Multiple embryonic sources converge to form the pectoral girdle skeleton in zebrafish

The morphological transformation of the pectoral/shoulder girdle is fundamental to the water-to-land transition in vertebrate evolution. Although previous studies have resolved the embryonic origins of tetrapod shoulder girdles, those of fish pectoral girdles remain uncharacterized, creating a gap in the understanding of girdle transformation mechanisms from fish to tetrapods. Here, we identify the embryonic origins of the zebrafish pectoral girdle, including the cleithrum as an ancestral girdle element lost in extant tetrapods. Our combinatorial approach of photoconversion and genetic lineage tracing demonstrates that cleithrum development combines four adjoining embryonic populations. A comparison of these pectoral girdle progenitors with extinct and extant vertebrates highlights that cleithrum loss, indispensable for neck evolution, is associated with the disappearance of its unique developmental environment at the head/trunk interface. Overall, our study establishes an embryological framework for pectoral/shoulder girdle formation and provides evolutionary trajectories from their origin in water to diversification on land.

Soft-tissue fossilization illuminates the stepwise evolution of the ray-finned fish brain

A complex brain is central to the success of backboned animals. However, direct evidence bearing on vertebrate brain evolution comes almost exclusively from extant species, leaving substantial knowledge gaps. Although rare, soft-tissue preservation in fossils can yield unique insights on patterns of neuroanatomical evolution. Paleontological evidence from an exceptionally preserved Pennsylvanian (∼318 Ma) actinopterygian, Coccocephalus, calls into question prior interpretations of ancestral actinopterygian brain conditions. However, the ordering and timing of major evolutionary innovations, such as an everted telencephalon, modified meningeal tissues, and hypothalamic inferior lobes, remain unclear. Here, we report two distinct actinopterygian morphotypes from the latest Carboniferous-earliest Permian (∼299 Ma) of Brazil that show extensive soft-tissue preservation of brains, cranial nerves, eyes, and potential cardiovascular tissues. These fossils corroborate inferences drawn from ✝Coccocephalus, while adding new information about neuroanatomical evolution. Skeletal features indicate that one of these Brazilian morphotypes is more closely related to living actinopterygians than the other, which is also reflected in soft-tissue features. Significantly, the more crownward morphotype shows a key neuroanatomical feature of extant actinopterygians-an everted telencephalon-that is absent in the other morphotype and ✝Coccocephalus. All preserved Paleozoic actinopterygian brains show broad similarities, including an invaginated cerebellum, hypothalamus inferior lobes, and a small forebrain. In each case, preserved brains are substantially smaller than the enclosing cranial chamber. The neuroanatomical similarities shared by this grade of Permo-Carboniferous actinopterygians reflect probable primitive conditions for actinopterygians, providing a revised model for interpreting brain evolution in a major branch of the vertebrate tree of life.

The Evolution of Ultraconserved Elements in Vertebrates

Ultraconserved elements were discovered two decades ago, arbitrarily defined as sequences that are identical over a length ≥ 200 bp in the human, mouse, and rat genomes. The definition was subsequently extended to sequences ≥ 100 bp identical in at least three of five mammalian genomes (including dog and cow), and shown to have undergone rapid expansion from ancestors in fish and strong negative selection in birds and mammals. Since then, many more genomes have become available, allowing better definition and more thorough examination of ultraconserved element distribution and evolutionary history. We developed a fast and flexible analytical pipeline for identifying ultraconserved elements in multiple genomes, dedUCE, which allows manipulation of minimum length, sequence identity, and number of species with a detectable ultraconserved element according to specified parameters. We suggest an updated definition of ultraconserved elements as sequences ≥ 100 bp and ≥97% sequence identity in ≥50% of placental mammal orders (12,813 ultraconserved elements). By mapping ultraconserved elements to ∼200 species, we find that placental ultraconserved elements appeared early in vertebrate evolution, well before land colonization, suggesting that the evolutionary pressures driving ultraconserved element selection were present in aquatic environments in the Cambrian-Devonian periods. Most (>90%) ultraconserved elements likely appeared after the divergence of gnathostomes from jawless predecessors, were largely established in sequence identity by early Sarcopterygii evolution-before the divergence of lobe-finned fishes from tetrapods-and became near fixed in the amniotes. Ultraconserved elements are mainly located in the introns of protein-coding and noncoding genes involved in neurological and skeletomuscular development, enriched in regulatory elements, and dynamically expressed throughout embryonic development.

Darwin, Haeckel, and the "Mikluskan gas organ theory"

A previously unknown reference to the Russian ethnologist, biologist, and traveler Nikolai N. Miklucho-Maclay (1846-1888) was discovered in correspondence between Charles Darwin (1809-1882) and Ernst Haeckel (1834-1919). This reference has remained unknown to science, even to Miklucho-Maclay's biographers, probably because Darwin used the Russian nickname "Mikluska" when alluding to this young scientist. Here, we briefly outline the story behind the short discussion between Darwin and his German counterpart Haeckel, and highlight its importance for the history of science. Miklucho-Maclay's discovery of a putative swim bladder anlage in sharks, published in 1867, was discussed in four letters between the great biologists. Whereas, Haeckel showed enthusiasm for the finding because it supported (his view on) evolutionary theory, Darwin was less interested, which highlights the conceptual differences between the two authorities. We discuss the scientific treatment of Miklucho-Maclay's observation in the literature and discuss the homology, origin, and destiny of gas organs-swim bladders and lungs-in vertebrate evolution, from an ontogenetic point of view. We show that the conclusions reached by Miklucho-Maclay and Haeckel were rather exaggerated, although they gave rise to fundamental insights, and we illustrate how tree-thinking may lead to differences in the conceptualization of evolutionary change.

