The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation

Science Advances, Journal Year: 2017, Volume and Issue: 3(8)

Published: Aug. 4, 2017

Accounting for specific alleles can be necessary to prevent the loss of significant biodiversity and ecosystem services.

Language: Английский

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On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes

Journal of Fish Biology, Journal Year: 2016, Volume and Issue: 89(6), P. 2519 - 2556

Published: Sept. 29, 2016

The first goal of this paper was to overview modern approaches local adaptation, with a focus on the use population genomics data detect signals natural selection in fishes. Several mechanisms are discussed that may enhance maintenance genetic variation and evolutionary potential, which have been overlooked should be considered future theoretical development predictive models: prevalence soft sweeps, polygenic basis balancing transient polymorphisms, parallel evolution, as well epigenetic variation. Research fish has provided ample evidence for adaptation at genome level. Pervasive adaptive however, seems almost never involve fixation beneficial alleles. Instead, apparently proceeds most commonly by sweeps entailing shifts frequencies alleles being shared between differentially adapted populations. One obvious factor contributing standing face selective pressures is phenotypic traits often highly polygenic, consequently response derive mostly from allelic co-variances among causative loci rather than pronounced allele frequency changes. Balancing its various forms also play an important role maintaining potential species cope environmental change. A large body literature fishes shows repeated evolution phenotypes ubiquitous phenomenon occur via different solutions, further adding options changing environment. Moreover, paradox emerging recent studies whereby populations reduced effective sizes impoverished diversity can retain their some circumstances. Although more empirical support needed, several suggest could account apparent paradox. Therefore, fully integrated considerations pertaining selection, involving towards improving models predicting world.

Language: Английский

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Understanding and monitoring the consequences of human impacts on intraspecific variation

Evolutionary Applications, Journal Year: 2016, Volume and Issue: 10(2), P. 121 - 139

Published: Oct. 7, 2016

Abstract Intraspecific variation is a major component of biodiversity, yet it has received relatively little attention from governmental and nongovernmental organizations, especially with regard to conservation plans the management wild species. This omission ill‐advised because phenotypic genetic variations within among populations can have dramatic effects on ecological evolutionary processes, including responses environmental change, maintenance species diversity, stability resilience. At same time, changes associated many human activities, such as land use climate often negative impacts intraspecific variation. We argue for need local, regional, global programs monitor suggest that monitoring should include two main strategies: (i) intensive multiple types in selected (ii) broad‐brush modeling representative predicting function population size range extent. Overall, we call collaborative efforts initiate urgently needed

Language: Английский

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Genomic Selection in Aquaculture: Application, Limitations and Opportunities With Special Reference to Marine Shrimp and Pearl Oysters

Frontiers in Genetics, Journal Year: 2019, Volume and Issue: 9

Published: Jan. 23, 2019

Within aquaculture industries, selection based on genomic information (genomic selection) has the profound potential to change genetic improvement programs and production systems. Genomic exploits use of realized relationships among individuals, from genome-wide markers in close linkage disequilibrium with genes biological economic importance. We discuss technical advances, practical requirements commercial applications that have made feasible a range particular focus molluscs (pearl oysters, Pinctada maxima) marine shrimp (Litopeneaus vannamei Penaeus monodon). The low-cost genome sequencing enabled cost-effective genotyping large-scale is value for species without reference or access arrays. highlight pitfalls offer solutions by approach, building appropriate resources undertake first-hand experience. describe capture phenotypes image analysis artificial intelligence through machine learning, as inputs calculation breeding values. application over traditional aquatic offers significant advantages being able accurately predict complex polygenic traits including disease resistance; increasing rates gain; minimizing inbreeding; negating limiting effects genotype environment interactions. Further selection, communal mating rearing systems are highlighted, well presenting rate-limiting steps which impact attaining maximum benefits adopting selection. now at tipping point where can be readily adopted short long-term sustainable profitable industries.

Language: Английский

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Genetic architecture and balancing selection: the life and death of differentiated variants

Molecular Ecology, Journal Year: 2017, Volume and Issue: 26(9), P. 2430 - 2448

Published: Feb. 7, 2017

Abstract Balancing selection describes any form of natural selection, which results in the persistence multiple variants a trait at intermediate frequencies within populations. By offering up snapshot co‐occurring functional and their interactions, systems under balancing can reveal evolutionary mechanisms favouring emergence adaptive variation We here focus on by several for given arise, process typically requiring epistatic mutations. highlight how favour specific features genetic architecture review molecular shaping this architecture. First, affects number loci underlying differentiated traits respective effects. Control one or few favours limiting intergenic recombination, its impact, may sometimes lead to evolution supergenes. Chromosomal rearrangements, particularly inversions, preventing combinations from being dissociated are increasingly noted as such systems. Similarly, due frequency heterozygotes maintained dominance be key property variants. High heterozygosity limited recombination also influence associated load, linked recessive deleterious mutations sheltered. The capture elements locus reinforce polymorphism further promoting heterozygotes. Finally, according recent genomewide scans, balanced might more pervasive than generally thought. stress need both ecological studies characterize operating these

Language: Английский

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Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment

Journal of Fish Biology, Journal Year: 2019, Volume and Issue: 95(3), P. 692 - 718

