An exceptionally preserved Late Devonian actinopterygian provides a new model for primitive cranial anatomy in ray-finned fishes

The early diversification of ray-finned fishes (Actinopterygii): hypotheses, challenges and future prospects

Actinopterygii makes up half of living vertebrate diversity, and study of fossil members during their Palaeozoic rise to dominance has a long history of descriptive work. Although research interest into Palaeozoic actinopterygians has increased in recent years, broader patterns of diversity and diversity dynamics remain critically understudied. Past studies have investigated macroevolutionary trends in Palaeozoic actinopterygians in a piecemeal fashion, variably using existing compendia of vertebrates or literature-based searches. Here, we present a comprehensive occurrence-based dataset of actinopterygians spanning the whole of the Palaeozoic. We use this to produce the first through-Palaeozoic trends in genus and species counts for Actinopterygii. Diversity through time generally tracks metrics for sampling, while major taxonomic problems pervading the Palaeozoic actinopterygian record obscure diversity trends. Many described species are concentrated in several particularly problematic 'waste-basket' genera, hiding considerable morphological and taxonomic diversity. This taxonomic confusion also feeds into a limited understanding of phylogenetic relationships. A heavy sampling bias towards Europe and North America exists in both occurrence databases and available phylogenetic matrices, with other regions underrepresented despite yielding important data. Scrutiny of the extent to which spatial biases influence the actinopterygian record is lacking, as is research on other forms of bias. Low richness in some time periods may be linked to geological biases, while the effects of taphonomic biases on Palaeozoic actinopterygians have not yet been investigated. Efforts are already underway both to redescribe poorly defined taxa and to describe taxa from underrepresented regions, helping to address taxonomic issues and accuracy of occurrence data. New methods of sampling standardisation utilising up-to-date occurrence databases will be critical in teasing apart biological changes in diversity and those resulting from bias. Lastly, continued phylogenetic work will enable the use of phylogenetic comparative methods to elucidate the origins of actinopterygian biogeography and subsequent patterns of radiation throughout their rise to dominate aquatic faunas.

Fitting fangs in a finite face: A novel fang accommodation strategy in a 280-million-year-old ray-finned fish

Though Paleozoic ray-finned fishes are considered to be morphologically conservative, we report a novel mode of fang accommodation (i.e., the fitting of fangs inside the jaw) in the Permian actinopterygian †Brazilichthys macrognathus, whereby the teeth of the lower jaw insert into fenestrae of the upper jaw. To better understand how fishes have accommodated lower jaw fangs through geologic time, we synthesize the multitude of ways living and extinct osteichthyans have housed large mandibular dentition. While the precise structure of fang accommodation seen in †Brazilichthys has not been reported in any other osteichthyans, alternate strategies of upper jaw fenestration to fit mandibular fangs are present in some extant ray-finned fishes-the needlejaws Acestrorhynchus and the gars of the genus Lepisosteus. Notably, out of our survey, only the two aforementioned neopterygians bear upper jaw fenestration for the accommodation of mandibular fangs. We implicate the kinetic jaws of neopterygians in this trend, whereby large mandibular fangs are more easily fit between the multitude of upper jaw and palatal bones. The restricted space available in early osteichthyan jaws may have led to a proliferation of novel ways to accommodate large dentition. We recommend a greater survey of Paleozoic actinopterygian jaw morphology, in light of these results and other recent reevaluations of jaw structure in early fossil ray-fins.

A Permian fish reveals widespread distribution of neopterygian-like jaw suspension

The actinopterygian crown group (comprising all living ray-finned fishes) originated by the end of the Carboniferous. However, most late Paleozoic taxa are stem actinopterygians, and broadly resemble stratigraphically older taxa. The early Permian †Brachydegma caelatum is notable for its three-dimensional preservation and past phylogenetic interpretations as a nested member of the neopterygian crown. Here, we use computed microtomography to redescribe †Brachydegma, uncovering an unanticipated combination of primitive (e.g., aortic canal; immobile maxilla) and derived (e.g., differentiated occipital ossifications; posterior stem of parasphenoid; two accessory hyoidean ossifications; double jaw joint) dermal and endoskeletal features relative to most other Paleozoic actinopterygians. Some of these features were previously thought to be restricted to the neopterygian crown. The precise phylogenetic position of †Brachydegma is unclear, with placements either on the polypterid stem, or as an early-diverging stem neopterygian. However, our analyses decisively reject previous placements of †Brachydegma in the neopterygian crown. Critically, we demonstrate that key-endoskeletal components of the hyoid portion of the suspensorium of crown neopterygians appeared deeper in the tree than previously thought.

