Population genomics of incipient allochronic divergence in the Pine Processionary Moth

Allochronic divergence is a key evolutionary mechanism that can frequently lead to incipient speciation. Although theoretical models suggest that such divergence is notably facilitated by small population size and genetic polymorphisms influencing reproductive timing, though constrained by genetic load, empirical validation remains limited. We investigated these predictions by re-analyzing a case of allochronic differentiation between two sympatric populations of pine processionary moth ( Thaumetopoea pityocampa ) in Portugal, using whole genome resequencing (IndSeq and PoolSeq) of those two populations and eight allopatric ones. We inferred the demographic history of those populations, assessed their genetic load, and searched for genomic regions associated with life cycle differences. Our analyses revealed a recent split between the sympatric allochronic populations, accompanied by a strong reduction in gene flow, bottlenecks, inbreeding and accumulation of deleterious variants. Genome scans identified several loci associated with life cycle variation, including genes putatively involved in circadian rhythm regulation. These loci were predominantly located on the Z chromosome, which overall exhibited a marked reduction in diversity in the population with the shifted phenology, likely caused by a bottleneck and an interruption of gene flow at the Z in this population. We discuss how these empirical genomic findings support theoretical expectations that assortative mating driven by differences in reproductive timing, underpinned by polymorphisms in circadian genes, along with genetic drift and purge of genetic load at high-impact sites, can promote the onset and persistence of allochronic divergence.