Conserved islands of divergence associated with adaptive variation in sockeye salmon are maintained by multiple mechanisms

Molecular Ecology, Journal Year: 2023, Volume and Issue: 33(24)

Published: Sept. 11, 2023

Local adaptation is facilitated by loci clustered in relatively few regions of the genome, termed genomic islands divergence. The mechanisms that create and maintain these how they contribute to adaptive divergence an active research topic. Here, we use sockeye salmon as a model investigate both responsible for creating patterns differentiation at islands. Previous suggested multiple contributed radiation salmon. However, low-density methods used studies made it difficult fully elucidate connect genotypes variation. We whole genome resequencing genotype millions genetic variation potentially created them. discovered 64 islands, including 16 four shared between two isolated populations. Characterisation three were likely structural variation, while one was processes not involving All small (< 600 kb), suggesting low recombination do have span megabases be important Differentiation consistently associated with established population attributes. In sum, landscape are complex; this complexity helps facilitate fine-scale local unique each population.

Language: Английский

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Evidence for the Functional Relevance of vgll3 and six6 οn Developmental Stages of Commercially Important Fish Species: Gilthead Seabream (Sparus aurata Linnaeus) and European Seabass (Dicentrarchus labrax Linnaeus)

Fishes, Journal Year: 2025, Volume and Issue: 10(3), P. 96 - 96

Published: Feb. 25, 2025

The six6 and vgll3 genes play evolutionarily conserved roles in developmental processes life history traits across species, including teleosts. Notable differences genotype allele frequencies of these have been observed between farmed wild populations European seabass gilthead seabream, suggesting potential associated with domestication. Here, we hypothesized that genetic variations the are distinct expression profiles underlie domestication-related two species. Using quantitative PCR (qPCR), examined early stages genotypes linked to Our results confirmed significantly influenced their statistically significant genotypes. In seabass, did not differ among genotypes, although heterozygous larvae showed higher variability decreased at juvenile stage. Meanwhile, no variation was vgll3, precluding genotype-specific analysis. Altogether, our findings provide first evidence confirming prior DNA-based associations domestication reflected mRNA level, particularly seabream. This highlights functional relevance shaping

Language: Английский

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Hierarchical Multi‐Dimensional Maturation Modeling to Isolate the Effects of Commercial Closure on a Great Lakes Fishery

Evolutionary Applications, Journal Year: 2025, Volume and Issue: 18(3)

Published: March 1, 2025

As anthropogenic disturbances rapidly change natural environments, species must respond to new selective pressures shaping rates of reproduction, growth, and mortality. One example is intense fisheries harvest, which can drive the evolution heavily fished populations toward maturation at smaller sizes younger ages. Changes in have often been measured using probabilistic reaction norms (PMRNs), were originally designed control for phenotypic plasticity while allowing detection maturation. However, multiple studies highlighted issues with PMRN estimation, particularly respect their accuracy when parameterized sparse data or applied experiencing myriad environmental stressors. We used a three-decade time series Laurentian Great Lakes yellow perch (Perca flavescens Mitchill) develop novel, hierarchical Bayesian estimation method that explicitly account these conceptual issues. Our results indicate commercial fishing was primary driver this population, relaxation harvest pressure via closure fishery late 1990s resulted adaptation older ages larger within 2-3 generations. Future pairing methods genome-wide will help reveal genetic underpinnings maturation, could lead avenues integrating PMRNs into management policy.

Language: Английский

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Genome-wide association for precocial maturation in juvenile male Spring Chinook salmon (Oncorhynchus tshawytscha)

Conservation Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: March 22, 2025

Language: Английский

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A Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook Salmon

Evolutionary Applications, Journal Year: 2025, Volume and Issue: 18(5)

Published: May 1, 2025

ABSTRACT Genetic methods have become an essential component of ecological investigation and conservation planning for fish wildlife. Among these is the use genetic marker data to identify individuals populations, or stocks, origin. More recently, that involve pedigree reconstruction relationships between within populations also common. We present here a novel set multiallelic microhaplotype markers Chinook salmon, which provide excellent resolution population discrimination relationship identification from rapidly economically assayed panel markers. show how this by sequencing 204 amplicons, in tandem with reference dataset 1636 individual samples 17 provides definitive power all known lineages salmon California. The inclusion loci associations phenotype were identified as outliers examination whole‐genome sequence allows stocks are not highly genetically differentiated but phenotypically distinct managed such. This same has ample variation accurately parent‐offspring full‐sibling pairs California including depauperate winter‐run lineage. Validation coastal previously studied modern reveals biological insights, presence single copy haplotype been documented part species range, clear signal mixed ancestry on geographic margins primary evolutionary

Language: Английский

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Steelhead (Oncorhynchus mykiss) lineages and sexes show variable patterns of association of adult migration timing and age‐at‐maturity traits with two genomic regions