The rapid evolution of lungfish durophagy

Innovations relating to the consumption of hard prey are implicated in ecological shifts in marine ecosystems as early as the mid-Paleozoic. Lungfishes represent the first and longest-ranging lineage of durophagous vertebrates, but how and when the various feeding specializations of this group arose remain unclear. Two exceptionally preserved fossils of the Early Devonian lobe-finned fish Youngolepis reveal the origin of the specialized lungfish feeding mechanism. Youngolepis has a radically restructured palate, reorienting jaw muscles for optimal force transition, coupled with radiating entopterygoid tooth rows like those of lungfish toothplates. This triturating surface occurs in conjunction with marginal dentition and blunt coronoid fangs, suggesting a role in crushing rather than piercing prey. Bayesian tip-dating analyses incorporating these morphological data indicate that the complete suite of lungfish feeding specializations may have arisen in as little as 7 million years, representing one of the most striking episodes of innovation during the initial evolutionary radiations of bony fishes.

It is unclear how Lungfishes evolved durophagy, the consumption of hard prey, despite being the longest lineage of vertebrates with this feeding mechanism. Here, the authors describe exceptionally preserved fossils of Youngolepis from the Early Devonian, showing early adaptations to durophagy.

A Bayesian approach to dynamic homology of morphological characters and the ancestral phenotype of jawed vertebrates

Phylogenetic analysis of morphological data proceeds from a fixed set of primary homology statements, the character-by-taxon matrix. However, there are cases where multiple conflicting homology statements can be justified from comparative anatomy. The upper jaw bones of placoderms have traditionally been considered homologous to the palatal vomer-dermopalatine series of osteichthyans. The discovery of 'maxillate' placoderms led to the alternative hypothesis that 'core' placoderm jaw bones are premaxillae and maxillae lacking external (facial) laminae. We introduce a BEAST2 package for simultaneous inference of homology and phylogeny, and find strong evidence for the latter hypothesis. Phenetic analysis of reconstructed ancestors suggests that maxillate placoderms are the most plesiomorphic known gnathostomes, and the shared cranial architecture of arthrodire placoderms, maxillate placoderms and osteichthyans is inherited. We suggest that the gnathostome ancestor possessed maxillae and premaxillae with facial and palatal laminae, and that these bones underwent divergent evolutionary trajectories in placoderms and osteichthyans.

Tanyrhinichthys mcallisteri, a long-rostrumed Pennsylvanian ray-finned fish (Actinopterygii) and the simultaneous appearance of novel ecomorphologies in Late Palaeozoic fishes

The Carboniferous radiation of fishes was marked by the convergent appearance of then-novel but now common ecomorphologies resulting from changes in the relative proportions of traits, including elongation of the front of the skull (rostrum). The earliest ray-finned fishes (Actinopterygii) with elongate rostra are poorly known, obscuring the earliest appearances of a now widespread feature in actinopterygians. We redescribe Tanyrhinichthys mcallisteri, a long-rostrumed actinopterygian from the Upper Pennsylvanian (Missourian) of the Kinney Brick Quarry, New Mexico. Tanyrhinichthys has a lengthened rostrum bearing a sensory canal, ventrally inserted paired fins, posteriorly placed median fins unequal in size and shape, and a heterocercal caudal fin. Tanyrhinichthys shares these features with sturgeons, but lacks chondrostean synapomorphies, indicating convergence on a bottom-feeding lifestyle. Elongate rostra evolved independently in two lineages of bottom-dwelling, freshwater actinopterygians in the Late Pennsylvanian of Euramerica, as well as in at least one North American chondrichthyan (Bandringa rayi). The near-simultaneous appearance of novel ecomorphologies among multiple, distantly related lineages of actinopterygians and chondrichthyans was common during the Carboniferous radiation of fishes. This may reflect global shifts in marine and freshwater ecosystems and environments during the Carboniferous favouring such ecomorphologies, or it may have been contingent on the plasticity of early actinopterygians and chondrichthyans.

