Convergent Evolution of Cichlid Fish Pharyngeal Jaw Dentitions in Mollusk-Crushing Predators: Comparative X-Ray Computed Tomography of Tooth Sizes, Numbers, and Replacement

Dental convergence is a hallmark of cichlid fish adaptive radiations. This type of repeated evolution characterizes both the oral jaws of these fishes as well as their pharyngeal jaws that are modified gill arches used to functionally process prey like hard-shelled mollusks. To test several hypotheses regarding the evolution of cichlid crushing pharyngeal dentitions, we used X-ray computed tomography scans to comparatively examine dental evolution in the pharyngeal jaw of a diversity of New World Heroine cichlid lineages. The substantial variation in erupted tooth sizes and numbers as well as replacement teeth found in these fishes showed several general patterns. Larger toothed species tended to have fewer teeth suggesting a potential role of spatial constraints in cichlid dental divergence. Species with larger numbers of erupted pharyngeal teeth also had larger numbers of replacement teeth. Replacement tooth size is almost exactly predicted (r = 0.99) from the size of erupted teeth across all of the species. Mollusk crushing was, therefore, highly associated with not only larger pharyngeal teeth, but also larger replacement teeth. Whether dental divergence arises as a result of environmental induced plasticity or originates via trophic polymorphism as found in the species Herichthys minckleyi, there appear to be general rules that structure interspecific divergence in cichlid pharyngeal erupted and replacement dentitions.

Non-trophic Functional Ecology of Vertebrate Teeth: A Review

Teeth are critical to the functional ecology of vertebrate trophic abilities, but are also used for a diversity of other non-trophic tasks. Teeth can play a substantial role in how animals move, manipulate their environment, positively interact with conspecifics, antagonistically interact with other organisms, and sense the environment. We review these non-trophic functions in an attempt to place the utility of human and all other vertebrate dentitions in a more diverse framework that emphasizes an expanded view of the functional importance and ecological diversity of teeth. In light of the extensive understanding of the developmental genetics, trophic functions, and evolutionary history of teeth, comparative studies of vertebrate dentitions will continue to provide unique insights into multi-functionality, many-to-one mapping, and the evolution of novel abilities.

Grand Challenges in Comparative Tooth Biology

Teeth are a model system for integrating developmental genomics, functional morphology, and evolution. We are at the cusp of being able to address many open issues in comparative tooth biology and we outline several of these newly tractable and exciting research directions. Like never before, technological advances and methodological approaches are allowing us to investigate the developmental machinery of vertebrates and discover both conserved and excitingly novel mechanisms of diversification. Additionally, studies of the great diversity of soft tissues, replacement teeth, and non-trophic functions of teeth are providing new insights into dental diversity. Finally, we highlight several emerging model groups of organisms that are at the forefront of increasing our appreciation of the mechanisms underlying tooth diversification.

The transcriptional correlates of divergent electric organ discharges in Paramormyrops electric fish

Background

Understanding the genomic basis of phenotypic diversity can be greatly facilitated by examining adaptive radiations with hypervariable traits. In this study, we focus on a rapidly diverged species group of mormyrid electric fish in the genus Paramormyrops, which are characterized by extensive phenotypic variation in electric organ discharges (EODs). The main components of EOD diversity are waveform duration, complexity and polarity. Using an RNA-sequencing based approach, we sought to identify gene expression correlates for each of these EOD waveform features by comparing 11 specimens of Paramormyrops that exhibit variation in these features.

Results

Patterns of gene expression among Paramormyrops are highly correlated, and 3274 genes (16%) were differentially expressed. Using our most restrictive criteria, we detected 145–183 differentially expressed genes correlated with each EOD feature, with little overlap between them. The predicted functions of several of these genes are related to extracellular matrix, cation homeostasis, lipid metabolism, and cytoskeletal and sarcomeric proteins. These genes are of significant interest given the known morphological differences between electric organs that underlie differences in the EOD waveform features studied.

Conclusions

In this study, we identified plausible candidate genes that may contribute to phenotypic differences in EOD waveforms among a rapidly diverged group of mormyrid electric fish. These genes may be important targets of selection in the evolution of species-specific differences in mate-recognition signals.

Evolutionary diversity as a catalyst for biological discovery

The tremendous diversity of animal behaviors has inspired generations of scientists from an array of biological disciplines. To complement investigations of ecological and evolutionary factors contributing to behavioral evolution, modern sequencing, gene editing, computational and neuroscience tools now provide a means to discover the proximate mechanisms upon which natural selection acts to generate behavioral diversity. Social behaviors are motivated behaviors that can differ tremendously between closely related species, suggesting phylogenetic plasticity in their underlying biological mechanisms. In addition, convergent evolution has repeatedly given rise to similar forms of social behavior and mating systems in distantly related species. Social behavioral divergence and convergence provides an entry point for understanding the neurogenetic mechanisms contributing to behavioral diversity. We argue that the greatest strides in discovering mechanisms contributing to social behavioral diversity will be achieved through integration of interdisciplinary comparative approaches with modern tools in diverse species systems. We review recent advances and future potential for discovering mechanisms underlying social behavioral variation; highlighting patterns of social behavioral evolution, oxytocin and vasopressin neuropeptide systems, genetic/transcriptional "toolkits," modern experimental tools, and alternative species systems, with particular emphasis on Microtine rodents and Lake Malawi cichlid fishes.

