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30 results for “deep-time”
Orogens of Big Sky Country: Reconstructing the Deep-Time Tectonothermal History of the Beartooth Mountains, Montana and Wyoming, USA (Supporting Information)
<p>Supporting datasets for Ronemus et al., "Orogens of Big Sky Country: Reconstructing the Deep-Time Tectonothermal History of the Beartooth Mountains, Montana and Wyoming, USA" in review at <em>Tectonics </em>as of August 16, 2022.</p> <p>Dataset S1. Detailed analytical settings and data for zircon U-Pb geochronology</p> <p>Dataset S2. Biotite <sup>40</sup>Ar/<sup>39</sup>Ar analytic results</p> <p>Dataset S3. Zircon (U-Th)/He analytic results</p> <p>Dataset S4. Apatite and zircon grain photomicrographs with measurements</p> <p>Dataset S5. Apatite (U-Th-Sm)/He analytic results</p> <p>Dataset S6. QTQt input and results files</p> <p> </p> <p>Datasets S1, S2, S3, and S5 are also available in the Tectonics submission supporting information.</p>
Deep-time convergent evolution in animal communication presented by shared adaptations for coping with noise in lizards and other animals
<p>Convergence in communication appears rare compared to other forms of adaptation. This is puzzling, given communication is acutely dependent on the environment and expected to converge in form when animals communicate in similar habitats. We uncover deep-time convergence in territorial communication between two groups of tropical lizards separated by over 140 million years of evolution: the Southeast Asian Draco and Caribbean Anolis. These groups have repeatedly converged in multiple aspects of display along common environmental gradients. Robot playbacks to free-ranging lizards confirmed the most prominent convergence in display is adaptive, as it improves signal detection. We then provide evidence from a sample of the literature to further show convergent adaptation among highly divergent animal groups is almost certainly widespread in nature. Signal evolution is therefore curbed towards the same set of adaptive solutions, especially when animals are challenged with the problem of communicating effectively in noisy environments.</p>
A double-edged sword: evolutionary novelty along deep-time diversity oscillation in an iconic group of predatory insects (Neuroptera: Mantispoidea)
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Deep-time convergent evolution in animal communication presented by shared adaptations for coping with noise in lizards and other animals
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Museum ‘dark data’ show variable impacts on deep-time biogeographic and evolutionary history
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Deep-Time Marine Sedimentary Element Database
<p>The Deep-Time Marine Sedimentary Element Database (DM-SED), built upon the Sedimentary Geochemistry and Paleoenvironments Project (SGP; n = 28,753) database with an additional 433 studies and 34,874 data entries, totaling 63,627 entries. This database contains 2,522,255 discrete proxy values covering the distributions of major and trace elements and some isotopes in ancient marine sediments. It includes 9,207 entries from the Precambrian and 54,420 entries from the Phanerozoic, thus providing significant references for reconstructing deep-time Earth system evolution.</p>
Data from: Decoding the drivers of deep-time wetland biodiversity: insights from an early Permian tropical lake ecosystem
<p><span>Wetlands are important to continental evolution, providing both the arenas and refugia for emerging and declining biotas, respectively. </span><span>Based on this significance and the high preservation potential, the resulting fossiliferous deposits play a key role in understanding past and future biodiversity. We reconstruct the trophic structure and age of the early Permian Manebach-Lake ecosystem, Germany, thriving in a wetland when the tropical biosphere faced profound upheaval in the peaking Late Palaeozoic Icehouse. Nine excavations, the high-resolution, spatiotemporal documentation of fossils and sediments, and the U-Pb radioisotopic dating of tuffs allow us to distinguish autogenic and allogenic factors that shaped the limnic biocoenosis. The Manebach Lake was an exorheic, stratified, perennial water body in the 10<sup>1</sup>–10<sup>2</sup> km<sup>2</sup> scale, integrated into the catchment draining much of the European Variscides. Lake formation paralleled an Asselian regional wet climatic interval and benefited from rising groundwater tables due to post-Variscan tectonics. Stromatolite-forming cyanobacteria, bivalves, several crustacean groups, amblypterids resembling <em>Paramblypterus duvernoyi</em> and xenacanthid sharks formed a differentiated biocoenosis. Digestive remains prove the rare presence of acanthodians, branchiosaurs, and large tetrapods. Anoxic events affected the mainly epilimnal community. The results indicate woody-debris-bearing lake littorals devoid of semi-aquatic and aquatic plants as places suitable for large stromatolites to grow, underpin the model of declining freshwater shark diversity in most Permian Variscan basins, demonstrate fish/amphibian ratios in limnic taphocoenoses to measure lake perenniality and reveal taphonomic biases in freshwater plant assemblages. Our outcomes highlight the need for more knowledge about the diversity, ecology, and fossilisation pathways of past limnic biotas, particularly microorganisms and actinopterygian fishes, to reconstruct deep-time continental ecosystems. </span></p>
