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Figure 2 from: Abdel-Dayem MS, Abu El-Ghiet UM, Elsheikh TM, Elgharbawy AA, Al-Fifi ZIA, Aldhafer HM (2020) The first survey of the beetles (Coleoptera) of the Farasan Archipelago of the southern Red Sea, Kingdom of Saudi Arabia. ZooKeys 959: 17-86. https://doi.org/10.3897/zookeys.959.51224
Figure 2 Climate data for Farasan Archipelago, southern Red Sea, Kingdom of Saudi Arabia (source of data http://www.worldclim.org).
Figure 4 from: Abdel-Dayem MS, Abu El-Ghiet UM, Elsheikh TM, Elgharbawy AA, Al-Fifi ZIA, Aldhafer HM (2020) The first survey of the beetles (Coleoptera) of the Farasan Archipelago of the southern Red Sea, Kingdom of Saudi Arabia. ZooKeys 959: 17-86. https://doi.org/10.3897/zookeys.959.51224
Figure 4 Proportion of genera represented in the Farasan Archipelago, Kingdom of Saudi Arabia by one (1), two (2), and three or more (> 3) species in Coleoptera (current data), Formicidae (based on Sharaf and Al-Zailaie 2006), mammals and herpetofauna (based on Masseti 2010, 2014), birds (based on Jennings 1988), and vascular plants (based on Alfarhan et al. 2002).
Figure 3 from: Abdel-Dayem MS, Abu El-Ghiet UM, Elsheikh TM, Elgharbawy AA, Al-Fifi ZIA, Aldhafer HM (2020) The first survey of the beetles (Coleoptera) of the Farasan Archipelago of the southern Red Sea, Kingdom of Saudi Arabia. ZooKeys 959: 17-86. https://doi.org/10.3897/zookeys.959.51224
Figure 3 Photographs of characteristic plants of the Farasan Archipelago, Kingdom of Saudi Arabia AAcacia ehrenbergiana, Commiphora gileadensis, Limonium axillare, and Tetraena alba in Al-Huseis BAcacia ehrenbergiana, Indigofera oblongifolia and Zygophyllum coccineum in Khotp CHyphaene thebaica, Caralluma acutangula, Euphorbia fractiflexa, Senna alexandrina, and Capparis sinaica in Khotp DIndigofera oblongifolia at Bridge ERhizophora mucronataFAvicennia marina in Al-Huseis GAcacia ehrenbergiana and Phoenix dactylifera in sand Sajid H sorghum field.
Decoupling the effects of food and density on life history plasticity of wild animals using field experiments: Insights from the steward who sits in the shadow of its tail, the North American red squirrel
<p>Long-term studies of wild animals provide the opportunity to investigate how phenotypic plasticity is used to cope with environmental fluctuations, and how the relationships between phenotypes and fitness can be dependent upon the ecological context.</p> <p>Most previous studies have only investigated life history plasticity in response to changes in temperature, yet wild animals often experience multiple environmental fluctuations simultaneously. This requires field experiments to decouple which ecological factor induces plasticity in fitness-relevant traits to better understand their population-level responses to those environmental fluctuations.</p> <p>For the past 32 years, we have conducted a long-term integrative study of individually marked North American red squirrels (<i>Tamiasciurus hudsonicus </i>Erxleben) in the Yukon, Canada. We have used multi-year field experiments to examine the physiological and life history responses of individual red squirrels to fluctuations in food abundance and conspecific density.</p> <p>Our long-term observational study and field experiments show that squirrels can anticipate increases in food availability and density, thereby decoupling the usual pattern where animals respond to, rather than anticipate, an ecological change.</p> <p>As in many other study systems, ecological factors that can induce plasticity (such as food and density) co-vary. However, our field experiments that manipulate food availability and social cues of density (frequency of territorial vocalizations) indicate that increases in social (acoustic) cues of density in the absence of additional food can induce similar life history plasticity, as does experimental food supplementation.</p> <p>Changes in the levels of metabolic hormones (glucocorticoids) in response to variation in food and density are one mechanism that seems to induce this adaptive life history plasticity. </p> <p>Although we have not yet investigated the energetic response of squirrels to elevated density or its association with life history plasticity, energetics research in red squirrels has overturned several standard pillars of knowledge in physiological ecology.</p> <p>We show how a tractable model species combined with integrative studies can reveal how animals cope with resource fluctuations through life history plasticity.</p>
Figure 1 from: Albano PG, Schnedl S-M, Eschner A (2020) An illustrated catalogue of Rudolf Sturany's type specimens in the Naturhistorisches Museum Wien, Austria (NHMW): more Red Sea species. Zoosystematics and Evolution 96(2): 571-576. https://doi.org/10.3897/zse.96.54707
Figure 1 Drillia levanderi Sturany, 1905, Massaua, Eritrea. A, C. Original figures in Sturany, 1905; B, D, E. Holotype NHMW-Mollusca 39903: front (B), side (D), apex detail (E); F. Original label. Scale bars: B, D: 3 mm, E: 0.5 mm.
