Microbiome composition shapes rapid genomic adaptation ofDrosophila melanogaster

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(40), P. 20025 - 20032

Published: Sept. 16, 2019

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. Shifts composition altered population dynamics led divergence between treatments allele frequencies, 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.

Language: Английский

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Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Molecular Biology and Evolution, Journal Year: 2020, Volume and Issue: 37(9), P. 2661 - 2678

Published: May 9, 2020

Genetic variation is the fuel of evolution, with standing genetic especially important for short-term evolution and local adaptation. To date, studies spatiotemporal 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 characterize among composition fly microbiome, five new DNA viruses our samples.

Language: Английский

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

Proceedings of the National Academy of Sciences, Journal Year: 2020, Volume and Issue: 117(34), P. 20672 - 20680

Published: Aug. 12, 2020

Significance A long-standing problem in evolutionary biology is to understand the processes that shape genetic composition of populations. In a population without migration, two change allele frequencies are selection, which increases beneficial alleles and removes deleterious ones, drift, randomly changes as some parents contribute more or fewer next generation. Previous efforts disentangle these have used genomic samples from single time point models how selection affects neighboring sites (linked selection). Here, we use data taken through quantify contributions drift genome-wide frequency changes. We show acts over short timescales three evolve-and-resequence studies has sizable impact.

Language: Английский

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Transposable elements in Drosophila

Mobile DNA, Journal Year: 2020, Volume and Issue: 11(1)

Published: July 3, 2020

has been studied as a biological model for many years and discoveries in biology rely on this species. Research transposable elements (TEs) is not an exception.

Language: Английский

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Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster

PLoS Genetics, Journal Year: 2020, Volume and Issue: 16(11), P. e1009110 - e1009110

Published: Nov. 20, 2020

Organisms living in seasonally variable environments utilize cues such as light and temperature to induce plastic responses, enabling them exploit favorable seasons avoid unfavorable ones. Local adapation can result variation seasonal but the genetic basis evolutionary history of this remains elusive. Many insects, including Drosophila melanogaster, are able undergo an arrest reproductive development (diapause) response conditions. In D. ability diapause is more common high latitude populations, where flies endure harsher winters, spring, reflecting differential survivorship overwintering populations. Using a novel hybrid swarm-based genome wide association study, we examined ovarian diapause. We exposed outbred females different temperatures day lengths, characterized for over 2800 flies, reconstructed their complete, phased genomes. found that diapause, scored at two developmental cutoffs, has modest heritability, identified hundreds SNPs associated with each phenotypes. Alleles one phenotypes tend be higher latitudes, these alleles do not show predictable variation. The collective signal many small-effect, clinally varying plausibly explain latitudinal seen North America. segregating Zambia, suggesting relies on ancestral polymorphisms, both pro- anti-diapause have experienced selection Finally, utilized outdoor mesocosms track under natural swarms reared outdoors evolved increased propensity late fall, whereas indoor control populations no change. Our results indicate complex, quantitative trait patterns across time space.

Language: Английский

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Different mechanisms drive the maintenance of polymorphism at loci subject to strong versus weak fluctuating selection

Evolution, Journal Year: 2019, Volume and Issue: 73(5), P. 883 - 896

Published: March 19, 2019

The long‐running debate about the role of selection in maintaining genetic variation has been given new impetus by discovery hundreds seasonally oscillating polymorphisms wild Drosophila, possibly stabilized an alternating summer‐winter regime. Historically, there skepticism potential temporal to balance polymorphism, because must be strong have a meaningful stabilizing effect—unless dominance also varies over time ("reversal dominance"). Here, we develop simplified model variable that simultaneously incorporates four different mechanisms, including two mechanisms ("cumulative overdominance" and reversal dominance), as well ecological "storage" ("protection from selection" boom‐bust demography). We use our compare effects these mechanisms. Although far greatest effect, argue three other could stabilize polymorphism under plausible conditions, particularly when all are present. With many loci subject diminishing returns epistasis, stabilizes alleles small effect. This makes combination which incapable effect alleles, better candidate for detectable frequency oscillations large alleles.