Data from: Decoding the drivers of deep-time wetland biodiversity: insights from an early Permian tropical lake ecosystem
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Data for: Deep-time demographic inference suggests ecological release as driver of Neoavian adaptive radiation
<p>Data for:</p> <p>Houde P, Braun EL, Zhou L. 2020. Deep-time demographic inference suggests ecological release as driver of Neoavian adaptive radiation. Diversity, in review</p> <p>**************************************************<br> The .tar.gz file will expand to yield a directory named "Houde_Braun_Zhou_data_files". That directory has three subdirectories:</p> <p>1. alignments<br> 2. indel_matrices<br> 3. trees</p> <p>The Houde_Braun_Zhou_data_files directory also includes a README.txt file with complete details regarding the contents of each subdirectory.</p>
Data from: Body-size trends of the extinct giant shark Carcharocles megalodon: a deep-time perspective on marine apex predators
The extinct shark Carcharocles megalodon is one of the largest marine apex predators ever to exist. Nonetheless, little is known about its body-size variations through time and space. Here, we studied the body-size trends of C. megalodon through its temporal and geographic range to better understand its ecology and evolution. Given that this species was the last of the megatooth lineage, a group of species that shows a purported size increase through time, we hypothesized that C. megalodon also displayed this trend, increasing in size over time and reaching its largest size prior to extinction. We found that C. megalodon body-size distribution was left-skewed (suggesting a long-term selective pressure favoring larger individuals), and presented significant geographic variation (possibly as a result of the heterogeneous ecological constraints of this cosmopolitan species) over geologic time. Finally, we found that stasis was the general mode of size evolution of C. megalodon (i.e., no net changes over time), contrasting with the trends of the megatooth lineage and our hypothesis. Given that C. megalodon is a relatively long-lived species with a widely distributed fossil record, we further used this study system to provide a deep-time perspective to the understanding of the body-size trends of marine apex predators. For instance, our results suggest that (1) a selective pressure in predatory sharks for consuming a broader range of prey may favor larger individuals and produce left-skewed distributions on a geologic time scale; (2) body-size variations in cosmopolitan apex marine predators may depend on their interactions with geographically discrete communities; and (3) the inherent characteristics of shark species can produce stable sizes over geologic time, regardless of the size trends of their lineages.
Amber fossils demonstrate deep-time stability of Caribbean lizard communities
<p>This is the dataset for the paper Sherratt et al. 2015 (PNAS, doi: ). Included are the X-ray microtomography (micro-CT) TIFF stacks for the amber encased anole lizard fossils studied. Also included are the morphometric data for the fossil and 100 modern specimens, and the phylogenetic character matrix for the fossils and 181 species (91 morphological characters, 4873 DNA bases).</p> <p>Abstract</p> <p>Whether the structure of ecological communities can exhibit stability over macroevolutionary timescales has long been debated. The similarity of independently evolved <em>Anolis</em> lizard communities on environmentally similar Greater Antillean islands supports the notion that community evolution is deterministic. However, a dearth of Caribbean <em>Anolis</em> fossils—only three have been described to date—has precluded direct investigation of the stability of anole communities through time. Here we report on an additional 17 fossil anoles in Dominican amber dating to 15–20 My before the present. Using data collected primarily by X-ray micro computed tomography (X-ray micro-CT), we demonstrate that the main elements of Hispaniolan anole ecomorphological diversity were in place in the Miocene. Phylogenetic analysis yields results consistent with the hypothesis that the ecomorphs that evolved in the Miocene are members of the same ecomorph clades extant today. The primary axes of ecomorphological diversity in the Hispaniolan anole fauna appear to have changed little between the Miocene and the present, providing evidence for the stability of ecological communities over macroevolutionary timescales.</p>
Figure 1 in The first known riodinid 'cuckoo' butterfly reveals deep-time convergence and parallelism in ant social parasites
Figure 1. Adult types of Aricoris described from Uruguay. A, Hamearis gauchoana, holotype female in dorsal view (left), ventral view (centre) and labels (right). B, Hamearis montana, lectotype male in dorsal view (left), ventral view (centre) and labels (right). C, H. montana, female paralectotype in dorsal view (left), ventral view (centre) and labels (right). D, Hamearis arenarum, lectotype male in dorsal view (left), ventral view (centre) and labels (right). E, H. arenarum, female paralectotype in dorsal view (left), ventral view (centre) and labels (right). Scale bar: 1 cm.
