Geographic and Genomic Signatures of a Dynamic Evolutionary History in Lake Tanganyika's Synodontis Catfish Radiation

Abstract

Aim Lacustrine systems generally exhibit greater habitat stability than riverine systems, yet some lakes have experienced substantial lake‐level fluctuations throughout the Pleistocene. These environmental perturbations repeatedly altered habitat availability critical to the evolution of their diverse fish communities. In this context, we inferred phylogenetic relationships and divergence times of lacustrine Synodontis catfishes in Lake Tanganyika. We then focused on three closely related species with distinct ecomorphological specializations ( Synodontis petricola , S. polli , S. irsacae ) to further investigate their evolutionary dynamics and elucidate responses to a temporally dynamic lacustrine environment. Location Lake Tanganyika, East Africa. Taxa Synodontis spp. (Mochokidae). Methods We used mitochondrial genomes for phylogenetic reconstruction and divergence time estimation, mitochondrial COI sequences for haplotype network analysis, and genome‐wide SNPs from ddRADseq to assess population structure, demographic history, and patterns of gene flow. Results Mitochondrial genomes indicate that diversification within lacustrine Synodontis of Lake Tanganyika occurred in two main phases during the Pleistocene (2.5–1.5 Ma and 1.0–0.5 Ma), coinciding with pronounced lake‐level fluctuations and palaeoclimatic shifts. Across three closely related but ecologically distinct species, S. petricola and S. polli exhibited mitonuclear discordance—with distinct mtDNA lineages in the northern and southern lake basins—and also showed strong population structure based on nuclear genomic SNP data, whereas S. irsacae lacked geographically structured mtDNA lineages and displayed weaker nuclear differentiation. Demographic reconstructions revealed asynchronous, species‐specific expansions across lake basins, and gene‐flow modelling indicated introgression across all species following a period of isolation after divergence. Main Conclusions Our results show that—in Lake Tanganyika—complex phylogeographic patterns in lacustrine fishes can arise through combined effects of lake‐level fluctuations, ecological specialization, and spatially variable gene flow. These findings highlight how dynamic environmental histories in lacustrine systems can profoundly shape diversification of their biodiversity.

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