A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation

Trends in Ecology & Evolution, Год журнала: 2020, Номер 35(7), С. 561 - 572

Опубликована: Апрель 6, 2020

Язык: Английский

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Redundancy analysis: A Swiss Army Knife for landscape genomics

Methods in Ecology and Evolution, Год журнала: 2021, Номер 12(12), С. 2298 - 2309

Опубликована: Сен. 20, 2021

Abstract Landscape genomics identifies how spatial and environmental factors structure the amount distribution of genetic variation among populations. genomic analyses have been applied across diverse taxonomic groups ecological settings, are increasingly used to analyse datasets composed large numbers markers multiple predictors. It is in this context that multivariate methods show their strengths. Redundancy analysis (RDA) a constrained ordination that, landscape framework, models linear relationships environment predictors variation, effectively identifying covarying allele frequencies associated with environment. RDA can be at both individual population levels, include covariates account for confounding directly infer genotype–environment associations on landscape. The modelling response explanatory variables allows accommodate complexity found nature, producing powerful efficient tool genomics. In review, we outline uses genomics, including variable selection, variance partitioning, associations, calculation adaptive indices offset. To illustrate these applications, use published dataset lodgepole pine includes genomic, phenotypic data. We provide an introduction statistical basis RDA, tutorial its interpretation discuss limitations guidelines avoid misuse. This review comprehensive resource community improve understanding as encourage appropriate applications. truly Swiss Army Knife genomics: multipurpose, adaptable versatile approach identifying, evaluating forecasting between variation.

Язык: Английский

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Insights into invasive species from whole‐genome resequencing

Molecular Ecology, Год журнала: 2021, Номер 30(23), С. 6289 - 6308

Опубликована: Май 27, 2021

Studies of invasive species can simultaneously inform management strategies and quantify rapid evolution in the wild. The role genomics invasion science is increasingly recognised, growing availability reference genomes for paving way whole-genome resequencing studies a wide range systems. Here, we survey literature to assess application data biology. For some applications, such as reconstruction routes time space, sequencing whole genome many individuals increase accuracy existing methods. In other cases, population genomic approaches haplotype analysis permit entirely new questions be addressed technologies applied. To date has only been used handful systems, but these have confirmed importance processes balancing selection hybridization allowing reuse adaptations rapidly overcome challenges foreign ecosystem. use does not constitute paradigm shift per se, by leveraging theory, tools, technologies, provide unprecedented insight into basic applied aspects science.

Язык: Английский

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The Evolutionary Consequences of Dams and Other Barriers for Riverine Fishes

BioScience, Год журнала: 2022, Номер 72(5), С. 431 - 448

Опубликована: Янв. 27, 2022

Abstract Dams and other anthropogenic barriers have caused global ecological hydrological upheaval in the blink of geological eye. In present article, we synthesize 307 studies a systematic review contemporary evolution following reduced connectivity habitat alteration on freshwater fishes. Genetic diversity loss was more commonly observed for small populations impounded patches many generations behind low-passability barriers. Studies show that impoundments can cause rapid adaptive migration timing, behavior, life history, temperature tolerance, morphology, as well reduce phenotypic variance, which alter potential roles. Fish passage structures restore migratory but also create artificial selection pressures body size migration. The accelerating pace dam removals paucity data fishes than salmonids, vertebrates, invertebrates, tropical southern hemisphere organisms highlights urgent need evolutionary effects dams.

Язык: Английский

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Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июль 8, 2024

Abstract Copy number variation (CNV) can drive rapid evolution in changing environments. In microbial pathogens, such adaptation is a key factor underpinning epidemics and colonization of new niches. However, the genomic determinants remain poorly understood. Here, we systematically investigate CNVs large genome sequencing dataset spanning worldwide collection 1104 genomes from major wheat pathogen Zymoseptoria tritici . We found overall strong purifying selection acting on most CNVs. Genomic defense mechanisms likely accelerated gene loss over episodes continental colonization. Local along climatic gradients was facilitated by affecting secondary metabolite production general. One strongest loci for highly conserved NAD-dependent Sirtuin family. The CNV locus localizes to an ~68-kb Starship mobile element unique species carrying genes expressed during plant infection. has lost ability transpose, demonstrating how ongoing domestication cargo-carrying selfish elements contribute selectable within populations. Our work highlights standing copy numbers at global scale be driving metabolic species.

