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FIGURE 3 in Tracking biases in the regular echinoid fossil record: The case of Paracentrotus lividus in recent and fossil shallow-water, high-energy environments
FIGURE 3. Remains of Paracentrotus lividus from Level A of the Is Mesas deposit (Late Pleistocene). A, 1) Fragment of test consisting of ambulacral and interambulacral plates still sutured together and showing interplate fracturing; 2) Isolated plates; 3) Fragments; 4) Spines. B, Large portion of ambulacral column showing intraplate fragmentation. C, Large portion of interambulacral column. D, Fragmented interambulacral plate. E, Madreporite. F, Hemipyramid. G, Rotula. H, Complete spine. A-C, H Scale bars equal 1 cm. E-G Scale bars equal 0.5 cm.
FIGURE 1 in Tracking biases in the regular echinoid fossil record: The case of Paracentrotus lividus in recent and fossil shallow-water, high-energy environments
FIGURE 1. Location of A, Late Pleistocene deposit of Is Mesas and B, Sa Mesa Longa Beach, Sardinia, Italy.
FIGURE 2. A in Tracking biases in the regular echinoid fossil record: The case of Paracentrotus lividus in recent and fossil shallow-water, high-energy environments
FIGURE 2. A, Field view of the Upper Pleistocene deposit of Is Mesas. B, Stratigraphic section of the deposit.
FIGURE 3. Fossilized bone fragments for the Vrabchov dol. 1 in Bone histology reveals the first record of titanosaur (Dinosauria: Sauropoda) from the Late Cretaceous of Bulgaria
FIGURE 3. Fossilized bone fragments for the Vrabchov dol. 1, Multiple views of specimen U.S., K21586, an undetermined long bone diaphyseal fragment; 2. Specimen NMNHS FR-16, possibly a partial diaphysis of undetermined long bone. Scale bar equals 3 cm.
FIGURE 2 in First record and a new species of the fossil dragonfly genus Proinogomphus (Odonata: Liassogomphidae) from the Early Jurassic of Bascharage in the Grand Duchy of Luxembourg
FIGURE 2. Photograph of holotype SMNS 67854 of Proinogomphus kreuzerorum sp. nov. Scale bar = 5 mm.
FIGURE 1 in Review of the fossil record of Bolitophilidae, with description of new taxa and discussion of position of Mangas Kovalev (Diptera: Sciaroidea)
FIGURE 1. Bolitophila warreni sp. nov., holotype USNM 595138. Scale bar equals 3 mm.
Figure 2 from: Casadei-Ferreira A, Chaul JCM, Feitosa RM (2019) A new species of Pheidole (Formicidae, Myrmicinae) from Dominican amber with a review of the fossil records for the genus. ZooKeys 866: 117-125. https://doi.org/10.3897/zookeys.866.35756
Figure 2 Illustrations of †Pheidoleanticua sp. nov. A Lateral view B full face view C dorsal view and D hypostomal margin. Scale bars: 0.2 mm.
Figure 1 from: Casadei-Ferreira A, Chaul JCM, Feitosa RM (2019) A new species of Pheidole (Formicidae, Myrmicinae) from Dominican amber with a review of the fossil records for the genus. ZooKeys 866: 117-125. https://doi.org/10.3897/zookeys.866.35756
Figure 1 †Pheidoleanticua sp. nov. A Lateral view B dorsal view C full face view and D hypostomal margin. Scale bars: 0.2 mm.
