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FIGURE 9 in Multigene phylogeny reveals the ribbed shell morphotypes in the land snail genus Sarika (Eupulmonata: Ariophantidae), with description of two new species from Thailand and Myanmar
FIGURE 9 Genitalia of Sarika spp. A, B) S. costabilis sp. nov. paratype CUMZ 7945. A) General view of the genital system. B) Internal structure of penis. C, D) S. costata sp. nov. paratype CUMZ 7947. C) General view of the genital system. D) Internal structure of penis. White arrows indicate the end of penis.
FIGURE 11 in Multigene phylogeny reveals the ribbed shell morphotypes in the land snail genus Sarika (Eupulmonata: Ariophantidae), with description of two new species from Thailand and Myanmar
FIGURE 11 Radula of Sarika spp. A) S. theodori specimen CUMZ 7942. B) S. siamensis specimen CUMZ 7951. C) S. costabilis sp. nov. paratype CUMZ 7945. D) S. costata sp. nov. paratype CUMZ 7947. Central tooth indicated by 'C' and blue colour; yellow colour indicates lateral teeth in the transition to marginal teeth.
FIGURE 8 in Multigene phylogeny reveals the ribbed shell morphotypes in the land snail genus Sarika (Eupulmonata: Ariophantidae), with description of two new species from Thailand and Myanmar
FIGURE 8 Shells of Sarika spp. A, B) S. costabilis sp. nov. A) Holotype CUMZ 7943. B) Paratype CUMZ 7944. C, D) S. costata sp. nov. C) Holotype CUMZ 7946. D) Paratype CUMZ 7947.
FIGURE 5 in Multigene phylogeny reveals the ribbed shell morphotypes in the land snail genus Sarika (Eupulmonata: Ariophantidae), with description of two new species from Thailand and Myanmar
FIGURE 5 Spermatophore of Sarika theodori, specimen CUMZ 7941. A) General view of spermatophore that was broken into two parts. B) Head filament. C–E) Tail filament. C) Three spines located close to the sperm sac. D) Region with and without branching spines. E) Branching spines on the tip region. Yellow arrow indicates the end of spines from the tip.
FIGURE 4 in Multigene phylogeny reveals the ribbed shell morphotypes in the land snail genus Sarika (Eupulmonata: Ariophantidae), with description of two new species from Thailand and Myanmar
FIGURE 4 Genitalia of Sarika spp. A, B) S. theodori, specimen CUMZ 7941. A) General view of the genital system. B) Internal structure of penis. C, D) S. siamensis, specimen CUMZ 7952. C) General view of the genital system. D) Internal structure of penis. Yellow arrow indicates the end of epiphallic caecum. White arrows indicate the end of penis.
FIGURE 2 in Multigene phylogeny reveals the ribbed shell morphotypes in the land snail genus Sarika (Eupulmonata: Ariophantidae), with description of two new species from Thailand and Myanmar
FIGURE 2 Bayesian inference tree based on a 1495 bp concatenated alignment dataset of COI + 16S + 28S genes. Numbers by the nodes are the Bayesian posterior probabilities (left) and ML bootstrap values (right); shown only for the nodes supported by BI ≥ 0.95 or ML ≥ 70%. Clade A consists of the S. resplendens-S. hainesi species groups. Clade B consists of the S. siamensis species group. Images of living snails are not to scale.
FIGURE 6 in Multigene phylogeny reveals the ribbed shell morphotypes in the land snail genus Sarika (Eupulmonata: Ariophantidae), with description of two new species from Thailand and Myanmar
FIGURE 6 Spermatophore of Sarika siamensis, specimen CUMZ 7951. A) General view of spermatophore that was broken into two parts. B) Head filament. C–E) Tail filament. C) Three spines located close to the sperm sac. D) Region with and without branching spines. E) Branching spines on the tip region. Yellow arrow indicates the end of spines from the tip.
FIGURE 1 in Multigene phylogeny reveals the ribbed shell morphotypes in the land snail genus Sarika (Eupulmonata: Ariophantidae), with description of two new species from Thailand and Myanmar
FIGURE 1 Geographic distribution of ribbed shell Sarika spp. based on the specimens examined herein. A) Distribution of S. theodori, S. costabilis sp. nov., and S. costata sp. nov. B) Distribution of S. siamensis. Black symbols indicate the DNA extracted specimens used in the molecular analysis; white symbols indicate shells or other preserved specimens.