Placoderms

For over 70 million years, during the Paleozoic, the placoderms (Greek for 'plated skin'), an extinct group of armoured fishes, were the most abundant and diverse vertebrates on our planet. Some of the first placoderm fossils discovered - such as Bothriolepis with its bone-covered pectoral fins - seemed so bizarre that they were thought to represent turtles or ancient beetles. All placoderms bear thick overlapping dermal plates around the head (called the 'head shield') and an area of the body covered in similar overlapping plates enveloping the pectoral to anal region (called the 'trunk-shield'). Placoderm fossils (Figure 1) are known from every continent on Earth ranging from the early Silurian (∼438 million years ago) to the end Devonian (∼359 million years ago) when they became extinct.

Microbially mediated fossil concretions and their characterization by the latest methodologies: a review

The study of well-preserved organic matter (OM) within mineral concretions has provided key insights into depositional and environmental conditions in deep time. Concretions of varied compositions, including carbonate, phosphate, and iron-based minerals, have been found to host exceptionally preserved fossils. Organic geochemical characterization of concretion-encapsulated OM promises valuable new information of fossil preservation, paleoenvironments, and even direct taxonomic information to further illuminate the evolutionary dynamics of our planet and its biota. Full exploitation of this largely untapped geochemical archive, however, requires a sophisticated understanding of the prevalence, formation controls and OM sequestration properties of mineral concretions. Past research has led to the proposal of different models of concretion formation and OM preservation. Nevertheless, the formation mechanisms and controls on OM preservation in concretions remain poorly understood. Here we provide a detailed review of the main types of concretions and formation pathways with a focus on the role of microbes and their metabolic activities. In addition, we provide a comprehensive account of organic geochemical, and complimentary inorganic geochemical, morphological, microbial and paleontological, analytical methods, including recent advancements, relevant to the characterization of concretions and sequestered OM. The application and outcome of several early organic geochemical studies of concretion-impregnated OM are included to demonstrate how this underexploited geo-biological record can provide new insights into the Earth's evolutionary record. This paper also attempts to shed light on the current status of this research and major challenges that lie ahead in the further application of geo-paleo-microbial and organic geochemical research of concretions and their host fossils. Recent efforts to bridge the knowledge and communication gaps in this multidisciplinary research area are also discussed, with particular emphasis on research with significance for interpreting the molecular record in extraordinarily preserved fossils.

Comment on "Exceptional preservation of organs in Devonian placoderms from the Gogo lagerstätte"

Trinajstic et al., (Science, 16 September 2022, p. 1311-1314) describe exceptionally well-preserved organs in fossilized Devonian placoderms to infer the early evolution of the vertebrate heart. We argue that the report has numerous shortcomings and examples of mixed specimen codes. Further, we question whether there indeed is any evidence for a mineralized chambered heart in these placoderms.

Response to comment on "Exceptional preservation of organs in Devonian placoderms from the Gogo largerstätte"

Jensen et al. (1) question evidence presented of a chambered heart within placoderms, citing its small size and apparently ventral atrium. However, they fail to note the belly-up orientation of the placoderm within one nodule, and the variability of heart morphology within extant taxa. Thus, we remain confident in our interpretation of the mineralized organ as the heart.

Exceptional fossil preservation and evolution of the ray-finned fish brain

Brain anatomy provides key evidence for the relationships between ray-finned fishes¹, but two major limitations obscure our understanding of neuroanatomical evolution in this major vertebrate group. First, the deepest branching living lineages are separated from the group's common ancestor by hundreds of millions of years, with indications that aspects of their brain morphology-like other aspects of their anatomy^2,3-are specialized relative to primitive conditions. Second, there are no direct constraints on brain morphology in the earliest ray-finned fishes beyond the coarse picture provided by cranial endocasts: natural or virtual infillings of void spaces within the skull^4-8. Here we report brain and cranial nerve soft-tissue preservation in Coccocephalus wildi, an approximately 319-million-year-old ray-finned fish. This example of a well-preserved vertebrate brain provides a window into neural anatomy deep within ray-finned fish phylogeny. Coccocephalus indicates a more complicated pattern of brain evolution than suggested by living species alone, highlighting cladistian apomorphies¹ and providing temporal constraints on the origin of traits uniting all extant ray-finned fishes^1,9. Our findings, along with a growing set of studies in other animal groups^10-12, point to the importance of ancient soft tissue preservation in understanding the deep evolutionary assembly of major anatomical systems outside of the narrow subset of skeletal tissues^13-15.

