An examination of the evolve-and-resequence method using Drosophila simulans

AbstractWe develop a set of analytical and simulation tools for Evolve-and-Resequence (E&R) experiments and apply them to a new study of rapid evolution in Drosophila simulans. Likelihood based test statistics applied to pooled population sequencing data suggest parallel evolution of 138 polymorphisms (SNPs) across the genome. This number is reduced by orders of magnitude from previous studies (thousands or tens of thousands), owing to differences in both experimental design and statistical analysis. Whole genome simulations calibrated from several Drosophila genetic datasets support the contention that the observed genome-wide response could be generated by as few as 30 loci under strong directional selection, with a corresponding hitch-hiking effect. Finally, the SNPs that showed strong parallel evolution in the novel laboratory environment exhibit an (initial) allele frequency spectrum indicative of balancing in nature. These loci also exhibit elevated differentiation among natural populations of D. simulans.

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Pervasive Linked Selection and Intermediate-Frequency Alleles Are Implicated in an Evolve-and-Resequencing Experiment of Drosophila simulans

Genetics ◽

10.1534/genetics.118.301824 ◽

2018 ◽

Vol 211 (3) ◽

pp. 943-961 ◽

Cited By ~ 22

Author(s):

John K. Kelly ◽

Kimberly A. Hughes

Keyword(s):

Balancing Selection ◽

Parallel Evolution ◽

Rapid Evolution ◽

Natural Populations ◽

Intermediate Frequency ◽

Drosophila Simulans ◽

Data Sets ◽

Sequencing Data ◽

Simulation Tools ◽

Genome Wide

We develop analytical and simulation tools for evolve-and-resequencing experiments and apply them to a new study of rapid evolution in Drosophila simulans. Likelihood test statistics applied to pooled population sequencing data suggest parallel evolution of 138 SNPs across the genome. This number is reduced by orders of magnitude from previous studies (thousands or tens of thousands), owing to differences in both experimental design and statistical analysis. Whole genome simulations calibrated from Drosophila genetic data sets indicate that major features of the genome-wide response could be explained by as few as 30 loci under strong directional selection with a corresponding hitchhiking effect. Smaller effect loci are likely also responding, but are below the detection limit of the experiment. Finally, SNPs showing strong parallel evolution in the experiment are intermediate in frequency in the natural population (usually 30–70%) indicative of balancing selection in nature. These loci also exhibit elevated differentiation among natural populations of D. simulans, suggesting environmental heterogeneity as a potential balancing mechanism.

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Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis

Communications Biology ◽

10.1038/s42003-021-02095-0 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Mariana G. Ferrarini ◽

Avantika Lal ◽

Rita Rebollo ◽

Andreas J. Gruber ◽

Andrea Guarracino ◽

...

Keyword(s):

Transposable Element ◽

Rna Binding ◽

Rna Binding Proteins ◽

Initiation Factor ◽

Sequence Variant ◽

The Novel ◽

Sequencing Data ◽

Genome Wide ◽

Respiratory Cells ◽

Nuclear Ribonucleoprotein

AbstractThe novel betacoronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a worldwide pandemic (COVID-19) after emerging in Wuhan, China. Here we analyzed public host and viral RNA sequencing data to better understand how SARS-CoV-2 interacts with human respiratory cells. We identified genes, isoforms and transposable element families that are specifically altered in SARS-CoV-2-infected respiratory cells. Well-known immunoregulatory genes including CSF2, IL32, IL-6 and SERPINA3 were differentially expressed, while immunoregulatory transposable element families were upregulated. We predicted conserved interactions between the SARS-CoV-2 genome and human RNA-binding proteins such as the heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) and eukaryotic initiation factor 4 (eIF4b). We also identified a viral sequence variant with a statistically significant skew associated with age of infection, that may contribute to intracellular host–pathogen interactions. These findings can help identify host mechanisms that can be targeted by prophylactics and/or therapeutics to reduce the severity of COVID-19.

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On the genetic architecture of rapidly adapting and convergent life history traits in guppies

10.1101/2021.03.18.435980 ◽

2021 ◽

Author(s):

James R Whiting ◽

Josephine R Paris ◽

Paul J Parsons ◽

Sophie Matthews ◽

Yuridia Reynoso ◽

...

