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Figure 4 in Diversification and species limits in scale-backed antbirds (Willisornis: Thamnophilidae), an Amazonian endemic lineage

Figure 4. Graphs of BAPS clusters and geographic distribution of individuals analysed when considering A, mitochondrial (K = 8); B, BF5 (K = 3); C, MUSK (K = 6) datasets. Samples were plotted on the map in the pie chart format representing the percentage of admixture recovered by the bar graphs.

Figure 2 in Diversification and species limits in scale-backed antbirds (Willisornis: Thamnophilidae), an Amazonian endemic lineage

Figure 2. Multilocus coalescent species tree of Willisornis lineages identified in previous molecular analyses (Fig. 1). Nodes contain posterior probabilities of clades (above line) and associated confidence intervals (95% HPD) for splitting times (blue bars). Numbers on the timescale below represent millions of years. The colours are the same as used for the recovered groups in Figure 1.

Figure 6 in Diversification and species limits in scale-backed antbirds (Willisornis: Thamnophilidae), an Amazonian endemic lineage

Figure 6. Ancestral range estimates for the genus Willisornis obtained with BioGeoBEARS. The model selected was DIVALIKE (see text for details). Node pie charts represent the likelihoods of ancestral area states. Colours represent major Amazonian geological provinces selected as areas for the analysis, with those differing from the ones in the map corresponding to combinations of areas: GUI, Guiana Shield; BAC, Amazonian foreland basins; BRA, Brazilian Shield; GUIBAC, Guiana Shield + Amazonian foreland basins; GUIBRA, Guiana Shield + Brazilian Shield; and BACBRA, Amazonian foreland basins + Brazilian Shield. Numbers on the timescale below represent millions of years.

Figure 3. A in Diversification and species limits in scale-backed antbirds (Willisornis: Thamnophilidae), an Amazonian endemic lineage

Figure 3. A, BP&P posterior probabilities for different prior settings corresponding to the degree of significant coalescence between reciprocally monophyletic Willisornis lineages. Θ corresponds to the population size parameter and τ to the divergence time priors at the root of the species tree. ε, α and m are different values of fine-tune parameters. B, overlapping coalescent trees for each scenario generated by BP&P.

Figure 5 in Diversification and species limits in scale-backed antbirds (Willisornis: Thamnophilidae), an Amazonian endemic lineage

Figure 5. Clusters of BAPS for Willisornis poecilinotus gutturalis and W. p. griseiventris A in western Amazonia. Each graph corresponds to analyses made with A, mitochondrial; B, BF5; C, MUSK datasets. The coloured bars represent the proportion of genetic similarity to each population for each specimen included in the analysis while the maps on the right show the geographic distribution of the samples used. Specimen CAM021 is highlighted by a red rectangle and arrow.

Data for figures 2 till4 of "Small-scale discharges observed near the top of a thunderstorm"

The data as well as the .gle files for generating figures 2 till 4 of the paper "Small-scale discharges observed near the top of a thunderstorm" by O.~Scholten, B.~M.~Hare, J.~Dwyer, N.~Liu, C.~Sterpka, J.~Assink, H.~Leijnse, S.~ter Veen submitted to JGR, see <a href="https://www.essoar.org/doi/10.1002/essoar.10512414.1">https://www.essoar.org/doi/10.1002/essoar.10512414.1</a> for an earlier version of this work

Sound pressure measurements and calculation of the cavitation volume for a full-scale 3500 TEU container vessel

Supplementary material comprising measurement data and MATLAB code corresponding to the published research article.

COJO ARG variants from "Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits"

These are COJO ARG variants accompanying the manuscript "Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits". For more details, view the README.md file and refer to our manuscript.

opencc-zeroDec 2021View details →

dryad40/100

Data for: Zebra finch song ecology: monitoring of breeding, observational transects, focal and year-round acoustic recordings, and a large-scale simultaneous playback experiment

Male songbirds sing to establish territories and to attract mates. However, increasing reports of singing in non-reproductive contexts and by females show that song use is more diverse than previously considered. Therefore, alternative functions of song, such as social cohesion and synchronisation of breeding, by and large were overlooked even in such well-studied species as the zebra finch (Taeniopygia guttata). In these social songbirds only the males sing and pairs breed synchronously in loose colonies following aseasonal rain events in their arid habitat. As males are not territorial, and pairs form long-term monogamous bonds early in life, conventional theory predicts that zebra finches should not sing much at all; yet they do and their song is the focus of hundreds of lab-based studies. We hypothesise that zebra finch song functions to maintain social cohesion and to synchronise breeding. Here we test this idea using data from five years of field studies, including observational transects, focal and year-round audio recordings, and a large-scale playback experiment. We show that zebra finches frequently sing while in groups, that breeding status influences song output at the nest and at aggregations, that they sing year-round, and that they predominantly sing when with their partner, suggesting that song remains important after pair formation. Our playback reveals that song actively features in social aggregations as it attracts conspecifics. Together, these results demonstrate that birdsong has important functions beyond territoriality and mate choice, illustrating its importance in coordination and cohesion of social units within larger societies.

