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This article summarizes the Special Issue of Evolutionary Applications focused on "Advances in Salmonid Genetics." Contributions to this Special Issue were primarily presented at the Coastwide Salmonid Genetics Meeting, held in Boise, ID in June 2023, with a focus on Pacific salmonids of the west coast region of North America. Contributions from other regions of the globe are also included and further convey the importance of various salmonid species across the world. This Special Issue is comprised of 22 articles that together illustrate major advances in genetic and genomic tools to address fundamental and applied questions for natural populations of salmonids, ranging from mixed‐stock analyses, to conservation of genetic diversity, to adaptation to local environments. These studies provide valuable insight for molecular ecologists since salmonid systems offer a window into evolutionary applications that parallel conservation efforts relevant and applicable beyond salmonid species. Here, we provide an introduction and a synopsis of articles in this Special Issue, along with future directions in this field. We present this Special Issue in honor of Fred Utter, a founder and leader in the field of salmonid genetics, who passed away in 2023. [ABSTRACT FROM AUTHOR]

ABSTRACT Limited approaches exist for studying population connectivity in widely dispersing marine benthic invertebrates. Genetic techniques can provide important insights toward identifying recruitment trajectories. Here, 10 microsatellite loci were used [...]

Dams have contributed to the decline of migratory fishes by blocking access to historical habitat. The active transport (trap and haul) of migratory fish species above existing dams can sometimes support population recovery when the use of fish ladders or dam removal is infeasible. However, little is known about the efficacy of trap and haul conservation strategies. Here we used genetic parentage assignments to evaluate the efficacy of reintroducing adult Chinook salmon (Oncorhynchus tshawytscha) above Cougar Dam on the South Fork McKenzie River, Oregon, USA, from 2008 to 2011. We found that mean reproductive success (RS) declined as adults were released later in the spawning season in 2009 and 2010; however, release location did not affect RS. In 2010 and 2011, we tested for RS differences between hatchery and natural origin (HOR and NOR, respectively) adults. HOR males were consistently less fit than NOR males, but little evidence for fitness differences was apparent between HOR and NOR females. Interestingly, the effect of origin on RS was not significant after accounting for variation explained by body length. Our results indicate that release date and location have inconsistent or no effect on the reproductive success of reintroduced adults when active transport strategies are employed for migratory fishes. Les barrages ont contribue au declin des poissons migrateurs en leur bloquant l'acces a des habitats historiques. Le transport actif (capture et deplacement) d'especes de poissons migrateurs par-dessus des barrages existants peut parfois appuyer le retablissement de populations quand l'utilisation d'echelles a poissons ou le retrait de barrages ne sont pas possibles. Les connaissances sur l'efficacite de strategies de conservation reposant sur la capture et le deplacement sont toutefois limitees. Nous utilisons des affectations de filiation genetique pour evaluer l'efficacite de la reintroduction de saumons quinnats (Oncorhynchus tshawytscha) adultes en amont du barrage Cougar sur la riviere South Fork McKenzie (Oregon, Etats-Unis), de 2008 a 2011. Nous avons constate que le succes de reproduction (SR) moyen etait plus faible quand les adultes etaient relaches plus tard dans la periode du frai en 2009 et 2010; le lieu du lacher n'avait toutefois pas d'incidence sur le SR. En 2010 et 2011, nous avons verifie la presence de differences du SR entre les adultes originaires d'ecloseries et de milieux naturels (HOR et NOR, respectivement). Si l'aptitude des males HOR etait uniformement plus faible que celle des males NOR, rien ne semblait indiquer une telle difference d'aptitude entre les femelles HOR et NOR. Fait interessant, l'effet de l'origine sur le SR n'etait pas significatif une fois prise en compte la variation expliquee par la longueur du corps. Nos resultats indiquent que la date et le lieu du lacher ont une incidence non uniforme ou nulle sur le succes de reproduction des adultes reintroduits quand des strategies de transport actif sont utilisees pour des poissons migrateurs. [Traduit par la Redaction], Introduction Reintroduction programs attempt to reestablish locally extirpated species to their historical habitat (IUCN-SSC 2013) and can serve to restore a species' distribution when access to habitat has simply been [...]

