African Cichlid Fish Research Articles

Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish

Epigenetic 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 focuses on two lake ecomorphs that diverged approximately 1,000 years ago and a population in the nearby river from which they separated approximately 10,000 years ago. The two lake ecomorphs show no fixed genetic differentiation, yet are characterized by different morphologies, depth preferences and diets. We report extensive genome-wide methylome divergence between the two lake ecomorphs, and 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, hemoglobin composition and erythropoiesis, consistent with their divergent habitat occupancy. Using a common-garden experiment, we found that global methylation profiles are often rapidly remodeled across generations but ecomorph-specific differences can be inherited. Collectively, our study suggests an epigenetic contribution to the early stages of vertebrate speciation.

Behavior and neural activation patterns of non-redundant visual and acoustic signaling during courtship in an African cichlid fish.

Animals evolve mechanisms to send and receive communication signals through multiple sensory channels during crucial behavioral contexts such as aggression and reproduction. This ensures the transmission of important context-dependent signals that supply either the same (redundant) or different (non-redundant) information to the receiver. Despite the importance of multimodal communication, there are relatively few species in which information on sender signals and receiver responses are known. Further, little is known about where context-dependent unimodal and multimodal information is processed in the brain to produce adaptive behaviors. We used the African cichlid, Astatotilapia burtoni, to investigate how unimodal and multimodal signals are processed within the female brain in a reproductive context. During courtship, dominant males produce low frequency sounds in conjunction with visual displays (quivers) directed towards receptive gravid females. We compared affiliation behaviors and neural activation patterns in gravid females exposed to visual, acoustic and visual-acoustic signals from courting dominant males. Females displayed reduced affiliation in auditory-only conditions, but similar affiliation during visual and visual-acoustic conditions, demonstrating that visual-acoustic signaling from males is non-redundant but vision dominates. Using the neural activation marker cfos, we identified differential activation in specific socially relevant brain nuclei between unimodal and multimodal conditions and distinct neural co-activation networks associated with each sensory context. Combined with our previous work on chemosensory signaling, we propose that A. burtoni represents a valuable vertebrate model for studying context-dependent behavioral and neural decision making associated with non-redundant multimodal communication.

Behavioral changes during social ascent and descent in replicate social networks of an African cichlid fish

Behavioral changes during social ascent and descent in replicate social networks of an African cichlid fish

Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations.

African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate the relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as the sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system. [African cichlids; Blenniiformes; Gene tree heterogeneity; Hybrid assembly; Phylogenetic network; Pseudocrenilabrinae; Species tree.].

Expression and localization of neuronal nitric oxide synthase in the brain and sensory tissues of the African cichlid fish Astatotilapia burtoni.

Nitric oxide (NO) produced by the enzyme neuronal nitric oxide synthase serves as an important neurotransmitter in the central nervous system that is involved in reproductive regulation, learning, sensory processing, and other forms of neural plasticity. Here, we map the distribution of nnos-expressing cells in the brain and retina of the cichlid fish Astatotilapia burtoni using in situ hybridization. In the brain, nnos-expressing cells are found from the olfactory bulbs to the hindbrain, including within specific nuclei involved in decision-making, sensory processing, neuroendocrine regulation, and the expression of social behaviors. In the retina, nnos-expressing cells are found in the inner nuclear layer, presumably in amacrine cells. We also used quantitative PCR to test for differences in nnos expression within the eye and olfactory bulbs of males and females of different reproductive states and social statuses. In the eye, males express more nnos than females, and socially dominant males express more nnos than subordinate males, but expression did not differ among female reproductive states. In the olfactory bulbs, dominant males had greater nnos expression than subordinate males. These results suggest a status-specific function for NO signaling in the visual and olfactory systems that may be important for sensory perception related to mating or territorial interactions to maintain the social hierarchy. The widespread distribution of nnos-expressing cells throughout the cichlid brain is similar to that in other teleosts, with some conserved localization patterns across vertebrates, suggesting diverse functions for this important neurotransmitter system.

