scholarly journals Ethanol resistance in Drosophila melanogaster has increased in parallel cold-adapted populations and shows a variable genetic architecture within and between populations

2021 ◽  
Author(s):  
Quentin Sprengelmeyer ◽  
John E Pool
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Biological Diversity ◽  
European Population ◽  
Membrane Composition ◽  
Trait Evolution ◽  
Adaptive Trait ◽  
Standing Variation ◽  
Ethanol Resistance

Understanding the genetic properties of adaptive trait evolution is a fundamental crux of biological inquiry that links molecular processes to biological diversity. Important uncertainties persist regarding the genetic predictability of adaptive trait change, the role of standing variation, and whether adaptation tends to result in the fixation of favored variants. Here, we use the recurrent evolution of enhanced ethanol resistance in Drosophila melanogaster during this species’ worldwide expansion as a promising system to add to our understanding of the genetics of adaptation. We find that elevated ethanol resistance has evolved at least three times in different cooler regions of the species’ modern range - not only at high latitude but also in two African high altitude regions - and that ethanol and cold resistance may have a partially shared genetic basis. Applying a bulk segregant mapping framework, we find that the genetic architecture of ethanol resistance evolution differs substantially not only between our three resistant populations, but also between two crosses involving the same European population. We then apply population genetic scans for local adaptation within our quantitative trait locus regions, and we find potential contributions of genes with annotated roles in spindle localization, membrane composition, sterol and alcohol metabolism, and other processes. We also apply simulation-based analyses that confirm the variable genetic basis of ethanol resistance and hint at a moderately polygenic architecture. However, these simulations indicate that larger-scale studies will be needed to more clearly quantify the genetic architecture of adaptive evolution, and to firmly connect trait evolution to specific causative loci.

Oligogenic Adaptation, Soft Sweeps, and Parallel Melanic Evolution in Drosophila melanogaster

2016 ◽  
Author(s):  
Héloïse Bastide ◽  
Jeremy D. Lange ◽  
Justin B. Lack ◽  
Yassin Amir ◽  
John E. Pool
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Evolutionary Biology ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Simulation Analysis ◽  
Mapping Method ◽  
Sub Saharan Africa ◽  
Mountain Ranges ◽  
Sub Saharan

AbstractUnraveling the genetic architecture of adaptive phenotypic divergence is a fundamental quest in evolutionary biology. In Drosophila melanogaster, high-altitude melanism has evolved in separate mountain ranges in sub-Saharan Africa, potentially as an adaptation to UV intensity. We investigated the genetic basis of this melanism in three populations using a new bulk segregant analysis mapping method. Although hundreds of genes are known to affect cuticular pigmentation in D. melanogaster, we identified only 19 distinct QTLs from 9 mapping crosses, with several QTL peaks being shared among two or all populations. Surprisingly, we did not find wide signals of genetic differentiation (Fst) between lightly and darkly pigmented populations at these QTLs, in spite of the pronounced phenotypic difference in pigmentation. Instead, we found small numbers of highly differentiated SNPs at the probable causative genes. A simulation analysis showed that these patterns of polymorphism are consistent with selection on standing genetic variation (leading to “soft sweeps“). Our results thus support a role for oligogenic selection on standing genetic variation in driving parallel ecological adaptation.

scholarly journals Genetic architecture of natural variation in cuticular hydrocarbon composition in Drosophila melanogaster

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Lauren M Dembeck ◽  
Katalin Böröczky ◽  
Wen Huang ◽  
Coby Schal ◽  
Robert R H Anholt ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Social Interactions ◽  
Individual Variation ◽  
Genetic Architecture ◽  
Natural Variation ◽  
Genetic Basis ◽  
Acid Metabolism ◽  
Cuticular Hydrocarbon ◽  
Principal Component ◽  
Hydrocarbon Composition

Insect cuticular hydrocarbons (CHCs) prevent desiccation and serve as chemical signals that mediate social interactions. Drosophila melanogaster CHCs have been studied extensively, but the genetic basis for individual variation in CHC composition is largely unknown. We quantified variation in CHC profiles in the D. melanogaster Genetic Reference Panel (DGRP) and identified novel CHCs. We used principal component (PC) analysis to extract PCs that explain the majority of CHC variation and identified polymorphisms in or near 305 and 173 genes in females and males, respectively, associated with variation in these PCs. In addition, 17 DGRP lines contain the functional Desat2 allele characteristic of African and Caribbean D. melanogaster females (more 5,9-C27:2 and less 7,11-C27:2, female sex pheromone isomers). Disruption of expression of 24 candidate genes affected CHC composition in at least one sex. These genes are associated with fatty acid metabolism and represent mechanistic targets for individual variation in CHC composition.

scholarly journals The Evolution of Larger Size in High Altitude Drosophila melanogaster has a Polymorphic Genetic Architecture

