Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation

Proceedings of the Royal Society B Biological Sciences, Год журнала: 2019, Номер 286(1900), С. 20182924 - 20182924

Опубликована: Апрель 3, 2019

Species delimitation is a major quest in biology and essential for adequate management of the organismal diversity. A challenging example comprises fish species red snappers Western Atlantic. Red have been traditionally recognized as two separate based on morphology: Lutjanus campechanus (northern snapper) L. purpureus (southern snapper). Recent genetic studies using mitochondrial markers, however, failed to delineate these nominal species, leading current lumping northern southern populations into single ( campechanus). This decision carries broad implications conservation commercially over-exploited across Atlantic are currently listed vulnerable. To address this conflict, we examine genome-wide data collected throughout range species. Population genomics, phylogenetic coalescent analyses favour existence independent evolutionary lineages, result that confirms morphology-based scenario agreement with conventional taxonomy. Despite finding evidence introgression geographically neighbouring South America, our genomic strongly support isolation differentiation suggesting should be treated distinct taxonomic entities.

Язык: Английский

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Biases in demographic modelling affect our understanding of recent divergence

Molecular Biology and Evolution, Год журнала: 2021, Номер unknown

Опубликована: Фев. 10, 2021

Testing among competing demographic models of divergence has become an important component evolutionary research in model and non-model organisms. However, the effect unaccounted events on choice parameter estimation remains largely unexplored. Using extensive simulations, we demonstrate that under realistic scenarios, failure to account for population size (Ne) changes daughter ancestral populations leads strong biases time estimates as well choice. We illustrate these issues reconstructing recent history North Sea Baltic turbots (Scophthalmus maximus) by testing 16 isolation with migration (IM) secondary contact (SC) modeling Ne effects linked selection barrier loci. Failure resulted selecting SC long periods strict times preceding formation Sea. In contrast, accounting suggest (<6 kya) constant gene flow. further show how interpreting genomic landscapes differentiation can help discerning models. For example, turbot data, islands signatures selective sweeps, rather than old resisting introgression. The results have broad implications study highlighting potential unmodeled inference. Tested should aim at representing scenarios target taxa, extreme caution always be exercised when modeling.

Язык: Английский

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Comparative genomics approach to evolutionary process connectivity

Evolutionary Applications, Год журнала: 2020, Номер 13(6), С. 1320 - 1334

Опубликована: Апрель 15, 2020

The influence of species life history traits and historical demography on contemporary connectivity is still poorly understood. However, these factors partly determine the evolutionary responses to anthropogenic landscape alterations. Genetic its outcomes depend a variety spatially dependent processes, such as population structure, local adaptation, genetic admixture, speciation. Over last years, genomic studies have been interrogating processes with increasing resolution, revealing large diversity structured landscapes. In parallel, multispecies meta-analyses usually based low-genome coverage data provided fundamental insights into ecological determinants connectivity, key structure. comparative lack thorough integration macro- micro-evolutionary scales fully realize their potential. Here, I present how genomics framework may provide deeper understanding process connectivity. This relies coupling inference long-term demographic selective an assessment consequences Standardizing this approach across several occupying same should help understand spatial environmental heterogeneity has shaped patterns in different taxa contrasted traits. will argue that reasonable amount genome sequence can be sufficient resolve connect complex histories. Ultimately, implementing varied taxonomic groups expected improve scientific guidelines for conservation management policies.

Язык: Английский

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Extensive standing genetic variation from a small number of founders enables rapid adaptation in Daphnia

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Июль 14, 2021

We lack a thorough understanding of the origin and maintenance standing genetic variation that enables rapid evolutionary responses natural populations. Whole genome sequencing resurrected Daphnia population shows in over 500 genes follows an trajectory parallels pronounced adaptive evolution multiple traits response to predator-driven selection its subsequent relaxation. Genetic carried by only five founding individuals from regional genotype pool is shown suffice at enabling observed evolution. Our results provide insight on how populations can acquire genomic variation, through colonization few genotypes, fuels strong pressures. While these our study involved hundreds genes, we no evidence erosion.