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.

New Sex Chromosomes in Lake Victoria Cichlid Fishes (Cichlidae: Haplochromini).

African cichlid fishes harbor an extraordinary diversity of sex-chromosome systems. Within just one lineage, the tribe Haplochromini, at least 6 unique sex-chromosome systems have been identified. Here we focus on characterizing sex chromosomes in cichlids from the Lake Victoria basin. In Haplochromis chilotes, we identified a new ZW system associated with the white blotch color pattern, which shows substantial sequence differentiation over most of LG16, and is likely to be present in related species. In Haplochromis sauvagei, we found a coding polymorphism in amh that may be responsible for an XY system on LG23. In Pundamilia nyererei, we identified a feminizing effect of B chromosomes together with XY- and ZW-patterned differentiation on LG23. In Haplochromis latifasciatus, we identified a duplication of amh that may be present in other species of the Lake Victoria superflock. We further characterized the LG5-14 XY system in Astatotilapia burtoni and identified the oldest stratum on LG14. This species also showed ZW differentiation on LG2. Finally, we characterized an XY system on LG7 in Astatoreochromis alluaudi. This report brings the number of distinct sex-chromosome systems in haplochromine cichlids to at least 13, and highlights the dynamic evolution of sex determination and sex chromosomes in this young lineage.

Social dominance and reproduction result in increased integration of oxidative state in males of an African cichlid fish

Oxidative stress is a potential cost of social dominance and reproduction, which could mediate life history trade-offs between current and future reproductive fitness. However, the evidence for an oxidative cost of social dominance and reproduction is mixed, in part because organisms have efficient protective mechanisms that can counteract oxidative insults. Further, previous studies have shown that different aspects of oxidative balance, including oxidative damage and antioxidant function, vary dramatically between tissue types, yet few studies have investigated oxidative cost in terms of interconnectedness and coordination within the system. Here, we tested whether dominant and subordinate males of the cichlid Astatotilapia burtoni differ in integration of different components of oxidative stress. We assessed 7 markers of oxidative stress, which included both oxidative damage and antioxidant function in various tissue types (total of 14 measurements). Across all oxidative stress measurements, we found more co-regulated clusters in dominant males, suggesting that components of oxidative state are more functionally integrated in dominant males than they are in subordinate males. We discuss how a high degree of functional integration reflects increased robustness or efficiency of the system (e.g. increased effectiveness of antioxidant machinery in reducing oxidative damage), but we also highlight potential costs (e.g. activation of cytoprotective mechanisms may have unwanted pleiotropic effects). Overall, our results suggest that quantifying the extent of functional integration across different components of oxidative stress could reveal insights into the oxidative cost of important life history events.

Molecular phylogeny and speciation patterns in host-specific monogeneans (Cichlidogyrus, Dactylogyridae) parasitizing cichlid fishes (Cichliformes, Cichlidae) in Lake Tanganyika

Cichlidogyrus (including Scutogyrus) is the most speciose dactylogyridean monogenean genus known from African and Levantine cichlid fishes (Cichlidae). While its taxonomy is well established, little is known about the phylogenetic relationships and evolutionary history of this ectoparasite, especially from hosts belonging to one of the most impressive vertebrate radiations, the cichlid fishes from the East African Great Lakes and surrounding hydrological systems. Phylogenetic inference based on DNA sequences of the nuclear 18S, internal transcribed spacer 1 and 28S rDNA genes revealed that Cichlidogyrus parasitizing mainly West African cichlid tribes is paraphyletic with respect to species parasitizing hosts belonging to the East African cichlid radiation, which constitute a well-supported monophylum. Members of Cichlidogyrus from tylochromine and oreochromine hosts that colonised Lake Tanganyika only recently, cluster with their non-Lake Tanganyika relatives, indicating that they colonised Lake Tanganyika with their current host species, and did not jump over from any of the many cichlid species already present in the lake. The diversification of Cichlidogyrus in Lake Tanganyika seems to be driven by failure to diverge in old lineages of cichlids, cospeciation in more recently evolved ones, and host switching followed by parasite duplication at the level of the various host tribes. Evaluation of host specificity and structural evolution of haptoral and reproductive organs in Lake Tanganyika Cichlidogyrus revealed that strict specialist species together with larval hook size represent the ancestral state of haptor configuration, suggesting that members of Cichlidogyrus in this system evolved from a very simple form to a more complex one similarly to their West African congeners. Generalist species among Cichlidogyrus with a sclerotized vagina parasitizing ancient Lake Tanganyika lineages seem to have developed a different hook configuration, most probably to ensure successful colonisation of new, phylogenetically unrelated hosts.

