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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Evolutionary genomics can improve prediction of species’ responses to climate change

Evolution Letters, Год журнала: 2020, Номер 4(1), С. 4 - 18

Опубликована: Янв. 14, 2020

Abstract Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and transformation entire ecosystems. Many species are challenged by pace GCC because they might not be able to respond fast enough changing biotic abiotic conditions. Species can either shifting their range, or persisting in local habitat. If populations persist, tolerate climatic changes phenotypic plasticity, genetically adapt conditions depending on genetic variability census population size allow for de novo mutations. Otherwise, will experience demographic collapses may go extinct. Current approaches predicting responses begin combine ecological evolutionary information distribution modelling. Including an dimension substantially improve projections which have accounted key processes such as dispersal, adaptive change, demography, interactions. However, eco-evolutionary models require new data methods estimation a species' potential, so far only been available small number model species. To represent global biodiversity, we need devise large-scale collection strategies define ecology potential broad range especially keystone We also standardized replicable modelling that integrate these account when impact survival. Here, discuss different genomic used investigate predict GCC. This serve guidance researchers looking appropriate experimental setup particular system. furthermore highlight future directions moving forward field allocating resources more effectively, implement mitigation measures before extinct ecosystems lose important functions.

Язык: Английский

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A beginner's guide to low‐coverage whole genome sequencing for population genomics

Molecular Ecology, Год журнала: 2021, Номер 30(23), С. 5966 - 5993

Опубликована: Июль 12, 2021

Abstract Low‐coverage whole genome sequencing (lcWGS) has emerged as a powerful and cost‐effective approach for population genomic studies in both model nonmodel species. However, with read depths too low to confidently call individual genotypes, lcWGS requires specialized analysis tools that explicitly account genotype uncertainty. A growing number of such have become available, but it can be difficult get an overview what types analyses performed reliably data, how the distribution effort between samples analysed per‐sample affects inference accuracy. In this introductory guide lcWGS, we first illustrate cost is now comparable RAD‐seq Pool‐seq many systems. We then provide software packages uncertainty different inference. Next, use simulated empirical data assess accuracy allele frequency, genetic diversity, linkage disequilibrium estimation, detection structure, selection scans under strategies. Our results show spreading given amount across more lower depth per sample consistently improves most inference, few notable exceptions. Finally, potential using imputation bolster from species, discuss current limitations future perspectives lcWGS‐based genomics research. With overview, hope make approachable stimulate its broader adoption.

Язык: Английский

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Prospects and limitations of genomic offset in conservation management

Evolutionary Applications, Год журнала: 2021, Номер 14(5), С. 1202 - 1212

Опубликована: Фев. 10, 2021

In nature conservation, there is keen interest in predicting how populations will respond to environmental changes such as climate change. These predictions can help determine whether a population be self-sustaining under future alterations of its habitat or it may require human intervention protection, restoration, assisted migration. An increasingly popular approach this respect the concept genomic offset, which combines and data from different time points and/or locations assess degree possible maladaptation new conditions. Here, we argue that offset holds great potential, but an exploration risks limitations needed use for recommendations conservation After briefly describing concept, list important issues consider (e.g., statistical frameworks, genetic structure, migration, independent evidence) when using developing these methods further. We conclude area development still lacks some features should used combination with other approaches inform measures.

Язык: Английский

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Conservation and the Genomics of Populations

Oxford University Press eBooks, Год журнала: 2022, Номер unknown

Опубликована: Фев. 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

Язык: Английский

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The importance of genomic variation for biodiversity, ecosystems and people

Nature Reviews Genetics, Год журнала: 2020, Номер 22(2), С. 89 - 105

Опубликована: Окт. 16, 2020

Язык: Английский

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Estimating the genome-wide contribution of selection to temporal allele frequency change

Proceedings of the National Academy of Sciences, Год журнала: 2020, Номер 117(34), С. 20672 - 20680

Опубликована: Авг. 12, 2020

Significance A long-standing problem in evolutionary biology is to understand the processes that shape genetic composition of populations. In a population without migration, two change allele frequencies are selection, which increases beneficial alleles and removes deleterious ones, drift, randomly changes as some parents contribute more or fewer next generation. Previous efforts disentangle these have used genomic samples from single time point models how selection affects neighboring sites (linked selection). Here, we use data taken through quantify contributions drift genome-wide frequency changes. We show acts over short timescales three evolve-and-resequence studies has sizable impact.

Язык: Английский

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Characterization of a Y‐specific duplication/insertion of the anti‐Mullerian hormone type II receptor gene based on a chromosome‐scale genome assembly of yellow perch, Perca flavescens

Molecular Ecology Resources, Год журнала: 2020, Номер 20(2), С. 531 - 543

Опубликована: Янв. 6, 2020

Abstract Yellow perch, Perca flavescens , is an ecologically and economically important species native to a large portion of the northern United States southern Canada also promising candidate for aquaculture. However, no yellow perch reference genome has been available facilitate improvements in both fisheries aquaculture management practices. By combining Oxford Nanopore Technologies long‐reads, 10X Genomics Illumina short linked reads chromosome contact map produced with Hi‐C, we generated high‐continuity chromosome‐scale assembly 877.4 Mb. It contains, agreement known diploid count, 24 chromosome‐size scaffolds covering 98.8% complete (N50 = 37.4 Mb, L50 11). We provide first characterization sex determination locus that contains male‐specific duplicate anti‐Mullerian hormone type II receptor gene ( amhr2by ) inserted at proximal end Y (chromosome 9). Using this sex‐specific information, developed simple PCR genotyping assay which accurately differentiates XY genetic males + from XX females − ). Our high‐quality genomic resource future studies on ecology, toxicology, research. In addition, as sex‐determining provides new example recurrent implication transforming growth factor beta pathway fish determination, highlights duplication mechanism emergence master genes.

Язык: Английский

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Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution

Science Advances, Год журнала: 2021, Номер 7(25)

Опубликована: Июнь 18, 2021

We perform an extensive genomic analysis of freshwater adaption in threespine stickleback to predict evolution other species.

Язык: Английский

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Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome

Evolution Letters, Год журнала: 2020, Номер 4(5), С. 430 - 443

Опубликована: Авг. 27, 2020

The study of local adaptation in the presence ongoing gene flow is natural selection action, revealing functional genetic diversity most relevant to contemporary pressures. In addition individual genes, genome-wide architecture can itself evolve enable adaptation. Distributed across a steep thermal gradient along east coast North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree suite traits, and capacity for rapid from standing variation, but we know little about patterns genomic variation species range that this remarkable adaptability. Here, use low-coverage, whole-transcriptome sequencing sampled environmental cline show marked signatures divergent neutral differentiation. 1371 km southern section its distribution have very low differentiation (median FST = 0.006 1.9 million variants), consistent with historical connectivity observations recent migrants. Yet almost 14,000 single nucleotide polymorphisms (SNPs) are nearly fixed (FST > 0.95) alternate alleles. Highly differentiated SNPs cluster into four tight linkage disequilibrium (LD) blocks span hundreds genes several megabases. Variants these LD disproportionately nonsynonymous concentrated enriched multiple functions related known adaptations silversides, including lipid storage, metabolic rate, spawning behavior. Elevated levels absolute divergence demographic modeling suggest maintaining under flow. These findings represent extreme case heterogeneity genome, highlight how shapes continuous populations. Locally adapted alleles may be common features populations distributed gradients, will likely key conserving future responses change.

Язык: Английский

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