Evolution and Developmental Diversity of Skin Spines in Pufferfishes

The Exploitation of Toxic Fish from the Terminal Pleistocene in Maritime Southeast Asia: A Case Study from the Mindoro Archaeological Sites, Philippines

Representatives of the Diodontidae family (porcupinefish) are known to have been fished by prehistoric Indo-Pacific populations; however, the antiquity of the use of this family is thus far unknown. We report here on the presence of Diodontidae in the archaeological sites of Bubog I, II, and Bilat in Mindoro, Philippines, dating back to c. 13,000 BP (Before Present). This evidence demonstrates the early exploitation by islanders of poisonous fish. Every part of porcupinefish can be toxic, but the toxicity is mostly concentrated in some organs, while other parts are edible. The continuous presence of Diodontidae remains throughout the stratigraphic record of these Philippines shell middens suggests that porcupinefish were prepared by human inhabitants of the sites to render them safe for consumption, indicating an advanced cultural knowledge of the preparation needed to separate the toxic principle from the edible parts. This constitutes one of the rare examples of poison processing by humans, aside from the contentious wooden stick poison applicator from Border Cave (South Africa).

Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes

Seadragons are widely recognized for their derived traits, which include leaf-like appendages and extreme spinal curvature. Efforts to understand the genetic basis of these unique traits and conserve these species and their relatives have been limited by genomic resource gaps. In this paper we present full, annotated genomes of leafy and weedy seadragons, which we use to uncover surprising features of gene family and genome architecture evolution that likely relate to the extravagant phenotypic traits of seadragons and their pipefish and seahorse relatives. These genomes and their analyses are important advances for the study of elaborate vertebrate traits, leveraging this diverse, morphologically exceptional group of fishes.

Seadragons are a remarkable lineage of teleost fishes in the family Syngnathidae, renowned for having evolved male pregnancy. Comprising three known species, seadragons are widely recognized and admired for their fantastical body forms and coloration, and their specific habitat requirements have made them flagship representatives for marine conservation and natural history interests. Until recently, a gap has been the lack of significant genomic resources for seadragons. We have produced gene-annotated, chromosome-scale genome models for the leafy and weedy seadragon to advance investigations of evolutionary innovation and elaboration of morphological traits in seadragons as well as their pipefish and seahorse relatives. We identified several interesting features specific to seadragon genomes, including divergent noncoding regions near a developmental gene important for integumentary outgrowth, a high genome-wide density of repetitive DNA, and recent expansions of transposable elements and a vesicular trafficking gene family. Surprisingly, comparative analyses leveraging the seadragon genomes and additional syngnathid and outgroup genomes revealed striking, syngnathid-specific losses in the family of fibroblast growth factors (FGFs), which likely involve reorganization of highly conserved gene regulatory networks in ways that have not previously been documented in natural populations. The resources presented here serve as important tools for future evolutionary studies of developmental processes in syngnathids and hold value for conservation of the extravagant seadragons and their relatives.

The ectodysplasin-A receptor is a candidate gene for lateral plate number variation in stickleback fish

Variation in lateral plating in stickleback fish represents a classical example of rapid and parallel adaptation in morphology. The underlying genetic architecture involves polymorphism at the ectodysplasin-A gene (EDA). However, lateral plate number is influenced by additional loci that remain poorly characterized. Here, we search for such loci by performing genome-wide differentiation mapping based on pooled whole-genome sequence data from a European stickleback population variable in the extent of lateral plating, while tightly controlling for the phenotypic effect of EDA. This suggests a new candidate locus, the EDA receptor gene (EDAR), for which additional support is obtained by individual-level targeted Sanger sequencing and by comparing allele frequencies among natural populations. Overall, our study illustrates the power of pooled whole-genome sequencing for searching phenotypically relevant loci and opens opportunities for exploring the population genetics and ecological significance of a new candidate locus for stickleback armor evolution.

Expression variations in ectodysplasin-A gene (eda) may contribute to morphological divergence of scales in haplochromine cichlids

BACKGROUND

Elasmoid scales are one of the most common dermal appendages and can be found in almost all species of bony fish differing greatly in their shape. Whilst the genetic underpinnings behind elasmoid scale development have been investigated, not much is known about the mechanisms involved in moulding of scales. To investigate the links between gene expression differences and morphological divergence, we inferred shape variation of scales from two different areas of the body (anterior and posterior) stemming from ten haplochromine cichlid species from different origins (Lake Tanganyika, Lake Malawi, Lake Victoria and riverine). Additionally, we investigated transcriptional differences of a set of genes known to be involved in scale development and morphogenesis in fish.

RESULTS

We found that scales from the anterior and posterior part of the body strongly differ in their overall shape, and a separate look on scales from each body part revealed similar trajectories of shape differences considering the lake origin of single investigated species. Above all, nine as well as 11 out of 16 target genes showed expression differences between the lakes for the anterior and posterior dataset, respectively. Whereas in posterior scales four genes (dlx5, eda, rankl and shh) revealed significant correlations between expression and morphological differentiation, in anterior scales only one gene (eda) showed such a correlation. Furthermore, eda displayed the most significant expression difference between species of Lake Tanganyika and species of the other two younger lakes. Finally, we found genetic differences in downstream regions of eda gene (e.g., in the eda-tnfsf13b inter-genic region) that are associated with observed expression differences. This is reminiscent of a genetic difference in the eda-tnfsf13b inter-genic region which leads to gain or loss of armour plates in stickleback.