The repeated evolution of stripe patterns is correlated with body morphology in the adaptive radiations of East African cichlid fishes.

Color patterns are often linked to the behavioral and morphological characteristics of an animal, contributing to the effectiveness of such patterns as antipredatory strategies. Species‐rich adaptive radiations, such as the freshwater fish family Cichlidae, provide an exciting opportunity to study trait correlations at a macroevolutionary scale. Cichlids are also well known for their diversity and repeated evolution of color patterns and body morphology. To study the evolutionary dynamics between color patterns and body morphology, we used an extensive dataset of 461 species. A phylogenetic supertree of these species shows that stripe patterns evolved ~70 times independently and were lost again ~30 times. Moreover, stripe patterns show strong signs of correlated evolution with body elongation, suggesting that the stripes’ effectiveness as antipredatory strategy might differ depending on the body shape. Using pedigree‐based analyses, we show that stripes and body elongation segregate independently, indicating that the two traits are not genetically linked. Their correlation in nature is therefore likely maintained by correlational selection. Lastly, by performing a mate preference assay using a striped CRISPR‐Cas9 mutant of a nonstriped species, we show that females do not differentiate between striped CRISPR mutant males and nonstriped wild‐type males, suggesting that these patterns might be less important for species recognition and mate choice. In summary, our study suggests that the massive rates of repeated evolution of stripe patterns are shaped by correlational selection with body elongation, but not by sexual selection.

Social ascent changes cognition, behaviour and physiology in a highly social cichlid fish.

When an individual ascends in dominance status within their social community, they often undergo a suite of behavioural, physiological and neuromolecular changes. While these changes have been extensively characterized across a number of species, we know much less about the degree to which these changes in turn influence cognitive processes like associative learning, memory and spatial navigation. Here, we assessed male Astatotilapia burtoni, an African cichlid fish known for its dynamic social dominance hierarchies, in a set of cognitive tasks both before and after a community perturbation in which some individuals ascended in dominance status. We assayed steroid hormone (cortisol, testosterone) levels before and after the community experienced a social perturbation. We found that ascending males changed their physiology and novel object recognition preference during the perturbation, and they subsequently differed in social competence from non-ascenders. Additionally, using a principal component analysis we were able to identify specific cognitive and physiological attributes that appear to predispose certain individuals to ascend in social status once a perturbation occurs. These previously undiscovered relationships between social ascent and cognition further emphasize the broad influence of social dominance on animal decision-making. This article is part of the theme issue 'The centennial of the pecking order: current state and future prospects for the study of dominance hierarchies'.

Speciation dynamics and extent of parallel evolution along a lake-stream environmental contrast in African cichlid fishes.

Understanding the dynamics of speciation is a central topic in evolutionary biology. Here, we investigated how morphological and genomic differentiation accumulated along the speciation continuum in the African cichlid fish Astatotilapia burtoni. While morphological differentiation was continuously distributed across different lake-stream population pairs, we found that there were two categories with respect to genomic differentiation, suggesting a “gray zone” of speciation at ~0.1% net nucleotide divergence. Genomic differentiation was increased in the presence of divergent selection and drift compared to drift alone. The quantification of phenotypic and genetic parallelism in four cichlid species occurring along a lake-stream environmental contrast revealed parallel and antiparallel components in rapid adaptive divergence, and morphological convergence in species replicates inhabiting the same environments. Furthermore, we show that the extent of parallelism was higher when ancestral populations were more similar. Our study highlights the complementary roles of divergent selection and drift on speciation and parallel evolution.

