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Migration-tracking integrated phylogeography supports long-distance dispersal-driven divergence for a migratory bird species in the Japanese archipelago
<p>Previous phylogeographic studies of migratory bird species have not discriminated long-distance dispersal (LDD) from vicariant speciation in their diversification process. We conducted an integrative phylogeographic approach to test the LDD hypothesis, which predicts that a Japanese migratory bird subspecies diverged from a population in the coastal region of the East China Sea (CRECS) via LDD over the East China Sea (ECS). We used the Brown Shrike as a model species, and we conducted molecular phylogenetics, species distribution models (SDMs) and migration tracking. We assessed whether the LDD hypothesis is applicable to the divergence history of the Japanese subspecies of the Brown Shrike.</p> <p>The datasets include three zipped files, namely DataS1.zip, DataS2.zip, and DataS3.zip. See the READ ME (AOKI_et_al_2021_DATASET_README.txt) for how each of the folder and files contained in them can be used to reproduce our results.</p> <p>DataS1.zip inlcudes an xml file to conduct the BEAST analysis. Molecular data, which include nucleotide sequences obtained for cytochrome b (cytb), cytochrome oxidase c subunit I (COI), myoglobin intron-2 (MB) and transforming growth factor beta 2 intron-5 (TGFb2), have been all reposited to DDBJ international nucleotide sequence database, and accession numbers have been already given to them. Accession numbers are provided in the appendix attached to the main manuscript.</p> <p>DataS2.zip includes several data that are related to produce occurrence data of the Brown Shrike used in the analysis and an R code to reproduce the SDMs. Explanatory climatic variables are all available at WorldClim v.1.4 (Hijmans et al., 2005), which are processed in the R code.</p> <p>DataS3.zip includes migratory route analyses using light-level geolocator data are available as the original light-level data and R codes. Sensitivity analyses were also conducted in these analyses, but their codes and results are seperately provided here.</p>
Replication Package for: "Pre-Colonial Warfare and Long-Run Development in India"
<p>Data and code to replicate all the results in the article Dincecco, Mark; Fenske, James; Menon, Anil; and Mukherjee, Shivaji "Pre-Colonial Warfare and Long-Run Development in India," Economic Journal.</p>
Long-term changes in flowering synchrony reflect climatic changes across an elevational gradient
<p>These are the data with the accompanying R code used in the article "Long-term changes in flowering synchrony reflect climatic changes across an elevational gradient", by Fisogni A, de Manincor N, Bertelsen CD, and Rafferty NE.</p> <p>We provide the raw data on flowering phenology, temperature and precipitation data in the study area, and overlap estimates used to evaluate temporal changes within and between elevations and their relationship with changing climatic variables.</p> <p>Data are .txt files with tab separated values.</p> <p>The raw dataset was created by C. David Bertelsen from field observations performed from 1984 to 2019 along a fixed transect in the Santa Catalina Mountains, Arizona, USA.</p>
Long-read genome sequencing accelerated the cloning of Pm69 by resolving the complexity of a rapidly evolving resistance gene cluster in wheat
<p>Oxford Nanopore assembly of <em>Triticum turgidum</em> ssp. <em>dicoccoides, </em>cv. G305-3M.</p>
FIGURE 5 in Rediscovery and an additional record of Terminalia kangeanensis (Combretaceae), a long lost threatened species from Indonesia
FIGURE 5. Leaves in flat shape (above) and fruits in cross-section (below). A). Terminalia kangeanensis from Tabuhan island (RIO 2971), B). Terminalia cf. microcarpa, misidentified as T. kangeanensis (Living collection in Bogor Botanic Gardens (XXIV.A.6)). Crosssection of fruits: outer layer is pulp, loculus and hollows drawn in black, sclerenchyma white, alveolar tissue dotted. Drawing by Destario Metusala.
FIGURE 4 in Rediscovery and an additional record of Terminalia kangeanensis (Combretaceae), a long lost threatened species from Indonesia
FIGURE 4. Terminalia kangeanensis from Tabuhan island (dried herbarium, RIO 9271). A), Leaves. B), Leaf gland on adaxial surface. C), Leaf domatia in vein axils. D), Inflorescence with fruits. E), Fruit variation. Square unit scale = 1×1 cm. Photos by Destario Metusala.
FIGURE 3 in Rediscovery and an additional record of Terminalia kangeanensis (Combretaceae), a long lost threatened species from Indonesia
FIGURE 3. Terminalia kangeanensis in Tabuhan island. A), Stem and branches. B), Leaf arrangements. C), Inflorescence with fruits. D), Fruits (close view). Photos by Destario Metusala.
