The tree of life and a new classification of bony fishes

Colonization of the ocean floor by jawless vertebrates across three mass extinctions

BACKGROUND

The deep (> 200 m) ocean floor is often considered to be a refugium of biodiversity; many benthic marine animals appear to share ancient common ancestry with nearshore and terrestrial relatives. Whether this pattern holds for vertebrates is obscured by a poor understanding of the evolutionary history of the oldest marine vertebrate clades. Hagfishes are jawless vertebrates that are either the living sister to all vertebrates or form a clade with lampreys, the only other surviving jawless fishes.

RESULTS

We use the hagfish fossil record and molecular data for all recognized genera to construct a novel hypothesis for hagfish relationships and diversification. We find that crown hagfishes persisted through three mass extinctions after appearing in the Permian ~ 275 Ma, making them one of the oldest living vertebrate lineages. In contrast to most other deep marine vertebrates, we consistently infer a deep origin of continental slope occupation by hagfishes that dates to the Paleozoic. Yet, we show that hagfishes have experienced marked body size diversification over the last hundred million years, contrasting with a view of this clade as morphologically stagnant.

CONCLUSION

Our results establish hagfishes as ancient members of demersal continental slope faunas and suggest a prolonged accumulation of deep sea jawless vertebrate biodiversity.

Morphological Diversity and Evolution of Jaw Morphologies in Zeiform Fishes (Teleostei, Paracanthopterygii)

Zeiformes (dories, tinselfishes, and oreos) are primarily benthopelagic acanthomorph fishes, distributed between 50 and 1000 m depth on continental slopes and on flanks of oceanic islands and seamounts. Among the interesting morphological adaptations of zeiform fishes are their unique and highly protrusible jaws involving premaxillae with long ascending processes and a four-bar linkage, including mobile palatines that pivot on their posterior articulation. This adaptation for increased jaw protrusion has enabled zeiform fishes to capture elusive prey more efficiently and is arguably a major factor in their morphological diversity and evolutionary success. This study examines the evolution of zeiform jaw morphologies using 3D landmark-based multivariate morphometrics as well as phylomorphospace analysis. Results show that the descendants of the zeiform ancestor branched rapidly early in their history, retaining conservative jaw morphologies during this early branching, but subsequently strongly diverged in many of the resulting lineages. Results from this study are compared with earlier research based on overall body form, demonstrating that morphological variation within Zeiformes arose along at least two distinct trajectories: body form and jaw morphology. Variation among genera in body form is not associated with variation among the same genera in jaw morphology, and vice versa. Hypotheses to explain the apparent decoupling of body shape and jaw morphology are addressed along with avenues for further study to better understand the morphological evolution of these iconic fishes.

A detailed 3D MRI brain atlas of the African lungfish Protopterus annectens

The study of the brain by magnetic resonance imaging (MRI) in evolutionary analyses is still in its incipient stage, however, it is particularly useful as it allows us to analyze detailed anatomical images and compare brains of rare or otherwise inaccessible species, evolutionarily contextualizing possible differences, while at the same time being non-invasive. A good example is the lungfishes, sarcopterygians that are the closest living relatives of tetrapods and thus have an interesting phylogenetic position in the evolutionary conquest of the terrestrial environment. In the present study, we have developed a three-dimensional representation of the brain of the lungfish Protopterus annectens together with a rostrocaudal anatomical atlas. This methodological approach provides a clear delineation of the major brain subdivisions of this model and allows to measure both brain and ventricular volumes. Our results confirm that lungfish show neuroanatomical patterns reminiscent of those of extant basal sarcopterygians, with an evaginated telencephalon, and distinctive characters like a small optic tectum. These and additional characters uncover lungfish as a remarkable model to understand the origins of tetrapod diversity, indicating that their brain may contain significant clues to the characters of the brain of ancestral tetrapods.

The evolution of NLRC3 subfamily genes in Sebastidae teleost fishes

BACKGROUND

With more than 36,000 valid fish species, teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. NLRC3 subfamily genes, which are specific to fishes, play vital roles in the immune system of teleosts. The evolution of teleosts has been impacted by several whole-genome duplication (WGD) events, which might be a key reason for the expansions of the NLRC3 subfamily, but detailed knowledge of NLRC3 subfamily evolution in the family Sebastidae is still limited.

RESULTS

Phylogenetic inference of NLRC3 subfamily protein sequences were conducted to evaluate the orthology of NLRC3 subfamily genes in black rockfish (Sebastes schlegilii), 13 other fish species from the families Sebastidae, Serranidae, Gasterosteidae and Cyclopteridae, and three species of high vertebrates (bird, reptile and amphibian). WGD analyses were used to estimate expansions and contractions of the NLRC3 subfamily, and patterns of expression of NLRC3 subfamily genes in black rockfish following bacterial infections were used to investigate the functional roles of these genes in the traditional and mucosal immune system of the Sebastidae. Different patterns of gene expansions and contractions were observed in 17 fish and other species examined, and one and two whole-genome duplication events were observed in two members of family Sebastidae (black rockfish and honeycomb rockfish, Sebastes umbrosus), respectively. Subsequently, 179 copy numbers of NLRC3 genes were found in black rockfish and 166 in honeycomb rockfish. Phylogenetic analyses corroborated the conservation and evolution of NLRC3 orthologues between Sebastidae and other fish species. Finally, differential expression analyses provided evidence of the immune roles of NLRC3 genes in black rockfish during bacterial infections and gene ontology analysis also indicated other functional roles.

CONCLUSIONS

We hypothesize that NLRC3 genes have evolved a variety of different functions, in addition to their role in the immune response, as a result of whole genome duplication events during teleost diversification. Importantly, this study had underscored the importance of sampling across taxonomic groups, to better understand the evolutionary patterns of the innate immunity system on which complex immunological novelties arose. Moreover, the results in this study could extend current knowledge of the plasticity of the immune system.

Marine and freshwater fishes of Alabama: a revised checklist and discussion of taxonomic issues

Checklists are fundamental and important tools for organizing information about biodiversity that provide a basis for conservation and additional scientific research. While Alabama is recognized as an aquatic biodiversity hotspot with the highest native freshwater fish diversity in the contiguous United States, we currently lack an up-to-date list of the states fishes. In particular, much has changed over the past ~20 years regarding our knowledge of fishes from Alabama and the Mobile River Basin, rendering past comprehensive treatments by Mettee et al. (1996) and Boschung and Mayden (2004) out of date. Here, we provide a revised checklist of marine and freshwater fishes known from the coastal and inland waters of Alabama that includes 463 species (335 primarily freshwater fishes, and 128 marine or diadromous fishes) in 35 orders, 78 families, and 176 genera. Extant, extirpated, and extinct species are included, as are putative candidate species. The checklist is based on prior work, searches of the literature and online sources, as well as parsing a large compilation of >140,000 fish records for Alabama and the Mobile River Basin from 37 data providers in the global Fishnet2 database (www.fishnet2.net) and >4000 marine survey records from the SEAMAP database (https://www.gsmfc.org/seamap.php). After editing and quality control checks, the final combined database contained 144,215 collection records, ~95% of which were georeferenced. We discuss the species descriptions, nomenclatural changes, and updates to marine species that account for changes to the state list, and we close with a discussion of ~13 candidate species forms that remain undescribed, which represent outstanding taxonomic issues in need of further research attention.