Evolutionary divergence of 3' UTRs in cichlid fishes

Background

Post-transcriptional regulation is crucial for the control of eukaryotic gene expression and might contribute to adaptive divergence. The three prime untranslated regions (3’ UTRs), that are located downstream of protein-coding sequences, play important roles in post-transcriptional regulation. These regions contain functional elements that influence the fate of mRNAs and could be exceptionally important in groups such as rapidly evolving cichlid fishes.

Results

To examine cichlid 3’ UTR evolution, we 1) identified gene features in nine teleost genomes and 2) performed comparative analyses to assess evolutionary variation in length, functional motifs, and evolutionary rates of 3’ UTRs. In all nine teleost genomes, we found a smaller proportion of repetitive elements in 3’ UTRs than in the whole genome. We found that the 3’ UTRs in cichlids tend to be longer than those in non-cichlids, and this was associated, on average, with one more miRNA target per gene in cichlids. Moreover, we provided evidence that 3’ UTRs on average have evolved faster in cichlids than in non-cichlids. Finally, analyses of gene function suggested that both the top 5% longest and 5% most rapidly evolving 3’ UTRs in cichlids tended to be involved in ribosome-associated pathways and translation.

Conclusions

Our results reveal novel patterns of evolution in the 3’ UTRs of teleosts in general and cichlids in particular. The data suggest that 3’ UTRs might serve as important meta-regulators, regulators of other mechanisms governing post-transcriptional regulation, especially in groups like cichlids that have undergone extremely fast rates of phenotypic diversification and speciation.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4821-8) contains supplementary material, which is available to authorized users.

Mechanical Transgressive Segregation and the Rapid Origin of Trophic Novelty

Hybrid phenotypes are often intermediate between those of parental species. However, hybridization can generate novel phenotypes when traits are complex. For instance, even when the morphologies of individual musculo-skeletal components do not segregate outside the parental range in hybrid offspring, complex functional systems can exhibit emergent phenotypes whose mechanics exceed the parental values. To determine if transgression in mechanics could facilitate divergence during an adaptive radiation, we examined three functional systems in the trophic apparatus of Lake Malawi cichlid fishes. We conducted a simulation study of hybridization between species pairs whose morphology for three functional systems was empirically measured, to determine how the evolutionary divergence of parental species influences the frequency that hybridization could produce mechanics that transgress the parental range. Our simulations suggest that the complex mechanical systems of the cichlid trophic apparatus commonly exhibit greater transgression between more recently diverged cichlid species. Because (1) all three mechanical systems produce hybrids with transgressive mechanics in Lake Malawi cichlids, (2) hybridization is common, and (3) single hybrid crosses often recapitulate a substantial diversity of mechanics, we conclude that mechanical transgressive segregation could play an important role in the rapid accumulation of phenotypic variation in adaptive radiations.

Mitochondrial genome primers for Lake Malawi cichlids

Resolving the evolutionary history of rapidly diversifying lineages like the Lake Malawi Cichlid Flock demands powerful phylogenetic tools. Although this clade of over 500 species of fish likely diversified in less than two million years, the availability of extensive sequence data sets, such as complete mitochondrial genomes, could help resolve evolutionary patterns in this group. Using a large number of newly developed primers, we generated whole mitochondrial genome sequences for 14 Lake Malawi cichlids. We compared sequence divergence across protein-coding regions of the mitochondrial genome and also compared divergence in the mitochondrial loci to divergence at two nuclear protein-coding loci, Mitfb and Dlx2. Despite the widespread sharing of haplotypes of identical sequences at individual loci, the combined use of all protein-coding mitochondrial loci provided a bifurcating phylogenetic hypothesis for the exemplars of major lineages within the Lake Malawi cichlid radiation. The primers presented here could have substantial utility for evolutionary analyses of mitochondrial evolution and hybridization within this diverse clade.

Low genetic and morphometric intraspecific divergence in peripheral copadichromis populations (perciformes: cichlidae) in the lake Malawi basin

Peripheral isolated populations may undergo rapid divergence from the main population due to various factors such as a bottleneck or a founder effect followed by genetic drift or local selection pressures. Recent populations of two economically important Copadichromis species in Lake Malombe, a satellite lake of Lake Malawi, were neither genetically nor morphometrically distinct from their source populations in the main lake. Evidence was found for a founder effect which had a different impact on the genetic composition of the two species. In addition, the increased fishing pressure in Lake Malombe may have led to a reduction of the body sizes of both species.

Comparative rates of lower jaw diversification in cichlid adaptive radiations

The lower jaw (LJ) provides an ideal trophic phenotype to compare rates and patterns of macroevolution among cichlid radiations. Using a novel phylogeny of four genes (ND2, dlx2, mitfb, and s7), we examined the evolutionary relationships among two of the most phylogenetically disparate cichlid radiations: (i) the Central America Heroines; and (ii) the East African Lake Malawi flock. To quantify jaw morphology, we measured two LJ lever systems in approximately 40 species from each lineage. Using geologic calibrations, we generated a chronogram for both groups and examined the rates of jaw evolution in the two radiations. The most rapidly evolving components of the LJ differed between the two radiations. However, the Lake Malawi flock exhibited a much faster rate of evolution in several components of the LJ. This rapid rate of divergence is consistent with natural selection, promoting unparalleled trophic diversification in Lake Malawi cichlids.