Adrian Indermaur

East African cichlids from Lakes Victoria, Malawi, and Tanganyika have undergone explosive adaptive radiation, generating extensive morphological, ecological, and behavioral diversity within a few million years. Understanding how genome-wide regulatory evolution contributes to this diversification requires comparative analyses of chromatin accessibility, transcription factor (TF) binding, and gene regulatory networks across species and tissues. Here, we combine high-coverage ATAC-seq with matched RNA-seq in forebrain, retina, liver, and testis from five East African cichlid species spanning radiating and nonradiating lineages to characterize the evolution of regulatory landscapes in this radiation. Thousands of promoter-associated accessible sites are conserved across species and tissues, yet more than half of these shared promoters show signatures of accelerated nucleotide evolution, particularly in genes linked to development and sensory function. In contrast, smaller sets of lineage- and tissue-specific accessible promoters, especially in retina, exhibit strong regulatory divergence and functional enrichment for visual system processes. Integrating TF footprinting and expression data uncovers pervasive TF binding site (TFBS) turnover at active promoters and extensive, tissue-dependent rewiring of motif-supported gene regulatory networks, with 86% to 97% of high-confidence edges being species-specific. Extending promoter TFBS variants into broader Malawi and tilapia phylogenies shows that functional variants in promoters of visual genes, such as actr1, segregate by clade and ecological niche. Together, these results demonstrate how accelerated regulatory sequence evolution, chromatin accessibility divergence, and TFBS turnover jointly reshape regulatory architecture genome-wide in an iconic vertebrate radiation, providing insights into how noncoding regulatory evolution can drive rapid phenotypic diversification.

Organisms have evolved a remarkable diversity of reproductive strategies in response to environmental variations and selective pressures. Although most vertebrates do reproduce biparentally, rare alternative modes such as selfing (self-fertilization) and different forms of parthenogenesis exist but remain poorly characterized. Here, we investigated an unusual reproductive event in the normally biparental cichlid fish Cyphotilapia frontosa, in which a female produced offspring in the absence of a male. Using whole-genome sequencing data, we analyzed whether reproduction occurred via selfing or parthenogenesis by comparing patterns of heterozygosity with those from a wild, genetically diverse C. frontosa family collected in Lake Tanganyika and a closely related inbred Ctenochromis benthicola family. The uniparental family exhibited reduced genetic diversity, elevated relatedness, and genome-wide patterns of heterozygosity distinct from those expected under parthenogenesis or inbreeding, but consistent with self-fertilization. Our study provides rare genomic evidence of selfing in a vertebrate and suggests that such alternative reproductive modes may be overlooked rather than truly absent. These findings contribute to a broader understanding of how alternative reproductive strategies evolve in vertebrate lineages.

Deep-water habitats have been colonized repeatedly by fishes, driving the evolution of visual systems under extremely low-light conditions. Here, we investigated visual adaptation in cichlids from the Barombi Mbo crater lake by comparing shallow- and deep-water species using retinal single-cell transcriptomics and analyses of retinal specializations. The shallow-water species Pungu maclareni expressed a broader repertoire of visual opsins across distinct populations of short-(SWS), medium-(RH2), and long-wavelength-sensitive (LWS) cone photoreceptors. In contrast, the deep-water species Myaka myaka lacked a distinct LWS cone population and instead relied predominantly on RH2Aα/β -expressing, green-sensitive photoreceptors. To assess whether these deep-water RH2 cones corresponded to canonical RH2 or LWS programmes, we compared conserved photoreceptor markers. Deep-water RH2 cones retained elements of both RH2- and LWS-associated transcriptional programmes, revealing a mixed profile lacking a clear canonical cone-type signature. LWS-associated transcriptional regulators also differed between species, with tbx2a absent from M. myaka cones, consistent with the loss of LWS opsin expression, whereas thrb persisted in M. myaka RH2 cones. We further examined retinal specialization across eight species from the radiation and found that retinal topography also differed in photoreceptor distributions and ganglion cell-based acuity centers in association with habitat depth but also with trophic ecology of the species. Together, our findings show that visual adaptation in a young adaptive radiation involves coordinated changes in visual opsin expression, cone-associated transcriptional programmes, and retinal organization, highlighting how sensory systems can quickly evolve through changes at multiple biological levels in response to ecological conditions.