FIGURE 3 in Multigene phylogeny reveals the ribbed shell morphotypes in the land snail genus Sarika (Eupulmonata: Ariophantidae), with description of two new species from Thailand and Myanmar
FIGURE 3 Shells of Sarika spp. A, B) S. theodori. A) Specimen NHMUK 1988.12.4.1514. B) Specimen CUMZ 7941. C, D) S. siamensis. C) Specimen CUMZ 7949. D) Specimen CUMZ 7950.
FUTURES land change forecasts in response to flooding in Charleston area, South Carolina (2019-2050)
<p>Climate-aware scenarios of FUTURES land change projections in Charleston area (Cherleston, Dorchester, Berkeley) for 2019-2050.</p> <p>Zipped folder <code>results</code> contains FUTURES v3 simulation runs for 3 counties in South Carolina, USA (Charleston, Berkeley, Dorchester) from 2019 to 2050. Included are five <em>climate-aware</em> scenarios (reactive, managed retreat, resist, polarized population, trapped population) and one scenario which does not take future climate conditions into account (<em>dynamic development</em>). Each folder contains 50 monte-carlo simulation results with <code>developed_seed_X.tif</code> and <code>adapted_seed_X.tif</code> where <code>X</code> goes from 1 to 50. Values of <code>developed_seed_X.tif</code> range from -31 to 31, where the positive values represent simulation step when an undeveloped pixel was developed and the negative values represent simulation step when a developed pixel was abandoned. Zero stands for initial development. For example, value -11 means the particular pixel was abandoned in 2030. Note that values of raster files in <code>Dynamic development</code> folder range from -1 to 31, where -1 means undeveloped and the rest is the same as above. Values of <code>adapted_seed_X.tif</code> range from 0 to 100, where 0 means trapped (flooded but no adaptation), the other values represent return period for which the pixel is adapted (e.g. 2-, 5-, 10-, 20-, 50- and 100-year flood). The files' CRS is Albers Conic Equal Area, NAD83(2011) datum.</p> <p>Additionally, we include <code>migration_matrix.csv</code> derived from IRS data, that contains probability values of moving from an origin county in the case study (row) to any other counties (columns).</p>
Figure 8 Shells. A–C. Taphrenalla diadema. A. specimen CUMZ 7175. B. specimen CUMZ 7177. C. specimen CUMZ 7171 showing channel-shaped suture with wide bottom. D, E. T in Integrative systematics reveals the new land-snail genus Taphrenalla (Eupulmonata: Ariophantidae) with a description of nine new species from Thailand
Figure 8 Shells. A–C. Taphrenalla diadema. A. specimen CUMZ 7175. B. specimen CUMZ 7177. C. specimen CUMZ 7171 showing channel-shaped suture with wide bottom. D, E. T. dalli sp. nov. D. holotype CUMZ 7183. E. specimen CUMZ 7189 showing channel-shaped suture with very wide bottom. Inset SEM image showing shell sculpture of each species.
Data and code from: Breakdown in seasonal dynamics of subtropical ant communities with land-cover change
<p><span>Concerns about widespread human-induced declines in insect populations are mounting, yet little is known about how land-use change modifies the dynamics of insect communities, particularly in understudied regions. Here, we examine how the seasonal activity patterns of ants—key drivers of terrestrial ecosystem functioning—vary with anthropogenic land-cover change on a subtropical island landscape, and whether differences in temperature or species composition can explain observed patterns. Using trap captures sampled biweekly over two years from a biodiversity monitoring network covering Okinawa Island, Japan, we processed 1.2 million individuals and reconstructed activity patterns within and across habitat types. Forest communities exhibited greater temporal variability of activity than those in more developed areas. Using time-series decomposition to deconstruct this pattern, we found that sites with greater human development exhibited ant communities with diminished seasonality, reduced synchrony, and higher stochasticity compared to sites with greater forest cover. Our results cannot be explained by variation in regional or site temperature patterns, or by differences in species richness or composition among sites. Our study raises the possibility that disruptions to natural seasonal patterns of functionally key insect communities may comprise an important and underappreciated consequence of global environmental change that must be better understood across Earth's biomes.</span></p>
Land cover data (30m) derived from GlobeLand30 for the China region
<p>This collection contains the land cover map (30m) derived from GlobeLand30 used in our study ‘<strong><em>Forestation at the right time with the right species can generate persistent carbon benefits in China</em></strong>’.</p> <p>Original maps were download from http://www.globallandcover.com/. The map was merged in ArcGIS 10.8 for the region of China (70°E-140°E, 15°N-55°N).</p> <p>Reference:<br> C. Jun, Y. Ban, S. Li, Open access to Earth land-cover map. Nature 514, 434–434 (2014). DOI:10.1038/514434c.</p>
