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opencc-zeroDec 2022View details →

Data from: Testing the success of palaeontological methods in the delimitation of clam shrimp (Crustacea, Branchiopoda) on extant species

Fossil spinicaudatan taxonomy heavily relies on carapace features (size, shape, ornamentation), and palaeontologists have greatly refined methods to study and describe carapace variability. Whether carapace features alone are sufficient for distinguishing between species of a single genus has remained untested. In our study, we tested common palaeontological methods on 481 individuals of the extant Australian genus Ozestheria that have been previously assigned to ten species based on genetic analysis. All species are morphologically distinct based on geometric morphometrics (p ≤ 0.001), but they occupy overlapping regions in Ozestheria morphospace. Linear discriminant analysis of Fourier shape coefficients reaches a mean model performance of 93.8% correctly classified individuals over all possible 45 pairwise species comparisons. This can be further increased by combining the size and shape datasets. Nine of the ten examined species are clearly sexually dimorphic but male and female morphologies strongly overlap within species with little influence on model performance. Ornamentation is commonly species-diagnostic; seven ornamentation types are distinguished of which six are species-specific while one is shared by four species. A transformation of main ornamental features (e.g. from punctate to smooth) can occur among closely related species suggesting short evolutionary timescales. Our overall results support the taxonomic value of carapace features, which should also receive greater attention in the taxonomy of extant species. The extensive variation in carapace shape and ornamentation is noteworthy and several species would probably have been assigned to different genera or families if these had been fossils, bearing implications for the systematics of fossil Spinicaudata.

publicDec 2022View details →

Data from: Testing the success of palaeontological methods in the delimitation of clam shrimp (Crustacea, Branchiopoda) on extant species

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publicFeb 2021View details →

Data from: Palaeontology meets metacommunity ecology: The Maastricthian dinosaur fossil record of North America as a case study

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publicAug 2018View details →

Data from: Quantifying the dark data in museum fossil collections as palaeontology undergoes a second digital revolution

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publicMar 2020View details →

Canada's first known dinosaurs: Palaeontology and collecting history of upper Cretaceous vertebrates in Southern Alberta and Saskatchewan, 1874-1889

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opencc-by-4.0Feb 2020View details →

Retrospect and prospect of a section-based stratigraphic and palaeontological database -- Geobiodiversity Database

Big data are significant to the quantitative analysis and contribute to the data-driven scientific research and discoveries. Here the thorough introduction is given on the Geobiodiversity database (GBDB), a comprehensive stratigraphic and palaeontological database. The GBDB includes abundant geological records from China and contributes a serial of scientific studies on early Palaeozoic palaeogeography, tectonic and biodiversity evolution of China. Nevertheless, the existing problems of the GBDB limited the using of its data. The turnover and improvement of the GBDB were started in 2019. Besides the data collecting, processing and visualization as the GBDB did previously, the database and the website are optimized and re-designed, the new GBDB working team pays more attention to data analyzing with the professional artificial intelligence techniques. GBDB is complementary to other related databases and further collaborations are proposed to mutually benefit and push forward the quantitative research of palaeontology and stratigraphy in the era of big data. The GBDB data associated with this article can be found at https://www.geobiodiversity.com/

opencc-by-sa-4.0Jul 2020View details →

Cave lynx Osteometrical Datasets from L'Escale Palaeontological site (South-East France)

