Introgression and Divergence in a Young Species Group.

The process of speciation concerns often multiple diverging and interacting taxa, not only taxon pairs. Understanding the evolution of species' diversity and their persistence therefore requires insight into how gene flow and evolution of reproductive isolation shape groups of closely related species. Using resequencing data, we disentangle genomic patterns of divergence and introgression in five Formica rufa group wood ant species at an early stage of speciation. We revise earlier mitochondrial phylogenies using a nuclear genomic tree and demonstrate that introgression has occurred in line with observations of current day natural hybridisation. Genome-wide correlations between divergence, differentiation, and diversity are in line with theoretical expectations for young species. However, despite previous evidence for polygenic species barriers, our data lack the genome-wide correlation between differentiation and divergence expected under a polygenic barriers model. This is likely explained by the dominating effect of ancestral diversity at these early stages of speciation. Interestingly, we find no strong positive genome-wide correlation between introgression and recombination, suggesting introgression is not predominantly deleterious. This contrasts with many previous empirical studies but aligns with new theoretical work on the interplay of divergence and introgression. Moreover, we observe low diversity in genomic regions with high introgression. This may signal that selection has favoured introgression in specific genomic regions. Such selection would be consistent with previous reports on wood ant hybrids, in which parental species ancestry is sorted likely due to positive selection, or because it allows reduction of genetic load. Benefiting from our focus on the whole F. rufa group and its introgression patterns, we show that interestingly, gene flow could cross multiple species boundaries even without direct interbreeding between each of the species. We discuss the long-term benefits and costs of introgression in young species, including the effect of environmental fluctuations and multi-species introgression.