Flux data kit, a comprehensive data set of ecosystem fluxes for land surface modelling
<blockquote> <p>Newer versions (>= v3.0) are released by Benjamin Stocker and can be found at his Zenodo account at: https://zenodo.org/records/10885934</p> </blockquote> <p>The Flux data kit is an effort to expand upon the existing work by Ukolla et a. (2022) to synthesize various sources of ecosystem flux data (i.e. the PLUMBER2 data set, gathered from all major networks). We further expand upon the original data set by integrating data which was either expanded upon (temporally) or where sites were added (e.g. the integration of ICOS data).</p> <p>The effort uses the FluxnetLSM package by the above mentioned authors, as well as their general workflow. In contrast to the PLUMBER2 data set we do not apply stringent quality control, and all quality control on the availability of variables and/or their duration <em>should be done by the user</em>. Furthermore, we include both leaf area index (LAI) and Fraction of Absorbed Photosynthetically Active Radiation (FAPAR) in the netcdf output, where PLUMBER2 only provided LAI. On all other parts the formatting and naming conventions as well as quality control specifications remain the same as in PLUMBER2. We therefore refer to Ukolla et al. (2022) for details.</p> <p><strong>Data included</strong></p> <p>The data included consists of three files, containing different versions of the same data. The FLUXDATAKIT_LSM.tar.gz file contains compressed netCDF files compatible with the ALMA scheme for land surface modelling. The FLUXDATAKIT_FLUXNET.tar.gz file contains data in a CSV format according to the FLUXNET specifications. And finally the rsofun_driver_data_clean.rds file is a compressed serialized R file containing data formatted for use with the `rsofun` R package.</p> <p><strong>Data generation</strong></p> <p>Data is generated using the FluxDataKit project. Although this project is not meant for continuous releases, and no support is provided in using this code with data provided AS IS, it might still be useful to some:</p> <p><a href="https://github.com/geco-bern/FluxDataKit">https://github.com/geco-bern/FluxDataKit</a></p> <p>The data can be further complimented using the FluxnetEO dataset, which is accessible through the package with the same name as found here:</p> <p><a href="https://github.com/geco-bern/FluxnetEO">https://github.com/geco-bern/FluxnetEO</a></p> <p><strong>Acknowledgements</strong></p> <p>The flux data kit is part of the LEMONTREE project and funded by Schmidt Futures and under the umbrella of the Virtual Earth System Research Institute (VESRI).</p> <p><strong>References:</strong></p> <ul> <li>Ukkola, Anna M., Gab Abramowitz, and Martin G. De Kauwe. "A flux tower dataset tailored for land model evaluation." Earth System Science Data 14.2 (2022): 449-461.</li> </ul>
Land based IMTA grow out production
<p>Data set of sea cucumber (<em>Holothuria sanctori</em>) and abalone (<em>Haliotis tuberculata</em> sp.) growth parameters during grow out in Land based IMTA systems when fed IMTA produced macroalgae (<em>Ulva rigida</em> and <em>Gracilaria cornea</em>) and compound feed.</p>
Vegetation Density Across NYC: Analysis of Land Cover Data (2017) within 200 meter Buffers of Points
<p><strong>Summary:</strong></p><p>This repository contains spatial data files representing the density of vegetation cover within a 200 meter radius of points on a grid across the land area of New York City (NYC), New York, USA based on 2017 six-inch resolution land cover data, as well as SQL code used to carry out the analysis. The 200 meter radius was selected based on a study led by researchers at the NYC Department of Health and Mental Hygiene, which found that for a given point in the city, cooling benefits of vegetation only begin to accrue once the vegetation cover within a 200 meter radius is at least 32% (Johnson et al. 2020). The grid spacing of 100 feet in north/south and east/west directions was intended to provide granular enough detail to offer useful insights at a local scale (e.g., within a neighborhood) while keeping the amount of data needed to be processed for this manageable. </p><p>The contained files were developed by the NY Cities Program of <a href="https://www.nature.org/newyork">The Nature Conservancy</a> and the <a href="https://nyc-eja.org/">NYC Environmental Justice Alliance</a> through the <a href="https://medium.com/gage-nyc/introducing-the-just-nature-nyc-partnership-513612e8c3b4">Just Nature NYC Partnership</a>. Additional context and interpretation of this work is available in a <a href="https://medium.com/gage-nyc/looking-at-cooling-benefits-of-plants-through-nyc-vegetation-data-ccdeb33cbe17">blog post</a>.