2021 ◽  
Author(s):  
Quentin D Sprengelmeyer ◽  
Justin B Lack ◽  
Dylan T Braun ◽  
Matthew J Monette ◽  
John E. Pool
Keyword(s):  
Drosophila Melanogaster ◽  
Qtl Mapping ◽  
Genetic Architecture ◽  
Natural Populations ◽  
Enrichment Analysis ◽  
Thorax Length ◽  
Adaptive Trait ◽  
Polygenic Adaptation ◽  
Trait Locus ◽  
Population Genetic Analyses

Important uncertainties persist regarding the genetic architecture of adaptive trait evolution in natural populations, including the number of genetic variants involved, whether they are drawn from standing genetic variation, and whether directional selection drives them to complete fixation. Here, we take advantage of a unique natural population of Drosophila melanogaster from the Ethiopian highlands, which has evolved larger body size than any other known population of this species. We apply a bulk segregant quantitative trait locus (QTL) mapping approach to four unique crosses between highland Ethiopian and lowland Zambian populations for both thorax length and wing length. Results indicated a persistently variable genetic basis for these evolved traits (with largely distinct sets of QTLs for each cross), and at least a moderately polygenic architecture with relatively strong effects present. We complemented these mapping experiments with population genetic analyses of QTL regions and gene ontology enrichment analysis, generating strong hypotheses for specific genes and functional processes that may have contributed to these adaptive trait changes. Finally, we find that the genetic architectures our QTL mapping results for size traits mirror those from similar experiments on other recently-evolved traits in this species. Collectively, these studies suggest a recurring pattern of polygenic adaptation in this species, in which causative variants do not approach fixation and moderately strong effect loci are present.

scholarly journals The genetic architecture and genomic context of glyphosate resistance

2020 ◽  
Author(s):  
J.M. Kreiner ◽  
P.J. Tranel ◽  
D. Weigel ◽  
J.R. Stinchcombe ◽  
S.I. Wright
Keyword(s):  
Herbicide Resistance ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Glyphosate Resistance ◽  
Target Site ◽  
Plant Performance ◽  
Comparable Amount ◽  
Standing Variation ◽  
Genome Wide ◽  
Target Site Resistance

AbstractAlthough much of what we know about the genetic basis of herbicide resistance has come from detailed investigations of monogenic adaptation at known target-sites, the importance of polygenic resistance has been increasingly recognized. Despite this, little work has been done to characterize the genomic basis of herbicide resistance, including the number and distribution of involved genes, their effect sizes, allele frequencies, and signatures of selection. Here we implement genome-wide association (GWA) and population genomic approaches to examine the genetic architecture of glyphosate resistance in the problematic agricultural weed, Amaranthus tuberculatus. GWA correctly identifies the gene targeted by glyphosate, and additionally finds more than 100 genes across all 16 chromosomes associated with resistance. The encoded proteins have relevant non-target-site resistance and stress-related functions, with potential for pleiotropic roles in resistance to other herbicides and diverse life history traits. Resistance-related alleles are enriched for large effects and intermediate frequencies, implying that strong selection has shaped the genetic architecture of resistance despite potential pleiotropic costs. The range of common and rare allele involvement implies a partially shared genetic basis of non-target-site resistance across populations, complemented by population-specific alleles. Resistance-related alleles show evidence of balancing selection, and suggest a long-term maintenance of standing variation at stress-response loci that have implications for plant performance under herbicide pressure. By our estimates, genome-wide SNPs explain a comparable amount of the total variation in glyphosate resistance to monogenic mechanisms, indicating the potential for an underappreciated polygenic contribution to the evolution of herbicide resistance in weed populations.

scholarly journals The Evolution of Larger Size in High Altitude Drosophila melanogaster has a Variable Genetic Architecture

2022 ◽  
Author(s):  
Quentin D Sprengelmeyer ◽  
Justin B Lack ◽  
Dylan T Braun ◽  
Matthew J Monette ◽  
John E Pool
Keyword(s):  
Drosophila Melanogaster ◽  
Qtl Mapping ◽  
Genetic Architecture ◽  
Natural Populations ◽  
Enrichment Analysis ◽  
Thorax Length ◽  
Adaptive Trait ◽  
Polygenic Adaptation ◽  
Trait Locus ◽  
Population Genetic Analyses

Abstract Important uncertainties persist regarding the genetic architecture of adaptive trait evolution in natural populations, including the number of genetic variants involved, whether they are drawn from standing genetic variation, and whether directional selection drives them to complete fixation. Here, we take advantage of a unique natural population of Drosophila melanogaster from the Ethiopian highlands, which has evolved larger body size than any other known population of this species. We apply a bulk segregant quantitative trait locus (QTL) mapping approach to four unique crosses between highland Ethiopian and lowland Zambian populations for both thorax length and wing length. Results indicated a persistently variable genetic basis for these evolved traits (with largely distinct sets of QTLs for each cross), and at least a moderately polygenic architecture with relatively strong effects present. We complemented these mapping experiments with population genetic analyses of QTL regions and gene ontology enrichment analysis, generating strong hypotheses for specific genes and functional processes that may have contributed to these adaptive trait changes. Finally, we find that the genetic architectures our QTL mapping results for size traits mirror those from similar experiments on other recently-evolved traits in this species. Collectively, these studies suggest a recurring pattern of polygenic adaptation in this species, in which causative variants do not approach fixation and moderately strong effect loci are present.