Control of testes mass by androgen receptor paralogs in a cichlid.

Steroid hormones play numerous important and diverse roles in the differentiation and development of vertebrate primary and secondary reproductive characteristics. However, the exact role of androgen receptors-which bind circulating androgens-in this regulatory pathway is unclear. Teleost fishes further complicate this question by having two paralogs of the androgen receptor (ARα and ARβ) resulting from a duplication of their ancestral genome. We investigated the functional role of these two ARs on adult testes mass, by eliminating receptor function of one or both paralogs using CRISPR/Cas9 genome edited Astatotilapia burtoni, an African cichlid fish. Fish with two or more functional AR alleles were more likely to be male compared to fish with one or fewer, suggesting that the two paralogs may play redundant roles in the A. burtoni sex determination system. We replicated previous work showing that fish lacking functional ARβ possess testes smaller than wild-type fish, while fish lacking ARα possess testes larger than wild-type fish. However, we found novel evidence supporting a complex relationship between the two AR paralogs in the regulation of testes mass. For instance, the effects of ARα mutation on testes mass are eliminated in homozygous ARβ mutants but the reverse is not true. These results suggest a dynamic relationship between these two AR paralogs where ARβ functions may be permissive to ARα functions in the control of testes mass. This mechanism may contribute to the robust physiological plasticity displayed by A. burtoni and other social teleost fishes.

Social dominance does not increase oxidative stress in a female dominance hierarchy of an African cichlid fish

AbstractIn many group living animal species, individuals use aggression to gain and maintain social dominance to secure access to ecological resources and potential mates. While social dominance has many fitness benefits, there are also potential costs associated with frequent agonistic interactions and status display. One potential cost of social dominance is oxidative stress, the imbalance of reactive oxygen species and antioxidant capacity. In the cichlid species Astatotilapia burtoni, dominant males are aggressive, hold a breeding territory, and have an activated reproductive system resulting in larger gonads. Subordinate males are submissive, school with females, and are nonreproductive. Females are submissive under natural conditions, but in a female‐only group, a dominance hierarchy will form with dominant females taking on male‐typical behaviours including aggression, territory defence, and increased androgen levels. However, in contrast to males, social dominance is not linked to increased activation of the reproductive system in females, allowing us to test whether social dominance alone exposes individuals to increased oxidative stress. We compared dominant and subordinate females in female‐only groups in five markers of oxidative stress. Dominant females did not have higher levels of oxidative damage compared to same‐sex subordinates. This result contrasted to the trend in males in which dominant males had higher oxidative damage than their subordinate counterparts. Our findings suggest that the oxidative cost of social dominance is limited and support the notion that previously reported associations between high rank and increased oxidative stress is most likely driven by increased investment in reproduction.

A 2b-RAD parentage analysis pipeline for complex and mixed DNA samples

Next-generation sequencing technology has revolutionized genotyping in many fields of study, yet parentage analysis often still relies on microsatellite markers that are costly to generate and are currently available only for a limited number of species. 2b-RAD sequencing (2b-RAD) is a DNA sequencing technique developed for ecological population genomics that utilizes type IIB restriction enzymes to generate consistent, uniform fragments across samples. This technology is inexpensive, effective with low DNA inputs, and robust to DNA degradation. Here, we developed a probabilistic genotyping-by-sequencing genetic testing pipeline for parentage analysis by using 2b-RAD for inferring familial relationships from mixed DNA samples and populations. Our approach to partial paternity assignment utilizes a novel weighted outlier paternity index (WOPI) adapted for next-generation sequencing data and an identity-by-state (IBS) matrix-based clustering method for pedigree reconstruction. The combination of these two parentage assignment methods overcomes two major obstacles faced by other genetic testing methods: 1) It allows detection of parentage when closely related or inbred individuals are in the alleged parent population (e.g., in laboratory strains); and 2) it resolves mixed DNA samples. We successfully demonstrate this novel approach by correctly inferring paternity for samples pooled from multiple offspring (i.e., entire clutches) in a highly inbred population of an East African cichlid fish. The unique advantages of 2b-RAD in combination with our bioinformatics pipeline enable straightforward and cost-effective parentage analysis in any species regardless of genomic resources available.

