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52 results for “Chromosomal Inversion”
An allozyme polymorphism is associated with a large chromosomal inversion in the marine snail Littorina fabalis
<p>This Zenodo archive contains the dataset analysed in the paper "An allozyme polymorphism is associated with a large chromosomal inversion in the marine snail Littorina fabalis" published in Evolutionary Application in 2022:</p> <ul> <li><a href="https://zenodo.org/api/files/cd560cff-56d4-4f72-95be-e70939f2b85f/FAB_LG3_maf1_SNP_Hexcess_depth10.vcf">FAB_LG3_maf1_SNP_Hexcess_depth10.vcf </a>: vcf for LG3 unpruned for LD containing 295 individuals genotyped at 58,246 filtered SNPs</li> <li><a href="https://zenodo.org/api/files/cd560cff-56d4-4f72-95be-e70939f2b85f/FAB_LG3_maf1_SNP_Hexcess_depth10_thin.vcf">FAB_LG3_maf1_SNP_Hexcess_depth10_thin.vcf </a>: vcf for LG3 pruned for LD containing 295 individuals genotyped at 9,905 filtered SNPs</li> <li><a href="https://zenodo.org/api/files/cd560cff-56d4-4f72-95be-e70939f2b85f/FAB_AK_maf1_SNP_Hexcess_depth10.vcf">FAB_AK_maf1_SNP_Hexcess_depth10.vcf</a> : vcf for contig265 containing the arginine kinase gene: 295 individuals genotyped at 70 filtered SNPs</li> </ul> <p>The archive also include some of the R script used to performed the analyses of the manuscrit:</p> <ul> <li> </li> <li><a href="https://zenodo.org/api/files/cd560cff-56d4-4f72-95be-e70939f2b85f/Population_genetic_Ark_analyses.R">Population_genetic_Ark_analyses.R </a>: Script to perform PCA +phenotypic cline + FST + Hobs + FIS</li> <li><a href="https://zenodo.org/api/files/cd560cff-56d4-4f72-95be-e70939f2b85f/Suspension_bridge_fit.R">Suspension_bridge_fit.R </a>: Script to perform the suspension bridge fit used to found evidence of gene flux inside the inversion.</li> <li><a href="https://zenodo.org/api/files/cd560cff-56d4-4f72-95be-e70939f2b85f/Cline_function.R">Cline_function.R </a>: function used to fit the allelic frequency variation (cline) along the transect</li> </ul> <p>The raw sequences are available in NCBI.</p> <p>Abstract of the study: Understanding the genetic targets of natural selection is one of the most challenging goalsof population genetics. Some of the earliest candidate genes were identified from associations between allozyme allele frequencies and environmental variation. One such example is the clinal polymorphism in the arginine kinase (<em>Ak</em>) gene in the marine snail <em>Littorina fabalis</em>. While other enzyme loci do not show differences in allozyme frequencies among populations, the <em>Ak</em> alleles are near differential fixation across repeated wave exposure gradients in Europe. Here, we use this case to illustrate how a new sequencing toolbox can be employed to characterize the genomic architecture associated with historical candidate genes. We found that the <em>Ak</em> alleles differ by 9 non-synonymous substitutions, which perfectly explain the different migration patterns of the allozymes during electrophoresis. Moreover, by exploring the genomic context of the <em>Ak</em> gene, we found that the three main <em>Ak</em> alleles are located on different arrangements of a putative chromosomal inversion that reaches near fixation at the opposing ends of two transects covering a wave exposure gradient. This shows <em>Ak</em> is part of a large (3/4 of the chromosome) genomic block of differentiation, in which <em>Ak</em> is unlikely to be the only target of divergent selection. Nevertheless, the non-synonymous substitutions among <em>Ak</em> alleles and the complete association of one allele with one inversion arrangement suggest that the <em>Ak</em> gene is a strong candidate to contribute to the adaptive significance of the inversion.</p> <p> </p> <p> </p>
Chromosomal inversions from an initial ecotypic divergence drive a gradual repeated radiation of Galápagos beetles
<p>Island faunas exhibit some of the most iconic examples where similar forms repeatedly evolve within different islands. Yet, whether these deterministic evolutionary trajectories within islands are driven by an initial, singular divergence and the subsequent exchange of individuals and adaptive genetic variation between islands remains unclear. Here, we address this issue using a gradual, repeated evolution of low-dispersive highland ecotypes from a dispersive lowland ecotype of <em>Calosoma</em> beetles along the island progression of the Galápagos. We show that repeated highland adaptation involved selection on multiple shared alleles within extensive chromosomal inversions that originated from an initial adaptation event on the oldest island. These highland inversions first spread through dispersal of highland individuals. Subsequent admixture with the widely distributed lowland ecotype resulted in polymorphic dispersive populations from which the highland populations evolved on the youngest islands. Our findings emphasize the significance of an ancient divergence in driving repeated evolution and highlight how a mixed contribution of inter-island colonization and within-island evolution can shape parallel species communities on islands.</p>
Experimental introgression in Drosophila: Asymmetric postzygotic isolation associated with chromosomal inversions and an incompatibility locus on the X chromosome