Teleost genomic repeat landscapes in light of diversification rates and ecology

Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we demonstrated that TE proportion correlates with genome size, but not to the proportion of short tandem repeats (STRs), which implies independent evolutionary paths. Marine and freshwater fish had large differences in STR content, with the most extreme propagation detected in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring.

The earliest evidence of deep-sea vertebrates

Vertebrate macroevolution has been punctuated by fundamental habitat transitions from shallow marine origins to terrestrial, freshwater, and aerial environments. Invasion of the deep sea is a less well-known ecological shift because of low fossilization potential and continual loss of abyssal fossil record by ocean floor subduction. Therefore, there has been a lack of convincing evidence of bottom-living vertebrates from pre-Paleogene deep seas. Here, we describe trace fossils from abyssal plain turbidites of the Tethys Ocean, which, combined with nannofossil dating, indicate that fishes have occupied the deep seafloor since at least the Early Cretaceous (Hauterivian-Barremian). These structures are identical to those produced by modern demersal fishes that feed by either scratching the substrate or expose their prey by water flow generated by suction or jetting. The trace fossils suggest activity of at least three fish species exploiting a productive abyssal invertebrate sediment fauna. These observations are consistent with Early Cretaceous vertebrate transition to the deep sea triggered by the availability of new food sources. Our results anticipate the appearance of deep-seafloor fishes in the fossil record by over 80 My while reassessing the mode of vertebrate colonization of the deep sea.

Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish, regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post-embryonic development. Understanding the mechanisms that regulate stripe patterning and scale morphogenesis may lead to the discovery of fundamental mechanisms that govern the development of animal form. To learn about cell types and signaling interactions that govern skin patterning and morphogenesis, we generated and analyzed single-cell transcriptomes of skin from wild-type fish as well as fish having genetic or transgenically induced defects in squamation or pigmentation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins, suggest hormonal control of epithelial-mesenchymal signaling, clarify the signaling network that governs scale papillae development, and identify a critical role for the hypodermis in supporting pigment cell development. Additionally, these comprehensive single-cell transcriptomic data representing skin phenotypes of biomedical relevance should provide a useful resource for accelerating the discovery of mechanisms that govern skin development and homeostasis.

Expanded olfactory system in ray-finned fishes capable of terrestrial exploration

BACKGROUND

Smell abilities differ greatly among vertebrate species due to distinct sensory needs, with exceptional variability reported in the number of olfactory genes and the size of the odour-processing regions of the brain. However, key environmental factors shaping genomic and phenotypic changes linked to the olfactory system remain difficult to identify at macroevolutionary scales. Here, we investigate the association between diverse ecological traits and the number of olfactory chemoreceptors in approximately two hundred ray-finned fishes.

RESULTS

We found independent expansions producing large gene repertoires in several lineages of nocturnal amphibious fishes, generally able to perform active terrestrial exploration. We reinforced this finding with on-purpose genomic and transcriptomic analysis of Channallabes apus, a catfish species from a clade with chemosensory-based aerial orientation. Furthermore, we also detected an augmented information-processing capacity in the olfactory bulb of nocturnal amphibious fishes by estimating the number of cells contained in this brain region in twenty-four actinopterygian species.

CONCLUSIONS

Overall, we report a convergent genomic and phenotypic magnification of the olfactory system in nocturnal amphibious fishes. This finding suggests the possibility of an analogous evolutionary event in fish-like tetrapod ancestors during the first steps of the water-to-land transition, favouring terrestrial adaptation through enhanced aerial orientation.

Phylogenetic and Evolutionary Comparison of Mitogenomes Reveal Adaptive Radiation of Lampriform Fishes

Lampriform fishes (Lampriformes), which primarily inhabit deep-sea environments, are large marine fishes varying from the whole-body endothermic opah to the world's longest bony fish-giant oarfish, with species morphologies varying from long and thin to deep and compressed, making them an ideal model for studying the adaptive radiation of teleost fishes. Moreover, this group is important from a phylogenetic perspective owing to their ancient origins among teleosts. However, knowledge about the group is limited, which is, at least partially, due to the dearth of recorded molecular data. This study is the first to analyze the mitochondrial genomes of three lampriform species (Lampris incognitus, Trachipterus ishikawae, and Regalecus russelii) and infer a time-calibrated phylogeny, including 68 species among 29 orders. Our phylomitogenomic analyses support the classification of Lampriformes as monophyletic and sister to Acanthopterygii; hence, addressing the longstanding controversy regarding the phylogenetic status of Lampriformes among teleosts. Comparative mitogenomic analyses indicate that tRNA losses existed in at least five Lampriformes species, which may reveal the mitogenomic structure variation associated with adaptive radiation. However, codon usage in Lampriformes did not change significantly, and it is hypothesized that the nucleus transported the corresponding tRNA, which led to function substitutions. The positive selection analysis revealed that atp8 and cox3 were positively selected in opah, which might have co-evolved with the endothermic trait. This study provides important insights into the systematic taxonomy and adaptive evolution studies of Lampriformes species.

Measuring the shape of mortality across animals and plants: Alternatives to H entropy metrics reveal hidden type IV survivorship curves and associations with parental care at macro-ecological scales

The shape of mortality, or how mortality is spread across an organism's life course, is fundamental to a range of biological processes, with attempts to quantify it rooted in ecology, evolution, and demography. One approach to quantify the distribution of mortality over an organism's life is the use of entropy metrics whose values are interpreted within the classical framework of survivorship curves ranging from type I distributions, with mortality concentrated in late life stages, to type III survivorship curves associated with high early stage mortality. However, entropy metrics were originally developed using restricted taxonomic groups and the behavior of entropy metrics over larger scales of variation may make them unsuitable for wider-ranging contemporary comparative studies. Here, we revisit the classic survivorship framework and, using a combination of simulations and comparative analysis of demography data spanning the animal and plant kingdoms, we show that commonly used entropy metrics cannot distinguish between the most extreme survivorship curves, which in turn can mask important macroecological patterns. We show how using H entropy masks a macroecological pattern of how parental care is associated with type I and type II species and for macroecological studies recommend the use of metrics, such as measures of area under the curve. Using frameworks and metrics that capture the full range of variation of survivorship curves will aid in our understanding of the links between the shape of mortality, population dynamics, and life history traits.

