn also well predicted by cumulative growing degree days calculated from these water temperatures. Most juveniles in the Burrishoole population migrated to sea as 2‐year‐old smolts, but our future projections indicate that the system should start producing a greater proportion of 1‐year‐old smolts, as increasingly more juveniles cross a size‐based threshold in their first summer for smoltification the following spring. Those failing to cross the size‐based threshold will instead become 2‐year‐old smolts, but at a larger length relative to 2‐year‐old smolts observed currently, owing to greater overall freshwater growth opportunity. These changes in age‐ and size‐at‐seaward migration could have cascading effects on age‐ and size‐at‐maturity and reproductive output. Consequently, the seemingly small changes that our results demonstrate have the potential to cause significant shifts in population dynamics over the full life cycle. This workflow is highly applicable across the range of the Atlantic salmon, as well as to other anadromous species, as it uses openly accessible climate data and a length‐at‐age model with minimal input requirements, fostering improved general understanding of phenotypic and demographic responses to climate change and management implications. [ABSTRACT FROM AUTHOR]

Reduction of freshwater habitat quality due to land use change can have major impacts on diadromous fish. Partitioning this impact from other potential drivers, such as changing marine conditions and climate, is hampered by a lack of long-term data sets. Here, four decades of data were used to assess the impact of land use change on Salmo salar and anadromous Salmo trutta in the Burrishoole catchment, Ireland, one of the few index sites for diadromous fish in the North Atlantic. Land use change was found to have no significant impact on the freshwater survival of either salmon or trout. However, climate impacted significantly on the survival of salmon and trout in fresh water, with poor survival in years with wetter, warmer winters, coinciding with positive North Atlantic Oscillation values. Additionally, cold springs were associated with higher survival in trout. The addition of hatchery fish into the salmon spawning cohort coincided with low freshwater survival. Our results highlight the necessity for a broad ecosystem approach in any conservation effort of these species. La baisse de la qualite des habitats d'eau douce decoulant de changements d'utilisation des sols peut avoir d'importants impacts sur les poissons diadromes. La capacite de departager ces impacts de ceux d'autres facteurs potentiels, comme des conditions marines changeantes et le climat, est limitee par l'absence d'ensembles de donnees de longue duree. Quatre decennies de donnees ont ete utilisees pour evaluer l'incidence de changements d'utilisation des sols sur le saumon atlantique Salmo salar et la truite de mer Salmo trutta. anadrome dans le bassin versant de Burrishoole en Irlande, un des rares lieux temoins pour les poissons diadromes dans l'Atlantique Nord. Nous avons constate que les changements d'utilisation des sols n'ont aucun impact significatif sur la survie en eau douce des saumons ou des truites. Le climat a toutefois une incidence significative sur la survie en eau douce des saumons et des truites, les annees de faible survie etant caracterisees par des hivers plus chauds et humides coincidant avec des valeurs positives de l'Oscillation nord-atlantique. Des printemps froids sont en outre associes a une plus grande survie des truites. L'ajout de poissons issus d'ecloseries dans la cohorte reproductrice de saumons coincide avec de faibles taux de survie en eau douce. Nos resultats soulignent la necessite d'une approche ecosystemique large dans tout effort de conservation de ces especes. [Traduit par la Redaction], Introduction The migratory nature of diadromous fish means that they are threatened by a unique set of multiple stressors, including habitat destruction, barriers, overexploitation, and climate change (Wilcove and Wikelski [...]

