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The Biomass and Plant Functional Traits of Leymus chinensis Affected by Genotypic Diversity and Soil Nitrogen Addition through a Two-year Experiment, Tianjin, China, 2021-2023
In order to investigate the effects of soil nitrogen addition on the genotypic diversity of Leymus chinensis, 12 genotypes of Leymus chinensis were used as plant material and a two-factor experimental design was carried out in this study. Factor one was genotypic diversity of L. chinensis, including three levels: mono-genotype (G1), three genotypes (G3), and six genotypes (G6). Factor two was the soil nitrogen addition level, which included four levels: no nitrogen addition (N0), 2.5 g N/(m²·a) nitrogen application (N2.5), 5 g N/(m²·a) nitrogen application (N5), and 10 g N/(m²·a) nitrogen application (N10). Each treatment had 12 combinations as replicates, and 12 genotypes of L. chinensis were used. The frequency of each genotype was standardized across all treatment levels of genotypic diversity × soil nitrogen addition. The experiment commenced in September 2021 and soil nitrogen was applied every 2 months. Plants were cultivated in the experimental field at Nankai University, but were moved to a greenhouse for overwintering from November to February each year. During the experiment, there were no stresses or disturbances such as shading, drought, or insect feeding; weeds were regularly removed.
Effects of factorial nitrogen, phosphorus, and potassium with micronutrient addition and Host Community on Fungal Endophyte Diversity at Cedar Creek Ecosystem Reserve, Minnesota, USA, 2014
The microbes contained within free-living organisms can alter host growth, reproduction, and interactions with the environment. In turn, processes occurring at larger scales determine the local biotic and abiotic environment of each host that may affect the diversity and composition of the microbiome community. Here, we examine variation in the diversity and composition of the foliar fungal microbiome in the grass host, Andropogon gerardii, across a factorial nitrogen, phosphorus, and potassium addition experiment in Minnesota, USA. We found limited evidence of direct effects of nutrients on endophyte diversity. Instead, the effects of nutrients on endophyte diversity appeared to be mediated by accumulation of plant litter and plant diversity loss. Specifically, nitrogen addition is associated with a 40% decrease in plant diversity and an 11% decrease in endophyte richness. Although nitrogen, phosphorus, and potassium addition increased aboveground live biomass and decreased relative Andropogon cover, endophyte diversity did not covary with live plant biomass or Andropogon cover. Our results suggest that fungal endophyte diversity within this focal host is determined in part by the diversity of the surrounding plant community and its potential impact on immigrant propagules and dispersal dynamics. Our results suggest that elemental nutrients reduce endophyte diversity indirectly via impacts on the local plant community, not direct response to nutrient addition.
Point-count bird censusing: long-term monitoring of bird abundance and diversity along the Salt River in the greater Phoenix metropolitan area, ongoing since 2013
Waterways are often the focus of restoration efforts in urban areas. In arid regions, passive discharge of urban water sources may stimulate the recovery or growth of wetland and riparian features in dewatered or ephemeral aquatic systems. In the greater Phoenix metropolitan area (GPMA), sections of the Salt and Gila Rivers have been the targets of active restoration through seeding, planting, and irrigation. At the same time, revegetation has occurred in some sections of the rivers in response to runoff from urban water sources (e.g., storm drains). This dataset catalogs the results of bird surveys conducted at several locations along the Salt River in and around the GPMA beginning in March 2013. Monitoring locations focus on reaches of the river with different characteristics, including: (1) urbanized with perennial water and actively restored (n=2 reaches), (2) urbanized with perennial water and passively restored (n=2 reaches), (3) urbanized with ephemeral water but not restored (n=2 reaches), and (4) non-urban reference areas with perennial water (n=1 reach). This program expands on bird monitoring that the CAP LTER conducts at other locations in and around the GPMA, and complements herpetological surveys that are performed at these locations along the Salt River where the bird surveys are performed. This is a long-term monitoring effort of the CAP LTER with on-going data collection.
FAB 1: Forests and Biodiversity Experiment - High density diversity experiment: carbon budget data
This data represents changes in above and belowground C pools in young stands six years after the initiation of the Forests and Biodiversity experiment (FAB1) in 2013, consisting of high density plots of one, two, five, or 12 tree species planted in a common garden. Trees were planted to represent a range of native functional diversity, including needle-leaf conifer and broadleaf deciduous species as well as ectomycorrhizal and arbuscular mycorrhizal species. We quantified the effects of species richness, phylogenetic diversity, and functional diversity on aboveground C accumulation, as well as on soil C accumulation, fine root C, and soil aggregation. To assess the role of the microbial community in mediating these effects, we further compared changes in soil C pools to phospholipid fatty acids (PLFAs) profiles collected in 2016.
Fall 2020 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites
Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in July 2020. Visual surveys were conducted along 8 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.
Fall 2021 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites
Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in August 2021. Visual surveys were conducted along 8 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.
Hubbard Brook Experimental Forest: Diversity of Forest Floor Vegetation under Ash, Beech, Sugar Maple, and Yellow Birch, 2021
As the interface between plants and soil, the organic horizon is the foundation of forest ecosystems. Two potential predictors of O-layer properties, vegetation and mineral soil type, are difficult to separate because they typically covary. We conducted a factorial study involving four canopy tree species and two soil types with distinctly different hydrology and topographic position to parse patterns in chemistry and microbiota of the O-layer in a north-temperate deciduous forest. There were frequent strong effects of tree species. White ash frequently differed from the other trees: e.g., lower cation exchange capacity and exchangeable acidity, thinner Oi layer, lower %C and C:N, and, from phospholipid fatty acids, more AM fungi and less gram+ bacteria. These patterns, presumably due to species-specific attributes of leaf litter quality, root exudates, and microbial associations, must arise over decades, given that the stands in the study age between 85 and 100 years. We also found patterns in the O-layer related to underlying soil type, independent of tree species: e.g., Bh podzols, compared to Typical podzols, had higher trace metals, thicker Oa layer, and more AM fungi. Relations between mineral soil type and the organic layer, which were larger than expected, could arise because landscape features that influence hydrology and therefore soil formation over millennia also influence biogeochemistry of the organic layer over decades. It could also involve bioturbation by organisms across horizons. There is basic and applied value in models that can predict properties of the O-layer based on vegetation and soil types.
The effects of changing vegetative composition on the abundance, species diversity and activity of birds at the Jornada Basin LTER site, 1997
This data package contains bird abundance data collected in plots that have had various plant functional groups or species experimentally removed at the Jornada Basin LTER site in southern New Mexico, USA. This data was collected in an effort to distinguish the differential effects of plant community biomass, plant community functional groups, and biodiversity within functional groups on plant community function, including effects on animals. To make these distinctions, treatments were established by the selective removal of plant species or functional groups within experimental plots. There are eight treatments: control (C, no removals); four functional group removal treatments (PG, perennial grass removed; S, shrubs removed; SSh, subshrubs removed; Succ, succulents removed), and three species richness manipulation treatments. Richness manipulations included a simplified treatment (Simp), where only the single most abundant species of each growth form is preserved and all other species in the growth form are removed, a reduced‐Larrea treatment (rL), where the Larrea is assumed to be the dominant and is removed while minority components remain, and a reduced-Prosopsis treatment (rP), where Prosopis rather than Larrea is removed as the shrub dominant. Following treatments, bird abundance and habitat preference data was collected in 1997. This data set consists of plot number, treatment type, and time of bird presence by taxa and by habitat and behavior. This study is complete.
