Geographic isolation is suggested to be among the most important processes in the generation of cichlid fish diversity in East Africa’s Great lakes, both through isolation by distance and fluctuating connectivity caused by changing lake levels. However, even broad scale phylogeographic patterns are currently unknown in many non-cichlid littoral taxa from these systems. To begin to address this we generated restriction-site associated DNA sequence (RADseq) data to investigate phylogeographic structure throughout Lake Tanganyika in two broadly sympatric rocky shore catfish species from independent evolutionary radiations with differing behaviours: the mouth-brooding claroteine, Lophiobagrus cyclurus, and the brood-parasite mochokid, Synodontis multipunctatus. Our results indicated contrasting patterns between these species, with strong lake-wide phylogeographic signal in L. cyclurus including a deep divergence between the northern and southern lake basins. Further structuring of these populations was observed across a heterogeneous habitat over much smaller distances. Strong population growth was observed in L. cyclurus sampled from shallow shorelines, suggesting population growth associated with the colonization of new habitats following lake level rises. Conversely, S. multipunctatus, which occupies a broader depth range, showed little phylogeographic structure and lower rates of population growth. Our findings suggest that isolation by distance and/or habitat barriers may play a role in the divergence of non-cichlid fishes in Lake Tanganyika but this effect varies by species.

All_Synodontis_multipunctatus-alignmentAn alignment of RADseq data for Synodontis multipunctatusAll_Synodontis_multipunctatus.phymlAll_Lophiobagrus-alignmentAlignment of RADseq data for Lophiobagrus cyclurus and Lophiobagrus aquilusAll_Lophiobagrus.phymlStructure_input_Synodontis_multipunctatusStructure_input_LophiobagrusStructure input for Lophiobagrus cyclurus and Lophiobagrus aquilus