The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: April 18, 2025

ABSTRACT The increasing feasibility of whole‐genome sequencing has been highly anticipated, promising to transform our understanding the biology nonmodel species. Notably, dramatic cost reductions beginning around 2007 with advent high‐throughput inspired publications heralding ‘genomics revolution’, predictions about its future impacts. Although such served as useful guideposts, value is added when statements are evaluated benefit hindsight. Here, we review 10 key made early in genomics revolution, highlighting those realised while identifying challenges limiting others. We focus on concerning applied aspects and examples involving salmonid species which, due their socioeconomic ecological significance, have frontrunners applications Predicted outcomes included enhanced analytical power, deeper insights into genetic basis phenotype fitness variation, disease management breeding program advancements. many materialised, several expectations remain unmet technological, knowledge barriers. Additionally, largely unforeseen advancements, including identification applicability large‐effect loci, close‐kin mark–recapture, environmental DNA gene editing under‐anticipated value. Finally, emerging innovations artificial intelligence bioinformatics offer new directions. This retrospective evaluation impacts genomic revolution offers for

Language: Английский

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Putting Structural Variants Into Practice: The Role of Chromosomal Inversions in the Management of Marine Environments

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: May 8, 2025

ABSTRACT Major threats to marine species and ecosystems include overfishing, invasive species, pollution climate change. The changing not only imposes direct through the impacts of severe heatwaves, cyclones ocean acidification but also complicates fisheries management by driving range shifts. dynamic nature these means that future our oceans will depend on ability adapt. This has led calls for genetic interventions focussed enhancing species' adaptive capacity, including translocations, restocking selective breeding. Assessing benefits risks such approaches requires an improved understanding architecture variation, in relation climate‐resilient phenotypes locally adapted populations fitness hybrids. Large structural variants as chromosomal inversions play important role local adaptation linking multiple loci. Consequently, are likely be particularly when managing capacity. However, under some circumstances, they accumulate deleterious mutations, potentially increasing risk inbreeding depression. Genetic takes account dual roles is more effective at ensuring population persistence. We summarise evolutionary factors influencing variation inversions, review found taxa, provide a framework predict consequences ignoring key scenarios. conclude describing practical methods bridge gap between theory application conservation.

Language: Английский

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Detecting parallel polygenic adaptation to novel evolutionary pressure in wild populations: a case study in Atlantic cod ( Gadus morhua )

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2023, Volume and Issue: 378(1881)

Published: May 29, 2023

Populations can adapt to novel selection pressures through dramatic frequency changes in a few genes of large effect or subtle shifts many small effect. The latter (polygenic adaptation) is expected be the primary mode evolution for life-history traits but tends more difficult detect than Atlantic cod ( Gadus morhua ) were subjected intense fishing pressure over twentieth century, leading abundance crashes and phenotypic shift toward earlier maturation across populations. Here, we use spatially replicated temporal genomic data test shared polygenic adaptive response using methods previously applied evolve-and-resequence experiments. Cod populations on either side show covariance allele change genome that are characteristic recent adaptation. Using simulations, demonstrate degree observed unlikely explained by neutral processes background selection. As human wild continue increase, understanding attributing modes adaptation similar those demonstrated here will important identifying capacity responses evolutionary rescue. This article part theme issue ‘Detecting causes biodiversity change: needs, gaps solutions’.