In several groups of anadromous fishes, but especially the salmonids, some populations migrate from the ocean to fresh water many months prior to spawning. This 'premature migration' reduces growth opportunities at sea, compels them to occupy much less productive freshwater habitats, and exposes them to extremes of flow and temperature, disease, and predation. We first review migration in salmonids and find great variation in timing patterns among and within species, relative to the timing of reproduction. Premature migration is widely distributed among species but not in all populations, and we propose two hypotheses to explain it. First, the fish may be making 'the best of a bad situation' by entering early because access to suitable breeding sites is constrained seasonally by flow or temperature regimes, so they sacrifice growing opportunities at sea. Alternatively or additionally, some populations may be 'balancing risks and benefits' as they trade off the benefits of growth at sea against the risk of mortality there. In this model, the reduced risk of mortality at sea must be balanced against the risk of mortality in freshwater habitats from thermal stress, disease, and predators. Premature migration may be favored where temperatures and flows are moderate or where lakes provide safety from predators and reduce energetic expenditure. Consistent with this hypothesis, early return is characteristic of larger, older salmonids (that would benefit less from additional time at sea to grow than would smaller fish). Finally, we consider the vulnerability of premature migrants to climate change and selective fisheries. Migration timing is an important part of the portfolio of phenotypic diversity that conveys resilience to species, population complexes, and the fisheries that depend on them. The premature migrants are often especially valued in fisheries and also often of particular conservation concern, and the phenomenon merits further research. Dans plusieurs groupes de poissons anadromes, mais particulierement chez les salmonides, certaines populations migrent de l'ocean vers l'eau douce plusieurs mois avant le frai. Cette << migration prematuree >> limite les possibilites de croissance en mer, amenent les poissons a occuper des habitats d'eau douce beaucoup moins productifs et les exposent a des extremes d'ecoulement et de temperature, ainsi qu'a la maladie et la predation. Nous passons d'abord en revue la migration chez les salmonides et notons d'importantes variations interspecifiques et intraspecifiques en ce qui concerne la distribution du moment de la migration par rapport au moment de la reproduction. La migration prematuree presente une large distribution entre les especes, mais pas dans toutes les populations, et nous proposons deux hypotheses pour expliquer cet etat de choses. D'abord, les poissons feraient << de leur mieux dans les circonstances >> en entrant tot en eau douce parce que l'acces a des sites de reproduction convenables est limite par les regimes d'ecoulement et de temperature a des periodes precises de l'annee, ce qui les amene a sacrifier des possibilites de croissance en mer. Par ailleurs, ou en plus, certaines populations pourraient << chercher un equilibre entre les differents risques et avantages >> en laissant tomber les avantages de la croissance en mer pour y eviter les risques de mortalite. Dans ce modele, la reduction du risque de mortalite en mer doit etre soupesee au vu du risque de mortalite dans les habitats d'eau douce associe au stress thermique, a la maladie et aux predateurs. La migration prematuree pourrait etre favorisee quand les temperatures et l'ecoulement sont moderes ou la oU les lacs offrent une protection contre les predateurs et reduisent les depenses energetiques. Selon cette hypothese, le retour precoce caracteriserait des salmonides plus grands et plus vieux (qui profiteraient moins d'une plus longue periode passee en mer pour croitre que les poissons plus petits). Enfin, nous nous penchons sur la vulnerabilite des migrants prematures aux changements climatiques et a la peche selective. Le moment de la migration constitue une part importante du portefeuille de diversite phenotypique qui confere de la resilience aux especes et aux complexes de populations, ainsi qu'aux peches qui en dependent. Une valeur particuliere est souvent accordee dans les peches aux migrants prematures, dont la conservation est, dans bien des cas, preoccupante; le phenomene merite de faire l'objet de travaux plus pousses. [Traduit par la Redaction], Introduction The need to obtain energy for maintenance, growth, and reproduction drives a wide range of behavioral and ecological processes. Migratory animals take advantage of seasonally predictable patterns of resource [...]

This paper reports an investigation of stock--recruitment relations for Atlantic salmon (Salmo salar). We regard these relations as stochastic functions characterized by an expected stock--recruitment relation and deviations from this expectation driven by observational error and uncharacterised environmental variability. We estimate model parameters by standard Bayesian methods. Analysis of the input--output characteristics of segments of the salmon life cycle in the Girnock Burn (Northeast Scotland) reveals two independent regulatory processes, one between ova and fry and the other between fry and smolts. Comparison of stock--recruitment relations for Atlantic salmon in Scotland, Ireland, and Canada, reinforced by an extended series of simulation studies, shows that even when comparatively long time series of high quality data are available, it is frequently difficult to exclude the possibility of low stock depensation--an effect whose implication of enhanced extinction risk implies that precautionary management policy would pay special attention to the posssibility of its occurence. A particular feature of our simulation results is their demonstration that inappropriate combination of distinct subpopulations both increases process noise and distorts the expected stock--recruitment relation, thereby greatly reducing the accuracy of any system identification process. Resume: Nous etudions les relations stock--recrutement chez le saumon atlantique (Salmo salar). Nous considerons ces relations comme des fonctions stochastiques caracterisees par une relation stock--recrutement attendue et des deviations de cette attente causees par des erreurs d'observation et une variabilite environnementale non caracterisee. Nous estimons les parametres du modele par des methodes bayesiennes standard. Une analyse des caracteristiques d'entree et de sortie des segments du cycle biologique des saumons de Girnock Burn (nord-est de l'Ecosse) revele l'existence de deux mecanismes independants de regulation, l'un entre l'oeuf et l'alevin et le second entre l'alevin et le saumoneau. Une comparaison des relations stock--recrutement chez les saumons atlantiques d'Ecosse, d'Irlande et du Canada, appuyee par une longue serie d'etudes de simulation, montre que, meme lorsque des series chronologiques comparativement longues de donnees de qualite sont disponibles, il est souvent difficile d'exclure la possibilite d'un effet de depensation sur les stocks bas--un effet qui implique un risque accru d'extinction, une possibilite dont une politique prudente de gestion doit tenir un compte special. Un aspect particulier de nos resultats de simulation est la demonstration qu'une combinaison inappropriee de sous-populations distinctes augmente le bruit de traitement et fausse la relation stock--recrutement--ce qui reduit grandement la precision de tout mecanisme d'identification des systemes. [Traduit par la Redaction], Introduction Overview The stock--recruitment paradigm dates from the pioneering work of Ricker (1954) and Beverton and Holt (1957). Despite evidence that some species have recruitment dynamics too subtle to be [...]