Developmental basis of phenotypic integration in two Lake Malawi cichlids

Comparative Hox genes expression within the dimorphic annelid Streblospio benedicti reveals patterning variation during development

Hox genes are transcriptional regulators that elicit cell positional identity along the anterior-posterior region of the body plan across different lineages of Metazoan. Comparison of Hox gene expression across distinct species reveals their evolutionary conservation, however their gains and losses in different lineages can correlate with body plan modifications and morphological novelty. We compare the expression of eleven Hox genes found within Streblospio benedicti, a marine annelid that produces two types of offspring with distinct developmental and morphological features. For these two distinct larval types, we compare Hox gene expression through ontogeny using HCR (hybridization chain reaction) probes for in-situ hybridization and RNA-seq data. We find that Hox gene expression patterning for both types is typically similar at equivalent developmental stages. However, some Hox genes have spatial or temporal differences between the larval types that are associated with morphological and life-history differences. This is the first comparison of developmental divergence in Hox genes expression within a single species and these changes reveal how body plan differences may arise in larval evolution.

Zebrafish crocc2 mutants exhibit divergent craniofacial shape, misregulated variability, and aberrant cartilage morphogenesis

BACKGROUND

Phenotypic variation is of paramount importance in development, evolution, and human health; however, the molecular mechanisms that influence organ shape and shape variability are not well understood. During craniofacial development, the behavior of skeletal precursors is regulated by both biochemical and environmental inputs, and the primary cilia play critical roles in transducing both types of signals. Here, we examine a gene that encodes a key constituent of the ciliary rootlets, crocc2, and its role in cartilage morphogenesis in larval zebrafish.

RESULTS

Geometric morphometric analysis of crocc2 mutants revealed altered craniofacial shapes and expanded variation. At the cellular level, we observed altered chondrocyte shapes and planar cell polarity across multiple stages in crocc2 mutants. Notably, cellular defects were specific to areas that experience direct mechanical input. Cartilage cell number, apoptosis, and bone patterning were not affected in crocc2 mutants.

CONCLUSIONS

Whereas "regulatory" genes are widely implicated in patterning the craniofacial skeleton, genes that encode "structural" aspects of the cell are increasingly implicated in shaping the face. Our results add crocc2 to this list, and demonstrate that it affects craniofacial geometry and canalizes phenotypic variation. We propose that it does so via mechanosensing, possibly through the ciliary rootlet. If true, this would implicate a new organelle in skeletal development and evolution.

Bone calcification rate as a factor of craniofacial transformations in salmonid fish: Insights from an experiment with hormonal treatment of calcium metabolism

Adaptation to different environments can be achieved by physiological shifts throughout development. Hormonal regulators shape the physiological and morphological traits of the evolving animals making them fit for the particular ecological surroundings. We hypothesized that the artificially induced hypersynthesis of calcitonin and parathyroid hormone mutually influencing calcium metabolism could affect bone formation during early ontogeny in fish imitating the heterochrony in craniofacial ossification in natural adaptive morphs. Conducting an experiment, we found that the long-standing treatment of salmonid juveniles with high doses of both hormones irreversibly shifts the corresponding hormone status for a period well beyond the time scale for total degradation of the injected hormone. The hormones program the ossification of the jaw suspension bones and neurocranial elements in a specific manner affecting the jaws position and pharingo-branchial area stretching. These morphological shifts resemble the adaptive variants found in sympatric pelagic and demersal morphs of salmonids. We conclude that solitary deviations in the regulators of calcium metabolism could determine functional morphological traits via transformations in skeletal development.

