The complete mitochondrial genome of endangered Enteromius thysi was determined from Cameroon in Western Africa. The genome was 16,688 bp in length, comprising 37 genes (13 PCGs, 2 rRNAs, 22 tRNAs, and an AT-rich control region). The heavy strand accommodates 28 genes (12 PCGs, 2 rRNAs, and 14 tRNAs), whereas the light strand holds 9 genes (NAD6 and 8 tRNAs). The E. thysi mitogenome is AT-biased (60.5%), as exhibited in other Enteromius species. Most of the PCGs start with the ATG initiation codon, except COI, with GTG, and seven PCGs end with the TAA termination codon, except some with an incomplete termination codon. Most of the tRNAs showed classical cloverleaf secondary structures, except tRNA-serine (trnS1). Bayesian phylogeny distinctly separated E. thysi from other congeners. The control regions of Enteromius species exhibited highly variable nucleotides, and parsimony-informative sites were found in the conserved sequence block-III (CSB-III) compared with other domains and a unique 9 bp tandem repeat (ATGCATGGT) in the variable-number tandem repeats (VNTRs) region of E. thysi. The present phylogeny with limited mitogenomes showed an uneven diversity and evolutionary patterns of Enteromius species distributed in the northwestern and southeastern riverine systems in Africa, which warrants further investigation. Based on the results of the present study, we recommend additional surveys, in-depth taxonomy, and the generation of more mitogenomes that could resolve the diversification pattern of Enteromius species in Africa.

The airbreathing walking catfish (Clariidae: Clarias) comprises 32 species that are endemic to African freshwater systems. The species-level identification of this group is challenging due to their complex taxonomy and polymorphism. Prior to this study, the biological and ecological studies were restricted to a single species, Clarias gariepinus, resulting in a biased view of their genetic diversity in African waters. Here, we generated the 63-mitochondrial Cytochrome c oxidase subunit 1 (COI) gene sequences of Clarias camerunensis and Clarias gariepinus from the Nyong River in Cameroon. Both C. camerunensis and C. gariepinus species maintained adequate intra-species (2.7% and 2.31%) and inter-species (6.9% to 16.8% and 11.4% to 15.1%) genetic distances with other Clarias congeners distributed in African and Asian/Southeast Asian drainages. The mtCOI sequences revealed 13 and 20 unique haplotypes of C. camerunensis and C. gariepinus, respectively. The TCS networks revealed distinct haplotypes of C. camerunensis and shared haplotypes of C. gariepinus in African waters. The multiple species delimitation approaches (ABGD and PTP) revealed a total of 20 and 22 molecular operational taxonomic units (MOTUs), respectively. Among the two Clarias species examined, we found more than one MOTU in C. camerunensis, which is consistent with population structure and tree topology results. The phylogeny generated through Bayesian Inference analysis clearly separated C. camerunensis and C. gariepinus from other Clarias species with high posterior probability supports. The present study elucidates the occurrence of possible cryptic diversity and allopatric speciation of C. camerunensis in African drainages. Further, the present study confirms the reduced genetic diversity of C. gariepinus across its native and introduced range, which might have been induced by unscientific aquaculture practices. The study recommends a similar approach to the same and related species from different river basins to illuminate the true diversity of Clarias species in Africa and other countries.