Morpho-molecular characterization of Gyrodactylus parasites of farmed tilapia and their spillover to native fishes in Mexico

Translocation of fishes for aquaculture has resulted in the co-introduction of some of their parasites. African cichlid fishes, generically called “tilapias” have been introduced worldwide, along with their monogenean parasites. In a nation-wide survey, we characterised monogeneans of the genus Gyrodactylus infecting farmed “tilapia” throughout Mexico. We also collected native fishes around farms, to look for potential parasite spillover from cultured fishes. Monogeneans were identified taxonomically using morphological and molecular characters. Originally African, pathogenic Gyrodactylus cichlidarum was recorded in every farm surveyed, infecting different “tilapia” varieties, as well as three native cichlid fish species. Previously, we had shown that G. cichlidarum also infects native, non-cichlid fishes in Mexico. We also recorded that Gyrodactylus yacatli is widely distributed in Mexico, infecting cultured “tilapia” and native fishes; and present data indicating that this is a further translocated African parasite. A third, unidentified gyrodactylid infected farmed and native fishes in Chiapas, southern Mexico; we describe the new species as Gyrodactylus shinni n. sp., and provide evidence that this is a third monogenean translocated with African fish. The wide distribution of exotic parasites co-introduced with “tilapia” and their spillover to native fishes may have an important impact on the ichthyofauna in Mexico, one the world’s megadiverse countries.

A behavioral logic underlying aggression in an African cichlid fish

AbstractSocial rank in a hierarchy determines which individuals have access to important resources such as food, shelter, and mates. In the African cichlid fish Astatotilapia burtoni, rank is under social control, such that larger males are more likely than smaller males to be dominant in rank. Although it is well known that the relative size of A. burtoni males is critical in controlling social rank, the specific behaviors underlying responses to males of different sizes are not well understood. In many other fish species, when size asymmetries between competing males are small, physical aggression is likely to be used to settle territorial disputes. Our goal was to characterize these responses in male A. burtoni by performing resident‐intruder assays, in which aggressive behaviors were measured in territorial males in response to the introduction of unfamiliar males that differed in relative standard length (SL). We found that the relative SL of intruders played an important role in determining behavioral performance. Resident males that were smaller than the intruder (resident >5% smaller in SL) or matched (resident between 0 and 5% smaller or larger in SL) in size to the intruder performed more lateral displays, a type of non‐physical aggression, than resident males that were larger than the intruder (resident >5% larger in SL). However, physical aggression, such as chases and bites, did not differ as a function of relative SL. Thus, contrary to what was expected based on work in other species, our results demonstrate that dominant resident A. burtoni increase non‐physical aggression to settle territorial disputes when non‐dominant intruders are closer in size. This behavioral strategy may aid in readily settling conflicts when size asymmetries are small.

Reproductive- and Social-State Plasticity of Multiple Sensory Systems in a Cichlid Fish.

