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Hard edges, soft edges, and species range evolution: A genomic analysis of the Cumberland Plateau salamander
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PLATE III. Species of southern Tibet and soft substrate habitats in the Caspian Basin. (A) P. theobaldi; (B) habitat of A, near Yangbajain, north of Lhasa, southern Tibet; (C) P. sogdianus; (D) P. interscapularis; (E) P. mystaceus; and (F) habitat of D and E, Karakum Desert. north of Ashkhabad, Turkmenistan. in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
PLATE III. Species of southern Tibet and soft substrate habitats in the Caspian Basin. (A) P. theobaldi; (B) habitat of A, near Yangbajain, north of Lhasa, southern Tibet; (C) P. sogdianus; (D) P. interscapularis; (E) P. mystaceus; and (F) habitat of D and E, Karakum Desert. north of Ashkhabad, Turkmenistan.
Versatile Macroscale Concentration Gradients of Nanoparticles in Soft Nanocomposites
<p>Nanocomposite materials benefit from the diverse physicochemical properties featured by nanoparticles, and the presence of nanoparticle concentration gradients can lend functions to macroscopic materials beyond the realm of classical nanocomposites. It is shown here that linearity and time‐shift invariance obtained via the synergism of two independent physical phenomena—translational self‐diffusion and shear‐driven dispersion—may give access to an exceptionally high degree of flexibility in the design of scalable and programmable long‐range concentration gradients of nanoparticles in solidifiable liquid matrices.</p>
Fig. 4. Cellular features associated with T in Soft-Tissue Vessels and Cellular Preservation in Tyrannosaurus rex
Fig. 4. Cellular features associated with T. rex and ostrich tissues. (A) Fragment of demin eralized cortical bone from T. rex, showing parallel-oriented fibers and cell-like microstruc tures among the fibers. The inset is a higher magnification of one of the microstructures seen embedded in the fibrous material. (B) Demin eralized and stained (3) ostrich cortical bone, showing fibrillar, parallel- oriented collagen matrix with osteocytes embed ded among the fibers. The inset shows a high er magnification of one of the osteocytes. Both inset views show elon gate bodies with multi ple projections arising from the external sur face consistent with filipodia. (C) Isolated microstructure from T. rex after fixation. In addition to the multiple filipodial-like projections, internal contents can be seen. The inset shows a second structure with long filipodia and an internal transparent nucleus-like structure. (D) Fixed ostrich osteocyte; inset, ostrich osteocyte fixed and stained for better visualization. Internal contents are discernible, and filipodia can be seen extending in multiple planes from the cell surface. (E and F) SEM images of aldehyde-fixed (3) microstructures isolated from T. rex cortical bone tissues. Scale bars in (A) and (B), 50 um; in (C) and (D), 20 um; in (E), 10 um; in (F), 1 um.
Fig. 3 in Soft-Tissue Vessels and Cellular Preservation in Tyrannosaurus rex
Fig. 3. SEM images of aldehyde-fixed vessels. (A) Isolated vessel from T. rex. (B) Vessel isolated from extant ostrich after demineralization and collagenase digestion (3). (C) Vessel from T. rex, showing internal contents and hollow character. (D) Exploded T. rex vessel showing small round microstructures partially embedded in internal vessel walls. (E) Higher magnification of a portion of T. rex vessel wall, showing hypothesized endothelial nuclei (EN). (F) Similar structures visible on fixed ostrich vessel. Striations are seen in both (E) and (F) that may represent endothelial cell junctions or alternatively may be artifacts of the fixation/dehydration process. Scale bars in (A) and (B), 40 um; in (C) and (D), 10 um; in (E) and (F), 1 um.
Fig. 3 in Analyses of Soft Tissue from Tyrannosaurus rex Suggest the Presence of Protein
Fig. 3. TOF-SIMS spectra of demineralized MOR 1125 medullary bone (A to C) and entombing sedimentary matrix (D to F). The imonium ions for Gly (m/z = 30), Ala (m/z = 44), and Pro (m/z = 70) can be unambiguously identified for MOR 1125; no signal was observed in sediment controls that corresponded to these amino acids. See text for discussion.
Figure 3 in Mechanisms of soft tissue and protein preservation in Tyrannosaurus rex
Figure 3. SR-FTIR full spectra of isolated T. rex vascular tissue and chicken type I collagen (no treatment). All key bands for the identification of protein (Amide I, Amide II, Amide III) are present in the dinosaur tissue spectrum. The T. rex spectrum also presents a strong non-peptide carbonyl (C=O) band at 1739 cm−1 and a carbohydrate band at ~1010 cm−1.