Figure 4 in The first known riodinid 'cuckoo' butterfly reveals deep-time convergence and parallelism in ant social parasites
Figure 4. Scanning electron micrographs of the first (A–E) and second (F–J) instars of Aricoris arenarum. A, lateral view. B, lateral setae on mesothorax. C, dorsal seta and PCO on mesothorax. D, opening of TNO (arrow). E, proleg of segment A4 in lateroventral view. F, lateral view; note reduce setae on metathorax (arrow). G, head in laterofrontal view. H, dorsal setae in lateral view; note reduced setae on metathorax (arrow). I, dendritic setae and PCOs on mesothorax. J, opening of TNO (arrow).
Figure 6 in The first known riodinid 'cuckoo' butterfly reveals deep-time convergence and parallelism in ant social parasites
Figure 6. Life cycle of Aricoris arenarum tended by 'black morphs' of Camponotus punctulatus ants on Geoffroea decorticans (Fabaceae), showing both free-living and social parasitic phases. A, female at post-alighting phase. B, eggs close to anttended treehoppers (dashed ellipse). C, eggs (white arrows) and first instar caterpillars (black arrows) close to scale insets, both tended by ant workers. D, first instar caterpillar (black arrow) close to ant-tended treehoppers. E, sequence of worker drinking honeydew from treehopper (top panel, white arrow) and first instar requesting trophallaxis from ant (bottom panel, white arrow); note the typical larval posture and long prothoracic setae. F, last instar caterpillar tended by ants inside brood chamber. G, penultimate instar (black arrow indicates the everted larval TNO) and pupa inside the ant nest (white arrow). Scale bars: 5 mm in A, B, C, D, F, G; 2 mm in E.
Figure 3 in The first known riodinid 'cuckoo' butterfly reveals deep-time convergence and parallelism in ant social parasites
Figure 3. Scanning electron micrographs of Aricoris arenarum egg. A, lateral view. B, hexagonal cells of the exochorion with aeropyles (Ac) in the rib intersections. C, micropylar area (Mp).
Figure 2 in The first known riodinid 'cuckoo' butterfly reveals deep-time convergence and parallelism in ant social parasites
Figure 2. Adults of Aricoris arenarum. (A) In copula in Castillos, Uruguay, showing the female (left) and male (right); note cryptic coloration on the ground. (B–F) Male (B–D) and female (E, F) genitalia of A. arenarum. B, lateral view. C, ventral view. D, eighth sternite in ventral view. E, ventral view. F, papilla analis. Scale bar: 0.5 mm.
Figure 5 in The first known riodinid 'cuckoo' butterfly reveals deep-time convergence and parallelism in ant social parasites
Figure 5. Scanning electron micrographs of the last instar (A–H) and pupa (I–L) of Aricoris arenarum. A, head and thorax in lateral view. B, head in laterofrontal view. C, long dorsal setae on mesothorax. D, vibratory papillae. E, detail of spiniform elevations (arrow) on cephalodorsal area. F, dendritic setae and PCOs on segment A2. G, opening of TNO (arrow). H, prothoracic spiracle. I, dorsal view of metathorax. J, cluster of dendritic setae and PCOs above spiracle (sp) on segment A5. K, detail of dendritic setae and PCOs. L, detail of cremaster crochet.