Text-fig. 2. Dentition and mandible of Panthera fossilis (REICHENAU, 1906) from Za Hájovnou Cave (Moravia, the Czech Republic), Middle Pleistocene. Scale bars: A = 1 cm (a–c), B = 3 cm (d–e). a – C dext. (Narozeninová chodba, layer 5,> MIS 9), lingual view; b – P4 dext. (Chodba naděje, layer 3–4, ~ MIS 9), buccal view; c – m1 dext. (Chodba naděje, layer 6,> MIS 9), lingual view; d – left mandible fragment with p4 and m1 (non-stratified record), buccal view; e – a detail occlusal view of p4 and m1 of the left mandible. in Panthera Fossilis (Reichenau, 1906) (Felidae, Carnivora) From Za Hájovnou Cave (Moravia, The Czech Republic): A Fossil Record From 1987-2007
Text-fig. 2. Dentition and mandible of Panthera fossilis (REICHENAU, 1906) from Za Hájovnou Cave (Moravia, the Czech Republic), Middle Pleistocene. Scale bars: A = 1 cm (a–c), B = 3 cm (d–e). a – C dext. (Narozeninová chodba, layer 5,> MIS 9), lingual view; b – P4 dext. (Chodba naděje, layer 3–4, ~ MIS 9), buccal view; c – m1 dext. (Chodba naděje, layer 6,> MIS 9), lingual view; d – left mandible fragment with p4 and m1 (non-stratified record), buccal view; e – a detail occlusal view of p4 and m1 of the left mandible.
Text-fig. 1. Taphonomic and pathological phenomena of cave bear bones from Late Pleistocene deposits from Vařekova chodba in Za Hájovnou Cave (Moravia, the Czech Republic); a – fragment of vertebra with bite marks; b – fragment of right humerus, proximal part with bite marks; c – thoracic vertebra with pathological rib facet; d–e – fused left astragalus with left calcaneus (d: medial view, e: dorsal view). in Basic Population And Taphonomic Analysis Of Bear Assemblages From Za Hájovnou Cave (Moravia, The Czech Republic): A Fossil Record From 1987-2007
Text-fig. 1. Taphonomic and pathological phenomena of cave bear bones from Late Pleistocene deposits from Vařekova chodba in Za Hájovnou Cave (Moravia, the Czech Republic); a – fragment of vertebra with bite marks; b – fragment of right humerus, proximal part with bite marks; c – thoracic vertebra with pathological rib facet; d–e – fused left astragalus with left calcaneus (d: medial view, e: dorsal view).
Data from: PaleoENM: applying ecological niche modeling to the fossil record
Ecological niche modeling (ENM) is a quantitative approach to predict species' abiotic requirements. It is a correlative technique, requiring geographically explicit information on species occurrences and the suites of environmental conditions experienced at each occurrence point. The output of these models is a set of environmental suitability rules that can be projected geographically and through time to test biogeographic, ecologic, and evolutionary hypotheses. Although developed by biologists and used extensively in the modern, ENM is in its early stages of application to the deep-time fossil record (hence PaleoENM). In part its limited use in the fossil record thus far reflects the methodological challenge of constructing paleoenvironmental layers needed for PaleoENM analysis, whereas in the modern these layers are available from large public databases (e.g., WorldClim). This paper provides a contextual and methodological framework for appropriately applying PaleoENM, including best practices for developing species occurrence and paleoenvironmental data sets for PaleoENM analyses.
Data from: Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record
Phylogeny-based approaches can be used to infer diversification dynamics and the rate and pattern of trait change. Applying these analyses to fossil data often requires time-scaling a cladogram of morphotaxon relationships. Although several time-scaling methods have been developed for this purpose, the incomplete sampling of the fossil record can distort the apparent timing of branching. It is unclear how well different time-scaling methods reconstruct the true temporal relationships or how any such inaccuracy could affect tree-based evolutionary analyses. I developed process-based simulations of the fossil record that allow the comparison of approximated time-scaled trees to true time-scaled trees. I used this simulation framework to test the effect of time-scaling methods on the fidelity of several commonly applied tree-based analyses, across a range of simulation conditions. When the fidelity of time-scaling methods differed, the stochastic "cal3" time-scaling method with ancestral assignment produced preferable results. Estimating rates and models of continuous trait evolution was particularly sensitive to bias from scenarios that forced the insertion of many short branch lengths, a bias that is not solved by any of the considered time-scaling methods in all scenarios. The cal3 method of time-scaling can be recommended as the preferred time-scaling method among those tested, but caution must be exercised because tree-based analyses are prone to easily overlooked biases.