Resolving homology in the face of shifting germ layer origins: Lessons from a major skull vault boundary

The vertebrate skull varies widely in shape, accommodating diverse strategies of feeding and predation. The braincase is composed of several flat bones that meet at flexible joints called sutures. Nearly all vertebrates have a prominent 'coronal' suture that separates the front and back of the skull. This suture can develop entirely within mesoderm-derived tissue, neural crest-derived tissue, or at the boundary of the two. Recent paleontological findings and genetic insights in non-mammalian model organisms serve to revise fundamental knowledge on the development and evolution of this suture. Growing evidence supports a decoupling of the germ layer origins of the mesenchyme that forms the calvarial bones from inductive signaling that establishes discrete bone centers. Changes in these relationships facilitate skull evolution and may create susceptibility to disease. These concepts provide a general framework for approaching issues of homology in cases where germ layer origins have shifted during evolution.

The pharynx of the stem-chondrichthyan Ptomacanthus and the early evolution of the gnathostome gill skeleton

The gill apparatus of gnathostomes (jawed vertebrates) is fundamental to feeding and ventilation and a focal point of classic hypotheses on the origin of jaws and paired appendages. The gill skeletons of chondrichthyans (sharks, batoids, chimaeras) have often been assumed to reflect ancestral states. However, only a handful of early chondrichthyan gill skeletons are known and palaeontological work is increasingly challenging other pre-supposed shark-like aspects of ancestral gnathostomes. Here we use computed tomography scanning to image the three-dimensionally preserved branchial apparatus in Ptomacanthus, a 415 million year old stem-chondrichthyan. Ptomacanthus had an osteichthyan-like compact pharynx with a bony operculum helping constrain the origin of an elongate elasmobranch-like pharynx to the chondrichthyan stem-group, rather than it representing an ancestral condition of the crown-group. A mixture of chondrichthyan-like and plesiomorphic pharyngeal patterning in Ptomacanthus challenges the idea that the ancestral gnathostome pharynx conformed to a morphologically complete ancestral type.

Our understanding of the origin of jaws is hampered by the poor fossil preservation of pharyngeal morphology. Here, Dearden et al. provide insight into the skull conditions of early jawed vertebrates through three-dimensional computed tomography imaging of a 415 million year old stem-chondrichthyan.

Internal cranial anatomy of Early Triassic species of †Saurichthys (Actinopterygii: †Saurichthyiformes): implications for the phylogenetic placement of †saurichthyiforms

BACKGROUND

†Saurichthyiformes were a successful group of latest Permian-Middle Jurassic predatory actinopterygian fishes and constituted important, widely-distributed components of Triassic marine and freshwater faunas. Their systematic affinities have long been debated, with †saurichthyiforms often being aligned with chondrosteans, a group today comprising sturgeons and paddlefishes. However, their character-rich endocranial anatomy has not been investigated in detail since the first half of the 20th century. Since then, major advances have occurred in terms of our understanding of early actinopterygian anatomy, as well as techniques for extracting morphological data from fossils.

RESULTS

We used μCT to study the internal cranial anatomy of two of the stratigraphically oldest representatives of †Saurichthys, from the Early Triassic of East Greenland and Nepal. Our work revealed numerous previously unknown characters (e.g., cryptic oticooccipital fissure; intramural diverticula of braincase; nasobasal canals; lateral cranial canal; fused dermohyal), and permitted the reevalution of features relating to the structure of cranial fossae, basicranial circulation and opercular anatomy of the genus. Critically, we reinterpret the former †saurichthyiform opercle as an expanded subopercle. For comparison, we also produced the first digital models of a braincase and endocast of a sturgeon (A. brevirostrum). New information from these taxa was included in a broad phylogenetic analysis of Actinopterygii. †Saurichthyiforms are resolved as close relatives of †Birgeria, forming a clade that constitutes the immediate sister group of crown actinopterygians. However, these and other divergences near the actinopterygian crown node are weakly supported.