Deep-time reticulation and ancient mitochondrial genome capture during the radiation of Jamaican Anolis lizards (Squamata; Iguanidae)
<p>Gene flow and reticulation are increasingly recognized as important processes in the diversification of many taxonomic groups. With the increasing ease of collecting genomic data and the development of multispecies coalescent network approaches, such reticulations can be accounted for when inferring phylogeny and diversification. Caribbean <i>Anolis</i> lizards are a classic example of an adaptive radiation in which species have independently radiated on the islands of the Greater Antilles into the same ecomorph classes. Within the Jamaican radiation at least one species, <i>A. opalinus</i>, has been documented to be polyphyletic in its mitochondrial DNA, which could be the result of an ancient reticulation event or incomplete lineage sorting. Here we generate mtDNA and genotyping-by-sequencing (GBS) data and implement gene-tree, species-tree, and multispecies coalescent network methods to infer the diversification of this group. Our mtDNA gene-tree recovers the same relationships previously inferred for this group, which is strikingly different from the species-tree inferred from our GBS data. Posterior predictive simulations suggest that our genomic data violate commonly adopted assumptions of the multispecies coalescent model, so we use network approaches to infer phylogenetic relationships. The inferred network topology contains a reticulation event but does not explain the mtDNA polyphyly observed in this group, however coalescent simulations suggest that the observed mtDNA topology is likely the result of past introgression. How common a signature of gene flow and reticulation is across the radiation of <i>Anolis</i> is unknown; however, the reticulation events that we demonstrate here may have allowed for adaptive evolution, as has been suggested in other, more recent adaptive radiations.</p>
Deep-time structural evolution of retroviral and filoviral surface envelope proteins
<p>The retroviral surface envelope protein subunit (SU) mediates receptor binding and triggers membrane fusion by the transmembrane (TM) subunit. SU evolves rapidly under strong selective conditions, resulting in seemingly unrelated SU structures in highly divergent retroviruses. Structural modeling of the SUs of several retroviruses and related endogenous retroviral elements with AlphaFold 2 identifies a TM-proximal SU β-sandwich structure that has been conserved in the orthoretroviruses for at least 110 million years. The SU of orthoretroviruses diversified by the differential expansion of the β-sandwich core to form domains involved in virus-host interactions. The β-sandwich domain is also conserved in the SU equivalent GP1 of Ebola virus although with a significantly different orientation in the trimeric envelope protein structure relative to the β-sandwich of human immunodeficiency virus type 1 gp120, with significant evidence for divergent rather than convergent evolution. The unified structural view of orthoretroviral SU and filoviral GP1 identifies an ancient, structurally conserved, and evolvable domain underlying the structural diversity of orthoretroviral SU and filoviral GP1.</p>
Phanerozoic tectonic and sedimentation history of the Arctic: constraints from deep-time low-temperature thermochronology data of Ellesmere Island and Northwest Greenland
<p>We present thermochronology and geochronology data from basement and (meta-)sedimentary samples collected on Ellesmere Island (Canadian High Arctic) and Northwest Greenland. The interpretations of our data are described and discussed in a paper in the journal Tectonics, titled “Phanerozoic tectonic and sedimentation history of the Arctic: constraints from deep-time low-temperature thermochronology data of Ellesmere Island and Northwest Greenland”. Our data include apatite fission track analyses, apatite (U-Th-Sm)/He analyses, and U-Pb analyses of detrital zircons. The data were used for inverse Monte Carlo simulations for obtaining time-temperature histories. We include descriptions of the analytical details related to the measurements, tests for potential effects of radiation damage on the (U-Th-Sm)/He age distributions, and we display the results of the Monte Carlo simulations for the individual samples. Our data set comprises a table summarizing constraints and specific parameters used for simulations (Table S1, summary input modelling), a table displaying the results of the simulations (Table S2, summary outcome thermal history inversions), a table displaying calculations of modelled overburden (Table S3, calculation of net burial and exhumation), a table summarizing the results of apatite fission track data, followed by several tables with the single-grain age and length data of fission track analyses (Table S4), a table with the detailed results of apatite (U-Th-Sm)/He thermochronology (Table S5), a table with single-grain zircon U-Pb data (Table S6), and a table with the results of statistical analysis for distinguishing individual age groups from the detrital zircon U-Pb age distributions (Table S7).</p>
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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.