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17 results for “balanced polymorphism”
Data from: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta
Background: Genomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta,is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergence subspecies. Here we delineate the evolutionary processes driving genetic diversity and population differentiation in this species. Results: Using whole genome re-sequencing data from 517 Boechera stricta accessions, we identify four genetic groups that diverged around 30 - 180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence (dXY) and lower relative divergence (FST) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome we also find regions with both high FST and DXY among groups, termed FST-islands. Population genetic signatures indicate that FST-islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms. Conclusions: Our results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation.
Data and scripts from: Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity
<p><em>Carcinus maenas</em> is a globally invasive species which spreads and thrives across a range of temperate environments. In the northwestern Pacific, the species has spread across >12 degrees of latitude in 10 years from a single source, following its introduction <35 years ago. Using six locations spanning >1,500 km, we examined genetic structure and selection to temperature using 9,376 Single Nucleotide Polymorphisms (SNPs) derived from cardiac transcriptome sequencing.</p> <p>Data in this repository includes information on sequenced samples (*.csv, *.txt), a cleaned transcriptome assembly after expression filtering (*.fasta), transcriptome annotation from EnTAP (*.tsv), list of transcripts removed from analysis after mapping (*.txt), high-quality SNPs identified from the transcriptome sequencing with GATK (seven files representing different SNP sets used in the analysis; *.vcf), and four custom scripts used in processing SNP data (*.py and *.R).</p> <p>Raw sequence data is archived in GenBank's SRA. 2015-2016 samples: BioProject ID PRJNA690934 and BioSample IDs SAMN17267686–SAMN17267781. 2011 samples: BioProject ID PRJNA283611 and BioSample IDs SAMN03653390–SAMN03653413.</p>
Balanced polymorphisms and their divergence in a Heliconius butterfly
<p>The evolution of mimicry in similarly defended prey is well described by Müllerian mimicry theory, which predicts the convergence of warning patterns in order to gain the most protection from predators. However, despite this prediction, we can find great diversity of color patterns amongst Müllerian mimics such as <i>Heliconius </i>butterflies in the neotropics. Furthermore, some species have evolved the ability to maintain multiple distinct warning patterns in single populations, a phenomenon known as polymorphic mimicry. The adaptive benefit of these polymorphisms is questionable since variation from the most common warning patterns is expected to be disadvantageous as novel signals are punished by predators naive to them. In this study we use artificial butterfly models throughout Central and South America to characterize the selective pressures maintaining polymorphic mimicry in <i>Heliconius doris.</i> Our results highlight the complexity of positive frequency-dependent selection, the principal selective pressure driving convergence amongst Müllerian mimics, and its impacts on interspecific variation of mimetic warning coloration. We further show how this selection regime can both limit and facilitate the diversification of mimetic traits.</p>
Data and scripts from: Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity
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Data from: Emergence of long-term balanced polymorphism under cyclic selection of spatially variable magnitude
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Data from: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta
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Data from: Multiple forms of balancing selection maintain inversion polymorphism
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Balanced polymorphisms and their divergence in a Heliconius butterfly
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Structural genomic variation and behavioral interactions underpin a balanced sexual mimicry polymorphism
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Data from: Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard
Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard (Podarcis muralis), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions, near genes associated with pterin (SPR) and carotenoid metabolism (BCO2), demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been co-opted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles and haplotype analysis revealed abundant trans-specific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.
Data from: Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird
Colour polymorphisms play a key role in sexual selection and speciation, yet the mechanisms that generate and maintain them are not fully understood. Here, we use genomic and transcriptomic tools to identify the precise genetic architecture and evolutionary history of a sex-linked colour polymorphism in the Gouldian finch Erythrura gouldiae that is also accompanied by remarkable differences in behaviour and physiology. We find that differences in colour are associated with an ~72-kbp region of the Z chromosome in a putative regulatory region for follistatin, an antagonist of the TGF-β superfamily genes. The region is highly differentiated between morphs, unlike the rest of the genome, yet we find no evidence that an inversion is involved in maintaining the distinct haplotypes. Coalescent simulations confirm that there is elevated nucleotide diversity and an excess of intermediate frequency alleles at this locus. We conclude that this pleiotropic colour polymorphism is most probably maintained by balancing selection.
Data from: Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird
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Data from: Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard
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Balancing selection and drift in a polymorphic salamander metapopulation
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Long-term balancing selection for pathogen resistance maintains trans-species polymorphisms in a planktonic crustacean
<p>Data related to the manuscript "Long-term balancing selection for pathogen resistance maintains trans-species polymorphisms in a planktonic crustacean"</p>
Use of single nucleotide polymorphism microarrays to distinguish between balanced and normal chromosomes in embryos from a translocation carrier
GEO Series GSE21732. Homo sapiens. 51 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae
GEO Series GSE14223. Saccharomyces cerevisiae. 54 samples. Type: Genome variation profiling by genome tiling array.
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