Drivers and dynamics of a massive adaptive radiation in cichlid fishes.

Adaptive radiation is the likely source of much of the ecological and morphological diversity of life1-4. How adaptive radiations proceed and what determines their extent remains unclear in most cases1,4. Here we report the in-depth examination of the spectacular adaptive radiation of cichlid fishes in Lake Tanganyika. On the basis of whole-genome phylogenetic analyses, multivariate morphological measurements of three ecologically relevant trait complexes (body shape, upper oral jaw morphology and lower pharyngeal jaw shape), scoring of pigmentation patterns and approximations of the ecology of nearly all of the approximately 240 cichlid species endemic to Lake Tanganyika, we show that the radiation occurred within the confines of the lake and that morphological diversification proceeded in consecutive trait-specific pulses of rapid morphospace expansion. We provide empirical support for two theoretical predictions of how adaptive radiations proceed, the 'early-burst' scenario1,5 (for body shape) and the stages model1,6,7 (for all traits investigated). Through the analysis of two genomes per species and by taking advantage of the uneven distribution of species in subclades of the radiation, we further show that species richness scales positively with per-individual heterozygosity, but is not correlated with transposable element content, number of gene duplications or genome-wide levels of selection in coding sequences.

Towards the phylogenetic placement of the enigmatic African genus Prolabeops Schultz, 1941.

The small cyprinid genus Prolabeops Schultz, 1941 is restricted to the Nyong and Sanaga River systems in Cameroon. In the past, the genus had been suggested to be either a member of the Labeoninae, Torinae or the Smiliogastrinae mainly on the basis of morphological similarities, and it is nowadays considered as incertae sedis within the Cypriniformes. This study provides the first attempt to reveal the phylogenetic position of Prolabeops using molecular data. For this purpose, the authors sequenced a large fraction of the mitochondrial genome (c. 13,600 bp), including all mitochondrial protein coding genes, of two Prolabeops melanhypopterus specimens and an additional four Enteromius specimens. The large-scale phylogenetic analysis was based on an alignment including all mitochondrial protein coding genes of 902 specimens representing c. 899 cypriniform species. Prolabeops was clearly recovered within the African Smiliogastrinae, forming a weakly supported clade together with Enteromius jae, Enteromius hulstaerti and Barboides gracilis. The study data underline the urgent need of a thorough taxonomic revision of the small African barbs collectively placed in the genus Enteromius.

Structural manipulations of a shelter resource reveal underlying preference functions in a shell-dwelling cichlid fish.

Many animals can modify the environments in which they live, thereby changing the selection pressures they experience. A common example of such niche construction is the use, creation or modification of environmental resources for use as nests or shelters. Because these resources often have correlated structural elements, it can be difficult to disentangle the relative contribution of these elements to resource choice, and the preference functions underlying niche-construction behaviour remain hidden. Here, we present an experimental paradigm that uses 3D scanning, modelling and printing to create replicas of structures that differ with respect to key structural attributes. We show that a niche-constructing, shell-dwelling cichlid fish, Neolamprologus multifasciatus, has strong open-ended preference functions for exaggerated shell replicas. Fish preferred shells that were fully intact and either enlarged, lengthened or had widened apertures. Shell intactness was the most important structural attribute, followed by shell length, then aperture width. We disentangle the relative roles of different shell attributes, which are tightly correlated in the wild, but nevertheless differentially influence shelter choice and therefore niche construction in this species. We highlight the broad utility of our approach when compared with more traditional methods (e.g. two-choice tasks) for studying animal decision-making in a range of contexts.

The taxonomic diversity of the cichlid fish fauna of ancient Lake Tanganyika, East Africa.