Figure 5 in Mechanisms of soft tissue and protein preservation in Tyrannosaurus rex
Figure 5. SR-FTIR analysis of T. rex vascular tissue, NaBH4 reduced T. rex vascular tissue, chicken type I collagen without treatment, and chicken type I collagen treated with Fenton reagent and iron-catalysed glycation. (a,b) Average FTIR spectra in the non-peptide carbonyl and protein amide I regions for all five samples. (a) Significant reduction in the non-peptide carbonyl band follows treatment of T. rex vascular tissue with NaBH4, which reduces (immature) peptide crosslinks. The blue-shifted Amide I band of the dinosaur tissue, Fenton reagent-treated chicken type I collagen, and Fe-catalysed glycation-treated chicken type I collagen indicate increasing α-helix structure (~1660 cm−1) as the higher-energy triple-helix and intermolecular sub-bands (see Fig. 1 for method of identification) increasingly predominate the spectra. The development of aldehydic carbonyl, ketoaldehyde, and/or immature ketoimine bands in both treated chicken tissues is consistent with the strong carbonyl band in the dinosaur tissue.
Figure 1. Amide I in Mechanisms of soft tissue and protein preservation in Tyrannosaurus rex
Figure 1. Amide I sub-band localisation of untreated and treated chicken type I collagen in SR-FTIR spectra. Sub-bands (β-sheet, ~1633 cm−1; triple-helix, ~1658–1660 cm−1; intermolecular, ~1683–1690 cm−1) are indicated in the figures. Red traces denote second derivatives of experimental curves. Although the intermolecular sub-band typically presents at lower wavenumber, the identified value was the nearest local minimum in each of the second derivative traces and consistently appears across all samples; therefore, in this sample, the intermolecular sub-band was indexed at 1697–1699 cm−1.
Softness and Weight from Shape: Material Properties Inferred from Local Shape Features
<p>Dataset relative to the following publication:</p> <p>Schmidt, F., Fleming, R. W., & Valsecchi, M. (2020). Softness and Weight from Shape: Material Properties Inferred from Local Shape Features. <em>Journal of Vision, 20(6):2</em>, 1-20. https://doi.org/10.1167/jov.20.6.2</p> <p>Each experiment folder contains the data relative to one experiment, the rating scale images and videos, and a text file with comments. The stimuli folder contains image files of all experimental stimuli.</p>
The evolution and fate of diversity under hard and soft selection - all data and code
<p><span>How genetic variation arises and persists over evolutionary time despite the depleting effects of natural selection remains a long-standing question. Here, we investigate the impacts of two extreme forms of population regulation – at the level of the total, mixed population (hard selection) and at the level of local, spatially distinct patches (soft selection) – on the emergence and fate of diversity under strong divergent selection. We find that while the form of population regulation has little effect on rates of diversification it can modulate the long-term fate of genetic variation, diversity being more readily maintained under soft selection compared to hard selection. The mechanism responsible for coexistence is negative frequency dependent selection which, while present initially under both forms of population regulation, persists over the long-term only under soft selection. Importantly, coexistence is robust to continued evolution of niche specialist types under soft selection but not hard selection. These results suggest that soft selection could be a general mechanism for the maintenance of ecological diversity over evolutionary time scales. </span></p>
Data Supplement for "A unified numerical model for wetting of soft substrates"
<p>This dataset contains the data for Fig. 3(a) of our publication</p> <p><em>Aland, S. & Mokbel, D.<br> A unified numerical model for wetting of soft substrates<br> (submitted to International Journal for Numerical Methods in Engineering 2020).</em></p> <p>The data are stored in the files "PresentSimulation.csv", <span class="math-tex">\(\)</span>"ReferenceSolution.csv" and "Experiments.csv".</p> <p>We provide a MLX-File (Live Code File Format), which can be called in a MATLAB editor by entering "Fig3a_live".<br> Alternatively, we also provide a M-File that can be used in the same manner, entering "Fig3a" in a MATLAB editor.</p> <p>We used MatlabR2019b.</p> <p> </p> <p> </p> <p> </p> <p> </p>
Data from: A new ankylosaurine dinosaur from the Judith River Formation of Montana, USA, based on an exceptional skeleton with soft tissue preservation
The terrestrial Judith River Formation of northern Montana was deposited over an approximately 4 Myr interval during the Campanian (Late Cretaceous). Despite having been prospected and collected continuously by palaeontologists for over a century, few relatively complete dinosaur skeletons have been recovered from this unit to date. Here we describe a new genus and species of ankylosaurine dinosaur, Zuul crurivastator, from the Coal Ridge Member of the Judith River Formation, based on an exceptionally complete and well-preserved skeleton (ROM 75860). This is the first ankylosaurin skeleton known with a complete skull and tail club, and it is the most complete ankylosaurid ever found in North America. The presence of abundant soft tissue preservation across the skeleton, including in situ osteoderms, skin impressions and dark films that probably represent preserved keratin, make this exceptional skeleton an important reference for understanding the evolution of dermal and epidermal structures in this clade. Phylogenetic analysis recovers Zuul as an ankylosaurin ankylosaurid within a clade of Dyoplosaurus and Scolosaurus, with Euoplocephalus being more distantly related within Ankylosaurini. The occurrence of Z. crurivastator from the upper Judith River Formation fills a gap in the ankylosaurine stratigraphic and geographical record in North America, and further highlights that Campanian ankylosaurines were undergoing rapid evolution and stratigraphic succession of taxa as observed for Laramidian ceratopsids, hadrosaurids, pachycephalosaurids and tyrannosaurids.
