Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania

Molecular phylogenetic evidence clearly resolves the African cichlid fish genus Ctenochromis, as defined by Greenwood (1979), as paraphyletic. Here, we redefine the genus Ctenochromis and assign Ctenochromis horei, a member of the Tropheini from Lake Tanganyika, to a new genus Shuja gen. nov. We restrict Ctenochromis to Ctenochromis pectoralis and Ctenochromis scatebra sp. nov., both of which are endemic to the Pangani River catchment in northern Tanzania, and are resolved as sister taxa in a phylogenetic analysis using genome-wide data. Ctenochromis pectoralis is the type species of the genus and described from specimens collected near Korogwe, Tanzania. The species was declared extinct in a 2016 IUCN Red List Assessment. We confirm the continued presence of a population of C. pectoralis within the Ruvu tributary linking Lake Jipe to Nyumba ya Mungu Reservoir. The new taxon Ctenochromis scatebra sp. nov. is described from Chemka Springs, and recognised on the basis of differences from C. pectoralis in tooth and jaw morphology

Sympatric and allopatric Alcolapia soda lake cichlid species show similar levels of assortative mating

Characterising reproductive barriers such as mating preferences within rapid evolutionary radiations is crucial for understanding the early stages of speciation. Cichlid fishes are well-known for their adaptive radiations and capacity for rapid speciation and as such we investigate assortative mating among Alcolapia species; a recent (<10,000 years), small adaptive radiation, endemic to the extreme soda lakes, Magadi (one species) and Natron (three species), in East Africa. In seminatural aquarium conditions, we observed both courtship and mate choice (tested by microsatellite paternity analysis) to be significantly assortative among the three sympatric Natron species in a three-way choice experiment. This was also the case between allopatric species from Natron and Magadi, as found in a two-way choice experiment. However, the proportion of disassortative matings was substantial in both of these experiments, with hybrids comprising 29% of offspring in sympatric species and 11.4% in allopatric species comparisons. . Previous work suggests that the Natron/Magadi split might not be much older than the radiation within Natron, so the similar rate of hybridisation in the allopatric comparison is surprising and inconsistent with predictions of reinforcement theory, which predicts a faster rate of accumulation of premating isolation in sympatry. The relatively weak assortative mating in sympatry suggests that additional reproductive barriers, such as microhabitat preferences or spatial structuring may contribute to genetic isolation in nature

Sympatric and allopatric Alcolapia soda lake cichlid species show similar levels of assortative mating

Characterizing reproductive barriers such as mating preferences within rapid evolutionary radiations is crucial for understanding the early stages of speciation. Cichlid fishes are well-known for their adaptive radiations and capacity for rapid speciation and as such we investigate assortative mating among Alcolapia species; a recent (<10,000 years), small adaptive radiation, endemic to the extreme soda lakes, Magadi (one species) and Natron (three species), in East Africa. In seminatural aquarium conditions, we observed both courtship and mate choice (tested by microsatellite paternity analysis) to be significantly assortative among the three sympatric Natron species in a three-way choice experiment. This was also the case between allopatric species from Natron and Magadi, as found in a two-way choice experiment. However, the proportion of disassortative matings was substantial in both of these experiments, with hybrids comprising 29% of offspring in sympatric species and 11.4% in allopatric species comparisons. Previous work suggests that the Natron/Magadi split might not be much older than the radiation within Natron, so the similar rate of hybridization in the allopatric comparison is surprising and inconsistent with predictions of reinforcement theory, which predicts a faster rate of accumulation of premating isolation in sympatry. The relatively weak assortative mating in sympatry suggests that additional reproductive barriers, such as microhabitat preferences or spatial structuring may contribute to genetic isolation in nature

Ctenochromis scatebra Genner, Ngatunga & Turner 2022, sp. nov.