Simultaneous NAD(P)H and FAD fluorescence lifetime microscopy of long UVA–induced metabolic stress in reconstructed human skin
<p>Solar ultraviolet longwave UVA1 exposure of human skin has short-term consequences at cellular and molecular level, leading at long-term to photoaging. Following exposure, reactive oxygen species (ROS) are generated, inducing oxidative stress that might impair cellular metabolic activity. However, the dynamic of UVA1 impact on cellular metabolism remains unknown because of lacking adequate live imaging techniques. Here we assess the UVA1-induced metabolic stress response in reconstructed human skin with multicolor two-photon fluorescence lifetime microscopy (FLIM). Simultaneous imaging of nicotinamide adenine dinucleotide (NAD(P)H) and flavin adenine dinucleotide (FAD) by wavelength mixing allows quantifying cellular metabolism in function of NAD(P)+/NAD(P)H and FAD/FADH2 redox ratios. After UVA1 exposure, we observe an increase of fraction of bound NAD(P)H and decrease of fraction of bound FAD indicating a metabolic switch from glycolysis to oxidative phosphorylation or oxidative stress possibly correlated to ROS generation. NAD(P)H and FAD biomarkers have unique temporal dynamic and sensitivity to skin cell types and UVA1 dose. While the FAD biomarker is UVA1 dose-dependent in keratinocytes, the NAD(P)H biomarker shows no dose dependence in keratinocytes, but is directly affected after exposure in fibroblasts, thus reflecting different skin cells sensitivities to oxidative stress. Finally, we show that a sunscreen including a UVA1 filter prevents UVA1 metabolic stress response from occurring.</p>
The dataset for the paper "Long-Lived and Continual Volcanic Eruptions, Tectonic Activity, Pit Chains Formation and Boulder Avalanches in Northern Tharsis Region: Implications for Late Amazonian Geodynamics and Seismo-Tectonic Processes on Mars" JGR: Planets.
<p>This dataset pertains to the following paper in Journal of Geophysical Research: Planets.</p> <p>Krishnan, V., and Kumar, P.S. (2022), Long-Lived and Continual Volcanic Eruptions, Tectonic Activity, Pit Chains Formation and Boulder Avalanches in Northern Tharsis Region: Implications for Late Amazonian Geodynamics and Seismo-Tectonic Processes on Mars, Journal of Geophysical Research: Planets (for full citation, please see the journal). AGU Manuscript No. 2022JE007511.</p> <p> </p>
Figure 7 in Adaptation to graviportality in Rhinocerotoidea? An investigation through the long bone shape variation in their hindlimb
Figure 7. Significant PGLS regression plots for proximal partial femur performed on shape data and log-transformed centroid size (CS) (A), log-transformed cubic root of mean body mass (BM) (B), log-transformed mean gracility index (GIMT3) (C). Point colour code follows Figure 1. Point size is proportional to mean log CS of each species. On the right, shapes associated with minimum and maximum fitted values (top row) and colour maps of the location and intensity of the shape deformation (bottom row). Blue: minimum value of the regression. Orange: maximum value of the regression. For each bone, the shape associated with the minimum was coloured depending on its distance to the shape associated with the maximum (blue indicates a low deformation intensity and red indicates a high deformation intensity). Orientation from left to right in each case: caudal, lateral, cranial and medial.
Figure 4 in Adaptation to graviportality in Rhinocerotoidea? An investigation through the long bone shape variation in their hindlimb
Figure 4. Results of the PCA performed on morphometric data of the complete femur and shape variation associated with the first axis of the PCA (cranial view). Blue: negative side of the axis. Orange: positive side of the axis. Phylogenetic relationships are plotted in the morphospace. Colour codes follow Figure 1 and abbreviations follow Table 1. Point size is proportional to the mean log centroid size of each species.
Figure 10 in Adaptation to graviportality in Rhinocerotoidea? An investigation through the long bone shape variation in their hindlimb
Figure 10. Significant PGLS regression plots for tibia performed on shape data and log-transformed cubic root of mean body mass (BM) (A), log-transformed mean gracility index (GI-MT3) (B), and fibula performed on shape data and logtransformed mean gracility index (GI-MT3) (C). Point colour code follows Figure 1. Point size is proportional to mean log CS of each species. On the right, shapes associated with minimum and maximum fitted values (top row) and colour maps of the location and intensity of the shape deformation (bottom row). Blue: minimum value of the regression. Orange: maximum value of the regression. For each bone, the shape associated with the minimum was coloured depending on its distance to the shape associated with the maximum (blue indicates a low deformation intensity and red indicates a high deformation intensity). Orientation from left to right in each case: caudal, lateral, cranial and medial.
Figure 3 in Adaptation to graviportality in Rhinocerotoidea? An investigation through the long bone shape variation in their hindlimb
Figure 3. Neighbour Joining trees computed on all PC scores obtained from the PCAs performed on shape data. Colour codes follow Figure 1 and abbreviations follow Table 1. Point size is proportional to the mean log centroid size of each species. A, complete femur; B, proximal partial femur; C, distal partial femur; D, tibia; E, fibula.