Ambient temperature as a factor contributing to the developmental divergence in sympatric salmonids

Factors and mechanisms promoting resource-based radiation in animals still represent a main challenge to evolutionary biology. The modifications of phenotype tied with adaptive diversification may result from an environmentally related shift having occurred at the early stage of development. Here, we study the role of temperature dynamics on the reproductive sites in the early-life divergence and adaptive radiation of the salmonid fish Salvelinus malma dwelling in the Lake Kronotskoe basin (North-East Asia). Local sympatric charr ecomorphs demonstrate strict homing behaviour guiding the preordained distribution along tributaries and, hence, further development under different temperatures. We thoroughly assessed the annual temperature dynamics at the spawning grounds of each morph as compared to an ancestral anadromous morph. Then we carried out an experimental rearing of both under naturally diverging and uniformed temperatures. To compare the morphs' development under the dynamically changing temperatures, we have designed a method based on calculating the accumulated heat by the Arrhenius equation. The proposed equation shows a strong predictive power and, at the same time, is not bias-susceptible when the developmental temperature approximates 0°C. The temperature was found to significantly affect the charrs' early ontogeny, which underlies the divergence of developmental and growth rates between the morphs, as well as morph-specific ontogenetic adaptations to the spawning site's temperatures. As opposed to the endemic morphs from Lake Kronotskoe, the anadromous S. malma, being unexposed to selection оn highly specific reproduction conditions, showed a wide temperature tolerance, Our findings demonstrate that the hatch, onset timing of external feeding, and size dissimilarities between the sympatric morphs reveal themselves during the development under contrast temperatures. As a result of the observed developmental disparities, the morphs occupy specific definitive foraging niches in the lake.

Stages of embryonic development in the live-bearing fish, Gambusia holbrooki

BACKGROUND

Divergent morphology and placentation of Poeciliids make them suitable model for investigating how evolutionary selection has altered and conserved the developmental mechanisms. However, there is limited description of their embryonic staging, despite representing a key evolutionary node that shares developmental strategy with placental vertebrates. Here, we describe the embryonic developmental stages of Gambusia holbrooki from zygote to parturition using freshly harvested embryos.

RESULTS

We defined 40 embryonic stages using a numbered (stages 0-39; zygote to parturition, respectively) and named (grouped into seven periods, ie, zygote, cleavage, blastula, gastrula, segmentation, pharyngula, and parturition) staging system. Two sets of quantitative (ie, egg diameter, embryonic total length, otic vesicle closure index, heart rates, the number of caudal fin rays and elements) and qualitative (ie, three-dimensional analysis of images and key morphological criteria) data were acquired and used in combination to describe each stage. All 40 stages are separated by well-defined morphological traits, revealing developmental novelties that are influenced by narrow perivitelline space, placentation, internal gestation, and sex differentiation.

CONCLUSIONS

The principal diagnostic features described are quick, reliable, and easy to apply. This system will benefit researchers investigating molecular ontogeny, particularly sexual differentiation mechanisms in G. holbrooki.

Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity

Background

The oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted trophic diversification and contributed to the success of cichlid adaptive radiations. Most studies until now have focused on the functional, morphological, or genetic aspects of cichlid jaw modularity. Here we extend this concept to include transcriptional modularity by sequencing whole transcriptomes of the two jaws and comparing their gene coexpression networks.

Results

We show that transcriptional decoupling of gene expression underlies the functional decoupling of cichlid oral and pharyngeal jaw apparatus and the two units are evolving independently in recently diverged cichlid species from Lake Tanganyika. Oral and pharyngeal jaw coexpression networks reflect the common origin of the jaw regulatory program as there is high preservation of gene coexpression modules between the two sets of jaws. However, there is substantial rewiring of genetic architecture within those modules. We define a global jaw coexpression network and highlight jaw-specific and species-specific modules within it. Furthermore, we annotate a comprehensive in silico gene regulatory network linking the Wnt and AHR signalling pathways to jaw morphogenesis and response to environmental cues, respectively. Components of these pathways are significantly differentially expressed between the oral and pharyngeal jaw apparatus.

Conclusion

This study describes the concerted expression of many genes in cichlid oral and pharyngeal jaw apparatus at the onset of the independent life of cichlid fishes. Our findings suggest that – on the basis of an ancestral gill arch network—transcriptional rewiring may have driven the modular evolution of the oral and pharyngeal jaws, highlighting the evolutionary significance of gene network reuse. The gene coexpression and in silico regulatory networks presented here are intended as resource for future studies on the genetics of vertebrate jaw morphogenesis and trophic adaptation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01787-9.