Ancient Lake Tanganyika in East Africa houses the world's ecologically and morphologically most diverse assemblage of cichlid fishes, and the third most species-rich after lakes Malawi and Victoria. Despite long-lasting scientific interest in the cichlid species flocks of the East African Great Lakes, for example in the context of adaptive radiation and explosive diversification, their taxonomy and systematics are only partially explored; and many cichlid species still await their formal description. Here, we provide a current inventory of the cichlid fish fauna of Lake Tanganyika, providing a complete list of all valid 208 Tanganyikan cichlid species, and discuss the taxonomic status of more than 50 undescribed taxa on the basis of the available literature as well as our own observations and collections around the lake. This leads us to conclude that there are at least 241 cichlid species present in Lake Tanganyika, all but two are endemic to the basin. We finally summarize some of the major taxonomic challenges regarding Lake Tanganyika's cichlid fauna. The taxonomic inventory of the cichlid fauna of Lake Tanganyika presented here will facilitate future research on the taxonomy and systematics and the ecology and evolution of the species flock, as well as its conservation.

Evolution of the visual sensory system in cichlid fishes from crater lake Barombi Mbo in Cameroon.

In deep-water animals, the visual sensory system is often challenged by the dim-light environment. Here, we focus on the molecular mechanisms involved in rapid deep-water adaptations. We examined visual system evolution in a small-scale yet phenotypically and ecologically diverse adaptive radiation, the species flock of cichlid fishes in deep crater lake Barombi Mbo in Cameroon, West Africa. We show that rapid adaptations of the visual system to the novel deep-water habitat primarily occurred at the level of gene expression changes rather than through nucleotide mutations, which is compatible with the young age of the radiation. Based on retinal bulk RNA sequencing of all eleven species, we found that the opsin gene expression pattern was substantially different for the deep-water species. The nine shallow-water species feature an opsin palette dominated by the red-sensitive (LWS) opsin, whereas the two unrelated deep-water species lack expression of LWS and the violet-sensitive (SWS2B) opsin, thereby shifting the cone sensitivity to the centre of the light spectrum. Deep-water species further predominantly express the green-sensitive RH2Aα over RH2Aß. We identified one amino acid substitution in the RH2Aα opsin specific to the deep-water species. We finally performed a comparative gene expression analysis in retinal tissue of deep- vs. shallow-water species. We thus identified 46 differentially expressed genes, many of which are associated with functions in vision, hypoxia management or circadian clock regulation, with some of them being associated with human eye diseases.

Adaptive Radiation from a Chromosomal Perspective: Evidence of Chromosome Set Stability in Cichlid Fishes (Cichlidae: Teleostei) from the Barombi Mbo Lake, Cameroon.

Cichlid fishes are the subject of scientific interest because of their rapid adaptive radiation, resulting in extensive ecological and taxonomic diversity. In this study, we examined 11 morphologically distinct cichlid species endemic to Barombi Mbo, the largest crater lake in western Cameroon, namely Konia eisentrauti, Konia dikume, Myaka myaka, Pungu maclareni, Sarotherodon steinbachi, Sarotherodon lohbergeri, Sarotherodon linnellii, Sarotherodon caroli, Stomatepia mariae, Stomatepia pindu, and Stomatepia mongo. These species supposedly evolved via sympatric ecological speciation from a common ancestor, which colonized the lake no earlier than one million years ago. Here we present the first comparative cytogenetic analysis of cichlid species from Barombi Mbo Lake using both conventional (Giemsa staining, C-banding, and CMA3/DAPI staining) and molecular (fluorescence in situ hybridization with telomeric, 5S, and 28S rDNA probes) methods. We observed stability on both macro and micro-chromosomal levels. The diploid chromosome number was 2n = 44, and the karyotype was invariably composed of three pairs of meta/submetacentric and 19 pairs of subtelo/acrocentric chromosomes in all analysed species, with the same numbers of rDNA clusters and distribution of heterochromatin. The results suggest the evolutionary stability of chromosomal set; therefore, the large-scale chromosomal rearrangements seem to be unlikely associated with the sympatric speciation in Barombi Mbo.

A complex mode of aggressive mimicry in a scale-eating cichlid fish.

Aggressive mimicry is an adaptive tactic of parasitic or predatory species that closely resemble inoffensive models in order to increase fitness via predatory gains. Although similarity of distantly related species is often intuitively implicated with mimicry, the exact mechanisms and evolutionary causes remain elusive in many cases. Here, we report a complex aggressive mimicry strategy in Plecodus straeleni, a scale-eating cichlid fish from Lake Tanganyika, which imitates two other cichlid species. Employing targeted sequencing on ingested scales, we show that P. straeleni does not preferentially parasitize its models but­contrary to prevailing assumptions­targets a variety of co-occurring dissimilar looking fish species. Combined with tests for visual resemblance and visual modelling from a prey perspective, our results suggest that complex interactions among different cichlid species are involved in this mimicry system.

