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Figure 7 in A comparative atlas of selected skeletal elements of European urodeles (Amphibia: Urodela) for palaeontological investigations
Figure 7. Atlantes of European urodeles. A, Calotriton asper (MNCN 16122). B, Euproctus montanus (BSPGM 4202). C, Ichthyosaura alpestris (MDHC 407). D, Ichthyosaura alpestris (MDHC 391). From left to right: anterior, dorsal, lateral (left lateral for A; right lateral for B–D), posterior and ventral views. Scale bars: 1 mm.
Figure 2 in A comparative atlas of selected skeletal elements of European urodeles (Amphibia: Urodela) for palaeontological investigations
Figure 2. Terminology followed for the atlas. Atlas of Ichthyosaura alpestris in anterior (A), dorsal (B), right lateral (C), posterior (D) and ventral (E) views. Abbreviations: cot, cotyle; fsn, foramen of the first spinal nerve; infcr, inferior crests; ivca, incisura vertebralis caudalis; ivcr, incisura vertebralis cranialis; lcr, lateral crest; na, neural arch; nc, neural canal; ncr, neural crest; odpr, odontoid process; oj, occipital joints; postz, postzygapophyses; scr, secondary crest. Scale bar: 1 mm.
Figure 5 in A comparative atlas of selected skeletal elements of European urodeles (Amphibia: Urodela) for palaeontological investigations
Figure 5. Otic–occipitum complexes of European Pleurodelinae. A, left complex of Calotriton asper (MNCN 16122). B, right complex of Euproctus montanus (BSPGM 4202). C, left complex of Ichthyosaura alpestris (MDHC 416). D, right complex of Lissotriton vulgaris (MDHC 133). E, left complex of Ommatotriton vittatus (MNCN 13193). F, right complex of Pleurodeles waltl (MDHC 253). G, right complex of Triturus carnifex (MDHC 38). H, left complex of Triturus carnifex (MDHC 299). From left to right: anterior, dorsal, lateral, posterior and ventral views. Scale bars: 1 mm.
Figure 6 in A comparative atlas of selected skeletal elements of European urodeles (Amphibia: Urodela) for palaeontological investigations
Figure 6. Atlantes of European urodeles. A, Salamandrella keyserlingii (BSPGM 5451), most probably not completely ossified (see the Material section). B, Proteus anguinus (BSPGM 4538). C, Speleomantes strinatii (MDHC 225), most probably not completely ossified (see the Material section). D, Salamandrina perspicillata (MDHC 407). E, Chioglossa lusitanica (MNCN 16099). F, Mertensiella caucasica (MNCN 23821). G, Salamandra salamandra (MDHC 396). From left to right: anterior, dorsal, lateral (right lateral for A–C, E, F; left lateral for D, G), posterior and ventral views. Scale bars: 1 mm.
Figure 4 in A comparative atlas of selected skeletal elements of European urodeles (Amphibia: Urodela) for palaeontological investigations
Figure 4. Otic–occipitum complexes of European urodeles (Plethodontidae, Salamandrininae and Salmandrinae). A, left complex of Speleomantes strinatii (MDHC 225). B, left complex of Salamandrina perspicillata (MDHC 407). C, right complex of Chioglossa lusitanica (MNCN 16099; ventral view of the left complex because the right one is anomalous; see main text). D, right complex of Mertensiella caucasica (MNCN 23821). E, left complex of Salamandra salamandra (MDHC 227). From left to right: dorsal, ventral, anterior, posterior, medial and lateral views. Scale bars: 1 mm.
