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.
Dams, utilized for hydroelectric or flood control purposes, obstruct organism dispersal and have contributed to the decline of many migratory fish populations. For threatened Chinook salmon ...(Oncorhynchus tshawytscha) from the Willamette River Basin in Oregon, human-assisted reintroductions are being used to facilitate dispersal to historical habitats located above dams. However, little is known about the reproductive outcomes of reintroduced individuals or the efficacy of reintroductions towards the goal of population demographic viability. Using genetic parentage assignments to 3-, 4-, and 5-year-old adult recruits, we estimated the fitness of hatchery and wild Chinook salmon reintroduced above Foster Dam on the South Santiam River, a tributary of the Willamette River. Our parentage assignments indicated that the fitness of reintroduced salmon was highly variable, with individuals producing a range of 0–40 adult progeny. We also detected a possible trend towards reduced fitness in mate pairs composed of hatchery versus wild salmon. For each of three brood years (2007, 2008, 2009), adult offspring recruitment achieved or exceeded population replacement. We observed the highest cohort replacement rate in 2009, the first year that managers aimed to release wild salmon solely above the dam. Taken together, our results suggest that human-assisted reintroductions of mature adult salmon to historical spawning habitats are a promising method of restoring natural production in populations affected by dams. Moreover, the continued used of wild fish in reintroduction operations may improve population productivity and the prospect of recovery within the South Santiam River.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
A critical seasonal event for anadromous Chinook salmon (Oncorhynchus tshawytscha) is the time at which adults migrate from the ocean to breed in freshwater. We investigated whether allelic variation ...at the circadian rhythm genes, OtsClock1a and OtsClock1b, underlies genetic control of migration timing among 42 populations in North America. We identified eight length variants of the functionally important polyglutamine repeat motif (PolyQ) of OtsClock1b while OtsClock1a PolyQ was highly conserved. We found evidence of a latitudinal cline in average allele length and frequency of the two most common OtsClock1b alleles. The shorter 335 bp allele increases in frequency with decreasing latitude while the longer 359 bp allele increases in frequency at higher latitudes. Comparison to 13 microsatellite loci showed that 335 and 359 bp deviate significantly from neutral expectations. Furthermore, a hierarchical gene diversity analysis based on OtsClock1b PolyQ variation revealed that run timing explains 40.9 per cent of the overall genetic variance among populations. By contrast, an analysis based on 13 microsatellite loci showed that run timing explains only 13.2 per cent of the overall genetic variance. Our findings suggest that length polymorphisms in OtsClock1b PolyQ may be maintained by selection and reflect an adaptation to ecological factors correlated with latitude, such as the seasonally changing day length.
Teleost fish are the most diverse group of vertebrates and provide opportunities to study the evolution of sex determination (SD) systems. Using genomic and functional analyses, we identified a ...male-specific duplication of
(
) gene as the male master sex-determining (MSD) gene in
. By resequencing 10 males and 10 females, we characterized a 5 kb-long fragment in HiC_Scaffold_12 as a male-specific region, which contained an
gene (named
). We then demonstrated that
is a duplication of autosomal
that was later translocated to the ancestral Y chromosome.
and
shared high-nucleotide identity with the most significant difference being two insertions in intron 4 of
. Furthermore,
overexpression triggered female-to-male sex reversal in
, displaying its fundamental role in driving testis differentiation. We developed a PCR assay which successfully identified sexes in two species of northwest Pacific rockfish related to
. However, the PCR assay failed to distinguish the sexes in a separate clade of northeast Pacific rockfish. Our study provides new examples of
as the MSD in fish and sheds light on the convergent evolution of
duplication as the driving force of sex determination in different fish taxa.
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.
