Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila

eLife, Journal Year: 2021, Volume and Issue: 10

Published: June 22, 2021

To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures seasonal occurring in parallel among Drosophila melanogaster populations. Specifically, estimated allele frequencies genome-wide from flies sampled early and late the growing season 20 widely dispersed We frequency shifts across North America Europe, demonstrating that is a general phenomenon temperate fly Seasonally fluctuating polymorphisms are enriched large chromosomal inversions, find broad concordance between spatial change. The direction change at seasonally variable can be predicted by weather conditions weeks prior sampling, linking environment genomic response selection. Our results suggest an important evolutionary force affecting patterns genetic variation .

Language: Английский

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Fish tissue accumulation and proteomic response to microcystins is species-dependent

Chemosphere, Journal Year: 2021, Volume and Issue: 287, P. 132028 - 132028

Published: Aug. 27, 2021

Language: Английский

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On the potential for GWAS with phenotypic population means and allele-frequency data (popGWAS)

Peer Community Journal, Journal Year: 2025, Volume and Issue: 5

Published: April 9, 2025

It is vital to understand the genomic basis of differences in ecologically important traits if we are impact global change on biodiversity and enhance our ability for targeted intervention. This study explores potential a novel genome-wide association (GWAS) approach identifying loci underlying quantitative polygenic natural populations, based phenotypic population means allele frequency data as obtained e.g. by PoolSeq approaches. Extensive genetic forward simulations demonstrate that generally effective oligogenic moderately relatively insensitive low heritability. However, applicability limited highly architectures pronounced structure. The required sample size moderate with very good results being already few dozen populations scored. When combined machine learning feature selection, method performs well predicting means. efficiency method, particularly when using pooled sequencing bulk phenotyping, makes GWAS studies more accessible research genomics. Moreover, direct comparison individual GWAS, proposed performed constistently better regard number true positive identified prediction accuracy. Overall, this highlights promise popGWAS dissecting complex populations.

Language: Английский

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The population genetics of convergent adaptation in maize and teosinte is not locally restricted

eLife, Journal Year: 2025, Volume and Issue: 12

Published: Feb. 13, 2025

What is the genetic architecture of local adaptation and what geographic scale over which it operates? We investigated patterns convergent in five sympatric population pairs traditionally cultivated maize its wild relative teosinte ( Zea mays subsp. parviglumis ). found that signatures based on inference adaptive fixations selective sweeps are frequently exclusive to individual populations, more so compared maize. However, for both teosinte, also shared by several often between subspecies. were further able infer among populations most via migration, though sharing standing variation was common. Our analyses suggest has been a continued source beneficial alleles maize, even after domestication, have facilitated moving across landscape. Taken together, our results an intermediate scale, one larger than but smaller species range.

Language: Английский

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Monitoring rapid evolution of plant populations at scale with Pool-Sequencing

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 4, 2022

Abstract The change in allele frequencies within a population over time represents fundamental process of evolution. By monitoring frequencies, we can analyze the effects natural selection and genetic drift on populations. To efficiently track time-resolved change, large experimental or wild populations be sequenced as pools individuals sampled using high-throughput genome sequencing (called Evolve & Resequence approach, E&R). Here, present set experiments hundreds genotypes model plant Arabidopsis thaliana to showcase power this approach study rapid evolution at scale. First, validate that DNA directly extracted from flowers multiple plants -- organs are relatively consistent size easy sample produces comparable results other, more expensive state-of-the-art approaches such sampling individual leaves. Sequencing 25-50 ∼40X coverage recovers genome-wide diverse with accuracy r > 0.95. Secondly, enable analyses evolutionary adaptation E&R highly replicated environments, provide open source tools streamline data curation calculate various statistics two orders magnitude faster than current software. demonstrate usefulness our method, conducted two-year outdoor experiment A. show signals genomic regions. We how these laboratory computational Pool-seq-based methods scaled across many climates.

