East African cichlid fishes

Genetic and Developmental Divergence in the Neural Crest Program between Cichlid Fish Species

Neural crest (NC) is a vertebrate-specific embryonic progenitor cell population at the basis of important vertebrate features such as the craniofacial skeleton and pigmentation patterns. Despite the wide-ranging variation of NC-derived traits across vertebrates, the contribution of NC to species diversification remains underexplored. Here, leveraging the adaptive diversity of African Great Lakes' cichlid species, we combined comparative transcriptomics and population genomics to investigate the evolution of the NC genetic program in the context of their morphological divergence. Our analysis revealed substantial differences in transcriptional landscapes across somitogenesis, an embryonic period coinciding with NC development and migration. This included dozens of genes with described functions in the vertebrate NC gene regulatory network, several of which showed signatures of positive selection. Among candidates showing between-species expression divergence, we focused on teleost-specific paralogs of the NC-specifier sox10 (sox10a and sox10b) as prime candidates to influence NC development. These genes, expressed in NC cells, displayed remarkable spatio-temporal variation in cichlids, suggesting their contribution to interspecific morphological differences, such as craniofacial structures and pigmentation. Finally, through CRISPR/Cas9 mutagenesis, we demonstrated the functional divergence between cichlid sox10 paralogs, with the acquisition of a novel skeletogenic function by sox10a. When compared with teleost models zebrafish and medaka, our findings reveal that sox10 duplication, although retained in most teleost lineages, had variable functional fates across their phylogeny. Altogether, our study suggests that NC-related processes-particularly those controlled by sox10s-are involved in generating morphological diversification between species and lays the groundwork for further investigations into the mechanisms underpinning vertebrate NC diversification.

Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination

Chromosomal inversions are an important class of genetic variation that link multiple alleles together into a single inherited block that can have important effects on fitness. To study the role of large inversions in the massive evolutionary radiation of Lake Malawi cichlids, we used long-read technologies to identify four single and two tandem inversions that span half of each respective chromosome, and which together encompass over 10% of the genome. Each inversion is fixed in one of the two states within the seven major ecogroups, suggesting they played a role in the separation of the major lake lineages into specific lake habitats. One exception is within the benthic sub-radiation, where both inverted and non-inverted alleles continue to segregate within the group. The evolutionary histories of three of the six inversions suggest they transferred from the pelagic Diplotaxodon group into benthic ancestors at the time the benthic sub-radiation was seeded. The remaining three inversions are found in a subset of benthic species living in deep waters. We show that some of these inversions are used as XY sex-determination systems but are also likely limited to a subset of total lake species. Our work suggests that inversions have been under both sexual and natural selection in Lake Malawi cichlids and that they will be important to understanding how this adaptive radiation evolved.

African cichlid fishes: morphological data and taxonomic insights from a genus-level survey of supraneurals, pterygiophores, and vertebral counts (Ovalentaria, Blenniiformes, Cichlidae, Pseudocrenilabrinae)

Background

The iconic freshwater cichlid fishes (Cichlidae) comprise about 1750 validly named species and hundreds more that are known, but not yet described and named. Cichlids are an important source of protein for millions of people on several continents, are model organisms in studies of evolution, speciation, ecology, development, behaviour and physiology and are popular as aquarium fishes. Yet, comparative studies of cichlid internal anatomy are rare. Even their osteology has not been taxonomically surveyed. The cichlid postcranial skeleton has been especially neglected.

New information

Here, I provide the first survey in cichlids of the considerable variation in numbers of vertebrae, supraneurals and dorsal- and anal-fin supports (pterygiophores), as well as the patterns with which the pterygiophores insert between the neural or haemal spines. The study includes some 1700 specimens of nearly 400 cichlid species. Focusing on the largest subfamily, the African cichlids or Pseudocrenilabrinae, the survey furnishes data from species in all but one of its 166 genera. Limited data from species in the other cichlid subfamilies (Etroplinae, Ptychochrominae and Cichlinae) and from the related leaffishes, Polycentridae, are also presented. Key examples of pterygiophore insertion patterns from throughout the range of variation are illustrated and discussed. Detailed analytical tables and all raw data are provided in supplementary files.A bizarre specialisation in Cyprichromis is noted, evidently for the first time. Uniquely in this Lake Tanganyikan genus, five to seven anal pterygiophores are abdominal in position, located anterior to the anal fin and inserting toward or between successive pairs of pleural ribs.Taxonomic changes: The most speciose tribe of African cichlids, currently known as Haplochromini, is correctly called Pseudocrenilabrini. Based chiefly on the molecular phylogenetic findings of other workers, I propose four pseudocrenilabrine subtribes, one occurring in rivers and three endemic to Lake Malawi. I also re-assign the Lake Tanganyikan tribe Tropheini as another subtribe of Pseudocrenilabrini, in line with numerous molecular studies placing tropheines firmly within this tribe. The remaining genera of Pseudocrenilabrini remain incertae sedis in this tribe pending clarification of their phylogenetic relationships.The character complex here surveyed is a promising source of taxonomically and phylogenetically informative characteristics distinguishing or uniting cichlid taxa at multiple hierarchical levels, from species through subfamily. This reference set of novel character data can also provide information for palaeontological studies of African cichlids. These attributes are skeletal features potentially available for study in well preserved fossils and may help determine their correct taxonomic placement.