Giant, swimming mouths: oral dimensions of extant sharks do not accurately predict body size in Dunkleosteus terrelli (Placodermi: Arthrodira)

Background

The size of Dunkleosteus and other late Devonian arthrodire placoderms has been a persistent problem in paleontology. The bony head and thoracic armor of these animals are typically the only elements preserved in the fossil record, with the rest of the body being lost during fossilization. Accurate length estimates of arthrodires are critical for reconstructing the paleobiology of these taxa and Devonian paleoecology more generally. Lengths of 5.3-8.8 m were proposed for Dunkleosteus based on allometric relationships between upper jaw perimeter and total length in extant large-bodied sharks. However, these methods were not statistically evaluated to determine if allometric relationships between body size and mouth size in sharks reliably predicted size in arthrodires. Several smaller arthrodire taxa are known from relatively complete remains, and can be used as independent case studies to test the accuracy of these methods.

Results

Length estimates for Dunkleosteus are evaluated through an examination of mouth proportions in complete arthrodires and fishes more generally. Currently accepted lengths of 5.3-8.8 m for D. terrelli are mathematically and biologically unlikely for three major reasons: (1) Arthrodires have larger mouths than sharks at similar body sizes. (2) upper jaw perimeter and mouth width produce extreme overestimates of body size (at least twice the actual value) in arthrodires known from complete remains. (3) Reconstructing Dunkleosteus using lengths predicted by upper jaw perimeter results in highly unusual body proportions, including extremely small, shrunken heads and hyper-anguilliform body plans, not seen in complete arthrodires or fishes more generally.

Conclusions

Length estimates for arthrodires based on the mouth dimensions of extant sharks are not reliable. Arthrodires have proportionally larger mouths than sharks, more similar to catfishes (Siluriformes). The disproportionately large mouths of arthrodires suggest these animals may have consumed larger prey relative to their body size than extant macropredatory sharks, and thus the paleobiology and paleoecology of these two groups may not have been exactly analogous within their respective ecosystems.

A New Large †Pachycormiform (Teleosteomorpha: †Pachycormiformes) from the Lower Jurassic of Germany, with Affinities to the Suspension-Feeding Clade, and Comments on the Gastrointestinal Anatomy of Pachycormid Fishes

Pachycormiformes is a diverse clade of stem-teleost actinopterygian fishes with a stratigraphic range from the Lower Jurassic (Toarcian) to Upper Cretaceous (Maastrichtian). The Toarcian Posidonienschiefer Formation in SW Germany records the earliest occurrence of †Pachycormiformes in the fossil record, offering unique and crucial insight into the clade’s origins and early adaptive radiation in the Early Jurassic. However, Early Jurassic taxa remain poorly studied with the taxonomic diversity and stratigraphic/geographic distributions insufficiently defined, thus masking the early part of this evolutionary radiation. Here, we report a new genus and species of pachycormid fish from the Posidonienschiefer Formation identified by phylogenetic analysis as falling in an intermediate position between Saurostomus and Ohmdenia at the base of the suspension-feeding clade. The new taxon shows a unique suite of cranial and postcranial characters. Several synapomorphies of the suspension-feeding clade, notably, the morphology of the hyomandibula, elongation of the skull, and reduced squamation are shared with the new taxon. The intestinal tract is exceptionally preserved, providing one of the most complete examples of pachycormid gastric anatomy. A comparison of the gastrointestinal anatomy of the new genus with other pachycormiforms indicates extensive taxonomic variation within the clade, in the configuration of both the midgut and spiral valve, potentially related to trophic divergence. The results highlight an underestimated high diversity and the rapid acquisition of trophic specializations in Pachycormiformes much earlier in the clade’s evolution than previously considered.

A new selenosteid placoderm from the Late Devonian of the eastern Anti-Atlas (Morocco) with preserved body outline and its ecomorphology

Placoderms are an extinct group of early jawed vertebrates that play a key role in understanding the evolution of the gnathostome body plan, including the origin of novelties such as jaws, teeth, and pelvic fins. As placoderms have a poorly ossified axial skeleton, preservation of the mainly cartilaginous axial and fin elements is extremely rare, contrary to the heavily mineralized bones of the skull and thoracic armor. Therefore, the gross anatomy of the animals and body shape is only known from a few taxa, and reconstructions of the swimming function and ecology are speculative. Here, we describe articulated specimens preserving skull roofs, shoulder girdles, most fins, and body outlines of a newly derived arthrodire. Specimens of the selenosteid Amazichthys trinajsticae gen. et sp. nov. display a skull roof with reticular ornamentation and raised sensory lines like Driscollaspis, a median dorsal plate with a unique sharp posterior depression, the pelvic girdle, the proportions and shape of the pectoral, dorsal, and caudal fins as well as a laterally enlarged region resembling the lateral keel of a few modern sharks and bony fishes. Our new phylogenetic analyses support the monophyly of the selenosteid family and place the new genus in a clade with Melanosteus, Enseosteus, Walterosteus, and Draconichthys. The shape of its body and heterocercal caudal fin in combination with the pronounced “lateral keel” suggest Amazichthys trinajsticae was an active macropelagic swimmer capable of reaching high swimming speeds.