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Publications (10 of 165) Show all publications
During, M. A. D., Matelsky, J. K., Gustafsson, F. K., Voeten, D. F. A., Chen, D., Wester, B. A., . . . Schön, T. B. (2025). Automated segmentation of synchrotron-scanned fossils. Fossil Record, 28(1), 103-114
Open this publication in new window or tab >>Automated segmentation of synchrotron-scanned fossils
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2025 (English)In: Fossil Record, ISSN 2193-0066, Vol. 28, no 1, p. 103-114Article in journal (Refereed) Published
Abstract [en]

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 structures that are 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 visualisation, 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 µm and 13.67 µm resolution (voxel size) 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.

Place, publisher, year, edition, pages
Pensoft Publishers, 2025
Keywords
AI-segmentation, Machine Learning, Open Source, Open Access, Propagation Phase-Contrast Synchrotron Radiation Micro-Computed Tomography (PPC-SRµCT), Random Forest
National Category
Computer Sciences Geology
Research subject
Artificial Intelligence
Identifiers
urn:nbn:se:uu:diva-538797 (URN)10.3897/fr.28.e139379 (DOI)001446793800001 ()2-s2.0-86000594308 (Scopus ID)
Funder
Swedish Research Council, 2020-03685Kjell and Marta Beijer Foundation
Note

De två första författarna delar förstaförfattarskapet

Available from: 2024-09-20 Created: 2024-09-20 Last updated: 2025-03-28Bibliographically approved
Ahlberg, P. (2025). Re-examining the strangest early vertebrate. NATIONAL SCIENCE REVIEW, 12(5), Article ID nwaf021.
Open this publication in new window or tab >>Re-examining the strangest early vertebrate
2025 (English)In: NATIONAL SCIENCE REVIEW, ISSN 2095-5138, Vol. 12, no 5, article id nwaf021Article in journal, Editorial material (Other academic) Published
Place, publisher, year, edition, pages
Oxford University Press, 2025
National Category
Palaeontology and Palaeoecology
Identifiers
urn:nbn:se:uu:diva-557635 (URN)10.1093/nsr/nwaf021 (DOI)001421774000001 ()40191257 (PubMedID)
Available from: 2025-06-02 Created: 2025-06-02 Last updated: 2025-06-02Bibliographically approved
During, M. A. D., Voeten, D. F. A., Van der Lubbe, J. L. & Ahlberg, P. E. (2024). Calibrations without raw data: A response to "Seasonal calibration of the end-cretaceous Chicxulub impact event". PeerJ, 12, Article ID e18519.
Open this publication in new window or tab >>Calibrations without raw data: A response to "Seasonal calibration of the end-cretaceous Chicxulub impact event"
2024 (English)In: PeerJ, E-ISSN 2167-8359, Vol. 12, article id e18519Article in journal (Refereed) Published
Abstract [en]

A recent article by DePalma et al. reported that the season of the End-Cretaceous mass extinction was confined to spring/summer on the basis of stable isotope analyses and supplementary observations. An independent study that was concurrently under review reached a similar conclusion using osteohistology and stable isotope analyses. We identified anomalies surrounding the stable isotope analyses reported by DePalma et al. Primary data are not provided, the laboratory where the analyses were performed is not identified, and the methods are insufficiently specified to enable accurate replication. Furthermore, isotopic graphs for carbon and oxygen contain irregularities such as missing data points, duplicate data points, and identical-length error bars for both elements despite different scales, that appear inconsistent with laboratory instrument outputs. A close examination of such methodological omissions and data irregularities can help to raise the standards for future studies of seasonality and prevent inaccurate claims or confirmation bias.

Place, publisher, year, edition, pages
PeerJ, 2024
Keywords
Mass spectrometry, Data, End Cretaceous, Seasonality, Osteohistology
National Category
Geochemistry
Identifiers
urn:nbn:se:uu:diva-538692 (URN)10.7717/peerj.18519 (DOI)001356218000001 ()39553725 (PubMedID)2-s2.0-85209928754 (Scopus ID)
Available from: 2024-09-19 Created: 2024-09-19 Last updated: 2024-12-03Bibliographically approved
Qvarnström, M., Vikberg Wernström, J., Wawrzyniak, Z., Barbacka, M., Pacyna, G., Górecki, A., . . . Niedźwiedzki, G. (2024). Digestive contents and food webs record the advent of dinosaur supremacy. Nature, 636(8042), 397-403
Open this publication in new window or tab >>Digestive contents and food webs record the advent of dinosaur supremacy
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2024 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 636, no 8042, p. 397-403Article in journal (Refereed) Published
Abstract [en]

