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55 results for “supergene”
Data and code for: A supergene controlling social structure in Alpine ants also affects the dispersal ability and fecundity of each sex
<p>Social organisation, dispersal and fecundity co-evolve, but whether they are genetically linked remains little known. Supergenes are prime candidates for coupling adaptive traits and mediating sex-specific trade-offs. Here, we test whether a supergene that controls social structure in <em>Formica selysi</em> also influences dispersal-related traits and fecundity within each sex. In this ant species, single-queen colonies contain only the ancestral supergene haplotype <em>M</em> and produce<em> MM</em> queens and <em>M</em> males, while multi-queen colonies contain the derived haplotype <em>P</em> and produce <em>MP </em>queens, <em>PP</em> queens, and <em>P</em> males. By combining multiple experiments, we show that the <em>M </em>haplotype induces phenotypes with higher dispersal potential and higher fecundity, for both sexes. Specifically, <em>MM</em> queens, <em>MP</em> queens, and <em>M </em>males are more aerodynamic and more fecund than <em>PP </em>queens and <em>P</em> males, respectively. Differences between <em>MP</em> and <em>PP</em> queens from the same colonies reveal a direct genetic effect of the supergene on dispersal-related traits and fecundity. The derived haplotype <em>P</em>, associated with multi-queen colonies, produces queens and males with reduced dispersal abilities and lower fecundity. More broadly, similarities between the <em>Formica </em>and <em>Solenopsis</em> systems reveal that supergenes play a major role in linking behavioural, morphological, and physiological traits associated with intraspecific social polymorphisms.</p>
A masculinizing supergene underlies an exaggerated male reproductive morph in a spider
<p>In many species, individuals can develop into strikingly different morphs, which are determined by a simple Mendelian locus. How selection shapes loci that control complex p henotypic differences remains poorly understood. In the spider gibbosus, males either develop into a 'hunched'morph with conspicuous head structures or as a fast developing 'flat'morph with a female- like appearance. We show that the hunched differs from the f lat-determinin g allele by a hunch-specific genomic fragment of approximately 3 megabases. This fragment comprises dozens of genes that duplicated from genes found at different chromosomes. All functional duplicates, including doublesex- a key sexual differentiation regulatory gene, show male-specific expression, which il lustrates their combined role as a masculinizing supergene. Our findings demonstrate how extensive indel polymorphisms and duplications of regulatory genes may contribute to t he evolution of co-adapted gene clusters, sex-limi ted reproductive morphs, and the enigmatic evolution of exaggerated sexual traits in general.</p>
Epistatic selection on a selfish Segregation Distorter supergene: drive, recombination, and genetic load
<p>Meiotic drive supergenes are complexes of alleles at linked loci that together subvert Mendelian segregation resulting in preferential transmission. In males, the most common mechanism of drive involves the disruption of sperm bearing one of a pair of alternative alleles. While at least two loci are important for male drive- the driver and the target- linked modifiers can enhance drive, creating selection pressure to suppress recombination. In this work, we investigate the evolution and genomic consequences of an autosomal, multilocus, male meiotic drive system, Segregation Distorter (SD) in the fruit fly, Drosophila melanogaster. In African populations, the predominant SD chromosome variant, SD-Mal, is characterized by two overlapping, paracentric inversions on chromosome arm 2R and nearly perfect (~100%) transmission. We study the SD-Mal system in detail, exploring its components, chromosomal structure, and evolutionary history. Our findings reveal a recent chromosome-scale selective sweep mediated by strong epistatic selection for haplotypes carrying Sd, the main driving allele, and one or more factors within the double inversion. While most SD-Mal chromosomes are homozygous lethal, SD-Mal haplotypes can recombine with other, complementing haplotypes via crossing over, and with wildtype chromosomes via gene conversion. SD-Mal chromosomes have nevertheless accumulated lethal mutations, excess non-synonymous mutations, and excess transposable element insertions. Therefore, SD-Mal haplotypes evolve as a small, semi-isolated subpopulation with a history of strong selection. These results may explain the evolutionary turnover of SD haplotypes in different populations around the world, and have implications for supergene evolution broadly.</p>
