The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond

True grit? Comparative anatomy and evolution of gizzards in fishes

Gut morphology frequently reflects the food organisms digest. Gizzards are organs of the gut found in archosaurs and fishes that mechanically reduce food to aid digestion. Gizzards are thought to compensate for edentulism and/or provide an advantage when consuming small, tough food items (e.g., phytoplankton and algae). It is unknown how widespread gizzards are in fishes and how similar these structures are among different lineages. Here, we investigate the distribution of gizzards across bony fishes to (1) survey different fishes for gizzard presence, (2) compare the histological structure of gizzards in three species, (3) estimate how often gizzards have evolved in fishes, and (4) explore whether anatomical and ecological traits like edentulism and microphagy predict gizzard presence. According to our analyses, gizzards are rare across bony fishes, evolving only six times in a broad taxonomic sampling of 51 species, and gizzard presence is not clearly correlated with factors like gut length or dentition. We find that gizzard morphology varies among the lineages where one is present, both macroscopically (presence of a crop) and microscopically (varying tissue types). We conclude that gizzards likely aid in the mechanical reduction of food in fishes that have lost an oral dentition in their evolutionary past; however, the relative scarcity of gizzards suggests they are just one of many possible solutions for processing tough, nutrient-poor food items. Gizzards have long been present in the evolutionary history of fishes, can be found in a wide variety of marine and freshwater clades, and likely have been overlooked in many taxa.

Different ways of evolving tool-using brains in teleosts and amniotes

In mammals and birds, tool-using species are characterized by their relatively large telencephalon containing a higher proportion of total brain neurons compared to other species. Some teleost species in the wrasse family have evolved tool-using abilities. In this study, we compared the brains of tool-using wrasses with various teleost species. We show that in the tool-using wrasses, the telencephalon and the ventral part of the forebrain and midbrain are significantly enlarged compared to other teleost species but do not contain a larger proportion of cells. Instead, this size difference is due to large fiber tracts connecting the dorsal part of the telencephalon (pallium) to the inferior lobe, a ventral mesencephalic structure absent in amniotes. The high degree of connectivity between these structures in tool-using wrasses suggests that the inferior lobe could contribute to higher-order cognitive functions. We conclude that the evolution of non-telencephalic structures might have been key in the emergence of these cognitive functions in teleosts.

Insights into the Mitochondrial Genetic Makeup and Miocene Colonization of Primitive Flatfishes (Pleuronectiformes: Psettodidae) in the East Atlantic and Indo-West Pacific Ocean

The mitogenomic evolution of the Psettodes flatfishes is still poorly known from their range distribution in eastern Atlantic and Indo-West Pacific Oceans. The study delves into the matrilineal evolutionary pathway of these primitive flatfishes, with a specific focus on the complete mitogenome of the Psettodes belcheri species, as determined through next-generation sequencing. The mitogenome in question spans a length of 16,747 base pairs and comprises a total of 37 genes, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Notably, the mitogenome of P. belcheri exhibits a bias towards AT base pairs, with a composition of 54.15%, mirroring a similar bias observed in its close relative, Psettodes erumei, which showcases percentages of 53.07% and 53.61%. Most of the protein-coding genes commence with an ATG initiation codon, except for Cytochrome c oxidase I (COI), which initiates with a GTG codon. Additionally, four protein-coding genes commence with a TAA termination codon, while seven others exhibit incomplete termination codons. Furthermore, two protein-coding genes, namely NAD1 and NAD6, terminate with AGG and TAG stop codons, respectively. In the mitogenome of P. belcheri, the majority of transfer RNAs demonstrate the classical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the control regions of two Psettodidae species unveiled that the CSB-II block extended to a length of 51 base pairs, surpassing the other blocks and encompassing highly variable sites. A comprehensive phylogenetic analysis using mitochondrial genomes (13 concatenated PCGs) categorized various Pleuronectiformes species, highlighting the basal position of the Psettodidae family and showed monophyletic clustering of Psettodes species. The approximate divergence time (35-10 MYA) between P. belcheri and P. erumei was estimated, providing insights into their separation and colonization during the early Miocene. The TimeTree analysis also estimated the divergence of two suborders, Psettodoidei and Pleuronectoidei, during the late Paleocene to early Eocene (56.87 MYA). The distribution patterns of Psettodes flatfishes were influenced by ocean currents and environmental conditions, contributing to their ecological speciation. In the face of climate change and anthropogenic activities, the conservation implications of Psettodes flatfishes are emphasized, underscoring the need for regulated harvesting and adaptive management strategies to ensure their survival in changing marine ecosystems. Overall, this study contributes to understanding the evolutionary history, genetic diversity, and conservation needs of Psettodes flatfishes globally. However, the multifaceted exploration of mitogenome and larger-scale genomic data of Psettodes flatfish will provide invaluable insights into their genetic characterization, evolutionary history, environmental adaptation, and conservation in the eastern Atlantic and Indo-West Pacific Oceans.

The cichlid pharyngeal jaw novelty enhances evolutionary integration in the feeding apparatus

The modified pharyngeal jaw system of cichlid fishes is widely viewed as a key innovation that substantially facilitated the evolutionary exuberance of this iconic evolutionary radiation. We conduct comparative phylogenetic analyses of integration, disparity, and rate of evolution among feeding-related, skeletal structures in Neotropical cichlids and North American centrarchids, which lack the specialized pharyngeal jaw. Contrasting evolutionary patterns in these two continental radiations, we test a classic decoupling hypothesis. Specifically, we ask whether the modified pharyngeal jaw in cichlids resulted in enhanced evolutionary independence of the oral and pharyngeal jaws, leading to increased diversity of trophic structures. Contrary to this prediction, we find significantly stronger evolutionary integration between the oral and pharyngeal jaws in cichlids compared to centrarchids, although the two groups do not differ in patterns of integration within each jaw system. Further, though we find no significant differences in disparity, centrarchids show faster rates of morphological evolution. Our results suggest that the modified pharyngeal jaw resulted in less evolutionary independence and slower rates of evolution within the feeding system. Thus, we raise the possibility that the cichlid novelty enhances feeding performance, but does not prompt increased morphological diversification within the feeding apparatus, as has long been thought.

Measuring the relative contribution to predictive power of modern nucleotide substitution modeling approaches

Traditional approaches to probabilistic phylogenetic inference have relied on information-theoretic criteria to select among a relatively small set of substitution models. These model selection criteria have recently been called into question when applied to richer models, including models that invoke mixtures of nucleotide frequency profiles. At the nucleotide level, we are therefore left without a clear picture of mixture models' contribution to overall predictive power relative to other modeling approaches. Here, we utilize a Bayesian cross-validation method to directly measure the predictive performance of a wide range of nucleotide substitution models. We compare the relative contributions of free nucleotide exchangeability parameters, gamma-distributed rates across sites, and mixtures of nucleotide frequencies with both finite and infinite mixture frameworks. We find that the most important contributor to a model's predictive power is the use of a sufficiently rich mixture of nucleotide frequencies. These results suggest that mixture models should be given greater consideration in nucleotide-level phylogenetic inference.