Evolutionary Applications, Journal Year: 2020, Volume and Issue: 13(10), P. 2836 - 2856

Published: Aug. 11, 2020

Abstract As life history diversity plays a critical role in supporting the resilience of exploited populations, understanding genetic basis those variations is important for conservation management. However, effective application requires robust strength and universality associations. Here, we examine variation single nucleotide polymorphisms genomic regions previously associated with migration phenology age‐at‐maturity steelhead ( Oncorhynchus mykiss ) from Columbia River. We found chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance timing both coastal inland steelhead. association was much greater than R 2 0.51 vs. 0.08), suggesting that background challenging pathways may act to moderate effects this region. Further, 25 candidate (SIX6 gene) were significantly age size at first return steelhead, pattern mediated by sex predictable (males = 0.139–0.170; females 0.096–0.111). While encourages using these predicting characteristics, suggest stock‐specific associations haplotype frequencies will be useful guiding implementation assays inform

Language: Английский

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Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods

Heredity, Journal Year: 2022, Volume and Issue: 129(6), P. 356 - 365

Published: Nov. 10, 2022

Characterizing the role of different mutational effect sizes in evolution fitness-related traits has been a major goal evolutionary biology for century. Such characterization diversity systems, both model and non-model, will help to understand genetic processes underlying fitness variation. However, well-characterized architectures such wild populations remain uncommon. In this study, we used haplotype-based multi-SNP Bayesian association methods with sequencing data 313 individuals from test composition known candidate regions sea age at maturation Atlantic salmon (Salmo salar). We detected an five loci out 116 candidates previously identified aquaculture strain timing salmon. found that four these loci, variation explained by locus was predominantly driven single SNP suggesting architecture trait includes multiple simple, non-clustered alleles potentially more complex alleles. This highlights can exist traits. Furthermore, study provides useful framework future work using characterize phenotypes populations.

Language: Английский

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A homology guide for Pacific salmon genus Oncorhynchus resolves patterns of ohnolog retention, resolution and local adaptation following the salmonid‐specific whole‐genome duplication event

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(4)

Published: April 1, 2023

Abstract Salmonid fishes have emerged as a tractable model to study whole‐genome duplications (WGDs) this group has undergone four rounds of WGDs. While most the salmonid genome returned diploid state, significant proportion genes are maintained duplicates and referred ohnologs. The fact that much modern gene repertoire is comprised ohnologs, while other their singleton state creates complications for genetic studies by obscuring homology relationships. difficulty particularly prominent in Pacific salmonids belonging genus Oncorhynchus who focus intense genetics‐based conservation management efforts owing important ecological cultural roles these fish play. To address gap, we generated guide six species with available genomes used describe patterns ohnolog retention resolution. Overall, find ohnologs comprise approximately half each repertoires, which functionally enriched involved DNA binding, less numerous heavily dosage‐sensitive processes such mitochondrial metabolism. Additionally, reanalyzing published expression data from locally adapted strains O. mykiss , show exhibit adaptive profiles; however, not more likely display signatures than either paralogs or singletons. Finally, demonstrate utility our investigating evolutionary relationship among highlighted playing role life‐history traits editing targets.

Language: Английский

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Development of supermale and all-male Atlantic salmon to research the vgll3 allele - puberty link

BMC Genomic Data, Journal Year: 2020, Volume and Issue: 21(1)

Published: Nov. 12, 2020

Abstract Background Farmed Atlantic salmon are one of the most economically significant global aquaculture products. Early sexual maturation farmed males represents a challenge to this industry and has been linked with vgll3 genotype. However, tools aid research topic, such as all-male clonal fish, still lacking. The present 6-year study examined if production is possible in salmon, species heteromorphic sex chromosomes (males being XY, females XX), fish can be applied further explore contribution on likelihood early maturation. Results Estrogen treatment mixed yolk sac larvae gave rise sexually mature hermaphrodite male genotype (XY) that was used produce both self-fertilized offspring androgenetic double haploid (dh) following egg activation UV treated sperm pressure shock block first mitotic division. There were YY supermales among types, which crossed dh females. Between 1 8% putative from eight crosses found have ovaries, 95% these phenotypic also genetically female. None supermale cross had ovaries. When assessing general locus post-smolt (jacking) populations we individuals homozygous for maturing (97%) more likely enter puberty than late (26%). jacking within an early/late heterozygous higher when allele came dam (94%) compared sire (45%). Conclusions results show viable fertile tool important aspects maturation, dependent parental genetic age at salmon. In addition, report fish.

Language: Английский

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A review of iteroparity in anadromous salmonids: biology, threats and implications

Reviews in Fish Biology and Fisheries, Journal Year: 2023, Volume and Issue: 33(4), P. 1005 - 1025

Published: April 11, 2023

Language: Английский

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