Cichlid visual systems can evolve rapidly during adaptive radiations. The Bermin crater lake species flock in Cameroon, comprising 13 (nine valid and four undescribed) Coptodon species, offers an ideal model to investigate visual adaptation to the deep-water light environments. Here, we examine visual opsin genes sequences and expression using 109 retina transcriptomes, focusing on interspecific variation with habitat depth, as well as on seasonal changes in the migratory species between depths. All species possess a multichromatic system with at least five cone opsins. While opsin coding sequences show limited divergence—consistent with the flock's recent origin—opsin expression profiles vary substantially. Deep-water species showed reduced sws1 and sws2b expression, in line with lower UV and violet light availability in deeper waters. Unexpectedly, proportional expression of the red-sensitive lws opsin gene increases with depth, contrasting with patterns in other lacustrine cichlids. In the seasonally migrating species Coptodon imbrifernus, opsin expression is plastic, with decreased sws2b levels in deeper-dwelling dry-season individuals. To contextualize our findings, we compared Bermin cichlids to the older Barombi Mbo crater lake radiation. While single cone adaptations to the depth were convergent (loss of UV/violet sensitivity, enhanced blue sensitivity), double cone response diverged: lws expression was lost in Barombi Mbo while increased in Bermin deep-water species. Our findings suggest that plasticity in opsin expression plays a crucial role at the onset of sensory evolution, potentially paving the way for future genetic change. This study underscores the power of young systems like Bermin for uncovering the mechanisms driving early visual system diversification.

Diet specialisation is a main driver of diversification in many adaptive radiations. Therefore, identifying diet items is essential to characterise trophic specialisations and to understand the dynamics of dietary adaptations. In this study, we explored the trophic niches of 56 species from the adaptive radiation of cichlid fishes in Lake Tanganyika, encompassing all major phylogenetic lineages and feeding specialisations. We employed a metagenomic sequencing approach to identify the food sources of the investigated species at high taxonomic resolution, sequencing over 400 digestive content samples from wild‐caught individuals at around 50 million paired‐end read depth per sample. Our analyses revealed Arthropoda, Chordata (fishes), Bacillariophyta and Streptophyta as the primary diet phyla of the Tanganyikan cichlids. Moreover, we confirmed the presence of other food sources and identified taxa not previously documented to be part of the cichlids' diet. Based on their dietary compositions, the Tanganyikan cichlids can be grouped into herbivores, invertivores, piscivores and mixed feeders. Further, we showed that trophic disparity in the radiation is shaped by rapid divergence and documented cases of dietary niche convergence. Diet composition correlated with carbon and nitrogen stable isotope values, gut length, and body morphology. Differences in diet—such as the consumption of diatoms, streptophytes and chlorophytes versus fish and arthropods—were associated with changes in body, upper oral jaw and lower pharyngeal jaw shape. Collectively, this study presents a comprehensive and detailed diet classification of the Tanganyikan cichlids, highlighting the power of metagenomic approaches in delineating dietary adaptations.

Cichlid visual systems can evolve rapidly during adaptive radiations. This study investigates the Bermin crater lake species flock in Cameroon, comprising thirteen (nine valid and four undescribed) Coptodon species, to explore the effects of deep-water light environments on visual evolution. We analyzed visual opsin genes and their expression using 109 retina transcriptomes, focusing on differences among species at varying depths, and seasonal changes in the visual system of a seasonally migrating species. All species exhibit a multichromatic system with at least five cone opsins. While opsin sequence variability among species was minimal due to the flock’s evolutionary youth, opsin expression patterns varied significantly. Deep-water species showed reduced SWS1 and SWS2B expression, consistent with diminished UV-to-violet light in deeper waters. Unexpectedly, we observed increased proportional expression of the red-sensitive LWS opsin gene, contrary to trends seen in other lacustrine fishes. Additionally, in the seasonally deep-dwelling species Coptodon imbriferna , opsin expression varied plastically between the rainy (shallow) and dry (deep) seasons, with reduced SWS2B expression when the fish reside in the deeper habitats. To add context of other cichlid systems and to explore shared patterns of molecular adaptation, we compared Bermin cichlids to the deep-water species of the Barombi Mbo crater lake. Both cases exemplify independent evolution of deep-water species, yet their visual systems adapted similarly in the single cones (less UV- and violet-sensitive and more blue-sensitive cones), whereas differently in the long-wavelength sensitive double cones (LWS expression lost in Barombi while increased in Bermin). Overall, our study focuses on an evolutionarily young example of cichlid adaptive radiation, providing a unique opportunity to examine the initial phases of molecular adaptation in visual systems.