CONCLUSIONS

Our phylogeny disagrees with the historically prevalent hypothesis favoring the chondrostean affinities of †saurichthyiforms. Previously-proposed synapomorphies uniting the two clades, such as the closure of the oticooccipital fissure, the posterior extension of the parasphenoid, and the absence of an opercular process, are all widespread amongst actinopterygians. Others, like those relating to basicranial circulation, are found to be based on erroneous interpretations. Our work renders the †saurichthyiform character complex adequately understood, and permits detailed comparisons with other stem and crown actinopterygians. Our phylogenetic scheme highlights outstanding questions concerning the affinity of many early actinopterygians, such as the Paleozoic-early Mesozoic deep-bodied forms, which are largely caused by lack of endoskeletal data.

The cranial endocast of the Upper Devonian dipnoan 'Chirodipterus' australis

One of the first endocasts of a dipnoan (lungfish) to be realised was that of the Upper Devonian taxon Chirodipterus australis. This early interpretation was based on observations of the shape of the cranial cavity alone and was not based on a natural cast or ‘steinkern’ nor from serial sectioning. The validity of this reconstruction is therefore questionable and continued reference to and use of this interpretation in analyses of sarcopterygian cranial evolution runs the risk of propagation of error. Here we present a new detailed anatomical description of the endocast of ‘Chirodipterus’ australis from the Upper Devonian Gogo Formation of Western Australia, known for exceptional 3D preservation which enables fine-scale scrutiny of endocranial anatomy. We show that it exhibits a suite of characters more typical of Lower and Middle Devonian dipnoan taxa. Notably, the small utricular recess is unexpected for a taxon of this age, whereas the ventral expansion of the telencephalon is more typical of more derived taxa. The presence of such ’primitive’ characters in ‘C.’ australis supports its relatively basal position as demonstrated in the most recent phylogenies of Devonian Dipnoi.

Neurocranial anatomy of an enigmatic Early Devonian fish sheds light on early osteichthyan evolution

The skull of 'Ligulalepis' from the Early Devonian of Australia (AM-F101607) has significantly expanded our knowledge of early osteichthyan anatomy, but its phylogenetic position has remained uncertain. We herein describe a second skull of 'Ligulalepis' and present micro-CT data on both specimens to reveal novel anatomical features, including cranial endocasts. Several features previously considered to link 'Ligulalepis' with actinopterygians are now considered generalized osteichthyan characters or of uncertain polarity. The presence of a lateral cranial canal is shown to be variable in its development between specimens. Other notable new features include the presence of a pineal foramen, the some detail of skull roof sutures, the shape of the nasal capsules, a placoderm-like hypophysial vein, and a chondrichthyan-like labyrinth system. New phylogenetic analyses place 'Ligulalepis' as a stem osteichthyan, specifically as the sister taxon to 'psarolepids' plus crown osteichthyans. The precise position of 'psarolepids' differs between parsimony and Bayesian analyses.

A primitive actinopterygian braincase from the Tournaisian of Nova Scotia

The vertebrate fossil record of the earliest Carboniferous is notoriously poorly sampled, obscuring a critical interval in vertebrate evolution and diversity. Recent studies of diversity across the Devonian-Carboniferous boundary have proposed a vertebrate mass extinction at the end-Devonian, and recent phylogenies suggest that the origin of the actinopterygian crown may have occurred in the earliest Carboniferous, as part of a broader recovery fauna. However, the data necessary to test this are limited. Here, we describe a partial actinopterygian skull, including diagnostic elements of the posterior braincase, from the Tournaisian Horton Bluff Formation of Blue Beach, Nova Scotia. The braincase surprisingly shows a confluence of characters common in Devonian taxa but absent in Mississippian forms, such as an open spiracular groove; lateral dorsal aortae that pass through open broadly separated, parallel grooves in the ventral otoccipital region, posterior to the articulation of the first infrapharyngobranchial and an intertemporal-supratemporal complex. Phylogenetic analysis places it deep within the actinopterygian stem, among Devonian moythomasiids and mimiids, suggesting more phylogenetically inclusive survivorship of stem group actinopterygians across the end-Devonian mass extinction. With a high lineage survivorship in tetrapods and lungfish across the Devonian-Carboniferous boundary and high vertebrate diversity at Tournaisian localities, this hints at a more gradual turnover between Devonian and Carboniferous vertebrate faunas.