Background These datasets provide osteometrical measurements for dental and postcranial remains in cave lynx from the Middle Pleistocene site of L’Escale (South-East France).  The cave lynx sample from L’Escale is probably one of the richest and most important population for the European (Middle) Pleistocene. L’Escale Cave, located about 30 km north to Aix-en-Provence, has been excavated during the 1960’s under the direction of Eugène and Marie-Françoise Bonifay. This site, dated to the first half of the Middle Pleistocene, yielded remarkable faunal associations, including abundant thar – Hemitragus bonali – remains as well as numerous and highly diverse carnivores such as the wolverine Gulo schlosseri, the « european » jaguar Panthera gombaszoegensis, the cave lynx Lynx spelaeus as well as the fossil striped hyena Hyaena prisca (Bonifay, 1971 ; Bonifay, 1974-75). L’Escale presents a unique palaeobiological record mixing phases of carnivore occupations (bears, striped hyenas?, jaguars?, wolves?, foxes) and natural trapping events (thar) (Coumont, 2006).   Method All the specimens have been described and measured (in millimeters with callipers to 0.1mm) by the authors. They are stored and curated in the MNP – Musée National de Préhistoire, Les Eyzies, Dordogne, France. Data description File title: Each file is named according to the following pattern:     • First part: abreviation of considered species (i.e., Lps = Lynx pardinus spelaeus);      • Second part: anatomical part codification:          ◦ MAND: Mandible          ◦ U: Upper / L: Lower         ◦ C: Canine / P: Premolar / M: Molar          ◦ 1 to 5: tooth or metapodials (metacarpals/metatarsals/phalanges) rank          ◦ HUM: Humerus / RAD: Radius / ULN: Ulna         ◦ FEM: Femur / TIB: Tibia         ◦ SCAPHL: Scapholunar (Carpal)         ◦ CALCA: Calcaneus (Tarsal)         ◦ TAL: Talus (Tarsal)         ◦ MTC: Metacarpals / MTT: Metatarsals File content:     • chrono: Chronology (i.e., Middle or Late Pleistocene);      • MIS: Marine Isotopic Stage (if applicable);      • species: specific (or sub-specific) identification (i.e., Lynx spelaea);      • country: Site location (i.e., France);      • site: Site name;      • label: Specimen label such as archaeological number or museum inventory number;      • side: Specimen laterality, it could be left (sin) or right (dext);      • L_cond_infra (in mm): length from the condyle process to infradental (in mm), applicable only for the mandible;     • L_angul_infra: length from the angular process to infradental (in mm), applicable only for the mandible;     • L_coron_infra: length from coronion to infradental (in mm), applicable only for the mandible;     • L_diast: Diastema length (in mm),  applicable only for the mandible;     • L_rawtth: Raw teeth length (in mm);     • H_p3: Horizontal ramus height before p3 (in mm), applicable only for the mandible;     • H_m1: Horizontal ramus height behind m1 (in mm), applicable only for the mandible;     • B_c: Horizontal ramus breadth at lower canine (in mm), applicable only for the mandible;     • B_p3: Horizontal ramus breadth before p3 (in mm), applicable only for the mandible;     • B_m1: Horizontal ramus breadth behind m1 (in mm), applicable only for the mandible;     • B: Breadth (in mm);      • L: Breadth (in mm);      • GL: Greatest length (in mm);     • Dp: Depth of the proximal end (in mm), applicable only for long bones and metapodials;     • Bp: Greatest breadth of the proximal end (in mm), applicable only for long bones and metapodials;     • Ds: Depth of the diaphysis (in mm), applicable only for long bones and metapodials;     • SD: Smallest breadth of the diaphysis (in mm), applicable only for long bones and metapodials;     • Dd: Depth of the distal end (in mm), applicable only for long bones and metapodials;     • Bd: Greatest breadth of the distal end (in mm), applicable only for long bones and metapodials;     • B_troch: Breadth of the trochlea (in mm), applicable only for the humerus;     • DPA: Depth across the processus anconaeus (in mm), applicable only for the ulna;     • SDO: Smallet depth of the olceranon (in mm), applicable only for the ulna;     • BPC: Greatest breadth across the coronoid process (in mm), applicable only for the ulna;     • GB: Greatest breadth (in mm), applicable only for carpals/tarsals;      • H: Greatest height (in mm), applicable only for carpals/tarsals;      • GD: Greatest depth (in mm), applicable only for carpals/tarsals;      • location: Curation place.  References • Bonifay, M.-F., 1974-1975. "Hemitragus bonali" Harlé et Stehlin, "Caprinae" de la grotte de l’Escale (Saint-Estève-Janson, Bouhes-du-Rhône). Quaternaria XVIII, 215–301. • Bonifay, M.-F., 1971. Carnivores quaternaires du Sud-Est de la France. Mémoires du Muséum national d’Histoire naturelle, Sér. C – Sciences de la Terre 21, 1–334. • Coumont, M.-P., 2006. Taphonomie préhistorique : mammifères fossiles en contexte naturel, les avens-pièges, apport pour l’étude des archéofaunes. Thèse de Doctorat. Université Aix-Marseille 1, Aix-en-Provence.

opencc-zeroAug 2020View details →

Data from: Bayesian analyses in phylogenetic palaeontology: interpreting the posterior sample

Establishing hypotheses of relationships is a critical prerequisite for any macroevolutionary analysis, but different approaches exist for achieving this goal. Amongst palaeontologists using morphological data the Bayesian approach is increasingly preferred over parsimony, but this shift also alters the way we think about samples of trees. Here we revisit stratigraphic congruence as a comparator between Bayesian and parsimony samples, but in a new visual context: treespace. Such spaces represent an ordination of unique topologies that can also be extended to create a "landscape" where altitude represents some comparative measure (here congruence with stratigraphy). By co-opting existing visualization tools and applying them to a meta-analysis of 128 cladistic data sets we show that there is no consistent favouring of either Bayesian or parsimony according to stratigraphic congruence metrics, and further that empirical treespace visualizations suggest a complex variety of topological landscapes. We conclude by arguing that treespaces should become a standard exploratory tool in phylogenetic analysis.