Ctenochromis scatebra Genner, Ngatunga & Turner sp. nov. urn:lsid:zoobank.org:act: 8B105DD6-6E73-4679-81D1-1A63CF668E5C Figs 6e–f, 7g –i, 8c Ctenochromis pectoralis – de Graaf 2011: 38 (specimens from Chemka Springs). — van Heusden 2015: 24–27, 29 (part, specimens from Chemka Springs). — Schedel et al. 2019: 27–30. — Carleton et al. 2020: 4961, 4964, fig 2. Ctenochromis sp. – Kalacska et al. 2017: 4 –6,18, fig. 2g –j. Diagnosis Ctenochromis scatebra sp. nov. is recognised as a member of Ctenochromis. This is because it possesses the diagnostic feature of a sharp break from small anterior scales to large posterior scales between the pectoral and pelvic fins, and it possesses scaleless areas on either side of the chest (Greenwood 1979). In C. scatebra sp. nov. squamation is absent from the ventral part of the cheek, which is characteristic of the genus Ctenochromis. Mature adult male C. scatebra sp. nov. possess at least one clear non-ocellate egg spot on the anal fin. Etymology The species is named from the Latin noun 'scatebra’, meaning 'spring’ or 'a gush of water from the ground’, referring to the type locality which is a spring in northern Tanzania. Material examined Holotype TANZANIA • &male; (54.9 mm SL); Chemka Springs; 3.443° S, 37.194° E; 17Aug. 2015; BMNH 2021.7.15.4 (Figs 6f, 7g –i, 8c). Paratypes TANZANIA • 9 individuals (between 33.8 and 59.1 mm SL); same collection data as for holotype; BMNH 2021.7.15.5 – BMNH 2021.7.15.13. Description Holotype and paratype measurements in Table 3. Body laterally compressed, deeper than wide. Head (lateral view) slightly convex between eye and dorsal fin. Snout straight in lateral view, rounded in dorsal view. Mouth retrognathus. Lips slightly thickened, equally developed. Teeth in outer row primarily unicuspid, widened (shovel shaped), often slanted. Side teeth in outer row unequally bicuspid and pointed. Teeth in inner rows small, in fleshy tissue. Pectoral fin origin above dorsal fin origin, pelvic fin origin slightly more anterior. Caudal-peduncle longer than deep (caudal-peduncle depth 62.0–83.4% of caudal-peduncle length). Scales ctenoid on flanks. Scales cycloid on head, between pectoral fin and anal fin, along dorsal-fin base. Scales absent from chest. Lateral-line scales 15–21/7–11, Dorsal fin XIV–XV, 8–9, Anal fin III, 7–8. Colour Live colouration from images of live specimens in natural habitat (Schedel 2019). Mature males: dorsal body grey-blue, flanks lighter than dorsal with blueish sheen. Depending on mood, a very faint midline stripe and 4–5 very faint vertical bars present. Head dark grey-blue, blue sheen below and posterior to eye. Blue tinge to lower lip. Dorsal fin grey-blue with orange-red lappets, red posteriorly. Pectoral fins black. Pelvic fins with red base. Anal fin grey/blue, red posteriorly, with one or two (rarely three) non-ocellate egg spots (multiple spots tightly packed). Caudal fin light grey-blue, with red tinges at the dorsal and ventral tips. Euthanised fish: colours darker (Fig. 6e). Females and subadult males: flank grey-brown base colour, white ventrally. Fins uniformly light grey-brown. Flank with 6–8 irregularly shaped and irregularly spaced vertical bars, alongside partially complete midlateral and dorsolateral stripes. Bar and stripe patterns variable among individuals, faded in some specimens (photo in van Heusden 2015). Preserved coloration: in ethanol brown or beige. Male non-ocellate egg spots on anal fin sometimes visible. Distribution The species is restricted to Chemka Springs and the surrounding water bodies immediately adjacent to the Springs. Water from Chemka Springs flows southwards into the Kikuletwa River towards Nyumba ya Mungu Reservoir. Surveys are needed further downstream from the site of the spring, into the river, to determine the full species distribution. Life history The species has been observed feeding upon epilithic and epiphytic algae in Chemka Springs, as well as sifting soft sediment (Schedel 2019), and pecking on skin of swimmers. The species is therefore most likely an omnivorous generalist. Only two other fish species are known from Chemka Springs, Garra cf. dembeensis (Rüppell, 1835) and Clarias gariepinus (Burchell, 1822). The water maintains a steady 28.4°C (Røhr et al. 2002). Remarks Phylogenetic analyses, based on genome-wide genetic markers, place C. scatebra sp. nov. as a sister to the type species C. pectoralis (Fig. 4). Specimens of C. scatebra sp. nov. can be distinguished from C. pectoralis based on two aspects of trophic morphology: 1) C. scatebra sp. nov. has front teeth in the outer row on both jaws that are primarily unicuspid, widened (shovel shaped) and often slanted (Fig. 7g), while side teeth in the outer row are unequally bicuspid and pointed; by contrast all front and side teeth in the outer row of C. pectoralis are all unequally bicuspid and pointed (Fig. 7a, d); 2) Ctenochromis scatebra sp. nov. has a retrognathus jaw, while C. pectoralis has a marginally prognathous jaw (Figs 6, 8).Published as part of Genner, Martin J., Hsu, Ling-Lan, Collins, Rupert A., Smith, Alan M., Saxon, Andrew D., Shechonge, Asilatu H., Ngatunga, Benjamin P. & Turner, George F., 2022, Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania, pp. 23-54 in European Journal of Taxonomy 819 on pages 46-47, DOI: 10.5852/ejt.2022.819.1775, http://zenodo.org/record/654437