XROMM Analysis of Feeding Mechanics in Toads: Interactions of the Tongue, Hyoid, and Pectoral Girdle

During feeding in many terrestrial vertebrates, the tongue acts in concert with the hyoid and pectoral girdle. In frogs, these three elements are interconnected by musculature. While the feeding mechanics of the anuran tongue are well-studied, little is known of how the motions of the tongue relate to the movements of the skeleton or how buccal structures move following closure of the mouth. Although features such as the pectoral girdle and hyoid are not externally visible in frogs, their motions can be tracked in X-ray video. We used XROMM (X-ray Reconstruction of Moving Morphology) techniques to track the 3D movements of the tongue, hyoid apparatus, pectoral girdle, skull, and jaw during the feeding cycle of the cane toad, Rhinella marina . We show how the movements of these elements are integrated during tongue protrusion and prey capture, as well as during prey transport, swallowing, and recovery. Our findings suggest that the hyoid apparatus is important both for prey manipulation and swallowing. The tongue consistently stretches posterior to the skull during swallowing, often more than it stretches during protrusion to reach the prey. Feeding kinematics are similar between individuals, and the kinematics of unsuccessful strikes generally resemble those of successful strikes. Our data also provide a new perspective on the potential role of the pectoral girdle, an element with a predominant locomotor function, during feeding events. This work raises new questions about the evolution of feeding in frogs, as well as how the diversity of pectoral and buccal anatomy observed across anurans may influence feeding kinematics.

Exon-based phylogenomics and the relationships of African cichlid fishes: tackling the challenges of reconstructing phylogenies with repeated rapid radiations

African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae, and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system.

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.

Terrestrial capabilities of invasive fishes and their management implications

Amphibious fishes have many adaptations that make them successful in a wide variety of conditions, including air-breathing, terrestrial locomotor capabilities, and extreme tolerance of poor water quality. However, the traits that make them highly adaptable may allow these fishes to successfully establish themselves outside of their native regions. In particular, the terrestrial capabilities of invasive amphibious fishes allow them to disperse overland, unlike fully aquatic invasive fishes, making their management more complicated. Despite numerous amphibious fish introductions around the world, ecological risk assessments and management plans often fail to adequately account for their terrestrial behaviors. In this review, I discuss the diversity of invasive amphibious fishes and what we currently know about why they emerge onto land, how they move around terrestrial environments, and how they orient while on land. In doing so, I use case studies of the performance and motivations of nonnative amphibious fishes in terrestrial environments to propose management solutions that factor in their complete natural history. Because of their terrestrial capabilities, we may need to manage amphibious fishes more like amphibians than fully aquatic fishes, but to do so, we need to learn more about how these species perform in a wide range of terrestrial environments and conditions.

Forensic odontology: Assessing bite wounds to determine the role of teeth in piscivorous fishes

Teeth facilitate the acquisition and processing of food in most vertebrates. However, relatively little is known about the functions of the diverse tooth morphologies observed in fishes. Piscivorous fishes (fish-eating fish) are crucial in shaping community structure and rely on their oral teeth to capture and/or process prey. However, how teeth are utilized in capturing and/or processing prey remains unclear. Most studies have determined the function of teeth by assessing morphological traits. The behavior during feeding, however, is seldom quantified. Here, we describe the function of teeth within piscivorous fishes by considering how morphological and behavioral traits interact during prey capture and processing. This was achieved through aquarium-based performance experiments, where prey fish were fed to 12 species of piscivorous fishes. Building on techniques in forensic odontology, we incorporate a novel approach to quantify and categorize bite damage on prey fish that were extracted from the piscivore’s stomachs immediately after being ingested. We then assess the significance of morphological and behavioral traits in determining the extent and severity of damage inflicted on prey fish. Results show that engulfing piscivores capture their prey whole and head-first. Grabbing piscivores capture prey tail-first using their teeth, process them using multiple headshakes and bites, before spitting them out, and then re-capturing prey head-first for ingestion. Prey from engulfers sustained minimal damage, whereas prey from grabbers sustained significant damage to the epaxial musculature. Within grabbers, headshakes were significantly associated with more severe damage categories. Headshaking behavior damages the locomotive muscles of prey, presumably to prevent escape. Compared to non-pharyngognaths, pharyngognath piscivores inflict significantly greater damage to prey. Overall, when present, oral jaw teeth appear to be crucial for both prey capture and processing (immobilization) in piscivorous fishes.

The complete mitogenomes of the spinyhead blenny, Acanthemblemaria spinosa (chaenopsidae) and the lofty triplefin, Enneanectes altivelis (Tripterygiidae)

The blennies, Acanthemblemaria spinosa (Chaenopsidae) and Enneanectes altivelis (Tripterygiidae) are representative members of two families spanning the deepest node of the Blennioidei tree. The mitogenomes of 16,507 bp for A. spinosa and 16,529 bp for E. altivelis each consisted of 37 genes and one control loop region. Phylogenetic analysis confirmed the placement of Chaenopsidae and Tripterygiidae within the Blenniiformes, however, there was instability in the placement of the triplefins between reconstruction methods, likely due to low taxon sampling. These mitogenomes represent an important milestone in uncovering relationships within Blenniiformes and Ovalentaria.

Quantitative Insights into the Contribution of Nematocysts to the Adaptive Success of Cnidarians Based on Proteomic Analysis

Nematocysts are secretory organelles in cnidarians that play important roles in predation, defense, locomotion, and host invasion. However, the extent to which nematocysts contribute to adaptation and the mechanisms underlying nematocyst evolution are unclear. Here, we investigated the role of the nematocyst in cnidarian evolution based on eight nematocyst proteomes and 110 cnidarian transcriptomes/genomes. We detected extensive species-specific adaptive mutations in nematocyst proteins (NEMs) and evidence for decentralized evolution, in which most evolutionary events involved non-core NEMs, reflecting the rapid diversification of NEMs in cnidarians. Moreover, there was a 33-55 million year macroevolutionary lag between nematocyst evolution and the main phases of cnidarian diversification, suggesting that the nematocyst can act as a driving force in evolution. Quantitative analysis revealed an excess of adaptive changes in NEMs and enrichment for positively selected conserved NEMs. Together, these findings suggest that nematocysts may be key to the adaptive success of cnidarians and provide a reference for quantitative analyses of the roles of phenotypic novelties in adaptation.

