Heterogeneous Selection at Specific Loci in Natural Environments in Arabidopsis thaliana

Genetics ◽  
2003 ◽  
Vol 165 (1) ◽  
pp. 321-329 ◽  
Author(s):  
Cynthia Weinig ◽  
Lisa A Dorn ◽  
Nolan C Kane ◽  
Zachary M German ◽  
Solveig S Halldorsdottir ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Variation ◽  
Natural Selection ◽  
Rhode Island ◽  
Plant Species ◽  
Allelic Variation ◽  
Balancing Selection ◽  
Wild Plant ◽  
Natural Environments ◽  
Fitness Effects

Abstract Genetic variation for quantitative traits is often greater than that expected to be maintained by mutation in the face of purifying natural selection. One possible explanation for this observed variation is the action of heterogeneous natural selection in the wild. Here we report that selection on quantitative trait loci (QTL) for fitness traits in the model plant species Arabidopsis thaliana differs among natural ecological settings and genetic backgrounds. At one QTL, the allele that enhanced the viability of fall-germinating seedlings in North Carolina reduced the fecundity of spring-germinating seedlings in Rhode Island. Several other QTL experienced strong directional selection, but only in one site and seasonal cohort. Thus, different loci were exposed to selection in different natural environments. Selection on allelic variation also depended upon the genetic background. The allelic fitness effects of two QTL reversed direction depending on the genotype at the other locus. Moreover, alternative alleles at each of these loci caused reversals in the allelic fitness effects of a QTL closely linked to TFL1, a candidate developmental gene displaying nucleotide sequence polymorphism consistent with balancing selection. Thus, both environmental heterogeneity and epistatic selection may maintain genetic variation for fitness in wild plant species.

scholarly journals A non-coding indel polymorphism in the fruitless gene of Drosophila melanogaster exhibits antagonistically pleiotropic fitness effects

2021 ◽  
Vol 288 (1950) ◽  
Author(s):  
Michael D. Jardine ◽  
Filip Ruzicka ◽  
Charlotte Diffley ◽  
Kevin Fowler ◽  
Max Reuter
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Balancing Selection ◽  
Antagonistic Pleiotropy ◽  
Multiple Target ◽  
Indel Polymorphism ◽  
Fitness Components ◽  
Fitness Effects ◽  
Males And Females ◽  
Opposing Effects

The amount of genetic variation for fitness within populations tends to exceed that expected under mutation–selection–drift balance. Several mechanisms have been proposed to actively maintain polymorphism and account for this discrepancy, including antagonistic pleiotropy (AP), where allelic variants have opposing effects on different components of fitness. Here, we identify a non-coding indel polymorphism in the fruitless gene of Drosophila melanogaster and measure survival and reproductive components of fitness in males and females of replicate lines carrying each respective allele. Expressing the fruitless region in a hemizygous state reveals a pattern of AP, with one allele generating greater reproductive fitness and the other conferring greater survival to adulthood. Different fitness effects were observed in an alternative genetic background, which may reflect dominance reversal and/or epistasis. Our findings link sequence-level variation at a single locus with complex effects on a range of fitness components, thus helping to explain the maintenance of genetic variation for fitness. Transcription factors, such as fruitless , may be prime candidates for targets of balancing selection since they interact with multiple target loci and their associated phenotypic effects.

scholarly journals Dispersal alters the nature and scope of sexually antagonistic variation

2020 ◽  
Author(s):  
Ewan O Flintham ◽  
Vincent Savolainen ◽  
Charles Mullon
Keyword(s):  
Genetic Variation ◽  
Balancing Selection ◽  
Sexual Antagonism ◽  
Previous Theory ◽  
Fitness Effects ◽  
Kin Competition ◽  
Spatial Subdivision ◽  
Subdivided Populations ◽  
Limited Dispersal ◽  
Intralocus Conflict

AbstractIntra-locus sexual conflict, or sexual antagonism, occurs when alleles have opposing fitness effects in the two sexes. Previous theory suggests that sexual antagonism is a driver of genetic variation by generating balancing selection. However, these studies assume that populations are well-mixed, neglecting the effects of spatial subdivision. Here we use mathematical modelling to show that limited dispersal can fundamentally change evolution at sexually antagonistic autosomal and X-linked loci due to inbreeding and sex-specific kin competition. We find that if the sexes disperse at different rates, kin competition within the philopatric sex biases intralocus conflict in favour of the more dispersive sex. Furthermore, kin competition diminishes the strength of balancing selection relative to genetic drift, reducing genetic variation in small subdivided populations. Meanwhile, by decreasing heterozygosity, inbreeding reduces the scope for sexually antagonistic polymorphism due to non-additive allelic effects, and this occurs to a greater extent on the X-chromosome than autosomes. Overall, our results demonstrate that spatial structure is an important factor in predicting where to expect sexually antagonistic alleles. We suggest that observed interspecific and intragenomic variation in sexual antagonism may be explained by sex-specific dispersal ecology and demography.