Differences in developmental potential predict the contrasting patterns of dental diversification in characiform and cypriniform fishes

Morphological diversification during adaptive radiation may depend on factors external or internal to the lineage. We provide evidence for the latter in characiform fishes (tetras and piranhas), which exhibit extensive dental diversity. Phylogenetic character mapping supported regain of lost teeth as contributing to this diversity. To test for latent potential for dentition that would facilitate its evolutionary expansion, we overexpressed a tooth initiation signal, the tumour necrosis factor pathway ligand ectodysplasin, in a model characiform, the Mexican tetra (Astyanax mexicanus). This manipulation resulted in extensive ectopic dentition, in contrast with its previously reported limited effect in the zebrafish (Danio rerio). Tooth location in the order Cypriniformes, to which the zebrafish belongs, is much more restricted than in characiforms, a pattern that may be explained by differences in the retention of ancestral developmental potential. Our results suggest that differences in evolvability between lineages may lead to contrasting patterns of diversification.

Trophic divergence of Lake Kivu cichlid fishes along a pelagic versus littoral habitat axis

Local adaptation to the littoral and pelagic zones in two cichlid haplochromine fish species from Lake Kivu was investigated using morphometrics. Cranial variation and inferred jaw mechanics in both sexes of the two species across the two habitat types were quantified and compared. Comparisons of littoral versus pelagic populations revealed habitat-specific differences in the shape of the feeding apparatus. Also, kinematic transmission of the anterior jaw four-bar linkage that promotes greater jaw protrusion was higher in the pelagic zone than in the littoral zone for both species. Inferred bite force was likewise higher in pelagic zone fish. There were also sex-specific differences in craniofacial morphology as males exhibited longer heads than females in both habitats. As has been described for other cichlids in the East African Great Lakes, local adaptation to trophic resources in the littoral and pelagic habitats characterizes these two Lake Kivu cichlids. Similar studies involving other types of the Lake Kivu fishes are recommended to test the evidence of the observed trophic patterns and their genetic basis of divergences.

Natural toxic impact and thyroid signalling interplay orchestrates riverine adaptive divergence of salmonid fish

Adaptive radiation in fishes has been actively investigated over the last decades. Along with numerous well-studied cases of lacustrine radiation, some examples of riverine sympatric divergence have been recently discovered. In contrast to the lakes, the riverine conditions do not provide evident stability in the ecological gradients. Consequently, external factors triggering the radiation, as well as developmental mechanisms underpinning it, remain unclear. Herein, we present the comprehensive study of external and internal drivers of the riverine adaptive divergence of the salmonid fish Salvelinus malma. In the Kamchatka River, north-east Asia, this species splits in the reproductively isolated morphs that drastically differ in ecology and morphology: the benthivorous Dolly Varden (DV) and the piscivorous stone charr (SC). To understand why and how these morphs originated, we performed a series of field and experimental work, including common-garden rearing, comparative ontogenetic, physiological and endocrinological analyses, hormonal 'engineering' of phenotypes and acute toxicological tests. We revealed that the type of spawning ground acts as the decisive factor driving the radiation of S. malma. In contrast to DV spawning in the leaf krummholz zone, SC reproduces in the zone of coniferous forest, which litter has a toxic impact on developing fishes. SC enhances resistance to the toxicants via metabolism acceleration provided by the elevated thyroid hormone expenditure. These physiological changes lead to the multiple heterochronies resulting in a specific morphology and ecology of SC. Salvelinus malma represents a notable example of how the thyroid axis contributes to the generation of diverse phenotypic outcomes underlying the riverine sympatric divergence. Our findings, along with the paleoecology data concerning spruce forest distribution during the Pleistocene, provide an opportunity to reconstruct a scenario of S. malma divergence. Taken together, obtained results with the data of the role of thyroid hormones in the ontogeny and diversification of fishes contribute a resource to consider the thyroid axis as a prime director orchestrating the phenotypic plasticity promoting evolutionary diversification under the changing environmental conditions.

Endochondral growth zone pattern and activity in the zebrafish pharyngeal skeleton

BACKGROUND

Endochondral ossification is a major bone forming mechanism in vertebrates, defects in which can result in skeletal dysplasia or craniofacial anomalies in humans. The zebrafish holds great potential to advance our understanding of endochondral growth zone development and genetics, yet several important aspects of its biology remain unexplored. Here we provide a comprehensive description of endochondral growth zones in the pharyngeal skeleton, including their developmental progression, cellular activity, and adult fates.