Keyword(s):

Life History ◽

Life Histories ◽

Genetic Architecture ◽

Genetic Basis ◽

Natural Populations ◽

Female Size ◽

Size At Maturity ◽

Sequencing Data ◽

Genome Wide ◽

Polygenic Traits

The genetic basis of traits can shape and constrain how adaptation proceeds in nature; rapid adaptation can be facilitated by polygenic traits, whereas polygenic traits may restrict re-use of the same genes in adaptation (genetic convergence). The rapidly evolving life histories of guppies in response to predation risk provide an opportunity to test this proposition. Guppies adapted to high- (HP) and low-predation (LP) environments in northern Trinidad evolve rapidly and convergently among natural populations. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use an F2 QTL design to examine the genetic basis of seven (five female, two male) guppy life history phenotypes. We use RAD-sequencing data (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform linkage mapping, estimates of genome-wide and per-chromosome heritability (multi-locus associations), and QTL mapping (single-locus associations). Our results are consistent with architectures of many-loci of small effect for male age and size at maturity and female interbrood period. Male trait associations are clustered on specific chromosomes, but female interbrood period exhibits a weak genome-wide signal suggesting a potentially highly polygenic component. Offspring weight and female size at maturity are also associated with a single significant QTL each. These results suggest rapid phenotypic evolution of guppies may be facilitated by polygenic trait architectures, but these may restrict gene-reuse across populations, in agreement with an absence of strong signatures of genetic convergence from recent population genomic analyses of wild HP-LP guppies.

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Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster

10.1101/632257 ◽

2019 ◽

Cited By ~ 3

Author(s):

Seth M. Rudman ◽

Sharon Greenblum ◽

Rachel C. Hughes ◽

Subhash Rajpurohit ◽

Ozan Kiratli ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Rapid Evolution ◽

Natural Populations ◽

Genomic Data ◽

Allele Frequencies ◽

Frequency Change ◽

Microbiome Composition ◽

Population Genomic ◽

Genome Wide ◽

Microbial Group

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

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The Recombinational Landscape in Daphnia pulex

10.1101/2020.03.03.974485 ◽

2020 ◽

Cited By ~ 1

Author(s):

Michael Lynch ◽

Zhiqiang Ye ◽

Takahiro Maruki

Keyword(s):

Linkage Disequilibrium ◽

Natural Populations ◽

Daphnia Pulex ◽

Physical Distance ◽

Sequencing Data ◽

Recombination Hotspots ◽

Genome Wide ◽

Nucleotide Mutation ◽

Suppressed Recombination ◽

The Relationship

AbstractThrough the analysis of linkage disequilibrium from genome-wide sequencing data for multiple individuals from eight populations, the general features of the recombinational landscape are revealed in the microcrustacean Daphnia pulex. The data suggest an exceptionally uniform pattern of recombination across the genome, while also confirming general patterns that are inconsistent with existing population-genetic models for the relationship between linkage dis-equilibrium and physical distances between genomic sites. Patterns of linkage disequilibrium are highly consistent among populations, and average rates of recombination are quite similar for all chromosomes. There is no evidence of recombination hotspots, and although there does appear to be suppressed recombination in the vicinity of gene bodies, this effect is quite small. Although this species reproduces asexually in ∼ 80% of generations, the mean per-generation recombination rate per nucleotide site is ∼ 37× the per-nucleotide mutation rate. Contrary to expectations for models in which crossing-over is the primary mechanism of recombination, and consistent with data for other species, the gradient of linkage disequilibrium with increasing physical distance between sites is far too high at short distances and far too low at long distances, suggesting an important role for factors such as the nonindependent appearance of pairs of mutations on haplotypes and long-range gene-conversion-like processes. Combined with other observations on patterns of nucleotide variation, these results provide a strong case for the utility of D. pulex as a model system for the study of mechanisms of evolution in natural populations.