Early members of 'living fossil' lineage imply later origin of modern ray-finned fishes

Modern ray-finned fishes (Actinopterygii) comprise half of extant vertebrate species and are widely thought to have originated before or near the end of the Middle Devonian epoch (around 385 million years ago). Polypterids (bichirs and ropefish) represent the earliest-diverging lineage of living actinopterygians, with almost all Palaeozoic taxa interpreted as more closely related to other extant actinopterygians than to polypterids. By contrast, the earliest material assigned to the polypterid lineage is mid-Cretaceous in age (around 100 million years old), implying a quarter-of-a-billion-year palaeontological gap. Here we show that scanilepiforms, a widely distributed radiation from the Triassic period (around 252-201 million years ago), are stem polypterids. Importantly, these fossils break the long polypterid branch and expose many supposedly primitive features of extant polypterids as reversals. This shifts numerous Palaeozoic ray-fins to the actinopterygian stem, reducing the minimum age for the crown lineage by roughly 45 million years. Recalibration of molecular clocks to exclude phylogenetically reassigned Palaeozoic taxa results in estimates that the actinopterygian crown lineage is about 20-40 million years younger than was indicated by previous molecular analyses. These new dates are broadly consistent with our revised palaeontological timescale and coincident with an interval of conspicuous morphological and taxonomic diversification among ray-fins centred on the Devonian-Carboniferous boundary. A shifting timescale, combined with ambiguity in the relationships of late Palaeozoic actinopterygians, highlights this part of the fossil record as a major frontier in understanding the evolutionary assembly of modern vertebrate diversity.

Fin modules: an evolutionary perspective on appendage disparity in basal vertebrates

BACKGROUND

Fishes are extremely speciose and also highly disparate in their fin configurations, more specifically in the number of fins present as well as their structure, shape, and size. How they achieved this remarkable disparity is difficult to explain in the absence of any comprehensive overview of the evolutionary history of fish appendages. Fin modularity could provide an explanation for both the observed disparity in fin configurations and the sequential appearance of new fins. Modularity is considered as an important prerequisite for the evolvability of living systems, enabling individual modules to be optimized without interfering with others. Similarities in developmental patterns between some of the fins already suggest that they form developmental modules during ontogeny. At a macroevolutionary scale, these developmental modules could act as evolutionary units of change and contribute to the disparity in fin configurations. This study addresses fin disparity in a phylogenetic perspective, while focusing on the presence/absence and number of each of the median and paired fins.

RESULTS

Patterns of fin morphological disparity were assessed by mapping fin characters on a new phylogenetic supertree of fish orders. Among agnathans, disparity in fin configurations results from the sequential appearance of novel fins forming various combinations. Both median and paired fins would have appeared first as elongated ribbon-like structures, which were the precursors for more constricted appendages. Among chondrichthyans, disparity in fin configurations relates mostly to median fin losses. Among actinopterygians, fin disparity involves fin losses, the addition of novel fins (e.g., the adipose fin), and coordinated duplications of the dorsal and anal fins. Furthermore, some pairs of fins, notably the dorsal/anal and pectoral/pelvic fins, show non-independence in their character distribution, supporting expectations based on developmental and morphological evidence that these fin pairs form evolutionary modules.

CONCLUSIONS

Our results suggest that the pectoral/pelvic fins and the dorsal/anal fins form two distinct evolutionary modules, and that the latter is nested within a more inclusive median fins module. Because the modularity hypotheses that we are testing are also supported by developmental and variational data, this constitutes a striking example linking developmental, variational, and evolutionary modules.