PRP02 Plant diversity, richness, and plant species cover in konza prairie restoration heterogeneity plots, since 1998
The experiment is a randomized complete block design with four whole plot hetereogeneity treatments replicated within each of four blocks (n=16 whole plots). The whole plot treatments were created using different combinations of soil depth and nutrient manipulations. The control plots contained no depth or nutrient manipulations. The maximum hetereogeneity plots contained three 2 m x 8 m vertical strips assigned to ambient, enriched and reduced N treatments and four 2 m x 6 m horizontal strips assigned to deep and shallow soil to result in six treatment combinations. The maximum heterogeneity plots are a split-block design. Every plot contained 12 subplots (2 m x 2 m) for sampling. Prior to sowing, all of the plots were excavatedto a depth of approximately 25 cm. Natural limestone slabs were laid in strips assigned to the shallow soil treatment. The soil from all plots was then replaced, leveled, and disked (2-3 cm deep). In February 1998, we incorporated sawdust (49% C; C:N ratio=122) into the strips assigned to the reduced-N treatment. The average C concentration and bulk density in the surface 15 cm following long-term cultivation was 1.5% and 1.2 g cm-3, respectively. Sawdust was tilled into the soil at a rate of 5.5 kg dry wt./m2 to achieve a C concentration representative of native prairie soil (approx. 3% C). Surface applications of granular sugar were initiated in 2004 at a rate of 200 g sucrose m-2 (84.22 g C/m2) 3-4 times each growing season. Strips assigned to the enriched-N treatment were fertilized with 5 g N m2/y (applied as ammonium-nitrate) in July of the first growing season and early June of each subsequent years.
Survey of pond habitats and aquatic diversity of Madison, Wisconsin from May to Aug 2019 and 2020 Data Set
1) Urbanization may lead to changes in local richness (alpha diversity) or in community composition (beta diversity), although the direction of change can be challenging to predict. For instance, introduced species may offset the loss of native specialist taxa, leading to no change in alpha diversity in urban areas, but decreased beta diversity (i.e., more homogenous community structure). Alternatively, because urban areas can have low connectivity and high environmental heterogeneity between sites, they may support distinct communities from one another over small geographic distances. 2) Wetlands and ponds provide critical ecosystem services and support diverse communities, making them important systems in which to understand consequences of urbanization. To determine how urban development shapes pond community structure, we surveyed 68 ponds around Madison, Wisconsin, USA, which were classified as urban, greenspace, or rural based on surrounding land use. We evaluated the influence of local abiotic factors, presence of nonnative fishes, and landscape characteristics on alpha diversity of aquatic plants, macroinvertebrates, and vertebrates. We also analyzed whether surrounding land cover was associated with changes in community composition and/or the presence of specific taxa. 3) We found a 23% decrease in mean richness (alpha diversity) from rural to urban pond sites, and a 15% decrease in richness from rural to urban greenspace pond sites. Among landscape factors, observed pond richness was negatively correlated with adjacent developed land and mowed lawns, as well as greater distances to other waterbodies. Among pond level factors, habitat complexity was associated with increased richness, while the presence of invasive fish was associated with decreased richness. 4) Beta diversity was relatively high for all ponds due to turnover in composition between sites. Urban ponds supported more introduced species, lacked a subset of native species found in rural ponds,
Catalogue of Diversity of Social Innovation
<p>The ‘Catalogue of Social Innovation Diversity in Rural Areas’ is the consolidated version of the research database of examples of social innovation in marginalised rural areas developed by the project SIMRA. The file contains a spreadsheet document that includes descriptive information of all the examples reviewed and recorded at some stage in the research database.</p> <p>The catalogue includes basic information for identifying and describing the examples and the characteristics of the social innovation. The total number of examples in the catalogue is 401. Of this number, 243 examples were positively validated using the SIMRA definition of social innovation. The information included in the catalogue for these examples is sufficient to meet the criteria of social innovation as defined by SIMRA. The remaining examples either demonstrate elements of social innovation without meeting all criteria, or include insufficient information to allow a positive validation. Examples can be filtered according to spatial scale, country, sector, topic, form and SIMRA validation.</p>
Perceptions of Diversity in Electronic Music: the Impact of Listener, Artist, and Track Characteristics
<p>Data Release and facsimile of the survey, presented in the submission 3238 to the CSCW 2021 conference.</p> <p> </p>
Mammal Diversity Database
<p>Accurate taxonomy is central to the study of biological diversity, as it provides the needed evolutionary framework for taxon sampling and interpreting results. While the number of recognized species in the class Mammalia has increased through time, tabulation of those increases has relied on the sporadic release of revisionary compendia like the <em>Mammal Species of the World</em> (MSW) series. Here, we present the <strong>Mammal Diversity Database</strong> (MDD), a digital, publically accessible, and updateable list of all mammalian species, now available online: <a href="https://mammaldiversity.org">https://mammaldiversity.org</a>. The MDD will continue to be updated as manuscripts describing new species and higher taxonomic changes are released. Starting from the baseline of the 3rd edition of MSW (MSW3), we performed a review of taxonomic changes published since 2004 and digitally linked species names to their original descriptions and subsequent revisionary articles in an interactive, hierarchical database. The MDD provides the mammalogical community with an updateable online database of taxonomic changes, joining digital efforts already established for amphibians (AmphibiaWeb, AMNH’s Amphibian Species of the World), birds (e.g., Avibase, IOC World Bird List, HBW Alive), non-avian reptiles (The Reptile Database), and fish (e.g., FishBase, Catalog of Fishes). Development for this work is funded primarily by the <a href="http://www.mammalsociety.org/">American Society of Mammalogists</a> (ASM; 2017-present), with logistical and planning support provided related grants at different time points (2025-present: <a href="https://reporter.nih.gov/search/jHonNExiyEulTWBDs1zc-Q/project-details/11022146">NIH R35</a> to Upham; 2021-2023: <a href="https://reporter.nih.gov/search/jHonNExiyEulTWBDs1zc-Q/project-details/10289637">NIH R21</a> to Upham, Reeder, Sterner, Sen; 2017-2019: <a href="http://vertlife.org/grant/">NSF Vertlife Terrestrial grant</a>). The <a href="http://www.mammalsociety.org/committees/biodiversity">ASM Biodiversity Committee</a> compiles and maintains the MDD, curating regular releases that are downloadable in comma-delimited format. Downstream goals include expanded hosting of ecological, trait, and taxonomic data. Overall, this initiative aims to promote the ASM’s role as a leader in high quality research on mammalian biology.