Ctenochromis pectoralis Pfeffer 1893

Ctenochromis pectoralis Pfeffer, 1893 Figs 6a–d, 7a–f, 8a–b Tilapia pectoralis – Boulenger 1899: 130. Haplochromis pectoralis – Regan 1922a: 685. — Jordan 1923: 219. — van Oijen et al. 1991: 161. non Harpagochromis pectoralis – Kaufman 1996: 1. Material examined Lectotype TANZANIA • Korogwe; 1888; F. Stuhlmann leg.; ZMH, ZMH402. Paralectotypes TANZANIA • 3 individuals; Korogwe; 1888; F. Stuhlmann leg.; ZMH403 1–3 • 1 individual; Korogwe; 1888; F. Stuhlmann leg.; BMNH 1899.2.27.1. Additional material TANZANIA – Ruvu River (between Lake Jipe and Nyumba ya Mungu Reservoir) • 3 specimens; 14 Aug. 2015; M. Genner, A. Shechonge, A. Smith and B.P. Ngatunga leg.; BMNH 2021.7.15.1 – BMNH 2021.7.15.3. Distribution Pangani River system, specimens only known from the Korogwe, Nyumba ya Mungu Reservoir, and the Ruvu River (between Lake Jipe and Nyumba ya Mungu Reservoir).Published as part of Genner, Martin J., Hsu, Ling-Lan, Collins, Rupert A., Smith, Alan M., Saxon, Andrew D., Shechonge, Asilatu H., Ngatunga, Benjamin P. & Turner, George F., 2022, Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania, pp. 23-54 in European Journal of Taxonomy 819 on pages 43-44, DOI: 10.5852/ejt.2022.819.1775, http://zenodo.org/record/654437