Investigations into the ancestry of the Grape-eye Seabass (Hemilutjanus macrophthalmos) reveal novel limits and relationships for the Acropomatiformes (Teleostei: Percomorpha)

Abstract For 175 years, an unremarkable bass, the Grape-eye Seabass (Hemilutjanus macrophthalmos), has been known from coastal waters in the Eastern Pacific. To date, its phylogenetic placement and classification have been ignored. A preliminary osteological examination of Hemilutjanus hinted that it may have affinities with the Acropomatiformes. To test this hypothesis, we conducted a phylogenetic analysis using UCE and Sanger sequence data to study the placement of Hemilutjanus and the limits and relationships of the Acropomatiformes. We show that Hemilutjanus is a malakichthyid, and our results corroborate earlier studies that have resolved a polyphyletic Polyprionidae; accordingly, we describe Stereolepididae, new family, for Stereolepis. With these revisions, the Acropomatiformes is now composed of the: Acropomatidae; Banjosidae; Bathyclupeidae; Champsodontidae; Creediidae; Dinolestidae; Epigonidae; Glaucosomatidae; Hemerocoetidae; Howellidae; Lateolabracidae; Malakichthyidae; Ostracoberycidae; Pempheridae; Pentacerotidae; Polyprionidae; Scombropidae; Stereolepididae, new family; Symphysanodontidae; Synagropidae; and Schuettea. Finally, using our new hypothesis, we demonstrate that acropomatiforms repeatedly evolved bioluminescence and transitioned between shallow waters and the deep sea.

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.

Tracing evolutionary decoupling of oral and pharyngeal jaws in cichlid fishes

Evolutionary innovations can facilitate diversification if the novel trait enables a lineage to exploit new niches or by expanding character space. The elaborate pharyngeal jaw apparatus of cichlid fishes is often referred to as an evolutionary "key innovation" that has promoted the spectacular adaptive radiations in these fishes. This goes back to the idea that the structural and functional independence of the oral and pharyngeal jaws for food capturing and food processing, respectively, permitted each jaw type to follow independent evolutionary trajectories. This "evolutionary decoupling" is thought to have facilitated novel trait combinations and, hence, ecological specialization, ultimately allowing more species to coexist in sympatry. Here, we test the hypotheses of evolutionary decoupling of the oral and pharyngeal jaws in the massive adaptive radiation of cichlid fishes in African Lake Tanganyika. Based on phylogenetic comparative analyses of oral jaw morphology and lower pharyngeal jaw shape across most of the ∼240 cichlid species occurring in that lake, we show that the two jaws evolved coupled along the main axes of morphological variation, yet most other components of these trait complexes evolved largely independently over the course of the radiation. Further, we find limited correlations between the two jaws in both overall divergence and evolutionary rates. Moreover, we show that the two jaws were evolutionary decoupled at a late stage of the radiation, suggesting that decoupling contributed to micro-niche partitioning and the associated rapidly increasing trophic diversity during this phase.

External reproductive structures of male Surfperches (Embiotocidae): Urogenital papilla

Fishes exhibit a dynamic array of reproductive diversity. Among the various forms of reproduction, internal fertilization has evolved at least 13 times and has been observed in 2-3% of teleost species, half of which are marine. Internal fertilization has led to the evolution of male intromittent organs to aid in sperm transfer during copulation. The intromittent organs of poeciliids have been widely investigated, but little research has focused on the intromittent organs of marine fishes. The surfperches are internally fertilizing, viviparous fishes with a ventrally located papilla. In this article, the external morphology of 19 Embiotocidae species was examined. Additionally, paraffin histology was used to investigate the walleye surfperch (Hyperprosopon argenteum), black perch (Embiotoca jacksoni), and dwarf perch (Micrometrus minimus) papilla to aid in the identification of tissue composition to determine its function. External morphology was documented via macro photography and males were dissected to observe the relationship between the testes, spermatic duct, and papilla. We provide histological evidence that the urogenital papilla is directly connected to the spermatic duct and testis and likely involved in spermatozeugmata transfer. Our research also determined that the papillae were composed of both urinary and reproductive tissues, thus we propose the papilla be referred to as a urogenital papilla. Our study contributes to an overall understanding of intromittent organs of marine fishes, particularly in the surfperches, which has not been previously documented.

The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes

The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century marked a paradigm shift in understanding the evolutionary history of half of living vertebrates. We review how the new ray-finned fish phylogeny radically departs from classical expectations based on morphology. We focus on evolutionary relationships that span the backbone of ray-finned fish phylogeny, from the earliest divergences among teleosts and nonteleosts to the resolution of major lineages of Percomorpha. Throughout, we feature advances gained by the new phylogeny toward a broader understanding of ray-finned fish evolutionary history and the implications for topics that span from the genetics of human health to reconsidering the concept of living fossils. Additionally, we discuss conceptual challenges that involve reconciling taxonomic classification with phylogenetic relationships and propose an alternate higher-level classification for Percomorpha. Our review highlights remaining areas of phylogenetic uncertainty and opportunities for comparative investigations empowered by this new phylogenetic perspective on ray-finned fishes.

A new species of the genus Acyrtus on the eastern Pacific: A cornerstone for the evolution and biogeography of the genus

The genus Acyrtus Schultz, 1944 currently includes four species distributed in the western Atlantic (WA), three occurring from the Bahamas to the southern Caribbean, and one endemic to the Fernando de Noronha Archipelago in north-east Brazil. We describe a new species of Acyrtus based on morphology and genetics from several individuals caught at artificial hard substrates deployed between 10 and 16 m deep at Malpelo Island, Colombian Pacific. The Malpelo clingfish, Acyrtus arturo new species, differs from all its WA congeners by a combination of morphology, meristics and genetics. This species is unique within Acyrtus in having the greatest number of caudal rays (12-13). It can also be distinguished by the greater body height (19.8-27.8% standard length), its longer disc (34.0-39.1% standard length) and the greater distance between anus and disc (13.9-18.1% standard length). A. arturo sp. nov. is the first Acyrtus so far recorded from the eastern Pacific and adds to the already high number of fishes endemic to Colombia's remote oceanic territory of Malpelo.

