A cosmopolitan inversion facilitates seasonal adaptation in overwintering Drosophila

Genetics, Journal Year: 2023, Volume and Issue: 226(2)

Published: Dec. 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.

Language: Английский

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From sub-Saharan Africa to China: Evolutionary history and adaptation of Drosophila melanogaster revealed by population genomics

Science Advances, Journal Year: 2024, Volume and Issue: 10(16)

Published: April 17, 2024

is a widely used model organism for studying environmental adaptation. However, the genetic diversity of populations in Asia poorly understood, leaving notable gap our knowledge global evolution and adaptation this species. We sequenced genomes 292

Language: Английский

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Inferring Signatures of Positive Selection in Whole-Genome Sequencing Data: An Overview of Haplotype-Based Methods

Genes, Journal Year: 2022, Volume and Issue: 13(5), P. 926 - 926

Published: May 22, 2022

Signatures of positive selection in the genome are a characteristic mark adaptation that can reveal an ongoing, recent, or ancient response to environmental change throughout evolution population. New sources food, climate conditions, and exposure pathogens only some possible selective pressure, rise advantageous genetic variants is crucial determinant survival reproduction. In this context, ability detect these signatures may pinpoint responsible for significant gene regulation, expression, protein synthesis, structure, function. This review focuses on statistical methods take advantage linkage disequilibrium haplotype determination whole-genome sequencing data, showing they emerge from different descriptions same underlying event. Moreover, considerations provided around application statistics species, their suitability DNA, usefulness discovering under biomedicine public health evolutionary medicine framework.

Language: Английский

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A Novel Approach Utilizing Domain Adversarial Neural Networks for the Detection and Classification of Selective Sweeps

Advanced Science, Journal Year: 2024, Volume and Issue: 11(14)

Published: Feb. 2, 2024

Abstract The identification and classification of selective sweeps are great significance for improving the understanding biological evolution exploring opportunities precision medicine genetic improvement. Here, a domain adaptation sweep detection (DASDC) method is presented to balance alignment two domains performance through domain‐adversarial neural network its adversarial learning modules. DASDC effectively addresses issue mismatch between training data real genomic in deep models, leading significant improvement generalization capability, prediction robustness, accuracy. demonstrates improved compared existing methods excels performance, particularly scenarios where there application data. successful implementation three distinct species highlights potential as useful tool identifying crucial functional genes investigating adaptive evolutionary mechanisms, with increasing availability

Language: Английский

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Dominance shifts increase the likelihood of soft selective sweeps

Evolution, Journal Year: 2022, Volume and Issue: 76(5), P. 966 - 984

Published: Feb. 25, 2022

Genetic models of adaptation to a new environment have typically assumed that the alleles involved maintain constant fitness dominance across old and environments. However, theories suggest this should often not be case. Instead, frequently shift from recessive deleterious in dominant beneficial environment. Here, we study consequences these expected shifts for genetics We find increase likelihood occurs standing variation, multiple variation are (a soft selective sweep). Furthermore, haplotypic diversity sweeps, rendering sweeps more detectable small genomic samples. In cases where an environmental change threatens viability population, show newly evolutionary rescue number involved. Finally, apply our results well‐studied case environment: evolution pesticide resistance at Ace locus Drosophila melanogaster. that, under reasonable demographic assumptions, resistant causes most frequent outcome case, with primary source being onset use, rather than recurrent mutation thereafter.

Language: Английский

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Rapid evolutionary change, constraints and the maintenance of polymorphism in natural populations of Drosophila melanogaster

Molecular Ecology, Journal Year: 2023, Volume and Issue: 33(10)

Published: May 24, 2023

Abstract Allele frequencies can shift rapidly within natural populations. Under certain conditions, repeated rapid allele frequency shifts lead to the long‐term maintenance of polymorphism. In recent years, studies model insect Drosophila melanogaster have suggested that this phenomenon is more common than previously believed and often driven by some form balancing selection, such as temporally fluctuating or sexually antagonistic selection. Here we discuss general insights into evolutionary change revealed large‐scale population genomic studies, well functional mechanistic causes adaptation uncovered single‐gene studies. As an example latter, consider a regulatory polymorphism D. fezzik gene. Polymorphism at site has been maintained intermediate over extended period time. Regular observations from single 7 years significant differences in derived its variance across collections between sexes. These patterns are highly unlikely arise genetic drift alone action selection individually. Instead, joint best explain observed shifts. Temporal those reviewed here further our understanding how changes improve knowledge forces driving limiting nature.

