Biology subjects

Ahlberg, P. E.

Publications and source records attributed to Ahlberg, P. E..

5 recordsLinked to original sources

bioRxiv2024

Automated segmentation of synchrotron-scanned fossils

Computed tomography has revolutionised the study of the internal three-dimensional structure of fossils. Historically, fossils typically spent years in preparation to be freed from the enclosing rock. Now, X-ray and synchrotron tomography reveal structure that is otherwise invisible and data acquisition can be fast. However, manual segmentation of these 3D volumes can still take months to years. This is especially challenging for resource-poor teams, as scanning may be free, but the computing power and (AI-assisted) segmentation software required to handle the resulting large data sets are complex to use and expensive. Here we present a free, browser-based segmentation tool that reduces computational overhead by splitting volumes into small chunks, allowing processing on low-memory, inexpensive hardware. Our tool also speeds up collaborative ground-truth generation and 3D visualization, all in-browser. We developed and evaluated our pipeline on various open-data scans of differing contrast, resolution, textural complexity, and size. Our tool successfully isolated the Thrinaxodon and Broomistega pair from an Early Triassic burrow. It isolated cranial bones from the Cretaceous acipenseriform Parapsephurus willybemisi on both 45.53 {micro}m and 13.67 {micro}m resolution scanning data. We also isolated bones of the Middle Triassic sauropterygian Nothosaurus and a challenging scan of a squamate embryo inside an egg dating back to the Early Cretaceous. Our tool reliably reproduces expert-supervised segmentation at a fraction of the time and cost, offering greater accessibility than existing tools. Beyond the online tool, all our code is open source, enabling contributions from the palaeontology community to further this emerging machine learning ecosystem.

paleontology↗

bioRxiv2021

Morphometric Analysis of Lungfish Endocasts Elucidates Early Dipnoan Palaeoneurological Evolution

Lungfish (Dipnoi) are lobe-finned fish (Sarcopterygii) that have persisted for over 400 million years from the Devonian Period to present day. They are the extant sister group to tetrapods and thus have the ability to provide unique insight into the condition of the earliest tetrapods as well as their own evolutionary history. The evolution of their dermal skull and dentition is relatively well understood, but this is not the case for the central nervous system. While the brain itself has very poor preservation potential and is not currently known in any fossil lungfish, substantial indirect information about it and associated structures such as the inner ears can be obtained from the cranial endocast. However, before the recent development of X-ray tomography as a palaeontological tool, these endocasts could not be studied non-destructively, and few detailed studies were undertaken. Here we describe and illustrate the endocasts of six Palaeozoic lungfishes (Iowadipterus halli, Gogodipterus paddyensis, Pillararhynchus longi, Griphognathus whitei, Orlovichthys limnatis, and Rhinodipterus ulrichi) from tomographic scans. We combine these with six previously described lungfish endocasts (4 fossil and 2 recent taxa), also based on tomographic studies, into a 12-taxon data set for multivariate morphometric analysis using 17 variables. We find that the olfactory region appears to be more highly plastic than the hindbrain, and undergoes significant elongation in several taxa. Further, while the semicircular canals covary as an integrated module, the utriculus and sacculus of the inner ear instead vary independently of each other. The functional and phylogenetic implications of our findings are discussed.

paleontology↗

bioRxiv2021

The extinction and survival of sharks across the end-Cretaceous mass extinction

Sharks (Selachimorpha) are iconic marine predators that have survived multiple mass extinctions over geologic time. Their fossil record is represented by an abundance of teeth, which traditionally formed the basis for reconstructing large-scale diversity changes among different selachimorph clades. By contrast, corresponding patterns in shark ecology, as measured through morphological disparity, have received comparatively limited analytical attention. Here, we use a geometric morphometric approach to comprehensively examine the dental morphology of multiple shark lineages traversing the catastrophic end-Cretaceous mass extinction -- this event terminated the Mesozoic Era 66 million years ago. Our results show that selachimorphs maintained virtually static levels of dental disparity in most of their constituent clades during the Cretaceous/Paleogene transition. Nevertheless, selective extinctions did impact on apex predator lineages characterized by triangular blade-like teeth, and in particular, lamniforms including the dominant Cretaceous anacoracids. Other groups, such as, triakid carcharhiniforms, squalids, and hexanchids, were seemingly unaffected. Finally, while some lamniform lineages experienced morphological depletion, others underwent a post-extinction disparity increase, especially odontaspidids, which are typified by narrow-cusped teeth adapted for feeding on fishes. This disparity shift coincides with the early Paleogene radiation of teleosts, a possible prey source, as well as the geographic relocation of shark disparity hotspots, perhaps indicating a regionally disjunct pattern of extinction recovery. Ultimately, our study reveals a complex morphological response to the end-Cretaceous mass extinction event, the dynamics of which we are only just beginning to understand.

paleontology↗

bioRxiv2020

Endocast and bony labyrinth of a stem gnathostome shed light on the earliest diversification of jawed vertebrates

Our understanding of the earliest evolution of jawed vertebrates depends on a credible phylogenetic assessment of the jawed stem gnathostomes collectively known as placoderms. However, their relationships, and even whether placoderms represent a single radiation or a paraphyletic array, remain contentious. Here we describe the endocranial cavity and inner ear of Brindabellaspis stensioi, commonly recovered as a taxon of uncertain affinity branching near the base of placoderms. While some features of its braincase and endocast resemble those of jawless vertebrates, its inner ear displays a repertoire of crown gnathostome characters. Both parsimony and Bayesian analyses suggest that established hypotheses of placoderm relationships are unstable, with newly-revealed anatomy pointing to a potentially radical revision of early gnathostome evolution. Our results call into question the appropriateness of fusiform placoderms as models of primitive gnathostome anatomy and raise questions of homology relating to key cranial features. One Sentence SummaryThe skull of a 400-million-year old fossil fish suggests that hypotheses of early jawed vertebrate relationships might have to be turned on their head.

paleontology↗

bioRxiv2020

Dental ontogeny in the most primitive bony fish Lophosteus reveals the developmental relationship between teeth and dermal odontodes

Ontogenetic data obtained by synchrotron microtomography of a marginal jawbone of Lophosteus superbus (Late Silurian, 422 Million years old), the phylogenetically basalmost stem osteichthyan, reveal developmental relationships between teeth and ornament that are not obvious from the adult morphology. The earliest odontodes are two longitudinal founder ridges formed at the ossification center. Subsequent odontodes that are added lingually to the ridges turn into conical teeth and undergo cyclic replacement, while those added labially achieve a stellate appearance. The stellate odontodes deposited directly on the bony plate are aligned with the alternate files of the teeth. Successive odontodes overgrowing the labial tooth rows become tooth-like and the replacement teeth near to them are ornament-like. We propose that teeth and ornament are modifications of a single odontode system regulated and differentiated by the oral and dermal signals; signal cross-communication between the two domains can occur around the oral-dermal boundary.

evolutionary biology↗