RESULTS

Postembryonic growth of the pharyngeal skeleton is supported by endochondral growth zones located either at skeletal epiphyses or synchondroses. Col2a1a and col10a1a in situ hybridization and anti-PCNA immunostaining identify resting-, hypertrophic- and proliferative zones, respectively, in pharyngeal synchondroses. Cellular hypertrophy and matrix deposition contribute little, if at all, to axial growth in most skeletal elements. Zebrafish endochondral growth zones develop during metamorphosis and arrest in adults.

CONCLUSIONS

Two endochondral growth zone configurations in the zebrafish pharyngeal skeleton produce either unidirectional (epiphyses) or bidirectional (synchondroses) growth. Cell proliferation drives endochondral growth and its modulation, in contrast to mammalian long bones in which bone length depends more on cell enlargement during hypertrophy and intramembranous ossification is the default mechanism of bone growth in zebrafish adults.

Experimental evidence of the role of heterochrony in evolution of the Mesoamerican cichlids pigment patterns

The Mesoamerican cichlids display a spectacular diversity of pigment patterns, which serve a variety of functions and serve as a strong selective trait for this lineage. The development and variation of coloration in the Mesoamerican cichlids have been detailed by several groups. In particular, Říčan, Musilová, Muška, and Novák () and Říčan, Piálek, Dragová, and Novák () determined homology of pattern and revealed four alternative types of coloration and their ontogeny. In this work, this group posed an "ontogenetic timing hypothesis" proposing heterochronic shifts underlying major transitions in the evolution of the Mesoamerican cichlids. Here, we experimentally test this hypothesis by experimentally altering timing of pigment pattern formation in the convict cichlid Amatitlania nigrofasciata, a member of the Mesoamerican cichlids, via manipulations of thyroid hormone (TH) function. The response of different pigment cell lineages to TH-perturbations revealed that the transition from larval to juvenile coloration in the convict cichlid is under the control of TH-signaling. Importantly, hormonally induced changes in the timing of pigment cell lineages' development resulted in shifts of coloration ontogeny type observed between lineages and led to the appearance of phenotypes mimicking those in phylogenetically close and distant species. Thus, our findings support the hypothesis that simple changes in ontogenetic timing underlies species specific patterns in pigmentation and provide new perspectives for studying the role of endocrine signaling in the evolution of cichlids.

Juvenile divergence in adaptive traits among seven sympatric fish ecomorphs arises before moving to different lacustrine habitats

Identifying the mechanisms initiating sympatric diversification in vertebrates has remained a conceptual challenge. Here, we analyse an assemblage of sympatric charr (Salvelinus malma) morphs from landlocked Lake Kronotskoe basin as a model to uncover the divergence pathways in freshwater fishes during the early life history stages. All morphs have distinct developmental biology, but a similar developmental rate retardation compared to the ancestor. Our study reveals that adult morphological differences, which acquire functionality at maturation, originate in the early juvenile stages due to heterochrony in skeletogenesis and allometric changes triggered by variation in metabolic activity. The craniofacial differences among the morphs result from asynchronous development of several skeletal modules. The accelerated ossification of teeth-armed bones occurs in predatory feeding morphs, whereas cranial cover ossification is promoted in benthivorous morphs. These contrasting growth patterns have led to seven phenotypes that span a range far beyond the ancestral variability. The most distinct morphs are a riverine spawning, epilimnetic predator and a lacustrine spawning, profundal benthic feeder. Taken together, we argue that the adaptive morphological differentiation in these sympatric freshwater fishes is driven by diverging patterns in ossification rate and metabolic activity against a background of uneven somatic growth. This divergence is primarily associated with basic environmental differences on the nursery grounds that might be unrelated to resource use. This nonheritable phenotype divergence is then exposed to natural selection that could result in further adaptive genetic changes.

