Diversification and adaptation along environmental gradients: identification of genes and traits involved in species differentiation in alpine butterflies – DIVALPS

Assembly and annotation of 5 reference genomes (2 parental species, 2 species originating from an ancient hybridization event, 1 recent hybrid);

Development of the structural variant genotyping software using long reads, SVJedi-graph, released as open-source via GitHub and Bioconda: github.com/SandraLouise/SVJedi-graph

structural variant detection;

population-level analysis: identification of genomic islands of differentiation, and of the genes and biological traits involved. Analysis of phenotypic clines (pheromones, cuticular compounds, morphometrics, thermal tolerance), genomic and environmental clines in contact zones between species, and genotype × phenotype × environment association analyses.

Five genomes assembled at the chromosomal level and annotated; publication in preparation Development of the Structure Variant genotyping software with long reads, SVJedi-graph, released in open-source via github and Bioconda: github.com/SandraLouise/SVJedi-graph;

Demographic analyses of the four species show that:

The two parental species diverged about 2 million years ago and have asynchronous demographic histories linked to Quaternary climatic fluctuations.

The two hybrid species originated from a hybridization event around 360,000 years ago and have experienced different recent introgression histories with the parental species, whose adaptive role remains to be demonstrated.

Differences in chemical compounds and egg thermal tolerance were identified between species.

Twelve large inversions (>100 kb) were identified between the parental species, including three on the Z chromosome. One of these inversions contains an olfactory receptor that may be involved in mate recognition. The hybrid species have mainly inherited the Z chromosome and inversions from their high-altitude parent, except for three autosomal inversions that were differentially inherited in the two hybrid species.

Studies of the contact zone between C. cephalidarwiniana and C. gardetta show that the Z chromosome once again plays an important role in keeping the species reproductively isolated. Interestingly, the reproductive barriers identified between C. arcania and C. gardetta are not present between cephalidarwiniana and gardetta, suggesting that new mechanisms of isolation have evolved. When looking at the relationship between traits and genes in the hybrid zone, we found that the traits studied—such as chemical cuticular compounds and wing patterns—are influenced by many genes, and the associated genes do not show especially sharp transitions across the contact zone. Reproductive isolation between the lowland species and the three alpine species may involve mate recognition through chemical signals (a form of prezygotic isolation), as well as the reduced heat tolerance of eggs from high-altitude species, which could select against hybrids. The exact mechanisms that prevent hybrid species from interbreeding with their high-altitude parent species, however, are still unknown.

SVJedi-graph: Open-source package for structural variants genotyping via github et Bioconda : github.com/SandraLouise/SVJedi-graph.

Repeated adaptation in related lineages to similar environmental conditions could result from natural selection acting independently in each lineage, or from adaptive introgression between lineages during periods of range overlap. Here we focus on a complex of butterfly species distributed along the altitudinal gradient, and with different histories of altitudinal adaptation, to understand how populations adapt to higher elevation. We will analyse genomes of butterflies in contact zones to identify introgressions and rearrangements between taxa, i.e. regions more or less permeable to gene flow, and associate them with adaptive phenotypic variation. By using hybrid taxa originating from ancient hybridization, we will untangle the effects of genome-wide differentiation due to allopatry and demography from those of selection on genes involved in local adaptation and reproductive isolation. We will reveal to what extent these genes were exchanged between lineages. To understand how the key traits conferring altitudinal adaptation are shared by introgression among alpine lineages or act as barriers to gene flow, we will use admixed populations in contact zones, taking advantage of a natural recombination experiment allowing the segregation of the phenotypic traits characterising each taxon through many generations of recombination. This will allow linking traits and candidate genes with adaptation to changes in climatic and biotic conditions with altitude. This system offers an excellent opportunity to decipher the processes involved in adaptation to new conditions along the altitudinal gradient, and identify the key traits and candidate genes involved. This project will mobilise forces from thres distinct labs with expertise in bioinformatics, population genomics, ecology, and experimental approaches.trogressions with adaptation to changes in climatic and biotic conditions with altitude.