<p>Interspecific gene flow (introgression) is an important source of new genetic variation, but selection against it can reinforce reproductive barriers between interbreeding species. We used an experimental approach to trace the role of chromosomal inversions and incompatibility genes in preventing introgression between two partly sympatric <em>Drosophila virilis</em> group species, <em>D. flavomontana </em>and<em> D. montana</em>. We backcrossed F<sub>1</sub> hybrid females from a cross between <em>D. flavomontana female </em>and<em> D. montana </em>male with the males of the parental species for two generations and sequenced pools of parental strains and their reciprocal 2<sup>nd</sup> generation backcross (BC<sub>2</sub>mon and BC<sub>2</sub>fla) females. Contrasting the observed amount of introgression (mean hybrid index, HI) in BC<sub>2</sub> female pools along the genome to simulations under different scenarios allowed us to identify chromosomal regions of restricted and increased introgression. We found no deviation from the HI expected under a neutral null model for any chromosome for the BC<sub>2</sub>mon pool, suggesting no evidence for genetic incompatibilities in backcrosses towards <em>D. montana</em>. In contrast, the BC<sub>2</sub>fla pool showed high variation in the observed HI between different chromosomes, and massive reduction of introgression on the X chromosome (large X-effect). We find that this observation is compatible with reduced recombination combined with at least one dominant incompatibility locus residing within the X inversion(s). Overall, our study suggests that genetic incompatibilities arising within chromosomal inversions can play an important role in speciation.</p>
Experimental introgression in Drosophila: Asymmetric postzygotic isolation associated with chromosomal inversions and an incompatibility locus on the X chromosome
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Chromosomal inversions from an initial ecotypic divergence drive a gradual repeated radiation of Galápagos beetles
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Data from: Chromosome inversions and ecological plasticity in the main African malaria mosquitoes
Chromosome inversions have fascinated the scientific community, mainly because of their role in the rapid adaption of different taxa to changing environments. However, the ecological traits linked to chromosome inversions have been poorly studied. Here, we investigated the roles played by 23 chromosome inversions in the adaptation of the four major African malaria mosquitoes to local environments in Africa. We studied their distribution patterns by using spatially explicit modeling and characterized the ecogeographical determinants of each inversion range. We then performed hierarchical clustering and constrained ordination analyses to assess the spatial and ecological similarities among inversions. Our results show that most inversions are environmentally structured, suggesting that they are actively involved in processes of local adaptation. Some inversions exhibited similar geographical patterns and ecological requirements among the four mosquito species, providing evidence for parallel evolution. Conversely, common inversion polymorphisms between sibling species displayed divergent ecological patterns, suggesting that they might have a different adaptive role in each species. These results are in agreement with the finding that chromosomal inversions play a role in Anopheles ecotypic adaptation. This study establishes a strong ecological basis for future genome-based analyses to elucidate the genetic mechanisms of local adaptation in these four mosquitoes.
Data from: Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion
Organisms exhibit an incredible diversity of life history strategies as adaptive responses to environmental variation. The establishment of novel life history strategies involves multilocus polymorphisms, which will be challenging to establish in the face of gene flow and recombination. Theory predicts that adaptive allelic combinations may be maintained and spread if they occur in genomic regions of reduced recombination, such as chromosomal inversion polymorphisms, yet empirical support for this prediction is lacking. Here, we use genomic data to investigate the evolution of divergent adaptive ecotypes of the yellow monkey flower Mimulus guttatus. We show that a large chromosomal inversion polymorphism is the major region of divergence between geographically widespread annual and perennial ecotypes. In contrast, ∼40,000 single nucleotide polymorphisms in collinear regions of the genome show no signal of life history, revealing genomic patterns of diversity have been shaped by localized homogenizing gene flow and large-scale Pleistocene range expansion. Our results provide evidence for an inversion capturing and protecting loci involved in local adaptation, while also explaining how adaptive divergence can occur with gene flow.
Data from: Dissecting the role of a large chromosomal inversion in life history divergence throughout the Mimulus guttatus species complex
Chromosomal inversions can play an important role in adaptation, but the mechanism of their action in many natural populations remains unclear. An inversion could suppress recombination between locally beneficial alleles, thereby preventing maladaptive reshuffling with less-fit, migrant alleles. The recombination suppression hypothesis has gained much theoretical support but empirical tests are lacking. Here, we evaluated the evolutionary history and phenotypic effects of a chromosomal inversion which differentiates annual and perennial forms of Mimulus guttatus. We found that perennials likely possess the derived orientation of the inversion. In addition, this perennial orientation occurs in a second perennial species, M. decorus, where it is strongly associated with life-history differences between co-occurring M. decorus and annual M. guttatus. One prediction of the recombination suppression hypothesis is that loci contributing to local adaptation will predate the inversion. To test whether the loci influencing perenniality pre-date this inversion, we mapped QTLs for life history traits that differ between annual M. guttatus and a more distantly related, collinear perennial species, M. tilingii. Consistent with the recombination suppression hypothesis we found that this region is associated with life-history in the absence of the inversion, and this association can be broken into at least two QTLs. However, the absolute phenotypic effect of the LG8 inversion region on life-history is weaker in M. tilingii than in perennials which possess the inversion. Thus, while we find support for the recombination suppression hypothesis, the contribution of this inversion to life history divergence in this group is likely complex.
Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype
<p>Both models and case studies suggest that chromosomal inversions can facilitate adaptation and speciation in the presence of gene flow by suppressing recombination between locally adapted alleles. Until recently, however, it has been laborious and time-consuming to identify and genotype inversions in natural populations. Here we apply RAD sequencing data and newly developed population genomic approaches to identify putative inversions that differentiate a sand dune ecotype of the prairie sunflower (<em>Helianthus petiolaris</em>) from populations found on the adjacent sand sheet. We detected seven large genomic regions that exhibit a different population structure than the rest of the genome and that vary in frequency between dune and non-dune populations. These regions also show high linkage disequilibrium and high heterozygosity between, but not within arrangements, consistent with the behavior of large inversions, an inference subsequently validated in part by comparative genetic mapping. Genome-environment association analyses show that key environmental variables, including vegetation cover and soil nitrogen, are significantly associated with inversions. The inversions co-locate with previously described "islands of differentiation," and appear to play an important role in adaptive divergence and incipient speciation within <em>H. petiolaris</em>.</p>
Data: Chromosomal inversions and the demography of speciation in Drosophila montana and Drosophila flavomontana
<p>Chromosome-level genome assemblies of Drosophila montana and Drosophila flavomontana that are associated with the publication "Chromosomal inversions and the demography of speciation in Drosophila montana and Drosophila flavomontana" by Poikela et al. (2024).</p> <p>Dmontana_chromosomes = only D. montana scaffolds assigned to chromosomes</p> <p>Dmontana_all_regions = all genomic D. montana regions</p> <p>Dflavomontana_chromosomes = only D. flavomontana scaffolds assigned to chromosomes</p> <p>Dflavomontana_all_regions = all genomic D. flavomontana regions</p>
Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes
<p>Geographic isolation is the primary driver of speciation in many vertebrate lineages. This trend is exemplified by North American darters, a clade of freshwater fishes where nearly all sister species pairs are allopatric and separated by millions of years of divergence. One of the only exceptions is the Lake Waccamaw endemic <em>Etheostoma perlongum</em> and its riverine sister species <em>E. maculaticeps</em>, which have no physical barriers to gene flow. Here we show that lacustrine speciation of <em>E. perlongum</em> is characterized by morphological and ecological divergence likely facilitated by a large chromosomal inversion. While <em>Etheostoma perlongum</em> is phylogenetically nested within the geographically widespread <em>E. maculaticeps</em>, there is a sharp genetic and morphological break coinciding with the lake-river boundary in the Waccamaw River system. Despite recent divergence, an active hybrid zone, and ongoing gene flow, analyses using a de novo reference genome reveal a 9 Mb chromosomal inversion with elevated divergence between <em>E. perlongum</em> and <em>E. maculaticeps</em>. This region exhibits striking synteny with known inversion supergenes in two distantly related fish lineages, suggesting deep evolutionary convergence of genomic architecture. Our results illustrate that rapid, ecological speciation with gene flow is possible even in lineages where geographic isolation is the dominant mechanism of speciation.</p>
Data from: Complex evolutionary processes maintain an ancient chromosomal inversion
<p>Genome re-arrangements such as chromosomal inversions are often involved in adaptation. As such, they experience natural selection, which can erode genetic variation. Thus, whether and how inversions can remain polymorphic for extended periods of time remains debated. Here we combine genomics, experiments, and evolutionary modeling to elucidate the processes maintaining an inversion polymorphism associated with the use of a challenging host plant (Redwood trees) in <em>Timema </em>stick insects. We show that the inversion is maintained by a combination of processes, finding roles for life-history trade-offs, heterozygote advantage, local adaptation to different hosts, and gene flow. We use models to show how such multi-layered regimes of balancing selection and gene flow provide resilience to help buffer populations against the loss of genetic variation, maintaining the potential for future evolution. We further show that the inversion polymorphism has persisted for millions of years and is not a result of recent introgression. We thus find that rather than being a nuisance, the complex interplay of evolutionary processes provides a mechanism for the long-term maintenance of genetic variation.</p>
Data from: Complex evolutionary processes maintain an ancient chromosomal inversion
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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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Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype
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Data from: Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion
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Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes
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Data from: Impact of Z chromosome inversions on gene expression in testes and liver tissues in the zebra finch
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Experimental test of the fitness effects of divergent marine-freshwater chromosomal inversions in stickleback under different salinity conditions
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Data from: Dissecting the role of a large chromosomal inversion in life history divergence throughout the Mimulus guttatus species complex
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