Language: Английский

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Genomically correlated trait combinations and antagonistic selection contributing to counterintuitive genetic patterns of adaptive diapause divergence in Rhagoletis flies

Journal of Evolutionary Biology, Journal Year: 2021, Volume and Issue: 35(1), P. 146 - 163

Published: Oct. 20, 2021

Adaptation to novel environments can result in unanticipated genomic responses selection. Here, we illustrate how multifarious, correlational selection helps explain a counterintuitive pattern of genetic divergence between the recently derived apple- and ancestral hawthorn-infesting host races Rhagoletis pomonella (Diptera: Tephritidae). The apple race terminates diapause emerges as adults earlier season than hawthorn race, coincide with fruiting phenology their hosts. However, alleles at many loci associated later emergence paradoxically occur higher frequencies sympatric populations compared race. We present evidence that historical over geographically varying environmental gradients across North America generated correlations two life history traits, intensity termination, Moreover, these traits are concentrated regions high linkage disequilibrium (LD). These antagonistic contemporary on local favours increased initial depth earlier, not later, termination. Thus, paradox flies appears due, part, pleiotropy or adult intensity, latter trait strongly selected for by apples. Our results demonstrate understanding multivariate combinations correlative nature selective forces acting them improve predictions concerning adaptive evolution help seemingly patterns diversity nature.

Language: Английский

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Not so local: the population genetics of convergent adaptation in maize and teosinte

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: Sept. 10, 2021

ABSTRACT What is the genetic architecture of local adaptation and what geographic scale over which it operates? We investigated patterns convergent in five sympatric population pairs traditionally cultivated maize its wild relative teosinte ( Zea mays subsp. parviglumis ). found that signatures based on inference adaptive fixations selective sweeps are frequently exclusive to individual populations, more so compared maize. However, for both teosinte, also shared by several often between subspecies. were further able infer among populations most via migration, though sharing standing variation was common. Our analyses suggest has been a continued source beneficial alleles maize, even after domestication, have facilitated moving across landscape. Taken together, our results an intermediate scale, one larger than but smaller species range.

Language: Английский

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On the potential for GWAS with phenotypic population means and allele-frequency data (popGWAS)

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 14, 2024

ABSTRACT It is vital to understand the genomic basis of differences in ecologically important traits if we are impact global change on biodiversity and enhance our ability for targeted intervention. This study explores potential a novel genome-wide association (GWAS) approach identifying loci underlying quantitative polygenic natural populations, based phenotypic population means allele frequency data as obtained e.g. by PoolSeq approaches. Extensive genetic forward simulations demonstrate that generally effective oligogenic moderately relatively insensitive low heritability. However, applicability limited highly architectures pronounced structure. The required sample size moderate with very good results being already few dozen populations scored. When combined machine learning feature selection, method performs well predicting means. efficiency method, particularly when using pooled sequencing bulk phenotyping, makes GWAS studies more accessible research genomics. Moreover, direct comparison individual GWAS, proposed performed constistently better regard number true positive identified prediction accuracy. Overall, this highlights promise popGWAS dissecting complex populations.

Language: Английский

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Population genomic time series data of a natural population suggests adaptive tracking of environmental changes

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2020, Volume and Issue: unknown

Published: June 16, 2020

Abstract Natural populations are constantly exposed to fluctuating environmental changes that negatively affect their fitness in unpredictable ways. While theoretical models show the possibility of counteracting these through rapid evolutionary adaptations, there have been few empirical studies demonstrating such adaptive tracking natural populations. Here, we analysed data, fitness-related phenotyping and genomic time-series data sampled over three years from a Chironomus riparius (Diptera, Insecta) population address this question. We population’s environment varied significantly on time scale sampling many selectively relevant dimensions, independently each other. Similarly, phenotypic components evolved same temporal (mean 0.32 Haldanes), likewise independent The allele frequencies 367,446 SNPs across genome showed evidence positive selection. Using correlation spatially coherent frequency revealed 35,574 haplotypes with more than one selected SNP. mean selection coefficient for was 0.30 (s.d. = 0.68). clustered 46 different patterns, indicating concerted, evolution polygenic traits. Nine patterns were strongly correlated measured variables. Thus, our results suggest C. tracks change adaptation dimensions. This is further pervasive at level ecological scales may not differ all, least some organisms.

Language: Английский

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Genomic Responses to Climate Change: Making the Most of the Drosophila Model

Frontiers in Genetics, Journal Year: 2021, Volume and Issue: 12

Published: July 13, 2021

It is pressing to understand how animal populations evolve in response climate change. We argue that new sequencing technologies and the use of historical samples are opening unprecedented opportunities investigate genome-wide responses changing environments. However, there important challenges interpreting emerging findings. First, it essential differentiate genetic adaptation from phenotypic plasticity. Second, extremely difficult map genotype, phenotype, fitness. Third, neutral demographic processes natural selection affect variation similar ways. Drosophila melanogaster , a classical model organism with decades research, uniquely suited overcome most these challenges. In near future, long-term time series datasets D. will provide exciting study recent change lay groundwork for related research non-model systems.

Language: Английский

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