Figure 1. Terminology followed for the otic–occipitum complex. A–F in A comparative atlas of selected skeletal elements of European urodeles (Amphibia: Urodela) for palaeontological investigations
Figure 1. Terminology followed for the otic–occipitum complex. A–F, left otic–occipitum complex of Salamandra salamandra from left to right in dorsal, ventral, anterior, posterior, medial and lateral views. G–L, right otic–occipitum complex of Lissotriton vulgaris from left to right in dorsal, ventral, anterior and lateral views. Abbreviations (newly introduced terms are in quotes): 'acav, auditory cavity'; bco, basicapsular commissure; bpr, processus basalis; crr, crista retrosellaris; fba, fenestra basicranialis posterioris; fend, foramen endolymphaticum; ffa, foramen faciale; fo, fenestra ovalis; fper, foramen perylimphaticum; fpo, foramen postoticum; fpro, foramen prooticum; hco, hypochordal commissure; 'lts, lamina of the tectum synoticum'; 'mcr, medial crest'; 'md, middle depression'; occ, occipital cotyle; otpr, otic process; pan, prominentia semicircularis anterioris; par, parietal crest; pcr, parotic crest; pla, prominentia semicircularis lateralis; ppr, parotic process; pps, prominentia semicircularis posterioris; preco, prefacial commissure; spe, sulcus petrosus; sulc, sulcus carotis; tsyn, tectum synoticum. Scale bars: 1 mm.
Data from: Early Triassic benthic invertebrates from the Great Bank of Guizhou, South China: systematic palaeontology and palaeobiology
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Data from: Phylogeny, palaeontology, and primates: do incomplete fossils bias the tree of life?
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Taxonomic identification using virtual palaeontology and geometric morphometrics: a case study of Jurassic nerineoidean gastropods
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Data from: A survey of palaeontological sampling biases in fishes based on the phanerozoic record of Great Britain
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Data from: Bayesian analyses in phylogenetic palaeontology: interpreting the posterior sample
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Data from: Integrating palaeontological and molecular data uncovers multiple ancient and recent dispersals in the pantropical Hamamelidaceae
Aim: The integration of palaeontological and phylogenetic data can improve our understanding in the spatio-temporal evolutionary processes of living organisms. However, how best to use fossil data in divergence time estimation and ancestral range reconstruction remains challenging. Here, we integrated palaeontological and molecular data to investigate the historical biogeography of Hamamelidaceae, a pantropical angiosperm family with abundant fossils outside its present distribution. Location: Global tropical/subtropical areas. Methods: Using seven DNA regions (> 7,500 bp) from plastid and nuclear genomes, we reconstructed a robust phylogenetic framework for Hamamelidaceae with the first complete genus-level sampling. We used the tip-dating method with the 22 fossils to estimate divergence times for the family, and inferred the ancestral range of lineages under the dispersal-extinction-cladogenesis model by incorporating the fossils. Results: Our biogeographic analysis indicates that extant Hamamelidaceae most likely originated in tropical Asia during the mid-Cretaceous, and in the family 20 dispersals occurred during three major time intervals: the Upper Cretaceous (c. 93–69 Ma), Paleocene–Eocene (c. 63–39 Ma) and late Oligocene (c. 27–23 Ma). Main conclusions: Overland migrations through available land bridges and island chains may have been mainly responsible for hamamelidaceous range expansions during these three episodes. This study contributes to our knowledge on the assembly and evolution of angiosperm-dominated tropical and subtropical forests.
