Genomic consequences and evolutionary causes of introgression in the late stages of speciation – IntroSpec

Gene flow has long been considered to take place within species only but we now realize that it often occurs between species as well. We still don’t know, however, how much gene flow effectively affects the genome of hybridizing species in the late stage of speciation. Such hybridization may be a source of adaptive genetic variation via the transfer of adaptations from the genome of one species to another, a phenomenon called “adaptive introgression”. While there are a few known prominent examples, its overall importance for adaptation is still largely unknown.
In this project, we address the following main questions: i) how much of the genome is affected by introgression and ii) what proportion of introgression is adaptive?
We have selected the Iberian wall lizard species complex because they have accumulated substantial genomic divergence; in spite of strong barriers to gene flow, nuclear and mitochondrial introgression still occurs; a transcriptome from our model and a reference genome from a close relative are available and we know their distribution, ecology and climatic niches. Last, we already have over 1000 tissue samples so sampling will be limited to additional locations specifically targeted for this project.
To achieve this, we will use whole-genome sequencing to quantify the proportion of the genome affected by admixture. We will then quantify which proportion of introgressed genome is better explained by positive selection. To do so, instead of trying to pinpoint which genes have been experienced adaptive introgression, we will develop a theoretical study using simulations to establish the neutral variance in admixture rates among loci then estimate which proportion of admixture events cannot be explained by neutral processes (see Task 4).
To overcome some of the limits of purely genomic approaches, we also propose an ecological test of the adaptation hypothesis based on candidate genes for climatic adaptation (mitochondrial DNA and the nuclear genes of the OXPHOS chain) in populations living in contrasted climatic conditions (Task 5). We will sample several pairs of populations within each species, each pair being composed of one population located in highly suitable climatic areas and the other in areas where climatic conditions resemble the climatic niche of a hybridizing (donor) species. Finding more loci that have been subjected to introgression in areas that resemble more the climatic conditions of the “donor” species would support the role of adaptive introgression.
Tasks 1 & 2 We will model the current realized climatic niche in all lineages. We will then sample populations in locations (2 per species) of high climatic suitability for the focal species and in the heart of their distribution and in locations (2 per species) where climatic suitability is higher for the other species that hybridizes with the focal species.
Task 3 We will obtain WGS data from 3 individuals in each sampled population (6 per species, 6 species).
Task 4 We will establish by simulation the neutral variance in introgression levels between nuclear loci in the absence of selection. This should give us the limits of the variation that can be reached between loci in terms of introgression level in absence of selection and allow developing methodological tools to identify loci that have been subject to adaptive introgression.
Task 5 We will identify introgressed genomic regions using already published methods then apply results from task 4 to test our idea that the proportion of loci affected by adaptive introgression (the proportion of high-frequency introgressed alleles that cannot be explained by neutral processes) is higher in areas where climatic conditions are closer to the climatic niche of the species which “gave” its genes through introgression, both for the whole genome data and for the OXPHOS genes and mtDNA.