Expression of SATB1 and SATB2 in the brain of bony fishes: what fish reveal about evolution

Satb1 and Satb2 belong to a family of homeodomain proteins with highly conserved functional and regulatory mechanisms and posttranslational modifications in evolution. However, although their distribution in the mouse brain has been analyzed, few data exist in other non-mammalian vertebrates. In the present study, we have analyzed in detail the sequence of SATB1 and SATB2 proteins and the immunolocalization of both, in combination with additional neuronal markers of highly conserved populations, in the brain of adult specimens of different bony fish models at key evolutionary points of vertebrate diversification, in particular including representative species of sarcopterygian and actinopterygian fishes. We observed a striking absence of both proteins in the pallial region of actinopterygians, only detected in lungfish, the only sarcopterygian fish. In the subpallium, including the amygdaloid complex, or comparable structures, we identified that the detected expressions of SATB1 and SATB2 have similar topologies in the studied models. In the caudal telencephalon, all models showed significant expression of SATB1 and SATB2 in the preoptic area, including the acroterminal domain of this region, where the cells were also dopaminergic. In the alar hypothalamus, all models showed SATB2 but not SATB1 in the subparaventricular area, whereas in the basal hypothalamus the cladistian species and the lungfish presented a SATB1 immunoreactive population in the tuberal hypothalamus, also labeled with SATB2 in the latter and colocalizing with the gen Orthopedia. In the diencephalon, all models, except the teleost fish, showed SATB1 in the prethalamus, thalamus and pretectum, whereas only lungfish showed also SATB2 in prethalamus and thalamus. At the midbrain level of actinopterygian fish, the optic tectum, the torus semicircularis and the tegmentum harbored populations of SATB1 cells, whereas lungfish housed SATB2 only in the torus and tegmentum. Similarly, the SATB1 expression in the rhombencephalic central gray and reticular formation was a common feature. The presence of SATB1 in the solitary tract nucleus is a peculiar feature only observed in non-teleost actinopterygian fishes. At these levels, none of the detected populations were catecholaminergic or serotonergic. In conclusion, the protein sequence analysis revealed a high degree of conservation of both proteins, especially in the functional domains, whereas the neuroanatomical pattern of SATB1 and SATB2 revealed significant differences between sarcopterygians and actinopterygians, and these divergences may be related to the different functional involvement of both in the acquisition of various neural phenotypes.

Species delimitation, molecular phylogeny and historical biogeography of the sweetlips fish (Perciformes, Haemulidae)

The subfamily Plectorhinchinae (sweetlips) is composed of poorly-known species with high commercially and ecologically values that exhibit phenotypic plasticity and various morphologies. Few studies have assessed the validity of sweetlips, intergeneric relationships and evolutionary survey in this subfamily, which have not yet been resolved. This study investigated the DNA sequences of (1) the mitochondrial COI gene to delimit species, and (2) two mitochondrial (COI and Cyt b), and one nuclear (RAG1) markers to infer phylogenetic relationships and evolutionary and biogeographic history. The molecular results could differentiate Diagramma punctatum from the other species, but failed to distinguish D. labiosum as a distinct species with considerably lower genetic distances for the COI (0.53%) and Cyt b (0.51%) markers. However, additional taxonomic investigations are required to shed light on this issue. All previously described nominal species of sweetlips in the northwest Indian Ocean were found to be well supported. The monophyly of Plectorhinchus is not supported and Diagramma pictum and D. punctatum should be assigned to the genus Plectorhinchus. The biogeographic history of Plectorhinchinae likely originated in the Indo-Pacific ca. 34 Ma (30–39 Ma; late Eocene/ middle Oligocene) and subsequently colonised the Western Indian Ocean and the Central Indo-Pacific. Maximum diversification within the subfamily occurred from the middle Miocene to Pliocene, coinciding with dispersal and vicariance events. Diversification was probably driven by both biological and geographical factors.

Skeletal ontogeny of the Plainfin Midshipman, Porichthys notatus (Percomorphacea: Batrachoidiformes)

Batrachoidiformes are benthic fishes that utilize the undersides of rocks as spawning nests. Their larvae are attached to the nest and nourished by a large yolk sac. The evolutionary shift from feeding, free-swimming larvae to sedentary larvae that are reliant on their yolk sac for nutrition can lead to changes in skeletal development. Batrachoidiformes also have many morphological specializations, such as five pectoral-fin radials (versus four in other acanthomorphs) that are of uncertain homology, the determination of which may have phylogenetic implications. A larval series of Porichthys notatus was collected and its skeletal ontogeny is described. In P. notatus the ossification of the pharyngeal toothplates occurs relatively later than in percomorphs with free-swimming larvae. The posterior basibranchial copula cartilage (= fourth basibranchial) in Porichthys notatus has a unique development among fishes: it initially develops as a paired element at 6.8-7.1 mm NL before fusing posteriorly and forming single median cartilage at 7.4 mm SL. Cartilages of hypobranchial four are transitory, being observed in two specimens of 6.8 and 7.3 mm NL before fusing with ceratobranchial four. The previously identified dorsalmost pectoral radial is a bone formed by a hypertrophied propterygium that ossifies later in development. The earliest stages of P. notatus have three dorsal spines, but during late larval development, the growth of the third dorsal spine is interrupted. The development of P. notatus is compared and discussed in context to that of other acanthomorph.

Platyfish bypass the constraint of the caudal fin ventral identity in teleosts

BACKGROUND

The caudal fin of teleosts is characterized by dorsoventral symmetry. Despite this external morphology, the principal rays of this appendage connect to bones below the notochord, indicating the ventral (hypochordal) identity of this organ.

RESULTS

Here, we report that this typical architecture of the caudal fin is not fully conserved in the platyfish (Xiphophorus maculatus) and the guppy (Poecilia reticulata), representatives of the Poeciliidae family. We show that in these species, 3-4 principal rays connect to bones above the notochord, suggesting an epichordal contribution. Consistently, as examined in platyfish, dorsal identity genes zic1/4 were highly expressed in these rays, providing molecular evidence of their epichordal origin. Developmental analysis revealed that the earliest rays above the notochord emerge at the 10-ray stage of fin morphogenesis. In contrast to zebrafish and medaka, platyfish and guppies display a mirrored shape of dorsal and ventral processes of the caudal endoskeleton. Our study suggests that an ancestral bauplan expanded in poeciliids by advancing its symmetrical pattern.

CONCLUSION

The platyfish evolved a fin architecture with the epichordal origin of its upper principal rays and a high level of symmetry in the caudal endoskeleton. This innovative architecture highlights the adaptation of the teleost skeleton.

Phylogenomics and classification of Notropis and related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups

North American minnows of the Shiner Clade, within the family Leuciscidae, represent one of the most taxonomically complex clades of the order Cypriniformes due to the large number of taxa coupled with conserved morphologies. Species within this clade were moved between genera and subgenera until the community decided to lump many of the unclassified taxa with similar morphologies into one genus, Notropis, which has held up to 325 species. Despite phylogentic studies that began to re-elevate some genera merged into Notropis, such as Cyprinella, Luxilus, Lythrurus, and Pteronotropis, the large genus Notropis remained as a taxonomic repository for many shiners of uncertain placement. Recent molecular advances in sequencing technologies have provided the opportunity to re-examine the Shiner Clade using phylogenomic markers. Using a fish probe kit, we sequenced 90 specimens in 87 species representing 16 genera included in the Shiner Clade, with a resulting dataset of 1,004 loci and 286,455 base pairs. Despite the large dataset, only 32,349 bp (11.29%) were phylogenetically informative. In our maximum likelihood tree, 78% of nodes are 100% bootstrap supported demonstrating the utility of the phylogenomic markers at lower taxonomic levels. Unsurprisingly, species within Notropis as well as Hudsonius, Luxilus, and Alburnops are not resolved as monophyletic groups. Cyprinella is monophyletic if Cyprinella callistia is excluded, and Pteronotropis is monophyletic if it includes Hudsonius cummingsae. Taxonomic changes we propose are: restriction of species included in Alburnops and Notropis, elevation of the subgenus Hydrophlox, expansion of species included in Miniellus, movement of Hudsonius cummingsae to Pteronotropis, and resurrection of the genera Coccotis and Paranotropis. We additionally had two specimens of three species, Notropis atherinoides, Ericymba amplamala, and Pimephales vigilax and found signficant differences between the localities (1,086, 1,424, and 845 nucleotides respectively).