Language: Английский

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Reduction of egg reappearance period of cyathostomins in naturally infected horses after increasing doses of ivermectin in Brazil: a grim picture for sustainable parasite control

Revista Brasileira de Parasitologia Veterinária/Brazilian Journal of Veterinary Parasitology, Journal Year: 2024, Volume and Issue: 33(3)

Published: Jan. 1, 2024

Abstract Cyathostomins are the largest group of parasites in horses that can be controlled by ivermectin (IVM). This study aimed to run a four-dose titration trial IVM 28 naturally infected Thoroughbred yearlings. The local Strongyle population had been recorded resistant (200 µg/kg). parasite fecal egg count (FEC) was performed investigate reappearance period (ERP) two and five weeks (w2pt w5pt) after treatment. FEC > 1000 on day zero for all groups. Although 100% reduction reported at w2pt concentrations, w5pt revealed < 83% efficacy. reports ERP using label dose as well 300, 400 µg/kg (double dose) IVM. protocol allowed significantly suppress although not eliminating adult worms, failing guarantee an extension its protection over 8 weeks. Moreover, possibly means infection cleared, worms reestablished laying. We raised possibility withdrawing control programs when drug has less than 80% w5pt.

Language: Английский

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Selective sweeps linked to the colonization of novel habitats and climatic changes in a wild tomato species

New Phytologist, Journal Year: 2022, Volume and Issue: 237(5), P. 1908 - 1921

Published: Nov. 24, 2022

Positive selection is the driving force underpinning local adaptation and leaves footprints of selective sweeps on underlying major genes. Quantifying timing revealing genetic bases in plant species occurring steep varying environmental gradients are crucial to predict a species' ability colonize new niches. We use whole-genome sequence data from six populations across three different habitats wild tomato Solanum chilense infer past demographic history search for genes under strong positive selection. then correlate current climatic projections with history, allele frequencies, age events distribution shifts. Several occur at regulatory networks involved root-hair development low altitude response photoperiod vernalization high-altitude populations. These appear concerted fashion given gene network particular periods substantial change. Using unique combination genome scans modelling data, we quantify likely semiarid habitats.

Language: Английский

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Population genetic concerns related to the interpretation of empirical outliers and the neglect of common evolutionary processes

Heredity, Journal Year: 2023, Volume and Issue: 130(3), P. 109 - 110

Published: Feb. 24, 2023

Language: Английский

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Genomic Signatures of a Major Adaptive Event in the Pathogenic Fungus Melampsora larici-populina

Genome Biology and Evolution, Journal Year: 2021, Volume and Issue: 14(1)

Published: Dec. 11, 2021

Abstract The recent availability of genome-wide sequencing techniques has allowed systematic screening for molecular signatures adaptation, including in nonmodel organisms. Host–pathogen interactions constitute good models due to the strong selective pressures that they entail. We focused on an adaptive event which affected poplar rust fungus Melampsora larici-populina when it overcame a resistance gene borne by its host, cultivated poplar. Based 76 virulent and avirulent isolates framing narrowly estimated date event, we examined selection. Using array genome scan methods based different features nucleotide diversity, detected single locus exhibiting consistent pattern suggestive sweep individuals (excess differentiation between samples, linkage disequilibrium, genotype–phenotype statistical association, long-range haplotypes). Our study pinpoints further amino acid replacement may have event. Although our samples are nearly contemporary sweep, does not seem diversity than immediate vicinity causal locus, can be explained soft (where selection acts standing variation) impact recombination mitigating Therefore, seems properties life cycle M. larici-populina, entails both high genetic outbreeding, facilitated adaptation.

Language: Английский

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