Intra- and inter-sexual communications are vital to the survival and reproductive success of animals. In species that cycle in and out of breeding or other physiological condition, sensory function can be modulated to optimize communication at crucial times. Little is known, however, about how widespread this sensory plasticity is across taxa, whether it occurs in multiple senses or both sexes within a species, and what potential modulatory substances and substrates are involved. Thus, studying modulation of sensory communication in a single species can provide valuable insights for understanding how sensory abilities can be altered to optimize detection of salient signals in different sensory channels and social contexts. The African cichlid fish Astatotilapia burtoni uses multimodal communication in social contexts such as courtship, territoriality, and parental care and shows plasticity in sensory abilities. In this review, we synthesize what is known about how visual, acoustic, and chemosensory communication is used in A. burtoni in inter- and intra-specific social contexts, how sensory funtion is modulated by an individual's reproductive, metabolic, and social state, and discuss evidence for plasticity in potential modulators that may contribute to changes in sensory abilities and behaviors. Sensory plasticity in females is primarily associated with the natural reproductive cycle and functions to improve detection of courtship signals (visual, auditory, chemosensory, and likely mechanosensory) from high-quality males for reproduction. Plasticity in male sensory abilities seems to function in altering their ability to detect the status of other males in the service of territory ownership and future reproductive opportunities. Changes in different classes of potential modulators or their receptors (steroids, neuropeptides, and biogenic amines) occur at both peripheral sensory organs (eye, inner ear, and olfactory epithelium) and central visual, olfactory, and auditory processing regions, suggesting complex mechanisms contributing to plasticity of sensory function. This type of sensory plasticity revealed in males and females of A. burtoni is likely more widespread among diverse animals than currently realized, and future studies should take an integrative and comparative approach to better understand the proximate and ultimate mechanisms modulating communication abilities across taxa.

Diversity in visual sensitivity across Neotropical cichlid fishes via differential expression and intraretinal variation of opsin genes.

The visual system of vertebrates has greatly contributed to our understanding of how different molecular mechanisms shape adaptive phenotypic diversity. Extensive work on African cichlid fishes has shown how variation in opsin gene expression mediates diversification as well as convergent evolution in colour vision. This trait has received less attention in Neotropical cichlids, the sister lineage to African cichlids, but the work done so far led to the conclusion that colour vision is much less variable in Neotropical species. However, as only few taxa have been investigated and as recent work found contradicting patterns, the diversity in meotropical cichlids might be greatly underestimated. Here, we survey patterns of opsin gene expression in 35 representative species of Neotropical cichlids, revealing much more variation than previously known. This diversity can be attributed to two main mechanisms: (i) differential expression of the blue-sensitive sws2a, the green-sensitive rh2a, and the red-sensitive lws opsin genes, and (ii) simultaneous expression of up to five opsin genes, instead of only three as commonly found, in a striking dorsoventral pattern across the retina. This intraretinal variation in opsin genes expression results in steep gradients in visual sensitivity that may represent a convergent adaptation to clear waters with broad light environments. These results highlight the role and flexibility of gene expression in generating adaptive phenotypic diversification.

Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika

With more than 1000 species, East African cichlid fishes represent the fastest and most species-rich vertebrate radiation known, providing an ideal model to tackle molecular mechanisms underlying recurrent adaptive diversification. We add high-quality genome reconstructions for two phylogenetic key species of a lineage that diverged about ~ 3–9 million years ago (mya), representing the earliest split of the so-called modern haplochromines that seeded additional radiations such as those in Lake Malawi and Victoria. Along with the annotated genomes we analysed discriminating genomic features of the study species, each representing an extreme trophic morphology, one being an algae browser and the other an algae grazer. The genomes of Tropheus moorii (TM) and Petrochromis trewavasae (PT) comprise 911 and 918 Mbp with 40,300 and 39,600 predicted genes, respectively. Our DNA sequence data are based on 5 and 6 individuals of TM and PT, and the transcriptomic sequences of one individual per species and sex, respectively. Concerning variation, on average we observed 1 variant per 220 bp (interspecific), and 1 variant per 2540 bp (PT vs PT)/1561 bp (TM vs TM) (intraspecific). GO enrichment analysis of gene regions affected by variants revealed several candidates which may influence phenotype modifications related to facial and jaw morphology, such as genes belonging to the Hedgehog pathway (SHH, SMO, WNT9A) and the BMP and GLI families.