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Small Mammal Exclosure Study (SMES) Vegetation Data from the Chihuahuan Desert Grassland and Shrubland at the Sevilleta National Wildlife Refuge, New Mexico (1995-2009)
This is data for vegetation canopy cover measured from each of the SMES study plots. Vegetation canopy cover was measured from each of the 36 one-meter2 quadrats twice each year. Animal consumers have important roles in ecosystems, determining plant species composition and structure, regulating rates of plant production and nutrient, and altering soil structure and chemistry. The purpose of this study is to determine whether or not the activities of small mammals regulate plant community structure, plant species diversity, and spatial vegetation patterns in Chihuahuan Desert shrublands and grasslands. The purpose of this study is to determine whether or not the activities of small mammals regulate plant community structure, plant species diversity, and spatial vegetation patterns in Chihuahuan Desert shrublands and grasslands. What role if any do indigenous small mammal consumers have in maintaining desertified landscapes in the Chihuahuan Desert? Additionally, how do the effects of small mammals interact with changing climate to affect vegetation patterns over time? This study will provide long-term experimental tests of the roles of consumers on ecosystem pattern and process across a latitudinal climate gradient. The following questions or hypotheses will be addressed. 1) Do small mammals influence patterns of plant species composition and diversity, vegetation structure, and spatial patterns of vegetation canopy cover and biomass in Chihuahuan Desert shrublands and grasslands? Are small mammals keystone species that determine plant species composition and physiognomy of Chihuahuan Desert communities? Do small mammals have a significant role in maintaining the existence of shrub islands and spatial heterogeneity of creosotebush shrub communities? 2) Do small mammals affect the taxonomic composition and spatial pattern of vegetation similarly or differently in grassland communities as compared to shrub communities? How do patterns compare between grassland and shru
Birdwood Mammal Trapping Data, Charlottesville, VA, 1974-1978
This data was collected by Ray Dueser, Bob Rose and their students (among them, Marcia Wilson, John Porter and Bill Ingoly). It is included in the VCR LTER database for comparative purposes. The data itself consists of trapping records for 10x10 trapping grids with 7.6m (25 foot) trap spacing. (note: grid 5 had an unusual geometry due to size constraints). Up to 4 captures of an individual may be recorded on each line of data. Trapping used modified Fitch live traps with a #10 tin can as the main chamber. Traps were baited with cracked corn or hen scratch and run for 3 sequential nights in each trapping session. In addition to the basic trapping data, there are additional files such as a fortran program for detecting inconsistencies in the data (KCHECK.FOR), a listing of known problems (ERRORLIS), a program for calculating Minimum Number Known Alive (MNAPROG.FOR) and a file containing minimum number alive (BIRDMNA.DAT) for each grid, week, sex and species combination.
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>
Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals
<p><strong>Supplementary Material for:</strong></p> <p>Emerling C.A., Springer M.S., Gatesy J., Jones Z., Hamilton D., Xia-Zhu D., Collin M.A., and Delsuc F. (2021). Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals.<strong><em> Open Research Europe</em></strong> 1:75. doi:10.12688/openreseurope.13795.1.</p> <p> </p> <p><strong>Supplementary File Legends:</strong></p> <p><strong>- Supplementary_Figure_S1.pdf:</strong> <em>AANAT</em> PAML ‘master model’ showing branch categories, corresponding to “Model 1: 24 ratio” in Supplementary Table S7.</p> <p><strong>- Supplementary_Figure_S2.pdf:</strong> <em>ASMT</em> PAML ‘master model’ showing branch categories, corresponding to “Model 2: 24 ratio” in Supplementary Table S8.