</p> <p>A new section on <strong>Subjective Decisions</strong> has been added to the <a href="https://www.mammaldiversity.org/about.html">MDD About page</a> for use in summarizing opinion-based decisions of the MDD team that depart from the most recently published peer-reviewed article on a given taxon. Some of these decisions are made in collaboratoration with the Global Bat Taxonomy Working Group of the <a href="https://www.iucnbsg.org/">IUCN SSC Bat Specialist Group</a> to promote harmonization between the MDD and batnames.org. Future subjective decisions will also be authored by the MDD Taxonomic Subcommittees that we are assembling in early 2024.</p> <p><em><strong>VERSIONS</strong></em></p> <p><strong>Version 2.3</strong> (1 Sep 2025). This is an incremental release that documents 6,836 total species, of which 113 are recently extinct (+1 from previous version: <em>Galea tixiensis, </em>found to have gone extinct in the past 500 years) and 6,723 are extant (17 domestic extant, 6,705 wild extant). There are 224 species flagged for further review. The <strong>Cell-by-Cell Tracked Differerences</strong> file ("Diff-AllChanges_v2.2-v2.3.csv") lists 1,325 changes to cells in the matrix that occurred between v2.2 and v2.3 as arranged by column, new value, and old value. This detailed tracking complements the <strong>Summary</strong> <strong>Tracked Differences</strong> file ("Diff_v2.2-v2.3.csv"), which documents 65 taxonomic changes made since MDD v2.2. Differences include 27 new species recognized (16 de novo, 11 split), 7 synonymizations (lumps), 4 genera newly added (<em>Nagasorex,</em><em> Breviforamen, Incanomys, Aethalodelphis</em>) and 2 genera lumped (<em>Sagmatias--</em>changed to <em>Aethalodelphis</em>; and <em>Maxomys</em>--all species transferred to <em>Crunomys</em>), as well as 27 species with genus name changes and 3 tribes added. The <strong>typeVoucher</strong> field is now filled for 6,189 accepted species, with corresponding <strong>typeKind</strong> categorizations for all those (e.g., holotype, lectotype, neotype, syntype). Hyperlinks to those type specimens are available in <strong>typeVoucherURIs</strong> for 3,682 species. Links to authority species citations in the <strong>authoritySpeciesLink</strong> field are now available for 6,442 species. In total, there was a net increase of 21 species and 2 genera of recognized extant or recently extinct mammals since MDD v2.2. Note also that the 1500th species of bat was also recognized in MDD v2.3 -- <em>Pipistrellus etula</em> described by Torrent et al. (2025) -- see press release by Bat Conservational International (forthcoming).</p> <p><strong>Version 2.2</strong> (13 Jun 2025). This is an incremental release that documents 6,815 total species, of which 112 are recently extinct (identical to previous version) and 6,703 are extant (17 domestic extant, 6,686 wild extant). There are still 223 species flagged for further review. The <strong>Cell-by-Cell Tracked Differerences</strong> file ("Diff-AllChanges_v2.1-v2.2.csv") lists 6,638 changes to cells in the matrix that occurred between v2.1 and v2.2 as arranged by column, new value, and old value. The majority of these changes are to higher taxonomic categories that were a focus of the curation this version (tribe: 533 changes; superorder: 133; superfamily: 1,541; suborder: 1,764; subgenus: 445; subfamily: 415; subclass: 5; specificEpithet: 8; parvorder: 572; infraorder: 287; genus: 20). This detailed tracking complements the <strong>Summary</strong> <strong>Tracked Differences</strong> file ("Diff_v2.1-v2.2.csv"), which documents 382 taxonomic changes made since MDD v2.1. Differences include 14 new species recognized (13 de novo, 4 split), 3 synonymizations (lumps), 2 genera split and newly added (<em>Pipistrellus</em> to <em>Alionoctula;</em> <em>Phodopus</em> to <em>Cricetiscus</em>), 20 species with genus name changes, 2 species epithet changes, 340 higher taxonomy changes (as mentioned above), and 107 species with common name changes (spelling or geographic consistency). The <strong>typeVoucher</strong> field is now filled for 5,948 accepted species, with corresponding <strong>typeKind</strong> categorizations for all those (e.g., holotype, lectotype, neotype, syntype). Hyperlinks to those type specimens are available in <strong>typeVoucherURIs</strong> for 3,649 species. Links to authority species citations in the <strong>authoritySpeciesLink</strong> field are now available for 6,420 species. In total, there was a net increase of 14 species and 2 genera of recognized extant or recently extinct mammals since MDD v2.1.</p> <p><strong>Version 2.1</strong> (6 Apr 2025). This is an incremental release that documents 6,801 total species, of which 112 are recently extinct (compared to 113 previously; <em>Lagostomus crassus</em> was lumped into <em>L. maximus</em>) and 6,689 are extant (17 domestic extant, 6,672 wild extant). There are now 223 species flagged for further review. A new addition to the MDD in v2.1 is the inclusion of a <strong>Cell-by-Cell Tracked Differerences</strong> file ("Diff-AllChanges_v2.0-v2.1.csv"), which lists 4,683 changes to cells in the matrix that occurred between v2.0 and v2.1 as arranged by column, new value, and old value. This detailed tracking complements the <strong>Summary</strong> <strong>Tracked Differences</strong> file ("Diff_v2.0-v2.1.csv"), which documents 215 taxonomic changes made since the MDD v2.0 taxonomic cutoff of 15 Aug 2024. Differences include 57 new species recognized (26 de novo, 31 split), 14 synonymizations (lumps), 1 species removal for unavailable name, 4 genera split and newly added (<em>Afropipistrellus, Casiomys, Megascapheus, Nyctinomus</em>), 20 species with genus name changes, 6 spelling changes, 2 tribe changes, and 114 species with common name changes (spelling or geographic consistency). The <strong>typeVoucher</strong> field is now filled for 5,918 accepted species, with corresponding <strong>typeKind</strong> categorizations for all those (e.g., holotype, lectotype, neotype, syntype). Hyperlinks to those type specimens are available in <strong>typeVoucherURIs</strong> for 3,641 species. Links to authority species citations in the <strong>authoritySpeciesLink</strong> field are now available for 6,406 species. In total, there was a net increase of 42 species and 4 genera of recognized extant or recently extinct mammals since MDD v2.0.