Demographic analyses of a new sample of haploid genomes from a Swedish population of Drosophila melanogaster

Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)

Published: Dec. 29, 2020

Abstract European and African natural populations of Drosophila melanogaster have been the focus several studies aiming at inferring demographic adaptive processes based on genetic variation data. However, in these analyses little attention has given to gene flow between samples. Here we present a dataset consisting 14 fully sequenced haploid genomes sampled from population northern species range (Umeå, Sweden). We co-analyzed this new data with an compare likelihood competing scenarios for show that improves fit models

Language: Английский

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Direct observation of adaptive tracking on ecological timescales inDrosophila

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

Published: April 28, 2021

Abstract Direct observation of evolution in response to natural environmental change can resolve fundamental questions about adaptation including its pace, temporal dynamics, and underlying phenotypic genomic architecture. We tracked fitness-associated phenotypes allele frequencies genome-wide ten replicate field populations Drosophila melanogaster over generations from summer late fall. Adaptation was evident each sampling interval (1-4 generations) with exceptionally rapid large frequency shifts at many independent loci. The direction basis the adaptive shifted repeatedly time, consistent action strong rapidly fluctuating selection. Overall, we find clear evidence tracking occurring contemporaneously change, demonstrating temporally dynamic nature adaptation. One sentence summary Rapid drives continuous polygenic adaptation, dynamism

Language: Английский

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Genomic analysis of EuropeanDrosophila melanogasterpopulations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2018, Volume and Issue: unknown

Published: May 3, 2018

Abstract Genetic variation is the fuel of evolution, with standing genetic especially important for short-term evolution and local adaptation. To date, studies spatio-temporal patterns in natural populations have been challenging, as comprehensive sampling logistically difficult, sequencing entire costly. Here, we address these issues using a collaborative approach, 48 pooled population samples from 32 locations, perform first continent-wide genomic analysis European Drosophila melanogaster . Our analyses uncover longitudinal structure, provide evidence selective sweeps, identify candidate genes climate adaptation, document clines chromosomal inversion transposable element frequencies. We also characterise among composition fly microbiome, five new DNA viruses our samples.

Language: Английский

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Predicting evolutionary change at the DNA level in a natural Mimulus population

PLoS Genetics, Journal Year: 2021, Volume and Issue: 17(1), P. e1008945 - e1008945

Published: Jan. 13, 2021

Evolution by natural selection occurs when the frequencies of genetic variants change because individuals differ in Darwinian fitness components such as survival or reproductive success. Differential has been demonstrated field studies many organisms, but it remains unclear how well we can quantitatively predict allele frequency changes from measurements. Here, characterize on millions Single Nucleotide Polymorphisms (SNPs) across genome annual plant Mimulus guttatus . We use estimates to calibrate population models that effectively into next generation. Hundreds SNPs experienced “male selection” 2013 with one at each SNP elevated among successful male gametes relative entire adults. In following generation, these consistently shifted predicted direction. A second year study revealed had effects both viability and success pervasive trade-offs between components. favored were, average, detrimental survival. These (antagonistic pleiotropy temporal fluctuations fitness) may be essential long-term maintenance alleles. Despite challenges measuring wild, strong correlation observed suggests have a much greater role play forward-time prediction evolutionary change.

Language: Английский

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Evolutionary insights from large scale resequencing datasets in Drosophila melanogaster

Current Opinion in Insect Science, Journal Year: 2018, Volume and Issue: 31, P. 70 - 76

Published: Nov. 20, 2018

Language: Английский

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Microbiome composition shapes rapid genomic adaptation ofDrosophila melanogaster

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2019, Volume and Issue: unknown