Extraoral expression and characterization of bitter taste receptors in Astyanax mexicanus (Mexican tetra fish)

The chemical senses of olfaction and taste are well developed in fish and play a vital role in its various activities such as navigation, mate recognition, and food detection. The small teleost fish Astyanax mexicanus consists of interfertile river-dwelling and cave-dwelling populations, referred to as "surface fish" and "cavefish" respectively. An important anatomical feature of cavefish is the lack of eyes leading them to be referred to as blind fish and suggesting an enhanced functional role for other senses such as taste. In this study, we characterize the expression of bitter taste receptors (T2Rs or Tas2Rs) in A. mexicanus and investigate their functionality in a heterologous expression system. The genome database of A. mexicanus (ensemble and NCBI) showed 7 Tas2Rs, among these Tas2R1, Tas2R3, Tas2R4, and Tas2R114 are well characterized in humans and mice but not in A. mexicanus. Therefore, the 4 Tas2Rs were selected for further analysis and their expression in A. mexicanus was confirmed by in situ hybridization and RT-PCR in early developmental stages. These Tas2Rs are expressed in various oral and extraoral organs (liver, fins, jaws, and gills) in A. mexicanus, and Tas2R1 has maximum expression and is localized throughout the fish body. Using the heterologous expression of A. mexicanus T2Rs in HEK293T cells coupled with cell-based calcium mobilization assays, we show that A. mexicanus T2Rs are activated by commonly used fish food and known bitter agonists, including quinine. This study provides novel insights into the extraoral expression of T2Rs in A. mexicanus and suggests their importance in extraoral food detection.

Evolutionary analysis of swimming speed in early vertebrates challenges the 'New Head Hypothesis'

The ecological context of early vertebrate evolution is envisaged as a long-term trend towards increasingly active food acquisition and enhanced locomotory capabilities culminating in the emergence of jawed vertebrates. However, support for this hypothesis has been anecdotal and drawn almost exclusively from the ecology of living taxa, despite knowledge of extinct phylogenetic intermediates that can inform our understanding of this formative episode. Here we analyse the evolution of swimming speed in early vertebrates based on caudal fin morphology using ancestral state reconstruction and evolutionary model fitting. We predict the lowest and highest ancestral swimming speeds in jawed vertebrates and microsquamous jawless vertebrates, respectively, and find complex patterns of swimming speed evolution with no support for a trend towards more active lifestyles in the lineage leading to jawed groups. Our results challenge the hypothesis of an escalation of Palaeozoic marine ecosystems and shed light into the factors that determined the disparate palaeobiogeographic patterns of microsquamous versus macrosquamous armoured Palaeozoic jawless vertebrates. Ultimately, our results offer a new enriched perspective on the ecological context that underpinned the assembly of vertebrate and gnathostome body plans, supporting a more complex scenario characterized by diverse evolutionary locomotory capabilities reflecting their equally diverse ecologies.

Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous

Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and account for more than a quarter of all living vertebrate species. Previous time-calibrated phylogenies and patterns from the fossil record explain this dominance by correlating the origin of major acanthomorph lineages with the Cretaceous-Palaeogene mass extinction. Here we infer a time-calibrated phylogeny using ultraconserved elements that samples 91.4% of all acanthomorph families and investigate patterns of body shape disparity. Our results show that acanthomorph lineages steadily accumulated throughout the Cenozoic and underwent a significant expansion of among-clade morphological disparity several million years after the end-Cretaceous. These acanthomorph lineages radiated into and diversified within distinct regions of morphospace that characterize iconic lineages, including fast-swimming open-ocean predators, laterally compressed reef fishes, bottom-dwelling flatfishes, seahorses and pufferfishes. The evolutionary success of spiny-rayed fishes is the culmination of multiple species-rich and phenotypically disparate lineages independently diversifying across the globe under a wide range of ecological conditions.

Absence of some cytochrome P450 (CYP) and hydroxysteroid dehydrogenase (HSD) enzymes in hagfishes

Corticosteroids are synthesized from cholesterol by steroidogenic enzyme catalysts belonging to two main families: the cytochrome p450s (CYPs) and hydroxysteroid dehydrogenases (HSDs). The action of these steroidogenic enzymes allows the genesis of the terminal active corticosteroids 11-deoxycortisol (S), 1ɑ-hydroxycorticosterone (1α-OH-B), or cortisol in different fish species. However, for Cyclostomes like hagfishes, the terminal corticosteroid is still undefined. In this study, we examined the presence or absence of CYPs and HSDs as traits in fishes to gain insight about the primary corticosteroid synthesis pathways of the hagfishes. We used published cytochrome c oxidase I (COXI) amino acid sequences to construct a phylogeny of fishes and then mapped the CYPs and HSDs as morphological traits onto the tree to predict the ancestral character states through ancestral character reconstruction (ACR). There is a clear phylogenetic signal for CYP (i.e., CYP11a1, 17, 21, and 11b) and HSD (i.e., 11-βHSD and 3β-HSD) derivatives of interest throughout the more derived fishes. Using trait-based ACR, we also found that hagfishes possess genes for 3β-HSD, CYP11a1, CYP17, and CYP21. Importantly, the presence of CYP21 implies that hagfish can synthesize 11-deoxycorticosterone (11-DOC) and S. Previous research demonstrated that despite hagfish having CYP21, neither 11-DOC nor S could be detected in hagfish. This discrepancy between the presence of steroidogenic enzymes and products brings into question the expression and/or function of CYP21 in hagfishes.

Imaging Intron Evolution

Intron evolution may be readily imaged through the combined use of the “dot plot” function of the NCBI BLAST, aligning two sequences at a time, and the Vertebrate “Multiz” alignment and conservation tool of the UCSC Genome Browser. With the NCBI BLAST, an ideal alignment of two highly conserved sequences generates a diagonal straight line in the plot from the lower left corner to the upper right corner. Gaps in this line correspond to non-conserved sections. In addition, the dot plot of the alignment of a sequence with the same sequence after the removal of the Transposable Elements (TEs) can be observed along the diagonal gaps that correspond to the sites of TE insertion. The UCSC Genome Browser can graph, along the entire sequence of a single gene, the level of overall conservation in vertebrates. This level can be compared with the conservation level of the gene in one or more selected vertebrate species. As an example, we show the graphic analysis of the intron conservation in two genes: the mitochondrial solute carrier 21 (SLC25A21) and the growth hormone receptor (GHR), whose coding sequences are conserved through vertebrates, while their introns show dramatic changes in nucleotide composition and even length. In the SLC25A21, a few short but significant nucleotide sequences are conserved in zebrafish, Xenopus and humans, and the rate of conservation steadily increases from chicken/human to mouse/human alignments. In the GHR, a less conserved gene, the earlier indication of intron conservation is a small signal in chicken/human alignment. The UCSC tool may simultaneously display the conservation level of a gene in different vertebrates, with reference to the level of overall conservation in Vertebrates. It is shown that, at least in SLC25A21, the sites of higher conservation are not always coincident in chicken and zebrafish nor are the sites of higher vertebrate conservation.