</p> <p><strong>Version 2.0</strong> (15 Aug 2024 cutoff date — 11 Mar 2025 publication date). This is a major release – MDD2 – that documents 7 years of taxonomic curation efforts since the taxonomic cutoff of MDD v1.0 (15 Aug 2017). The MDD2 includes 6,759 total species, of which 113 are recently extinct and 6,646 are extant (17 domestic extant, 6,629 wild extant). There are now 217 species flagged for further review (125 Artiodactyla, 57 Primates, 12 Lagomorpha, 7 Rodentia, 8 Carnivora, 6 Perissodactyla, 1 Microbiotheria, 1 Diprotodontia). Key updates in MDD2 include:</p> <ol> <li>Codings of US state, country, continent, and biogeographic realm geographic categories for each species (fields of <strong>subregionDistribution</strong>, <strong>countryDistribution</strong>, <strong>continentDistribution</strong>, <strong>biogeographicRealm</strong>, respectively);</li> <li>Curated <strong>Species-level Synonyms</strong> file ("Species_Syn_v2.0.csv") containing 50,230 valid and synonymous species-rank names, including name combinations and type locality and specimen information for the first time; and</li> <li>Integration between the MDD and the databases Hesperomys and Batnames for greater data accuracy and completeness.</li> <li>Updated data presentations by MDD student programmer <a href="https://www.hhandika.com/">Heru Handika</a>: <ol> <li>Improved website at <a href="https://www.mammaldiversity.org/">https://www.mammaldiversity.org/</a> that is fully re-written, including a migration from Jekyll (<a href="https://jekyllrb.com/">https://jekyllrb.com/</a>) to the Astro web-framework (<a href="https://astro.build/">https://astro.build/</a>) with TypeScript (<a href="https://www.typescriptlang.org/">https://www.typescriptlang.org/</a>), and Tailwind CSS (<a href="https://tailwindcss.com/">https://tailwindcss.com/</a>) integration</li> <li>New MDD app wrote using the Flutter framework (<a href="https://flutter.dev/">https://flutter.dev/</a>) and the Rust programming language (<a href="https://www.rust-lang.org/">https://www.rust-lang.org/</a>). It supports iOS, iPadOS, Android, Windows, Linux, and macOS. Details on installing the app are available at <a href="https://github.com/mammaldiversity/mdd_app">https://github.com/mammaldiversity/mdd_app</a>.</li> </ol> </li> </ol> <p>The <strong>typeVoucher</strong> field (formerly called 'holotypeVoucher') is now filled for 5,837 accepted species, with corresponding <strong>typeKind</strong> categorizations for all those (e.g., holotype, lectotype, neotype, syntype). Hyperlinks to those type specimens are available in <strong>typeVoucherURIs</strong> for 3,617 species. Links to authority species citations in the <strong>authoritySpeciesLink</strong> field are now available for 6,072 species. The <strong>Tracked Differences</strong> file ("Diff_v1.13-v2.0.csv") documents taxonomic changes made since the last MDD version, including 41 during the one month between taxonomic cutoffs. Differences include 6 new species recognized (2 de novo, 4 split), 0 synonymizations (lumps), 0 species with genus or other name changes, and 35 species with common name spelling changes (including 25 to add accent marks). In total, there was a net increase of 6 species and 0 genera of recognized extant or recently extinct mammals since MDD v1.13.</p> <p><strong>Version 1.13</strong> (13 July 2024). This is an incremental release that documents 6,753 total species, of which 113 are recently extinct (addition of 6 species since v1.12) and 6,640 are extant (17 domestic extant, 6,623 wild extant). There are still 27 species flagged for further review. The <strong>typeVoucher</strong> field (formerly called 'holotypeVoucher') is now filled for an incredible 5,801 accepted species, as compared to 2,727 species previously, thanks to the efforts of the MDD team with expanding the field to non-holotypes. The new field <strong>typeKind</strong> denotes which kind of type specimen is listed (e.g., holotype, lectotype, neotype, syntype). Also newly expanded is the direct link to authority species citations in the <strong>authoritySpeciesLink</strong> field — which went from 2,782 in the v1.12 to 6,057 links in the present version! The <strong>Tracked Differences</strong> file ("Diff_v1.12.1-v1.13.csv") documents taxonomic changes made since the last MDD version, including 85 during the last 6 months (compares to 115 changes from v1.11-v1.12). Differences include 49 new species recognized (24 de novo, 25 split), 12 synonymizations (lumps), 2 species with genus name changes, 2 genus additions (<em>Pudu</em> to <em>Pudella</em>, <em>Petinomys</em> to <em>Olisthomys</em>), 2 species with epithet changes (based on priority/preoccupation), 12 species with epithet spelling changes (based on gender matching), and 2 species of Ctenomys that were removed due to unavailable names (to help flag that available names need to be proposed). In total, there was a net increase of 35 species and 2 genera of recognized extant or recently extinct mammals since MDD v1.12.</p> <p><strong>Version 1.12.1</strong> (30 January 2024). This is minor release that fixes a spelling error in a new species to <em>Euryoryzomys cerqueirai </em>(from <em>E. cerqueriai</em>). This version is also the first to display country-based maps on the per species pages as populated from the 'countryDistribution' field (e.g., see: https://www.mammaldiversity.org/explore.html#genus=Peromyscus&species=maniculatus&id=1002307). Thanks to Jorrit Poelen for some stellar work here!</p> <p><strong>Version 1.12</strong> (5 January 2024). This is an incremental release that documents 6,718 total species, of which 107 are recently extinct (addition of 2 species since v1.11) and 6,611 are extant (17 domestic extant, 6,594 wild extant). There are now 27 species flagged for further review. The <strong>holotypeVoucher</strong> field is filled for 2,727 accepted species thanks to the efforts of the MDD team (35 NA's indicate a real lack of actual voucher--in need of neotype). The <strong>Tracked Differences</strong> file ("Diff_v1.11-v1.12.csv") documents taxonomic changes made since the last MDD version, which include 115 changes during the last 8 months (compares to 194 changes from v1.10-v1.11 and 117 changes from v1.9 to v1.10, and ~30 changes between versions before that). Differences include 77 new species recognized (38 de novo, 38 split, 1 revalidation), 8 synonymizations (lumps), 31 species with genus name changes, 7 genus additions (<em>Bisbalus, Passalites, Subulo, Neoeptesicus, Mictomys, Cnephaeus, Cordimus</em>) and 1 genus lump <em>(Nesoromys</em>), and 1 removed domestic species (<em>Homo sapiens</em>, given a revised MDD definition of domestication to be 'domesticated by human artificial selection'; see About page). In total, there was a net increase of 69 species and net increase of 6 genera of recognized extant or recently extinct mammals since MDD v1.11.