Epistatic selection on a selfish Segregation Distorter supergene: drive, recombination, and genetic load
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A masculinizing supergene underlies an exaggerated male reproductive morph in a spider
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Code and datasets associated with: A sex-linked supergene with large effects on sperm traits has little impact on reproductive traits in female zebra finches
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Data and code for: A supergene controlling social structure in Alpine ants also affects the dispersal ability and fecundity of each sex
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Disentangling the mechanisms linking dispersal and sociality in supergene-mediated ant social forms
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Functional genetic elements of a butterfly mimicry supergene
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Vasoactive intestinal peptide as a mediator of the effects of a supergene on social behavior
<p>Supergenes, or linked groups of alleles that are inherited together, present excellent opportunities to understand gene-behavior relationships. In white-throated sparrows (<i>Zonotrichia albicollis</i>), a supergene on the second chromosome associates with a more aggressive and less parental phenotype. This supergene includes the gene for vasoactive intestinal peptide (VIP), a neuropeptide known to play a causal role in both aggression and parental behavior. Here, using a free-living population, we compared levels of VIP mRNA between birds with and without the supergene. We focused on the anterior hypothalamus and infundibular region, two brain regions containing VIP neurons known to play a causal role in aggression and parental behavior, respectively. First, we show that the supergene enhances VIP expression in the anterior hypothalamus and that expression positively predicts vocal aggression independently of genotype in both sexes. Next, we show that the supergene reduces VIP expression in the infundibular region, which suggests reduced secretion of prolactin, a pro-parental hormone. Thus, patterns of VIP expression in these two regions are consistent with the enhanced aggression and reduced parental behavior of birds with the supergene allele. Our results illustrate mechanisms by which elements of genomic architecture, such as supergenes, can contribute to the evolution of alternative behavioral phenotypes.</p>
Fine-scale habitat heterogeneity favours the coexistence of supergene-controlled social forms in Formica selysi
<p><b>Background:</b> Social insects vary widely in social organization, yet the genetical and ecological factors influencing this variation remain poorly known. In particular, whether spatially varying selection influences the maintenance of social polymorphisms in ants has been rarely investigated. To fill this gap, we examined whether fine-scale habitat heterogeneity contributes to the co-existence of alternative forms of social organization within populations. Single-queen colonies (monogyne social form) are generally associated with better colonization abilities, whereas multiple-queen colonies (polygyne social form) are predicted to be better competitors and monopolize saturated habitats. We hypothesize that each social form colonizes and thrives in distinct local habitats, as a result of their alternative dispersal and colony founding strategies. Here, we test this hypothesis in the Alpine silver ant, in which a supergene controls polymorphic social organization.</p> <p><b>Results:</b> Monogyne and polygyne colonies predominate in distinct habitats of the same population. The analysis of 59 sampling plots distributed across six habitats revealed that single-queen colonies mostly occupy unconnected habitats that were most likely reached by flight. This includes young habitats isolated by water and old habitats isolated by vegetation. In contrast, multiple-queen colonies were abundant in young, continuous and saturated habitats. Hence, alternative social forms colonize and monopolize distinct niches at a very local scale.</p> <p><b>Conclusions:</b> Alternative social forms colonized and monopolized different local habitats, in accordance with differences in colonization and competition abilities. The monogyne social form displays a colonizer phenotype, by efficiently occupying empty habitats, while the polygyne social form exhibits a competitor phenotype, thriving in saturated habitats. The combination of the two phenotypes, coupled with fine-scale habitat heterogeneity, may allow the coexistence of alternative social forms within populations. Overall, these results suggest that spatially varying selection may be one of the mechanisms contributing to the maintenance of genetic polymorphisms in social organization.</p>