Investigating the utility of Anchored Hybrid Enrichment data to investigate the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes

The Killifishes (Cyprinodontiformes) are a diverse and well-known group of fishes that contains sixteen families inclusive of Anablepidae, Aphaniidae Aplocheilidae, Cubanichthyidae, Cyprinodontidae, Fluviphylacidae, Fundulidae, Goodeidae, Nothobranchiidae, Orestiidae, Pantanodontidae, Poeciliidae, Procatopodidae, Profundulidae, Rivulidae, and Valenciidae and more than 1,200 species that are globally distributed in tropical and temperate, freshwater and estuarine habitats. The evolutionary relationships among the families within the group, based on different molecular and morphological data sets, have remained uncertain. Therefore, the objective of this study was to use a targeted approach, anchored hybrid enrichment, to investigate the phylogenetic relationships among the families within the Cyprindontiformes. This study included more than 100 individuals, representing all sixteen families within the Cyprinodontiformes, including many recently diagnosed families. We recovered an average of 244 loci per individual. These data were submitted to phylogenetic analyses (RaxML and ASTRAL) and although we recovered many of the same relationships as in previous studies of the group, several novel sets of relationships for other families also were recovered. In addition, two well-established clades (Suborders Cyprinodontoidei and Aplocheilodei) were recovered as monophyletic and are in agreement with most previous studies. We also assessed the degree of gene tree discordance in our dataset to evaluate support for alternative topological hypotheses for interfamilial relationships within the Cyprinodontiformes using a variety of different analyses. The results from this study will provide a robust, historical framework needed to investigate a plethora of biogeographic, taxonomic, ecological, and physiological questions for this group of fishes.

FISHES (Actinopteri, Characiformes) FROM THE TAPYTA RESERVE WITH THREE NEW ADDITIONS TO THE PARAGUAYAN ICHTHYOFAUNA

The Characiform fish species from the Tapyta Reserve and surrounding area, Caazapa, Paraguay, were inventoried during a year with electrofishing, netting, and trapping. A total of 20 species were registered, being Characidae the richest family. We also report three species as new records to the Paraguayan ichthyofauna and discuss the update of the inventory of fishes from Paraguay.

The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics

Ophisternoninfernale is one of the 200+ troglobitic fish species worldwide, and one of the two cave-dwelling fishes endemic to the karstic aquifer of the Yucatán Peninsula, Mexico. Because of its elusive nature and the relative inaccessibility of its habitat, there is virtually no genetic information on this enigmatic fish. Herein we report the complete mitochondrial genome of O.infernale, which overall exhibits a configuration comparable to that of other synbranchiforms as well as of more distantly related teleosts. The K_A/K_S ratio indicates that most mtDNA PCGs in synbranchiforms have evolved under strong purifying selection, preventing major structural and functional protein changes. The few instances of PCGs under positive selection might be related to adaptation to decreased oxygen availability. Phylogenetic analysis of mtDNA comparative data from synbranchiforms and closely related taxa (including the indostomid Indostomusparadoxus) corroborate the notion that indostomids are more closely related to synbranchiforms than to gasterosteoids, but without rendering the former paraphyletic. Our phylogenetic results also suggest that New World species of Ophisternon might be more closely related to Synbranchus than to the remaining Ophisternon species. This novel phylogenetic hypothesis, however, should be further tested in the context of a comprehensive systematic study of the group.

Diversification Rate is Associated with Rate of Molecular Evolution in Ray-Finned Fish (Actinopterygii)

Understanding the factors that drive diversification of taxa across the tree of life is a key focus of macroevolutionary research. While the effects of life history, ecology, climate and geography on diversity have been studied for many taxa, the relationship between molecular evolution and diversification has received less attention. However, correlations between rates of molecular evolution and diversification rate have been detected in a range of taxa, including reptiles, plants and birds. A correlation between rates of molecular evolution and diversification rate is a prediction of several evolutionary theories, including the evolutionary speed hypothesis which links variation in mutation rates to differences in speciation rates. If it is widespread, such correlations could also have significant practical impacts, if they are not adequately accounted for in phylogenetic inference of evolutionary rates and timescales. Ray-finned fish (Actinopterygii) offer a prime target to test for this relationship due to their extreme variation in clade size suggesting a wide range of diversification rates. We employ both a sister-pairs approach and a whole-tree approach to test for correlations between substitution rate and net diversification. We also collect life history and ecological trait data and account for potential confounding factors including body size, latitude, max depth and reef association. We find evidence to support a relationship between diversification and synonymous rates of nuclear evolution across two published backbone phylogenies, as well as weak evidence for a relationship between mitochondrial nonsynonymous rates and diversification at the genus level.

A high-quality chromosome-level genome of the endangered roughskin sculpin provides insights into its evolution and adaptation

The cottids (Cottidae) are a taxonomically diverse and ecologically important component of many marine and freshwater ecosystems. Despite recent breakthroughs in long-read sequencing, high quality genomic resources are still limited for studies of ecological and evolutionary processes in cottids. Here we generated a high-quality, chromosome-scale genome assembly (521.26 Mb) of the catadromous roughskin sculpin (Trachidermus fasciatus Heckel) with a contig N50 of 2.93 Mb and a scaffold N50 of 24.06 Mb. Approximately 21.97% of the genome was composed of repetitive elements. A total of 21,872 protein-coding genes were predicted, of which 19,900 genes (90.98%) were functionally annotated. Phylogenetic analysis supported the validity of Scorpaenoidei and Cottioidei as two suborders of the Perciformes. Chromosome-scale collinearity analyses identified four chromosome fusions leading to the reduction of chromosome number in T. fasciatus. Gene families related to cell apoptosis and cell death were expanded and those related to immune system were contracted, suggesting that these gene families might be relevant to a host of phenotypic differences between T. fasciatus and other teleosts. Gene families associated with osmoregulation were also expanded, which might be associated with its catadromous life history. A total of 50 aging-associated genes were found to be under positive selection, which might be associated with the short lifespan of T. fasciatus. The high-quality genome assembly and annotation will promote researches into the evolution of catadromous life history and short lifespan for T. fasciatus and facilitate comparative genomic studies of cottids in the near future.

Morphological characters in light of new molecular phylogenies: the caudal-fin skeleton of Ovalentaria

The Ovalentaria is a taxon of teleosts that has been proposed based on molecular analyses only. Previously widely separated families are assembled in this taxon. For the first time, the Ovalentaria are analysed using a comparative morphological approach. The caudal-fin skeleton of 355 species covering all 48 ovalentarian families are examined in cleared and stained specimens, µCT datasets and X-ray images as well as from the literature. A total of 38 morphological characters are evaluated and used for ancestral character state reconstructions and phylogenetic analyses. Results provide hypotheses for a scenario of the evolution of the caudal-fin skeleton and its ground plan in Ovalentaria. An evolutionary trend towards the reduction of skeletal elements in the caudal fin is observed. Connections between the evolution of the caudal-fin skeleton and modes of locomotion found in ovalentarian taxa are discussed. Phylogenetic analyses based on the caudal-fin morphology provide topologies for intra-ovalentarian relationships that largely agree with molecular hypotheses.