</p> <p><strong>Version 1.11</strong> (15 April 2023). This is an incremental release that documents 6,649 total species, of which 105 are recently extinct (addition of 4 species since v1.10) and 6,544 are extant (18 domestic extant, 6,526 wild extant). There are now only 21 species flagged for further review. The <strong>holotypeVoucher</strong> field is filled for 2,731 accepted species thanks to the efforts of the MDD team (NA's indicate a real lack of actual voucher--in need of neotype). The <strong>Tracked Differences</strong> file ("Diff_v1.10-v1.11.csv") documents taxonomic changes made since the last MDD version, which have been extensive recently due to enhanced activity, leading to a whopping 194 changes during the last 4 months (compares to 117 changes in the last version, and ~30 changes between previous versions). Differences include 64 new species recognized (15 de novo, 49 split), 29 synonymizations (lumps, including 2 domestic species<em>: Bos domesticus</em> into <em>Bos javanicus</em>, and <em>Bos indicus</em> into <em>Bos taurus</em>), 1 species removal (<em>Makalata obscura</em>, now considered nomen dubium), 36 species with genus name changes, 5 genus additions (<em>Otohylomys, Baeodon, Neusticomys, Poecilictis, </em>and <em>Parachoerus</em>) and 7 genus lumps (<em>Crossogale, Aeorestes, Dasypterus, Koopmania, Pediolagus, Petropseudes, Catagonus</em>), 5 species epithet changes to clear up confusion, 47 species epithet spelling changes to match gender or the original description (this was a major emphasis of this version– to come into harmony with batnames.org and hesperomys.com), and 1 error fix in the spelling of the common name "Australian Humpback Dolphin". In total, there was a net increase of 34 species and net decrease of 2 genera of recognized extant or recently extinct mammals since MDD v1.10.</p> <p><strong>Version 1.10</strong> (3 Dec 2022). This is an incremental release that documents 6,615 total species, of which 101 are recently extinct and 6,514 are extant (20 domestic extant, 6,494 wild extant). There are now 33 species flagged for further review (subtraction of <em>Dromiciops mondaca</em>, which was synonymized under <em>D. gliroides</em>). The <strong>holotypeVoucher</strong> field is now filled for 2,731 accepted species thanks to the continued efforts of Ingrid Rochon, Connor Burgin, and also now Bruce Patterson (NA's indicate a real lack of actual voucher--in need of neotype). The <strong>Tracked Differences</strong> file ("Diff_v1.9-v1.10.csv") documents taxonomic changes made since the last MDD version, which was 8 months ago (1 April 2022) so 117 changes are included now versus the ~30 changes between previous versions. Differences include 49 new species recognized (22 de novo, 27 split), 30 synonymizations (lumps), 29 species with genus name changes (affecting <em>Lissonycteris -> Myonycteris, Aonyx/Lutrogale -> Lutra, Eothenomys -> Anteliomys, Ellobius -> Bramus, Proedromys -> Mictomicrotus, Lasiopodomys </em>back to <em>Stenocranius, and Cephalophus -> Cephalophorus</em>), 3 species epithet changes to clear up confusion, 5 species epithet spelling changes to match gender or the original description, and 1 error fix shifting <em>Capra hircus</em> to domestic status as the domestic form of <em>C. aegagrus</em>. In total, there was a net increase of 19 species and 5 genera of recognized extant or recently extinct mammals since MDD v1.9.</p> <p><strong>Version 1.9.1</strong> (29 Jun 2022). This is a patch release that adds the field '<strong>holotypeVoucherURIs</strong>' to the MDD taxonomy file for use in linking the type specimens to external website(s), including the hosting museum collection. Currently this feature is experimental. The taxonomy still includes 6,596 total species, of which 101 are recently extinct & 6,495 are extant (19 domestic extant, 6,476 wild extant).</p> <p><strong>Version 1.9</strong> (1 Apr 2022). This is an incremental release that documents 6,596 total species, of which 101 are recently extinct and 6,495 are extant (19 domestic extant, 6,476 wild extant). There are now 34 species flagged for further review (addition of 6 species related to the split of <em>Lagenorhynchus</em> dolphins, along with the previous inclusion of some Cebus species). The <strong>holotypeVoucher</strong> field is now filled for 2,662 accepted species thanks to the continued efforts of Ingrid Rochon and Connor Burgin (NA's indicate a real lack of actual voucher--in need of neotype). The <strong>Tracked Differences</strong> file ("Diff_v1.8-v1.9.csv") documents taxonomic changes made since the last MDD version, and here includes 15 new species recognized (8 de novo, 7 split), 10 synonymizations (lumps), 2 species with genus name changes (<em>Brachylagus idahoensis</em> to <em>Sylvilagus idahoensis </em>and <em>Nycticebus pygmaeus</em> to <em>Xanthonycticebus pygmaeus</em>), and 1 range extension (for <em>Marmosa alstoni</em> extended to Panama; https://doi.org/10.5281/zenodo.6374907). In total, there was a net increase of 5 recognized species of extant or recently extinct mammals since MDD v1.8.</p> <p><strong>Version 1.8</strong> (1 Feb 2022). This is an incremental release that documents 6,591 total species, of which 101 are recently extinct and 6,490 are extant (19 domestic extant, 6,471 wild extant). There are still 28 species flagged for further review (e.g., some Cebus species). The <strong>holotypeVoucher</strong> field is now filled for 2,665 accepted species thanks to the continued efforts of Ingrid Rochon and Connor Burgin (NA's indicate a real lack of actual voucher--in need of neotype). The <strong>Tracked Differences</strong> file ("Diff_v1.7-v1.8.csv") documents taxonomic changes made since the last MDD version, and here includes 27 new species recognized (21 de novo, 6 split), 3 synonymizations, 1 genus change (Nasuella into Nasua, resulting in a reduction in the total number of genera), and 3 species name changes (2 based on new genetic evidence and naming priority, 1 on a spelling change). In total, there was a net increase of 24 recognized species of extant or recently extinct mammals since MDD v1.7.</p> <p><strong>Version 1.7</strong> (6 Nov 2021). This is an incremental release that documents 6,567 total species, of which 101 are recently extinct and 6,466 are extant (19 domestic extant, 6,447 wild extant). There are now 28 species flagged for further review (e.g., some Cebus species). The <strong>holotypeVoucher</strong> field is now filled for 2,512 accepted species thanks to the continued efforts of Ingrid Rochon and Connor Burgin (including a reduction of NA's from 103 to 26). The <strong>Tracked Differences</strong> file ("Diff_v1.6-v1.7.csv") documents taxonomic changes made since the last MDD version, and here includes 19 new species recognized (13 de novo, 6 split), 9 synonymizations, 12 genus changes, and 2 de-extinctions due to taxonomic changes (extinct <em>Gazella bilkis</em> synonymized under extant <em>Gazella arabica</em> following Bärmann et al. 2013<em>; </em>extinct <em>Pseudomys gouldii </em>changed to extant since extant <em>Pseudomys fieldi</em> was synonymized under it in the MDD v1.6 following Roycroft et al. 2021). In total, there was a net increase of 10 recognized species of extant or recently extinct mammals since MDD v1.6.