Phylogeny of the damselfishes (Pomacentridae) and patterns of asymmetrical diversification in body size and feeding ecology

The damselfishes (family Pomacentridae) inhabit near-shore communities in tropical and temperature oceans as one of the major lineages in coral reef fish assemblages. Our understanding of their evolutionary ecology, morphology and function has often been advanced by increasingly detailed and accurate molecular phylogenies. Here we present the next stage of multi-locus, molecular phylogenetics for the group based on analysis of 12 nuclear and mitochondrial gene sequences from 345 of the 422 damselfishes. The resulting well-resolved phylogeny helps to address several important questions about higher-level damselfish relationships, their evolutionary history and patterns of divergence. A time-calibrated phylogenetic tree yields a root age for the family of 55.5 mya, refines the age of origin for a number of diverse genera, and shows that ecological changes during the Eocene-Oligocene transition provided opportunities for damselfish diversification. We explored the idea that body size extremes have evolved repeatedly among the Pomacentridae, and demonstrate that large and small body sizes have evolved independently at least 40 times and with asymmetric rates of transition among size classes. We tested the hypothesis that transitions among dietary ecotypes (benthic herbivory, pelagic planktivory and intermediate omnivory) are asymmetric, with higher transition rates from intermediate omnivory to either planktivory or herbivory. Using multistate hidden-state speciation and extinction models, we found that both body size and dietary ecotype are significantly associated with patterns of diversification across the damselfishes, and that the highest rates of net diversification are associated with medium body size and pelagic planktivory. We also conclude that the pattern of evolutionary diversification in feeding ecology, with frequent and asymmetrical transitions between feeding ecotypes, is largely restricted to the subfamily Pomacentrinae in the Indo-West Pacific. Trait diversification patterns for damselfishes across a fully resolved phylogeny challenge many recent general conclusions about the evolution of reef fishes.

Phylogeny, body morphology, and trophic level shape intestinal traits in coral reef fishes

Trait-based approaches are increasingly used to study species assemblages and understand ecosystem functioning. The strength of these approaches lies in the appropriate choice of functional traits that relate to the functions of interest. However, trait-function relationships are often supported by weak empirical evidence.Processes related to digestion and nutrient assimilation are particularly challenging to integrate into trait-based approaches. In fishes, intestinal length is commonly used to describe these functions. Although there is broad consensus concerning the relationship between fish intestinal length and diet, evolutionary and environmental forces have shaped a diversity of intestinal morphologies that is not captured by length alone.Focusing on coral reef fishes, we investigate how evolutionary history and ecology shape intestinal morphology. Using a large dataset encompassing 142 species across 31 families collected in French Polynesia, we test how phylogeny, body morphology, and diet relate to three intestinal morphological traits: intestinal length, diameter, and surface area.We demonstrate that phylogeny, body morphology, and trophic level explain most of the interspecific variability in fish intestinal morphology. Despite the high degree of phylogenetic conservatism, taxonomically unrelated herbivorous fishes exhibit similar intestinal morphology due to adaptive convergent evolution. Furthermore, we show that stomachless, durophagous species have the widest intestines to compensate for the lack of a stomach and allow passage of relatively large undigested food particles.Rather than traditionally applied metrics of intestinal length, intestinal surface area may be the most appropriate trait to characterize intestinal morphology in functional studies.

The cichlid oral and pharyngeal jaws are evolutionarily and genetically coupled

Evolutionary constraints may significantly bias phenotypic change, while "breaking" from such constraints can lead to expanded ecological opportunity. Ray-finned fishes have broken functional constraints by developing two jaws (oral-pharyngeal), decoupling prey capture (oral jaw) from processing (pharyngeal jaw). It is hypothesized that the oral and pharyngeal jaws represent independent evolutionary modules and this facilitated diversification in feeding architectures. Here we test this hypothesis in African cichlids. Contrary to our expectation, we find integration between jaws at multiple evolutionary levels. Next, we document integration at the genetic level, and identify a candidate gene, smad7, within a pleiotropic locus for oral and pharyngeal jaw shape that exhibits correlated expression between the two tissues. Collectively, our data show that African cichlid evolutionary success has occurred within the context of a coupled jaw system, an attribute that may be driving adaptive evolution in this iconic group by facilitating rapid shifts between foraging habitats, providing an advantage in a stochastic environment such as the East African Rift-Valley.

Ecological limits on the decoupling of prey capture and processing in fishes

Ray-finned fishes have two jaw systems, the oral and pharyngeal jaws, which perform functions associated with prey capture and processing, respectively. The structural independence of the jaw systems is recognized as having broad implications for the functional and ecological diversity of the radiation. Cichlids (and a few other lineages) possess a modified pharyngeal jaw system that enhances prey processing versatility and capacity. This innovation, pharyngognathy, is hypothesized to have freed the oral jaws to diversify in terms of prey capture. We test the relative role of prey capture properties (e.g., evasiveness) and prey processing (e.g., crushing) in driving divergent selection in the oral and pharyngeal jaws using a macroevolutionary model fitting framework. Evolutionary outcomes were asymmetric. All transitions between different properties of prey capture had a corresponding transition in properties of prey processing. In contrast, fewer than half the transitions in the properties of prey processing had a corresponding prey capture transition. This discrepancy was further highlighted by multi-peak models that reflect the opposing function of each jaw system, which fit better than null models for oral jaw traits, but not pharyngeal jaw traits. These results suggest that pharyngeal jaw function can change independently from the function of the oral jaws, but not vice versa. This finding highlights the possibility of ecological limits to the evolutionary decoupling of jaw systems. The independent actions of prey capture and processing may be decoupled, but their respective functional demands (and evolution) are not. Therefore, prey likely impose some degree of coordinated evolution between acquisition and processing functional morphology, even in decoupled jaw systems.

A review of linkage mechanisms in animal joints and related bioinspired designs

This paper presents a review of biological mechanical linkage mechanisms. One purpose is to identify the range of kinematic functions that they are able to perform. A second purpose is to review progress in bioinspired designs. Ten different linkage mechanisms are presented. They are chosen because they cover a wide range of functionality and because they have potential for bioinspired design. Linkage mechanisms enable animal joints to perform highly sophisticated and optimised motions. A key function of animal linkage mechanisms is the optimisation of actuator location and mechanical advantage. This is crucially important for animals where space is highly constrained. Many of the design features used by engineers in linkage mechanisms are seen in nature, such as short coupler links, extended bars, elastic energy storage and latch mechanisms. However, animal joints contain some features rarely seen in engineering such as integrated cam and linkage mechanisms, nonplanar four-bar mechanisms, resonant hinges and highly redundant actuators. The extreme performance of animal joints together with the unusual design features makes them an important area of investigation for bioinspired designs. Whilst there has been significant progress in bioinspiration, there is the potential for more, especially in robotics where compactness is a key design driver.