Adaptive divergence between lake and stream populations of an East African cichlid fish.

Divergent natural selection acting in different habitats may build up barriers to gene flow and initiate speciation. This speciation continuum can range from weak or no divergence to strong genetic differentiation between populations. Here, we focus on the early phases of adaptive divergence in the East African cichlid fish Astatotilapia burtoni, which occurs in both Lake Tanganyika (LT) and inflowing rivers. We first assessed the population structure and morphological differences in A. burtoni from southern LT. We then focused on four lake-stream systems and quantified body shape, ecologically relevant traits (gill raker and lower pharyngeal jaw) as well as stomach contents. Our study revealed the presence of several divergent lake-stream populations that rest at different stages of the speciation continuum, but show the same morphological and ecological trajectories along the lake-stream gradient. Lake fish have higher bodies, a more superior mouth position, longer gill rakers and more slender pharyngeal jaws, and they show a plant/algae and zooplankton-biased diet, whereas stream fish feed more on snails, insects and plant seeds. A test for reproductive isolation between closely related lake and stream populations did not detect population-assortative mating. Analyses of F1 offspring reared under common garden conditions indicate that the detected differences in body shape and gill raker length do not constitute pure plastic responses to different environmental conditions, but also have a genetic basis. Taken together, the A. burtoni lake-stream system constitutes a new model to study the factors that enhance and constrain progress towards speciation in cichlid fishes.

Revision of the cichlid fish genus Gnathochromis (Teleostei: Cichlidae) from Lake Tanganyika with the description of a new genus Jabarichromis gen. nov.

The cichlid species flock from Lake Tanganyika is a well-studied system for evolutionary biology research because its species assemblage shows a high degree of endemism and is a product of adaptive radiation. While our understanding of the evolutionary history of Lake Tanganyika cichlids has advanced tremendously over the past decades, their taxonomy received considerably less attention, despite numerous taxonomic misplacements (e.g., polyphyletic genera and species) that have been revealed by phylogenetic studies. One prominent example of a polyphyletic genus is Gnathochromis, which includes two distantly related species, belonging to two different tribes. To resolve this issue, here we present a taxonomic revision based on an extensive morphological dataset obtained from a comprehensive taxon sampling including 587 specimens from 63 taxa. We introduce a new monotypic genus, Jabarichromis gen. nov. for Gnathochromis pfefferi, a member of the tribe Tropheini, thereby separating it from the type species of Gnathochromis, G. permaxillaris. As a result, the genus Gnathochromis, which belongs to the tribe Limnochromini, is rendered monophyletic. Further, we provide an additional character to distinguish the recently described genus Shuja, which also belongs to the Tropheini, from its former mostly riverine congeners.

The ecological and genetic basis of convergent thick-lipped phenotypes in cichlid fishes.

The evolution of convergent phenotypes is one of the most interesting outcomes of replicate adaptive radiations. Remarkable cases of convergence involve the thick-lipped phenotype found across cichlid species flocks in the East African Great Lakes. Unlike most other convergent forms in cichlids, which are restricted to East Africa, the thick-lipped phenotype also occurs elsewhere, for example in the Central American Midas Cichlid assemblage. Here, we use an ecological genomic approach to study the function, the evolution and the genetic basis of this phenotype in two independent cichlid adaptive radiations on two continents. We applied phylogenetic, demographic, geometric morphometric and stomach content analyses to an African (Lobochilotes labiatus) and a Central American (Amphilophus labiatus) thick-lipped species. We found that similar morphological adaptations occur in both thick-lipped species and that the 'fleshy' lips are associated with hard-shelled prey in the form of molluscs and invertebrates. We then used comparative Illumina RNA sequencing of thick vs. normal lip tissue in East African cichlids and identified a set of 141 candidate genes that appear to be involved in the morphogenesis of this trait. A more detailed analysis of six of these genes led to three strong candidates: Actb, Cldn7 and Copb. The function of these genes can be linked to the loose connective tissue constituting the fleshy lips. Similar trends in gene expression between African and Central American thick-lipped species appear to indicate that an overlapping set of genes was independently recruited to build this particular phenotype in both lineages.