Uncovering developmental diversity in the field

Many developmental biologists seldom leave the lab for research, relying instead on establishing colonies of traditional and emerging model systems. However, to fully understand the mechanisms and principles of development and evolution, including the role of ecology and the environment, it is important to study a diverse range of organisms in context. In this Perspective, we hear from five research teams from around the world about the importance and challenges of going into the field to study their organisms of interest. We also invite you to share your own fieldwork stories on the Node.

A whole-body micro-CT scan library that captures the skeletal diversity of Lake Malawi cichlid fishes

Here we describe a dataset of freely available, readily processed, whole-body μCT-scans of 56 species (116 specimens) of Lake Malawi cichlid fishes that captures a considerable majority of the morphological variation present in this remarkable adaptive radiation. We contextualise the scanned specimens within a discussion of their respective ecomorphological groupings and suggest possible macroevolutionary studies that could be conducted with these data. In addition, we describe a methodology to efficiently μCT-scan (on average) 23 specimens per hour, limiting scanning time and alleviating the financial cost whilst maintaining high resolution. We demonstrate the utility of this method by reconstructing 3D models of multiple bones from multiple specimens within the dataset. We hope this dataset will enable further morphological study of this fascinating system and permit wider-scale comparisons with other cichlid adaptive radiations.

Genome assemblies for Chromidotilapia guntheri (Teleostei: Cichlidae) identify a novel candidate gene for vertebrate sex determination, RIN3

Advances in genome sequencing have greatly accelerated the identification of sex chromosomes in a variety of species. Many of these species have experienced structural rearrangements that reduce recombination between the sex chromosomes, allowing the accumulation of sequence differences over many megabases. Identification of the genes that are responsible for sex determination within these sometimes large regions has proved difficult. Here, we identify an XY sex chromosome system on LG19 in the West African cichlid fish Chromidotilapia guntheri in which the region of differentiation extends over less than 400 kb. We develop high-quality male and female genome assemblies for this species, which confirm the absence of structural variants, and which facilitate the annotation of genes in the region. The peak of differentiation lies within rin3, which has experienced several debilitating mutations on the Y chromosome. We suggest two hypotheses about how these mutations might disrupt endocytosis, leading to Mendelian effects on sexual development.

Diversity of Sex Chromosomes in Vertebrates: Six Novel Sex Chromosomes in Basal Haplochromines (Teleostei: Cichlidae)

African cichlid fishes are known for their high rates of phenotypic evolution. A rapid rate of diversification is apparent also in the diversity of their sex chromosomes. To date, sex determiners have been identified on 18 of 22 chromosomes in the standard karyotype. Here, we use whole-genome sequencing to characterize the sex chromosomes of seven populations of basal haplochromines, focusing on the genus Pseudocrenilabrus. We identify six new sex chromosome systems, including the first report of a cichlid sex-determining system on linkage group 12. We then quantify the rates and patterns of sex chromosome turnover in this clade. Finally, we test whether some autosomes become sex chromosomes in East African cichlids more often than expected by chance.

Genetic and developmental divergence in the neural crest programme between cichlid fish species

Neural crest (NC) is a vertebrate-specific embryonic progenitor cell population at the basis of important vertebrate features such as the craniofacial skeleton and pigmentation patterns. Despite the wide-ranging variation of NC-derived traits across vertebrates, the contribution of NC to species diversification remains underexplored. Here, leveraging the adaptive diversity of African Great Lakes' cichlid species, we combined comparative transcriptomics and population genomics to investigate the evolution of the NC genetic programme in the context of their morphological divergence. Our analysis revealed substantial differences in transcriptional landscapes across somitogenesis, an embryonic period coinciding with NC development and migration. This included dozens of genes with described functions in the vertebrate NC gene regulatory network, several of which showed signatures of positive selection. Among candidates showing between-species expression divergence, we focused on teleost-specific paralogs of the NC-specifier sox10 (sox10a and sox10b) as prime candidates to influence NC development. These genes, expressed in NC cells, displayed remarkable spatio-temporal variation in cichlids, suggesting their contribution to inter-specific morphological differences. Finally, through CRISPR/Cas9 mutagenesis, we demonstrated the functional divergence between cichlid sox10 paralogs, with the acquisition of a novel skeletogenic function by sox10a. When compared to the teleost models zebrafish and medaka, our findings reveal that sox10 duplication, although retained in most teleost lineages, had variable functional fates across their phylogeny. Altogether, our study suggests that NC-related processes - particularly those controlled by sox10s - might be involved in generating morphological diversification between species and lays the groundwork for further investigations into mechanisms underpinning vertebrate NC diversification.