The impact of small-scale green infrastructure on the affective wellbeing associated with urban sites

The database contains participants' reported affective perceptions of 18 images of street images with different levels of green coverage.

opencc-by-4.0Jan 2023View details →

Atmospheric Dust Source Contributions and Synoptic Scale Adjustments in the East Asian Region in April of 2021

The WRF-Chem simulations were conducted to assess the source contributions to the concentrations and ratios across the East Asian region in April 2021. The WRF-Chem baseline was compiled, and sensitivity simulations were conducted regarding the source contributions to the concentrations of PM10 BASE, PM10 Anthro, PM10 Dust, and PM10 Biomass.   In our dataset, you can find PM10 concentrations of WRF-Chem baseline simulations and other sensitivity-simulated PM10 concentrations of multi-sources of anthropogenic, wind-blown dust, and biomass-burning emissions. Furthermore, model meteorological variables of air temperature, wind, surface level pressure, and geopotential height can be found here. If you have any difficulty downloading these datasets, please feel free to contact the first author, kimhsung@gmail.com. All references and acknowledgments can be found in our paper.

opencc-by-4.0Jan 2023View details →

Phantom imaging data and analysis macros for the article "Monochromatic computed tomography using laboratory-scale setup"

The raw and processed data and analysis macros of the article A.-P. Honkanen et S. J. Huotari, Monochromatic computed tomography using laboratory-scale setup, Scientific Reports (2023), doi:<a href="http://doi.org/10.1038/s41598-023-27409-6">10.1038/s41598-023-27409-6</a> The data set consists of the raw and reconstructed computed tomography projection data taken of an PMMA phantom embedded with three different chemical species of selenium taken with a monochromatic X-ray imaging setup based on a laboratory-scale Johann-type crystal X-ray spectrometer. In addition to the imaging data, the set contains also the Jupyter Notebooks used to process and analyse the data. The details of the instrument and the analysis are presented in the article. The dataset is licensed under Creative Commons Attribution 4.0 International License <a href="https://creativecommons.org/licenses/by/4.0/">https://creativecommons.org/licenses/by/4.0/</a>

Text-fig. 50. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c–f) images of "Foveolate seed sp. 2"; Catefica locality, Portugal. a, b) Lateral (a) and apical (b) views of seed showing the coarsely foveolate surface; note the truncate apex and the slightly depressed hilar-micropylar region; c) Longitudinal section (volume rendering cut between orthoslices xz0740 and xz0840) through the middle of seed showing the truncate apex with slightly depressed hilar-micropylar region and basal rounded chalazal region; note thick outer integument (oi) composed of an exotesta of thickwalled palisade-like cells and a thin inner integument (ii); d, e, f) Transverse (d, orthoslice xy0800) and longitudinal sections (e, orthoslice xz1100, f, orthoslice yz0800) through seed hilar-micropylar region, showing the exotesta comprised of the thick-walled palisade-like cells of the outer integument (oi), small, thin-walled meso- endotestal cells of the outer integument (arrows) and thin inner integument (ii). Specimen, Catefica 153-S172332 (a–f). Scale bars = 300 Μm (a–f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 50. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c–f) images of "Foveolate seed sp. 2"; Catefica locality, Portugal. a, b) Lateral (a) and apical (b) views of seed showing the coarsely foveolate surface; note the truncate apex and the slightly depressed hilar-micropylar region; c) Longitudinal section (volume rendering cut between orthoslices xz0740 and xz0840) through the middle of seed showing the truncate apex with slightly depressed hilar-micropylar region and basal rounded chalazal region; note thick outer integument (oi) composed of an exotesta of thickwalled palisade-like cells and a thin inner integument (ii); d, e, f) Transverse (d, orthoslice xy0800) and longitudinal sections (e, orthoslice xz1100, f, orthoslice yz0800) through seed hilar-micropylar region, showing the exotesta comprised of the thick-walled palisade-like cells of the outer integument (oi), small, thin-walled meso- endotestal cells of the outer integument (arrows) and thin inner integument (ii). Specimen, Catefica 153-S172332 (a–f). Scale bars = 300 Μm (a–f).