</p> <p><strong>- Supplementary_Figure_S3.pdf:</strong> <em>MTNR1A</em> PAML ‘master model’ showing branch categories, corresponding to “Model 1: 27 ratio” in Supplementary Table S9.</p> <p><strong>- Supplementary_Figure_S4.pdf:</strong> <em>MTNR1B</em> PAML ‘master model’ showing branch categories, corresponding to “Model 1: 46 ratio” in Supplementary Table S10.</p> <p><strong>- Supplementary_Figure_S5.pdf:</strong> RAxML <em>AANAT</em> gene tree. Numbers at nodes correspond to bootstrap support values.</p> <p><strong>- Supplementary_Figure_S6.pdf: </strong>RAxML <em>ASMT</em> gene tree. Numbers at nodes correspond to bootstrap support values.</p> <p><strong>- Supplementary_Figure_S7.pdf: </strong>RAxML <em>MTNR1A</em>+<em>MTNR1B</em> tree. Numbers at nodes correspond to bootstrap support values.</p> <p><strong>- Supplementary_Figure_S8.pdf: </strong>Supporting data showing the inactivation of <em>MTNR1A</em> exon 2 in cetaceans. Read Supplementary Table S13 for further details.</p> <p><strong>- Supplementary_Figure_S9.pdf: </strong>Supporting data showing the inactivation of <em>ASMT</em> in spalacids and <em>Fukomys damarensis</em>. Read Supplementary Table S13 for further details.</p> <p><strong>- Supplementary_Figure_S10.pdf: </strong>Supporting data showing the inactivation of <em>MTNR1A</em> in hyracoids and <em>Cyclopes didactylus</em>. Read Supplementary Table S13 for further details.</p> <p><strong>- Supplementary_Figure_S11.pdf: </strong>Supporting data showing the inactivation of <em>MTNR1A</em> in sirenians. Read Supplementary Table S13 for further details.</p> <p><strong>- Supplementary_Figure_S12.pdf: </strong>Supporting data showing the inactivation of <em>AANAT</em> in sirenians and a polymorphic premature stop codon in exon 5 of <em>ASMT</em> in <em>Trichechus manatus</em>. Read Supplementary Table S13 for further details.</p> <p><strong>- Supplementary_Figure_S13.pdf: </strong>Supporting data showing the inactivation of <em>MTNR1A</em> in <em>Condylura cristata</em>. Read Supplementary Table S13 for further details.</p> <p><strong>- Supplementary_Figure_S14.pdf: </strong>Supporting data showing the inactivation of <em>MTNR1A</em> in <em>Phataginus tricuspis</em>. Read Supplementary Table S14 for further details.</p> <p><strong>- Supplementary_Figure_S15.pdf: </strong>PAML <em>AANAT</em> results, Model 1: 24 ratio (see Supplementary Table S7).</p> <p><strong>- Supplementary_Figure_S16.pdf: </strong>PAML <em>ASMT</em> results, Model 2: 24 ratio (see Supplementary Table S8).</p> <p><strong>- Supplementary_Figure_S17.pdf: </strong>PAML <em>MTNR1A</em> results, Model 1: 27 ratio (see Supplementary Table S9).</p> <p><strong>- Supplementary_Figure_S18.pdf: </strong>PAML <em>MTNR1B</em> results, Model 1: 46 ratio (see Supplementary Table S10).</p> <p><strong>- Supplementary_Table_S1.xlsx: </strong>List of species examined in this study and the sources of the genes. Source key: WGS: Sequences derived from NCBI's Whole Genome Shotgun database, with accession prefix provided; Whole Genome Sequencing of Short Reads: whole genomes were sequenced using short-read technologies. The methodologies varied for the species, and will be or have been published with other projects, so please contact the author(s) for information on the specific methodology and samples used (Xenarthrans, <em>Proteles cristatus</em>, <em>Otocyon megalotis</em>: Frédéric Delsuc, e-mail: Frederic.Delsuc@umontpellier.fr; Crocodylians: John Gatesy, e-mail: jgatesy@amnh.org; <em>Dugong dugon</em>: Mark Springer, e-mail: mark.springer@ucr.edu; SRA: sequences derived from NCBI's Sequence Read Archive; GenBank: sequences derived from NCBI's nucleotide collection; Bowhead Whale Genome Resource: sequences derived from http://www.bowhead-whale.org; Ensembl: sequences derived from Ensembl genome browser (www.ensembl.org)l; Discovar de novo: sequences derived genomes assembled via Discovar de novo (<a href="https://software.broadinstitute.org/software/discovar/blog/">https://software.broadinstitute.org/software/discovar/blog/</a>). Coverage: indicates coverage of the whole genome (reported in NCBI or other source) or individual genes (derived from short read mapping). Scaffold and contig N50: reported in NCBI or other source.