Developmental plasticity and variability in the formation of egg-spots, a pigmentation ornament in the cichlid Astatotilapia calliptera

Vertebrate pigmentation patterns are highly diverse, yet we have a limited understanding of how evolutionary changes to genetic, cellular, and developmental mechanisms generate variation. To address this, we examine the formation of a sexually-selected male ornament exhibiting inter- and intraspecific variation, the egg-spot pattern, consisting of circular yellow-orange markings on the male anal fins of haplochromine cichlid fishes. We focus on Astatotilapia calliptera, the ancestor-type species of the Malawi cichlid adaptive radiation of over 850 species. We identify a key role for iridophores in initializing egg-spot aggregations composed of iridophore-xanthophore associations. Despite adult sexual dimorphism, aggregations initially form in both males and females, with development only diverging between the sexes at later stages. Unexpectedly, we found that the timing of egg-spot initialization is plastic. The earlier individuals are socially isolated, the earlier the aggregations form, with iridophores being the cell type that responds to changes to the social environment. Furthermore, we observe apparent competitive interactions between adjacent egg-spot aggregations, which strongly suggests that egg-spot patterning results mostly from cell-autonomous cellular interactions. Together, these results demonstrate that A. calliptera egg-spot development is an exciting model for investigating pigment pattern formation at the cellular level in a system with developmental plasticity, sexual dimorphism, and intraspecific variation. As A. calliptera represents the ancestral bauplan for egg-spots, these findings provide a baseline for informed comparisons across the incredibly diverse Malawi cichlid radiation.

Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.

Mechanisms Underlying the Formation and Evolution of Vertebrate Color Patterns

Vertebrates exhibit a wide range of color patterns, which play critical roles in mediating intra- and interspecific communication. Because of their diversity and visual accessibility, color patterns offer a unique and fascinating window into the processes underlying biological organization. In this review, we focus on describing many of the general principles governing the formation and evolution of color patterns in different vertebrate groups. We characterize the types of patterns, review the molecular and developmental mechanisms by which they originate, and discuss their role in constraining or facilitating evolutionary change. Lastly, we outline outstanding questions in the field and discuss different approaches that can be used to address them. Overall, we provide a unifying conceptual framework among vertebrate systems that may guide research into naturally evolved mechanisms underlying color pattern formation and evolution.

Genome editing in East African cichlids and tilapias: state-of-the-art and future directions

African cichlid fishes of the Cichlidae family are a group of teleosts important for aquaculture and research. A thriving research community is particularly interested in the cichlid radiations of the East African Great Lakes. One key goal is to pinpoint genetic variation underlying phenotypic diversification, but the lack of genetic tools has precluded thorough dissection of the genetic basis of relevant traits in cichlids. Genome editing technologies are well established in teleost models like zebrafish and medaka. However, this is not the case for emerging model organisms, such as East African cichlids, where these technologies remain inaccessible to most laboratories, due in part to limited exchange of knowledge and expertise. The Cichlid Science 2022 meeting (Cambridge, UK) hosted for the first time a Genome Editing Workshop, where the community discussed recent advances in genome editing, with an emphasis on CRISPR/Cas9 technologies. Based on the workshop findings and discussions, in this review we define the state-of-the-art of cichlid genome editing, share resources and protocols, and propose new possible avenues to further expand the cichlid genome editing toolkit.

Mitogenomic Characterization of Cameroonian Endemic Coptodon camerunensis (Cichliformes: Cichlidae) and Matrilineal Phylogeny of Old-World Cichlids

The mitogenomic evolution of old-world cichlids is still largely incomplete in Western Africa. In this present study, the complete mitogenome of the Cameroon endemic cichlid, Coptodon camerunensis, was determined by next-generation sequencing. The mitogenome was 16,557 bp long and encoded with 37 genes (13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region). The C. camerunensis mitogenome is AT-biased (52.63%), as exhibited in its congener, Coptodon zillii (52.76% and 53.04%). The majority of PCGs start with an ATG initiation codon, except COI, which starts with a GTG codon and five PCGs and ends with the TAA termination codon and except seven PCGs with an incomplete termination codon. In C. camerunensis mitogenome, most tRNAs showed classical cloverleaf secondary structures, except tRNA-serine with a lack of DHU stem. Comparative analyses of the conserved blocks of two Coptodonini species control regions revealed that the CSB-II block was longer than other blocks and contained highly variable sites. Using 13 concatenated PCGs, the mitogenome-based Bayesian phylogeny easily distinguished all the examined old-world cichlids. Except for Oreochromini and Coptodinini tribe members, the majority of the taxa exhibited monophyletic clustering within their respective lineages. C. camerunensis clustered closely with Heterotilapia buttikoferi (tribe Heterotilapiini) and had paraphyletic clustering with its congener, C. zillii. The Oreochromini species also displayed paraphyletic grouping, and the genus Oreochromis showed a close relationship with Coptodinini and Heterotilapiini species. In addition, illustrating the known distribution patterns of old-world cichlids, the present study is congruent with the previous hypothesis and proclaims that prehistoric geological evolution plays a key role in the hydroclimate of the African continent during Mesozoic, which simultaneously disperses and/or colonizes cichlids in different ichthyological provinces and Rift Lake systems in Africa. The present study suggests that further mitogenomes of cichlid species are required, especially from western Africa, to understand their unique evolution and adaptation.