Text-fig. 49. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c–e) images of "Foveolate seed sp. 1"; Catefica locality, Portugal. a) Lateral view of seed showing foveolate surface; note the slightly pointed hilar-micropylar region with the preservation of a presumed secretion (arrow) from the micropyle; b) Detail of seed surface showing shallow pitting and very faint outlines of the undulate anticlinal walls of the exotestal cells; c) Longitudinal section (volume rendering cut between orthoslices yz0450 and yz0460) through the middle of the seed showing the slightly pointed hilarmicropylar region and the rounded chalazal region; note the thick exotesta of the outer integument composed of thick-walled palisade-like cells (oi); note partial preservation of large cells of the nutritive tissue (nu) and the smaller cells of the embryo (em) at the micropylar end of the seed; d, e) Longitudinal sections (d, orthoslice xz0750, e, orthoslice yz0485) through middle of the seed perpendicular to each other showing the hilar-micropylar region with the preservation of a presumed secretion from micropyle (e, arrow), thick palisade-like cells of outer integument (oi), larger cells of the nutritive tissue (nu) and remains of the smaller cells of the embryo (em). Specimen, Catefica 49-S172316 (a–e). Scale bars = 300 Μm (a, c–e), 50 Μm (b). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 49. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c–e) images of "Foveolate seed sp. 1"; Catefica locality, Portugal. a) Lateral view of seed showing foveolate surface; note the slightly pointed hilar-micropylar region with the preservation of a presumed secretion (arrow) from the micropyle; b) Detail of seed surface showing shallow pitting and very faint outlines of the undulate anticlinal walls of the exotestal cells; c) Longitudinal section (volume rendering cut between orthoslices yz0450 and yz0460) through the middle of the seed showing the slightly pointed hilarmicropylar region and the rounded chalazal region; note the thick exotesta of the outer integument composed of thick-walled palisade-like cells (oi); note partial preservation of large cells of the nutritive tissue (nu) and the smaller cells of the embryo (em) at the micropylar end of the seed; d, e) Longitudinal sections (d, orthoslice xz0750, e, orthoslice yz0485) through middle of the seed perpendicular to each other showing the hilar-micropylar region with the preservation of a presumed secretion from micropyle (e, arrow), thick palisade-like cells of outer integument (oi), larger cells of the nutritive tissue (nu) and remains of the smaller cells of the embryo (em). Specimen, Catefica 49-S172316 (a–e). Scale bars = 300 Μm (a, c–e), 50 Μm (b).

Text-fig. 48. Scanning electron microscope (SEM, a, b, d–i) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c) images of "One-seeded fruit sp. 2" (a–c), "Unassigned, unnamed fruits" (d–f), Pazliopsis sp. (g, h) and "Follicular fruit with exotestal seeds" (i); Catefica locality, Portugal. a) Lateral view of fruit showing remains of tepals (te) and a single stamen (st); b) Detail of fruit surface showing short, scale-like, peltate trichomes (arrows); c) Transverse section (orthoslice xy0475) of fruit containing a single seed showing tepals (te) and fruit surface with peltate trichomes (arrow); note partial preservation of internal nutritive tissue; d) Fruit in lateral view showing the almost smooth epidermis with scattered openings; e) Detail of fruit surface from (d) showing the scattered openings in the epidermis interpreted as burst secretory cells (arrows); f) Dorsi-ventral view of tiny fruit with an irregular surface; g) Lateral view of exotestal seed assigned to cf. Pazliopsis sp.; h) Detail of fruit surface of seed in (g) showing faint facets of outer palisade layer with fine jigsaw-puzzle outlines of the anticlinal walls; i) Lateral view of fragmentary follicular fruit showing two exposed exotestal seeds. Specimens, Catefica 153-S174314 (a–c), Catefica 50-S170420 (d, e), Catefica 152-S174300 (f), Catefica 49-S172319 (g, h), Catefica MM158-P0272 (i). Scale bars = 300 Μm (a, c, d, f, g, i), 100 Μm (e), 50 Μm (b, h). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 48. Scanning electron microscope (SEM, a, b, d–i) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c) images of "One-seeded fruit sp. 2" (a–c), "Unassigned, unnamed fruits" (d–f), Pazliopsis sp. (g, h) and "Follicular fruit with exotestal seeds" (i); Catefica locality, Portugal. a) Lateral view of fruit showing remains of tepals (te) and a single stamen (st); b) Detail of fruit surface showing short, scale-like, peltate trichomes (arrows); c) Transverse section (orthoslice xy0475) of fruit containing a single seed showing tepals (te) and fruit surface with peltate trichomes (arrow); note partial preservation of internal nutritive tissue; d) Fruit in lateral view showing the almost smooth epidermis with scattered openings; e) Detail of fruit surface from (d) showing the scattered openings in the epidermis interpreted as burst secretory cells (arrows); f) Dorsi-ventral view of tiny fruit with an irregular surface; g) Lateral view of exotestal seed assigned to cf. Pazliopsis sp.; h) Detail of fruit surface of seed in (g) showing faint facets of outer palisade layer with fine jigsaw-puzzle outlines of the anticlinal walls; i) Lateral view of fragmentary follicular fruit showing two exposed exotestal seeds. Specimens, Catefica 153-S174314 (a–c), Catefica 50-S170420 (d, e), Catefica 152-S174300 (f), Catefica 49-S172319 (g, h), Catefica MM158-P0272 (i). Scale bars = 300 Μm (a, c, d, f, g, i), 100 Μm (e), 50 Μm (b, h).