Dynamic marine environments can shape complex spatial and temporal patterns in the population connectivity of marine species, and this is often exemplified in species with long larval phases. Here, ...we used a genotyping-by-sequencing (GBS) approach to examine fine-scale spatial and temporal genomic variation among Dungeness crab Cancer magister larval recruits sampled in the California Current Ecosystem. Specifically, we compared samples collected during expected- and late-season recruitment time periods within 2 consecutive years (2017 and 2018) at 2 sites in Oregon, USA (Yaquina Bay and Coos Bay). Evidence was found for high gene flow between the expected- and late-season recruits within each year and at both sites based on 1389 neutral loci. In contrast, strong genetic differentiation was observed between these 2 groups within each year and at both sites based on variation at 2 putatively adaptive loci. Contrary to prediction, the magnitude of genetic differentiation between these 2 seasonal groups was greater in 2017 when the Pacific Decadal Oscillation was stronger, upwelling was weaker, and the spring transition was later. Spatial genetic variation was not observed within 2017 or 2018. Comparing across years, expected- and late-season groups were differentiated at putatively adaptive loci. Interestingly, strong genetic differentiation was also observed between late-season groups across years. We found no evidence for cohesive larval dispersal among recruits based on genetic related ness estimates. Overall, our findings provide evidence for high connectivity within Dungeness crab, but suggest that selective pressures and ocean conditions influence the genetic composition of larval recruits both intra- and inter-annually.
Understanding connectivity of marine organisms is necessary for determining the appropriate scale of conservation and management strategies. For species that inhabit both the coastal ocean and ...partially enclosed water bodies (i.e., estuaries or fjords), this information is even more critical since estuaries and fjords are often characterized by hydrological complexities which can limit dispersal potential and promote population subdivision. In this study, genetic connectivity of Dungeness crab
Cancer magister
in Puget Sound and coastal Washington, USA, was examined to test the hypothesis of genetic structure in partially enclosed versus open environments. Dungeness crab that were sampled at five sites in Puget Sound in 2015 and three sites in coastal Washington in 2014 were genotyped at ten microsatellite loci. We observed similar levels of heterozygosity and allelic richness within Puget Sound and coastal Washington. Pairwise
F
ST
estimates indicated that Hood Canal was significantly differentiated from other Puget Sound sites, except Nisqually, suggesting larval retention within the Hood Canal basin. No evidence for significant genetic differentiation was found among the four remaining Puget Sound sites or among the three coastal sites. Analysis of molecular variance indicated that, in aggregate, Puget Sound sites significantly differed from coastal sites. On a site by site basis, we found evidence for significant differentiation between three sites in Puget Sound and coastal Washington. Based upon the observed patterns of genetic differentiation, our findings did not support our hypothesis of restricted genetic connectivity within Puget Sound, with the exception of Hood Canal. However, our results demonstrate that there is stronger genetic connectivity within Puget Sound and coastal Washington than between these two areas.
Abstract
The increasing feasibility of assembling large genomic datasets for non-model species presents both opportunities and challenges for applied conservation and management. A popular theme in ...recent studies is the search for large-effect loci that explain substantial portions of phenotypic variance for a key trait(s). If such loci can be linked to adaptations, 2 important questions arise: 1) Should information from these loci be used to reconfigure conservation units (CUs), even if this conflicts with overall patterns of genetic differentiation? 2) How should this information be used in viability assessments of populations and larger CUs? In this review, we address these questions in the context of recent studies of Chinook salmon and steelhead (anadromous form of rainbow trout) that show strong associations between adult migration timing and specific alleles in one small genomic region. Based on the polygenic paradigm (most traits are controlled by many genes of small effect) and genetic data available at the time showing that early-migrating populations are most closely related to nearby late-migrating populations, adult migration differences in Pacific salmon and steelhead were considered to reflect diversity within CUs rather than separate CUs. Recent data, however, suggest that specific alleles are required for early migration, and that these alleles are lost in populations where conditions do not support early-migrating phenotypes. Contrasting determinations under the US Endangered Species Act and the State of California’s equivalent legislation illustrate the complexities of incorporating genomics data into CU configuration decisions. Regardless how CUs are defined, viability assessments should consider that 1) early-migrating phenotypes experience disproportionate risks across large geographic areas, so it becomes important to identify early-migrating populations that can serve as reliable sources for these valuable genetic resources; and 2) genetic architecture, especially the existence of large-effect loci, can affect evolutionary potential and adaptability.
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.
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.
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