Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout

Molecular Ecology, Journal Year: 2022, Volume and Issue: 32(4), P. 800 - 818

Published: Dec. 7, 2022

Abstract Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence climate conditions on body temperature. We investigated in redband trout ( Oncorhynchus mykiss gairdneri ) using genome scans for 547 samples 11 populations across a wide range habitats and thermal gradients interior Columbia River. estimated allele frequencies millions single nucleotide polymorphism loci (SNPs) low‐coverage whole resequencing, used population structure outlier analyses identify regions under divergent selection between populations. Twelve showed signatures adaptation, including two associated with genes known migration developmental timing salmonids GREB1L , ROCK1 SIX6 ). Genotype–environment association indicated that diurnal temperature variation was driver primarily divergence northern extreme subspecies range. also found evidence adaptive differences high‐elevation desert vs. montane at smaller geographical scale. Finally, we vulnerability future change ecological niche modelling genetic offset scenarios. These substantial habitat loss shifts necessary habitats, greatest Our results provide new insight into complexity salmonids, important predictions regarding responses change.

Language: Английский

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Genomic vulnerability of a freshwater salmonid under climate change

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

Published: Oct. 27, 2023

Abstract Understanding the adaptive potential of populations and species is pivotal for minimizing loss biodiversity in this era rapid climate change. Adaptive has been estimated various ways, including based on levels standing genetic variation, presence potentially beneficial alleles, and/or severity environmental Kokanee salmon, non‐migratory ecotype sockeye salmon ( Oncorhynchus nerka ), culturally economically important already impacted by effects To assess its vulnerability moving forward, we integrated analyses genotype‐environment associations, modeling sequence structural genomic variation from 224 whole genomes sampled 22 lakes British Columbia Yukon (Canada). We found that variables extreme temperatures, particularly warmer had most pervasive signature selection genome were strongest predictors putatively both structural. Genomic offset estimates, a measure vulnerability, significantly correlated with higher increases warm further highlighting risk summer heat waves are predicted to increase frequency future. Levels an metric population viability resilience, not offset. Nonetheless, our combined approach highlights importance integrating different sources information data formulate more comprehensive accurate predictions future

Language: Английский

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The integration of whole‐genome resequencing and ecological niche modelling to conserve profiles of local adaptation

Diversity and Distributions, Journal Year: 2024, Volume and Issue: 30(6)

Published: April 11, 2024

Abstract Background Ecological and genomic attributes of populations can provide two orthologous perspectives on the biological profiles associated with local adaptation. The ability organisms to track suitable habitats (ecological adaptability) shift allele frequencies (adaptive potential) are prerequisite for population sustainability. Aims Many contemporary threatened by habitat loss vulnerability) a lack adaptive potential (evolutionary vulnerability). Technical advances new opportunities address these challenges in conservation: Future shifts be predicted ecological niche modelling genetic diversity discerned using genome sequence data. Together, approaches illuminate adaptation profile help identify environmental conditions that should maximize evolutionary fitness. Materials Methods Here, we reviewed primary literature key studies utilize both whole‐genome resequencing (WGR) (ENM) an effort envisage future research directions may benefit conservation efforts. Results We identified ways integrate different approaches, such as ENM‐informed genomics genomics‐informed ENMs, used delineate conserve profiles. Discussion Integrative characteristics, vulnerable subject changes, patterns from geographic analyses. discuss directions, limitations their solutions suggestions collaborative workflows. Conclusion integration WGR ENM is promising continuous advancement. An integrative approach evaluate eco‐evolutionary attributes, at organismal molecular levels,

Language: Английский

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Environmental Variation Influences Genome Evolution in Hispaniolan Trunk Anoles (Anolis distichus)

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

Published: Jan. 14, 2025

Environmental variation often drives evolutionary processes like population differentiation, local adaptation and speciation. We used genome-scale data to investigate the contribution of environmental evolution North Caribbean bark anole (Anolis distichus), a widespread common lizard that exhibits impressive phenotypic across varying habitats on island Hispaniola. obtained new double-digest restriction-associated DNA sequence (ddRADseq) from nearly 200 individuals 53 GIS layers representing range variables. first asked how has contributed genome-wide differentiation found Hispaniola's three major mountain ranges contribute deep divergence patterns migration, some deeply genomically divergent populations occupy significantly different environments, is broadly capable explaining more range-wide genomic than geographic distance alone. then whether specific loci exhibit evidence using genotype-environment association (GEA) methods. initially identified hundreds distributed genome are correlated with one or variables, but ultimately fewer 100 these candidate shared GEA methods applied our entire dataset, only 10 by independent analyses two regional subsets suggesting parallel infrequent. Our study shows abiotic played critical role in diversity phenotypically diverse species.