</p> <p><strong>Version 1.6</strong> (10 Aug 2021). This is an incremental release that documents 6,557 total species, of which 103 are recently extinct and 6,454 are extant (19 domestic extant, 6,435 wild extant). There are 29 species still flagged for further review (e.g., some Cebus species). The <strong>holotypeVoucher</strong> field is now filled for 2,548 accepted species thanks to the continued efforts of Ingrid Rochon. The <strong>Tracked Differences</strong> file ("Diff_v1.5-v1.6.csv") documents taxonomic changes made since the last MDD version, and here includes 9 new species recognized (5 de novo, 4 split), 5 synonymizations, 1 removal (<em>Dryomys yarkandensis</em> invalid while in pre-print), and 18 genus changes.</p> <p><strong>Version 1.5</strong> (11 Jun 2021). This is an incremental release that documents 6,554 total species, of which 103 are recently extinct and 6,451 are extant (19 domestic extant, 6,432 wild extant). There are 29 species still flagged for further review (e.g., some Cebus species). The <strong>holotypeVoucher</strong> field, which now filled for 2,459 accepted species thanks to the continued efforts of Ingrid Rochon. We also continue to maintain the <strong>Tracked Differences</strong> file ("Diff_v1.4-v1.5.csv") which documents which taxonomic changes were made per species since the last MDD version. We still plan to retrospectively assemble these diff files for previous versions as well.</p> <p><strong>Version 1.4</strong> (11 Apr 2021). This is an incremental release that documents 6,533 total species, of which 103 are recently extinct, 19 are domestic extant, and 6,411 are wild extant. There are 29 species still flagged for further review (e.g., some Cebus species). Especially improved in this version is the <strong>holotypeVoucher</strong> field, which now filled for 2,153 accepted species thanks to the heroic efforts of Ingrid Rochon (nearly 1/3 of mammals!!). Additionally, this time we added a <strong>Tracked Differences</strong> file ("Diff_v1.31-v1.4.csv") which documents which taxonomic changes were made per species since the last MDD version. We plan to retrospectively assemble these diff files for previous versions as well. Note also that the per-species notes (<strong>taxonomyNotes</strong>) are now updated through all mammals including Chiroptera thanks to the careful efforts of David Huckaby and Connor Burgin. Those notes should help clarify changes since MSW3, which is the well-recognized baseline for mammal taxonomy from which the MDD is updating.</p> <p><strong>Version 1.3.1</strong> (8 Jan 2021). This is an patch release that, like v1.3, documents 6,513 total species, but also (i) fixes some bugs in the type locality listings; and (ii) completes the improved documentation in the <strong>per-species notes</strong> across all orders including Chiroptera (carefully curated by David Huckaby and Connor Burgin; thanks both!). These completed notes clarify changes since MSW3, which is the well-recognized baseline for mammal taxonomy from which the MDD is updating.</p> <p><strong>Version 1.3</strong> (28 Dec 2020). This is an incremental release that documents 6,513 total species, of which 103 are recently extinct, 19 are domestic extant, and 6,391 are wild extant. There are 29 species still flagged for further review (e.g., some Cebus species). Especially improved in this version are the <strong>per-species notes</strong>, which have been carefully curated by David Huckaby and Connor Burgin for all mammal orders except Chiroptera (expect those updates in the next version). These notes were written to help clarify changes since MSW3, which is the well-recognized baseline for mammal taxonomy from which the MDD is updating.</p> <p><strong>Version 1.2</strong> (24 Sep 2020). This is a major update, though still incremental toward a more definitive forthcoming release. This release documents 6,485 total species, of which 103 are recently extinct, 19 are domestic extant, and 6,363 are wild extant. Ten species are still "flagged" for further review. This taxonomy and associated data (type locality, authorities, common names) are improved by reference to the <em>Handbook of the Mammals of the World</em> series. Additionally, justifications and citations are now provided for any subjective decisions made, the most substantial of which has been the recommendations of Groves and Grubb (2011)’s compendium <em>Ungulate Taxonomy</em>. That taxonomy of Perissodactyla and non-cetacean Artiodactyla was fully included in the v1.0 release of the MDD (Burgin et al. 2018). However, since Groves and Grubb (2011) was based primarily on qualitative morphological diagnoses with small sample sizes, it has since become controversial in the mammalogical community (e.g., (Holbrook 2013; Gutiérrez and Garbino 2018)). Many specialists have subsequently reverted to the taxonomic arrangement presented by Peter Grubb in MSW3. In current versions of the MDD, we use MSW3 as a baseline for ungulate taxonomy, leaving out all changes made by Groves and Grubb (2011) with the exception of those supported by other published research. Note: this MDD v1.2 taxonomy is also paired with <strong>species-level geographic range maps</strong> for 6,362 species, available at <a href="https://doi.org/10.5281/zenodo.6644198">https://doi.org/10.5281/zenodo.6644198</a> as mirrored from the data publication of Marsh et al. 2022 (<a href="https://doi.org/10.1111/jbi.14330">https://doi.org/10.1111/jbi.14330</a>). This range map data set differs from the 6,485 total species in MDD v1.2, as follows:</p> <ul> <li>excludes all recently extinct (103) and domestic species (20; correcting for <em>Capra hircus</em> that was coded as 'domestic=0' rather than 'domestic=1' originally);</li> <li>excludes 2 species for which no spatial information was available (<em>Nycticeius aenobarbus</em> and <em>Phoniscus aerosus</em>); and</li> <li>includes 2 species<em> </em>(<em>Elaphurus davidianus</em> and <em>Oryx dammah</em>) that are extinct in the wild (EW) in IUCN, but which have recent range information and were coded in the MDD as extant.</li> </ul> <p><strong>Version 1.1</strong> (29 Mar 2019). This is an incremental release that documents 6,526 total species, of which 100 are recently extinct, 17 are domestic extant, and 6,409 are wild extant. Of those, 212 species are "flagged" for further review (mostly ungulates from Groves & Grubb, 2011).</p> <p><strong>Version 1.0</strong> (1 Feb 2018; described in <a href="https://doi.org/10.1093/jmammal/gyx147">https://doi.org/10.1093/jmammal/gyx147</a>). We found 6,495 species of currently recognized mammals (96 recently extinct, 6,399 extant), compared to 5,416 in MSW3 (75 extinct, 5,341 extant)—an increase of 1,079 species in about 13 years, including 11 species newly described as having gone extinct in the last 500 years. We tabulate 1,251 new species recognitions, at least 172 unions, and multiple major, higher-level changes, including an additional 88 genera (1,314 now, compared to 1,226 in MSW3) and 14 newly recognized families (167 compared to 153). Analyses of the description of new species through time and across biogeographic regions show a long-term global rate of ~25 species recognized per year, with the Indomalayan biogeographic region as the overall most species-dense for mammals globally (127.1 species/km<sup>2</sup>), followed by Australasia-Oceania (90.6) and the Neotropics (85.1).