Data from: Taxonomy and phylogeny can yield comparable results in comparative palaeontological analyses
Many extinct taxa with extensive fossil records and mature taxonomic classifications have not yet been the subject of formal phylogenetic analysis. Here, we test whether the taxonomies available for such groups represent useful (i.e., non-misleading) substitutes for trees derived from matrix-based phylogenetic analyses. We collected data for 52 animal clades that included fossil representatives, and for which a recent cladogram and pre-cladistic taxonomy were available. We quantified the difference between the time-scaled phylogenies implied by taxonomies and cladograms using the matching cluster distance metric. We simulated phenotypic trait values and used them to estimate a series of commonly used, phylogenetically explicit measures (phylogenetic signal [Blomberg's K], phylogenetic generalized least squares [PGLS], mode of evolution [Brownian vs. Ornstein–Uhlenbeck], and phylogenetic clustering of extinction [Fritz and Purvis' D]) in order to determine the degree to which they co-varied on taxonomic and cladistic trees. With respect to topology taxonomies are good approximations of the underlying evolutionary relationships as recorded in inferred cladograms. Detection of phylogenetic clustering of extinction could not be properly assessed. For all other evolutionary analyses, results from taxonomy-based phylogenies (TBPs) co-varied with those from cladogram-based phylogenies (CBPs), but individual comparisons could be misleading. The relative length of terminal branches (influenced by stratigraphy and sampling rate) is a key control on the shared information between, and therefore the relative performance of, TBP and CBP. Collectively these results suggest that under particular circumstances and after careful consideration some taxonomies, or composite trees that incorporate taxonomic information, could be used in place of a formal analytical solution, but workers must be cautious. This opens certain parts of a previously inaccessible section of the fossil record to interrogation within an explicit comparative framework, which will help to test many classical macroevolutionary hypotheses formulated for groups that currently lack formal phylogenetic estimates.
Data from: Coupling of palaeontological and neontological reef coral data improves forecasts of biodiversity responses under global climatic change
Reef corals are currently undergoing climatically-driven poleward range expansions, with some evidence for equatorial range retractions. Predicting their response to future climate scenarios is critical to their conservation, but ecological models are based only on short-term observations. The fossil record provides the only empirical evidence for the long-term response of organisms under perturbed climate states. The palaeontological record from the Last Interglacial (LIG; 125,000 years ago), a time of global warming, suggests that reef corals experienced poleward range shifts and an equatorial decline relative to their modern distribution. However, this record is spatiotemporally biased, and existing methods cannot account for data absence. Here, we use ecological niche modelling to estimate reef corals' realised niche and LIG distribution, based on modern and fossil occurrences. We then make inferences about modelled habitability under two future climate change scenarios (RCP4.5, RCP8.5). Reef coral ranges during the LIG were comparable to the present, with no prominent equatorial decrease in habitability. Reef corals are likely to experience poleward range expansion and large equatorial declines under RCP4.5 and RCP8.5. However, this range expansion is likely optimistic in the face of anthropogenic climate change. Incorporation of fossil data in niche models improves forecasts of biodiversity responses under global climatic change.
Data from: Molecular palaeontology illuminates the evolution of ecdysozoan vision
Colour vision is known to have arisen only twice – once in Vertebrata and once within the Ecdysozoa, in Arthropoda. However, the evolutionary history of ecdysozoan vision is unclear. At the molecular level, visual pigments, composed of a chromophore and a protein belonging to the opsin family, have different spectral sensitivities and these mediate colour vision. At the morphological level, ecdysozoan vision is conveyed by eyes of variable levels of complexity; from the simple ocelli observed in the velvet worms (phylum Onychophora) to the marvellously complex eyes of insects, spiders and crustaceans. Here we explore the evolution of ecdysozoan vision at both the molecular and morphological level; combining analysis of a large-scale opsin dataset that includes previously-unknown ecdysozoan opsins with morphological analyses of key Cambrian fossils with preserved eye structures. We found that while several non-arthropod ecdysozoan lineages have multiple opsins, arthropod multi-opsin vision evolved through a series of gene duplications were fixed in a period of 35 to 71 Million years (Ma) along the stem-arthropod lineage. Our integrative study of the fossil and molecular record of vision indicates that fossils with more complex eyes were likely to have possessed a larger complement of opsin genes.
Fig. 30 in Diversity and taxonomy of the Late Triassic sauropodomorphs (Saurischia, Sauropodomorpha) stored in the Palaeontological Collection of Tübingen, Germany, historically referred to Plateosaurus
Fig. 30. Skeletal elements of specimen GPIT-PV-30789 on display in the diorama, referred to as Plateosaurus 'quenstedti' by von Huene (see Fig. 14) comprising a right hindlimb, with a femur, a tibia, a fibula, and a complete pes.
