An overview of current population genomics methods for the analysis of whole‐genome resequencing data in eukaryotes

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(23), P. 6036 - 6071

Published: May 19, 2021

Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation agronomy. The constant improvement high-throughput sequencing techniques has facilitated production whole genome data wide range species. Population genomics now provides tools to better integrate selection into historical framework, take account when reconstructing demographic history. However, this come with profusion analytical that can confuse discourage users. Such confusion limits amount information effectively retrieved from complex genomic sets, impairs diffusion most recent fields such as biology. It may also lead redundancy among methods. To address these isssues, we propose an overview more than 100 state-of-the-art methods deal data. We summarize strategies they use infer selection, discuss some their limitations. A website listing available at www.methodspopgen.com.

Language: Английский

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Domestic chicken diversity: Origin, distribution, and adaptation

Animal Genetics, Journal Year: 2021, Volume and Issue: 52(4), P. 385 - 394

Published: May 31, 2021

Summary Chicken is the most numerous among domesticated livestock species. Across cultures, religions, and societies, chicken widely accepted with little or no taboo compared to other domestic animals. Its adaptability diverse environmental conditions demonstrated potential for breeding improvement provide a unique genetic resource addressing challenges of food security in world impacted by climatic change human population growth. Recent studies, shedding new knowledge on genomes, have helped reconstruct its past evolutionary history. Here, we review literature concerning origin, dispersion, adaptation chicken. We highlight role natural selection shaping diversity species few examples gaps that may be focus future research.

Language: Английский

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Extensive introgression and mosaic genomes of Mediterranean endemic lizards

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: May 12, 2021

The Mediterranean basin is a hotspot of biodiversity, fuelled by climatic oscillation and geological change over the past 20 million years. Wall lizards genus Podarcis are among most abundant, diverse, conspicuous fauna. Here, we unravel remarkably entangled evolutionary history wall sequencing genomes 34 major lineages covering 26 species. We demonstrate an early (>11 MYA) separation into two clades centred on Iberian Balkan Peninsulas, island endemics. Diversification within these was pronounced between 6.5-4.0 MYA, period spanning Messinian Salinity Crisis, during which Sea nearly dried up before rapidly refilling. However, genetic exchange has been pervasive feature throughout entire lizards. This resulted in highly reticulated pattern evolution across group, characterised mosaic with contributions from or more parental taxa. These hybrid gave rise to several extant species that endemic islands. endemics may have promoted their extraordinary adaptability striking diversity body size, shape colouration, puzzled biologists for centuries.

Language: Английский

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Rapid adaptive radiation of Darwin’s finches depends on ancestral genetic modules

Science Advances, Journal Year: 2022, Volume and Issue: 8(27)

Published: July 8, 2022

Recent adaptive radiations are models for investigating mechanisms contributing to the evolution of biodiversity. An unresolved question is relative importance new mutations, ancestral variants, and introgressive hybridization phenotypic speciation. Here, we address this issue using Darwin’s finches investigate genomic architecture underlying their diversity. Admixture mapping beak body size in small, medium, large ground revealed 28 loci showing strong genetic differentiation. These represent haplotype blocks with origins predating speciation events during finch radiation. Genes expressed developing overrepresented these regions. Ancestral haplotypes constitute modules selection act as key determinants unusual diversity finches. Such can be critical how species adapt environmental variability change.

Language: Английский

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Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(2)

Published: Jan. 10, 2022

Hybridization and resulting introgression are important processes shaping the tree of life appear to be far more common than previously thought. However, how genome evolution was shaped by various genetic evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data 227 individuals from multiple widespread Populus species characterize their contemporary patterns quantify genomic signatures past introgression. We observe a high frequency confirm that ambiguous in fact F1 hybrids. Seven were identified, which experienced different demographic histories resulted strikingly varied efficacy selection burdens deleterious mutations. Frequent has been found pervasive feature throughout speciation these species. The retained introgressed regions, generally, tend contain reduced load located regions recombination. also find pairs with substantial differences effective population size, inferred have undergone selective sweeps at greater expected frequencies lower suggesting likely higher potential provide beneficial variation for small populations. Our results, therefore, illustrate demography recombination interplayed both positive negative determining hybridization.

Language: Английский

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