Budding speciation, mitochondrial capture and introgression between surface and cave lineages in the Asellus...

Replicated pairs of ancestral and evolutionarily derived populations provide opportunities to test hypotheses about the deterministic laws of evolution. The Asellus aquaticus species complex is an invertebrate model system with several independent surface-to-cave transitions and a complicated and unresolved evolutionary history. Here, we sampled all known major lineages and surface-cave population pairs, and used genome-wide ddRAD sequencing to improve phylogenetic resolution. We present a robust phylogenetic backbone that is essential for testing hypotheses of ecological transitions, trait evolution and comparative analyses. Our results support an emerging new perspective on the evolution of cave invertebrates from surface ancestors. First, frequent admixture between distinct surface lineages may preclude pinpointing a single surface sister lineage for each cave colonization. Second, the mitochondrial genomes of some cave lineages have been replaced by mitogenomes of adjacent surface populations during sporadic Pleistocene hybridization events. The resulting new phylogenetic view of Asellus aquaticus is one of continuously admixing surface lineages with several isolated cave lineages budding off from the omnipresent surface progenitor. Some cave lineages have been described as separate species. Hence, the taxonomic structure of the species complex is shaped by ecologically driven budding speciation rather than by a usual succession of dichotomous lineage splits.