Diversification and hybridization within the Spirochona gemmipara complex driven by gammarid host range shifts.

Hybridizing multispecies complexes represent understudied genetic systems within unicellular eukaryotes. Using integrated morphological, morphometric, and multilocus phylogenetic data, we show that Spirochona gemmipara, a widespread ciliate epibiont of European freshwater gammarids, constitutes a hybridizing network of at least nine lineages forming a sympatric multispecies syngameon. Time-calibrated phylogenies indicate that its five main lineages originated in the Miocene through allopatric divergence on isolated European paleoislands colonized independently by freshwater gammarids. Subsequent reconnection of continental freshwater systems following the regression of the Paratethys Sea enabled secondary contact and hybridization among emerging S. gemmipara-like species, with later Pleistocene range shifts likely maintaining compatibility within the syngameon. Discordant mitochondrial signals within the syngameon are consistent with heteroplasmy and may also reflect phylogenetic noise or nuclear mitochondrial pseudogenes (NUMTs), and only tentatively suggest the possibility of mitogenome recombination. This added complexity underscores the need for whole-genome analyses to clarify mechanisms driving mitochondrial diversity and hybridization in ciliates.