FIG. 4 in The d'Orbigny Palaeontological Collection of the National Museum of Natural History and Science, Lisbon, Portugal: Historical perspective and revision of Cretaceous Cephalopoda
FIG. 4. — Cretaceous ammonites and belemnites of the d'Orbigny Collection of the National Museum of Natural History and Science (Museu Nacional de História Natural e da Ciência): A-C, Coilopoceras requienianus (d'Orbigny, 1840) in lateral (A) and ventral (B) views, and original label (C): Nº 518/Ammonites Requienianus (d'Orb), Andar 21º [corrected] Turoniense, Terreno Cretaceo, Localidade Uchaux (Vanduse);D-F, Turrilites (Turrilites) costatus Lamarck,1801 in lateral (D) and basal (E) views, and original label (F): Nº 466/Turrilites costatus (Lamarck), Andar 20º Cenomaniense, Terreno Cretaceo,Localidade Rouen (Seine inf.re); G-J, Duvalia dilatata (de Blainville, 1827) in dorsal view (G), section (H), lateral view (I), and original label (J): Nº 351/Belemnites dilatatus (Blainville),Andar 17º Neocomiense,Terreno Cretaceo,Localidade Cheiron perto de [near of] Castellanne (Basses Alpes);K-N, Hibolithes subfusiformis(Raspail,1829) in dorsal view (K), section (L), ventral view (M), and original label (N):Nº 352/Belemnites subfusiformis (Raspail), Andar 17º Neocomiense, Terreno Cretaceo, Localidade Cheiron (Basses Alpes); O-R, Belemnitella mucronata (von Schlotheim, 1813) in dorsal view (O), section (P), ventral view (Q), and original label (R): Nº 556/Belemnitella mucronata (d'Orb), Andar 22º Senoniense, Terreno Cretaceo, Localidade Epernay (Marne). Scale bar: 2 cm.
Text-fig. 8. Mhengere Hill fossiliferous localities (1–3). Silicified tree trunks and fragments of wood are abundant in the poorly indurated basal deposits (marly sand and conglomerate) as well as in the silicified lime-rich sandstones that form the hill, which is interpreted to be the remains of a palaeopan. Image modified from Google Earth. in Stratigraphy, Chronology And Palaeontology Of The Tertiary Rocks Of The Cheringoma Plateau, Mozambique
Text-fig. 8. Mhengere Hill fossiliferous localities (1–3). Silicified tree trunks and fragments of wood are abundant in the poorly indurated basal deposits (marly sand and conglomerate) as well as in the silicified lime-rich sandstones that form the hill, which is interpreted to be the remains of a palaeopan. Image modified from Google Earth.
Fig. 4 in Photography in the ultraviolet and visible violet spectra: Unravelling methods and applications in palaeontology
Fig. 4. Bivalves photographed under visible, UV, and VV light. A. Arcoid bivalve Glycymeris nummaria (Linnaeus, 1758) from the Lower Pleistocene Arda River section, Italy. MPUM 12162 (ACG261-1), right valve in external (A1–A3) and internal (A4–A6) view, visible light (A1, A4), 365 nm (A2, A5) and 440 nm (A3, A6). B. Hippuritid bivalve Vaccinites sp. from the Upper Cretaceous Samhan Formation, Oman. MPUM 12167 (OMAN-1), conical valve, visible light (B1), 365 nm (B2) and 440 nm (B3).
FIGURE 4 in Injured trilobites within a collection of dinosaurs: Using the Royal Tyrrell Museum of Palaeontology to document Cambrian predation
FIGURE 4. The first record of a Hemirhodon amplipyge specimen with an abnormality (TMP.2006.036.0102). A: Complete specimen. B: Close up of the abnormality on left side of pygidium, showing a truncated 'W'- (white arrows) and 'V'-shape (black arrow) on pygidial margin.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.