51 research outputs found
A latitudinal cline in the Chinook salmon (Oncorhynchus tshawytscha) Clock gene: evidence for selection on PolyQ length variants
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 335âbp allele increases in frequency with decreasing latitude while the longer 359âbp allele increases in frequency at higher latitudes. Comparison to 13 microsatellite loci showed that 335 and 359âbp 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
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A latitudinal cline in the Chinook salmon (Oncorhynchus tshawytscha) Clock gene: evidence for selection on PolyQ length variants
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
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Big fishery, big data, and little crabs: Using genomic methods to examine the seasonal recruitment patterns of early life stage Dungeness crab (Cancer magister) in the California Current Ecosystem
The California Current Ecosystem (CCE) is a dynamic marine ecosystem from which many socioeconomically important fisheries species are harvested. Here, a genotyping- by-sequencing (GBS) approach was used to examine genomic variation in an early life stage (megalopae) of the Dungeness crab (Cancer magister), which constitutes the most valuable single-species commercial fishery in the CCE. Variation in abundance and timing of megalopae recruitment has been extensively studied for over two decades in Coos Bay, Oregon, United States. Within the CCE, documented timing of Dungeness crab life history events indicates that coastal megalopae recruitment is expected to occur April through July; however, long-term studies in Coos Bay have observed late-season recruitment from August to October. Based on variation at 1,913 presumably neutral loci, evidence was found for weak, yet significant differentiation (FST estimate = 0.0011) between the 2014 expected-season recruits (n = 47) and late- season recruits (n = 47) collected in Coos Bay. However, two putatively adaptive loci with a high FST estimate (0.2036) between expected-season and late-season recruits were identified. These findings support the hypothesis that expected-season and late- season megalopae recruiting to Coos Bay within the same year may have originated from different locations or from different breeding groups. Understanding marine species connectivity between ecosystems is important when considering how future changes in ocean conditions may impact fishery harvests
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Fine-scale spatial and temporal genomic variation among Dungeness crab Cancer magister larval recruits in the California Current Ecosystem
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 relatedness 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
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Characterizing neutral and adaptive genomic differentiation in a changing climate: The most northerly freshwater fish as a model
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 lifeâhistory diversity and adaptability. Using a genotypingâbyâseâ quencing 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 Ìvatn (Anadromous, Normal, and Dwarf) and EllasjĂžen (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 EllasjĂžen, we found evidence for moderate (Anadromous vs. Normal) to high genetic differentiation (Anadromous and Normal vs. Dwarf) among morphs within Linne Ìvatn based on two adaptive loci. As these freshwater ecosystems become more producâ tive, the frequency of sympatric morphs in EllasjĂžen will likely shift based on foraging opportunities, whereas the propensity to migrate may decrease in Linne Ìvatn, inâ creasing the frequency of the Normal morph. The Dwarf charr was the most genetiâ cally distinct group. Identifying the biological basis for small body size should elucidate the potential for increased growth and subsequent interbreeding with symâ patric morphs. Overall, neutral and adaptive genomic differentiation between alâ lopatric and some sympatric morphs suggests that the response of Arctic charr to climate change will be variable across freshwater ecosystems
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Sex identification PCRâRFLP assay tested in eight species of Sebastes rockfish
The phenotypic identification of sex in Sebastes rockfish is difficult and often impractical from a management perspective, and the genetic basis of sex determination in the genus is currently uncertain. We tested a previously developed sex identifi- cation polymerase chain reaction restriction fragment length polymorphism (PCRâRFLP) assay in eight species of Sebastes rockfish. Results indicated that the association of this restriction site with sex is species-dependent
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Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow
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.Keywords: conservation genetics, ecological genetics, captive populations, conservation biology, life history evolution, hybridization, population genetics, fisheries managemen
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Microsatellite Markers for Red Drum, Sciaenops ocellatus
Polymerase chain reaction (PCR) primers are reported for 68 nuclear-encoded microsatellites developed during the past several years from genomic libraries of red drum (Sciaenops ocelwtus). All68 microsatellites were tested for reproducibility and polymorphism on a sample of five to 12 red drum; 60 of the microsatellites were found to be polymorphic. Estimates of observed and expected heterozygos- ity (gene diversity) and tests of conformity of genotypes to Hardy-Weinberg equi- librium were carried out for a subset of 31 microsatellites on a larger sample of 45 adults provided by Texas Parks and Wildlife. Levels of allelic and gene diversity were average relative to values observed for marine and anadromous fishes. The set of genetic markers should be useful for a variety of studies, including moni- toring and assessment of red drum stock enhancement
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Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)
Little is known about intraspecific variation within the deacon rockfish (Sebastes diâ aconus), a recently described species found in the northeast Pacific Ocean. We inâ vestigated population structure among fish sampled from two nearshore reefs (Siletz Reef and Seal Rock) and one offshore site (Stonewall Bank) within a 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 asâ sociated with sex, potentially indicating differential selection between males and feâ males. 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 inâ traspecific variation within the deacon rockfish and the potential management impliâ cations. Since differentiation among the three sample sites was small, we consider the results to be suggestive of a single stock. However, future studies should evaluâ ate how the stock is affected by differences in sex, age, and gene flow between the nearshore and offshore environments
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Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test
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.Keywords: Microsatellites, Oncorhynchus tshawytscha, Individual-identificationKeywords: Microsatellites, Oncorhynchus tshawytscha, Individual-identificatio
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