Figure 3 from: Albano PG, Schnedl S-M, Eschner A (2020) An illustrated catalogue of Rudolf Sturany's type specimens in the Naturhistorisches Museum Wien, Austria (NHMW): more Red Sea species. Zoosystematics and Evolution 96(2): 571-576. https://doi.org/10.3897/zse.96.54707
Figure 3 Raeta jickelii Sturany, 1905, Massaua, Eritrea. A, D. Original figures in Sturany, 1905; B, C, E. Illustrated syntype NHMW-Mollusca 39925: left valve outside view (B), left valve inside view (C), hinge detail (E). Scale bars: B, C: 10 mm, E: 2 mm.
Figure 2 from: Albano PG, Schnedl S-M, Eschner A (2020) An illustrated catalogue of Rudolf Sturany's type specimens in the Naturhistorisches Museum Wien, Austria (NHMW): more Red Sea species. Zoosystematics and Evolution 96(2): 571-576. https://doi.org/10.3897/zse.96.54707
Figure 2 Levanderia erythraeensis Sturany, 1905, Massaua, Eritrea. A, B. Original figures in Sturany, 1905; C, D. Holotype NHMW-Mollusca 39894: outside view (C), inside view (D); E. Original label. Scale bar: 1 mm.
Exploring human splenic red pulp vasculature in virtual reality. Details of sheathed capillaries and the open capillary network. Supplementary material
<p>Supplementary files demonstrate our data in an interactive application. Please download und unpack the file, then launch file "start.bat". Please note that loading the original images takes some time. If you have a Steam VR headset, it is detected and used automatically.</p> <ol> <li><strong>Supplementary file 1 </strong><br> Localization of arteries and arterioles in ROI 4.<br> ROI 4 with all endothelia and some periarterial fibroblasts colored blue (CD34), smooth muscle alpha-actin (SMA) colored white and capillary sheaths depicted in green (CD271). Most arteries and arterioles can be localized by white color. White appears in a vertex of the blue reconstruction of CD34 staining, if a surface reconstructed for SMA labelling is closer than 8.75 µm to this vertex. Capillary sheaths connected to the selected arterioles (marked red in Suppl. file 2) are green and non-connected sheaths fed by other arterioles are dark green (CD271).</li> <li><strong>Supplementary file 2</strong><br> Relation of capillary sheaths to terminal arterioles in ROI4.<br> ROI 4 with all endothelia and some periarterial fibroblasts colored blue (CD34), selected terminal artery and terminal arterioles manually labelled red and capillary sheaths connected to the labelled arterioles in green (CD271). Non-connected sheaths fed by other arterioles are dark green (CD271). Follicular dendritic cells (FDCs) in follicles are light green (CD271). This file corresponds to Fig. 3 and to Suppl. Video 1-3.</li> <li><strong>Supplementary file 3</strong><br> Relation of capillary sheaths to terminal arterioles in ROI 2.<br> ROI 2 with all endothelia and some periarterial fibroblasts colored blue (CD34), selected terminal artery and terminal arterioles manually labelled red and capillary sheaths connected to the labelled arterioles in green (CD271). Non-connected sheaths fed by other arterioles are dark green (CD271). FDCs in follicles are light green (CD271). This file corresponds to Fig. 4a,b.</li> <li><strong>Supplementary file 4</strong><br> Relation of capillary sheaths to terminal arterioles in ROI 1.<br> ROI 1 with all endothelia and some periarterial fibroblasts colored blue (CD34), selected terminal artery and terminal arterioles manually labelled red and capillary sheaths connected to the labelled arterioles in green (CD271). Non-connected sheaths fed by other arterioles are dark green (CD271). FDCs in follicles are light green (CD271)</li> <li><strong>Supplementary file 5</strong><br> White pulp in 3D (ROI 3).