Jing Lu

Sharks exhibit extraordinary morphological diversity across a wide range of ecological niches, yet large-scale, high-resolution digital datasets of their internal anatomy remain limited. Here we present an open-access 3D shark anatomical repository derived from published X-ray computed tomography (CT) data, featuring manually segmented and systematically annotated models of the chondrocranium, visceral arches, axial skeleton, musculature, and viscera in standard STL format. The dataset comprises 117 individuals, representing 72 species across 25 families and all nine extant shark orders, with 115 full-body reconstructions and two head-only models. This open-access dataset offers a comprehensive resource for comparative anatomy, biomechanical simulations, evolutionary developmental biology and biomimetics research of extant sharks.

Osteichthyans (bony fishes and tetrapods) encompass 98% of modern vertebrate species. However, our understanding of the sequence of character evolution among stem osteichthyans has been substantially limited by the fragmentary nature of known stem osteichthyan fossils^1-4. Here we investigate newly discovered articulated head and trunk material of Megamastax amblyodus⁵, which yields previously unseen morphological details of a Silurian stem osteichthyan. Megamastax-previously interpreted as a lobe-finned fish⁵-exhibits distinct osteichthyan traits in the dermatocranium, such as resorptive tooth shedding and the presence of extrascapular bones. However, the arrangement of its dorsal aortae is reminiscent of crown-group chondrichthyans. The premaxilla with extensive palatal lamina and the elongated post-hypophyseal region of the braincase recall the condition in maxillate placoderms^6-8. Crucially, the discovery of an inner dental arcade of discrete tooth cushions on individual attachment bases aligns Megamastax with the fragmentary genera Lophosteus and Andreolepis^2-4, corroborating the previous interpretation of isolated tooth cushions as part of the jaw dentition^3,9 and verifying their identity as stem osteichthyans. Phylogenetic analysis places Megamastax within the osteichthyan stem, near the osteichthyan crown-group node, and provides a framework for exploring the sequence of character acquisition along the osteichthyan stem. Together, these new findings help to bridge the morphological gap between stem gnathostomes and modern osteichthyans, offering insights into the sequence of early evolutionary steps that shaped the osteichthyan lineage.

Osteichthyans, comprising sarcopterygians and actinopterygians, dominate modern vertebrate biodiversity^1,2,3, yet their pre-Devonian fossil record remains scarce and fragmentary^4,5. The oldest articulated sarcopterygian⁶ and stem osteichthyan⁷ date to the late Silurian, whereas undisputed actinopterygian fossils in articulation appear only in the Middle Devonian⁸. Here we report an articulated, near-complete osteichthyan from the early Silurian Chongqing Lagerstätte (approximately 436 million years ago)^9,10,11, representing the oldest osteichthyan occurrence including microfossils. This tiny fish exhibits a fusiform, generalized osteichthyan body outline, with plesiomorphic osteichthyan characters, including the lack of lepidotrichia and the presence of serial median dorsal plates, pectoral and dorsal fin spines and an anal fin spine reported previously exclusively in stem chondrichthyans¹² and one placoderm¹³. It also displays features, such as a single dorsal fin and caudal fulcra, seen commonly in actinopterygians. Bayesian inference and the 50% majority rule consensus of the maximum-parsimony analysis place the new fish on the osteichthyan stem, whereas the strict consensus leaves its position unresolved within osteichthyans. This discovery increases Silurian osteichthyan diversity and further populates the osteichthyan stem group. The morphological disparity among early osteichthyans implies a more extensive Silurian to Early Devonian radiation of bony fishes than previous lines of evidence suggested.