Ctenochromis Pfeffer 1893

Genus Ctenochromis Pfeffer, 1893 Type species Ctenochromis pectoralis Pfeffer, 1893 (by original designation). Diagnosis Ctenochromis is a haplochromine cichlid genus restricted to species with the combination of four key characters, following Greenwood (1979): 1) “The abrupt size transition between the very small chest scales and the larger scales on the ventrolateral aspects of the anterior flanks”, 2) “a naked area on either side of the chest”, 3) “a failure of cheek squamation to reach the ventral margin of the cheek”, and 4) “anal fin markings of male fishes are in the form of one or two (rarely three) non-ocellate spots”. Remarks As noted by Greenwood (1979: 288), non-ocellate spots are “without a dark margin or clear surround”. In Greenwood (1979) the significance of the non-ocellate male egg spots in the diagnosis of Ctenochromis is unclear, hence a rediagnosis has been provided here. Using the four diagnostic characters for Ctenochromis listed above, the genus currently includes only C. pectoralis and Ctenochromis scatebra sp. nov. described herein. Of Greenwood’s (1979) five species of Ctenochromis, namely C. pectoralis, C. horei, C. luluae, C. oligacanthus and C. polli, Greenwood notes that three species have non-ocellate egg spots but did not specifically mention which species, although it is likely that Greenwood considered his C. polli to have this trait, given the mention of a colour photograph of the species in Voss (1977: 74). Based on photographs of field collected specimens, or specimens kept in aquaria, we are aware of only one of Greenwood’s five species that unquestionably possesses non-ocellate egg spots, namely the type species C. pectoralis (Fig. 6). Aquarium specimens of Greenwood’s C. horei (herein Shuja horei gen. et comb. nov.) are clearly in possession of ocellate egg spots (see Konings 2015). In contrast to Greenwood, we consider Voss (1977: 74) to show a specimen of Greenwood’s C. polli with an ocellate spot, as does a photograph in Lamboj (2004: 212). There is a photograph of a specimen of C. luluae in Lamboj (2004: 211) with ocellate eggspots. We are unaware of any unambiguous evidence of the precise egg spot characteristics of Greenwood’s C. oligacanthus. Hence, we follow Daget et al. (1991) and Fricke et al. (2021) in assigning Greenwood’s C. polli, C. luluae and C. oligacanthus to the catchall genus Haplochromis, as Haplochromis polli, Haplochromis luluae and Haplochromis oligacanthus, respectively. These three taxa will require a comprehensive taxonomic evaluation. In addition, the specimens we observed of Shura horei gen. et comb. nov. do not possess the “naked area on either side of the chest” characteristic of Ctenochromis, but instead have a single scaleless area at the anterior of the chest. This single scaleless area at the anterior of the chest is also shared with the phylogenetically proximate Gnathochromis pfefferi.Published as part of Genner, Martin J., Hsu, Ling-Lan, Collins, Rupert A., Smith, Alan M., Saxon, Andrew D., Shechonge, Asilatu H., Ngatunga, Benjamin P. & Turner, George F., 2022, Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania, pp. 23-54 in European Journal of Taxonomy 819 on pages 42-43, DOI: 10.5852/ejt.2022.819.1775, http://zenodo.org/record/654437

Shuja Genner, Ngatunga & Turner 2022, gen. nov.

