Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

Molecular Biology and Evolution, Год журнала: 2021, Номер 38(12), С. 5782 - 5805

Опубликована: Сен. 1, 2021

Abstract Drosophila melanogaster is a leading model in population genetics and genomics, growing number of whole-genome data sets from natural populations this species have been published over the last years. A major challenge integration disparate sets, often generated using different sequencing technologies bioinformatic pipelines, which hampers our ability to address questions about evolution species. Here we these issues by developing bioinformatics pipeline that maps pooled (Pool-Seq) reads D. hologenome consisting fly symbiont genomes estimates allele frequencies either heuristic (PoolSNP) or probabilistic variant caller (SNAPE-pooled). We use generate largest repository genomic available for date, encompassing 271 previously unpublished samples 100 locations >20 countries on four continents. Several sampled at seasons across multiple This set, call Evolution Space Time (DEST), coupled with sampling environmental metadata. web-based genome browser web portal provide easy access SNP set. further guidelines how Pool-Seq model-based demographic inference. Our aim scalable platform as community resource can be easily extended via future efforts an even more extensive cosmopolitan will enable geneticists analyze spatiotemporal genetic patterns evolutionary dynamics unprecedented detail.

Язык: Английский

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Evolutionary gain and loss of a pathological immune response to parasitism

Science, Год журнала: 2022, Номер 377(6611), С. 1206 - 1211

Опубликована: Сен. 8, 2022

Parasites impose fitness costs on their hosts. Biologists often assume that natural selection favors infection-resistant Yet, when the immune response itself is costly, theory suggests may sometimes favor loss of resistance, which result in alternative stable states where some populations are resistant and others tolerant. Intraspecific variation rarely surveyed a manner tests evolutionary patterns, there few examples adaptive resistance. Here, we show marine threespine stickleback colonized freshwater lakes, they gained resistance to freshwater-associated cestode Schistocephalus solidus. Extensive peritoneal fibrosis inflammation commonly observed phenotype contributes suppression growth viability but also imposes substantial cost fecundity. Combining genetic mapping population genomics, find opposing generates system differences between tolerant populations, consistent with divergent optimization.

Язык: Английский

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grenedalf: Population genetic statistics for the next generation of Pool sequencing

Bioinformatics, Год журнала: 2024, Номер 40(8)

Опубликована: Авг. 1, 2024

Abstract Summary Pool sequencing is an efficient method for capturing genome-wide allele frequencies from multiple individuals, with broad applications such as studying adaptation in Evolve-and-Resequence experiments, monitoring of genetic diversity wild populations, and genotype-to-phenotype mapping. Here, we present grenedalf, a command line tool written C++ that implements common population statistics θ, Tajima’s D, FST sequencing. It orders magnitude faster than current tools, focused on providing usability scalability, while also offering plethora input file formats convenience options. Availability implementation grenedalf published under the GPL-3, freely available at github.com/lczech/grenedalf.

Язык: Английский

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Multi‐omics analysis identifies a CYP9K1 haplotype conferring pyrethroid resistance in the malaria vector Anopheles funestus in East Africa

Molecular Ecology, Год журнала: 2022, Номер 31(13), С. 3642 - 3657

Опубликована: Май 12, 2022

Abstract Metabolic resistance to pyrethroids is a menace the continued effectiveness of malaria vector controls. Its molecular basis complex and varies geographically across Africa. Here, we used multi‐omics approach, followed‐up with functional validation show that directionally selected haplotype cytochrome P450, CYP9K1 major driver in Anopheles funestus . A PoolSeq GWAS using mosquitoes alive dead after permethrin exposure, from Malawi Cameroon, detected candidate genomic regions, but lacked consistency replicates. Targeted sequencing genes several SNPs associated known pyrethroid QTLs. The most significant were P450 CYP304B1 (Cameroon), CYP315A1 (Uganda) ABC transporter gene ABCG4 (Malawi). However, when comparing field resistant laboratory susceptible, locus rp1 around consistently significant, except for Uganda where was markedly significant. In vitro heterologous metabolism assays recombinant revealed it metabolises type II (deltamethrin; 64% depletion) not I (permethrin; 0%), while moderately metabolising DDT (17%). exhibited reduced genetic diversity underlying an extensive selective sweep. Furthermore, glycine alanine (G454A) amino acid change fixed Ugandan other An populations. This study sheds further light on evolution metabolic by implicating more variants can be design field‐applicable markers better track Africa‐wide.

Язык: Английский

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Mismatch between lab-generated and field-evolved resistance to transgenic Bt crops in Helicoverpa zea

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(47)

Опубликована: Ноя. 6, 2024

Transgenic crops producing crystalline (Cry) proteins from the bacterium

Язык: Английский

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Leveraging graphical model techniques to study evolution on phylogenetic networks

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2025, Номер 380(1919)

Опубликована: Фев. 13, 2025

The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be tree, or network if it includes reticulations, representing events such as hybridization admixture. Computing the likelihood data observed at leaves costly size complexity grows. Efficient algorithms exist for trees, but cannot applied to networks. We show that vast array models trait phylogenetic networks reformulated graphical models, which efficient belief propagation exist. provide brief review on general then focus linear Gaussian continuous traits. how techniques exact approximate (but more scalable) gradient calculations, prove novel results parameter inference some models. highlight possible fruitful interactions between methods. For example, approaches have potential greatly reduce computational costs phylogenies with reticulations.