</p> <p> </p> <p><em><strong>CITATIONS</strong></em></p> <p>BURGIN, C. J., J. P. COLELLA, P. L. KAHN, AND N. S. UPHAM. 2018. How many species of mammals are there? Journal of Mammalogy 99:1–14.</p> <p>GROVES, C., AND P. GRUBB. 2011. Ungulate Taxonomy. JHU Press.</p> <p>GUTIÉRREZ, E. E., AND G. S. T. GARBINO. 2018. Species delimitation based on diagnosis and monophyly, and its importance for advancing mammalian taxonomy. Zoological Research:97.</p> <p>HOLBROOK, L. T. 2013. Taxonomy Interrupted. Journal of Mammalian Evolution 20:153–154.</p> <p>WILSON, D. E., AND D. M. REEDER. 2005. Mammal species of the world: a taxonomic and geographic reference, 3rd ed. 3rd edition. Johns Hopkins University Press, Baltimore, MD.</p>
Data: Disentangling drivers of temporal changes in urban pond macroinvertebrate diversity
<p>Data for: (i) presence and abundance of Odonata and Trichoptera (larvae), and Coleoptera and Hemiptera (larvae and adults) species in ponds in Stockholm, Sweden, in 2014 and 2019, (ii) environmental data 2014 and 2019 (pond data like water chemistry, and land-change data), (iii) coordinates of ponds and pond area, (iv) and R script to reproduce analyses presented in Granath et al. 2024 (Urban Ecosystems, https://doi.org/10.1007/s11252-023-01500-2). A meta-data file with descriptions of the data files is also included.</p>
heat of hydrogenation for diverse organic compounds -- experimental and calculated data for 166 unique reactions
<h3>General remarks</h3> <p>The experimental data was drawn from reactions involving H2 that are available at <a href="https://webbook.nist.gov/cgi/cbook.cgi?Name=H2&Units=SI&cTR=on" target="_blank" rel="noopener">NIST</a> (accessed on 15/03/2024). Only reactions of type<strong><em> M + H2 => MH2</em></strong>, where M is a neutral, closed-shell organic molecule that accepts one equivalent of H2, were included in the collection. M corresponds to the oxidized form of the molecule ( => suffix '_ox'), MH2 to the reduced form (=> suffix '_red'). For reasons of clarity, the references to original publications were abbreviated in the main table (look up in separate table).</p> <p>For the molecules involved, Smiles were manually assigned. From those, 3D structures were generated and evaluated in order to match the thermodynamic properties as accurately as possible (for details on the procedure refer to the related work, see below).</p> <p>In addition to the experimental uncertainty, a significant scatter is seen for replicate measurements.</p> <p><strong>Please note</strong>: To compute the heat of hydrogenation from the calculated data for M/MH2 the contribution of H2 needs to be considered, take e.g. -1.164816 hartree (Energy at 298.15K, calculated at CCSD(T)=FULL/aug-cc-pVDZ) from <a href="https://cccbdb.nist.gov/energy3x.asp?method=63&basis=17&charge=0" target="_blank" rel="noopener">CCCBDB</a> (accessed on 15/03/2024).</p> <h3> </h3> <h3>Description of files</h3> <p>The file <strong>01_heat_of_hydrogenation_XP+QM.csv</strong> contains experimentally measured and calculated data.</p> <ul> <li>columns are separated by "|"</li> <li>column names and explanations: <ul> <li><strong>NIST_idx</strong> -- index of original reaction, mostly unique. In a few cases, data of the reverse reaction were subsumed under a different index</li> <li><strong>env</strong> -- if available, information about the environment a reported reaction took place in, e.g. gas phase, hexane, etc...</li> <li><strong>method</strong> -- if available, reference about the experimental technique, e.g. 'Eqk' = Heat of equilibrium, 'Cm' = Calorimetry, 'Chyd' = Calorimetry of hydrogenation</li> <li><strong>Temperature K</strong> -- if available, reported values </li> <li><strong>reference</strong> -- Abbreviation of reference to original publication</li> <li><strong>experimental heat of reaction kJ/mol</strong> -- measured value as reported by experimentalists</li> <li><strong>experimental uncertainty </strong>-- if available, uncertainty of measurement reported by experimentalists</li> <li><strong>comments</strong> -- notes relating to identification of compounds</li> <li><strong>SMILES_ox</strong> -- isomeric canonical SMILES for oxidized form M</li> <li><strong>InChI_ox</strong> -- InChI for oxidized form M </li> <li><strong>SMILES_red</strong> -- isomeric canonical SMILES for reduced form M</li> <li><strong>InChI_red </strong>-- InChI for reduced form M</li> <li><strong>reaction_index </strong>-- consequtively numbered for identical pairs (SMILES_ox, SMILES_red)<strong><br></strong></li> <li>the calculated properties are given for the oxidized and reduced form of the molecule (in hartree) <ul> <li><strong>E(B3LYP/6-31G(2df,p))</strong></li> <li><strong>E_thermal</strong></li> <li><strong>E(G4(MP2))@0K</strong></li> <li><strong>E(G4(MP2))@298K</strong></li> <li><strong>H(G4(MP2))</strong></li> <li><strong>heat_of_formation@0K</strong></li> <li><strong>heat_of_formation@298K</strong></li> </ul> </li> </ul> </li> </ul> <p><strong>02_molecules.sdf:</strong> provides for each molecule a low-energy geometry along with some descriptors and calculated energetic properties:</p> <blockquote> <ul> <li>coordinate block + bond information</li> <li>properties <ul> <li><strong>SMILES</strong> -- isomeric canonical smiles linking compound to reactions defined in 01_heat_of_hydrogenation_XP+QM.csv</li> <li><strong>radical_electrons</strong> -- number of unpaired electrons as determined by RDKit</li> <li><strong>empirical_formula</strong> -- elemental composition of molecule</li> <li><strong>molecular_weight</strong> -- as determined by RDKit in g/mol</li> <li><strong>TPSA </strong>-- topological polar surface area (<em>TPSA</em>) as determined by RDKit</li> <li><strong>logP </strong>-- octanol/water partition coefficient as predicted by RDKit</li> <li><strong>nof_heavy_atoms --</strong> number of non-hydrogen atoms in molecule</li> <li><strong>degree_of_unsaturation</strong> -- sum of multiplebonds and/or rings present in the compound</li> <li><strong>rings</strong> -- number of rings in the compound as determined by RDKit</li> <li><strong>multiplicity</strong> -- spin multiplicity for use as input for QM calculations</li> <li><strong>nof_multiple_bonds</strong> -- number of multiple bonds as determined by RDKit</li> <li><strong>Std_InChI</strong> -- standard InChi</li> <li><strong>FixedH_InChI</strong> -- variant of InChI to differentiate tautomers</li> <li><strong>tag </strong>-- dataset label</li> <li><strong>total_atoms </strong>-- total number of atoms (including H)</li> <li><strong>net_charge</strong> -- total charge of molecule in units of elementary charge</li> <li> <p>energetic properties (in