Язык: Английский

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Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations

Evolutionary Applications, Год журнала: 2024, Номер 17(3)

Опубликована: Март 1, 2024

Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and known to contribute evolutionary processes in various organisms. However, they inherently difficult detect genotype from readily available short-read sequencing data, therefore remain poorly documented wild populations. Salmonid species displaying strong interpopulation variability both life history traits habitat characteristics, such Atlantic salmon (

Язык: Английский

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Copy number variation contributes to parallel local adaptation in an invasive plant

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(10)

Опубликована: Март 3, 2025

Adaptation is a critical determinant of the diversification, persistence, and geographic range limits species. Yet genetic basis adaptation often unknown potentially underpinned by wide mutational types-from single nucleotide changes to large-scale alterations chromosome structure. Copy number variation (CNV) thought be an important source adaptive variation, as indicated decades candidate gene studies that point CNVs underlying rapid strong selective pressures. Nevertheless, population-genomic face unique logistical challenges not encountered other forms variation. Consequently, few have systematically investigated contributions at genome-wide scale. We present analysis CNV contributing invasive weed, Ambrosia artemisiifolia. show clear signatures parallel local between North American (native) European (invaded) ranges, implying widespread reuse during shared heterogeneous patterns selection. used principal component (PCA) genotype regions in whole-genome sequences samples collected over last two centuries. identified 16 large up 11.85 megabases length, eight which signals evolutionary change, with pronounced frequency shifts historic modern populations. Our results provide compelling evidence underlies contemporary timescales natural

Язык: Английский

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Copy number variations in response to chronic pollution: Basilichthys microlepidotus in central Chile

Neotropical Ichthyology, Год журнала: 2025, Номер 23(1)

Опубликована: Янв. 1, 2025

Abstract Pollution, driven by land use, industrial operations, and urban growth, significantly affects biodiversity in freshwater ecosystems. Studies have shown how organisms adapt to pollution, observing mechanisms like directional selection, balancing introgression. They focused on genetic changes populations exposed particularly single nucleotide polymorphisms (SNPs) copy number variants (CNVs) DNA. CNVs been linked environmental disturbances. This study investigates Basilichthys microlepidotus Chile’s polluted Maipo River watershed. were associated with pollution chronically populations, though population structure was weak, making it difficult distinguish between reference contaminated sites. However, outliers related functions consistently identified. Eleven CNV loci correlated three historical physical variables electroconductivity, pH, total dissolved solids accounting for 5% of all detected loci. These markers revealed a subtle but significant structure, linking gene expression SNPs potentially affected pollution-driven selection. The effects these are unknown, further analysis is required unveil them, they could help contamination.

Язык: Английский

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Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern

Molecular Ecology, Год журнала: 2021, Номер 30(23), С. 5949 - 5965

Опубликована: Авг. 23, 2021

Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and content structure of chromosomes. As a result, SVs significant source functional genomic variation, is, variation at regions underpinning phenotype differences, can have effects on individual population fitness. While there increasing opportunities to investigate in threatened species via single nucleotide polymorphism (SNP) data sets, remain understudied despite their potential influence fitness traits conservation interest. In this future-focused Opinion, we contend characterizing offers genomics community an exciting opportunity complement SNP-based approaches enhance recovery. We also leverage existing literature-predominantly human health, agriculture ecoevolutionary biology-to identify for readily consider how integrating these into toolbox may transform way manage some world's most species.

Язык: Английский

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The role of structural variants in pest adaptation and genome evolution of the Colorado potato beetle, Leptinotarsa decemlineata (Say)

Molecular Ecology, Год журнала: 2023, Номер 32(6), С. 1425 - 1440

Опубликована: Янв. 2, 2023

Structural variation has been associated with genetic diversity and adaptation. Despite these observations, it is not clear what their relative importance for evolution, especially in rapidly adapting species. Here, we examine the significance of structural polymorphisms pesticide resistance evolution agricultural super-pest, Colorado potato beetle, Leptinotarsa decemlineata. By employing a parent offspring trio sequencing procedure, develop highly contiguous reference genomes to characterize variation. These updated assemblies represent >100-fold improvement contiguity include derived pest ancestral nonpest individuals. We identify >200,000 variations, which appear be nonrandomly distributed across genome as they co-occur transposable elements genes. variations intersect exons large proportion gene annotations (~20%) that are insecticide (including cytochrome P450s), development, transcription. To understand role play adaptation, measure allele frequencies among an additional 57 individuals using whole resequencing data, represents populations North America. Incorporating multiple independent tests detect signature natural selection SNP 14 genes probably under positive selection, SNPs elevated frequency within lineages. Among these, three based on previous research. One genes, CYP4g15, coinduced during exposure glycosyltransferase-13, duplicated enclosed variant adjacent CYP4g15 genic region. results demonstrate genomic feature describe species history, diversity,

Язык: Английский

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