Palaeospondylus gunni Traquair, 1890, is represented by thousands of similarly preserved articulated fossils from the Achannaras quarry (∼390 Mya) in Caithness, Scotland. With radically different interpretations of its structure, it has been assigned to almost all major jawless and jawed vertebrate groups. Here we report a new and older species of Palaeospondylus from the Early Devonian of Australia (c. 400 Ma), investigated using high-resolution computed tomography. Its 3D-preserved braincase demonstrates a combination of primitive gnathostome features including an anteriorly positioned transverse cranial fissure of uncertain homology, a large dorsal fontanelle and a small hypophysial fossa. Contrary to recent interpretations of P. gunni, the new braincase shows that Palaeospondylus lacks both a postorbital process and an intracranial joint. Our new Australian species extends the history of Palaeospondylus back some 10 million years prior to its occurrence in Scotland. The newly identified neurocranial characters have been coded into a phylogenetic analysis that places Palaeospondylus as a sister group of the Chondrichthyes, but some neurocranial characters could indicate a phylogenetic position within the gnathostome stem group.

3D visualization and segmentation are increasingly widely used in physical, biological and medical science, facilitating advanced investigative methodologies. However, the integration and reproduction of segmented volumes or results across the spectrum of mainstream 3D visualization platforms remain hindered by compatibility constraints. These barriers not only challenge the replication of findings but also obstruct the process of cross-validating the accuracy of 3D visualization outputs. To address this gap, we developed an innovative revisualization method implemented within the open-source framework of Drishti , a 3D visualization software. Leveraging four animal samples alongside three mainstream 3D visualization platforms as case studies, our method demonstrates the seamless transferability of segmented results into Drishti . This capability effectively fosters a new avenue for authentication and enhanced scrutiny of segmented data. By facilitating this interoperability, our approach underscores the potential for significant advancements in accuracy validation and collaborative research efforts across diverse scientific domains.

When first described based on isolated scales, Ligulalepis was assigned to thePalaeoniscoidea, a basal group of actinopterygians (ray-finned fishes). Recent cladisticanalyses, mainly based on skull and neurocranial characters, have mostly recovered thetaxon (or, ‘Ligulalepis’) as a stem osteichthyan. Here we present information on Ligulalepisdermal elements other than scales and skulls, that include a cheek fragment, a premaxilla,other marginal jaw elements and teeth, an accessory vomer, a partial shoulder girdle,incomplete spine-like elements, and a gular plate. The shoulder girdle and premaxilla compareclosely with those of basal actinopterygians, whereas the spine-like element showssome similarity to the distal end of the spines on medial dorsal plates of the Chinese LateSilurian stem osteichthyans Guiyu and Sparalepis, or alternatively to fin rays on the stemosteichthyan Dialipina. One of the jaw elements appears to be a compound jugal plate pluspart of the dentate maxilla, an arrangement not previously known in any Devonian stemosteichthyan, or actinopterygian. Histological structure of dermal plates somewhat resemblesthat of Meemannia, but pore openings in Ligulalepis lead only to the vascular canalnetwork at the base of the ornament layer and not to a pore canal network. Like previousphylogenetic analyses, our analysis incorporating post-cranial dermal skeleton charactersalso recovered Ligulalepis as a stem osteichthyan.

Colonies are the basic geometric building blocks of coral reefs. However, the forming regulations of both colonies and reefs are still not understood adequately. Therefore, in this study, we reconstructed 25 samples using high‐resolution micro‐computed tomography to investigate coral growth patterns and parameters. Our skeleton and canal reconstructions revealed the characteristics of different coral species, and we further visualized the growth axes and growth rings to understand the coral growth directions. We drew a skeleton grayscale map and calculated the coral skeleton void ratios to ascertain the skeletal diversity, devising a method to quantify coral growth. On the basis of the three‐dimensional (3D) reconstructions and growth parameters, we investigated the growth strategies of different coral species. This research increases the breadth of knowledge on how reef‐building corals grow their colonies, providing information on reef‐forming regulations. The data in this paper contain a large amount of coral growth information, which can be used in further research on reef‐forming patterns under different conditions. The method used in this study can also be applied to animals with porous skeletons.