Data from: Individual marking of soft-bodied subtidal invertebrates in situ - a novel staining technique applied to the giant plumose anemone Metridium farcimen (Tilesius, 1809)
The ability to recognize individuals and track growth over time is crucial to population dynamics research as well as studies of animal behavior. Invertebrates are particularly difficult to track as they often molt, have regenerative capabilities, or lack hard parts to attach markers. We tested, in laboratory and field studies, a new way of marking sea anemones (order Actiniaria) by injection of three vital stains (i.e., neutral red, methylene blue, and fluorescein). Neutral red and methylene blue did not affect growth or survival, but fluorescein was lethal at high concentrations. Marked individuals could be identified up to seven months after injection with neutral red, six weeks with methylene blue, and three days with low concentrations of fluorescein. Neutral red could be used for long-term monitoring of growth and survival in the field, and in combination with methylene blue could be used to mark individuals in distinguishable patterns for short-term studies such as examining predator-prey interactions, movement of individuals, and recruitment survival.
Data from: Differences between hard and soft phylogenetic data
When building the tree of life, variability of phylogenetic signal is often accounted for by partitioning gene sequences and testing for differences. The same considerations however are rarely applied to morphological data, potentially undermining its use in evolutionary contexts. Here we apply partition heterogeneity tests to 59 animal datasets to demonstrate that significant differences exist between the phylogenetic signal conveyed by 'hard' and 'soft' characters (bones, teeth and shells versus myology, integument etc). Furthermore, the morphological partitions differ significantly in their consistency relative to independent molecular trees. The observed morphological differences correspond with missing data biases, and as such their existence presents a problem not only for phylogeny reconstruction, but also for interpretations of fossil data. Evolutionary inferences drawn from clades in which hard, readily-fossilizable characters are relatively less consistent and different from other morphology (mammals, bivalves) may be less secure. More secure inferences might be drawn from the fossil record of clades that exhibit fewer differences, or exhibit more consistent hard characters (fishes, birds). In all cases it will be necessary to consider the impact of missing data on empirical data, and the differences that exist between morphological modules.
Data from: Ontogeny, morphology and taxonomy of the soft-bodied Cambrian 'mollusc' Wiwaxia
The soft-bodied Cambrian organism Wiwaxia poses a taxonomic conundrum. Its imbricated dorsal scleritome suggests a relationship with the polychaete annelid worms, whereas its mouthparts and naked ventral surface invite comparison with the molluscan radula and foot. 476 new and existing specimens from the 505-Myr-old Burgess Shale cast fresh light on Wiwaxia's sclerites and scleritome. My observations illuminate the diversity within the genus and demonstrate that Wiwaxia did not undergo discrete moult stages; rather, its scleritome developed gradually, with piecewise addition and replacement of individually secreted sclerites. I recognize a digestive tract and creeping foot in Wiwaxia, solidifying its relationship with the contemporary Odontogriphus. Similarities between the scleritomes of Wiwaxia, halkieriids, Polyplacophora and Aplacophora hint that the taxa are related. A molluscan affinity is robustly established, and Wiwaxia provides a good fossil proxy for the ancestral aculiferan – and perhaps molluscan – body plan.