Distinct genetic origins of eumelanin intensity and barring patterns in cichlid fishes

Pigment patterns are incredibly diverse across vertebrates and are shaped by multiple selective pressures from predator avoidance to mate choice. A common pattern across fishes, but for which we know little about the underlying mechanisms, is repeated melanic vertical bars. In order to understand genetic factors that modify the level or pattern of vertical barring, we generated a genetic cross of 322 F2 hybrids between two cichlid species with distinct barring patterns, Aulonocara koningsi and Metriaclima mbenjii. We identify 48 significant quantitative trait loci that underlie a series of seven phenotypes related to the relative pigmentation intensity, and four traits related to patterning of the vertical bars. We find that genomic regions that generate variation in the level of eumelanin produced are largely independent of those that control the spacing of vertical bars. Candidate genes within these intervals include novel genes and those newly-associated with vertical bars, which could affect melanophore survival, fate decisions, pigment biosynthesis, and pigment distribution. Together, this work provides insights into the regulation of pigment diversity, with direct implications for an animal's fitness and the speciation process.

Social deprivation in maternal mouthbrooders Tropheus sp. "Caramba" (Teleostei: Cichlidae) decreases the success rate of reproduction and survival rate of fish fry

Early offspring separation from mothers causes social deprivation. Mouthbrooding, when eggs and fry are incubated in the buccal cavity of the parent, is one of the reproductive strategies in fish. The mother is the incubating parent in African lake cichlids from the genus Tropheus. Many of these are produced in captivity and some producers use artificial incubators in which eggs are incubated separately from the mother. We hypothesized that this practice may dramatically modify the reproduction rate of fish individuals produced by the method of artificial incubation. The long-term experiment focused on Tropheus sp. "Caramba" had been carried out for 10 years when maternally incubated and separated individuals were compared. We found a negative effect of artificial egg and offspring incubation out of the mother's buccal cavity. The deprived females laid the same number of eggs as maternally incubated females, but most eggs were lost during the incubation. Moreover, the reproduction frequency was significantly lower in deprived females in comparison with those maternally incubated. This study should be perceived as preliminary. For this reason and with respect to welfare principles, we strongly recommend similarly designed experiments focused on other potentially sensitive fish mouthbrooders. Once the syndrome would be confirmed, we recommend avoiding artificial incubation of mouthbrooding fish in general.

The Effects of Humic Acids on the Early Developmental Stages of African Cichlids during Artificial Breeding

The aim of this study was to compare the effect of humic acid (HA) obtained by extraction from alginate on the incubation of roes and fry development in African cichlids, Labidochormis caeruleus, as well as their influence on the stabilization of the physicochemical parameters of water in an aquarium during artificial breeding. The roes were obtained by extruding from a female buccal cavity immediately after fertilization. For the experiment, 4 groups of 40 roes were formed in an incubator with an artificial hatchery. Groups 1-3 were exposed to 1%, 5%, and 10% concentrations of HA, respectively. The control group C was not exposed to HA. In all groups, the mortality and size differences of the fry, as well as the temperature, pH, hardness, nitrite, and nitrate levels in the tanks, were determined during a 30-day monitoring period until the resorption of the yolk sac. The results of this study indicated the ability of HA in 5% and 10% concentrations to reduce nitrite and nitrate levels in the aquatic environment, which significantly reduced the mortality of roes and the survivability of the fry. The determination of the morphological measurements of the fry revealed an increased body length in the groups exposed to 5% and 10% HA concentrations compared to the control group by the end of the monitored period. It was also noted that the yolk sac was resorbed two days earlier in the same groups than in the control. Thus, the results showed that HAs are suitable for use in the artificial aquarium incubation of roes and fry development, which are increasingly exposed to adverse environmental factors. The knowledge obtained in this study and its transfer into practice can allow even less experienced aquarists to successfully breed aquarium fish species that could not normally be bred under artificial conditions without the addition of HA.