The consequences of supergene evolution – Supergene

The Supergene project employs a range of approaches to explore chromosomal inversions and their impact on evolution.

Sequencing: The genomes of the species studied are sequenced using next-generation sequencing technologies, allowing for rapid and precise analysis of genetic variations. The development of advanced computational tools is essential for detecting and analyzing chromosomal inversions and for genotyping these variations from various sequencing data sets.

Mathematical Models and Simulations: In parallel, mathematical models and computer simulations are used to understand the conditions under which these inversions are maintained and influence complex traits in organisms. Field studies and laboratory experiments are conducted to link observed genetic variations to phenotypic adaptations, such as behaviors or different color elements.

Ecological and Genomic Consequences: Finally, the research examines the ecological and genomic consequences of these inversions on the overall genetic variation and population structure. This integrative approach provides a comprehensive understanding of supergenes and their role in adaptation and evolution of species.

Genome structure Researchers used advanced technologies to analyse the genomes of butterflies. They identified "inverted" segments of chromosomes that can reorganize and influence wing colour.

Identification of genes involved in phenotype formation Researchers discovered that three chromosomal inversions, P1, P2, and P3, are associated with variations in wing colour in butterflies. They confirmed the involvement of known genes and discovered new coloration genes with previously unknown functions.

Gene annotation and expression The study included the description of genes and other genetic elements, as well as the analysis of the breakpoints of inversions to understand their impact on gene function. Most of the supergene's genes are well expressed during the development of butterfly wings, but significant changes in expression were observed between different supergene variants.

Dominance In the supergene region, heterozygotes show gene expression similar to that of homozygotes. The gene called cortex is identified as an important player in colour variation, but it does not explain everything. Other genes also play a role.

Evolution and ecological consequences Research has shown suppression of recombination around mutations affecting the expression of different colour elements on the wings. However, the evolution of inversions seems linked to the accumulation of transposable elements and deleterious mutations, which results in a significant advantage for heterozygotes but very low larval survival for homozygotes.

Disassortative mating and modelling Mathematical models have been used to analyse the conditions under which heterogamous sexual preferences evolve, showing that these preferences can develop in response to associated deleterious mutations.

Behavioural studies and mate choice signals Behavioural tests in captivity revealed a strong heterogamous preference associated with inversions, influenced by olfactory and visual signals. Manipulating odours showed that these olfactory signals play a crucial role in interaction with visual signals.

Demographic consequences and geographic structuring Genomic simulations and demographic tests showed that inversions can promote large-scale genetic mixing, thus inhibiting population differentiation.

In conclusion, the Supergene project has provided better understanding of how supergenes and chromosomal inversions play a crucial role in the evolution and adaptation of species, paving the way for new perspectives in evolutionary genetics

The Supergene project has opened many perspectives in our understanding of the evolution and adaptation of complex traits. Among the perspectives, we can suggest:

1. By analyzing genomic sequences and their history, we can try to understand why supergenes are complex genetic segments often composed of several adjacent or nested inversions.

2. Continuing to develop methods for detecting and analyzing chromosomal rearrangements will improve our ability to study genomes in a wide variety of species, and thus better measure their consequences.

3. We need to determine why some inversion polymorphisms stabilize in populations while others disappear. This involves testing different models of natural selection and genetic drift to understand the conditions that favor the stability of inversions.

4. A more precise question is to understand why certain genetic combinations show better survival while others have reduced survival. What are the mutations involved, and how do they compensate (or not) in their effects?

In summary, the Supergene project paves the way for new research on how chromosomal inversions shape the evolution and adaptation of species.

There is growing evidence for the prevalence of inversions among genomes of closely-related species, as well as within populations. Yet contributions of chromosomal rearrangements to adaptive evolution are still relatively poorly known. Even less is known on the effect of inversion polymorphisms on population dynamics. A supergene is a master locus composed of tightly-linked genes inherited as a single Mendelian locus, and controlling complex polymorphisms via the co-variation of many characters. Using the supergene controlling adaptive mimicry in a polymorphic, ubiquitous butterfly from the Amazon basin (H. numata), we will investigate the evolution of inversions involved in adaptive polymorphism and their consequences on population biology. Mimicry is the protective resemblance which evolves between toxic prey species, and mimetic butterflies enjoy protection from predators when they display a wing colour pattern used by other local species. H. numata displays several mimetic forms, and the supergene switching between them is associated with polymorphic inversions. Given that the fitness landscape associated with polymorphic mimicry in H. numata can be predicted by spatial variations in butterfly communities, and because we have access to populations with and without inversions polymorphism, this species provide a unique opportunity to disentangle the effect of supergene genetic architecture and ecological variations to genome evolution and population dynamics. In this proposal we will tackle three main questions: (1) What are the characteristics of inversions associated with the supergene, as compared to other inversions occurring in the genome? (2) What are the evolutionary forces driving the persistence of inversion polymorphism, and specifically what are the contributions of the mating system and of deleterious variation associated with inversions? and (3) What are the consequences of inversion polymorphism on population genomics and dynamics ? By combining theoretical, experimental and cutting-edge bioinformatic approaches, and by bringing together researchers from CNRS and INRIA labs from Montpellier, Rennes and Paris, we will provide general conclusions on the role of inversions associated with adaptive polymorphism in the evolution of complex adaptive traits and population biology.