<br> ROI 3 with all endothelia and some periarterial fibroblasts colored blue (CD34) and capillary sheaths in green (CD271). FDCs in follicles are light green (CD271). Arteries and terminal arterioles were not labelled.</li> <li><strong>Supplementary file 6 </strong><br> Sheathed capillaries exhibit short open-ended side branches.<br> ROI 2 with all endothelia and some periarterial fibroblasts colored blue (CD34) and with selected terminal artery and terminal arterioles labelled light blue. Capillary sheaths connected to the selected arterioles are green (CD271) and unconnected sheaths are dark green (CD271). The open-ended side branches of the selected sheathed capillaries were manually labelled red and are visualized in their entire length. This file corresponds to Fig. 4c.</li> <li><strong>Supplementary file 7</strong><br> Terminal arterioles may have a few unsheathed connections to the red pulp capillary network.<br> ROI 2 with all endothelia and some periarterial fibroblasts colored blue (CD34) and with selected terminal artery and terminal arterioles labelled light blue. Capillary sheaths connected to the selected arterioles are green (CD271) and unconnected sheaths are dark green (CD271). Connections from a terminal arteriole to the red pulp capillary network lacking sheaths were manually labelled red. A part of the capillary network after the connection is colored yellow. This file corresponds to Figs. 4d,e.</li> <li><strong>Supplementary file 8</strong><br> B-lymphocytes accumulate around terminal arteries and in/around capillary sheaths.<br> Lower part of ROI 2 with selected terminal artery and terminal arterioles colored blue and connected capillary sheaths in green (CD271). B-lymphocytes were digitally reduced in number and automatically labelled red (CD20). The B-cells accumulate around a terminal artery and around (and inside) capillary sheaths. This file corresponds to Fig. 6 and to Suppl. Video 4.</li> <li><strong>Supplementary file 9</strong><br> Reduction of B-lymphocytes is inevitable for visualization.<br> ROI 2 showing Suppl. file 8 integrated into the entire ROI 2. A large number of B-lymphocytes is present in the red pulp of ROI 2 (CD20 visualized in white). These cells are self-occluding and necessitate reducing B-lymphocytes as shown in Suppl. Fig. 8 to highlight accumulations.</li> <li><strong>Supplementary file 10</strong><br> Red pulp venule with potential connections to capillary network.<br> A red pulp venule with capillaries in ROI 1. Capillary and venous endothelium is shown in light blue (CD34). A part of a red pulp venule with potential contributing capillaries (CD34, blue) was manually selected in addition to a terminal arteriole (light red). The capillary sheaths connected with this arteriole are green (CD271). Non-connected sheaths are dark green (CD 271) and FDCs in follicles are light green (CD271). Capillaries from the red pulp network, which appear to be connected to the venule were manually colored red. Two of the red capillaries seem to originate from a sheathed capillary. This file corresponds to Fig. 5a-d and to Suppl. Video 5.</li> </ol> <p>Bounding boxes for all files have a side length of 1 mm with exception of Suppl. File 8 which is 800 (b) x 620 (h) x 614 (d) µm.</p> <p>As for videos, each video is in three quality settings:</p> <ul> <li>..._h264_8bit.mov is the most generic H.264 HQ setting. Should play everywhere, also with QuickTime.</li> <li>..._h265_10bit.mov is the 10 bit video version, encoded with HEVC encoder. Should be the same or higher quality with less size. Might not play everywhere.