Language: Английский

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A clinal polymorphism in the insulin signaling transcription factorfoxocontributes to life‐history adaptation inDrosophila*

Evolution, Journal Year: 2019, Volume and Issue: 73(9), P. 1774 - 1792

Published: May 21, 2019

A fundamental aim of adaptation genomics is to identify polymorphisms that underpin variation in fitness traits. In Drosophila melanogaster, latitudinal life‐history clines exist on multiple continents and make an excellent system for dissecting the genetics adaptation. We have previously identified numerous clinal single‐nucleotide polymorphism insulin/insulin‐like growth factor signaling (IIS), a pathway known from mutant studies affect life history. However, effects natural variants this remain poorly understood. Here we investigate how two alternative alleles at foxo, transcriptional effector IIS, components (viability, size, starvation resistance, fat content). assessed North American cline by reconstituting outbred populations, fixed either low‐ or high‐latitude allele, inbred DGRP lines. Because diet temperature modulate phenotyped across temperatures (18°C, 25°C) diets differing sugar source content. Consistent with expectations, allele conferred larger body size reduced wing loading. Alleles also differed resistance expression insulin‐like receptor, target FOXO. Allelic reaction norms were mostly parallel, few GxE interactions. Together, our results suggest IIS makes major contribution

Language: Английский

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Benchmarking the performance of Pool‐seq SNP callers using simulated and real sequencing data

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 21(4), P. 1216 - 1229

Published: Feb. 5, 2021

Population genomics is a fast-developing discipline with promising applications in growing number of life sciences fields. Advances sequencing technologies and bioinformatics tools allow population to exploit genome-wide information identify the molecular variants underlying traits interest evolutionary forces that modulate these through space time. However, cost genomic analyses multiple populations still too high address them individual genome sequencing. Pooling individuals for can be more effective strategy Single Nucleotide Polymorphism (SNP) detection allele frequency estimation because higher total coverage. compared sequencing, SNP calling from pools has additional difficulty distinguishing rare errors, which often avoided by establishing minimum threshold analysis. Finding an optimal balance between minimizing loss reducing costs essential ensure success studies. Here, we have benchmarked performance callers Pool-seq data, based on different approaches, under conditions, using computer simulations real data. We found varied frequencies up 0.35. also Bayesian (SNAPE-pooled) or maximum likelihood (MAPGD) approaches outperform two heuristic tested (VarScan PoolSNP), terms sensitivity FDR both simulated Our results will help inform selection most appropriate caller not only large-scale studies but cases where option, such as metagenomic polyploid

Language: Английский

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Population Genomics on the Fly: Recent Advances in Drosophila

Methods in molecular biology, Journal Year: 2020, Volume and Issue: unknown, P. 357 - 396

Published: Jan. 1, 2020

Abstract Drosophila melanogaster , a small dipteran of African origin, represents one the best-studied model organisms. Early work in this system has uniquely shed light on basic principles genetics and resulted versatile collection genetic tools that allow to uncover mechanistic links between genotype phenotype. Moreover, given its worldwide distribution diverse habitats moderate genome-size, proven very powerful for population inference was first eukaryotes whose genome fully sequenced. In book chapter, we provide brief historical overview research then focus recent advances during genomic era. After describing different types sources data, discuss mechanisms neutral evolution including demographic history effects recombination biased gene conversion. Then, review detecting genome-wide signals selection, such as soft hard selective sweeps. We further introduction background selection noncoding DNA codon usage role structural variants, transposable elements chromosomal inversions, adaptive process. Finally, how data helps dissect evolutionary shape phenotypic variation natural populations along environmental gradients. summary, chapter serves starting point genomics provides an sources, important concepts field.

Language: Английский

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Footprints of natural selection at the mannose-6-phosphate isomerase locus in barnacles

Proceedings of the National Academy of Sciences, Journal Year: 2020, Volume and Issue: 117(10), P. 5376 - 5385

Published: Feb. 25, 2020

The mannose-6-phosphate isomerase ( Mpi ) locus in Semibalanus balanoides has been studied as a candidate gene for balancing selection more than two decades. Previous work shown that allozyme genotypes (fast and slow) have different frequencies across Atlantic intertidal zones due to on postsettlement survival (i.e., allele zonation). We present the complete sequence of quantify nucleotide polymorphism S. , well divergence its sister taxon cariosus . show slow contains derived charge-altering amino acid polymorphism, both classes correspond haplogroups with multiple internal haplotypes. shows several footprints around fast/slow site: an enrichment positive Tajima’s D nonsynonymous mutations, excess spike levels silent relative divergence, site frequency spectrum enriched midfrequency mutations. observe other departures from neutrality coding noncoding regions. These include trans-species recent mutation under within fast haplogroup. latter suggests ongoing allelic replacement functionally relevant variants. Moreover, predicted models protein structure provide insight into functional significance putatively selected polymorphisms. While are widespread range our data zonation patterns variable spatial temporal scales. further evidence heterogeneous

Language: Английский

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