Data from: Unexpected patterns of segregation distortion at a selfish supergene in the fire ant Solenopsis invicta
Background: The Sb supergene in the fire ant Solenopsis invicta determines the form of colony social organization, with colonies whose inhabitants bear the element containing multiple reproductive queens and colonies lacking it containing only a single queen. Several features of this supergene — including suppressed recombination, presence of deleterious mutations and abundant transposable elements, association with a large centromere, and "green-beard" behavior — suggest that it may be a selfish genetic element that engages in transmission ratio distortion (TRD), defined as significant departures in progeny allele frequencies from Mendelian inheritance ratios. We tested this possibility by surveying segregation ratios in embryo progenies of 101 queens of the "polygyne" social form (3512 embryos) using three supergene-linked markers and twelve markers not associated with the supergene. Results: Significant departures from Mendelian ratios were observed at the supergene loci in 3-5 times more progenies than expected in the absence of TRD and than found, on average, among non-supergene loci. Also, supergene loci displayed the greatest mean deviations from Mendelian ratios among all study loci, although these typically were modest. A surprising feature of the observed inter-progeny variation in TRD was that significant deviations involved not only excesses of supergene alleles but also similarly frequent excesses of the alternate alleles on the homologous chromosome. As expected given the common occurrence of such "drive reversal," alleles associated with the supergene evidently gain no consistent transmission advantage over their alternate alleles at the population level. Finally, we observed low levels of recombination and incomplete gametic disequilibrium across the supergene, including between adjacent markers within a single inversion. Conclusions: Our data confirm the prediction that the Sb supergene is a selfish genetic element capable of biasing its own transmission during reproduction, yet counterselection for suppressor loci evidently has produced an evolutionary stalemate in TRD between the variant homologous haplotypes on the "social chromosome". Evidence implicates prezygotic segregation distortion as responsible for the TRD we document, with "true" meiotic drive the most likely mechanism. Low levels of recombination and incomplete gametic disequilibrium across the supergene suggest that selection does not act to preserve a single uniform supergene haplotype.
Data from: The fire ant social supergene is characterized by extensive gene and transposable element copy number variation
In the fire ant Solenopsis invicta, a supergene composed of ~600 genes and having two variants, SB and Sb, regulates colony social form. In single queen colonies all individuals carry only the SB allele, while in multiple queen colonies, some individuals carry the Sb allele. In this study we characterized genes with copy number variation between SB and Sb-carrying individuals. We showed extensive acquisition of gene duplicates in Sb genome, with some likely involved in polygyne-related phenotypes. We found 260 genes with differences in copy number between SB and Sb, of which 239 are in greater copy number in Sb. We observed TE accumulation on Sb, likely due to the accumulation of repetitive elements on the non-recombining chromosome. We found a weak correlation between TE copy number and differential expression, suggesting some TEs may still be proliferating in Sb, however many of the duplicated TEs were already silenced. Among the 115 non-TE genes with higher copy in Sb, enzymes responsible for cuticular hydrocarbon synthesis were highly represented. These include a desaturase and an elongase; both potentially responsible for differential queen odor and likely beneficial for polygyne ants. These genes seem to have translocated into the supergene from other chromosomes and proliferated by multiple duplication events. While the presence of transposable elements (TEs) in supergenes is well documented, little is known about duplication of non-TE genes and their possible adaptive role. Overall, our results suggest that gene duplications may be an important factor leading to monogyne and polygyne ant societies.