The accessory neural arch: development, morphology, and systematic distribution

The accessory neural arch is an oddly distributed character present in several non-acanthomorph teleostean taxa. Its homology was often implied but never satisfyingly tested. In this study, we attended this pending problem. We analyzed the morphology, development, and systematic distribution of the accessory neural arch in teleosts. Using a comprehensive taxon sampling of cleared and stained specimens, we evaluated if the accessory neural arch fulfils existing homology criteria. We then combined these data with recent genetic phylogenies and ancestral character state estimation to reconstruct the evolutionary history of the accessory neural arch. While its gross morphology and development fit homology criteria, results from ancestral character state estimations suggest multiple independent evolutions within teleosts. Although the accessory neural arch cannot be homologous between several teleostean taxa, the concept of parallelism may explain the presence of such a similar character in a variety of non-acanthomorph teleostean taxa.

Evolution of the DAN gene family in vertebrates

The DAN gene family (DAN, Differential screening-selected gene Aberrant in Neuroblastoma) is a group of genes that is expressed during development and plays fundamental roles in limb bud formation and digitation, kidney formation and morphogenesis and left-right axis specification. During adulthood the expression of these genes are associated with diseases, including cancer. Although most of the attention to this group of genes has been dedicated to understanding its role in physiology and development, its evolutionary history remains poorly understood. Thus, the goal of this study is to investigate the evolutionary history of the DAN gene family in vertebrates, with the objective of complementing the already abundant physiological information with an evolutionary context. Our results recovered the monophyly of all DAN gene family members and divide them into five main groups. In addition to the well-known DAN genes, our phylogenetic results revealed the presence of two new DAN gene lineages; one is only retained in cephalochordates, whereas the other one (GREM3) was only identified in cartilaginous fish, holostean fish, and coelacanth. According to the phyletic distribution of the genes, the ancestor of gnathostomes possessed a repertoire of eight DAN genes, and during the radiation of the group GREM1, GREM2, SOST, SOSTDC1, and NBL1 were retained in all major groups, whereas, GREM3, CER1, and DAND5 were differentially lost.

A highly contiguous nuclear genome assembly of the mandarinfish Synchiropus splendidus (Syngnathiformes: Callionymidae)

The fish order Syngnathiformes has been referred to as a collection of misfit fishes, comprising commercially important fish such as red mullets as well as the highly diverse seahorses, pipefishes, and seadragons-the well-known family Syngnathidae, with their unique adaptations including male pregnancy. Another ornate member of this order is the species mandarinfish. No less than two types of chromatophores have been discovered in the spectacularly colored mandarinfish: the cyanophore (producing blue color) and the dichromatic cyano-erythrophore (producing blue and red). The phylogenetic position of mandarinfish in Syngnathiformes, and their promise of additional genetic discoveries beyond the chromatophores, made mandarinfish an appealing target for whole-genome sequencing. We used linked sequences to create synthetic long reads, producing a highly contiguous genome assembly for the mandarinfish. The genome assembly comprises 483 Mbp (longest scaffold 29 Mbp), has an N50 of 12 Mbp, and an L50 of 14 scaffolds. The assembly completeness is also high, with 92.6% complete, 4.4% fragmented, and 2.9% missing out of 4584 BUSCO genes found in ray-finned fishes. Outside the family Syngnathidae, the mandarinfish represents one of the most contiguous syngnathiform genome assemblies to date. The mandarinfish genomic resource will likely serve as a high-quality outgroup to syngnathid fish, and furthermore for research on the genomic underpinnings of the evolution of novel pigmentation.

Exon-capture data and locus screening provide new insights into the phylogeny of flatfishes (Pleuronectoidei)

There is an extensive collection of literature on the taxonomy and phylogenetics of flatfishes (Pleuronectiformes) that extends over two centuries, but consensus on many of their evolutionary relationships remains elusive. Phylogenetic uncertainty stems from highly divergent results derived from morphological and genetic characters, and between various molecular datasets. Deciphering relationships is complicated by rapid diversification early in the Pleuronectiformes tree and an abundance of studies that incompletely and inconsistently sample taxa and genetic markers. We present phylogenies based on a genome-wide dataset (4,434 nuclear markers via exon-capture) and wide taxon sampling (86 species spanning 12 of 16 families) of the largest flatfish suborder (Pleuronectoidei). Nine different subsets of the data and two tree construction approaches (eighteen phylogenies in total) are remarkably consistent with other recent molecular phylogenies, and show strong support for the monophyly of all families included except Pleuronectidae. Analyses resolved a novel phylogenetic hypothesis for the family Rhombosoleidae as being within the Pleuronectoidea rather than the Soleoidea, and failed to support the subfamily Hippoglossinae as a monophyletic group. Our results were corroborated with evidence from previous phylogenetic studies to outline regions of persistent phylogenetic uncertainty and identify groups in need of further phylogenetic inference.

A brief review of vertebrate sex evolution with a pledge for integrative research: towards 'sexomics'

Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue a sexomics integrative research initiative across vertebrates. The vertebrate sexome comprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. The sexome also includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of the sexomes of many key vertebrate species. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.

Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences

Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher order relationships. Such analyses are rightfully regarded as the 'gold standard' for phylogenetics. However, DNA retrieval requires modern or well-preserved tissue and is less likely to be preserved in archaeological or fossil specimens. By contrast, some proteins, such as collagen, are phylogenetically informative and can survive into deep time. Here, we test the utility of collagen type I amino acid sequences for phylogenetic estimation of ray-finned fishes. We estimate topology using Bayesian approaches and compare the congruence of our estimated trees with published genomic phylogenies. Furthermore, we apply a Bayesian molecular clock approach and compare estimated divergence dates with previously published genomic clock analyses. Our collagen-derived trees exhibit 77% of node positions as congruent with recent genomic-derived trees, with the majority of discrepancies occurring in higher order node positions, almost exclusively within the Percomorpha. Our molecular clock trees present divergence times that are fairly comparable with genomic-based phylogenetic analyses. We estimate the mean node age of Actinopteri at ∼293 million years (Ma), the base of Teleostei at ∼211 Ma and the radiation of percomorphs beginning at ∼141 Ma (∼350 Ma, ∼250-283 Ma and ∼120-133 Ma in genomic trees, respectively). Finally, we show that the average rate of collagen (I) sequence evolution is 0.9 amino acid substitutions for every million years of divergence, with the α3 (I) sequence evolving the fastest, followed by the α2 (I) chain. This is the quickest rate known for any vertebrate group. We demonstrate that phylogenetic analyses using collagen type I amino acid sequences generate tangible signals for actinopterygians that are highly congruent with recent genomic-level studies. However, there is limited congruence within percomorphs, perhaps due to clade-specific functional constraints acting upon collagen sequences. Our results provide important insights for future phylogenetic analyses incorporating extinct actinopterygian species via collagen (I) sequencing.

Behavioural red-light sensitivity in fish according to the optomotor response

Various procedures have been adopted to investigate spectral sensitivity of animals, e.g. absorption spectra of visual pigments, electroretinography, optokinetic response, optomotor response (OMR) and phototaxis. The use of these techniques has led to various conclusions about animal vision. However, visual sensitivity should be evaluated consistently for a reliable comparison. In this study, we retrieved behavioural data of several fish species using a single OMR procedure and compared their sensitivities to near-infrared light. Besides cavefish that lack eyes, some species were not appropriate for the OMR test because they either stayed still or changed swimming direction frequently. Eight of 13 fish species tested were OMR positive. Detailed analyses using medaka, goldfish, zebrafish, guppy, stickleback and cichlid revealed that all the fish were sensitive to light at a wavelength greater than or equal to 750 nm, where the threshold wavelengths varied from 750 to 880 nm. Fish opsin repertoire affected the perception of red light. By contrast, the copy number of long-wavelength-sensitive (LWS) genes did not necessarily improve red-light sensitivity. While the duplication of LWS and other cone opsin genes that has occurred extensively during fish evolution might not aid increasing spectral sensitivity, it may provide some other advantageous ophthalmic function, such as enhanced spectral discrimination.