</li> <li>..._h264_8bit_small.mov is the H.264 LQ setting with much lower resolution, use this if your download bandwidth is limited.</li> </ul> <p>Now, there are 5 videos to supplement the submission:</p> <ol> <li><a href="https://zenodo.org/record/3993324/files/suppl%20video%201%20-%20sheath%20video%20r4%20full%20h264%208bit.mov">suppl video 1 - sheath r4 full .</a>.. shows the region ROI4 with full vasculature, similar to Fig. 3 of the manuscript,</li> <li><a href="https://zenodo.org/record/3993324/files/suppl%20video%202%20-%20sheath%20video%20r4%20select%20h264%208bit.mov">suppl video 2 - sheath r4 select .</a>... shows only the selection of the vasculature from ROI4, similar to Fig. 3 of the manuscript,</li> <li><a href="https://zenodo.org/record/3993324/files/suppl%20video%203%20-%20sheath%20video%20r4%20clipping%20h264%208bit.mov">suppl video 3 - sheath r4 clipping .</a>... showcases the front plane clipping technique we used for diagnostics in VR. This demonstrates the contents of Fig. 8 in dynamics.</li> <li><a href="https://zenodo.org/record/3993324/files/suppl%20video%204%20-%20sheath%20video%20r2%20bcell%20h264%208bit.mov">suppl video 4 - sheath bcell .</a>.. shows the selection of the B-cells to supplement Fig. 6 in the manuscript.</li> <li><a href="https://zenodo.org/record/3993324/files/suppl%20video%205%20-%20sheath%20video%20r1%20vene%20h264%208bit.mov">suppl video 5 - sheath r1 vene .</a>.. shows a red pulp venule and its apparent connections, this supplements Fig. 5 of the manuscript.</li> </ol>
Fragmentation and translocation distort the genetic landscape of ungulates: red deer in the Netherlands
<p>Many ungulate populations have a complex history of isolation and translocation. Consequently, ungulate populations may have experienced substantial reductions in the level of overall gene flow, yet simultaneously have augmented levels of long distance gene flow. To investigate the effect of this dual anthropogenic effect on the genetic landscape of ungulates, we genotyped 35K SNPs in 47 red deer (Cervus elaphus) of Netherlands, including putative autochthonous relic populations as well as allochthonous populations established in private estates and rewilding areas. We applied FST and ordination analyses to determine the meta-population genetic structure and thereby the occurrence of hybridization. At population level, we investigated levels of inbreeding through individual-based diversity measures, including Runs of Homozygosity. We documented that both spatial genetic structure and within-population genetic variation differed markedly from patterns assumed from present-day abundance and distribution. Notwithstanding the small spatial scale, red deer populations formed distinct genetic clusters, and some had higher genetic similarity to distant than to nearby populations. Moreover, the putative autochthonous relic deer populations had much reduced levels of polymorphism and multi-locus heterozygosity, despite relatively large current population sizes. Accordingly, genomes of these deer contained a high proportion of long (>5 Mb) Runs of Homozygosity. Whereas the observed high levels of inbreeding warrant defragmentation measures, the presence of adjacent autochthonous and allochthonous genetic stocks imply that facilitation of gene flow would cause genetic homogenization. Such distortions of the genetic landscape of ungulates creates management dilemmas that cannot be properly anticipated without baseline genetic monitoring.</p>
The Genome sequences of Calonectria ilicicola (anamorph Cylindrocladium parasiticum) causing Cylindrocladium black rot of peanut and red crown rot of soybean