Text-fig. 47. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of "One-seeded fruit sp. 1"; Catefica locality, Portugal. a, b) Lateral view of fruits showing slightly sinuous ventral margin and the curved stalk; c, d) Longitudinal sections perpendicular to each other through the median part of fruit and its single seed (c, orthoslice yz0652, d, xz0739) showing the bitegmic seed closely adhering to the fruit wall (fw); the several cell layer thick outer integument (oi) and the membranous inner integument (ii); note the vascular bundle (vb) branching into a dorsal and lateral bundle near the base of the fruit; e) Transverse section (orthoslice xy0600) showing fruit wall (fw) and outer (oi) and inner (ii) integuments of the seed; f) Longitudinal section (orthoslice yz0871) through the micropylar region showing micropyle (mi) formed from membranous inner integument (ii). Specimens, Catefica 49-S174927 (a), Catefica 49-S174923 (b, f), Catefica 49-S174769 (c–e). Scale bars = 300 Μm (a–d), 100 Μm (e, f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 47. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of "One-seeded fruit sp. 1"; Catefica locality, Portugal. a, b) Lateral view of fruits showing slightly sinuous ventral margin and the curved stalk; c, d) Longitudinal sections perpendicular to each other through the median part of fruit and its single seed (c, orthoslice yz0652, d, xz0739) showing the bitegmic seed closely adhering to the fruit wall (fw); the several cell layer thick outer integument (oi) and the membranous inner integument (ii); note the vascular bundle (vb) branching into a dorsal and lateral bundle near the base of the fruit; e) Transverse section (orthoslice xy0600) showing fruit wall (fw) and outer (oi) and inner (ii) integuments of the seed; f) Longitudinal section (orthoslice yz0871) through the micropylar region showing micropyle (mi) formed from membranous inner integument (ii). Specimens, Catefica 49-S174927 (a), Catefica 49-S174923 (b, f), Catefica 49-S174769 (c–e). Scale bars = 300 Μm (a–d), 100 Μm (e, f).

Text-fig. 46. Scanning electron microscope (SEM) images of "Rugulate fruit"; Catefica locality, Portugal. a, b) Lateral (a) and ventral (b) views of a rugulate fruit showing the short extension of the sessile stigma at the apex (arrows); c) Irregular surface of fruit that probably reflects an irregular endocarp; note the isodiametric outlines of the epidermal cells; d) Semi-tectate reticulate pollen grains embedded in the remains of a secretion on the stigmatic surface. Specimen, Catefica 154-S101291 (a–d). Scale bars = 300 Μm (a, b), 100 Μm (c), 6 Μm (d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 46. Scanning electron microscope (SEM) images of "Rugulate fruit"; Catefica locality, Portugal. a, b) Lateral (a) and ventral (b) views of a rugulate fruit showing the short extension of the sessile stigma at the apex (arrows); c) Irregular surface of fruit that probably reflects an irregular endocarp; note the isodiametric outlines of the epidermal cells; d) Semi-tectate reticulate pollen grains embedded in the remains of a secretion on the stigmatic surface. Specimen, Catefica 154-S101291 (a–d). Scale bars = 300 Μm (a, b), 100 Μm (c), 6 Μm (d).