Chromosome-level genome assembly of the endangered humphead wrasse Cheilinus undulatus: Insight into the expansion of opsin genes in fishes

Wrasses are dominant components of major coral reef systems. Among wrasses, Cheilinus undulatus is an endangered species with high economic and ecological value that exhibits sex reversal of females to males, while sexual selection occurs in breeding aggregations. However, the molecular-associated mechanism underlying this remains unclear. Opsin gene diversification is regarded as a potent force in sexual selection. Here we present a genome assembly of C. undulatus, using Illumina, Nanopore and Hi-C sequencing. The 1.17 Gb genome was generated from 328 contigs with an N50 length of 16.5 Mb and anchored to 24 chromosomes. In total, 22,218 genes were functionally annotated, and 96.36% of BUSCO genes were fully represented. Transcriptomic analyses showed that 96.79% of the predicted genes were expressed. Transposons were most abundant, accounting for 39.88% of the genome, with low divergence, owing to their evolution with close species ~60.53 million years ago. In total, 567/1,826 gene families were expanded and contracted in the reconstructed phylogeny, respectively. Forty-six genes were under positive selection. Comparative genomic analyses with other fish revealed expansion of opsin SWS2B, LWS1 and Rh2. The elevated duplicates of SWS2B were generated by gene conversions via transposition of transposons followed by nonallelic homologous recombination. Amino acid substitutions of opsin paralogues occurred at key tuning sites, causing a spectral shift in maximal absorbance of visual pigment to capture functional changes. Among these opsin genes, SWS2B-3 and 4 and Rh1 are expressed in the retina. The genome sequence of C. undulatus provides valuable resources for future investigation of the conservation, evolution and behaviour of fishes.

Ecological Opportunity from Innovation, not Islands, Drove the Anole Lizard Adaptive Radiation

Islands are thought to facilitate adaptive radiation by providing release from competition and predation. Anole lizards are considered a classic example of this phenomenon: different ecological specialists ('ecomorphs') evolved in the Caribbean Greater Antilles (Cuba, Hispaniola, Jamaica, and Puerto Rico), resulting in convergent assemblages that are not observed in mainland Latin America. Yet, the role of islands in facilitating adaptive radiation is more often implied than directly tested, leaving uncertain the role of biogeography in stimulating diversification. Here, we assess the proposed "island effect" on anole diversification using Bayesian phylogenetic comparative methods that explicitly incorporate rate heterogeneity across the tree and demonstrate two cases of would-be false positives. We discovered that rates of speciation and morphological evolution of island and mainland anoles are equivalent, implying that islands provide no special context for exceptionally rapid diversification. Likewise, rates of evolution were equivalent between island anoles that arose via in situ versus dispersal-based mechanisms, and we found no evidence for island-specific rates of speciation or morphological evolution. Nonetheless, the origin of Anolis is characterized by a speciation pulse that slowed over time - a classic signature of waning ecological opportunity. Our findings cast doubt on the notion that islands catalyzed the anole adaptive radiation and instead point to a key innovation, adhesive toe pads, which facilitated the exploitation of many arboreal niches sparsely utilized by other iguanian lizards. The selective pressures responsible for arboreal niche diversification differ between islands and the mainland, but the tempo of diversification driven by these discordant processes is indistinguishable.

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.

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.

Multiple Degrees of Freedom in the Fish Skull and Their Relation to Hydraulic Transport of Prey in Channel Catfish

Fish perform many complex manipulation behaviors without hands or flexible muscular tongues, instead relying on more than 20 movable skeletal elements in their highly kinetic skulls. How fish use their skulls to accomplish these behaviors, however, remains unclear. Most previous mechanical models have represented the fish skull using one or more planar four-bar linkages, which have just a single degree of freedom (DoF). In contrast, truncated-cone hydrodynamic models have assumed up to five DoFs. In this study, we introduce and validate a 3D mechanical linkage model of a fish skull that incorporates the pectoral girdle and mandibular and hyoid arches. We validate this model using an in vivo motion dataset of suction feeding in channel catfish and then use this model to quantify the DoFs in the fish skull, to categorize the motion patterns of the cranial linkage during feeding, and to evaluate the association between these patterns and food motion. We find that the channel catfish skull functions as a 17-link, five-loop parallel mechanism. Despite having 19 potential DoFs, we find that seven DoFs are sufficient to describe most of the motion of the cranial linkage, consistent with the fish skull functioning as a multi-DoF, manipulation system. Channel catfish use this linkage to generate three different motion patterns (rostrocaudal wave, caudorostral wave, and compressive wave), each with its own associated food velocity profile. These results suggest that biomechanical manipulation systems must have a minimum number of DoFs to effectively control objects, whether in water or air.

Rise and fall of †Pycnodontiformes: Diversity, competition and extinction of a successful fish clade

†Pycnodontiformes was a successful lineage of primarily marine fishes that broadly diversified during the Mesozoic. They possessed a wide variety of body shapes and were adapted to a broad range of food sources. Two other neopterygian clades possessing similar ecological adaptations in both body morphology (†Dapediiformes) and dentition (Ginglymodi) also occurred in Mesozoic seas. Although these groups occupied the same marine ecosystems, the role that competitive exclusion and niche partitioning played in their ability to survive alongside each other remains unknown. Using geometric morphometrics on both the lower jaw (as constraint for feeding adaptation) and body shape (as constraint for habitat adaptation), we show that while dapediiforms and ginglymodians occupy similar lower jaw morphospace, pycnodontiforms are completely separate. Separation also occurs between the clades in body shape so that competition reduction between pycnodontiforms and the other two clades would have resulted in niche partitioning. Competition within pycnodontiforms seemingly was reduced further by evolving different feeding strategies as shown by disparate jaw shapes that also indicate high levels of plasticity. Acanthomorpha was a teleostean clade that evolved later in the Mesozoic and which has been regarded as implicated in driving the pycnodontiforms to extinction. Although they share similar body shapes, no coeval acanthomorphs had similar jaw shapes or dentitions for dealing with hard prey like pycnodontiforms do and so their success being a factor in pycnodontiform extinction is unlikely. Sea surface temperature and eustatic variations also had no impact on pycnodontiform diversity patterns according to our results. Conversely, the occurrence and number of available reefs and hardgrounds as habitats through time seems to be the main factor in pycnodontiform success. Decline in such habitats during the Late Cretaceous and Palaeogene might have had deleterious consequences for pycnodontiform diversity. Acanthomorphs occupied the niches of pycnodontiforms during the terminal phase of their existence.

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics

Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon-capture sequence data into an existing data matrix of 1,104 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR-generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR-based exon and mitochondrial data.

Flexibility of intraoral food processing in the salamandrid newt Triturus carnifex: effects of environment and prey type

Intraoral food processing mechanisms are known for all major vertebrate groups, but the form and function of systems used to crush, grind or puncture food items can differ substantially between and within groups. Most vertebrates display flexible mechanisms of intraoral food processing with respect to different environmental conditions or food types. It has recently been shown that newts use cyclical loop-motions of the tongue to rasp prey against the palatal dentition. However, it remains unknown whether newts can adjust their food processing behavior in response to different food types or environmental conditions. Newts are interesting models for studying the functional adaptation to different conditions because of their unique and flexible lifestyle: they seasonally change between aquatic and terrestrial habitats, adapt their prey-capture mode to the respective environment, and consume diverse food types with different mechanical properties. Using X-ray high-speed recordings, anatomical investigations, behavioral analyses and mechanical property measurements, we tested the effects of the medium in which feeding occurs (water/air) and the food type (maggot, earthworm, cricket) on the processing behavior in Triturus carnifex We discovered that food processing, by contrast to prey capture, differed only slightly between aquatic and terrestrial habitats. However, newts adjusted the number of processing cycles to different prey types: while maggots were processed extensively, earthworm pieces were barely processed at all. We conclude that, in addition to food mechanical properties, sensory feedback such as smell and taste appear to induce flexible processing responses, while the medium in which feeding occurs appears to have less of an effect.