Data from: Model adequacy and microevolutionary explanations for stasis in the fossil record
Long-term phenotypic stasis is frequently observed in the fossil record, but not readily predicted from microevolutionary theory. To test competing explanations for stasis on macroevolutionary time scales we need reliably estimated parameters from appropriate evolutionary models that adequately describe the evolutionary trait dynamics. Here, we develop tests to assess the adequacy of the most commonly used stasis model in evolutionary biology and apply them to time series of phenotypic traits from fossil lineages. Of the 572 fossil time series we analyzed from the literature, 263 times series showed a better fit to the stasis model relative to alternative models, but only 172 of those fitted the stasis model both in relative and absolute terms. The estimated trait variances from these 172 time series do not correlate with rough proxies of effective population size. Our preliminary investigation of the fixed-optimum hypothesis hence fails to give empirical support to the idea that genetic drift around a constant trait optimum is an explanation for stasis in the fossil record. We argue that optima following stationary processes on the adaptive landscape is a viable hypothesis for stasis that needs further investigation. We end by discussing how investigations of model adequacy can be a valuable approach for increasing our understanding of the dynamics of the adaptive landscape on macroevolutionary time scales.
Data from: An expansion of age constraints for microbial clades that lack a conventional fossil record using phylogenomic dating
Most microbial taxa lack a conventional microfossil or biomarker record, and so we currently have little information regarding how old most microbial clades and their associated traits are. Building on the previously published oxygen age constraint, two new age constraints are proposed based on the ability of microbial clades to metabolize chitin and aromatic compounds derived from lignin. Using the archaeal domain of life as a test case, phylogenetic analyses, along with published metabolic and genetic data, showed that members of the Halobacteriales and Thermococcales are able to metabolize chitin. Ancestral state reconstruction combined with phylogenetic analysis of the genes underlying chitin degradation predicted that the ancestors of these two groups were also likely able to metabolize chitin or chitin-related compounds. These two clades were therefore assigned a maximum age of 1.0 Ga (when chitin likely first appeared). Similar analyses also predicted that the ancestor to the Sulfolobus solfataricus-Sulfolobus islandicus clade was able to metabolize phenol using catechol dioxygenase, so this clade was assigned a maximum age of 475 Ma. Inferred ages of archaeal clades using relaxed molecular clocks with the new age constraints were consistent with those inferred with the oxygen age constraints. This work expands our current toolkit to include Paleoproterozoic, Neoproterozoic, and Paleozoic age constraints, and should aid in our ability to phylogenetically reconstruct the antiquity of a wide array of microbial clades and their associated morphological and biogeochemical traits, spanning deep geologic time. Such hypotheses-although built upon evolutionary inferences-are fundamentally testable.
Data from: The mosasaur fossil record through the lens of fossil completeness
The quality of the fossil record affects our understanding of macroevolutionary patterns. Palaeodiversity is filtered through geological and human processes; efforts to correct for these biases are part of a debate concerning the role of sampling proxies and standardization in biodiversity models. We analyse the fossil record of mosasaurs in terms of fossil completeness as a measure of fossil quality, using three novel, correlating metrics of fossil completeness and 4083 specimens. A new qualitative measure of character completeness (QCM) correlates with the phylogenetic character completeness metric. Mean completeness by species decreases with specimen count; average completeness by substage varies significantly. Mean specimen completeness is higher for species‐named fossils than those identified to genus and family. We consider the effect of tooth‐only specimens. Importantly, we find that completeness of species does not correlate with completeness of specimens. Completeness varies by palaeogeography: North American specimens show higher completeness than those from Eurasia and Gondwana. These metrics can be used to identify exceptional preservation; specimen completeness varies significantly by both formation and lithology. The Belgian Ciply Formation displays the highest completeness; clay lithologies show higher completeness values. Neither species diversity nor sea level correlates significantly with fossil completeness. A generalized least squares (GLS) analysis using multiple variables agrees with this result, but reveals two variables with significant predictive value for modelling averaged diversity: sea level, and mosasaur and plesiosaur‐bearing formations (the latter is redundant with diversity). Mosasaur completeness is not driven by sea level, nor does completeness limit the mosasaur diversity signal.
