A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation

Trends in Ecology & Evolution, Journal Year: 2020, Volume and Issue: 35(7), P. 561 - 572

Published: April 6, 2020

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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Genomics for monitoring and understanding species responses to global climate change

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 25(3), P. 165 - 183

Published: Oct. 20, 2023

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish species' potential adapt future environments. Understanding monitoring how organisms respond human-driven change is therefore major priority for conservation rapidly changing environment. Recent developments genomic, transcriptomic epigenomic technologies enabling unprecedented insights into evolutionary processes molecular bases adaptation. This Review summarizes methods that apply integrate omics tools experimentally investigate, monitor predict species communities wild cope with change, which by genetically adapting new conditions, through range shifts or phenotypic plasticity. We identify advantages limitations each method discuss research avenues would improve our understanding responses highlighting need holistic, multi-omics approaches ecosystem during Species can shifting their these responses.

Language: Английский

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The importance of genomic variation for biodiversity, ecosystems and people

Nature Reviews Genetics, Journal Year: 2020, Volume and Issue: 22(2), P. 89 - 105

Published: Oct. 16, 2020

Language: Английский

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Discovery and population genomics of structural variation in a songbird genus

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: July 7, 2020

Abstract Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover genome-wide spectrum intra- and interspecific SV segregating in natural populations seven songbird species genus Corvus . Combining short-read ( N = 127) long-read re-sequencing 31), as well optical mapping 16), apply both assembly- read approaches to detect characterize a total 220,452 insertions, deletions inversions. We exploit sampling across wide phylogenetic timescales validate genotypes assess contribution evolutionary processes avian model incipient speciation. reveal young (~530,000 years) cis -acting 2.25-kb LTR retrotransposon insertion reducing expression NDP gene with consequences premating isolation. Our results attest wealth significance highlight need reliable genotyping.

Language: Английский

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Balancing selection via life-history trade-offs maintains an inversion polymorphism in a seaweed fly

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Feb. 3, 2020

Abstract How natural diversity is maintained an evolutionary puzzle. Genetic variation can be eroded by drift and directional selection but some polymorphisms persist for long time periods, implicating a role balancing selection. Here, we investigate the maintenance of chromosomal inversion polymorphism in seaweed fly Coelopa frigida . Using experimental evolution quantifying fitness, show that underlies life-history trade-off, whereby each haplotype has opposing effects on larval survival adult reproduction. Numerical simulations confirm such antagonistic pleiotropy maintain polymorphism. Our results also highlight importance sex-specific effects, dominance environmental heterogeneity, whose interaction enhances through pleiotropy. Overall, our findings directly demonstrate how overdominance sexual antagonism emerge from inviting reconsideration as key part multi-headed processes enable persistence genetic variation.

Language: Английский

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Current status of structural variation studies in plants

Plant Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19(11), P. 2153 - 2163

Published: June 8, 2021

Structural variations (SVs) including gene presence/absence and copy number are a common feature of genomes in plants and, together with single nucleotide polymorphisms epigenetic differences, responsible for the heritable phenotypic diversity observed within between species. Understanding contribution SVs to plant variation is important breeders assist producing improved varieties. The low resolution early genetic technologies inefficient methods have previously limited our understanding plants. However, rapid expansion genomic technologies, it possible assess an ever-greater accuracy. Here, we review current status SV studies plants, examine roles that play traits, compare future challenges studies.

Language: Английский

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The structural variation landscape in 492 Atlantic salmon genomes

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Oct. 14, 2020

Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type hence poorly characterized in most species. We present an approach for reliable SV discovery non-model species using whole genome sequencing report 15,483 high-confidence SVs 492 Atlantic salmon (Salmo salar L.) sampled from broad phylogeographic distribution. These recover population structure with high resolution, include active DNA transposon, widely affect functional features, overlap more duplicated genes retained ancestral salmonid autotetraploidization event than expected. Changes allele frequency between wild farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked neurological disorders humans. This study offers novel insights into the role evolution architecture domestication traits, along resources supporting

Language: Английский

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Deleterious mutation accumulation and the long-term fate of chromosomal inversions

PLoS Genetics, Journal Year: 2021, Volume and Issue: 17(3), P. e1009411 - e1009411

Published: March 4, 2021

Chromosomal inversions contribute widely to adaptation and speciation, yet they present a unique evolutionary puzzle as both their allelic content frequency evolve in feedback loop. In this simulation study, we quantified the role of determining long-term fate inversion. Recessive deleterious mutations accumulated on arrangements with most them being private given arrangement. This led increasing overdominance, allowing for maintenance inversion polymorphism generating strong non-adaptive divergence between arrangements. The accumulation was mitigated by gene conversion but nevertheless fitness decline at least one homokaryotype under all considered conditions. Surprisingly, degradation could be permanently halted branching an arrangement into multiple highly divergent haplotypes. Our results highlight dynamic features showing how evolution can play major

Language: Английский

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Copy number variants outperform SNPs to reveal genotype–temperature association in a marine species

Molecular Ecology, Journal Year: 2020, Volume and Issue: 29(24), P. 4765 - 4782

Published: Aug. 17, 2020

Abstract Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. To date, our knowledge evolution has largely been acquired by means single nucleotide polymorphism (SNPs) analyses. Until recently, the adaptive role structural (SVs) particularly that CNVs overlooked wild populations, partly due to their challenging identification. Here, we document usefulness Rapture, derived reduced‐representation shotgun sequencing approach, detect investigate copy alongside SNPs American lobster ( Homarus americanus ) populations. We conducted comparative study examine potential local adaptation 1,141 lobsters from 21 sampling sites within southern Gulf St. Lawrence, which experiences highest yearly thermal variance Canadian marine coastal waters. Our results demonstrated account for higher genetic differentiation than SNP markers. Contrary SNPs, no significant genetic–environment association was found, 48 CNV candidates were significantly associated with annual sea surface temperature, leading clustering locations despite geographic separation. Altogether, provide strong empirical case putatively contribute species unveil stronger spatial signal population structure SNPs. provides nonmodel highlights importance considering enhance understanding ecological evolutionary processes shaping structure.

Language: Английский

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