</p><p> </p><p><i>References:</i></p><p>Johnson, S., Z. Ross, I. Kheirbek, and K. Ito. 2020. Characterization of intra-urban spatial variation in observed summer ambient temperature from the New York City Community Air Survey. <i>Urban Climate</i> 31:100583. <a href="https://doi.org/10.1016/j.uclim.2020.100583">https://doi.org/10.1016/j.uclim.2020.100583</a></p><p> </p><p><strong>Files in this Repository:</strong></p><p>Spatial Data (all data are in the New York State Plane Coordinate System - Long Island Zone, North American Datum 1983, <a href="https://epsg.io/2263">EPSG 2263</a>):</p><p>Points with unique identifiers (<i>fid</i>) and data on proportion tree canopy cover (<i>prop_canopy</i>), proportion grass/shrub cover (<i>prop_grassshrub</i>), and proportion total vegetation cover (<i>prop_veg</i>) within a 200 meter radius (same data made available in two commonly used formats, Esri File GeoDatabase and GeoPackage):</p><p><i>nyc_propveg2017_200mbuffer_100ftgrid_nowater.gdb.zip</i></p><p><i>nyc_propveg2017_200mbuffer_100ftgrid_nowater.gpkg</i> </p><p>Raster Data with the proportion total vegetation within a 200 meter radius of the center of each cell (pixel centers align with the spatial point data)</p><p><i>nyc_propveg2017_200mbuffer_100ftgrid_nowater.tif</i></p><p>Computer Code:</p><p>Code for generating the point data in PostgreSQL/PostGIS, assuming the data sources listed below are already in a PostGIS database.</p><p><i>nyc_point_buffer_vegetation_overlay.sql</i></p><p> </p><p><strong>Data Sources and Methods:</strong></p><p>We used two openly available datasets from the City of New York for this analysis:</p><p>Borough Boundaries (Clipped to Shoreline) for NYC, from the NYC Department of City Planning, available at <a href="https://www.nyc.gov/site/planning/data-maps/open-data/districts-download-metadata.page">https://www.nyc.gov/site/planning/data-maps/open-data/districts-download-metadata.page</a> </p><p>Six-inch resolution land cover data for New York City as of 2017, available at <a href="https://data.cityofnewyork.us/Environment/Land-Cover-Raster-Data-2017-6in-Resolution/he6d-2qns">https://data.cityofnewyork.us/Environment/Land-Cover-Raster-Data-2017-6in-Resolution/he6d-2qns</a> </p><p>All data were used in the New York State Plane Coordinate System, Long Island Zone (<a href="https://epsg.io/2263">EPSG 2263</a>). Land cover data were used in a polygonized form for these analyses.</p><p>The general steps for developing the data available in this repository were as follows:</p><p>Create a grid of points across the city, based on the full extent of the Borough Boundaries dataset, with points 100 feet from one another in east/west and north/south directions</p><p>Delete any points that do not overlap the areas in the Borough Boundaries dataset.</p><p>Create circles centered at each point, with a radius of 200 meters (656.168 feet) in line with the aforementioned paper (Johnson et al. 2020).</p><p>Overlay the circles with the land cover data, and calculate the proportion of the land cover that was grass/shrub and tree canopy land cover types. Note, because the land cover data consistently ended at the boundaries of NYC, for points within 200 meters of Nassau and Westchester Counties, the area with land cover data was smaller than the area of the circles.</p><p>Relate the results from the overlay analysis back to the associated points.</p><p>Create a raster data layer from the point data, with 100 foot by 100 foot resolution, where the center of each pixel is at the location of the respective points. Areas between the Borough Boundary polygons (open water of NY Harbor) are coded as "no data."</p><p>All steps except for the creation of the raster dataset were conducted in PostgreSQL/PostGIS, as documented in <i>nyc_point_buffer_vegetation_overlay.sql</i>. The conversion of the results to a raster dataset was done in QGIS (version 3.28), ultimately using the <a href="https://gdal.org/programs/gdal_rasterize.html">gdal_rasterize</a> function.</p>
Figs 52–55 in Revision of the land snail genus Landouria Godwin-Austen, 1918 (Gastropoda, Camaenidae) from Java
Figs 52–55 (opposite page). Distribution of species of Landouria in Java (10′ grid). 52. L. winteriana (Pfeiffer, 1842), L. naggsi sp. nov., L. nusakambangensis sp. nov., L. petrukensis sp. nov., L. tholiformis sp. nov., L. tonywhitteni sp. nov., L. smimensis (Mousson, 1848). 53. L. conoidea (Leschke, 1914), L. abdidalem sp. nov., L. sewuensis sp. nov., L. sukoliloensis sp. nov., L. pacitanensis sp. nov., L. intumescens (Martens, 1867), L. madurensis sp. nov. 54. L. rotatoria (Pfeiffer, 1842), L. nodifera sp. nov., L. parahyangensis sp. nov., L. schepmani (Möllendorff, 1897), L. zonifera sp. nov., L. ciliocincta (Möllendorff, 1897), L. pakidulan sp. nov. 55. L. epiplatia (Möllendorff, 1897), L. monticola van Benthem Jutting, 1950, L. davini Dharma, 2015, L. menorehensis sp. nov., L. dharmai sp. nov., L. moussoniana (Martens, 1867).