Diversification of Neotropical Freshwater Fishes

Neotropical freshwater fishes (NFFs) constitute the most diverse continental vertebrate fauna on Earth, with more than 6,200 named species compressed into an aquatic footprint <0.5% of the total regional land-surface area and representing the greatest phenotypic disparity and functional diversity of any continental ichthyofauna. Data from the fossil record and time-calibrated molecular phylogenies indicate that most higher taxa (e.g., genera, families) diversified relatively continuously through the Cenozoic, across broad geographic ranges of the South American platform. Biodiversity data for most NFF clades support a model of continental radiation rather than adaptive radiation, in which speciation occurs mainly in allopatry, and speciation and adaptation are largely decoupled. These radiations occurred under the perennial influence of river capture and sea-level oscillations, which episodically fragmented and merged portions of adjacent river networks. The future of the NFF fauna into the Anthropocene is uncertain, facing numerous threats at local, regional, and continental scales.

Complete mitochondrial genome of Iniistius trivittatus and unique variation in two observed inserts between rRNA and tRNA genes in wrasses

Background

The family Labridae made up of 519 species in the world. The functional evolution of the feeding-related jaws leaded to differentiation of species, and the pharyngeal jaw apparatus evolved independently, but evolutionary mechanism still remain unaddressed in wrasses. Mitogenomes data can be used to infer genetic diversification and investigate evolutionary history of wrasses, whereas only eight complete mitogenomes in this family have been sequenced to date. Here, we sequenced the complete mitogenomes of Iniistius trivittatus to investigate genetic differentiation among wrasse species.

Results

We sequenced the complete mitogenomes of I. trivittatus using a novel PCR strategy. The I. trivittatus mitogenomes is 16,820 bp in length and includes 13 protein -coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. Compared to eight known mitochondrial genome, 2 additional noncoding regions (lengths of 121 and 107 bp), or so-called inserts, are found in the intergenic regions 12S rRNA - tRNA^Val - 16S rRNA. The presumed origin of the two rare inserts is from tRNA- related retrotransposons. Compared with cytochrome b gene, the two insert sequences are highly conserved at the intraspecies level, but they showed significant variation and low similarity (< 70%) at the interspecies level. The insert events were only observed in I. trivittatus by checking the phylogenetic trees based on the complete mitogenomes of Labrida species. This finding provides evidence that in the mitogenomes, retrotransposon inserts result in intraspecific homoplasmy and interspecific heteroplasmy by natural selection and adaptation to various environments.

Conclusions

This study found additional mitogenome inserts limited in wrasse species. The rRNA genes with inserts might have experienced a selective pressure for adaptation to feeding modes. Such knowledge can enable a better understanding of molecular mechanism underlying morphological evolution in wrasses.

Do key innovations unlock diversification? A case-study on the morphological and ecological impact of pharyngognathy in acanthomorph fishes

Key innovations may allow lineages access to new resources and facilitate the invasion of new adaptive zones, potentially influencing diversification patterns. Many studies have focused on the impact of key innovations on speciation rates, but far less is known about how they influence phenotypic rates and patterns of ecomorphological diversification. We use the repeated evolution of pharyngognathy within acanthomorph fishes, a commonly cited key innovation, as a case study to explore the predictions of key innovation theory. Specifically, we investigate whether transitions to pharyngognathy led to shifts in the rate of phenotypic evolution, as well as shifts and/or expansion in the occupation of morphological and dietary space, using a dataset of 8 morphological traits measured across 3,853 species of Acanthomorpha. Analyzing the 6 evolutionarily independent pharyngognathous clades together, we found no evidence to support pharyngognathy as a key innovation; however, comparisons between individual pharyngognathous lineages and their sister clades did reveal some consistent patterns. In morphospace, most pharyngognathous clades cluster in areas that correspond to deeper-bodied morphologies relative to their sister clades, while occupying greater areas in dietary space that reflects a more diversified diet. Additionally, both Cichlidae and Labridae exhibited higher univariate rates of phenotypic evolution compared with their closest relatives. However, few of these results were exceptional relative to our null models. Our results suggest that transitions to pharyngognathy may only be advantageous when combined with additional ecological or intrinsic factors, illustrating the importance of accounting for lineage-specific effects when testing key innovation hypotheses. Moreover, the challenges we experienced formulating informative comparisons, despite the ideal evolutionary scenario of multiple independent evolutionary origins of pharyngognathous clades, illustrates the complexities involved in quantifying the impact of key innovations. Given the issues of lineage specific effects and rate heterogeneity at macroevolutionary scales we observed, we suggest a reassessment of the expected impacts of key innovations may be warranted.

A conceptual framework of evolutionary novelty and innovation

Since 1990 the recognition of deep homologies among metazoan developmental processes and the spread of more mechanistic approaches to developmental biology have led to a resurgence of interest in evolutionary novelty and innovation. Other evolutionary biologists have proposed central roles for behaviour and phenotypic plasticity in generating the conditions for the construction of novel morphologies, or invoked the accessibility of new regions of vast sequence spaces. These approaches contrast with more traditional emphasis on the exploitation of ecological opportunities as the primary source of novelty. This definitional cornucopia reflects differing stress placed on three attributes of novelties: their radical nature, the generation of new taxa, and ecological and evolutionary impact. Such different emphasis has led to conflating four distinct issues: the origin of novel attributes (genes, developmental processes, phenotypic characters), new functions, higher clades and the ecological impact of new structures and functions. Here I distinguish novelty (the origin of new characters, deep character transformations, or new combinations) from innovation, the ecological and evolutionary success of clades. Evidence from the fossil record of macroevolutionary lags between the origin of a novelty and its ecological success demonstrates that novelty may be decoupled from innovation, and only definitions of novelty based on radicality (rather than generativity or consequentiality) can be assessed without reference to the subsequent history of the clade to which a novelty belongs. These considerations suggest a conceptual framework for novelty and innovation, involving: (i) generation of the potential for novelty; (ii) the formation of novel attributes; (iii) refinement of novelties through adaptation; (iv) exploitation of novelties by a clade, which may coincide with a new round of ecological or environmental potentiation; followed by (v) the establishment of innovations through ecological processes. This framework recognizes that there is little empirical support for either the dominance of ecological opportunity, nor abrupt discontinuities (often caricatured as 'hopeful monsters'). This general framework may be extended to aspects of cultural and social innovation.

