![]() ![]() If each of the arrangements contains alleles contributing to local adaptation in a specific habitat, arrangement and habitat will become associated due to selection. A crucial consequence is that effective recombination between standard (ancestral) arrangements and inverted arrangements is reduced or largely prevented due to problems in meiosis. Supergenes might be generated by chromosomal inversions, which reverse the gene order in the affected chromosomal region. This key feature of allowing a ‘switch’ between alternative genotypes without intermediates is useful where a set of optimal discrete phenotypes exists within a population, or where different discrete phenotypes are favoured in different populations connected by gene flow. In the most extreme scenario, a supergene acts as a single locus with a small number of discrete alleles, while with free recombination a variety of genotypes could be produced. Supergenes are genomic regions where alleles at multiple loci contributing to alternative phenotypes are kept in tight linkage. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. However, little is known about whether inversions also contribute disproportionately to parallel evolution. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Local adaptation leads to differences between populations within a species. ![]()
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