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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]

Reintroduction is an important tool for the recovery of imperiled species. For threatened Pacific salmonids (Oncorhynchus spp.) species, hatchery‐origin (HOR) individuals from a nearby source are often used to reestablish populations in vacant, historically occupied habitat. However, this approach is challenged by the relatively low reproductive success that HOR Pacific salmonids experience when they spawn in the wild, relative to their natural‐origin (NOR) counterparts. In this study, we used genetic parentage analysis to compare the reproductive success of three groups of adult Chinook salmon (Oncorhynchus tshawytscha) reintroduced above Cougar Dam on the South Fork McKenzie River, Oregon: HOR Chinook salmon from an integrated stock; first‐generation, wild‐born descendants (hereafter F1s) of Chinook salmon produced at the same hatchery; and NOR Chinook salmon that are presumed to have been produced below the dam, on the mainstem McKenzie River, or elsewhere and volitionally entered a trap below Cougar Dam. We found that F1s produced nearly as many adult offspring as NORs, and 1.8‐fold more adult offspring than HORs. This result suggests that, for the South Fork McKenzie reintroduction program, a single generation in the wild increases fitness for the descendants of HOR Chinook salmon. Although these results are encouraging, care must be taken before extrapolating our results to other systems. [ABSTRACT FROM AUTHOR]

Climate change is a global phenomenon, but natural selection occurs within landscapes. Many global analyses predict how climate change will shape behavior and physiology, but few incorporate information from the landscape scales at which animals actually respond to selective pressure. We compared cold‐water fish (redband trout Oncorhynchus mykiss newberrii) from neighboring habitats in a naturally warm, recently fragmented basin to understand how different responses to warming may arise from landscape constraints. Trout in warm, hydrologically connected Upper Klamath Lake fled summer temperatures and sought refuge in cool tributaries, while trout in an equally warm but fragmented reach of the Klamath River endured summer conditions. Trout in the river were more physiologically tolerant of high temperatures than trout in the lake across multiple metrics, including capacity for aerobic activity, recovery from exertion, and loss of equilibrium. Two independent metrics of energetic condition indicated that the behavioral strategy of trout in the lake came at a substantial energetic cost, while the physiological strategy of trout in the river was able to mitigate most energetic consequences of high temperatures. No clear genetic basis for increased tolerance was found in trout from the river, which may suggest tolerance was derived from plasticity, although our analysis could not rule out genetic adaptation. Our results show that landscape processes such as fragmentation can cause different climate survival strategies to emerge in neighboring populations. Connecting the mechanisms that favor similar survival strategies among related organisms at broad scales with mechanisms that drive landscape‐scale variability within taxa should be a major goal for future predictions of biological responses to climate change. [ABSTRACT FROM AUTHOR]

Albacore (Thunnus alalunga) support an economically valuable global fishery, but surprisingly little is known about the population structure of this highly migratory species. Physical tagging data suggest that Albacore from the North and South Pacific Ocean are separate stocks, but results from previous genetic studies did not support this two stock hypothesis. In addition, observed biological differences among juveniles suggest that there may be population substructure in the North Pacific. We used double‐digest restriction site‐associated DNA sequencing to assess population structure among 308 Albacore caught in 12 sample areas across the Pacific Ocean (10 North, 2 South). Since Albacore are highly migratory and spawning areas are unknown, sample groups were not assumed to be equivalent to populations and the genetic data were analyzed iteratively. We tested for putatively adaptive differences among groups and for genetic variation associated with sex. Results indicated that Albacore in the North and South Pacific can be distinguished using 84 putatively adaptive loci, but not using the remaining 12,788 presumed neutral sites. However, two individuals likely represent F1 hybrids between the North and South Pacific populations, and 43 Albacore potentially exhibit lower degrees of mixed ancestry. In addition, four or five cross‐hemisphere migrants were potentially identified. No genetic evidence was found for population substructure within the North Pacific, and no loci appeared to distinguish males from females. Potential functions for the putatively adaptive loci were identified, but an annotated Albacore genome is required for further exploration. Future research should try to locate spawning areas so that life history, demography, and genetic population structure can be linked and spatiotemporal patterns can be investigated. [ABSTRACT FROM AUTHOR]