opencc-zeroDec 2020View details →

Taxonomic identification using virtual palaeontology and geometric morphometrics: a case study of Jurassic nerineoidean gastropods

Taxonomic identification of fossils is fundamental to a wide range of geological and biological disciplines. Many fossil groups are identified based on expert judgment, which requires extensive experience and is not always available for the specific taxonomic group at hand. Nerineoideans, a group of extinct gastropods that formed a major component of Mesozoic shallow marine environments, have distinctive internal spiral folds that form the basis for their classification at the genus level. However, their identification is often inconsistent because it is based on a set of selected characters reliant upon individual interpretation. This study shows a non-destructive and quantitative method for their identification using micro-CT and geometric morphometrics. We examined and micro-CT-scanned nerineoidean specimens from five main families that dominated Europe, Arabia and Africa during the Middle-Late Jurassic. Optimal longitudinal slices were selected from the tomographic reconstructions or from images of polished cross-sections compiled from fossil collections, published work and online databases. Internal whorl outlines were represented by thirty evenly distributed sliding semilandmarks and shape variations were studied using the Procrustes-based geometric morphometrics method. Multivariate analysis shows that Ceritellidae and Ptygmatididae are distinct families, whereas Nerinellidae, Eunerineidae and Nerineidae fall within the same shape variance and cannot be distinguished based on internal whorl outlines. The suggested method can be applied to images from various sources as well as to poorly preserved specimens. Our case study demonstrates the importance of quantitatively re-evaluating taxonomy in the fossil record, promoting the future utility of large datasets.

opencc-zeroDec 2011View details →

Data from: A survey of palaeontological sampling biases in fishes based on the phanerozoic record of Great Britain

Fishes represent more than half of all living vertebrate species, but patterns of fish diversity remain little explored in the fossil record. A compendium of fossil occurrences from Great Britain was assembled in order to address a series of questions concerning the palaeontological record of fishes. There are broad similarities between British richness trajectories and those compiled from global data, including an initial peak in the mid-Palaeozoic (Devonian or Carboniferous, depending on the compilation), with a late Palaeozoic trough followed by a sharp rise in diversity in the Late Cretaceous and Paleogene. The British dataset is too small to reveal any significant differences in richness between time bins using subsampling, but a modeling approach based on sampling and geological proxies consistently shows lower-than-predicted richness in the Silurian-Devonian and higher-than-predicted richness in the Late Cretaceous and Eocene. This positive excursion is robust to the exclusion of data from the early Eocene London Clay Lagerstätte. Chondrichthyans (sharks, rays, and ratfishes) and osteichthyans (ray-finned and lobe-finned fishes) show contrasting relationships with geological and sampling proxies, possibly reflecting different taphonomic profiles or idiosyncratic variation in the relative proportion of freshwater and marine deposits over the British Phanerozoic.

opencc-zeroDec 2018View details →

Data from: Early Triassic benthic invertebrates from the Great Bank of Guizhou, South China: systematic palaeontology and palaeobiology

To further our understanding on the evolution, selectivity, and ecological composition of marine communities following the latest Permian mass extinction, new collections from underrepresented regions in the immediate extinction aftermath are required. Here, we provide new systematic data and the first palaeobiological account of the benthic invertebrate community from the Great Bank of Guizhou, South China. We systematically describe 3 brachiopod species, 26 bivalve species, 11 gastropod species, 1 microconchid, and 1 crinoid species. The descriptions include five new species; two bivalve species (Hoernesia? danisae, Atomodesma? hautmanni) and three gastropod species (Donaldina erwini, Cossmannina alfischeri, and Vernelia samae). This is the most species-rich benthic community known so far from the extinction aftermath, which is typically characterised by a high proportion of Permian holdover genera and cosmopolitan taxa. Taxonomically, this community is different from coeval faunas with dissimilarity values > 60%. Ecologically, however, this fauna is similar to faunas from the Dolomites (Italy), and East Greenland. This new data, therefore, suggests that the lower Griesbachian invertebrate faunas were taxonomically heterogeneous, whereas ecologically they were relatively homogenous. The marine community on the Great Bank of Guizhou records genera that survived the mass extinction event with some, but not all, recording a size reduction, i.e., the Lilliput effect. The absence of large body fossils and the preferential survival of small species suggest that the mass extinction event was size-selective.

