An enrichment‐based capture method from nuclear environmental DNA presents new opportunities for population genomics: A case study on the common frog DOI Creative Commons
Stéphanie Manel, Jérémy Gauthier, Laura Benestan

et al.

Methods in Ecology and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: May 12, 2025

Abstract Population genetics is a powerful tool for studying evolutionary processes and informing conservation biology. Traditional approaches typically rely on tissue sampling, which poses challenges in aquatic environments where specimen collection often difficult. Recent efforts to conduct non‐invasive studies using environmental DNA (eDNA) have shown promise but face limitations. For instance, the use of limited number markers or unintended capture fragments from off‐target species can hinder their effectiveness population genetic studies. As proof concept species‐specific genome‐wide nuclear loci detection eDNA, we targeted common frog, Rana temporaria , comparative experimental design. Field eDNA replicates were collected four Alpine ponds, alongside samples 20 live tadpoles per pond. These also placed separate tanks collect under controlled conditions. Frog subset individuals was analysed through ddRAD genotyping subsequently used design custom probes capturing frog individually tissues, modified hyRAD protocol. Although observed substantial heterogeneity data retrieved across replicates, recovered line with those obtained classical ddRAD, proving sufficient investigate variation. We identified total 17,617 single polymorphisms shared individual, pond tank samples, enabling us detect structuring sampling locations, consistent individual‐based estimates. Our study opens new perspectives corroborates potential conducting genomics analyses by using, first time, thousands highlights areas further improvement.

Language: Английский

Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource DOI Creative Commons
Martin Kapun, Joaquin C. B. Nunez, María Bogaerts-Márquez

et al.

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(12), P. 5782 - 5805

Published: Sept. 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.

Language: Английский

Citations

58
Evolutionary gain and loss of a pathological immune response to parasitism DOI
Jesse N. Weber, Natalie C. Steinel, Foen Peng

et al.

Science, Journal Year: 2022, Volume and Issue: 377(6611), P. 1206 - 1211

Published: Sept. 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.

Language: Английский

Citations

41
grenedalf: Population genetic statistics for the next generation of Pool sequencing DOI Creative Commons
Lucas Czech, Jeffrey P. Spence, Moisés Expósito‐Alonso

et al.

Bioinformatics, Journal Year: 2024, Volume and Issue: 40(8)

Published: Aug. 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.

Language: Английский

Citations

10
Mismatch between lab-generated and field-evolved resistance to transgenic Bt crops in Helicoverpa zea DOI Creative Commons
Andrew W. Legan, Carson W. Allan,

Zoe N. Jensen

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(47)

Published: Nov. 6, 2024

Transgenic crops producing crystalline (Cry) proteins from the bacterium

Language: Английский

Citations

10
Multi‐omics analysis identifies a CYP9K1 haplotype conferring pyrethroid resistance in the malaria vector Anopheles funestus in East Africa DOI Creative Commons
Jack Hearn, Carlos S. Djoko Tagne, Sulaiman S. Ibrahim

et al.

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(13), P. 3642 - 3657

Published: May 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.

Language: Английский

Citations

30
Leveraging graphical model techniques to study evolution on phylogenetic networks DOI
Benjamin Teo, Paul Bastide, Cécile Ané

et al.

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 380(1919)

Published: Feb. 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.

Language: Английский

Citations

1
Two distinct host-specialized fungal species cause white-nose disease in bats DOI Creative Commons
Nicola M. Fischer, Imogen Dumville, Benoît Nabholz

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: May 28, 2025

Language: Английский

Citations

1
Opportunities and inherent limits of using environmental DNA for population genetics DOI Creative Commons
Marjorie Couton, Frédérique Viard, Florian Altermatt

et al.

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(5), P. 1048 - 1064

Published: Aug. 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.

Language: Английский

Citations

14
Building integrated plant health surveillance: a proactive research agenda for anticipating and mitigating disease and pest emergence DOI Creative Commons
Samuel Soubeyrand, Arnaud Estoup, Astrid Cruaud

et al.

CABI Agriculture and Bioscience, Journal Year: 2024, Volume and Issue: 5(1)

Published: Aug. 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.

Language: Английский

Citations

6
Population genomics of Drosophila suzukii reveal longitudinal population structure and signals of migrations in and out of the continental United States DOI Creative Commons
Kyle M. Lewald, Antoine Abrieux,

Derek A. Wilson

et al.

G3 Genes Genomes Genetics, Journal Year: 2021, Volume and Issue: 11(12)

Published: Oct. 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.

Language: Английский

Citations

29