The early radiation of dinosaurs remains a complex and poorly understood evolutionary event1,2,3,4. Here we use hundreds of fossils with direct evidence of feeding to compare trophic dynamics across five vertebrate assemblages that record this event in the Triassic–Jurassic succession of the Polish Basin (central Europe). Bromalites, fossil digestive products, increase in size and diversity across the interval, indicating the emergence of larger dinosaur faunas with new feeding patterns. Well-preserved food residues and bromalite-taxon associations enable broad inferences of trophic interactions. Our results, integrated with climate and plant data, indicate a stepwise increase of dinosaur diversity and ecospace occupancy in the area. This involved (1) a replacement of non-dinosaur guild members by opportunistic and omnivorous dinosaur precursors, followed by (2) the emergence of insect and fish-eating theropods and small omnivorous dinosaurs. Climate change in the latest Triassic5,6,7 resulted in substantial vegetation changes that paved the way for ((3) and (4)) an expansion of herbivore ecospace and the replacement of pseudosuchian and therapsid herbivores by large sauropodomorphs and early ornithischians that ingested food of a broader range, even including burnt plants. Finally, (5) theropods rapidly evolved and developed enormous sizes in response to the appearance of the new herbivore guild. We suggest that the processes shown by the Polish data may explain global patterns, shedding new light on the environmentally governed emergence of dinosaur dominance and gigantism that endured until the end-Cretaceous mass extinction.

Place, publisher, year, edition, pages
Springer Nature, 2024
National Category
Evolutionary Biology Geology
Identifiers
urn:nbn:se:uu:diva-551464 (URN)10.1038/s41586-024-08265-4 (DOI)001365217000001 ()39604731 (PubMedID)2-s2.0-85210484332 (Scopus ID)
Funder
Swedish Research Council, 2020-06445Knut and Alice Wallenberg FoundationUppsala UniversitySwedish Research Council, 2017-05248
Available from: 2025-02-27 Created: 2025-02-27 Last updated: 2025-04-23Bibliographically approved
Jimenez-Mejias, P., Carlsson, B., Svensson, B., Guerrero-Bosagna, C., Arnqvist, G., Cárdenas, P., . . . Fitzpatrick, M. (2024). Protecting stable biological nomenclatural systems enables universal communication: A collective international appeal. BioScience, 74(7), 467-472
Open this publication in new window or tab >>Protecting stable biological nomenclatural systems enables universal communication: A collective international appeal
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2024 (English)In: BioScience, ISSN 0006-3568, E-ISSN 1525-3244, Vol. 74, no 7, p. 467-472Article in journal (Refereed) Published
Abstract [en]

The fundamental value of universal nomenclatural systems in biology is that they enable unambiguous scientific communication. However, the stability of these systems is threatened by recent discussions asking for a fairer nomenclature, raising the possibility of bulk revision processes for "inappropriate" names. It is evident that such proposals come from very deep feelings, but we show how they can irreparably damage the foundation of biological communication and, in turn, the sciences that depend on it. There are four essential consequences of objective codes of nomenclature: universality, stability, neutrality, and transculturality. These codes provide fair and impartial guides to the principles governing biological nomenclature and allow unambiguous universal communication in biology. Accordingly, no subjective proposals should be allowed to undermine them.

Place, publisher, year, edition, pages
Oxford University Press, 2024
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-557489 (URN)10.1093/biosci/biae043 (DOI)001380658700001 ()39156614 (PubMedID)2-s2.0-85201776125 (Scopus ID)
Note

For complete list of authors see http://dx.doi.org/10.1093/biosci/biae043

Available from: 2025-05-27 Created: 2025-05-27 Last updated: 2025-05-27Bibliographically approved
Gess, R. & Ahlberg, P. (2023). A high latitude Gondwanan species of the Late Devonian tristichopterid Hyneria (Osteichthyes: Sarcopterygii). PLOS ONE, 18(2), Article ID e0281333.
Open this publication in new window or tab >>A high latitude Gondwanan species of the Late Devonian tristichopterid Hyneria (Osteichthyes: Sarcopterygii)
2023 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 18, no 2, article id e0281333Article in journal (Refereed) Published
Abstract [en]