Genetic methods can guide and improve the management of recreational mixed‐stock fisheries by informing stock‐specific estimates of harvest. We applied genetic stock identification and parentage‐based tagging to a recreational Chinook Salmon Oncorhynchus tshawytscha fishery in the Columbia River to illustrate the value of genetic analysis in management. We sampled landed catch in 2017 and 2018, assigned the fish to genetic reporting groups, explored temporal trends in harvest composition within and between seasons, and assessed the accuracy and precision of genetic methods against estimates from conventional tagging methodology. The genetic stock identification and parentage‐based tagging produced concordant stock assignments, and the harvest composition estimates were validated with independent data. High assignment rates, relative to expended sampling effort, and precise harvest composition estimates with adequate sample sizes demonstrate that both genetic methods can be complementary, effective tools in advancing harvest assessment and recreational fisheries management. The success of genetic stock identification and parentage‐based tagging supports the expanded application of genetics to similar fisheries, potentially alongside existing or emerging assessment methods, and guides future improvements in data collection and analysis. [ABSTRACT FROM AUTHOR]

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]

Little is known about intraspecific variation within the deacon rockfish (Sebastes diaconus), a recently described species found in the northeast Pacific Ocean. We investigated population structure among fish sampled from two nearshore reefs (Siletz Reef and Seal Rock) and one offshore site (Stonewall Bank) within a <50‐km2 area off the Oregon coast. Fish from the three sample sites exhibited small but statistically significant differences based on genetic variation at >15,000 neutral loci, whether analyzed independently or classified into nearshore and offshore groups. Male and females were readily distinguished using genetic data and 92 outlier loci were associated with sex, potentially indicating differential selection between males and females. Morphometric results indicated that there was significant secondary sexual dimorphism in otolith shape, but further sampling is required to disentangle potential confounding influence of age. This study is the first step toward understanding intraspecific variation within the deacon rockfish and the potential management implications. Since differentiation among the three sample sites was small, we consider the results to be suggestive of a single stock. However, future studies should evaluate how the stock is affected by differences in sex, age, and gene flow between the nearshore and offshore environments. [ABSTRACT FROM AUTHOR]

Arctic freshwater ecosystems have been profoundly affected by climate change. Given that the Arctic charr (Salvelinus alpinus) is often the only fish species inhabiting these ecosystems, it represents a valuable model for studying the impacts of climate change on species life‐history diversity and adaptability. Using a genotyping‐by‐sequencing approach, we identified 5,976 neutral single nucleotide polymorphisms and found evidence for reduced gene flow between allopatric morphs from two high Arctic lakes, Linne'vatn (Anadromous, Normal, and Dwarf) and Ellasjøen (Littoral and Pelagic). Within each lake, the degree of genetic differentiation ranged from low (Pelagic vs. Littoral) to moderate (Anadromous and Normal vs. Dwarf). We identified 17 highly diagnostic, putatively adaptive SNPs that differentiated the allopatric morphs. Although we found no evidence for adaptive differences between morphs within Ellasjøen, we found evidence for moderate (Anadromous vs. Normal) to high genetic differentiation (Anadromous and Normal vs. Dwarf) among morphs within Linne'vatn based on two adaptive loci. As these freshwater ecosystems become more productive, the frequency of sympatric morphs in Ellasjøen will likely shift based on foraging opportunities, whereas the propensity to migrate may decrease in Linne'vatn, increasing the frequency of the Normal morph. The Dwarf charr was the most genetically distinct group. Identifying the biological basis for small body size should elucidate the potential for increased growth and subsequent interbreeding with sympatric morphs. Overall, neutral and adaptive genomic differentiation between allopatric and some sympatric morphs suggests that the response of Arctic charr to climate change will be variable across freshwater ecosystems. The Arctic charr Salvelinus alpinus (Linnaeus, 1758) has a broad, circumpolar distribution and is the most northerly distributed freshwater fish species (primarily above 60°N; Klemetsen, 2010; Wilson et al., 2004). Using a genotyping‐by‐sequencing approach (Elshire et al., 2011), we investigate how Arctic charr morphs may respond to climate change by identifying neutral and putatively adaptive loci to determine the degree of reproductive isolation among morphs that can be attributed to genetic drift or local adaptation. [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]