The Role of Alternative Splicing and Differential Gene Expression in Cichlid Adaptive Radiation

Species diverge eco-morphologically through the continuous action of natural selection on functionally important structures, producing alternative adaptive morphologies. In cichlid fishes, the oral and pharyngeal jaws are such key structures. Adaptive variation in jaw morphology contributes to trophic specialization, which is hypothesized to fuel their rapid speciation in the East African Great Lakes. Much is known about the genes involved in cichlid jaw and craniofacial development. However, it is still unclear what salient sources of variation gave rise to trophic-niche specialization, facilitating adaptive radiation. Here, we explore two sources of transcriptional variation that may underlie species-specific disparities in jaw morphology. Using whole transcriptome RNA-sequencing, we analyze differences in gene expression and alternative splicing, at the end of postlarval development, in fully functional jaws of six species of cichlids from the Lake Tanganyika tribe Tropheini. Our data reveal a surprisingly high degree of alternative splicing events compared with gene expression differences among species and trophic types. This suggests that differential trophic adaptation of the jaw apparatus may have been shaped by transcriptional rewiring of splicing as well as gene expression variation during the rapid radiation of the Tropheini. Specifically, genes undergoing splicing across most species were found to be enriched for pharyngeal jaw gene ontology terms. Overall, jaw transcriptional patterns at postlarval developmental stage were highly dynamic and species-specific. In conclusion, this work indicates that shifts in alternative splicing could have played a more important role in cichlid adaptive radiation, and possibly adaptive radiation in general, than currently recognized.

Thyroid Hormone Stimulates the Onset of Adult Feeding Kinematics in Zebrafish

The physical demands for swimming and feeding change dramatically over the course of development for many aquatic animals. Indeed, in teleosts, the transition from larva to adult involves major shifts in both trophic morphology and feeding behavior. A spike in thyroid hormone (TH) coordinates many developmental processes that occur during this adult transition in numerous vertebrate species. Using mutant and transgenic zebrafish, we tested the hypothesis that TH is essential for the transition from larval to adult feeding kinematic profiles. We found that every measured kinematic variable that distinguished larvae from adults also differentiated hypothyroid from wild-type (WT) euthyroid adults, suggesting that TH is indeed necessary for the onset of mature feeding behaviors. In contrast, feeding kinematics in hyperthyroid adults were extremely similar to those measured in euthyroid adults. Altered TH signaling underlies pedomorphosis in some amphibian species, and Danionella is a pedomorphic danionin genus. We therefore tested whether feeding kinematics of adult Danionella would more closely match larval zebrafish (and hypothyroid adults) than WT adult zebrafish. We found Danionella feeding kinematics resemble those of larval (and hypothyroid) zebrafish in multiple respects. Overall, we conclude that TH is essential in stimulating the onset of adult feeding kinematics in zebrafish, and that some of the underlying developmental pathways may have been lost in Danionella.

The evolution of jaw protrusion mechanics is tightly coupled to bentho-pelagic divergence in damselfishes (Pomacentridae)

Most species-rich lineages of aquatic organisms have undergone divergence between forms that feed from the substrate (benthic feeding) and forms that feed from the water column (pelagic feeding). Changes in trophic niche are frequently accompanied by changes in skull mechanics, and multiple fish lineages have evolved highly specialized biomechanical configurations that allow them to protrude their upper jaws toward the prey during feeding. Damselfishes (family Pomacentridae) are an example of a species-rich lineage with multiple trophic morphologies and feeding ecologies. We sought to determine whether bentho-pelagic divergence in the damselfishes is tightly coupled to changes in jaw protrusion ability. Using high-speed video recordings and kinematic analysis, we examined feeding performance in 10 species that include three examples of convergence on herbivory, three examples of convergence on omnivory and two examples of convergence on planktivory. We also utilized morphometrics to characterize the feeding morphology of an additional 40 species that represent all 29 damselfish genera. Comparative phylogenetic analyses were then used to examine the evolution of trophic morphology and biomechanical performance. We find that pelagic-feeding damselfishes (planktivores) are strongly differentiated from extensively benthic-feeding species (omnivores and herbivores) by their jaw protrusion ability, upper jaw morphology and the functional integration of upper jaw protrusion with lower jaw abduction. Most aspects of cranial form and function that separate these two ecological groups have evolved in correlation with each other and the evolution of the functional morphology of feeding in damselfishes has involved repeated convergence in form, function and ecology.