Язык: Английский

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Opportunities and inherent limits of using environmental DNA for population genetics

Environmental DNA, Год журнала: 2023, Номер 5(5), С. 1048 - 1064

Опубликована: Авг. 9, 2023

Abstract Molecular techniques using DNA retrieved from community or environmental samples, in particular (eDNA), are becoming increasingly popular for detecting individual species, assessing biodiversity, and quantifying ecological indices. More recently, eDNA has also been proposed as a template population genetics, several studies have already tested the feasibility of this approach, mostly looking at vertebrate species. Their results along with general opportunities offered by these types “community‐based” such possibility to target multiple species same time, generated great enthusiasm expectations genetics. However, not every aspect genetics can be addressed eDNA‐based data some inherent limitations may challenge its conclusions. Here, we firstly review state current knowledge samples Then, focusing on eDNA, summarize but detail four main use population‐level inferences, namely, (1) difficulty retrieve species‐specific dataset, (2) potential lack correlation between observed true allelic frequencies, (3) loss information multi‐locus genotyping linkage loci, (4) uncertainty about individuals contributing sampled pool (e.g., number, life‐stage, sex). Some might overcome development new technologies models that account specificities eDNA. Others, however, inherent, their effect inferences must thoroughly evaluated. The gaining insights into genetic diversity structure is appealing scientists, conservation managers, other practitioners. Yet, avoid false incorrect it imperative known considered alongside advantages.

Язык: Английский

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Building integrated plant health surveillance: a proactive research agenda for anticipating and mitigating disease and pest emergence

CABI Agriculture and Bioscience, Год журнала: 2024, Номер 5(1)

Опубликована: Авг. 17, 2024

Abstract In an era marked by rapid global changes, the reinforcement and modernization of plant health surveillance systems have become imperative. Sixty-five scientists present here a research agenda for enhanced modernized to anticipate mitigate disease pest emergence. Our approach integrates wide range scientific fields (from life, social, physical engineering sciences) identifies key knowledge gaps, focusing on anticipation, risk assessment, early detection, multi-actor collaboration. The directions we propose are organized around four complementary thematic axes. first axis is anticipation emergence, encompassing innovative forecasting, adaptive potential, effects climatic cropping system changes. second addresses use versatile broad-spectrum tools, including molecular or imaging diagnostics supported artificial intelligence, monitoring generic matrices such as air water. third focuses known pests from new perspectives, i.e., using novel approaches detect species but also anticipating detecting, within species, populations genotypes that pose higher risk. fourth advocates management commons through establishment cooperative long-term data-driven alert information dissemination. We stress importance integrating data multiple sources open science databases metadata, alongside developing methods interpolating extrapolating incomplete data. Finally, advocate Integrated Health Surveillance in One context, favoring tailored solutions problems recognizing interconnected risks plants, humans, animals environment, food insecurity, pesticide residues, environmental pollution alterations ecosystem services.

Язык: Английский

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Population genomics of Drosophila suzukii reveal longitudinal population structure and signals of migrations in and out of the continental United States

G3 Genes Genomes Genetics, Год журнала: 2021, Номер 11(12)

Опубликована: Окт. 2, 2021

Abstract Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native East Asia, D. suzukii infestations started United States a decade ago, occupying wide range climates. To better understand invasion ecology this pest, knowledge past migration events, population structure, and genetic diversity needed. In study, we sequenced whole genomes 237 individual flies collected across continental States, as well several sites Europe, Brazil, identify analyze hundreds thousands markers. We observed strong structure between Western Eastern US populations, but no evidence any different latitudes within suggesting that there are broad-scale adaptations occurring response differences winter detect admixture from Hawaii agreement with previously identified introduction routes inferred microsatellite analysis. also potential signals back which could have important implications for shipping quarantine policies exported agriculture. anticipate large genomic dataset will spur future research into underlying activity development novel control methods agricultural pest.

Язык: Английский

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A cosmopolitan inversion facilitates seasonal adaptation in overwintering Drosophila

Genetics, Год журнала: 2023, Номер 226(2)

Опубликована: Дек. 5, 2023

Abstract Fluctuations in the strength and direction of natural selection through time are a ubiquitous feature life on Earth. One evolutionary outcome such fluctuations is adaptive tracking, wherein populations rapidly adapt from standing genetic variation. In certain circumstances, tracking can lead to long-term maintenance functional polymorphism despite allele frequency change due selection. Although likely common process, we still have limited understanding aspects its architecture relative other forces as drift. Drosophila melanogaster living temperate regions evolve track seasonal an excellent system tackle these gaps knowledge. By sequencing orchard collected across multiple years, characterized genomic signal demography identified that cosmopolitan inversion In(2L)t facilitates shows molecular footprints A meta-analysis phenotypic studies loci within associated with behavior, history, physiology, morphological traits. We identify candidate experimentally link them phenotype. Our work contributes our general fluctuating highlights dynamics contemporary inversions.

Язык: Английский

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