<p>The fungus <em>Calonectria ilicicola</em> (anamorph <em>Cylindrocladium parasiticum</em>) is an important plant pathogen causing Cylindrocladium black rot (CBR) on peanut and Red crown rot (RCR) on soybean. CBR infection of peanuts cause symptoms such as chlorosis of leaves, blackening of taproots, and wilting, while RCR infection of soybeans lead to root and interveinal necrosis of soybean. In the present study, we sequenced the genome of four CBR-related<em> Ca. ilicicola</em> strains and three RCR-related<em> Ca. ilicicola</em> strains. The draft genome of <em>Ca. ilicicola</em>, ranged from 68.63 Mb to 70.35 Mb in genome size, containing 18536 to 19361 protein-coding genes. The described genome sequences will provide insights into factors that contribute to pathogenicity toward peanut and soybean and will be useful for future research in population genomics and molecular diagnostic marker development to quickly detect this pathogen.</p>
Figure 3 from: Li Z, Zheng H-L, Tang M (2020) Synotis panzhouensis (Asteraceae, Senecioneae), a distinct new species with red-purple pappus from southwestern Guizhou, China. PhytoKeys 166: 79-86. https://doi.org/10.3897/phytokeys.166.58654
Figure 3 Synotis nayongensis in the wild (Luzui village, Nayong, Guizhou,China). A habitat B habit C portion of vegetative stem D leaf blades from the adaxil view E synflorescence F portion of synflorescence (side view, note the white phyllaries with green apex, and also note the white pappus). Scale bars: 5 mm (C); 6 mm (F).
Figure 1 from: Li Z, Zheng H-L, Tang M (2020) Synotis panzhouensis (Asteraceae, Senecioneae), a distinct new species with red-purple pappus from southwestern Guizhou, China. PhytoKeys 166: 79-86. https://doi.org/10.3897/phytokeys.166.58654
Figure 1 Holotype of Synotis panzhouensis (Panzhou, Guizhou, China, Z. Li & M. Tang 2020-0901 (JXAU)).
Figure 2 from: Li Z, Zheng H-L, Tang M (2020) Synotis panzhouensis (Asteraceae, Senecioneae), a distinct new species with red-purple pappus from southwestern Guizhou, China. PhytoKeys 166: 79-86. https://doi.org/10.3897/phytokeys.166.58654
Figure 2 Synotis panzhouensis in the wild (Dazhai village, Panzhou, Guizhou, China). A habitat B general habit C portion of vegetative stem D leaf blades (left two: adaxial surface; right four: abaxial surface) E synflorescence F capitulum (top view) G capitulum (side view) H a disk floret with red-purple pappus. Scale bars: 5 mm (C); 10 cm (D); 4 mm (F); 1 cm (G, H).
Figure 6 from: Sheffield CS, Oram R, Heron JM (2020) Bombus (Pyrobombus) johanseni Sladen, 1919, a valid North American bumble bee species, with a new synonymy and comparisons to other "red-banded" bumble bee species in North America (Hymenoptera, Apidae, Bombini). ZooKeys 984: 59-81. https://doi.org/10.3897/zookeys.984.55816
Figure 6 Faces (A, C, E) and thorax in dorsal view (B, D, F) in female bumble bees A, BBombus johanseniC, DB. melanopygusE, FB. lapponicus sylvicola.
Figure 3 from: Sheffield CS, Oram R, Heron JM (2020) Bombus (Pyrobombus) johanseni Sladen, 1919, a valid North American bumble bee species, with a new synonymy and comparisons to other "red-banded" bumble bee species in North America (Hymenoptera, Apidae, Bombini). ZooKeys 984: 59-81. https://doi.org/10.3897/zookeys.984.55816
Figure 3 Bombus johanseni female from Sachs Harbour, Banks Island, Northwest Territories, Canada. A Left arrow shows the characteristic black pubescence of the face, right arrow shows the solid area of darker pubescence on the anterior part of thorax B left arrow shows the solid area of darker pubescence on the anterior part of thorax, right arrow shows the typical "red-banding" of the abdomen. Photographs by JMH.