Species diversity and phylogeography of the Australoheros autrani group (Teleostei, Cichlidae) in eastern Brazil.

Cichlid fishes are an important model system in evolutionary biology, primarily because of their exceptional diversity. However, while some cichlid assemblages, such as the ones of the African Great Lakes, have received considerable attention, others are not well studied, including many riverine species. Here, we focus on the Australoheros autrani species group and first report a new record of Australoheros in the upper Paranaíba River drainage, extending the known distribution range of this genus. Through Bayesian inference and maximum likelihood phylogenetic analyses of the mitochondrial cytochrome b gene of these specimens as well as available sequences, we assigned the newly discovered population to Australoheros barbosae. We corroborate the monophyly of the A. autrani species group and the presence of three species in the upper/middle Paraíba do Sul River basin as well as molecular diagnostic characters for each. Finally, we provide evidence for a recent expansion of A. barbosae. Supplementary Information: The online version contains supplementary material available at 10.1007/s10228-022-00888-9.

Gene expression dynamics during rapid organismal diversification in African cichlid fishes.

Changes in gene expression play a fundamental role in phenotypic evolution. Transcriptome evolutionary dynamics have so far mainly been compared among distantly related species and remain largely unexplored during rapid organismal diversification, in which gene regulatory changes have been suggested as particularly effective drivers of phenotypic divergence. Here we studied gene expression evolution in a model system of adaptive radiation, the cichlid fishes of African Lake Tanganyika. By comparing gene expression profiles of 6 different organs in 74 cichlid species representing all subclades of this radiation, we demonstrate that the rate of gene expression evolution varies among organs, transcriptome parts and the subclades of the radiation, indicating different strengths of selection. We found that the noncoding part of the transcriptome evolved more rapidly than the coding part, and that the gonadal transcriptomes evolved more rapidly than the somatic ones, with the exception of liver. We further show that the rate of gene expression change was not constant over the course of the radiation but accelerated at its later phase. Finally, we show that-at the per-gene level-the evolution of expression patterns is dominated by stabilizing selection.

Where Am I? Niche constraints due to morphological specialization in two Tanganyikan cichlid fish species.

Food resource specialization within novel environments is considered a common axis of diversification in adaptive radiations. Feeding specializations are often coupled with striking morphological adaptations and exemplify the relation between morphology and diet (phenotype-environment correlations), as seen in, for example, Darwin finches, Hawaiian spiders, and the cichlid fish radiations in East African lakes. The cichlids' potential to rapidly exploit and occupy a variety of different habitats has previously been attributed to the variability and adaptability of their trophic structures including the pharyngeal jaw apparatus. Here we report a reciprocal transplant experiment designed to explore the adaptability of the trophic structures in highly specialized cichlid fish species. More specifically, we forced two common but ecologically distinct cichlid species from Lake Tanganyika, Tropheus moorii (rock-dweller), and Xenotilapia boulengeri (sand-dweller), to live on their preferred as well as on an unpreferred habitat (sand and rock, respectively). We measured their overall performance on the different habitat types and explored whether adaptive phenotypic plasticity is involved in adaptation. We found that, while habitat had no effect on the performance of X. boulengeri, T. moorii performed significantly better in its preferred habitat. Despite an experimental duration of several months, we did not find a shift in the morphology of the lower pharyngeal jaw bone that would be indicative of adaptive phenotypic plasticity in this trait.

Point-Combination Transect (PCT): Incorporation of small underwater cameras to study fish communities.