Data from: Stepwise evolution of a butterfly supergene via duplication and inversion
<p>Supergenes maintain adaptive clusters of alleles in the face of genetic mixing. Although usually attributed to inversions, supergenes can be complex, and reconstructing the precise processes that led to recombination suppression and their timing is challenging. We investigated the origin of the BC supergene, which controls variation in warning colouration in the African Monarch butterfly, <em>Danaus chrysippus</em>. By generating chromosome-scale assemblies for all three alleles, we identified multiple structural differences. Most strikingly, we find that a region of >1 million bp underwent several segmental duplications at least 7.5 million years ago. The resulting duplicated fragments appear to have triggered four inversions in surrounding parts of the chromosome, resulting in stepwise growth of the region of suppressed recombination. Phylogenies for the inversions are incongruent with the species tree, and suggest that structural polymorphisms have persisted for at least 4.1 million years. In addition to the role of duplications in triggering inversions, our results suggest a previously undescribed mechanism of recombination suppression through independent losses of divergent duplicated tracts. Overall, our findings add support for a stepwise model of supergene evolution involving a variety of structural changes.</p>
Multiscale processes controlling niobium mobility during supergene weathering
<p>This metadata file gathers diffraction, spectroscopic and geochemical raw data supporting the manuscript entitled “<strong>Multiscale processes controlling niobium mobility during supergene weathering</strong>“ submitted to <em>Geochimica et Cosmochima Acta</em>.</p> <p><strong>- X-ray diffraction:</strong> "spinner_PIMI_xx.xrdml". Duricrust: PIMI01, 02. Bauxitic horizon: PIMI03. Lateritic horizon: PIMI04, 05. Clayey mottled zone: PIMI06,07.</p> <p><strong>- X-ray absorption data:</strong></p> <p><strong>1) References: </strong>"XAS_L3/K-EDGE_<em>references</em>". Raw X-ray absorption spectra of Nb mineralogial references at the Nb L<sub>3</sub>- and K-edges.</p> <p><strong>2) Bulk sample of laterite: </strong>"XAS_L3/K-EDGE_<em>pimi_XX</em>". Raw X-ray absorption spectra of lateritic bulk samples from Pitinga.</p> <p><strong>3) Microanalyses: </strong>"MICRO_XAS_L3_<em>minerals</em>". Micro-XAS spectra collected on thin sections from Pitinga.</p> <p>- <strong>Bulk chemistry </strong>"geochemistry_pitinga". Bulk geochemical analyses of Pitinga lateritic regolith.</p>
Supergene genotypes and associated phenotypes in Formica cinerea samples
<p class="MsoNormal"><span>Antagonistic selection has long been considered a major driver of the formation and expansion of sex chromosomes. For example, sexually antagonistic variation on an autosome can select for suppressed recombination between that autosome and the sex chromosome, leading to a neo-sex chromosome. Autosomal supergenes, chromosomal regions containing tightly linked variants affecting the same complex trait, share similarities with sex chromosomes, raising the possibility that sex chromosome evolution models can explain the evolution of genome structure and recombination in other contexts. </span><span> </span><span>We tested this premise in a <em><span>Formica </span></em>ant species wherein we identified four supergene haplotypes on chromosome 3 underlying colony social organization and sex ratio. We discovered a novel rearranged supergene variant (9r) on chromosome 9 underlying queen miniaturization. The 9r is in strong linkage disequilibrium with one chromosome 3 haplotype (P<sub>2</sub>) found in multi-queen (polygyne) colonies. We suggest that queen miniaturization is strongly disfavored in the single queen (monogyne) background, and thus socially antagonistic. As such, divergent selection experienced by ants living in alternative social 'environments' (monogyne and polygyne) may have contributed to the emergence of a genetic polymorphism on chromosome 9 and associated queen-size dimorphism. Consequently, an ancestral polygyne-associated haplotype may have expanded to include the polymorphism on chromosome 9, resulting in a larger region of suppressed recombination spanning two chromosomes. This process is analogous to the formation of neo-sex chromosomes and consistent with models of expanding regions of suppressed recombination. We propose that miniaturized queens, 16-20% smaller than queens without 9r, could be incipient intraspecific social parasites.</span></p>
Supergene genotypes and associated phenotypes in Formica cinerea samples
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Data from: The role of breakpoint mutations, supergene effects, and ancient nested rearrangements in the evolution of adaptive chromosome inversions in the yellow monkey flower, Mimulus guttatus
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Data from: Unexpected absence of a multiple-queen supergene haplotype from supercolonial populations of Formica ants
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Male and female adult zebra finch (Taeniopygia guttata) gonad RNAseq associated with: Relaxed purifying selection maintains a sex-linked supergene polymorphism in zebra finches
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