Figure 6 in Adaptation to graviportality in Rhinocerotoidea? An investigation through the long bone shape variation in their hindlimb
Figure 6. Results of the PCA performed on morphometric data of proximal partial femur (A) and distal partial femur (B) and shape variation associated with the first two axes of the PCA (caudal view). Blue: negative side of the axis. Orange: positive side of the axis. Phylogenetic relationships are plotted in the morphospace. Colour codes follow Figure 1 and abbreviations follow Table 1. Point size is proportional to the mean log centroid size of each species.
Figure 2 in Adaptation to graviportality in Rhinocerotoidea? An investigation through the long bone shape variation in their hindlimb
Figure 2. Evolution of BM and GI-MT3 along the phylogeny for the studied species. Left: mean BM. Right: mean GI-MT3. Computations were made on the log-transformed cubic root of mean BM and the log-transformed GI-MT3. Values at nodes and along branches were reconstructed based on a Brownian Motion model of evolution (Revell, 2012). Colour codes for taxa follow Figure 1. Evolution of the third metatarsal shape depending on the GI-MT3 value is illustrated by specimens Hyrachyus eximius AMNH FM 12675 (minimum) and Teleoceras fossiger YPM VP 039358 (maximum).
Figure 9 in Adaptation to graviportality in Rhinocerotoidea? An investigation through the long bone shape variation in their hindlimb
Figure 9. Results of the PCA performed on morphometric data of tibia (A) and fibula (B) and shape variation associated with the first two axes of the PCA (caudal view). Blue: negative side of the axis. Orange: positive side of the axis. Phylogenetic relationships are plotted in the morphospace. Colour codes follow Figure 1 and abbreviations follow Table 1. Point size is proportional to the mean log centroid size of each species.
Figure 8 in Adaptation to graviportality in Rhinocerotoidea? An investigation through the long bone shape variation in their hindlimb
Figure 8. Significant PGLS regression plot for distal partial femur performed on shape data and log-transformed mean gracility index (GI-MT3). Point colour code follows Figure 1. Point size is proportional to mean log CS of each species. On the right, shapes associated with minimum and maximum fitted values (top row) and colour maps of the location and intensity of the shape deformation (bottom row). Blue: minimum value of the regression. Orange: maximum value of the regression. For each bone, the shape associated with the minimum was coloured depending on its distance to the shape associated with the maximum (blue indicates a low deformation intensity and red indicates a high deformation intensity). Orientation from left to right: caudal, lateral, cranial and medial.
Figure 11 in Adaptation to graviportality in Rhinocerotoidea? An investigation through the long bone shape variation in their hindlimb
Figure 11. Evolution of centroid size (CS) along the phylogeny for the studied species. A, distal partial femur; B, tibia; C, fibula. The cladogram used here is the same composite one as used in Figure 1. Computations were made on log-transformed CS. Values at nodes and along branches were reconstructed based on a Brownian Motion model of evolution (Revell, 2012). Colour codes for taxa follow Figure 1.
Figure 12 in Adaptation to graviportality in Rhinocerotoidea? An investigation through the long bone shape variation in their hindlimb
Figure 12. Schematic summary of the relations between bone shape and the different variables tested in this work and in Mallet et al. (2022). Blue indicates a shape variation dominated by evolutionary legacy over other parameters. Red indicates a shape variation mainly dominated by brachypody and/or body mass over other parameters. This relative influence is based on the results obtained through the NJ trees, the PCA and the regression plots of the PGLS described in the previous chapters. The size of the font and arrows for each variable is proportional to its relation with the shape for each bone or part of bone based on the overall previous results. Faded colours on the hindlimb indicate a lower association with body mass in general. Bones modified from Archeozoo.org under the Creative Commons license.
Figure 5 in Adaptation to graviportality in Rhinocerotoidea? An investigation through the long bone shape variation in their hindlimb
Figure 5. Significant PGLS regression plots for complete femur performed on shape data and log-transformed centroid size (CS) (A), log-transformed cubic root of mean body mass (BM) (B), log-transformed mean gracility index (GI-MT3) (C). Point colour code follows Figure 1. Point size is proportional to mean log CS of each species. On the right, shapes associated with minimum and maximum fitted values (top row) and colour maps of the location and intensity of the shape deformation (bottom row). Blue: minimum value of the regression. Orange: maximum value of the regression. For each bone, the shape associated with the minimum was coloured depending on its distance to the shape associated with the maximum (blue indicates a low deformation intensity and red indicates a high deformation intensity). Orientation from left to right in each case: caudal, lateral, cranial and medial.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.