Figs 48–51 in Revision of the land snail genus Landouria Godwin-Austen, 1918 (Gastropoda, Camaenidae) from Java
Figs 48–51 (opposite page). Shells of species of Landouria from Java. 48. L. parahyangensis sp. nov., West Java, Karangnunggal, surroundings of Pasir Taraje Cave (holotype, MZB 20429). 49. L. nusakambangensis sp. nov., Central Java, Nusa Kambangan Island, nature monument Gligir (holotype, ZMA 412298a). 50. L. petrukensis sp. nov., Central Java, Karangbolong, way to Petruk Cave (holotype, MZB 19203). 51. L. tholiformis sp. nov., Yogyakarta, Gunung Kidul, Tepus, near Poktunggal Beach (holotype, MZB 17999). Scale bar: 5 mm.
Figs 29–47 in Revision of the land snail genus Landouria Godwin-Austen, 1918 (Gastropoda, Camaenidae) from Java
Figs 29–47. Flagella of species of Landouria from Java. 29. L. winteriana (Pfeiffer, 1842), West Java, Padalarang, Gunung Masigit (neotype, ZMA 376193a). 30. L. rotatoria (Pfeiffer, 1842), West Java, Gunung Salak, 1166 m a.s.l. (neotype, MZB 19205). 31. L. epiplatia (Möllendorff, 1897)?, West Java, Bogor, Gunung Gede (ZMH 79946). 32. L. nusakambangensis sp. nov., Central Java, Nusa Kambangan Island, nature monument Gligir (holotype, ZMA 412298a). 33. L. petrukensis sp. nov., Central Java, Karangbolong, way to Petruk Cave (holotype, MZB 19203). 34. L. tholiformis sp. nov., Yogyakarta, Gunung Kidul, Tepus, near Poktunggal Beach (holotype, MZB 17999). 35. L. abdidalem sp. nov., Yogyakarta, Kulonprogo, Sabrang Kidul (holotype, MZB 17664). 36. L. madurensis sp. nov., East Java, Madura Island, Sampang, Nepa Monkey lowland rainforest (paratype, MZB 19209). 37. L. sewuensis sp. nov., Yogyakarta, Gunung Kidul, Tepus, Mbajo Hill (holotype, MZB 19255). 38. L. sukoliloensis sp. nov., Central Java, Kayen, near Watu Payung (holotype, MZB 19219). 39. L. tonywhitteni sp. nov., Central Java, Taruman Village, near Sendang Sedayu (holotype, MZB 19214). 40. L. nodifera sp. nov., Central Java, Larangan Village, Lanang Spring (holotype, MZB 19227). 41. L. pacitanensis sp. nov., East Java, Pacitan, near Srau Beach (MZB 19231). 42. L. intumescens (Martens, 1867), East Java, Guwoterus (MZB 19207). 43. L. smimensis (Mousson, 1848), East Java, Tosari (ZMA 390881). 44. L. zonifera sp. nov., Yogyakarta, Kulonprogo, Sibolong (holotype, MZB 17727). 45. L. ciliocincta (Möllendorff, 1897), East Java, Malang, Kondangmerak (MZB 19211). 46. L. pakidulan sp. nov., Central Java, Nusa Kambangan Island, nature monument Gligir (holotype, ZMA 417011a). 47. L. menorehensis sp. nov., Yogyakarta, Kulonprogo, Sibolong (holotype, MZB 19201). Scale bar: 1 mm.
Figs 56–59 in Revision of the land snail genus Landouria Godwin-Austen, 1918 (Gastropoda, Camaenidae) from Java
Figs 56–59 (opposite page). Shells of species of Landouria from Java. 56. L. abdidalem sp. nov., Yogyakarta, Kulonprogo, Sabrang Kidul (holotype, MZB 17664). 57. L. madurensis sp. nov., East Java, Madura Island, Sampang, Nepa Monkey lowland rainforest (holotype MZB 21432). 58. L. sewuensis sp. nov., Yogyakarta, Gunung Kidul, Tepus, Mbajo Hill (holotype, MZB 19255). 59. L. sukoliloensis sp. nov., Central Java, Kayen, near Watu Payung (holotype, MZB 19219). Scale bar: 5 mm.
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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.