Figure 4 from: Belokobylskij SA, Dubovikoff DA, Manukyan AR, Zharkov DM (2021) Braconid parasitoids of ants (Hymenoptera, Braconidae, Euphorinae, Neoneurini) from Baltic amber with a discussion of records of fossil larvae parasitizing ant workers. In: Proshchalykin MYu, Gokhman VE (Eds) Hymenoptera studies through space and time: A collection of papers dedicated to the 75th anniversary of Arkady S. Lelej. Journal of Hymenoptera Research 84: 29-43. https://doi.org/10.3897/jhr.84.67749
Figure 4 A worker of the ant Lasius schiefferdeckeri Mayr, 1868 (Baltic amber) with emerging larva of an Elasmosomites species A general view, right side B general view, left side C gastral apex of the ant with Elasmosomites larva D micro-CT reconstruction showing the position of the parasitoid larva inside the ant.
Figure 3 from: Belokobylskij SA, Dubovikoff DA, Manukyan AR, Zharkov DM (2021) Braconid parasitoids of ants (Hymenoptera, Braconidae, Euphorinae, Neoneurini) from Baltic amber with a discussion of records of fossil larvae parasitizing ant workers. In: Proshchalykin MYu, Gokhman VE (Eds) Hymenoptera studies through space and time: A collection of papers dedicated to the 75th anniversary of Arkady S. Lelej. Journal of Hymenoptera Research 84: 29-43. https://doi.org/10.3897/jhr.84.67749
Figure 3 Elasmosomites primordialis Brues, 1933 (male, Baltic amber, # BX 9/21.2) A fore wing B hind wing C posterior margin of hind wing.
Figure 2 from: Belokobylskij SA, Dubovikoff DA, Manukyan AR, Zharkov DM (2021) Braconid parasitoids of ants (Hymenoptera, Braconidae, Euphorinae, Neoneurini) from Baltic amber with a discussion of records of fossil larvae parasitizing ant workers. In: Proshchalykin MYu, Gokhman VE (Eds) Hymenoptera studies through space and time: A collection of papers dedicated to the 75th anniversary of Arkady S. Lelej. Journal of Hymenoptera Research 84: 29-43. https://doi.org/10.3897/jhr.84.67749
Figure 2 Elasmosomites primordialis Brues, 1933 (male, Baltic amber, # BX 9/21.2) A habitus, dorso-lateral view B habitus, ventro-lateral view C head, antenna and metasoma, dorsal view D head and mesosoma, ventro-lateral view E mesosoma, dorsal view F metasoma, ventral view.
Figure 1 from: Belokobylskij SA, Dubovikoff DA, Manukyan AR, Zharkov DM (2021) Braconid parasitoids of ants (Hymenoptera, Braconidae, Euphorinae, Neoneurini) from Baltic amber with a discussion of records of fossil larvae parasitizing ant workers. In: Proshchalykin MYu, Gokhman VE (Eds) Hymenoptera studies through space and time: A collection of papers dedicated to the 75th anniversary of Arkady S. Lelej. Journal of Hymenoptera Research 84: 29-43. https://doi.org/10.3897/jhr.84.67749
Figure 1 Elasmosomites arkadyleleji sp. nov. (female, holotype, Baltic amber, # BX 9/21.1) A habitus, dorsal view B habitus, ventral view C antenna D head and mesosoma, dorsal view E head, mesosoma and legs, ventral view F metasoma and distal part of fore wing, dorsal view J metasoma, middle and hind legs, ventral view H fore wing.
Figure 5 in Phylogeny of families in the Pectinoidea (Mollusca: Bivalvia): importance of the fossil record
Figure 5. Diagrammatic shell structure map of Propeamussium modified from Waller (1972). The dotted lines outline calcitic internal ribs that are covered by the aragonitic inner layer. Muscle scars and pallial lines are areas of secretion of aragonitic myostracum.
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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.