Язык: Английский

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Using natural laboratories to study evolution to global warming: contrasting altitudinal, latitudinal, and urbanization gradients

Current Opinion in Insect Science, Год журнала: 2019, Номер 35, С. 10 - 19

Опубликована: Июнь 8, 2019

Язык: Английский

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Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins

Science Advances, Год журнала: 2021, Номер 7(44)

Опубликована: Окт. 27, 2021

Old genetic variants were key to the ability of bottlenose dolphins repeatedly adapt coastal waters across world.

Язык: Английский

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Reinventing the wheel? Reassessing the roles of gene flow, sorting and convergence in repeated evolution

Molecular Ecology, Год журнала: 2021, Номер 30(17), С. 4162 - 4172

Опубликована: Июнь 16, 2021

Abstract Biologists have long been intrigued by apparently predictable and repetitive evolutionary trajectories inferred across a variety of lineages systems. In recent years, high‐throughput sequencing analyses started to transform our understanding such shifts. While researchers traditionally categorized shifts as either “convergent” or “parallel,” based on relatedness the involved, emerging genomic insights provide an opportunity better describe actual mechanisms at play. A synthesis confirms that convergence is predominant driver evolution among species, whereas repeated sorting standing variation major within species. However, data reveal numerous notable exceptions these expectations, with examples de novo mutations underpinning convergent even very closely related lineages, while processes occurred deeply divergent taxa, sometimes via introgression. number found evidence for both occurring different scales taxa. We suggest relative importance versus depends interplay between gene flow populations, phylogenetic involved.

Язык: Английский

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Butterfly Mimicry Polymorphisms Highlight Phylogenetic Limits of Gene Reuse in the Evolution of Diverse Adaptations

Molecular Biology and Evolution, Год журнала: 2019, Номер 36(12), С. 2842 - 2853

Опубликована: Авг. 27, 2019

Some genes have repeatedly been found to control diverse adaptations in a wide variety of organisms. Such gene reuse reveals not only the diversity phenotypes these unique but also composition developmental networks and genetic routes available taken by organisms during adaptation. However, causes remain unclear. A small number large-effect Mendelian loci huge mimetic butterfly wing color patterns, reasons for their are difficult identify because basis mimicry has primarily studied two systems with correlated factors: female-limited Batesian Papilio swallowtails (Papilionidae) non-sex-limited Müllerian Heliconius longwings (Nymphalidae). Here, we break correlation between phylogenetic relationship sex-limited identifying controlling polymorphism Hypolimnas misippus (Nymphalidae) clytia (Papilionidae). The is controlled genome region containing cortex, classic P supergene numata, pattern variation across Lepidoptera. In contrast, associated locus previously implicated patterning. Thus, although many species converged on cortex its neighboring over 120 My evolution polymorphisms each evolved using different gene. Our results support conclusions that occurs mainly within ∼10 highlight puzzling seemingly complex polymorphisms.

Язык: Английский

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Evolution at two time frames: ancient structural variants involved in post-glacial divergence of the European plaice (Pleuronectes platessa)

Heredity, Год журнала: 2021, Номер 126(4), С. 668 - 683

Опубликована: Фев. 2, 2021

Язык: Английский

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Sex chromosome evolution in beetles

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Янв. 20, 2023

Abstract Beetles are the most species-rich group of animals and harbor diverse karyotypes. Most species have XY sex chromosomes, but X0 determination mechanisms also common in some groups. We generated a whole-chromosome assembly beetle with neo-sex chromosome utilize eleven additional genomes, to reconstruct karyotype evolution across Coleoptera. identify ancestral linkage groups, termed Stevens elements, that share conserved set genes beetles. While X is maintained beetles, we find independent additions autosomes chromosomes. These chromosomes evolve stereotypical properties including dosage compensation, non-random distribution sex-biased expression. thus provide novel model gain better understanding forces driving evolution.

Язык: Английский

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