High chromosomal evolutionary dynamics in sleeper gobies (Eleotridae) and notes on disruptive biological factors in Gobiiformes karyotypes (Osteichthyes, Teleostei)

The order Gobiiformes is made up of more than 2200 species, representing one of the most diverse groups among teleost fishes. The biological causes for the tachytelic karyotype evolution of the gobies have not yet been fully studied. Here we expanded cytogenetic data for the Eleotridae family, analyzing the neotropical species Dormitator maculatus, Eleotris pisonis, Erotelis smaragdus, and Guavina guavina. In addition, a meta-analytical approach was followed for elucidating the karyotype diversification versus biological aspects (habitat and egg type) of the Gobiiformes. The species E. smaragdus and E. pisonis present 2n = 46 acrocentric chromosomes (NF = 46), D. maculatus 2n = 46 (36sm + 4st + 6a; NF = 86), and G. guavina, the most divergent karyotype, with 2n = 52 acrocentric chromosomes (NF = 52). Besides numeric and structural diversification in the karyotypes, the mapping of rDNAs and microsatellites also showed noticeable numerical and positional variation, supporting the high chromosomal evolutionary dynamism of these species. In Gobiiformes, karyotype patterns which are more divergent from the basal karyotype (2n = 46a) are associated with characteristics less effective to dispersion, such as the benthic habit. These adaptive characteristics, connected with the organization of the repetitive DNA content in the chromosomes, likely play a synergistic role in the remarkable karyotype diversification of this group.

Evolutionary Modifications Are Moderate in the Astroglial System of Actinopterygii as Revealed by GFAP Immunohistochemistry

The present paper is the first comparative study on the astroglia of several actinopterygian species at different phylogenetical positions, teleosts (16 species), and non-teleosts (3 species), based on the immunohistochemical staining of GFAP (glial fibrillary acidic protein), the characteristic cytoskeletal intermediary filament protein, and immunohistochemical marker of astroglia. The question was, how the astroglial architecture reflexes the high diversity of this largest vertebrate group. The actinopterygian telencephalon has a so-called ‘eversive’ development in contrast to the ‘evagination’ found in sarcopterygii (including tetrapods). Several brain parts either have no equivalents in tetrapod vertebrates (e.g., torus longitudinalis, lobus inferior, lobus nervi vagi), or have rather different shapes (e.g., the cerebellum). GFAP was visualized applying DAKO polyclonal anti-GFAP serum. The study was focused mainly on the telencephalon (eversion), tectum (visual orientation), and cerebellum (motor coordination) where the evolutionary changes were most expected, but the other areas were also investigated. The predominant astroglial elements were tanycytes (long, thin, fiber-like cells). In the teleost telencephala a ‘fan-shape’ re-arrangement of radial glia reflects the eversion. In bichir, starlet, and gar, in which the eversion is less pronounced, the ‘fan-shape’ re-arrangement did not form. In the tectum the radial glial processes were immunostained, but in Ostariophysi and Euteleostei it did not extend into their deep segments. In the cerebellum Bergmann-like glia was found in each group, including non-teleosts, except for Cyprinidae. The vagal lobe was uniquely enlarged and layered in Cyprininae, and had a corresponding layered astroglial system, which left almost free of GFAP the zones of sensory and motor neurons. In conclusion, despite the diversity and evolutionary alterations of Actinopterygii brains, the diversity of the astroglial architecture is moderate. In contrast to Chondrichthyes and Amniotes; in Actinopterygii true astrocytes (stellate-shaped extraependymal cells) did not appear during evolution, and the expansion of GFAP-free areas was limited.

Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes

The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1,288 ultraconserved element loci (UCE) spanning 293 species, 211 genera and 21 families of characoid fishes to reconstruct a new, fossil-calibrated phylogeny and infer the most likely diversification scenario for a clade that includes a third of Neotropical fish diversity. This phylogeny implies paraphyly of the traditional delimitation of Characiformes because it resolves the largely Neotropical Characoidei as the sister lineage of Siluriformes (catfishes), rather than the African Citharinodei. Time-calibrated phylogenies indicate an ancient origin of major characoid lineages and reveal a much more recent emergence of most characoid species. Diversification rate analyses infer increased speciation and decreased extinction rates during the Oligocene at around 30 million years ago (Ma) during a period of mega-wetland formation in the proto-Orinoco-Amazonas. Three species-rich and ecomorphologically diverse lineages (Anostomidae, Serrasalmidae, and Characidae) that originated more than 60 Ma in the Paleocene experienced particularly notable bursts of Oligocene diversification and now account collectively for 68% of the approximately 2,150 species of Characoidei. In addition to paleogeographic changes, we discuss potential accelerants of diversification in these three lineages. While the Neotropics accumulated a museum of ecomorphologically diverse characoid lineages long ago, this geologically dynamic region also cradled a much more recent birth of remarkable species-level diversity.

The biogeographic history of eelpouts and related fishes: Linking phylogeny, environmental change, and patterns of dispersal in a globally distributed fish group

Modern genetic data sets present unprecedented opportunities to understand the evolutionary origins of diverse taxonomic groups. When the timing of key events is known, it is possible to investigate biogeographic history in the context of major phenomena (e.g., cooling of a major ocean). In this study, we investigated the biogeographic history of the suborder Zoarcoidei, a globally distributed fish group that includes species inhabiting both poles that produce antifreeze proteins to survive chronic subfreezing temperatures. We first generated a multi-locus, time-calibrated phylogeny for the group. We then used biogeographic modeling to reconstruct ancestral ranges across the tree and to quantify the type and frequency of biogeographic events (e.g., founder, dispersal). With these results, we considered how the cooling of the Southern and Arctic Oceans, which reached their present-day subfreezing temperatures 10-15 million years ago (Mya) and 2-3 Mya, respectively, may have shaped the group's evolutionary history, with an emphasis on the most speciose and widely distributed family, eelpouts (family Zoarcidae). Our phylogenetic results clarified the Zoarcoidei taxonomy and showed that the group began to diversify in the Oligocene ~31-32 Mya, with the center of origin for all families in north temperate waters. Within-area speciation was the most common biogeographic event in the group's history (80% of all events) followed by dispersal (20%). Finally, we only found evidence, albeit limited, for ocean cooling underpinning diversification of eelpouts living in the high Antarctic over the last 10 million years.

Phylogeny of Micronesian emperor fishes and evolution of trophic types

Island communities that rely on reef fish are currently faced with declining marine resources due to unsustainable fishing and climate change. Identification of genetic stocks through phylogenetic analyses has become a growing field of study with conservation implications, but genetic information on reef fish in Micronesia is limited. In this study we focus on Lethrinidae, one of the most commonly fished reef fish families in Micronesia. Our main goal was to establish a phylogeny for Lethrinidae based on Micronesian data with the intent to help future conservation efforts and clarify the evolutionary history of trophic types in this family. Thirty-eight Lethrinidae specimens collected across five Micronesian islands were used to build a phylogeny with three mitochondrial and one nuclear gene. The phylogenetic analyses allowed us to clarify the identity and position of 11 commonly harvested species and provided a novel genetic identification for Monotaxis heterodon in Micronesia. Our improved and dated phylogeny supports a new hypothesis for the ancestral trophic type of emperor fishes: "stalkers" with low-bodies and conical teeth. We correlated the radiation of most Lethrinidae species with the radiation of major scleractinian coral lineages in the middle Miocene, highlighting the tight relationships between declining reefs and the survival of emperor fishes.

