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

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

10.1101/337188 ◽

2018 ◽

Cited By ~ 1

Author(s):

John K. Kelly ◽

Kimberly A. Hughes

Keyword(s):

Parallel Evolution ◽

Rapid Evolution ◽

Natural Populations ◽

Drosophila Simulans ◽

The Novel ◽

Test Statistics ◽

Sequencing Data ◽

Simulation Tools ◽

Allele Frequency Spectrum ◽

Genome Wide

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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A New Catalog of Structural Variants in 1,301 A. thaliana Lines from Africa, Eurasia, and North America Reveals a Signature of Balancing Selection at Defense Response Genes

Molecular Biology and Evolution ◽

10.1093/molbev/msaa309 ◽

2020 ◽

Author(s):

Mehmet Göktay ◽

Andrea Fulgione ◽

Angela M Hancock

Keyword(s):

North America ◽

Defense Response ◽

Balancing Selection ◽

Natural Populations ◽

Housekeeping Genes ◽

Intermediate Frequency ◽

Genomic Variation ◽

Nucleotide Polymorphisms ◽

Structural Variants ◽

Defense Response Genes

Abstract Genomic variation in the model plant Arabidopsis thaliana has been extensively used to understand evolutionary processes in natural populations, mainly focusing on single-nucleotide polymorphisms. Conversely, structural variation has been largely ignored in spite of its potential to dramatically affect phenotype. Here, we identify 155,440 indels and structural variants ranging in size from 1 bp to 10 kb, including presence/absence variants (PAVs), inversions, and tandem duplications in 1,301 A. thaliana natural accessions from Morocco, Madeira, Europe, Asia, and North America. We show evidence for strong purifying selection on PAVs in genes, in particular for housekeeping genes and homeobox genes, and we find that PAVs are concentrated in defense-related genes (R-genes, secondary metabolites) and F-box genes. This implies the presence of a “core” genome underlying basic cellular processes and a “flexible” genome that includes genes that may be important in spatially or temporally varying selection. Further, we find an excess of intermediate frequency PAVs in defense response genes in nearly all populations studied, consistent with a history of balancing selection on this class of genes. Finally, we find that PAVs in genes involved in the cold requirement for flowering (vernalization) and drought response are strongly associated with temperature at the sites of origin.

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Genotyping and De Novo Discovery of Allelic Variants at the Brassicaceae Self-Incompatibility Locus from Short-Read Sequencing Data

Molecular Biology and Evolution ◽

10.1093/molbev/msz258 ◽

2019 ◽

Vol 37 (4) ◽

pp. 1193-1201 ◽

Cited By ~ 2

Author(s):

Mathieu Genete ◽

Vincent Castric ◽

Xavier Vekemans

Keyword(s):

De Novo ◽

Balancing Selection ◽

Methodological Approach ◽

Natural Populations ◽

Sequence Divergence ◽

Reference Database ◽

Self Incompatibility ◽

Sequencing Data ◽

Allelic Series ◽

S Alleles

Abstract Plant self-incompatibility (SI) is a genetic system that prevents selfing and enforces outcrossing. Because of strong balancing selection, the genes encoding SI are predicted to maintain extraordinarily high levels of polymorphism, both in terms of the number of functionally distinct S-alleles that segregate in SI species and in terms of their nucleotide sequence divergence. However, because of these two combined features, documenting polymorphism of these genes also presents important methodological challenges that have so far largely prevented the comprehensive analysis of complete allelic series in natural populations, and also precluded the obtention of complete genic sequences for many S-alleles. Here, we develop a powerful methodological approach based on a computationally optimized comparison of short Illumina sequencing reads from genomic DNA to a database of known nucleotide sequences of the extracellular domain of SRK (eSRK). By examining mapping patterns along the reference sequences, we obtain highly reliable predictions of S-genotypes from individuals collected from natural populations of Arabidopsis halleri. Furthermore, using a de novo assembly approach of the filtered short reads, we obtain full-length sequences of eSRK even when the initial sequence in the database was only partial, and we discover putative new SRK alleles that were not initially present in the database. When including those new alleles in the reference database, we were able to resolve the complete diploid SI genotypes of all individuals. Beyond the specific case of Brassicaceae S-alleles, our approach can be readily applied to other polymorphic loci, given reference allelic sequences are available.