The application of DNA-based markers toward the task of discriminating among alternate salmon runs has evolved in accordance with ongoing genomic developments and increasingly has enabled resolution of which genetic markers associate with important life-history differences. Accurate and efficient identification of the most likely origin for salmon encountered during ocean fisheries, or at salvage from fresh water diversion and monitoring facilities, has far-reaching consequences for improving measures for management, restoration and conservation. Near-real-time provision of high-resolution identity information enables prompt response to changes in encounter rates. We thus continue to develop new tools to provide the greatest statistical power for run identification. As a proof of concept for genetic identification improvements, we conducted simulation and blind tests for 623 known-origin Chinook salmon ( Oncorhynchus tshawytscha) to compare and contrast the accuracy of different population sampling baselines and microsatellite loci panels. This test included 35 microsatellite loci (1266 alleles), some known to be associated with specific coding regions of functional significance, such as the circadian rhythm cryptochrome genes, and others not known to be associated with any functional importance. The identification of fall run with unprecedented accuracy was demonstrated. Overall, the top performing panel and baseline ( HMSC21) were predicted to have a success rate of 98%, but the blind-test success rate was 84%. Findings for bias or non-bias are discussed to target primary areas for further research and resolution. [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]

Local adaptation is a dynamic process driven by selection that can vary both in space and time. One important temporal adaptation for migratory animals is the time at which individuals return to breeding sites. Chinook salmon ( Oncorhynchus tshawytscha) are excellent subjects for studying the genetic basis of temporal adaptation because their high seasonal homing fidelity promotes reproductive isolation leading to the formation of local populations across diverse environments. We tested for adaptive genetic differentiation between seasonal runs of Chinook salmon using two candidate loci; the circadian rhythm gene, OtsClock1b, and Ots515NWFSC, a microsatellite locus showing sequence identity to three salmonid genes central to reproductive development. We found significant evidence for two genetically distinct migratory runs in the Feather River, California ( OtsClock1b: FST = 0.042, P = 0.02; Ots515NWFSC: FST = 0.058, P = 0.003). In contrast, the fall and threatened spring runs are genetically homogenous based on neutral microsatellite data ( FST = –0.0002). Similarly, two temporally divergent migratory runs of Chinook salmon from New Zealand are genetically differentiated based on polymorphisms in the candidate loci ( OtsClock1b: FST = 0.083, P-value = 0.001; Ots515NWFSC: FST = 0.095, P-value = 0.000). We used an individual-based assignment method to confirm that these recently diverged populations originated from a single source in California. Tests for selective neutrality indicate that OtsClock1b and Ots515NWFSC exhibit substantial departures from neutral expectations in both systems. The large FST estimates could therefore be the result of directional selection. Evidence presented here suggests that OtsClock1b and Ots515NWFSC may influence migration and spawning timing of Chinook salmon in these river systems. [ABSTRACT FROM AUTHOR]

Development of nine polymorphic microsatellites from a genomic library of hybrid striped bass (female Morone chrysops × male Morone saxatilus) DNA is described. Breeding of hybrid striped bass for aquaculture is based largely on breeding wild fish. Molecular markers such as microsatellites will be useful tools for developing broodstock, estimating heritability for production traits, and selective breeding via marker-assisted selection. The nine polymorphic microsatellites include six dinucleotide and three complex repeat motifs. The number of alleles detected among a sample of 10 individuals of each species was relatively low. All polymerase chain reaction primer pairs also amplified products in the sea bass Dicentrarchus labrax. [ABSTRACT FROM AUTHOR]

Thirty-eight nuclear-encoded microsatellites were isolated from the marine fish Sciaenops ocellatus (red drum). The species is of economic importance in the southeastern United States, and declines in abundance have led to augmentation of the 'wild' fishery with hatchery-raised fingerlings. The microsatellites will be useful for studies designed to assess larval/juvenile recruitment of hatchery-raised individuals at varying spatial and temporal scales and for assessment of genetic components contributing to variation in performance and survival of hatchery-produced fingerlings in the wild. The microsatellites also will prove useful as 'anchor' loci in constructing a genetic map. [ABSTRACT FROM AUTHOR]