hartree) </p> <ul> <li> <p><code>E(B3LYP/6-31G(2df,p))</code></p> </li> <li> <p><code>E</code><code>(HF/maug-cc-p(T+d)Z) </code></p> </li> <li> <p><code>E(HF/CBS)</code></p> </li> <li> <p><code>E(HF/maug-cc-p(Q+d)Z) </code></p> </li> <li> <p><code>E(MP2/6-31G(d))</code></p> </li> <li> <p><code>E(CCSD(T)/6-31G(d))</code></p> </li> <li> <p><code>E(HF/G3MP2LARGEXP) </code></p> </li> <li> <p><code>E(MP2/G3MP2LARGEXP)</code></p> </li> <li> <p><code>DE(MP2) hartreeDE(HF)</code></p> </li> <li> <p><code>ZPE(B3LYP) hartree</code></p> </li> <li> <p><code>ZPE_scale_factor hartree</code></p> </li> <li> <p><code>E(HLC) hartree</code></p> </li> <li> <p><code>E_thermal hartree</code></p> </li> <li> <p><code>H_thermal hartree</code></p> </li> <li> <p><code>E(G4(MP2))@0K hartree</code></p> </li> <li> <p><code>E(G4(MP2))@298K hartree</code></p> </li> <li> <p><code>H(G4(MP2)) hartree</code></p> </li> <li> <p><code>heat_of_formation@0K kcal/mol</code></p> </li> <li> <p><code>heat_of_formation@298K kcal/mol</code></p> </li> </ul> </li> </ul> </li> </ul> </blockquote> <p><strong>03_references.csv</strong> (separated by "|") lists abbreviations and corresponding full reference to original publication of individual data points.</p>
(Fastq Files) Amplicon sequencing of ama1 and mdr1 to track within-host P. falciparum diversity in Kilifi, KENYA
<p>These data were generated from amplicon sequencing of <em>Plasmodium falciparum</em> <em>ama1 </em>and<em> </em><em>mdr1</em> genes in samples collected from Kilifi, at the coast of Kenya.</p> <p>The two papers that reference these data will soon be included here:</p> <ol> <li> The Journal of Infectious Diseases - https://doi.org/10.1093/infdis/jiac144</li> <li>Wellcome Open Research - https://wellcomeopenresearch.org/articles/7-95</li> </ol> <p>Two objectives were explored:</p> <ol> <li>To determine temporal changes in the genetic diversity of malaria parasites in asymptomatic and febrile infections.</li> <li>To track within-host parasite diversity, throughout treatment in a clinical drug trial.</li> </ol>
Soil visible–near infrared (vis–NIR) spectra for the Biomes of Australian Soil Environments (BASE) soil microbial diversity database
<p>Visible–near infrared spectra of 695 soil samples collected in the Biomes of Australian Soil Environments (BASE) soil microbial diversity project (Bissett et al., 2016). The spectra represent reflectance values from 2151 wavelengths that range from 350 nm to 2500 nm with a 1 nm interval. The dataset has unique sample identification numbers and the date of sampling, which can be related to the BASE (Australian Microbiome) database (https://data.bioplatforms.com/organization/australian-microbiome)</p>
Data on 'Gelatinous macrozooplankton diversity and distribution in the North Sea and Skagerrak/Kattegat during January-February 2021'
<p>This dataset includes raw and analysed data from '<strong>Gelatinous macrozooplankton diversity and distribution in the North Sea and Skagerrak/Kattegat during January-February 2021</strong>'</p> <p><strong>Louise G. Køhler<sup>1</sup>, Bastian Huwer<sup>2</sup>, José Martín Pujolar<sup>1</sup>, Malin Werner<sup>3</sup>, Karolina Wikström<sup>3</sup>, Anders Wernbo<sup>3</sup>, Maria Ovegård<sup>3</sup>, Cornelia Jaspers<sup>1*</sup></strong></p> <p> </p> <p><sup>1</sup>Centre for Gelatinous Zooplankton Ecology and Evolution, National Institute of Aquatic Resources, Technical University of Denmark, Kemitorvet 202, 2800 Kgs. Lyngby, Denmark</p> <p><sup>2</sup>National Institute of Aquatic Resources, Technical University of Denmark, Kemitorvet 201, 2800 Kgs. Lyngby, Denmark</p> <p><sup>3</sup>Institute of Marine Research, Department of Aquatic Resources (SLU Aqua), Swedish University of Agricultural Sciences, Turistgatan 5, S- 453 30 Lysekil, Sweden</p> <p>* Corresponding author: <a href="mailto:coja@aqua.dtu.dk">coja@aqua.dtu.dk</a></p> <p>This dataset includes data on the qualitative and quantitative description of the gelatinous macrozooplankton community of the North Sea during January-February 2021. Sampling was conducted during the 1<sup>st</sup> quarter International Bottom Trawl Survey (IBTS) on board the Danish R/V DANA (DTU Aqua Denmark) and the Swedish R/V Svea (SLU Sweden), as part of the ichthyoplankton investigation during night-time. A total of 147 stations were investigated in the western, central and eastern North Sea as well as the Skagerrak and Kattegat. Sampling was conducted with a 13 m long Midwater Ring Net (MIK net, Ø 2 m, mesh size 1.6 mm, cod end with smaller mesh size of 500 µm), equipped with a flow meter. The MIK net was deployed in double oblique hauls from the surface to c. 5 m above the sea floor. Samples were visually analysed unpreserved on a light table and/or with a stereomicroscope or magnifying lamp within 2 hours after catch. A total of 13,610 individuals were counted/sized. Twelve gelatinous macrozooplankton species or genera were encountered, namely the hydrozoan <em>Aequorea vitrina</em>, <em>Aglantha digitale</em>, <em>Clytia</em> spp., <em>Leuckartiara octona,</em> <em>Tima bairdii, Muggiaea atlantica</em>; the scyphozoans <em>Cyanea</em> <em>capillata and Cyanea lamarckii</em> and the ctenophores <em>Beroe</em> spp., <em>Bolinopsis infundibulum</em>, <em>Mnemiopsis leidyi</em>, <em>Pleurobrachia pileus</em>. Abundance data are presented on a volume specific (m<sup>-3</sup>) and area specific (m<sup>-2</sup>) basis. Size data have been used to estimate wet weights based on published length-weight regressions (see reference column in the dataset). This dataset contributes baseline information about the gelatinous macrozooplankton diversity and its specific distribution pattern in the extended North Sea area during winter (January-February) 2021. These data can be an important contribution to address global change impacts on marine systems, especially considering gelatinous macrozooplankton abundance changes in relation to anthropogenic stressors.</p>
DATASET: characterization of the seed coat extractable phenolic profile and color in 308 common bean lines of the Spanish Diversity Panel
<p>Characterizarion of the seed coat extractable phenolic profile and color in 308 common bean lines of the Spanish Diversity Panel</p>
WS22 database: combining Wigner Sampling and geometry interpolation towards configurationally diverse molecular datasets
<p>The WS22 database provides a collection of molecular datasets that explores a broad configurational space of flexible organic molecules with varying sizes and complexity. It includes several chemical properties calculated with a quantum chemical (QM) method. Complementary to the structured datasets, this repository also provides the molecular geometries for the equilibrium structures together with the corresponding output of the QM frequency calculations. Details about the methodology, content, and structure of the WS22 datasets are provided in the README file included in this repository.</p>
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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.