A peacock bass (Cichla) functional novelty relaxes a constraint imposed by the classic cichlid pharyngeal jaw innovation

Innovations may provide access to new resources but often result in significant trade-offs. Pharyngognathy is a classic pharyngeal jaw innovation in which the left and right lower pharyngeal jaw (LPJ) bones are united into a single structure, producing a strong bite but reduced gape. Throughout cichlids, pharyngeal suturing occurs along the entire medial border between LPJ bones, except in peacock bass (Cichla), where these bones are connected by ligaments only in their anterior region. We show that this limited attachment permits the jaw bones to spread apart and we link this feature to an increase in pharyngeal gape that is comparable to non-pharyngognathous species. The capacity of the LPJ bones to spread apart is strongest in juveniles and is mostly lost during development. Juvenile Cichla exhibit size-specific pharyngeal gape similar to non-pharyngognathous percomorphs; however, adults exhibit pharyngeal gape on par with other predatory cichlids. Relaxation of pharyngeal suturing offsets a major deleterious consequence of pharyngognathy by reducing gape limitation and we propose this may accelerate the ontogenetic transition to piscivory. Partial reversal of the classic cichlid pharyngeal jaw innovation highlights the functional trade-offs that often accompany innovations and may be a major cause of variation in their macroevolutionary consequences.

The Prevalence and Impact of Model Violations in Phylogenetic Analysis

In phylogenetic inference, we commonly use models of substitution which assume that sequence evolution is stationary, reversible, and homogeneous (SRH). Although the use of such models is often criticized, the extent of SRH violations and their effects on phylogenetic inference of tree topologies and edge lengths are not well understood. Here, we introduce and apply the maximal matched-pairs tests of homogeneity to assess the scale and impact of SRH model violations on 3,572 partitions from 35 published phylogenetic data sets. We show that roughly one-quarter of all the partitions we analyzed (23.5%) reject the SRH assumptions, and that for 25% of data sets, tree topologies inferred from all partitions differ significantly from topologies inferred using the subset of partitions that do not reject the SRH assumptions. This proportion increases when comparing trees inferred using the subset of partitions that rejects the SRH assumptions, to those inferred from partitions that do not reject the SRH assumptions. These results suggest that the extent and effects of model violation in phylogenetics may be substantial. They highlight the importance of testing for model violations and possibly excluding partitions that violate models prior to tree reconstruction. Our results also suggest that further effort in developing models that do not require SRH assumptions could lead to large improvements in the accuracy of phylogenomic inference. The scripts necessary to perform the analysis are available in https://github.com/roblanf/SRHtests, and the new tests we describe are available as a new option in IQ-TREE (http://www.iqtree.org).

The Future is Bright for Evolutionary Morphology and Biomechanics in the Era of Big Data

In recent years, the fields of evolutionary biomechanics and morphology have developed into a deeply quantitative and integrative science, resulting in a much richer understanding of how structural relationships shape macroevolutionary patterns. This issue highlights new research at the conceptual and experimental cutting edge, with a special focus on applying big data approaches to classic questions in form-function evolution. As this issue illustrates, new technologies and analytical tools are facilitating the integration of biomechanics, functional morphology, and phylogenetic comparative methods to catalyze a new, more integrative discipline. Although we are at the cusp of the big data generation of organismal biology, the field is nonetheless still data-limited. This data bottleneck is primarily due to the rate-limiting steps of digitizing specimens, recording and tracking organismal movements, and extracting patterns from massive datasets. Automation and machine-learning approaches hold great promise to help data generation keep pace with ideas. As a final and important note, almost all the research presented in this issue relied on specimens-totaling the tens of thousands-provided by museum collections. Without collection, curation, and conservation of museum specimens, the future of the field is much less bright.

Vision using multiple distinct rod opsins in deep-sea fishes

Vertebrate vision is accomplished through light-sensitive photopigments consisting of an opsin protein bound to a chromophore. In dim light, vertebrates generally rely on a single rod opsin [rhodopsin 1 (RH1)] for obtaining visual information. By inspecting 101 fish genomes, we found that three deep-sea teleost lineages have independently expanded their RH1 gene repertoires. Among these, the silver spinyfin (Diretmus argenteus) stands out as having the highest number of visual opsins in vertebrates (two cone opsins and 38 rod opsins). Spinyfins express up to 14 RH1s (including the most blueshifted rod photopigments known), which cover the range of the residual daylight as well as the bioluminescence spectrum present in the deep sea. Our findings present molecular and functional evidence for the recurrent evolution of multiple rod opsin-based vision in vertebrates.

Head Shape Modulates Diversification of a Classic Cichlid Pharyngeal Jaw Innovation

Functional innovations are often invoked to explain the uneven distribution of ecological diversity. Innovations may provide access to new adaptive zones by expanding available ecological opportunities and may serve as catalysts of adaptive radiation. However, diversity is often unevenly distributed within clades that share a key innovation, highlighting the possibility that the impact of the innovation is mediated by other traits. Pharyngognathy is a widely recognized innovation of the pharyngeal jaws that enhances the ability to process hard and tough prey in several major radiations of fishes, including marine wrasses and freshwater cichlids. We explored diversification of lower pharyngeal jaw shape, a key feature of pharyngognathy, and the extent to which it is influenced by head shape in Neotropical cichlids. While pharyngeal jaw shape was unaffected by either head length or head depth, its disparity declined dramatically with increasing head width. Head width also predicted the rate of pharyngeal jaw evolution such that higher rates were associated with narrow heads. Wide heads are associated with exploiting prey that require intense processing by pharyngeal jaws that have expanded surfaces for the attachment of enlarged muscles. However, we show that a wide head constrains access to adaptive peaks associated with several trophic roles. A constraint on the independent evolution of pharyngeal jaw and head shape may explain the uneven distribution of ecological diversity within a clade that shares a major functional innovation.

Functional implications of dentition-based morphotypes in piscivorous fishes

Teeth are crucial in elucidating the life history of vertebrates. However, most studies of teeth have focused on mammals. In heterodont mammals, tooth function is based on tooth shape and position along the jaw. However, the vast majority of vertebrates are homodont, and tooth function might not be based on the same principles (in homodonts, tooth shape is broadly similar along the jaw). We provide a quantitative framework and establish dentition-based morphotypes for piscivorous fishes. We then assess how these morphotypes relate to key functional feeding traits. We identified three broad morphotypes: edentulate, villiform and macrodont, with edentulate and villiform species displaying considerable functional overlap; macrodont species are more distinct. When analysing macrodonts exclusively, we found a major axis of variation between 'front-fanged' and 'back-fanged' species. The functional interpretations of this axis suggest that tooth-based functional decoupling could exist, even in homodont vertebrates, where teeth have similar shapes. This diversity is based not only on tooth shape but also solely on the position along the jaw.