CONCLUSION

These findings provide evidence for cross-species transcriptional differences of an important morphogenetic factor, eda, which is involved in formation of ectodermal appendages. These expression differences appeared to be associated with morphological differences observed in the scales of haplochromine cichlids indicating potential role of eda mediated signal in divergent scale morphogenesis in fish.

Pacific Spiny Lumpsucker armor - development, damage, and defense in the intertidal

Predation, combat, and the slings and arrows of an abrasive and high impact environment, represent just some of the biotic and abiotic stressors that fishes are armored against. The Pacific Spiny Lumpsucker (Eumicrotremus orbis) found in the subtidal of the Northern Pacific Ocean is a rotund fish covered with epidermal, cone-shaped, enamel odontodes. The Lumpsucker is a poor swimmer in the wave swept rocky intertidal, and this armor may be a lightweight solution to the problem of collisions with abiotic obstacles. We use micro-CT and SEM to reveal the morphology and ontogeny of the armor, and to quantify the amount of mineralization relative to the endoskeleton. The non-overlapping odontodes are organized into eight rows - six rows on the body, one row surrounding the eye, and one row underneath the chin. Odontodes start as a single, hooked cone; and they grow by the addition of cusps that accrete into a spiral. The mineral investment in armor compared to skeleton increases over ontogeny. Damage to the armor occurs both through passive abrasion and breakage from impact; and there is no evidence of replacement, or repair of damaged odontodes.

Evolutionary patterns of scale morphology in damselfishes (Pomacentridae)

Fish scales are bony plates embedded in the skin that vary extensively in shape across taxa. Despite a plethora of hypotheses regarding form–function relationships in scales, we know little about the ecological selective factors that shape their diversity. Here we examine evolutionary patterns of scale morphology using novel three-dimensional topography from the surfaces of 59 species of damselfishes, a prominent radiation of coral reef fishes. We find evidence that scale morphology changes with different flow environments, such that species that spend more time in open-water habitats have smoother scales. We also show that other aspects of ecology lead to highly derived scales. For example, anemonefishes show an evolutionary transition to smaller scales and smaller ctenii (scale spines). Moreover, changes in body shape, which may reflect ecological differentiation, are related to scale shape but not surface properties. We also demonstrate weak evolutionary integration among multiple aspects of scale morphology; however, scale size and shape are related, and scale morphology is correlated between different body regions. Finally, we also identify a relationship between aspects of lateral line pore morphology, such that the number of lateral line pores per scale and the size of those pores are inversely related. Overall, our study provides insights into the multidimensionality of scale evolution and improves our understanding of some of the factors that can give rise to the diversity of scales seen across fishes.

Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution

Seahorses have a circum-global distribution in tropical to temperate coastal waters. Yet, seahorses show many adaptations for a sedentary, cryptic lifestyle: they require specific habitats, such as seagrass, kelp or coral reefs, lack pelvic and caudal fins, and give birth to directly developed offspring without pronounced pelagic larval stage, rendering long-range dispersal by conventional means inefficient. Here we investigate seahorses' worldwide dispersal and biogeographic patterns based on a de novo genome assembly of Hippocampus erectus as well as 358 re-sequenced genomes from 21 species. Seahorses evolved in the late Oligocene and subsequent circum-global colonization routes are identified and linked to changing dynamics in ocean currents and paleo-temporal seaway openings. Furthermore, the genetic basis of the recurring "bony spines" adaptive phenotype is linked to independent substitutions in a key developmental gene. Analyses thus suggest that rafting via ocean currents compensates for poor dispersal and rapid adaptation facilitates colonizing new habitats.

The Genetic Basis of Scale-Loss Phenotype in the Rapid Radiation of Takifugu Fishes

Rapid radiation associated with phenotypic divergence and convergence provides an opportunity to study the genetic mechanisms of evolution. Here we investigate the genus Takifugu that has undergone explosive radiation relatively recently and contains a subset of closely-related species with a scale-loss phenotype. By using observations during development and genetic mapping approaches, we show that the scale-loss phenotype of two Takifugu species, T. pardalis Temminck & Schlegel and T. snyderi Abe, is largely controlled by an overlapping genomic segment (QTL). A search for candidate genes underlying the scale-loss phenotype revealed that the QTL region contains no known genes responsible for the evolution of scale-loss phenotype in other fishes. These results suggest that the genes used for the scale-loss phenotypes in the two Takifugu are likely the same, but the genes used for the similar phenotype in Takifugu and distantly related fishes are not the same. Meanwhile, Fgfrl1, a gene predicted to function in a pathway known to regulate bone/scale development was identified in the QTL region. Since Fgfr1a1, another memebr of the Fgf signaling pathway, has been implicated in scale loss/scale shape in fish distantly related to Takifugu, our results suggest that the convergence of the scale-loss phenotype may be constrained by signaling modules with conserved roles in scale development.