Language: Английский

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Assortative mating for reproductive timing affects population recruitment and resilience in a quantitative genetic model

Evolutionary Applications, Journal Year: 2023, Volume and Issue: 16(3), P. 657 - 672

Published: Jan. 20, 2023

Quantitative models that simulate the inheritance and evolution of fitness-linked traits offer a method for predicting how environmental or anthropogenic perturbations can affect dynamics wild populations. Random mating between individuals within populations is key assumption many such used in conservation management to predict impacts proposed actions. However, recent evidence suggests non-random may be underestimated play an important role diversity-stability relationships. Here we introduce novel individual-based quantitative genetic model incorporates assortative reproductive timing, defining attribute aggregate breeding species. We demonstrate utility this framework by simulating generalized salmonid lifecycle, varying input parameters, comparing outputs theoretical expectations several eco-evolutionary, population dynamic scenarios. Simulations with systems resulted more resilient productive than those were randomly mating. In accordance established ecological evolutionary theory, also found decreasing magnitude trait correlations, variability, strength selection each had positive effect on growth. Our constructed modular so future components easily added address pressing issues as effects supportive breeding, variable age structure, differential sex age, fishery interactions growth resilience. With code published public Github repository, tailored specific study parameterizing empirically generated values from long-term monitoring programs.

Language: Английский

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Population structure and adaptive differentiation in the sea cucumber Apostichopus californicus and implications for spatial resource management

PLoS ONE, Journal Year: 2023, Volume and Issue: 18(3), P. e0280500 - e0280500

Published: March 16, 2023

A growing body of evidence suggests that spatial population structure can develop in marine species despite large sizes and high gene flow. Characterizing is important for the effective management exploited species, as it be used to identify appropriate scales fishery aquaculture contexts. The California sea cucumber, Apostichopus californicus , one such whose could benefit from further characterization structure. Using restriction site-associated DNA (RAD) sequencing, we developed 2075 single nucleotide polymorphisms (SNPs) quantify genetic over a broad section species’ range along North American west coast within Salish Sea, region supporting Washington State . developing production species. We found (global fixation index ( F ST ) = 0.0068) with limited dispersal driving two patterns differentiation: isolation-by-distance latitudinal gradient differentiation. Notably, detectable differences among collection sites Sea (pairwise 0.001–0.006). outlier detection gene-environment association, identified 10.2% total SNPs putatively adaptive. Environmental variables (e.g., temperature, salinity) surface were more correlated variation than those same measured near benthos, suggesting selection on pelagic larvae may drive adaptive differentiation greater degree adults. Our results consistent previous estimates this other extents range. Additionally, neutral co-varied, barriers limit dispersal. study provides guidance decision-makers regarding designation units adds literature identifying large, nominally connected populations.

Language: Английский

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Re‐evaluating Coho salmon (Oncorhynchus kisutch) conservation units in Canada using genomic data

Evolutionary Applications, Journal Year: 2022, Volume and Issue: 15(11), P. 1925 - 1944

Published: Oct. 18, 2022

Abstract Conservation units (CUs) are important tools for supporting the implementation of standardized management practices exploited species. Following adoption Wild Salmon Policy in Canada, CUs were defined Pacific salmon based on characteristics related to ecotype, life history and genetic variation using microsatellite markers as indirect measures local adaptation. Genomic data sets have potential improve definition by reducing variance around estimates population parameters, thereby increasing power detect more subtle patterns structure providing an opportunity incorporate adaptive information directly with identification variants putatively under selection. We used one largest genomic recently published a nonmodel species, comprising 5662 individual Coho ( Oncorhynchus kisutch ) from 149 sampling locations total 24,542 high‐quality SNPs obtained genotyping‐by‐sequencing mapped reference genome (1) evaluate current delineation Canada (2) compare observed neutral outlier loci genotype–environment association analyses determine whether separate that capture diversity needed. Our results reflected CU boundaries whole, majority managed same clustering together within groups. However, additional groups not currently represented also uncovered. considerable overlap clusters identified or candidate loci, indicating general congruence driven adaptation gene flow this Consequently, we suggest largely well‐suited meeting Canadian Policy's objective defining biologically distinct groups, but highlight specific areas where may be refined.

