Importance of balancing selection in species adaptation and underlying evolutionary mechanisms – BalanSe

Balancing selection is a form of natural selection that results in the maintenance of genetic diversity, and which can arise from contrasted evolutionary dynamics. Recently, with the accumulation of genomic data and the development of more robust methods, it has been suggested that it might be more common than previously thought. However, most studies have focused on model organisms and have used methods benchmarked only under heterozygote advantage. The overall prevalence of balancing selection in natural populations and the contribution of various mechanisms such as negative frequency-dependent, temporally fluctuating, or spatially-variable selection thus remain largely unknown. Furthermore, the role of balancing selection in maintaining polymorphic structural variations has received recent attention, and the contribution of pseudo-overdominance (resulting from the accumulation of recessive deleterious mutations) in the maintenance of inversions is debated.
The BalanSe project aims at revisiting the question of the importance of balancing selection in nature at the micro- and macro-evolutionary scale, both on point mutations and structural variants. To do so, we will generate simulation data to assess the power of existing methods under contrasted dynamics and explore new combinations of methods to distinguish them, notably using haplotype-based statistics. We will further obtain long-read sequencing data and combine them with short-read data using pangenome-based approaches in four taxa for which we have data from multiple populations of the same species, as well as closely-related and more distant species: primates (Pan/Homo), birds (Ficedula), butterflies (Morpho) and flies (Coelopa). We will assess the genomic prevalence of balancing selection and investigate the underlying evolutionary mechanisms in these taxonomically and ecologically diverse species, controlling for power differences between taxa as predicted based on dedicated simulations. This will inform us on the universality of our results and allow us to test specific evolutionary and ecological hypotheses. In addition, we will explore which biological functions are enriched for balancing selection signals. We will also test whether structural variants, notably inversions, are preferentially found under balancing selection and assess how pseudo-overdominance contribute to maintaining polymorphic inversions.