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Molecular Signatures Related to the Virulence of Bacillus cereus Sensu Lato, a Leading Cause of Devastating Endophthalmitis

mSystems ◽

10.1128/msystems.00745-19 ◽

2019 ◽

Vol 4 (6) ◽

Author(s):

Jian Yuan ◽

Yu-Yu Li ◽

Yi Xu ◽

Bian-Jin Sun ◽

Jiao Shao ◽

...

Keyword(s):

Bacillus Cereus ◽

Association Studies ◽

Whole Genome Sequence ◽

Data Sets ◽

Molecular Signatures ◽

Sequencing Data ◽

Content Type ◽

Genome Wide ◽

Medical University ◽

Bacillus Toyonensis

ABSTRACT Bacillus endophthalmitis is a devastating eye infection that causes rapid blindness through extracellular tissue-destructive exotoxins. Despite its importance, knowledge of the phylogenetic relationships and population structure of intraocular Bacillus spp. is lacking. In this study, we sequenced the whole genomes of eight Bacillus intraocular pathogens independently isolated from 8/52 patients with posttraumatic Bacillus endophthalmitis infections in the Eye Hospital of Wenzhou Medical University between January 2010 and December 2018. Phylogenetic analysis revealed that the pathogenic intraocular isolates belonged to Bacillus cereus, Bacillus thuringiensis and Bacillus toyonensis. To determine the virulence of the ocular isolates, three representative strains were injected into mouse models, and severe endophthalmitis leading to blindness was observed. Through incorporating publicly available genomes for Bacillus spp., we found that the intraocular pathogens could be isolated independently but displayed a similar genetic context. In addition, our data provide genome-wide support for intraocular and gastrointestinal sources of Bacillus spp. belonging to different lineages. Importantly, we identified five molecular signatures of virulence and motility genes associated with intraocular infection, namely, plcA-2, InhA-3, InhA-4, hblA-5, and fliD using pangenome-wide association studies. The characterization of overrepresented genes in the intraocular isolates holds value to predict bacterial evolution and for the design of future intervention strategies in patients with endophthalmitis. IMPORTANCE In this study, we provided a detailed and comprehensive clinicopathological and pathogenic report of Bacillus endophthalmitis over the 8 years of the study period. We first reported the whole-genome sequence of Bacillus spp. causing devastating endophthalmitis and found that Bacillus toyonensis is able to cause endophthalmitis. Finally, we revealed significant endophthalmitis-associated virulence genes involved in hemolysis, immunity inhibition, and pathogenesis. Overall, as more sequencing data sets become available, these data will facilitate comparative research and will reveal the emergence of pathogenic “ocular bacteria.”

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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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Integrating Phenotypic Data For Depression

Journal of Integrative Bioinformatics ◽

10.1515/jib-2010-136 ◽

2010 ◽

Vol 7 (3) ◽

pp. 290-299 ◽

Cited By ~ 1

Author(s):

Amy W. Butler ◽

Sarah Cohen-Woods ◽

Anne Farmer ◽

Peter McGuffin ◽

Cathryn M. Lewis

Keyword(s):

Association Studies ◽

Molecular Genetic ◽

Genetic Research ◽

Data Sets ◽

Full Potential ◽

Genome Wide Association Studies ◽

Sequencing Data ◽

Phenotypic Data ◽

Genome Wide ◽

Meta Analyses

Abstract The golden era of molecular genetic research brings about an explosion of phenotypic, genotypic and sequencing data. Building on the common aims to exploit understanding of human diseases, it also opens up an opportunity for scientific communities to share and combine research data. Genome-wide association studies (GWAS) have been widely used to locate genetic variants, which are susceptible for common diseases. In the field of medical genetics, many international collaborative consortiums have been established to conduct meta-analyses of GWAS results and to combine large genotypic data sets to perform mega genetic analyses. Having an integrated phenotype database is significant for exploiting the full potential of extensive genotypic data. In this paper, we aim to share our experience gained from integrating four heterogeneous sets of major depression phenotypic data onto the MySQL platform. These data sets constitute clinical data which had been gathered for various genetic studies for the past decade. We also highlight in this report some generic data handling techniques, the costs and benefits regarding the use of integrated phenotype database within our own institution and under the consortium framework.