Language: Английский

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Genomic Insights Into Inbreeding and Adaptive Divergence of Trout Populations to Inform Genetic Rescue

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

Published: March 1, 2025

Genetic rescue, specifically translocation to facilitate gene flow among populations and reduce the effects of inbreeding, is an increasingly used approach in conservation. However, this comes with trade-offs, wherein may fitness when have adaptive differentiation (i.e., outbreeding depression). A better understanding interaction between isolation, divergence key traits, such as life history will help inform genetic rescue efforts. Stream-dwelling salmonids, westslope cutthroat trout (Oncorhynchus lewisi; WCT), are well-suited for examining these trade-offs because they isolated by habitat degradation, exhibit substantial variation traits populations, include many species conservation concern. few genomic studies examined potential inbreeding versus depression salmonids. We > 150,000 SNPs examine coefficients 565 individuals across 25 WCT that differed their isolation status demographic histories. Analyses runs homozygosity revealed several had "flatlined" having extremely low high coefficients. Additionally, we conducted genome scans identify outlier loci could explain differences 10 populations. Genome identified one candidate region influenced maximum length age-1 age-2 growth. limited number suggests be driven genes small effect or phenotypic plasticity. Although should considered, suggest benefit most genetically depauperate

Language: Английский

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Whole-genome resequencing reveals the selection of adaptive evolution during the domestication of pearl oyster Pinctada maxima

Comparative Biochemistry and Physiology Part D Genomics and Proteomics, Journal Year: 2025, Volume and Issue: unknown, P. 101494 - 101494

Published: March 1, 2025

Language: Английский

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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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Comparative analysis of commonly used bioinformatics software based on omics

Gene Reports, Journal Year: 2023, Volume and Issue: 32, P. 101800 - 101800

Published: June 12, 2023

Language: Английский

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Population structure and adaptability analysis of Schizothorax o’connori based on whole-genome resequencing

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Feb. 6, 2024

Abstract Background Schizothorax o’connori is an endemic fish distributed in the upper and lower reaches of Yarlung Zangbo River China. It has experienced a fourth round whole gene replication events good model for exploring genetic differentiation environmental adaptability Qinghai-Tibet Plateau. The uplift Plateau led to changes river system, thereby affecting exchange population between populations. With release genome data, resequencing been widely used evolutionary analysis screening selected genes fish, which can better elucidate basis molecular adaptation mechanisms fish. Therefore, our purpose this study was understand structure adaptive characteristics S. using whole-genome method . Results results showed that 23,602,746 SNPs were identified from seven populations, mostly on chromosomes 2 23. There no significant diversity relatively low. However, Zangga could be separated Bomi, Linzhi, Milin populations cluster analysis. Based historical dynamics population, size ancestral affected by late accelerated Qinghai Tibet Fourth Glacial Age. sites enriched pathways related DNA repair energy metabolism. Conclusion Overall, provides valuable insights into obvious at level upstream downstream River. current distribution pattern are influenced Ice metabolism adapt low temperature strong ultraviolet radiation environment high altitude.

Language: Английский

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Whole-genome resequencing reveals genetic diversity and selection signals in warm temperate and subtropical Sillago sinica populations

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

Published: Sept. 15, 2023

Abstract Background Genetic diversity and heterogeneous genomic signatures in marine fish populations may result from selection pressures driven by the strong effects of environmental change. Nearshore fishes are often exposed to complex environments human activities, especially those with small ranges. However, studies on genetic population signals these species have mostly been based a relatively number markers. As newly recorded Sillaginidae, genetics Sillago sinica fragmented or even absent. Results To address this theoretical gap, we performed whole-genome resequencing 43 S. individuals Dongying (DY), Qingdao (QD) Wenzhou (WZ) obtained 4,878,771 high-quality SNPs. Population analysis showed that was low, but WZ higher than other two populations. Interestingly, three were not strictly clustered within group defined their sampling location an obvious geographic structure signal warm temperate subtropics. With further analysis, warm-temperate exhibited regions related nervous system development, sensory function immune function. subtropical more selective signalling for tolerance stress transduction. Conclusions Genome-wide SNPs provide data support localization The reduction be bottleneck effect. Considering low leads reduced adaptability, conservation efforts monitoring should increased future. Differences between activities changes complexity. This study deepened understanding nearshore provided basis exploring potential mechanisms variation pressures.

Language: Английский

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