Text-fig. 45. Scanning electron microscope (SEM) images of "Staminate structure"; Catefica locality, Portugal. a–c) Staminate structure in oblique apical (a), oblique basal (b) and lateral (c) views showing distinct stalk and head with a cluster of about 20 stamens; note bracts at the base of the structure (asterisks) and probable secretory openings in the anther tissues (arrows). Specimen, Catefica 358-S135451 (a–c). Scale bars = 600 Μm (a–c). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 45. Scanning electron microscope (SEM) images of "Staminate structure"; Catefica locality, Portugal. a–c) Staminate structure in oblique apical (a), oblique basal (b) and lateral (c) views showing distinct stalk and head with a cluster of about 20 stamens; note bracts at the base of the structure (asterisks) and probable secretory openings in the anther tissues (arrows). Specimen, Catefica 358-S135451 (a–c). Scale bars = 600 Μm (a–c).

Text-fig. 41. Scanning electron microscope (SEM) images of "Pollen clump with tricolpate pollen sp. 5"; Catefica locality, Portugal. a) Pollen clump, probably coprolite but containing one kind of pollen; b, c) Pollen grains from pollen clump in oblique equatorial view (b) and polar view (c) showing the three apertures with a distinct aperture margin and the coarse reticulum; d) Detail of wall of a broken pollen grain showing long straight columellae and a thin foot layer. Specimen, Catefica 50-S115858 (a–d). Scale bars = 600 Μm (a), 6 Μm (b, c), 1.5 Μm (d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 41. Scanning electron microscope (SEM) images of "Pollen clump with tricolpate pollen sp. 5"; Catefica locality, Portugal. a) Pollen clump, probably coprolite but containing one kind of pollen; b, c) Pollen grains from pollen clump in oblique equatorial view (b) and polar view (c) showing the three apertures with a distinct aperture margin and the coarse reticulum; d) Detail of wall of a broken pollen grain showing long straight columellae and a thin foot layer. Specimen, Catefica 50-S115858 (a–d). Scale bars = 600 Μm (a), 6 Μm (b, c), 1.5 Μm (d).

Text-fig. 43. Synchrotron radiation X-ray tomographic microscopy SRXTM images of "Tricarpellate flower sp. 2"; Catefica locality, Portugal. a) Lateral view of floral structure (volume rendering) showing the apical projection of the carpels and the semiinferior organization; b) Apical view of floral structure (volume rendering) showing the triangular shape of the hypanthial rim, the tricarpellate ovary with a single apical style; note that one locule is fully developed while the other two are collapsed; note also slits of unknown nature in the corners of the triangular hypanthial rim (arrows); c) Transverse section (orthoslice xy0712) close to the floral apex showing the locule of the one fully developed carpel with ovules borne along ventral placentae; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; d) Longitudinal section (orthoslice xz0858) through the locule of the one fully developed carpel showing the semi-inferior organization and ovules arranged along the full length of the carpel; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; e) Tangential longitudinal section (orthoslice yz1019) through the one fully developed locule, showing the densely packed ovules and the amorphous substance (asterisk) with which they are associated. Specimen, Catefica 50-S174901 (a–e). Scale bars = 300 Μm (a–e). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 43. Synchrotron radiation X-ray tomographic microscopy SRXTM images of "Tricarpellate flower sp. 2"; Catefica locality, Portugal. a) Lateral view of floral structure (volume rendering) showing the apical projection of the carpels and the semiinferior organization; b) Apical view of floral structure (volume rendering) showing the triangular shape of the hypanthial rim, the tricarpellate ovary with a single apical style; note that one locule is fully developed while the other two are collapsed; note also slits of unknown nature in the corners of the triangular hypanthial rim (arrows); c) Transverse section (orthoslice xy0712) close to the floral apex showing the locule of the one fully developed carpel with ovules borne along ventral placentae; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; d) Longitudinal section (orthoslice xz0858) through the locule of the one fully developed carpel showing the semi-inferior organization and ovules arranged along the full length of the carpel; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; e) Tangential longitudinal section (orthoslice yz1019) through the one fully developed locule, showing the densely packed ovules and the amorphous substance (asterisk) with which they are associated. Specimen, Catefica 50-S174901 (a–e). Scale bars = 300 Μm (a–e).