Data from: Soft selective sweeps in fungicide resistance evolution: recurrent mutations without fitness costs in grapevine downy mildew
Adaptation produces hard or soft selective sweeps depending on the supply of adaptive genetic polymorphism. The evolution of pesticide resistance in parasites is a striking example of rapid adaptation that can shed light on selection processes. Plasmopara viticola, which causes grapevine downy mildew, forms large populations, in which resistance has rapidly evolved due to excessive fungicide use. We investigated the pathways by which fungicide resistance has evolved in this plant pathogen, to determine whether hard or soft selective sweeps were involved. An analysis of nucleotide polymorphism in 108 field isolates from the Bordeaux region revealed recurrent mutations of cytb and CesA3 conferring resistance to quinone outside inhibiting (QoI) and carboxylic acid amide (CAA) fungicides, respectively. Higher levels of genetic differentiation were observed for nucleotide positions involved in resistance than for neutral microsatellites, consistent with local adaptation of the pathogen to fungicide treatments. No hitchhiking was found between selected sites and neighbouring polymorphisms in cytb and CesA3, confirming multiple origins of resistance alleles. We assessed resistance costs, by evaluating the fitness of the 108 isolates through measurements of multiple quantitative pathogenicity traits under controlled conditions. No significant differences were found between sensitive and resistant isolates, suggesting that fitness costs may be absent or negligible. Our results indicate that the rapid evolution of fungicide resistance in P. viticola has involved a soft sweep.
Data from: Soft-surface grasping: radular opening in Aplysia californica
Grasping soft, irregular material is challenging both for animals and robots. The feeding systems of many animals have adapted to this challenge. In particular, the feeding system of the marine mollusk, Aplysia californica, a generalist herbivore, allows it to grasp and ingest seaweeds of varying shapes, textures and toughness. On the surface of Aplysia's grasper is a structure known as the radula, a thin flexible cartilaginous sheet with fine teeth. Previous in vitro studies suggested that an intrinsic muscle, I7, is responsible for opening the radula. Lesioning I7 in vivo does reduce opening width, but does not prevent animals from grasping and ingesting food. New in vitro studies demonstrate that a set of fine muscle fibers on the ventral surface of the radula, the subradular fibers (SRFs), mediate opening movements even if the I7 muscles are absent. Both in vitro and in vivo lesions demonstrate that removing the subradular fibers leads to profound deficits in radular opening, and significantly reduces feeding efficiency. A theoretical biomechanical analysis of the actions of the subradular fibers suggests that they induce the radular surface to open around a central crease in the radular surface and to arch the radular surface, allowing it to softly conform to irregular material. A three-dimensional model of the radular surface, based on in vivo observations and magnetic resonance imaging of intact animals, provides support for the biomechanical analysis. These results suggest how a soft grasper can work during feeding, and suggest novel designs for artificial soft graspers.
Data from: A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan
Reconstructing the evolutionary assembly of animal body plans is challenging when there are large morphological gaps between extant sister taxa, as in the case of echinozoans (echinoids and holothurians). However, the inclusion of extinct taxa can help bridge these gaps. Here we describe a new species of echinozoan, Sollasina cthulhu, from the Silurian Herefordshire Lagerstätte, UK. S. cthulhu belongs to the ophiocistioids, an extinct group that shares characters with both echinoids and holothurians. Using physical-optical tomography and computer reconstruction, we visualize the internal anatomy of S. cthulhu in three dimensions, revealing inner soft tissues that we interpret as the ring canal, a key part of the water vascular system that was previously unknown in fossil echinozoans. Phylogenetic analyses strongly suggest that Sollasina and other ophiocistioids represent a paraphyletic group of stem holothurians, as previously hypothesized. This allows us to reconstruct the stepwise reduction of the skeleton during the assembly of the holothurian body plan, which may have been controlled by changes in the expression of biomineralization genes.
Figure 5 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada
Figure 5. Non-metric multidimensional scaling (nMDS) plots showing infaunal invertebrate community at three intertidal sandy shore sites on the north coast of British Columbia, Canada during the summer of 2017. (a) the infaunal community by sandy shore site and sampling round and (b) the vector overlay indicates the direction of increased density, with correlations>0.3 shown. BO: Boulder Beach. GU: Coast Guard Beach. PI: Prescott Inlet. Round A: 23 May–1 June. Round B: 21–26 June. Round C: 19–25 July. Round D: 18–24 August.
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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.