Large-scale sequencing of flatfish genomes provides insights into the polyphyletic origin of their specialized body plan

The evolutionary and genetic origins of the specialized body plan of flatfish are largely unclear. We analyzed the genomes of 11 flatfish species representing 9 of the 14 Pleuronectiforme families and conclude that Pleuronectoidei and Psettodoidei do not form a monophyletic group, suggesting independent origins from different percoid ancestors. Genomic and transcriptomic data indicate that genes related to WNT and retinoic acid pathways, hampered musculature and reduced lipids might have functioned in the evolution of the specialized body plan of Pleuronectoidei. Evolution of Psettodoidei involved similar but not identical genes. Our work provides valuable resources and insights for understanding the genetic origins of the unusual body plan of flatfishes.

Development of the caudal-fin skeleton reveals multiple convergent fusions within Atherinomorpha

Background

The caudal fin of teleosts is a highly diverse morphological structure and a valuable source of information for comparative analyses. Within the Atherinomorpha a high variation of conditions of the caudal-fin skeleton can be found. These range from complex but basal configurations to simple yet derived configurations. When comparing atherinomorph taxa, it is often difficult to decide on the homology of skeletal elements if only considering adult specimens. However, observing the development of caudal-fin skeletons allows one to evaluate complex structures, reveal homologies and developmental patterns, and even reconstruct the grundplan of the examined taxa.

Results

We studied the development of the caudal-fin skeleton in different atheriniform, beloniform and cyprinodontiform species using cleared and stained specimens. Subsequently we compared the development to find similarities and differences in terms of 1) which structures are formed and 2) which structures fuse during ontogeny. For many structures, i.e., the parhypural, the epural(s), the haemal and neural spines of the preural centra and the uroneural, there were either no or only minor differences visible between the three taxa. However, the development of the hypurals revealed a high variation of fusions within different taxa that partly occurred independently in atheriniforms, beloniforms and cyprinodontiforms. Moreover, comparing the development of the ural centra exposed two ways of formation of the compound centrum: 1) in atheriniforms and the beloniforms Oryzias and Hyporhamphus limbatus two ural centra develop and fuse during ontogeny while 2) in cyprinodontiforms and Exocoetidae (Beloniformes) only a single ural centrum is formed during ontogeny.

Conclusions

We were able to reconstruct the grundplan of the developmental pattern of the caudal-fin skeleton of the Atheriniformes, Beloniformes and Cyprinodontiformes as well as their last common ancestors. We found two developmental modes of the compound centrum within the Atherinomorpha, i.e., the fusion of two developing ural centra in atheriniforms and beloniforms and the development of only one ural centrum in cyprinodontiforms. Further differences and similarities for the examined taxa are discussed, resulting in the hypothesis that the caudal-fin development of a last common ancestor to all atherinomorphs is very much similar to that of extant atheriniforms.

Adult neurogenesis in the central nervous system of teleost fish: from stem cells to function and evolution

Adult neurogenesis, the generation of functional neurons from adult neural stem cells in the central nervous system (CNS), is widespread, and perhaps universal, among vertebrates. This phenomenon is more pronounced in teleost fish than in any other vertebrate taxon. There are up to 100 neurogenic sites in the adult teleost brain. New cells, including neurons and glia, arise from neural stem cells harbored both in neurogenic niches and outside these niches (such as the ependymal layer and parenchyma in the spinal cord, respectively). At least some, but not all, of the stem cells are of astrocytic identity. Aging appears to lead to stem cell attrition in fish that exhibit determinate body growth but not in those with indeterminate growth. At least in some areas of the CNS, the activity of the neural stem cells results in additive neurogenesis or gliogenesis - tissue growth by net addition of cells. Mathematical and computational modeling has identified three factors to be crucial for sustained tissue growth and correct formation of CNS structures: symmetric stem cell division, cell death and cell drift due to population pressure. It is hypothesized that neurogenesis in the CNS is driven by continued growth of corresponding muscle fibers and sensory receptor cells in the periphery to ensure a constant ratio of peripheral versus central elements. This 'numerical matching hypothesis' can explain why neurogenesis has ceased in most parts of the adult CNS during the evolution of mammals, which show determinate growth.

A Pliocene-Pleistocene continental biota from Venezuela

The Pliocene-Pleistocene transition in the Neotropics is poorly understood despite the major climatic changes that occurred at the onset of the Quaternary. The San Gregorio Formation, the younger unit of the Urumaco Sequence, preserves a fauna that documents this critical transition. We report stingrays, freshwater bony fishes, amphibians, crocodiles, lizards, snakes, aquatic and terrestrial turtles, and mammals. A total of 49 taxa are reported from the Vergel Member (late Pliocene) and nine taxa from the Cocuiza Member (Early Pleistocene), with 28 and 18 taxa reported for the first time in the Urumaco sequence and Venezuela, respectively. Our findings include the first fossil record of the freshwater fishes Megaleporinus, Schizodon, Amblydoras, Scorpiodoras, and the pipesnake Anilius scytale, all from Pliocene strata. The late Pliocene and Early Pleistocene ages proposed here for the Vergel and Cocuiza members, respectively, are supported by their stratigraphic position, palynology, nannoplankton, and ⁸⁶Sr/⁸⁸Sr dating. Mammals from the Vergel Member are associated with the first major pulse of the Great American Biotic Interchange. In contrast to the dry conditions prevailing today, the San Gregorio Formation documents mixed open grassland/forest areas surrounding permanent freshwater systems, following the isolation of the northern South American basin from western Amazonia. These findings support the hypothesis that range contraction of many taxa to their current distribution in northern South America occurred rapidly during at least the last 1.5 million years.

A fossil-calibrated time-tree of all Australian freshwater fishes

Australian freshwater fishes are a relatively species-poor assemblage, mostly comprising groups derived from older repeated freshwater invasions by marine ancestors, plus a small number of Gondwanan lineages. These taxa are both highly endemic and highly threatened, but a comprehensive phylogeny for Australian freshwater fishes is lacking. This has hampered efforts to study their phylogenetic diversity, distribution of extinction risk, speciation rates, and rates of trait evolution. Here, we present a comprehensive dated phylogeny of 412 Australian fishes. We include all formally recognized freshwater species plus a number of genetically distinct subpopulations, species awaiting formal description, and predominantly brackish-water species that sometimes enter fresh water. The phylogeny was inferred using maximum-likelihood analysis of a multilocus data set comprising six mitochondrial and three nuclear genes from 326 taxa. We inferred the evolutionary timescale using penalized likelihood, then used a statistical approach to add 86 taxa for which no molecular data were available. The time-tree inferred in our study will provide a useful resource for macroecological studies of Australian freshwater fishes by enabling corrections for phylogenetic non-independence in evolutionary and ecological comparative analyses.