The cranial endocast of Dipnorhynchus sussmilchi (Sarcopterygii: Dipnoi) and the interrelationships of stem-group lungfishes

The first virtual cranial endocast of a lungfish from the Early Devonian, Dipnorhynchus sussmilchi, is described. Dipnorhynchus, only the fourth Devonian lungfish for which a near complete cranial endocast is known, is a key taxon for clarifying primitive character states within the group. A ventrally-expanded telencephalic cavity is present in the endocast of Dipnorhynchus demonstrating that this is the primitive state for “true” Dipnoi. Dipnorhynchus also possesses a utricular recess differentiated from the sacculolagenar pouch like that seen in stratigraphically younger lungfish (Dipterus, Chirodipterus, Rhinodipterus), but absent from the dipnomorph Youngolepis. We do not find separate pineal and para-pineal canals in contrast to a reconstruction from previous authors. We conduct the first phylogenetic analysis of Dipnoi based purely on endocast characters, which supports a basal placement of Dipnorhynchus within the dipnoan stem group, in agreement with recent analyses. Our analysis demonstrates the value of endocast characters for inferring phylogenetic relationships.

A new method for reconstructing brain morphology: applying the brain-neurocranial spatial relationship in an extant lungfish to a fossil endocast

Lungfish first appeared in the geological record over 410 million years ago and are the closest living group of fish to the tetrapods. Palaeoneurological investigations into the group show that unlike numerous other fishes-but more similar to those in tetrapods-lungfish appear to have had a close fit between the brain and the cranial cavity that housed it. As such, researchers can use the endocast of fossil taxa (an internal cast of the cranial cavity) both as a source of morphological data but also to aid in developing functional and phylogenetic implications about the group. Using fossil endocast data from a three-dimensional-preserved Late Devonian lungfish from the Gogo Formation, Rhinodipterus, and the brain-neurocranial relationship in the extant Australian lungfish, Neoceratodus, we herein present the first virtually reconstructed brain of a fossil lungfish. Computed tomographic data and a newly developed 'brain-warping' method are used in conjunction with our own distance map software tool to both analyse and present the data. The brain reconstruction is adequate, but we envisage that its accuracy and wider application in other taxonomic groups will grow with increasing availability of tomographic datasets.

Bony labyrinth morphology in early neopterygian fishes (Actinopterygii: Neopterygii)

Endocasts of the osseous labyrinth have the potential to yield information about both phylogenetic relationships and ecology. Although bony labyrinth morphology is well documented in many groups of fossil vertebrates, little is known for early Neopterygii, the major fish radiation containing living teleosts, gars and the bowfin. Here, we reconstruct endocasts of the bony labyrinth and associated structures for a sample of Mesozoic neopterygian fishes using high-resolution computed tomography. Our sample includes taxa unambiguously assigned to either the teleost (Dorsetichthys, "Pholidophorus," Elopoides) and holostean ("Aspidorynchus," "Caturus," Heterolepidotus) total-groups, as well as examples of less certain phylogenetic position (an unnamed parasemionotid and Dapedium). Our models provide a test of anatomical interpretations for forms where bony labyrinths were reconstructed based on destructive tomography ("Caturus") or inspection of the lateral wall of the cranial chamber (Dorsetichthys), and deliver the first detailed insights on inner ear morphology in the remaining taxa. With respect to relationships, traits apparent in the bony labyrinth and associated structures broadly support past phylogenetic hypotheses concerning taxa agreed to have reasonably secure systematic placements. Inner ear morphology supports placement of Dapedium with holosteans rather than teleosts, while preserved structure in the unnamed parasemionotid is generalized to the degree that it provides no evidence of close affinity with either of the crown neopterygian lineages. This study provides proof-of-concept for the systematic utility of the inner ear in neopterygians that, in combination with similar findings for earlier-diverging actinopterygian lineages, points to the substantial potential of this anatomical system for addressing the longstanding questions in the relationships of fossil ray-finned fishes to one another and living groups. J. Morphol. 279:426-440, 2018. © 2016 Wiley Periodicals, Inc.