We describe the largest bony fish in the Late Devonian (late Famennian) fossil assemblage from Waterloo Farm near Makhanda/Grahamstown, South Africa. It is a giant member of the extinct clade Tristichopteridae (Sarcopterygii: Tetrapodomorpha) and most closely resembles Hyneria lindae from the late Famennian Catskill Formation of Pennsylvania, USA. Notwithstanding the overall similarity, it can be distinguished from H. lindae on a number of morphological points and is accordingly described as a new species, H. udlezinye sp. nov. The preserved material comprises most of the dermal skull, lower jaw, gill cover and shoulder girdle. The cranial endoskeleton appears to have been unossified and is not preserved, apart from a fragment of the hyoid arch adhering to a subopercular, but the postcranial endoskeleton is represented by an ulnare, some semi-articulated neural spines, and the basal plate of a median fin. The discovery of H. udlezinye shows that Hyneria is a cosmopolitan genus extending into the high latitudes of Gondwana, not a Euramerican endemic. It supports the contention that the derived clade of giant tristichopterids, which alongside Hyneria includes such genera as Eusthenodon, Edenopteron and Mandageria, originated in Gondwana.

Place, publisher, year, edition, pages
Public Library of Science (PLoS), 2023
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-500587 (URN)10.1371/journal.pone.0281333 (DOI)000942161600060 ()36812170 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationEU, European Research Council, ERC-2020-ADG 10101963
Available from: 2023-04-21 Created: 2023-04-21 Last updated: 2023-04-21Bibliographically approved
Stundl, J., Martik, M. L., Chen, D., Raja, D. A., Franek, R., Pospisilova, A., . . . Bronner, M. E. (2023). Ancient vertebrate dermal armor evolved from trunk neural crest. Proceedings of the National Academy of Sciences of the United States of America, 120(30), Article ID e2221120120.
Open this publication in new window or tab >>Ancient vertebrate dermal armor evolved from trunk neural crest
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2023 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 120, no 30, article id e2221120120Article in journal (Refereed) Published
Abstract [en]

Bone is an evolutionary novelty of vertebrates, likely to have first emerged as part of ancestral dermal armor that consisted of osteogenic and odontogenic components. Whether these early vertebrate structures arose from mesoderm or neural crest cells has been a matter of considerable debate. To examine the developmental origin of the bony part of the dermal armor, we have performed in vivo lineage tracing in the sterlet sturgeon, a representative of nonteleost ray- finned fish that has retained an extensive postcranial dermal skeleton. The results definitively show that sterlet trunk neural crest cells give rise to osteoblasts of the scutes. Transcriptional profiling further reveals neural crest gene signature in sterlet scutes as well as bichir scales. Finally, histological and microCT analyses of ray- finned fish dermal armor show that their scales and scutes are formed by bone, dentin, and hypermineralized covering tissues, in various combinations, that resemble those of the first armored vertebrates. Taken together, our results support a primitive skeletogenic role for the neural crest along the entire body axis, that was later progressively restricted to the cranial region during vertebrate evolution. Thus, the neural crest was a crucial evolutionary innovation driving the origin and diversification of dermal armor along the entire body axis.

Place, publisher, year, edition, pages
Proceedings of the National Academy of Sciences (PNAS), 2023
Keywords
neural crest, vertebrate evolution, scales, sterlet sturgeon, skeleton
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-511895 (URN)10.1073/pnas.2221120120 (DOI)001055246900002 ()37459514 (PubMedID)
Funder
EU, Horizon 2020, 897949Knut and Alice Wallenberg Foundation
Available from: 2023-09-21 Created: 2023-09-21 Last updated: 2023-09-21Bibliographically approved
Hilton, E. J., During, M. A. D., Grande, L. & Ahlberg, P. (2023). New paddlefishes (Acipenseriformes, Polyodontidae) from the Late Cretaceous Tanis Site of the Hell Creek Formation in North Dakota, USA. Journal of Paleontology, 97(3), 675-692
Open this publication in new window or tab >>New paddlefishes (Acipenseriformes, Polyodontidae) from the Late Cretaceous Tanis Site of the Hell Creek Formation in North Dakota, USA
2023 (English)In: Journal of Paleontology, ISSN 0022-3360, E-ISSN 1937-2337, Vol. 97, no 3, p. 675-692Article in journal (Refereed) Published
Abstract [en]