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Faculty Opinions recommendation of From parasite to mutualist: rapid evolution of Wolbachia in natural populations of Drosophila.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1086782.539699 ◽

2007 ◽

Author(s):

Nina Wedell

Keyword(s):

Rapid Evolution ◽

Natural Populations

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Experimental Evidence for the Rapid Evolution of Behavioral Canalization in Natural Populations

The American Naturalist ◽

10.2307/40306070 ◽

2009 ◽

Vol 174 (3) ◽

pp. 434

Author(s):

Edgell ◽

Lynch ◽

Trussell ◽

Palmer

Keyword(s):

Experimental Evidence ◽

Rapid Evolution ◽

Natural Populations

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The Genetic Architecture of Ovariole Number in Drosophila melanogaster: Genes with Major, Quantitative, and Pleiotropic Effects

G3 Genes|Genome|Genetics ◽

10.1534/g3.117.042390 ◽

2017 ◽

Vol 7 (7) ◽

pp. 2391-2403 ◽

Cited By ~ 11

Author(s):

Amanda S Lobell ◽

Rachel R Kaspari ◽

Yazmin L Serrano Negron ◽

Susan T Harbison

Keyword(s):

Candidate Genes ◽

Genome Wide Association Study ◽

Natural Populations ◽

Direct Role ◽

Genome Wide ◽

A Genome ◽

Fitness Trait ◽

Sleep Parameters ◽

Activity Behavior ◽

Ovariole Number

Abstract Ovariole number has a direct role in the number of eggs produced by an insect, suggesting that it is a key morphological fitness trait. Many studies have documented the variability of ovariole number and its relationship to other fitness and life-history traits in natural populations of Drosophila. However, the genes contributing to this variability are largely unknown. Here, we conducted a genome-wide association study of ovariole number in a natural population of flies. Using mutations and RNAi-mediated knockdown, we confirmed the effects of 24 candidate genes on ovariole number, including a novel gene, anneboleyn (formerly CG32000), that impacts both ovariole morphology and numbers of offspring produced. We also identified pleiotropic genes between ovariole number traits and sleep and activity behavior. While few polymorphisms overlapped between sleep parameters and ovariole number, 39 candidate genes were nevertheless in common. We verified the effects of seven genes on both ovariole number and sleep: bin3, blot, CG42389, kirre, slim, VAChT, and zfh1. Linkage disequilibrium among the polymorphisms in these common genes was low, suggesting that these polymorphisms may evolve independently.

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Genetic characterization of novel polymorphic microsatellite markers for Epilobium nankotaizanense (Onagraceae), an endemic and threatened herb in Taiwan

Plant Genetic Resources ◽

10.1017/s1479262121000289 ◽

2021 ◽

pp. 1-4

Author(s):

Yu-Wei Tseng ◽

Chi-Chun Huang ◽

Chih-Chiang Wang ◽

Chiuan-Yu Li ◽

Kuo-Hsiang Hung

Keyword(s):

Microsatellite Markers ◽

Natural Populations ◽

Conservation Strategy ◽

Sequencing Data ◽

Germplasm Collections ◽

The Family ◽

Conservation Genetic ◽

Population Sizes ◽

Polymorphic Microsatellite

Abstract Epilobium belongs to the family Onagraceae, which consists of approximately 200 species distributed worldwide, and some species have been used as medicinal plants. Epilobium nankotaizanense is an endemic and endangered herb that grows in the high mountains in Taiwan at an elevation of more than 3300 m. Alpine herbs are severely threatened by climate change, which leads to a reduction in their habitats and population sizes. However, only a few studies have addressed genetic diversity and population genetics. In the present study, we developed a new set of microsatellite markers for E. nankotaizanense using high-throughput genome sequencing data. Twenty polymorphic microsatellite markers were developed and tested on 30 individuals collected from three natural populations. These loci were successfully amplified, and polymorphisms were observed in E. nankotaizanense. The number of alleles per locus (A) ranged from 2.000 to 3.000, and the observed (Ho) and expected (He) heterozygosities ranged from 0.000 to 0.929 and from 0.034 to 0.631, respectively. The developed polymorphic microsatellite markers will be useful in future conservation genetic studies of E. nankotaizanense as well as for developing an effective conservation strategy for this species and facilitating germplasm collections and sustainable utilization of other Epilobium species.

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