Published: May 10, 2019

Abstract Brown trout Salmo trutta is endemic to Europe, western Asia and north‐western Africa; it a prominent member of freshwater coastal marine fish faunas. The species shows two resident (river‐resident, lake‐resident) three main facultative migratory life histories (downstream–upstream within river system, fluvial–adfluvial potamodromous; from lake, lacustrine–adfluvial (inlet) or allacustrine (outlet) the sea, anadromous). River‐residency v . migration balance between enhanced feeding thus growth advantages particular habitat costs potentially greater mortality energy expenditure. Fluvial–adfluvial usually has less improvement, but risk, than anadromous, latter vary among catchments as which favoured. Indirect evidence suggests that around 50% variability in S. residency, individuals population, due genetic variance. This dichotomous decision can best be explained by threshold‐trait model quantitative genetics. Thus, an individual's physiological condition ( e.g ., status) regulated environmental factors, genes non‐genetic parental effects, acts cue. magnitude this cue relative genetically predetermined individual threshold, governs whether will migrate sexually mature river‐resident. threshold occurs early and, if choice migrate, second probably follows determining age timing migration. Migration destination (mainstem river, sea) also appears programmed. Decisions ultimate result number subsequent consequential changes such parr–smolt transformation, sexual maturity return Strong associations with one few have been found for most aspects syndrome indirect supports involvement all parts. evolve natural anthropogenic changes, alter survival reproduction. Knowledge determinants various components lags substantially behind Oncorhynchus mykiss other salmonines. Identification markers linked especially migration–residency decision, prerequisite facilitating detailed empirical studies. In order predict effectively, through modelling, effects quantification fitness different traits their heritabilities, across range conditions, urgently required face increasing pace changes.

Language: Английский

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Conservation and the Genomics of Populations

Oxford University Press eBooks, Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 10, 2022

Abstract Loss of biodiversity is among the greatest problems facing world today. Conservation and Genomics Populations gives a comprehensive overview essential background, concepts, tools needed to understand how genetic information can be used conserve species threatened with extinction, manage ecological or commercial importance. New molecular techniques, statistical methods, computer programs, principles, methods are becoming increasingly useful in conservation biological diversity. Using balance data theory, coupled basic applied research examples, this book examines phenotypic variation natural populations, principles mechanisms evolutionary change, interpretation from these conservation. The includes examples plants, animals, microbes wild captive populations. This third edition has been thoroughly revised include advances genomics contains new chapters on population genomics, monitoring, genetics practice, as well sections climate emerging diseases, metagenomics, more. More than one-third references were published after previous edition. Each 24 Appendix end Guest Box written by an expert who provides example presented chapter their own work. for advanced undergraduate graduate students genetics, resource management, biology, professional biologists policy-makers working wildlife habitat management agencies. Much will also interest nonprofessionals curious about role

Language: Английский

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Genome‐wide association and genomic selection in aquaculture

Reviews in Aquaculture, Journal Year: 2022, Volume and Issue: 15(2), P. 645 - 675

Published: Nov. 17, 2022

Abstract Recent advancements in genomic technologies have led to the discovery and application of DNA‐markers [e.g. single nucleotide polymorphisms (SNPs)] for genetic improvement several aquaculture species. The identification specific regions associated with economically important traits, using, example, genome‐wide association studies (GWAS), has allowed incorporation markers linked quantitative trait loci (QTL) into breeding programs through marker‐assisted selection (MAS). However, most traits economic relevance are expected be controlled by many QTLs, each one explaining only a small proportion variation. For under polygenic control, prediction merit animals based on sum effects at positions across entire genome (i.e. estimated values, GEBV, which used what become known as selection), been demonstrated speed rate gain breeding. aim this review was provide an overview development uncovering basis complex accelerating progress species, well providing future perspectives about deployment novel molecular selective coming years.

Language: Английский

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Amplification is the primary mode of gene-by-sex interaction in complex human traits

Cell Genomics, Journal Year: 2023, Volume and Issue: 3(5), P. 100297 - 100297

Published: April 6, 2023

Sex differences in complex traits are suspected to be part due widespread gene-by-sex interactions (GxSex), but empirical evidence has been elusive. Here, we infer the mixture of ways which polygenic effects on physiological covary between males and females. We find that GxSex is pervasive acts primarily through systematic sex magnitude many genetic ("amplification") rather than identity causal variants. Amplification patterns account for trait variance. In some cases, testosterone may mediate amplification. Finally, develop a population-genetic test linking contemporary natural selection sexually antagonistic variants affecting levels. Our results suggest amplification common mode contribute fuel their evolution.

Language: Английский

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Dominance reversals: the resolution of genetic conflict and maintenance of genetic variation

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 291(2018)

Published: March 13, 2024

Beneficial reversals of dominance reduce the costs genetic trade-offs and can enable selection to maintain variation for fitness. are characterized by beneficial allele a given context (e.g. habitat, developmental stage, trait or sex) being dominant in that but recessive where deleterious. This dependence at least partially mitigates fitness consequence heterozygotes carrying one non-beneficial their result balancing maintains alternative alleles. Dominance theoretically plausible supported mounting empirical evidence. Here, we highlight importance as mechanism mitigation conflict review theory evidence them. We identify some areas need further research development outline three methods could facilitate identification antagonistic (dominance ordination, allele-specific expression ATAC-Seq (assay transposase-accessible chromatin with sequencing)). There is ample scope new well reanalysis existing data through lens reversals. A greater focus on this topic will expand our understanding mechanisms resolve whether they variation.

Language: Английский

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