Background Cichlids are a prime model system in evolutionary research and several of the most prominent examples of adaptive radiations are found in the East African Lakes Tanganyika, Malawi and Victoria, all part of the East African cichlid radiation (EAR). In the past, great effort has been invested in reconstructing the evolutionary and biogeographic history of cichlids (Teleostei: Cichlidae). In this study, we present new divergence age estimates for the major cichlid lineages with the main focus on the EAR based on a dataset encompassing representative taxa of almost all recognized cichlid tribes and ten mitochondrial protein genes. We have thoroughly re-evaluated both fossil and geological calibration points, and we included the recently described fossil † Tugenchromis pickfordi in the cichlid divergence age estimates. Results Our results estimate the origin of the EAR to Late Eocene/Early Oligocene (28.71 Ma; 95% HPD: 24.43–33.15 Ma). More importantly divergence ages of the most recent common ancestor (MRCA) of several Tanganyika cichlid tribes were estimated to be substantially older than the oldest estimated maximum age of the Lake Tanganyika: Trematocarini (16.13 Ma, 95% HPD: 11.89–20.46 Ma), Bathybatini (20.62 Ma, 95% HPD: 16.88–25.34 Ma), Lamprologini (15.27 Ma; 95% HPD: 12.23–18.49 Ma). The divergence age of the crown haplochromine H-lineage is estimated to 22.8 Ma (95% HPD: 14.40–26.32 Ma) and of the Lake Malawi radiation to 4.07 Ma (95% HDP: 2.93–5.26 Ma). In addition, we recovered a novel lineage within the Lamprologini tribe encompassing only Lamprologus of the lower and central Congo drainage with its divergence estimated to the Late Miocene or early Pliocene. Furthermore we recovered two novel mitochondrial haplotype lineages within the Haplochromini tribe: ‘ Orthochromis ’ indermauri and ‘ Haplochormis ’ vanheusdeni. Conclusions Divergence time estimates of the MRCA of several Tanganyika cichlid tribes predate the age of the extant Lake Tanganyika basin, and hence are in line with the recently formulated “Melting-Pot Tanganyika” hypothesis. The radiation of the ‘Lower Congo Lamprologus clade’ might be linked with the Pliocene origin of the modern lower Congo rapids as has been shown for other Lower Congo cichlid assemblages. Finally, the age of origin of the Lake Malawi cichlid flock agrees well with the oldest age estimate for lacustrine conditions in Lake Malawi. Electronic supplementary material The online version of this article (10.1186/s12862-019-1417-0) contains supplementary material, which is available to authorized users.

Fossil tip‐dating allows for the inclusion of morphological data in divergence time estimates based on both extant and extinct taxa. Neoselachii have a cartilaginous skeleton, which is less prone to fossilization compared to skeletons of Osteichthyans. Therefore, the majority of the neoselachian fossil record is comprised of single teeth, which fossilize more easily. Neoselachian teeth can be found in large numbers as they are continuously replaced. Tooth morphologies are of major importance on multiple taxonomic levels for identification of shark and ray taxa. Here, we review dental morphological characters of squalomorph sharks and test these for their phylogenetic signal. Subsequently, we combine DNA sequence data (concatenated exon sequences) with dental morphological characters from 85 fossil and extant taxa to simultaneously infer the phylogeny and re‐estimate divergence times using information of 61 fossil tip‐dates as well as eight node age calibrations of squalomorph sharks. Our findings show that the phylogenetic placement of fossil taxa is mostly in accordance with their previous taxonomic allocation. An exception is the phylogenetic placement of the extinct genus †Protospinax, which remains unclear. We conclude that the high number of fossil taxa as well as the comprehensive DNA sequence data for extant taxa may compensate for the limited number of morphological characters identifiable on teeth, serving as a backbone for reliably estimating the phylogeny of both extinct and extant taxa. In general, tip‐dating mostly estimates older node ages compared to previous studies based on calibrated molecular clocks.

Five new rheophilic haplochromine cichlid species are described from the Upper Congo drainage of Zambia and the Democratic Republic of the Congo: Orthochromis mporokoso sp. nov. and O. katumbii sp. nov. from the Bangwelu-Mweru ecoregion, O. kimpala sp. nov. and O. gecki sp. nov. from the Upper Lualaba ecoregion, and O. indermauri sp. nov. from the Lufubu River of the Lake Tanganyika ecoregion. Orthochromis kimpala sp. nov, O. gecki sp. nov., and O. indermauri sp. nov. are distinguished from all currently valid species of the genus Orthochromis Greenwood 1954, except for O. torrenticola (Thys van den Audenaerde 1963), by the presence of eggspots or eggspot-like maculae on the anal fin (vs. no eggspots). The three species can be easily distinguished from O. torrenticola by having three anal spines (vs. four anal spines). Moreover, all five new species can be individually distinguished from all currently known rheophilic taxa placed in the genera Orthochromis, Schwetzochromis Poll 1948 and the rheophilic species of the genus Haplochromis Hilgendorf 1888 (e.g. H. bakongo Thys van den Audenaerde 1964, H. snoeksi Wamuini Lunkayilako & Vreven 2010, H. vanheusdeni Schedel et al. 2014) either based on meristic values, morphometric distances and colouration patterns, or on a combination of them.

Hemibates koningsi, new species, is described from southern Lake Tanganyika (Republic of Zambia) as the second species of Hemibates Regan, 1920. Males of the new species are easily distinguished from H. stenosoma (Boulenger, 1901) based on their adult color pattern, i.e. black vertical bars on the anterior flanks part and posterior horizontal bands on a silvery-whitish body coloration vs. an anterior flank color pattern of black blotches of variable number, size and shape and posterior horizontal bands. Males and females of the new species are further distinguished by their longer lower pharyngeal jaw (37.6–38.2% HL vs. 27.8–32.5% HL) with a characteristically curved keel, which is straight or only slightly curved towards the tips in H. stenosoma. The new species has on average fewer gill rakers on the first gill arch than its only congener (33–37 vs 35–43).

Located in the central region of northern Nigeria, the Jos Plateau covers approximately 9,400 km² with an average altitude of 1,280 m and constitutes a unique terrestrial ecoregion known as the Jos Plateau forest-grassland mosaic. The biota of the Jos Plateau include endemic elements, but very limited information is available on its ichthyofauna. This is despite the fact that the ancient plateau contributes to several large rivers spanning multiple major drainage systems including the Niger and Benue Rivers, and Lake Chad. This study provides the first species list for the fishes of the Jos Plateau based mainly on 175 DNA barcoded museum voucher specimens representing 20 species, and another three species without a DNA barcode. In total, 23 species from eight families and 17 genera were collected from the Jos Plateau including five putatively new species, four in the family Cyprinidae and one in the Clariidae. With ten species, the Cyprinidae is the most diverse fish family on the Jos Plateau, followed by Clariidae and Cichlidae, each with three species. The study also provides data on species distribution and habitat parameters including information on water chemistry that strongly suggests that selected water bodies are heavily impacted by anthropogenic activities. Urgent management steps are required to preserve the unique and diverse fish communities of the Jos Plateau and their habitats.