Published: May 9, 2019

Abstract Population genomic data has revealed patterns of genetic variation associated with adaptation in many taxa. Yet understanding the adaptive process that drives such is challenging - it requires disentangling ecological agents selection, determining relevant timescales over which evolution occurs, and elucidating architecture adaptation. Doing so for hosts to their microbiome particular interest growing recognition importance complexity host-microbe interactions. Here, we track pace an experimental manipulation replicate populations Drosophila melanogaster field mesocosms. Manipulation altered population dynamics increased divergence between treatments allele frequencies genome-wide, regions showing strong found on all chromosomes. Moreover, at divergent loci previously across natural populations, more common fly experimentally enriched a certain microbial group was also high relative abundance group. These results suggest microbiomes may be agent selection shapes pattern and, broadly, single factor within complex environment can drive rapid, polygenic short timescales. Significance statement Natural However, there little factors are capable driving rapid how this alters genome. Here combine experiment from latitudinal gradient assess whether composition host populations. We find differences cause including genes local observed concordance terms direction frequency change, suggesting wild.

Language: Английский

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A map of climate change-driven natural selection in Arabidopsis thaliana

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2018, Volume and Issue: unknown

Published: May 14, 2018

Through the lens of evolution, climate change is an agent natural selection that forces populations to and adapt, or face extinction. Current assessments risk biodiversity associated with 1 , however, do not typically take into account genetic makeup how impacts it 2 . We made use extensive genome information in Arabidopsis thaliana measured rainfall-manipulation affected fitness 517 lines grown Spain Germany. This allowed us directly infer along 3 Natural was particularly strong hot-dry Spanish location, killing 63% significantly changing frequency ~5% all genome-wide variants. A significant portion this climate-driven over variants predictable from signatures local adaptation (R =29-52%), as found geographic areas climates more similar experimental sites were positively selected. Field-validated predictions across species range indicated Mediterranean Western Siberian — at edges species’ environmental limits currently experience strongest selection. With frequent droughts rising temperatures Europe 4 we forecast increase directional moving northwards southern end, putting many native A. evolutionary risk.

Language: Английский

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The promise and deceit of genomic selection component analyses

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2021, Volume and Issue: 288(1961)

Published: Oct. 27, 2021

Selection component analyses (SCA) relate individual genotype to fitness components such as viability, fecundity and mating success. SCA are based on population genetic models yield selection estimates directly in terms of predicted allele frequency change. This paper explores the statistical properties gSCA: experiments that apply genome-wide scoring SNPs field sampled individuals. Computer simulations indicate gSCA involving a few thousand genotyped samples can detect changes magnitude has been documented diverse taxa. To selection, imprecise genotyping from low-level sequencing large individuals provides much greater power than precise smaller samples. The also demonstrate efficacy ‘haplotype matching’, method combine information limited collection whole genome sequence (the reference panel) with larger sample measured for fitness. Pooled is demonstrated another way increase power. Finally, I discuss interpretation relation Beavis effect, overestimation intensities at significant loci.

Language: Английский

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Estimating the genome-wide contribution of selection to temporal allele frequency change

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2019, Volume and Issue: unknown

Published: Oct. 9, 2019

Abstract Rapid phenotypic adaptation is often observed in natural populations and selection experiments. However, detecting the genome-wide impact of this difficult, since proceeds from standing variation on polygenic traits, both which may leave faint genomic signals indistinguishable a noisy background genetic drift. One promising signal comes covariance between allele frequency changes observable temporal data, e.g. evolve-and-resequence studies. These covariances reflect how heritable fitness population leads frequencies at one timepoint to be predictive later timepoints, as alleles are indirectly selected due remaining associations with alleles. Since drift does not lead covariance, we can use these estimate what fraction change through time driven by linked selection. Here, reanalyze three experiments quantify effects over short timescales using among time-points across replicates. We that least 17% 37% Against positive also identify negative corresponding reversals direction for reasonable proportion loci course experiment. Overall, find studies analyzed, has large short-term dynamics readily distinguishable Significance Statement A long-standing problem evolutionary biology understand processes shape composition populations. In without migration, two selection, increases beneficial removes deleterious ones, randomly some parents contribute more or less next generation. Previous efforts disentangle have used samples single models affects neighboring sites (linked selection). data taken contributions changes. show acts sizable impact.

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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