The paleoichthyofauna housed in the Colección Nacional de Paleontología of Universidad Nacional Autónoma de México

Fishes are a paraphyletic group composed by craniates except for the four-limbed clade Tetrapoda. This group was the only vertebrate representative until the Devonian but now comprises almost half of the vertebrate species, dominating nearly all aquatic environments. The fossil record is the key to understand the ancient paleobiodiversity and the patterns that lead the modern fish fauna, and paleontological collections play a fundamental role in providing accommodation, maintenance, and access to the specimens and their respective metadata. Here we present a systematic checklist of fossil fishes housed in the type collection of the Colección Nacional de Paleontología which is located at the Instituto de Geología of Universidad Nacional Autónoma de México. Currently housed in the type collection are 14 chondrichthyan specimens, belonging to two superorders, five orders, seven families, 10 genera, and five nominal species, and 361 osteichthyan specimens, belonging to eight orders, nine families, nine genera, and 26 nominal species. These fossils come from 32 localities and 15 geological units, which range temporally from the Jurassic to the Pleistocene. The paleoichthyofauna housed in the type collection of the Colección Nacional de Paleontología is remarkable for its singularity and reveals new insights about the origin and diversification of many groups of fishes. The recovery and curation of this fossil material indicates that knowledge of Mexican fossil fish diversity and its role in understanding lower vertebrate evolution are just emerging and reaffirms the importance of the biological and paleontological collections to the future biodiversity research.

New fossil cichlid from the middle Miocene of East Africa revealed as oldest known member of the Oreochromini

A new genus and species of fossil cichlid fishes of middle Miocene age (12.5 Ma) is described from the Ngorora fish Lagerstätte (Tugen Hills, Kenya) in the East African Rift Valley. Parsimony analysis of morphological characters using published phylogenetic frameworks for extant cichlids combined with the application of a comprehensive best-fit approach based on morphology was employed to place the new fossil taxon in the phylogenetic context of the African cichlids. The data reveal that the fossil specimens can be assigned to the tribe Oreochromini within the haplotilapiines. †Oreochromimos kabchorensis gen. et sp. nov. shows a mosaic set of characters bearing many similarities to the almost pan-African Oreochromis and the East African lake-endemic Alcolapia. As the striking diversity of present-day African cichlids, with 1100 recognised species, has remained largely invisible in the fossil record, the material described here adds significantly to our knowledge of the Miocene diversity of the group. It effectively doubles the age of a fossil calibration point, which has hitherto been used to calibrate divergence times of the East African cichlids in molecular phylogenetic investigations. Furthermore, the comparative dataset derived from extant cichlids presented here will greatly facilitate the classification of fossil cichlids in future studies.

Do Coral Reefs Promote Morphological Diversification? Exploration of Habitat Effects on Labrid Pharyngeal Jaw Evolution in the Era of Big Data

Coral reefs are complex marine habitats that have been hypothesized to facilitate functional specialization and increased rates of functional and morphological evolution. Wrasses (Labridae: Percomorpha) in particular, have diversified extensively in these coral reef environments and have evolved adaptations to further exploit reef-specific resources. Prior studies have found that reef-dwelling wrasses exhibit higher rates of functional evolution, leading to higher functional variation than in non-reef dwelling wrasses. Here, we examine this hypothesis in the lower pharyngeal tooth plate of 134 species of reef and non-reef-associated labrid fishes using high-resolution morphological data in the form of micro-computed tomography scans and employing three-dimensional geometric morphometrics to quantify shape differences. We find that reef-dwelling wrasses do not differ from non-reef-associated wrasses in morphological disparity or rates of shape evolution. However, we find that some reef-associated species (e.g., parrotfishes and tubelips) exhibit elevated rates of pharyngeal jaw shape evolution and have colonized unique regions of morphospace. These results suggest that while coral reef association may provide the opportunity for specialization and morphological diversification, species must still be able to capitalize on the ecological opportunities to invade novel niche space, and that these novel invasions may prompt rapid rates of morphological evolution in the associated traits that allow them to capitalize on new resources.

The Role of Developmental Integration and Historical Contingency in the Origin and Evolution of Cypriniform Trophic Novelties

While functional morphologists have long studied the evolution of anatomical structures, the origin of morphological novelties has received less attention. When such novelties first originate they must become incorporated into an integrated system to be rendered fully functional. Thus, developmental integration is key at the origin of morphological novelties. However, given enough evolutionary time such integration may be broken, allowing for a division of labor that is facilitated by subsequent decoupling of structures. Cypriniformes represent a diverse group of freshwater fishes characterized by several trophic novelties that include: kinethmoid-mediated premaxillary protrusion, a muscular palatal and post-lingual organ, hypertrophied lower pharyngeal jaws that masticate against the base of the neurocranium, novel pharyngeal musculature controlling movement of the hypertrophied lower pharyngeal jaws, and in a few species an incredibly complex epibranchial organ used to aggregate filtered phytoplankton. Here, we use the wealth of such trophic novelties in different cypriniform fishes to present case studies in which developmental integration allowed for the origin of morphological innovations. As proposed in case studies 1 and 2 trophic innovations may be associated with both morphological and lineage diversification. Alternatively, case studies 3 and 4 represent a situation where ecological niche was expanded but with no concomitant increase in species diversity.

Tempo and mode of mandibular shape and size evolution reveal mixed support for incumbency effects in two clades of island-endemic rodents (Muridae: Murinae)

Existing radiations in a spatially limited system such as an oceanic island may limit the ecological opportunity experienced by later colonists, resulting in lower macroevolutionary rates for secondary radiations. Additionally, potential colonists may be competitively excluded by these incumbent (resident) species, unless they are biologically distinct (biotic filtering). The extant phenotypic diversity of secondary colonists may thus be impacted by lower rates of phenotypic evolution, exclusion from certain phenotypes, and transitions to new morphotypes to escape competition from incumbent lineages. We used geometric morphometric methods to test whether the rates and patterns of mandibular evolution of the Luzon "old endemic" rodent clades, Phloeomyini and Chrotomyini, are consistent with these predictions. Each clade occupied nearly completely separate shape space and partially separate size space. We detected limited support for decelerating and clade-specific evolutionary rates for both shape and size, with strong evidence for a shift in evolutionary mode within Chrotomyini. Our results suggest that decelerating phenotypic evolutionary rates are not a necessary result of incumbency interactions; rather, incumbency effects may be more likely to determine which clades can become established in the system. Nonincumbent clades that pass a biotic filter can potentially exhibit relatively unfettered evolution.