The recently discovered mass mortality of fishes from the Tanis Site in the North Dakota portion of the Late Cretaceous Hell Creek Formation contains many well-preserved, three-dimensional skeletons. Among these are representatives of two acipenseriform families, Acipenseridae (sturgeons) and Polyodontidae (paddlefishes). This paper describes two new monotypic polyodontid genera, expanding our knowledge of polyodontid diversity. The first of the new species described here is +Parapsephurus willybemisi n. gen. n. sp. It is distinguished from all other known species by having a combination of posteriorly elongate parietals, the middle fenestra longitudinalis bordered medially by the parietal and frontal and laterally by the dermopterotic, slender and numerous dorsal caudal fulcra, an elongate hyomandibula that is not hourglass shaped, and gill rakers that are short and widely spaced. The second polyodontid species described here is dagger Pugiopsephurus inundatus n. gen. n. sp. It is diagnosed by a combination of having stellate bones that are exceptionally poorly developed or absent and having a dermopalatine with a medial expansion and lacking an ectopterygoid process. The two species of paddlefishes described in this paper add to the morphological and taxonomic diversity of Polyodontidae. The presence of these taxa within the Hell Creek Formation hints at substantial diversity of polyodontids at this stage of their evolutionary history.

Place, publisher, year, edition, pages
Cambridge University Press, 2023
National Category
Other Earth Sciences
Identifiers
urn:nbn:se:uu:diva-512262 (URN)10.1017/jpa.2023.19 (DOI)000969104200001 ()
Funder
Swedish Research Council, 2020-03685
Available from: 2023-09-26 Created: 2023-09-26 Last updated: 2025-02-07Bibliographically approved
Trinajstic, K., Long, J., Sanchez, S., Boisvert, C. A., Snitting, D., Tafforeau, P., . . . Ahlberg, P. E. (2023). Response to comment on "Exceptional preservation of organs in Devonian placoderms from the Gogo largerstätte" [Letter to the editor]. Science, 380(6645), Article ID eadg3748.
Open this publication in new window or tab >>Response to comment on "Exceptional preservation of organs in Devonian placoderms from the Gogo largerstätte"
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2023 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 380, no 6645, article id eadg3748Article in journal, Letter (Other academic) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
American Association for the Advancement of Science (AAAS), 2023
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-524986 (URN)10.1126/science.adg3748 (DOI)001169212000001 ()37167391 (PubMedID)
Funder
Australian Research Council, DP1092870Australian Research Council, ARC-DP140104161Australian Research Council, DP1096002Australian Research Council, ARC-DP110101127Australian Research Council, ARCDP200103219EU, European Research Council, 233111Knut and Alice Wallenberg Foundation
Available from: 2024-03-15 Created: 2024-03-15 Last updated: 2024-03-15Bibliographically approved
Dupret, V., Byrne, H., Castro, N. A., Hammer, Ø., Higgs, K. T., Long, J. A., . . . Ahlberg, P. (2023). The Bothriolepis (Placodermi, Antiarcha) material from the Valentia Slate Formation of the Iveragh Peninsula (middle Givetian, Ireland): Morphology, evolutionary and systematic considerations, phylogenetic and palaeogeographic implications. PLOS ONE, 18(2), Article ID e0280208.
Open this publication in new window or tab >>The Bothriolepis (Placodermi, Antiarcha) material from the Valentia Slate Formation of the Iveragh Peninsula (middle Givetian, Ireland): Morphology, evolutionary and systematic considerations, phylogenetic and palaeogeographic implications
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2023 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 18, no 2, article id e0280208Article in journal (Refereed) Published
Abstract [en]

Material of the antiarch placoderm Bothriolepis from the middle Givetian of the Valentia Slate Formation in Iveragh Peninsula, Ireland, is described and attributed to a new species, B. dairbhrensis sp. nov. A revision of the genus Bothriolepis is proposed, and its taxonomic content and previous phylogenetic analyses are reviewed, as well as the validity of morphologic characteristics considered important for the establishment of the genus, such as the shape of the preorbital recess of the neurocranium. A series of computerised phylogenetic analyses was performed, which reveals that our new species is the sister taxon to the Frasnian Scottish form B. gigantea. New phylogenetic and biogeographic analyses of the genus Bothriolepis together with comparisons between faunal assemblages reveal a first northward dispersal wave from Gondwana to Euramerica at the latest in the mid Givetian. Other Euramerican species of Bothriolepis seem to belong to later dispersal waves from Gondwana, non-excluding southward waves from Euramerica. Questions remain open such as the taxonomic validity and stratigraphic constraints for the most ancient forms of Bothriolepis in China, and around the highly speciose nature of the genus.

Place, publisher, year, edition, pages
Public Library of Science (PLoS), 2023
National Category
Biological Systematics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-499915 (URN)10.1371/journal.pone.0280208 (DOI)000942237800004 ()36821588 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationEU, European Research Council, ERC-2020-ADG 101019613
Available from: 2023-04-05 Created: 2023-04-05 Last updated: 2023-04-05Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-9054-2900

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