Available underwater visual census (UVC) methods such as line transects or point count observations are widely used to obtain community data of underwater species assemblages, despite their known pit-falls. As interest in the community structure of aquatic life is growing, there is need for more standardized and replicable methods for acquiring underwater census data.Here, we propose a novel approach, Point-Combination Transect (PCT), which makes use of automated image recording by small digital cameras to eliminate observer and identification biases associated with available UVC methods. We conducted a pilot study at Lake Tanganyika, demonstrating the applicability of PCT on a taxonomically and phenotypically highly diverse assemblage of fishes, the Tanganyikan cichlid species-flock.We conducted 17 PCTs consisting of five GoPro cameras each and identified 22,867 individual cichlids belonging to 61 species on the recorded images. These data were then used to evaluate our method and to compare it to traditional line transect studies conducted in close proximity to our study site at Lake Tanganyika.We show that the analysis of the second hour of PCT image recordings (equivalent to 360 images per camera) leads to reliable estimates of the benthic cichlid community composition in Lake Tanganyika according to species accumulation curves, while minimizing the effect of disturbance of the fish through SCUBA divers. We further show that PCT is robust against observer biases and outperforms traditional line transect methods.

Mouth dimorphism in scale-eating cichlid fish from Lake Tanganyika advances individual fitness.

Random asymmetry, that is the coexistence of left- and right-sided (or -handed) individuals within a population, is a particular case of natural variation; what triggers and maintains such dimorphisms remains unknown in most cases. Here, we report a field-based cage experiment in the scale-eating Tanganyikan cichlid Perissodus microlepis, which occurs in two morphs in nature: left-skewed and right-skewed individuals with respect to mouth orientation. Using underwater cages stocked with scale-eaters and natural prey fish, we first confirm that, under semi-natural conditions, left-skewed scale-eaters preferentially attack the right flank of their prey, whereas right-skewed individuals feed predominantly from the left side. We then demonstrate that scale-eaters have a higher probability for successful attacks when kept in dimorphic experimental populations (left- and right-skewed morphs together) as compared to monomorphic populations (left- or right-skewed morphs), most likely because prey fishes fail to accustom to strikes from both sides. The significantly increased probability for attacks appears to be the selective agent responsible for the evolution and maintenance of mouth dimorphism in P. microlepis, lending further support to the hypothesis that negative frequency-dependent selection is the stabilizing force balancing the mouth dimorphism at quasi-equal ratios in scale-eating cichlids.

Back to Tanganyika: a case of recent trans-species-flock dispersal in East African haplochromine cichlid fishes.

The species flocks of cichlid fishes in the East African Great Lakes are the largest vertebrate adaptive radiations in the world and illustrious textbook examples of convergent evolution between independent species assemblages. Although recent studies suggest some degrees of genetic exchange between riverine taxa and the lake faunas, not a single cichlid species is known from Lakes Tanganyika, Malawi and Victoria that is derived from the radiation associated with another of these lakes. Here, we report the discovery of a haplochromine cichlid species in Lake Tanganyika, which belongs genetically to the species flock of haplochromines of the Lake Victoria region. The new species colonized Lake Tanganyika only recently, suggesting that faunal exchange across watersheds and, hence, between isolated ichthyofaunas, is more common than previously thought.

Convergent evolution within an adaptive radiation of cichlid fishes.

The recurrent evolution of convergent forms is a widespread phenomenon in adaptive radiations (e.g., [1-9]). For example, similar ecotypes of anoles lizards have evolved on different islands of the Caribbean, benthic-limnetic species pairs of stickleback fish emerged repeatedly in postglacial lakes, equivalent sets of spider ecomorphs have arisen on Hawaiian islands, and a whole set of convergent species pairs of cichlid fishes evolved in East African Lakes Malawi and Tanganyika. In all these cases, convergent phenotypes originated in geographic isolation from each other. Recent theoretical models, however, predict that convergence should be common within species-rich communities, such as species assemblages resulting from adaptive radiations. Here, we present the most extensive quantitative analysis to date of an adaptive radiation of cichlid fishes, discovering multiple instances of convergence in body and trophic morphology. Moreover, we show that convergent morphologies are associated with adaptations to specific habitats and resources and that Lake Tanganyika's cichlid communities are characterized by the sympatric occurrence of convergent forms. This prevalent coexistence of distantly related yet ecomorphologically similar species offers an explanation for the greatly elevated species numbers in cichlid species flocks.