Hatcheries support fisheries and aid in the recovery of endangered wild populations. Evidence for reduced reproductive success (RS) in wild-spawning hatchery-reared salmon compared with that in wild-born fish invites questions about the impact on subsequent generations. Immune gene-dependent mate preference is one mechanism known to influence salmonid fitness. We evaluated mate choice and correlates of RS to better understand fitness differences between hatchery-reared and wild-born fish using a previously constructed genetic pedigree of coho salmon (Onchorhynchus kisutch) from the Umpqua River, Oregon. Two years (2005 and 2006) of three wild-spawning mate pair classes were examined: wild x wild (W x W), hatchery x hatchery (H x H), and wild x hatchery (W x H). We found no evidence for mate choice within mate pair classes based on microsatellites linked to the major histocompatibility complex (MHC) and immune-relevant expressed sequence tags. Greater W x W mate pair RS was associated with increased MHC diversity in 2005 and 2006, while greater W x H mate pair RS was correlated to intermediate MHC diversity in 2006. We found no correlation between MHC diversity and H x H mate pair RS. Our results suggest that greater MHC diversity between wild-born coho pairs may increase offspring survival. Les alevinieres appuient les peches et aident au retablissement des populations sauvages menacees. Des indications voulant que le succes de reproduction (SR) de saumons eleves en alevinieres et frayant en milieu naturel soit plus faible que celui de poissons nes en milieu naturel soulevent des questions quant a l'incidence sur les generations subsequentes. Il est etabli que la selection de partenaires dependante des genes de l'immunite est un mecanisme qui influence la valeur adaptative des salmonides. Nous avons evalue le choix des partenaires et les correlats du SR afin de mieux comprendre les variations de la valeur adaptative entre les poissons eleves en aleviniere et les poissons nes en milieu naturel en utilisant la genetique deja etablie des saumons cohos (Onchorhynchus kisutch) de la riviere Umpqua, en Oregon. Trois classes de paires de partenaires frayant en milieu naturel ont ete examinees pour deux annees (2005 et 2006): sauvage x sauvage (W x W), aleviniere x aleviniere (H x H) et sauvage x aleviniere (W x H). L'analyse de microsatellites relies au complexe majeur d'histocompatibilite (CMH) et d'etiquettes de sequences transcrites associees a l'immunite n'a rien revele qui appuierait le choix de partenaire issu de la meme classe de paires de partenaires. Un plus grand SR des paires de partenaires W x W etait associe a une diversite accrue du CMH en 2005 et 2006, alors qu'un plus grand SR des paires W x H etait correle a une diversite intermediate du CMH en 2006. Nous n'avons trouve aucune correlation entre la diversite du CMH et le SR des paires de partenaires HxH. Nos resultats donnent a penser qu'une plus grande diversite du CMH entre paires de saumons cohos nes en milieu naturel pourrait accroitre la survie de la progeniture. [Traduit par la Redaction], Introduction Artificially propagated salmonids have been released from hatcheries since the early 20th century to supplement declining wild populations. While in a hatchery environment, fish experience selective pressures of a [...]

The Arctic will be especially affected by climate change, resulting in altered seasonal timing. Anadromous Arctic char (Salvelinus alpinus) is strongly influenced by sea surface temperature (SST) delimiting time periods available for foraging in the sea. Recent studies of salmonid species have shown variation at phenology‐related loci associated with timing of migration and spawning. We contrasted genetic population structure at 53 SNPs versus four phenology‐related loci among 15 anadromous Arctic char populations from Western Greenland and three outgroup populations. Among anadromous populations, the time period available for foraging at sea (>2°C) ranges from a few weeks to several months, motivating two research questions: (a) Is population structure compatible with possibilities for evolutionary rescue of anadromous populations during climate change? (b) Does selection associated with latitude or SST regimes act on phenology‐related loci? In Western Greenland, strong isolation by distance at SNPs was observed and spatial autocorrelation analysis showed genetic patch size up to 450 km, documenting contingency and gene flow among populations. Outlier tests provided no evidence for selection at phenology‐related loci. However, in Western Greenland, mean allele length at OtsClock1b was positively associated with the time of year when SST first exceeded 2°C and negatively associated with duration of the period where SST exceeded 2°C. This is consistent with local adaptation for making full use of the time period available for foraging in the sea. Current adaptation may become maladaptive under climate change, but long‐distance connectivity of anadromous populations could redistribute adaptive variation across populations and lead to evolutionary rescue. [ABSTRACT FROM AUTHOR]

