Genomewide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids‐adapted clade of cichlids from the Congo River

The lower Congo River is a freshwater biodiversity hot spot in Africa characterized by some of the world's largest rapids. However, little is known about the evolutionary forces shaping this diversity, which include numerous endemic fishes. We investigated phylogeographic relationships in Teleogramma, a small clade of rheophilic cichlids, in the context of regional geography and hydrology. Previous studies have been unable to resolve phylogenetic relationships within Teleogramma due to lack of variation in nuclear genes and discrete morphological characters among putative species. To sample more broadly across the genome, we analysed double‐digest restriction‐associated sequencing (ddRAD) data from 53 individuals across all described species in the genus. We also assessed body shape and mitochondrial variation within and between taxa. Phylogenetic analyses reveal previously unrecognized lineages and instances of microallopatric divergence across as little as ~1.5 km. Species ranges appear to correspond to geographic regions broadly separated by major hydrological and topographic barriers, indicating these features are likely important drivers of diversification. Mitonuclear discordance indicates one or more introgressive hybridization events, but no clear evidence of admixture is present in nuclear genomes, suggesting these events were likely ancient. A survey of female fin patterns hints that previously undetected lineage‐specific patterning may be acting to reinforce species cohesion. These analyses highlight the importance of hydrological complexity in generating diversity in certain freshwater systems, as well as the utility of ddRAD‐Seq data in understanding diversification processes operating both below and above the species level.     

Genetic isolation and morphological divergence mediated by high-energy rapids in two cichlid genera from the lower Congo rapids

Background  

It is hypothesized that one of the mechanisms promoting diversification in cichlid fishes in the African Great Lakes has been the well-documented pattern of philopatry along shoreline habitats leading to high levels of genetic isolation among populations. However lake habitats are not the only centers of cichlid biodiversity - certain African rivers also contain large numbers of narrowly endemic species. Patterns of isolation and divergence in these systems have tended to be overlooked and are not well understood.     

Are characiform Fishes Gondwanan in Origin? Insights from a Time-Scaled Molecular Phylogeny of the Citharinoidei (Ostariophysi: Characiformes)

Fishes of the order Characiformes are a diverse and economically important teleost clade whose extant members are found exclusively in African and Neotropical freshwaters. Although their transatlantic distribution has been primarily attributed to the Early Cretaceous fragmentation of western Gondwana, vicariance has not been tested with temporal information beyond that contained in their fragmentary fossil record and a recent time-scaled phylogeny focused on the African family Alestidae. Because members of the suborder Citharinoidei constitute the sister lineage to the entire remaining Afro-Neotropical characiform radiation, we inferred a time-calibrated molecular phylogeny of citharinoids using a popular Bayesian approach to molecular dating in order to assess the adequacy of current vicariance hypotheses and shed light on the early biogeographic history of characiform fishes. Given that the only comprehensive phylogenetic treatment of the Citharinoidei has been a morphology-based analysis published over three decades ago, the present study also provided an opportunity to further investigate citharinoid relationships and update the evolutionary framework that has laid the foundations for the current classification of the group. The inferred chronogram is robust to changes in calibration priors and suggests that the origins of citharinoids date back to the Turonian (ca 90 Ma) of the Late Cretaceous. Most modern citharinoid genera, however, appear to have originated and diversified much more recently, mainly during the Miocene. By reconciling molecular-clock- with fossil-based estimates for the origins of the Characiformes, our results provide further support for the hypothesis that attributes the disjunct distribution of the order to the opening of the South Atlantic Ocean. The striking overlap in tempo of diversification and biogeographic patterns between citharinoids and the African-endemic family Alestidae suggests that their evolutionary histories could have been strongly and similarly influenced by Miocene geotectonic events that modified the landscape and produced the drainage pattern of Central Africa seen today.     

Phylogenetic relationships and the temporal context for the diversification of African characins of the family Alestidae (Ostariophysi: Characiformes): evidence from DNA sequence data

Phylogenetic relationships within the family Alestidae were investigated using parsimony, maximum likelihood, and Bayesian approaches based on a molecular dataset that included both nuclear and mitochondrial markers. Multiple representatives of all but two of the recognized alestid genera were included, which allowed for testing previous hypotheses of intergeneric relationships and the monophyly of several genera. The phylogenetic position of the Neotropical genus Chalceus with respect to the family Alestidae was also examined. In order to understand the temporal context of alestid diversification, Bayesian methods of divergence time estimation using fossil data in the form of calibration priors were used to date the nodes of the phylogenetic tree. Our results rejected the monophyly of the family as currently recognized (Alestidae sensu lato) and revealed several instances of poly- and paraphyly among genera. The genus Chalceus was recovered well nested within Neotropical characiforms, thus rejecting the hypothesis that this taxon is the most basal alestid. The estimated mean divergence time for the alestid clade (Alestidae sensu stricto) was 54 Mya with a 95% credibility interval of 63-49 Mya. These results are incongruent with the hypothesis that the origin of the family Alestidae predates the African-South American Drift-Vicariance event.     

Review of the cichlid genus Thysochromis (Teleostei: Ovalentaria) with the description of a new species from the Kouilou Province in the Republic of Congo,west–Central Africa

A new species of the chromidotilapiine genus Thysochromis, is described from the Noumbi and Kouilou River drainages in the Republic of Congo. Based on the current investigation, Thysochromis is resolved as containing two geographically disjunct species, T. ansorgii from localities in the upper Guinean ichthyofaunal province (Ivory Coast, Ghana, Benin and Nigeria) and Thysochromis emili sp. nov. restricted to coastal regions of the Republic of Congo in the lower Guinean province.     

Can an eel be a flatfish? Observations on enigmatic asymmetrical heterenchelyids from the Guinea coast of West Africa

Morphological asymmetry is described in the heterenchelyid mud eel Pythonichthys cf. macrurus from inshore coastal waters of Guinea, West Africa. The intensity of asymmetry differs between two examined specimens, with the more extreme case exhibiting strong asymmetry in both external and internal features, including unilateral depigmentation, reductive degeneration and embedding of a blind‐side eye, skewed jaws with reduced dentition and tooth loss. The extent and nature of asymmetry suggests that this individual probably lived primarily on its left lateral side, not unlike sinistral pleuronectiform flatfishes.