Incipient speciation and secondary contact in a fossorial island endemic, the São Tomé caecilian

Secondary contact of lineages in the early stages of divergence can result in lineage fusion or promote reproductive isolation through reinforcement. While these processes are well studied in many taxonomic groups, we know little about their contribution to diversification of the secretive and enigmatic caecilians (Amphibia: Gymnophiona). Here, we combine genetic (mtDNA and genome-wide SNPs) and phenotypic data to investigate the divergence history of caecilians endemic to the oceanic island of São Tomé in the Gulf of Guinea archipelago. Consistent with a previous mtDNA study, we find two phenotypically and genetically distinct lineages that occur along a north-to-south axis with extensive admixture in the centre of the island. Demographic modelling supports divergence in allopatry (~300 kya) followed by secondary contact (~95 kya). Contrary to a morphological study that interpreted latitudinal phenotypic variation in these caecilians as a cline within a single widespread species, our analyses suggest a history of allopatric lineage divergence and subsequent hybridization that may have blurred species boundaries. We propose that late Pleistocene volcanic activity favoured allopatric divergence between these lineages with local adaptation to climate maintaining a stable hybrid zone in the centre of São Tomé Island.