opencc-by-4.0Dec 2023View details →

The code and software to identify putative trace makers of horizontal trace fossils: Palaeontology

These are the code ("CurveGithub.m") and the free software ("Curvesoftware.exe") that help you identify putative trace makers of horizontal trace fossils with frequency spectrum and autocorrelation function. You can also use it to study the frequency and size of self-repeating patterns in a horizontal trace. You can use the metrics to quantify ichnotaxonomy as well. An example of the coordinates of a horizontal trace is "A curve-Github.txt", which is output from Getdata Graph Digitizer, with the first describing sentence in the output file removed, leaving cooridnates only. Zero-value is not allowed in the coordinates. The paper is published in Palaeontology, with doi: 10.1111/pala.12686, <a title="Quantitative Ichnology" href="https://onlinelibrary.wiley.com/doi/abs/10.1111/pala.12686">https://onlinelibrary.wiley.com/doi/abs/10.1111/pala.12686</a>  IMPORTANT NOTICE !!!!! MATLAB code Line 41: "plot(ss,YY(M:M+99)/max(YY(M:M+99)),'r-'); " means plotting the autocorrelation over sampling steps; If you would like to plot the autocorrelation over normalized length (as in both the manuscript and the free software), it should be "plot(ss/Fs,YY(M:M+99)/max(YY(M:M+99)),'r-'); "

Figure 17 in The skeletal remains of the euryhaline sclerorhynchoid †Onchopristis (Elasmobranchii) from the 'Mid'-Cretaceous and their palaeontological implications

Figure 17. Enlarged dermal denticles of †Onchopristis numidus from the 'Kem Kem Beds'. A–C. B–C, Charles Underwood personal collection, lateral view, longitudinal section and close up of the enameloid layer. D–F, IGR 2819, lateral, anterior and basal views. G, IGR 2820, lateral view. H, IGR 2821, antero-apical view. Scale bars: 1 cm.

Figure 16. A–F in The skeletal remains of the euryhaline sclerorhynchoid †Onchopristis (Elasmobranchii) from the 'Mid'-Cretaceous and their palaeontological implications

Figure 16. A–F, ventral rostral denticles from the section of the rostrum of †Onchopristis numidus (NHMUK PV P 75502). A–C, Morpho 1. D–F, Morpho 2 (scale bar: 2 mm) NHMUK PV P 74051. G, anterior part of the ventral surface of IPUW 353500 rostrum (scale bar: 1 cm).

Figure 15. A, B in The skeletal remains of the euryhaline sclerorhynchoid †Onchopristis (Elasmobranchii) from the 'Mid'-Cretaceous and their palaeontological implications

Figure 15. A, B, vertebral centra of †Onchopristis numidus from the 'Kem Kem Beds' collection sites Boulalou (KK5: easting: 418413; northing: 3479178 UTM) NHMUK PV P 74052. A, B, sagittal section of vertebra. C, articulation surface of the vertebra. Scale bars: 1 cm.

Figure 13 in The skeletal remains of the euryhaline sclerorhynchoid †Onchopristis (Elasmobranchii) from the 'Mid'-Cretaceous and their palaeontological implications

Figure 13. Micro-CT-based volume renderings and virtual sections of oral teeth of † found associated with IPUW 353500. A–E, broken main cusp in: A, labial; B, occlusal; C, lingual; D, medial; D, E, profile views. F–L, incomplete tooth lacking part of the labial apron and root in: F, labial; H, lingual; I, apical; J, L, profile views; tooth sections in (G) axial and (K) sagittal aspects; M–S, tooth with a broken main cusp in: M, labial; N, lingual; O, occlusal; P, basal; Q, S, profile views tooth section in (R).

Figure 10. A, B in The skeletal remains of the euryhaline sclerorhynchoid †Onchopristis (Elasmobranchii) from the 'Mid'-Cretaceous and their palaeontological implications

Figure 10. A, B, neurocranium of †Onchopristis numidus. A, picture of IPUW 353500. B, line drawing. C, picture of IGR 2818. D, line drawing. Scale bar 4 cm. Note: darken areas on drawing represent sediments.

Figure 9 in The skeletal remains of the euryhaline sclerorhynchoid †Onchopristis (Elasmobranchii) from the 'Mid'-Cretaceous and their palaeontological implications

Figure 9. Fragment of the rostrum of †Onchopristis numidus. A, IPUW 353500 (scale bar: 1 cm). B, NHMUK PV P 75503 (scale bar: 5 cm). C, hypothetical scheme of the growth and addition of rostral denticles in †Onchopristis. Denticles in grey in (C) are larger denticles replacing smaller ones that fell.