Abstract: Using a combination of population‐ and individual‐based analytical approaches, we provide a comprehensive examination of genetic connectivity of Dungeness crab (Cancer magister) along ~1,200 km of the California Current System (CCS). We sampled individuals at 33 sites in 2012 to establish a baseline of genetic diversity and hierarchal population genetic structure and then assessed interannual variability in our estimates by sampling again in 2014. Genetic diversity showed little variation among sites or across years. In 2012, we observed weak genetic differentiation among sites (FST range = −0.005–0.014) following a pattern of isolation by distance (IBD) and significantly high relatedness among individuals within nine sampling sites. In 2014, pairwise FST estimates were lower (FST range = −0.014–0.007), there was no spatial autocorrelation, and fewer sites had significant evidence of relatedness. Based on these findings, we propose that interannual variation in the physical oceanographic conditions of the CCS influences larval recruitment and thus gene flow, contributing to interannual variation in population genetic structure. Estimates of effective population size (Ne) were large in both 2012 and 2014. Together, our results suggest that Dungeness crab in the CCS may constitute a single evolutionary population, although geographically limited dispersal results in an ephemeral signal of IBD. Furthermore, our findings demonstrate that populations of marine organisms may be susceptible to temporal changes in population genetic structure over short time periods; thus, interannual variability in population genetic measures should be considered. [ABSTRACT FROM AUTHOR]

Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive versus neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid high gene flow owing to artificial propagation and habitat alteration. We compared seven putative migration timing genes to ten microsatellite loci in delineating three migratory groups of Chinook in the Feather River, CA: offspring of fall-run hatchery broodstock that returned as adults to freshwater in fall (fall run), spring-run offspring that returned in spring (spring run), and fall-run offspring that returned in spring (FRS). We found evidence for significant differentiation between the fall and federally listed threatened spring groups based on divergence at three circadian clock genes (OtsClock1b, OmyFbxw11, and Omy1009UW), but not neutral markers. We thus demonstrate the importance of genetic marker choice in resolving complex life history types. These findings directly impact conservation management strategies and add to previous evidence from Pacific and Atlantic salmon indicating that circadian clock genes influence migration timing. [ABSTRACT FROM AUTHOR]

We examined the distribution of Umpqua ChubOregonichthys kalawatseti, an endemic, vulnerable minnow in western Oregon, and whether six ecological populations (based on distribution patterns) had sufficient genetic cohesion to be considered evolutionary populations. We also evaluated the influence of Holocene geological events and recent nonnative predator introductions on the timing of population formation or fragmentation. Based on data from 10 microsatellite loci, we found evidence for four evolutionary populations of Umpqua Chub. One population, in the Smith River, is isolated by the Umpqua estuary and is more than 100 river kilometers from the other three populations: Elk Creek, Calapooya Creek–Olalla Creek, and Cow Creek–South Umpqua River. Quantile regression was used to examine the timing of genetic divergence among evolutionary populations assuming a genetic isolation-by-distance model. The quantile regression suggested that the genetic differentiation index (FST) should change by at least 0.0002/km; most fragmentation was recent and with similar timing, but the Smith River isolation event may have been about 2–4 times older. We could not distinguish whether the timing of the Smith River isolation corresponded to the last major tsunami event or the introduction of Striped BassMorone saxatilis, a likely predator. All population fragmentation appears to be relatively recent, with the three upstream populations restricted to third- and fourth-order streams, most likely fragmented by either nonnative Smallmouth BassMicropterus dolomieu, which now dominate sixth-order streams, or in the case of Elk Creek, a dam. The mid-drainage Calapooya–Olalla population was the most genetically diverse and appeared to be a mix of the other populations, which showed a significant isolation-by-distance relationship to this population. We hypothesize that Umpqua Chub populations have formed and fragmented by peripheral isolation from a larger population, the remnant of which is the mid-drainage Calapooya–Olalla population. Received April 20, 2012; accepted August 25, 2012 [ABSTRACT FROM AUTHOR]

Using a combination of population- and individual-based analytical approaches, we provide a comprehensive examination of genetic connectivity of Dungeness crab (Cancer magister) along ~1,200 km of the California Current System (CCS). We sampled individuals at 33 sites in 2012 to establish a baseline of genetic diversity and hierarchal population genetic structure and then assessed interannual variability in our estimates by sampling again in 2014. Genetic diversity showed little variation among sites or across years. In 2012, we observed weak genetic differentiation among sites (F ST range = -0.005-0.014) following a pattern of isolation by distance (IBD) and significantly high relatedness among individuals within nine sampling sites. In 2014, pairwise F ST estimates were lower (F ST range = -0.014-0.007), there was no spatial autocorrelation, and fewer sites had significant evidence of relatedness. Based on these findings, we propose that interannual variation in the physical oceanographic conditions of the CCS influences larval recruitment and thus gene flow, contributing to interannual variation in population genetic structure. Estimates of effective population size (N e ) were large in both 2012 and 2014. Together, our results suggest that Dungeness crab in the CCS may constitute a single evolutionary population, although geographically limited dispersal results in an ephemeral signal of IBD. Furthermore, our findings demonstrate that populations of marine organisms may be susceptible to temporal changes in population genetic structure over short time periods; thus, interannual variability in population genetic measures should be considered., (© 2017 John Wiley & Sons Ltd.)