Genus Shuja Genner, Ngatunga & Turner gen. nov. urn:lsid:zoobank.org:act: 7862EC4A-51D5-4535-98D5-650D6CC165A7 Type species Chromis horei Günther, 1894. Diagnosis Shuja gen. nov. can be diagnosed as a genus of haplochromine cichlid within the Tropheini. According to Takahashi (2003: 379), the Tropheini have “extensively granulated cycloid scales at midbody”, with the “granulations comprising irregularly arranged, variously shaped protrusions over almost entire exposed surface”. Shuja gen. nov. is the only representative of the Tropheini with a prognathous lower jaw, versus the retrognathus or isognathus jaw in other genera within the Tropheini (Table 2). Etymology The genus name is derived from the Swahili noun 'shujaa’, translated into English as 'brave person’ or 'warrior’, referring to the notable territorial behaviour of the males of this genus. Description One species in genus Shuja horei gen. et comb. nov. Species description, from original German text (Günther 1894: 630): “Dorsal fin 14 spines 8 rays, L. lat 28, L. trans. 4/9. Teeth bicuspid, cusps subequal, slightly tinged with brown; 28–31 each side of upper jaw outer series. Cheeks naked or few extremely thin scales. In specimen nearly 5 inches (12.70 cm) long eye diameter nearly equal to depth of soft part of cheek, a little less than width of preorbital and interorbital space, which is flat. Preopercular limbs at right angle. Body height less than length of head, and one third of total (without caudal). Last dorsal spine longest, two fifths of head length. Pectoral fin to, or nearly to, origin of anal fin. Caudal scaleless. Scales rough, some with margins ciliated. Body light greenish, with incomplete brownish cross-bands on upper part of body. Largest specimen cheek and snout with irregular deep brown spots. Soft dorsal and caudal fin with scattered ocelli; milky-white spot between last two anal rays.” In Shuja horei gen. et comb. nov. hypertrophied lips absent. Remarks Shuja gen. nov. belongs to Tropheini tribe of African cichlids, originally defined by Poll (1986). The diagnosis of Tropheini is the presence of “extensively granulated cycloid scales at midbody” (Takahashi 2003: 379). Our observations suggest such granularity of the flank/midbody scales in Tropheini is present in Shuja horei gen. et comb. nov., Gnathochromis pfefferi and Lobochilotes labiata, at least, but also small ctenii are present. These ctenii are sparse and largely restricted on the margins of this caudal edge of the scale. Viertler et al. (2021) report multiple species in the Tropheini with ctenoid scales on the central flank area. Further detailed work of all described species is needed to determine if the distribution of the granulation and ctenii on midbody scales is diagnostic of the Tropheini. Nevertheless, irrespective of morphological traits, the tribe is unambiguously monophyletic in genome-scale molecular phylogenetic analyses (Ronco et al. 2021), and endemic to Lake Tanganyika and immediate river systems. Within the tribe, Shuja gen. nov. is a monotypic genus and can be distinguished from other representatives of the Tropheini by the presence of a prognathous jaw (Fig. 5a–c), when all other described species in the Tropheini have a retrognathus or isognathus jaw (Table 2). These include Gnathochromis pfefferi, and representatives of Interochromis, Limnotilapia, Lobochilotes, Petrochromis, Pseudosimochromis, Simochromis and Tropheus (Table 2).Published as part of Genner, Martin J., Hsu, Ling-Lan, Collins, Rupert A., Smith, Alan M., Saxon, Andrew D., Shechonge, Asilatu H., Ngatunga, Benjamin P. & Turner, George F., 2022, Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania, pp. 23-54 in European Journal of Taxonomy 819 on pages 40-41, DOI: 10.5852/ejt.2022.819.1775, http://zenodo.org/record/654437

Nuclear environmental DNA resolves fine-scale population genetic structure in an aquatic habitat

Summary: There is considerable potential for nuclear genomic material in environmental DNA (eDNA) to inform us of population genetic structure within aquatic species. We tested if nuclear allelic composition data sourced from eDNA can resolve fine scale spatial genetic structure of the cichlid fish Astatotilapia calliptera in Lake Masoko, Tanzania. In this ∼35 m deep crater lake the species is diverging into two genetically distinguishable ecomorphs, separated by a thermo-oxycline at ∼15 m that divides biologically distinct water masses. We quantified population genetic structure along a depth transect using single nucleotide polymorphisms (SNPs) derived from genome sequencing of 530 individuals. This population genetic structure was reflected in a focal set of SNPs that were also reliably amplified from eDNA — with allele frequencies derived from eDNA reflecting those of fish within each depth zone. Thus, by targeting known genetic variation between populations within aquatic eDNA, we measured genetic structure within the focal species

Data from Blackwell et al. - Newly discovered tilapia cichlid fish biodiversity threatened by hybridization with non-native species

Morphological and genetic data from Oreochromis cichlid fishes from Tanzani