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

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

Epigenetic Divergence during Early Stages of Speciation in an African Crater Lake Cichlid Fish

Funder: Wellcome Trust (Wellcome); doi: https://doi.org/10.13039/100004440Funder: Cancer Research UK (CRUK); doi: https://doi.org/10.13039/501100000289Funder: EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions); doi: https://doi.org/10.13039/100010665Funder: NERCFunder: Leverhulme Trust; doi: https://doi.org/10.13039/501100000275Epigenetic variation can alter transcription and promote phenotypic divergence between populations facing different environmental challenges. Here, we assess the epigenetic basis of diversification during the early stages of speciation. Specifically, we focus on the extent and functional relevance of DNA methylome divergence in the very young radiation of Astatotilapia calliptera in crater Lake Masoko, southern Tanzania. Our study focusses on two lake ecomorphs that diverged ~1,000 years ago, as well as a population in the nearby river from which they separated ~10,000 years ago. The two lake ecomorphs show no fixed genetic differentiation, yet are characterised by different morphologies, depth preferences and diet. We report extensive genome-wide methylome divergence between the two lake ecomorphs, as well as between the lake and river populations, linked to key biological processes and associated with altered transcriptional activity of ecologically-relevant genes. Such genes differing between lake ecomorphs include those involved in steroid metabolism, haemoglobin composition and erythropoiesis, consistent with their divergent habitat occupancy. Using a common garden experiment, we found that global methylation profiles are often rapidly remodelled across generations, but ecomorph-specific differences can be inherited. Collectively, our study suggests an epigenetic contribution to early stages of vertebrate speciation