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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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ESTIMATION OF GENETIC VARIABILITY IN NATURAL POPULATIONS OF DROSOPHILA SIMULANS BY TWO-DIMENSIONAL AND STARCH GEL ELECTROPHORESIS

Genetics ◽

10.1093/genetics/100.1.127 ◽

1982 ◽

Vol 100 (1) ◽

pp. 127-136

Author(s):

Seido Ohnishi ◽

Andrew J Leigh Brown ◽

Robert A Voelker ◽

Charles H Langley

Keyword(s):

Sibling Species ◽

Natural Populations ◽

Genetic Distances ◽

Drosophila Simulans ◽

Data Sets ◽

Starch Gel Electrophoresis ◽

Two Dimensional ◽

Two Dimensional Electrophoresis ◽

Starch Gel ◽

Dimensional Electrophoresis

ABSTRACT Genic variation in natural populations of Drosophila simulans was surveyed using allozymic and two-dimensional electrophoretic techniques. Consistent with some previous reports, allozymic heterozygosity appeared lower than in the sibling species D. melanogaster (0.07 vs. 0.16). No variation was detected by two-dimensional electrophoresis of 19 lines scored for 70 abundant proteins. This is consistent with reported reductions in estimates of genic heterozygosity by two-dimensional electrophoresis in D. melanogaster, Mus musculus, and man. Although the amount of intraspecific variation detected in abundant proteins was lower than that detected for allozymes in D. simulans and D. melanogaster, the genetic distances between the sibling species calculated from the two data sets are not significantly different (0.35 and 0.20). The allozyme and two-dimensional electrophoresis data confirmed the impression from other measures of genetic variation (mitochondrial DNA restriction maps and inversion polymorphisms) that D. simulans is substantially less variable than D. melanogaster.

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The genetic basis of cooperation and conflict in natural populations of a model symbiont

10.1101/2021.07.19.452989 ◽

2021 ◽

Author(s):

Rebecca T Batstone ◽

Liana T Burghardt ◽

Katy D Heath

Keyword(s):

Nucleotide Diversity ◽

Genetic Basis ◽

Balancing Selection ◽

Association Studies ◽

Natural Populations ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Ensifer Meliloti ◽

Single Versus

Although mutualisms are defined as net beneficial interactions among species, whether fitness conflict or alignment drive the evolution of these interactions is unclear. Examining the relationships between host and symbiont fitness proxies at both the organismal and genomic levels can provide new insights. Here, we utilized data from several genome-wide association studies (GWAS) that involved 191 strains of the N-fixing rhizobium symbiont, Ensifer meliloti, collected from natural populations being paired in single or mixed inoculation with two genotypes of the host Medicago truncatula to determine how different proxies of microbial fitness were related to one another, and examine signatures of fitness conflict and alignment between host and symbiont at both the whole-organism and genomic levels. We found little evidence for fitness conflict; instead, loci tended to have concordant effects on both host and symbiont fitness and showed heightened nucleotide diversity and signatures of balancing selection compared to the rest of the genome. We additionally found that single versus competitive measures of rhizobium fitness are distinct, and that the latter should be used given that they better reflect the ecological conditions rhizobia experience in nature. Our results suggest that although conflict appears to be largely resolved in natural populations of rhizobia, mutualistic coevolution between legumes and rhizobia can nonetheless maintain genetic diversity, potentially explaining why variation in symbiotic traits persists in nature.

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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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