The lamprologine cichlid genus Telmatochromis was long considered primarily lacustrine and endemic to Lake Tanganyika until an undescribed Telmatochromis species was reported from the Lufubu River (Lake Tanganyika drainage, Zambia). A phylogenomic study in 2021 confirmed the association of Telmatochromis sp. “lufubu” with Telmatochromis along with another riverine species, Neolamprologus devosi (Malagarasi drainage, Tanzania). Here, we quantify the morphological diversity of the genus Telmatochromis and the two associated riverine species using a multivariate dataset combining geometric and classical morphometrics, as well as meristics. We identify three distinct morphological clusters: the “Telmatochromis vittatus complex” with highly elongated bodies and short heads, the “Telmatochromis temporalis complex” with deeper bodies, and the two riverine species with intermediate body elongation and large heads. Further, we formally describe the species endemic to the lower Lufubu River as Telmatochromis salzburgeri sp. nov. and reassign N. devosi to Telmatochromis. Telmatochromis devosi comb. nov. differs from all congeners by the absence of bi‐ and tricuspid teeth in the inner tooth rows of the oral dentition. T. salzburgeri sp. nov. can be distinguished from all other Telmatochromis species by a prominent orange stripe along the base of the dorsal fin and from T. devosi comb. nov. by the relatively smaller size of the lower pharyngeal jaw. Both riverine species differ from all lacustrine Telmatochromis by a lower number of dorsal‐fin spines. Additionally, the riverine species can be distinguished from the T. vittatus complex by having larger heads and longer oral jaws, and from the T. temporalis complex by their lower relative body depth. With the inclusion of new riverine members, the genus Telmatochromis is revealed to be more morphologically and ecologically diverse than previously recognized.

Adaptations related to how nutrients are acquired and processed play a central role in the colonization of novel ecological niches and, therefore, in organismal diversification. While the evolution of feeding structures has been studied extensively in this context, the nature of dietary adaptations in the digestive tract remains largely unexplored. Here, we investigate the cellular and molecular basis of dietary adaptations in the massive radiation of cichlid fishes in Lake Tanganyika using comprehensive single-cell transcriptomic data derived from the intestines of 24 endemic cichlid species with distinct habitats and diets. We show that, at the cellular level, dietary adaptations are primarily driven by anterior enterocytes, and that both the relative abundance and gene expression profiles of these cells have evolved in response to rapid dietary specializations. These dietary adaptations are driven by rapidly evolving cell population-specific genes, suggesting that alterations in epithelial cell specification programs and molecular makeup promote ecological diversification.

Fish biologists have long assumed a link between intestinal length and diet, and relative gut length or Zihler’s index are often used to classify species into trophic groups. This has been done for specific fish taxa or specific ecosystems, but not for a global fish dataset. Here, we assess these relationships across a dataset of 468 fish species (254 marine, 191 freshwater, and 23 that occupy both habitats) in relation to body mass and fish length. Herbivores had significantly relatively stouter bodies and longer intestines than omni- and faunivores. Among faunivores, corallivores had longer intestines than invertivores, with piscivores having the shortest. There were no detectable differences between herbivore groups, possibly due to insufficient understanding of herbivorous fish diets. We propose that reasons for long intestines in fish include (i) difficult-to-digest items that require a symbiotic microbiome, and (ii) the dilution of easily digestible compounds with indigestible material (e.g., sand, wood, exoskeleton). Intestinal indices differed significantly between dietary groups, but there was substantial group overlap. Counter-intuitively, in the largest dataset, marine species had significantly shorter intestines than freshwater fish. These results put fish together with mammals as vertebrate taxa with clear convergence in intestine length in association with trophic level, in contrast to reptiles and birds, even if the peculiar feeding ecology of herbivorous fish is probably more varied than that of mammalian herbivores.

Hemoglobin is a crucial element of the oxygen transport system in vertebrates. It exhibits remarkable gene diversity across teleost fishes, reflecting their evolutionary adaptations for thriving in various aquatic environments. In this study, we present the dynamic evolution of hemoglobin subunit genes based on a comparison of high quality long-read genome assemblies of 24 vertebrate species, including 16 teleosts (of which six are cichlids). Our findings indicate that teleost genomes contain between five (fugu) and 43 (salmon) hemoglobin genes, representing the largest hemoglobin gene repertoire among vertebrates. We find evidence that the ancestor of teleosts had at least four Hbα and three or four Hbβ subunit genes, and that the current gene diversity emerged during subsequent teleost radiation, driven primarily by (tandem) gene duplications, genome compaction, and rearrangement dynamics. We provide insights into the genomic organization of hemoglobin clusters, revealing the parallel origin of multiple clusters in tetrapods and in teleosts. Importantly, we show that the presence of paralogous rhbdf1 genes flanking both teleost hemoglobin clusters (LA and MN) supports the hypothesis for the origin of the LA cluster by rearrangement within teleosts, rather than by the teleost specific whole-genome duplication. We specifically focus on cichlid fishes, where adaptation to low oxygen environments has been shown to play roles in species diversification. Our analysis of six cichlid genomes, including the Pungu maclareni from crater lake Barombi Mbo, for which we sequenced the representative genome, reveals 18 to 31 copies of the Hb genes, and elevated rates of non- synonymous substitutions compared to other teleosts. Overall, this work facilitates a deeper understanding of how hemoglobin genes contribute to the adaptive and diversification potential of teleosts.