Figure 10 from: Sheffield CS, Oram R, Heron JM (2020) Bombus (Pyrobombus) johanseni Sladen, 1919, a valid North American bumble bee species, with a new synonymy and comparisons to other "red-banded" bumble bee species in North America (Hymenoptera, Apidae, Bombini). ZooKeys 984: 59-81. https://doi.org/10.3897/zookeys.984.55816
Figure 10 Distribution map of known specimens of B. johanseni, including B. interacti. Specimens identified in the literature as B. gelidus are also included as it is likely that some of these, especially the eastern record, are actually B. johanseni, and not dark specimens of B. sylvicola.
Figure 5 from: Sheffield CS, Oram R, Heron JM (2020) Bombus (Pyrobombus) johanseni Sladen, 1919, a valid North American bumble bee species, with a new synonymy and comparisons to other "red-banded" bumble bee species in North America (Hymenoptera, Apidae, Bombini). ZooKeys 984: 59-81. https://doi.org/10.3897/zookeys.984.55816
Figure 5 A A typical "red-banded" bumble bee, Bombus huntii, showing the two red bands (terga 2 and 3) with yellow bands on either side (arrows, terga 1 and 4), and "red-tailed" bumble bees BB. centralis, with red band (terga 3 and 4) preceded by a yellow band (terga 1 and 2) with black apically (arrow) CB. mixtus, with a black band (arrow) separating the basal yellow and apical red bands. Photographs by CSS.
Figure 1 from: Sheffield CS, Oram R, Heron JM (2020) Bombus (Pyrobombus) johanseni Sladen, 1919, a valid North American bumble bee species, with a new synonymy and comparisons to other "red-banded" bumble bee species in North America (Hymenoptera, Apidae, Bombini). ZooKeys 984: 59-81. https://doi.org/10.3897/zookeys.984.55816
Figure 1 Maximum likelihood tree constructed with 500 bootstraps for selected taxa of Pyrobombus, with B. (Bombus) terricola as an outgroup. The taxon Bombus johanseni consists of specimens identified in BOLD as Bombus sp. and B. johanseni, in addition to the holotype male of B. interacti.
Figure 2 from: Sheffield CS, Oram R, Heron JM (2020) Bombus (Pyrobombus) johanseni Sladen, 1919, a valid North American bumble bee species, with a new synonymy and comparisons to other "red-banded" bumble bee species in North America (Hymenoptera, Apidae, Bombini). ZooKeys 984: 59-81. https://doi.org/10.3897/zookeys.984.55816
Figure 2 Holotype female of Bombus sylvicola var. johanseniA face B lateral view C associated specimen labels D dorsal view. Photographs by Joel Kits, Ottawa Research and Development Centre.
Figure 7 from: Sheffield CS, Oram R, Heron JM (2020) Bombus (Pyrobombus) johanseni Sladen, 1919, a valid North American bumble bee species, with a new synonymy and comparisons to other "red-banded" bumble bee species in North America (Hymenoptera, Apidae, Bombini). ZooKeys 984: 59-81. https://doi.org/10.3897/zookeys.984.55816
Figure 7 Examples of "red-banded" bumble bees. ABombus huntii female. Top arrow shows the complete yellow hair patch on the rear of the thorax (scutellum), bottom arrow shows the completely black tegum 5 BB. ternarius female. Top arrow shows the face with both yellow and black hairs, middle arrow shows the entirely yellow anterior area of the thorax, bottom arrow shows the yellow hair patch on the rear of the thorax (scutellum) divided in two by a wedge of black hairs. Photographs by CSS C, DB. ternarius female, from Newfoundland. Arrow in C shows the atypical intermixed black hair on the anterior area of the thorax. Top arrow in D shows the yellow hair patch on the rear of the thorax (scutellum) divided in two by a wedge of black hairs, bottom arrow shows all black tergum 5. Photographs by Carolyn Parsons EB. vancouverensis female (red form). Left arrow shows the pale hair patch on the rear of the thorax (scutellum) divided in two by a wedge of black hairs, right arrow shows the incomplete red band of tergum 2, with black hairs in basal half FB. rufocinctus female (red form). Arrow shows the incomplete red band of tergum 2, being yellow medially in the basal half. Photographs by CSS.
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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)
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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.
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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.