Rethinking the Nile Perch Species Complex: Diversification and Phenotypic Plasticity in the most widespread fisheries keystone species in African Freshwaters

Abstract

Studying the diversity of freshwater fish species, in particular, the Nile perch complex is crucial for understanding and managing African freshwater ecosystems. As top predators, they play a significant role in regulating fish populations and influencing ecosystem functioning. Taxonomic uncertainties within the complex necessitate further investigation. We study the morphological diversification of lates perches (Latidae) across Afrotropical freshwaters. We hypothesize morphological differentiation between Nile perches from various basins and habitats, particularly between the Congo and Nile rivers. We expect an increased morphospace in lacustrine environments compared with riverine environments, reflecting the presence of more species in the lakes. We aim to assess the status of two sympatric species in Lake Turkana. Specimens of lates perches were collected from various historical collections and included in the morphological study. A subsample underwent X-ray or CT scanning. Morphological measurements (37 parameters) were obtained using a digital caliper. Meristic data, including fin formulas, scale counts, and vertebral counts were recorded. Genetic data were retrieved from ten specimens of Lake Turkana (Kenya). Fin clips were collected and DNA extraction was performed, followed by Illumina sequencing (with targeted bait capture), and Sanger sequencing of the targeted markers (11 mitochondrial, 1 nuclear). Phylogenetic analyses were conducted using maximum likelihood estimation and Bayesian inference. The morphological data reveal a remarkably conserved morphology with local variation. Based on the combined genetic and morphological evidence, we classify Lates niloticus var. macrolepidota from the Congo River as a distinct species, elevated to Lates macrolepidotus Pellegrin, 1922. We observe east-west clinal variation, with Guinean populations showing greater similarity in meristics to L. macrolepidotus, likely influenced by the predominance of rainforest ecosystems and habitats. The endemic species from lakes Turkana and Albert exhibit morphological differences from the co-occurring L. niloticus, but without species-level genetic differentiation in Lake Turkana.