scholarly journals Intragenic Recombination in the Adh Locws of the Wild Plant Arabidopsis thaliana

Genetics ◽  
1996 ◽  
Vol 143 (4) ◽  
pp. 1761-1770 ◽  
Author(s):  
Hideki Innan ◽  
Fumio Tajima ◽  
Ryohei Terauchi ◽  
Naohiko T Miyashita
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Species ◽  
Dna Polymorphism ◽  
Geographic Origin ◽  
Wild Plant ◽  
Intragenic Recombination ◽  
Nucleotide Variation ◽  
Nucleotide Mutation ◽  
Sequence Types ◽  
Plant Arabidopsis Thaliana

Abstract Nucleotide variation in the Adh region of the wild plant Arabidopsis thaliana was analyzed in 17 ecotypes sampled worldwide to investigate DNA polymorphism in natural plant populations. The investigated 2.4kb Adh region was divided into four blocks by intragenic recombinations between two parental sequence types that diverged 6.3 million years (Myr) ago, if the nucleotide mutation rate μ = 10−9 is assumed. Within each block, dimorphism of segregating variations was observed with intermediate frequencies, which caused a substantial amount of nucleotide variation in A. thaliana at the species level. The first recombination introduced the divergent variation that resulted in dimorphism in this plant species ~3.3 Myr ago, and three subsequent intragenic recombinations have occurred sporadically in ~1.1-Myr intervals. It was shown that there was only a limited number (six) of sequence types in this species and that no clear association was observed between sequence type and geographic origin. Taken together, these results suggest that A. thaliana has spread over the world only recently. It can be concluded that recombination played an important role in the evolutionary history of A. thaliana, especially through the generation of DNA polymorphism in the natural populations of this plant species.

scholarly journals A non-coding indel polymorphism in the fruitless gene of Drosophila melanogaster exhibits antagonistically pleiotropic fitness effects

2020 ◽  
Author(s):  
Michael D. Jardine ◽  
Filip Ruzicka ◽  
Charlotte Diffley ◽  
Kevin Fowler ◽  
Max Reuter
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Balancing Selection ◽  
The Other ◽  
Antagonistic Pleiotropy ◽  
Indel Polymorphism ◽  
Fitness Components ◽  
Fitness Effects ◽  
Males And Females ◽  
Opposing Effects

AbstractThe amount of genetic variation for fitness within populations tends to exceed that expected under mutation-selection-drift balance. Several mechanisms have been proposed to actively maintain polymorphism and account for this discrepancy, including antagonistic pleiotropy (AP), where allelic variants have opposing effects on different components of fitness. Here we identify a non-coding indel polymorphism in the fruitless gene of Drosophila melanogaster and measure survival and reproductive components of fitness in males and females of replicate lines carrying one or the other allele. Expressing the fruitless region in a hemizygous state we observe a pattern of AP, with one allele resulting in greater reproductive fitness while the other confers greater survival to adulthood. Different fitness effects were observed in an alternative genetic background, suggesting widespread epistatic effects. Our findings link sequence-level variation at a single locus with complex effects on a range of fitness components, thus helping to explain the maintenance of genetic variation for fitness. Transcription factors, such as fruitless, may be prime candidates for targets of balancing selection since they interact with multiple target loci and their associated phenotypic effects.

scholarly journals EXAMINATION OF ALLELIC VARIATION AT THE HEXOKINASE LOCI OF DROSOPHILA PSEUDOOBSCURA AND D. PERSIMILIS BY DIFFERENT METHODS

Genetics ◽  
1977 ◽  
Vol 87 (4) ◽  
pp. 743-761
Author(s):  
Andrew T Beckenbach ◽  
Satya Prakash
Keyword(s):  
Genetic Variation ◽  
Allelic Variation ◽  
Balancing Selection ◽  
Heat Stability ◽  
Relative Activity ◽  
Allelic Frequency ◽  
Drosophila Pseudoobscura ◽  
Urea Denaturation ◽  
Thiol Reagent ◽  
Electrophoretic Techniques