Language: Английский

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Whole-genome resequencing reveals genetic differences and the genetic basis of parapodium number in Russian and Chinese Apostichopus japonicus

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Jan. 16, 2023

Abstract Background Apostichopus japonicus is an economically important species in the global aquaculture industry. Russian A. , mainly harvested Vladivostok region, exhibits significant phenotypic differentiation, including many traits, compared with Chinese owing to differences their habitat. However, both genetic basis for divergence and population structure of are unknown. Result In this study, 210 individuals from seven populations were sampled whole-genome resequencing. The analysis differentiated into two groups. Population analyses indicated that showed a high degree allelic linkage had undergone stronger positive selection populations. Gene ontology terms enriched among candidate genes group involved immunity, such as inflammatory response, antimicrobial peptides, humoral apoptosis. Genome-wide association yielded eight single-nucleotide polymorphism loci significantly associated parapodium number, these located regions genomic differentiation between Russia These SNPs five genes. expression validation revealed three differentially expressed differing number. AJAP08772 AJAP08773 may directly affect production by promoting endothelial cell proliferation metabolism, whereas AJAP07248 indirectly affects participating immune responses. Conclusions This we performed GWAS on found related number parapodium. results provide in-depth understanding China Russia, information subsequent breeding species.

Language: Английский

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Genetic divergence and one‐way gene flow influence contemporary evolution and ecology of a partially migratory fish

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(6)

Published: June 1, 2024

Recent work has revealed the importance of contemporary evolution in shaping ecological outcomes. In particular, rapid evolutionary divergence between populations been shown to impact ecology populations, communities, and ecosystems. While studies have focused largely on role adaptive generating ecologically important variation among much less is known about gene flow After divergence, may continue interact through flow, which influence processes. Here, we investigate recently diverged anadromous steelhead resident rainbow trout (

Language: Английский

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Genetic variation associated with adult migration timing in lineages of Steelhead and Chinook Salmon in the Columbia River

Evolutionary Applications, Journal Year: 2023, Volume and Issue: 17(2)

Published: Dec. 28, 2023

Abstract With the discovery of a major effect region (GREB1L, ROCK1) for adult migration timing in genomes both Chinook Salmon and Steelhead, several subsequent studies have investigated size distribution early late alleles among populations Columbia River. Here, we synthesize results these lineages Steelhead that include highly distinct groups interior River exhibit atypical life histories from most coastal lineage two species. Whole‐genome with high marker density provided extensive insight into SNPs associated timing, suites markers each species been genotyped large numbers individuals to further validate phenotypic effects. For largest sizes observed (36% variation passage at Bonneville Dam; 43% tributary arrival timing) compared inland (7.5% 8.4% overwinter freshwater prior spawning. Salmon, all three multiple phenotypes (Coastal lineage: percentage 27.9% Dam, 28.7% spawning; Interior ocean type: 47.6% 39.6% 77.9% stream 35.3% 9.8% 4.7% spawning). Together, extended our understanding genetic history diversity River, however, much research remains necessary determine causal mechanism this on

Language: Английский

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Loci associated with maturation, migration and appetite control are linked with signals of fine-scale local selection in a large Atlantic salmon population

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 23, 2023

Abstract Insights into the genetic basis of local adaptation and drivers population differentiation improve our understanding evolution maintenance biological diversity. Characterising adaptively important variation also allows more efficient planning conservation management actions. We used a genome-wide SNP array to analyse structure large Atlantic salmon ( Salmo salar ) in interconnected Tornio/Torne Kalix River system Baltic Sea basin, identify genomic signatures fine-scale selection within it. identified signals genotype-environment associations (GEA) especially on chromosome (Chr) 9, including haploblock containing six6 gene other loci that have been earlier suggested be salmonids. detected genome regions genes ecological relevance, such as two known appetite-controlling melanocortin pomca Chr 9 mc4r 14), maturation-associated taar13c-like (on 21). Variation these candidate may potentially reflect differential selective pressures experienced by from different parts river system, regarding traits related e.g. vision, feeding growth, age at maturity and/or migratory timing. This indicates need for strategies consider ecologically these, order protect adaptive diversity wild populations.

Language: Английский

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