Monogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to offer genetic resources for work on African monogeneans by providing mitogenomic data of four species (two belonging to Gyrodactylidae, two to Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective. Using Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasites Gyrodactylus nyanzae, Cichlidogyrus halli, Cichlidogyrus mbirizei (near-complete mitogenome) and the catfish parasite Macrogyrodactylus karibae (near-complete mitogenome). Complete nuclear ribosomal operons were also retrieved, as molecular vouchers. The start codon TTG is new for Gyrodactylus and for Dactylogyridae, as is the incomplete stop codon TA for Dactylogyridae. Especially the nad2 gene is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500 bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparous Aglaiogyrodactylus forficulatus takes a sister group position with respect to the other gyrodactylids, instead of the supposedly ‘primitive’ African Macrogyrodactylus. Inclusion of the African Gyrodactylus nyanzae confirms the paraphyly of Gyrodactylus. The position of the African dactylogyrid Cichlidogyrus is unresolved, although gene order suggests it is closely related to marine ancyrocephalines. The amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available.

This study represents the first exploration of the parasite fauna of cichlid fishes in the Mweru-Luapula subregion (Central Africa). Twelve species of cichlids and 14 species of Monogenea from three genera (Cichlidogyrus, Gyrodactylus and Scutogyrus) were collected. We present a first record of the gill parasite fauna of eight host species, Oreochromis mweruensis, Orthochromis sp. ‘Mambilima’, Sargochromis mellandi, Serranochromis angusticeps, S. stappersi, S. thumbergi and Tylochromis mylodon. The host range of ten parasite species was expanded. The study further includes the description of Cichlidogyrus consobrini sp. n. from S. mellandi and Orthochromis sp. ‘Mambilima’. A new morphotype of C. halli is characterized, and three species – C. papernastrema, C. quaestio and C. zambezensis – are redescribed. Furthermore, the biodiversity and host specificity of these parasites is compared with that of cichlid parasites from Lake Kariba and Cameroon. Two species, including C. consobrini sp. n. and a new morphotype of C. halli, are putative endemics. The parasite fauna in Bangweulu-Mweru is highly similar in species composition to Lake Kariba, but in Bangweulu-Mweru the same parasite species are more host-specific, probably because of hydrogeographical differences between the two regions.

The Lower Congo Basin is characterized by a mangrove-lined estuary at its mouth and, further upstream, by many hydrogeographical barriers such as rapids and narrow gorges. Five localities in the mangroves and four from (upstream) left bank tributaries or pools were sampled. On the gills of Coptodon tholloni, Coptodon rendalli, Hemichromis elongatus, Hemichromis stellifer and Tylochromis praecox, 17 species of parasites (Dactylogyridae & Gyrodactylidae, Monogenea) were found, eight of which are new to science. Six of these are herein described: Cichlidogyrus bixlerzavalai n. sp. and Cichlidogyrus omari n. sp. from T. praecox, Cichlidogyrus calycinus n. sp. and Cichlidogyrus polyenso n. sp. from H. elongatus, Cichlidogyrus kmentovae n. sp. from H. stellifer and Onchobdella ximenae n. sp. from both species of Hemichromis. On Cichlidogyrus reversati a ridge on the accessory piece was discovered that connects to the basal bulb of the penis. We report a putative spillback effect of the native parasites Cichlidogyrus berradae, Cichlidogyrus cubitus and Cichlidogyrus flexicolpos from C. tholloni to the introduced C. rendalli. From our results, we note that the parasite fauna of Lower Congo has a higher affinity with the fauna of West African and nearby freshwater ecoregions than it has with fauna of other regions of the Congo Basin and Central Africa.