ABSTRACT Recently a number of electrophoretic techniques have been applied to reveal the presence of additional genetic variation among the electrophoretic mobility classes of the highly polymorphic xanthine dehydrogenase (XDH) and esterase-5 (est-5) loci. We examined the hexokinase loci of Drosophila pseudoobscura and D. persimilis using a variety of techniques to determine whether further allelic variation could be revealed for these much less polymorphic loci and to analyze the nature of the known variation at the hexokinase-1 (hex-1) locus. The following studies were conducted: 135 strains of the two species from six localities were examined with buffer pH ranging from 5.5 to 10.0; 40 strains of D. pseudoobscura and 9 strains of D. persimilis from Mather were studied using starch gel concentrations ranging from 8.5 to 15.5% and were examined for differences in heat stability and reactivity to the thiol reagent p CMSA; strains were also tested for susceptibility to urea denaturation and differences in relative activities. Major findings of the work are: (1) No additional allelic variation could be detected at any of the hexokinase loci by applying these techniques. The finding of abundant hidden genetic variation in XDH and est-5 does not extend to all enzyme loci. (2) Evidence from studies using p CMSA indicates that the hex-1 alleles 0.6, 0.8, 1.0 and 1.2 of the two species form a series of unit charge steps. Since the 0.94 allele of D. persimilis has mobility intermediate between 0.8 and 1.0, it is argued that routine electrophoretic techniques are sensitive to at least some conservative amino acid substitutions. (3) Strong correlations were found at the hex-1locus between low allelic frequency, reduced relative activity and reduced stability to heat and urea denaturation. Since the three sibling species, D. pseudoobscura, D. persimilis and D. miranda, all appear to share a common high frequency allele (1.0) at that locus, these findings are taken as evidence that the observed allelic frequencies are a result of directional selection and mutation, rather than any form of balancing selection.

scholarly journals Long-term balancing selection drives evolution of immunity genes in Capsella

2018 ◽  
Author(s):  
Daniel Koenig ◽  
Jörg Hagmann ◽  
Rachel Li ◽  
Felix Bemm ◽  
Tanja Slotte ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Natural Selection ◽  
Balancing Selection ◽  
Population Bottleneck ◽  
Genomic Variability ◽  
Immune Systems ◽  
Immunity Genes ◽  
Evolution Of Immunity

ABSTRACTGenetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. Our data point to long term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.

scholarly journals The Arabidopsis thaliana mobilome and its impact at the species level

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Leandro Quadrana ◽  
Amanda Bortolini Silveira ◽  
George F Mayhew ◽  
Chantal LeBlanc ◽  
Robert A Martienssen ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Natural Selection ◽  
Transposable Elements ◽  
Genome Evolution ◽  
Plant Species ◽  
Genome Sequencing ◽  
Genetic Factors ◽  
Species Level ◽  
Adaptive Responses ◽  
Sequencing Data

Transposable elements (TEs) are powerful motors of genome evolution yet a comprehensive assessment of recent transposition activity at the species level is lacking for most organisms. Here, using genome sequencing data for 211 Arabidopsis thaliana accessions taken from across the globe, we identify thousands of recent transposition events involving half of the 326 TE families annotated in this plant species. We further show that the composition and activity of the 'mobilome' vary extensively between accessions in relation to climate and genetic factors. Moreover, TEs insert equally throughout the genome and are rapidly purged by natural selection from gene-rich regions because they frequently affect genes, in multiple ways. Remarkably, loci controlling adaptive responses to the environment are the most frequent transposition targets observed. These findings demonstrate the pervasive, species-wide impact that a rich mobilome can have and the importance of transposition as a recurrent generator of large-effect alleles.

scholarly journals Compensatory evolution via cryptic genetic variation: Distinct trajectories to phenotypic and fitness recovery

2017 ◽  
Author(s):  
Sudarshan Chari ◽  
Christian Marier ◽  
Cody Porter ◽  
Emmalee Northrop ◽  
Alexandra Belinky ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Allelic Variation ◽  
Courtship Behavior ◽  
Natural Populations ◽  
Wing Morphology ◽  
Cryptic Genetic Variation ◽  
Compensatory Evolution ◽  
Compensatory Adaptation ◽  
Deleterious Alleles

AbstractPopulations are constantly exposed to deleterious alleles, most of which are purged via natural selection. However, deleterious fitness effects of alleles can also be suppressed by compensatory adaptation. Compensatory mutations can act directly to reduce deleterious effects of an allele. Alternatively, compensation may also occur by altering other aspects of an organisms’ phenotype or performance, without suppressing the phenotypic effects of the deleterious allele. Moreover, the origin of allelic variation contributing to compensatory adaptation remains poorly understood. Compensatory evolution driven by mutations that arise during the selective process are well studied. However less is known about the role standing (cryptic) genetic variation plays in compensatory adaptation. To address these questions, we examined evolutionary trajectories of natural populations of Drosophila melanogaster fixed for mutations that disrupt wing morphology, resulting in deleterious effects on several components of fitness. Lineages subjected only to natural selection, evolved modifications to courtship behavior and several life history traits without compensation in wing morphology. Yet, we observed rapid phenotypic compensation of wing morphology under artificial selection, consistent with segregating variation for compensatory alleles. We show that alleles contributing to compensation of wing morphology have deleterious effects on other fitness components. These results demonstrate the potential for multiple independent avenues for rapid compensatory adaptation from standing genetic variation, which ultimately may reveal novel adaptive trajectories.

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