scholarly journals Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima

2018 ◽  
Author(s):  
Markus G Stetter ◽  
Kevin Thornton ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Genetic Architecture ◽  
Genetic Basis ◽  
Stabilizing Selection ◽  
Relative Importance ◽  
Selective Sweeps ◽  
Weak Selection ◽  
Standing Variation ◽  
Polygenic Adaptation ◽  
Maize Domestication ◽  
New Mutations

ABSTRACTUnderstanding the genetic basis of phenotypic adaptation to changing environments is an essential goal of population and quantitative genetics. While technological advances now allow interrogation of genome-wide genotyping data in large panels, our understanding of the process of polygenic adaptation is still limited. To address this limitation, we use extensive forward-time simulation to explore the impacts of variation in demography, trait genetics, and selection on the rate and mode of adaptation and the resulting genetic architecture. We simulate a population adapting to an optimum shift, modeling sequence variation for 20 QTL for each of 12 different demographies for 100 different traits varying in the effect size distribution of new mutations, the strength of stabilizing selection, and the contribution of the genomic background. We then use random forest regression approaches to learn the relative importance of input parameters in determining a number of aspects of the process of adaptation including the speed of adaptation, the relative frequency of hard sweeps and sweeps from standing variation, or the final genetic architecture of the trait. We find that selective sweeps occur even for traits under relatively weak selection and where the genetic background explains most of the variation. Though most sweeps occur from variation segregating in the ancestral population, new mutations can be important for traits under strong stabilizing selection that undergo a large optimum shift. We also show that population bottlenecks and expansion impact overall genetic variation as well as the relative importance of sweeps from standing variation and the speed with which adaptation can occur. We then compare our results to two traits under selection during maize domestication, showing that our simulations qualitatively recapitulate differences between them. Overall, our results underscore the complex population genetics of individual loci in even relatively simple quantitative trait models, but provide a glimpse into the factors that drive this complexity and the potential of these approaches for understanding polygenic adaptation.Author summaryMany traits are controlled by a large number of genes, and environmental changes can lead to shifts in trait optima. How populations adapt to these shifts depends on a number of parameters including the genetic basis of the trait as well as population demography. We simulate a number of trait architectures and population histories to study the genetics of adaptation to distant trait optima. We find that selective sweeps occur even in traits under relatively weak selection and our machine learning analyses find that demography and the effect sizes of mutations have the largest influence on genetic variation after adaptation. Maize domestication is a well suited model for trait adaptation accompanied by demographic changes. We show how two example traits under a maize specific demography adapt to a distant optimum and demonstrate that polygenic adaptation is a well suited model for crop domestication even for traits with major effect loci.

Genetic Basis for Repeated Mating in Drosophila melanogaster

1981 ◽  
Vol 117 (2) ◽  
pp. 133-146 ◽  
Author(s):  
Donald W. Pyle ◽  
Mark H. Gromko
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Basis ◽  
Repeated Mating

scholarly journals INTRACISTRONIC MAPPING OF ELECTROPHORETIC SITES IN DROSOPHILA MELANOGASTER: FIDELITY OF INFORMATION TRANSFER BY GENE CONVERSION

Genetics ◽  
1974 ◽  
Vol 76 (2) ◽  
pp. 289-299
Author(s):  
Margaret McCarron ◽  
William Gelbart ◽  
Arthur Chovnick
Keyword(s):  
Drosophila Melanogaster ◽  
Information Transfer ◽  
Large Scale ◽  
Genetic Basis ◽  
Xanthine Dehydrogenase ◽  
Specific Protein ◽  
Wild Type ◽  
Electrophoretic Variation ◽  
The Stability ◽  
Recombination Experiments

ABSTRACT A convenient method is described for the intracistronic mapping of genetic sites responsible for electrophoretic variation of a specific protein in Drosophila melanogaster. A number of wild-type isoalleles of the rosy locus have been isolated which are associated with the production of electrophoretically distinguishable xanthine dehydrogenases. Large-scale recombination experiments were carried out involving null enzyme mutants induced on electrophoretically distinct wild-type isoalleles, the genetic basis for which is followed as a nonselective marker in the cross. Additionally, a large-scale recombination experiment was carried out involving null enzyme rosy mutants induced on the same wild-type isoallele. Examination of the electrophoretic character of crossover and convertant products recovered from the latter experiment revealed that all exhibited the same parental electrophoretic character. In addition to documenting the stability of the xanthine dehydrogenase electrophoretic character, this observation argues against a special mutagenesis hypothesis to explain conversions resulting from allele recombination studies.

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