</p> <p><strong>- Supplementary_Table_S2.xlsx: </strong>Accession numbers and functionality of <em>AANAT</em> in species examined. If Accession # indicated as “New”, sequence generated for this study and can be found in Supplementary Dataset S1. Parentheses after accession number indicates coordinates for sequence on the contig / scaffold. Exon colors code for the following: green = putatively functional; yellow = missing (e.g., negative BLAST results, negative mapping results); pink = one or more inactivating mutations found. Abbreviations for mutations are as follows: del = deletion; ins = insertion; start = start codon mutation; stop = premature stop codon; ? = ambiguity whether the mutation is shared among all members of the clade. Abbreviations in brackets following an inactivating mutation indicate shared inactivating mutation. Key for each abbreviation follows: Bacu = <em>Balaenoptera acutorostrata</em>; BALA = Balaenidae; BALAEN = Balaenopteridae; Bbon = <em>Balaenoptera bonaerensis</em>; CAB = <em>Cabassous</em>; Ccap = <em>Cebus capucinus</em>; CETA = Cetacea; CHLAM = Chlamyphoridae; CHOL = <em>Choloepus</em>; Cjac = <em>Callithrix jacchus</em>; CING = Cingulata; DASY = Dasypodidae; DELP = Delphinidae; DERM = Dermoptera; Erob = <em>Eschrichtius robustus</em>; INIA = <em>Inia</em>; FOLI = Folivora; GALE = <em>Galeopterus</em>; LIPO = <em>Lipotes</em>; Lobl = <em>Lagenorhynchus obliquidens</em>; MANI = Manidae; MONO = Monodontidae; MYRM = Myrmecophagidae; MYST = Mysticeti; NPP = Not present in <em>Platanista</em> or Physeteroidea, but present in other Odontocetes; NPZ = Not present in Ziphiidae, but present in other Odontocetes; Oorc = <em>Orcinus orca</em>; PEUT = Tolypeutinae; PHOC = Phocoenidae; PHOL = Pholidota; PHOR = Chlamyphorinae; PILO = Pilosa; PHYS = Physeteroidea; PONT = <em>Pontoporia</em>; Schi = <em>Sousa chinensis</em>; SIRE = Sirenia; Tadu = <em>Tursiops aduncus</em>; TOLY = <em>Tolypeutes</em>; VERM = Vermilingua; XEN = Xenarthra.</p> <p><br> <strong>- Supplementary_Table_S3.xlsx: </strong>Accession numbers and functionality of <em>ASMT</em> in species examined. See Table S2 caption for details.</p> <p><strong>- Supplementary_Table_S4.xlsx: </strong>Accession numbers and functionality of <em>MTNR1A</em> in species examined. See Table S2 caption for details.</p> <p><strong>- Supplementary_Table_S5.xlsx: </strong>Accession numbers and functionality of <em>MTNR1B</em> in species examined. See Table S2 caption for details.</p> <p><strong>- Supplementary_Table_S6.xlsx: </strong>Codon frequency model selection. These are the results from one ratio dN/dS analyses using different codon frequency models. AIC = Akaike Information Criterion.</p> <p><strong>- Supplementary_Table_S7.xlsx: </strong>Results of <em>AANAT</em> PAML dN/dS analyses for mammals. Model: BG = branch(es) grouped with background; fixed 1 = branch(es) fixed at 1. p’-value: p-value after Holm-Bonferroni correction for multiple testing. Model Comparison: if model comparison yields statistically significant differences (p < 0.05), model comparison bolded and given green background; if model comparison is still significant after Holm-Bonferroni correction, asterisk (*) added. For most models, w only shown for branch(es) of interest. Numbers in front of taxonomic names in first row correspond to numbers in the master model shown in Supplementary Figure S1.</p> <p><strong>- Supplementary_Table_S8.xlsx: </strong>Results of <em>ASMT</em> PAML dN/dS analyses for mammals. Refer to Table S7 caption for additional details. Numbers in front of taxonomic names in first row correspond to numbers in the master model shown in Supplementary Figure S2.</p> <p><strong>- Supplementary_Table_S9.xlsx: </strong>Results of <em>MTNR1A</em> PAML dN/dS analyses for mammals. Refer to Table S7 caption for additional details. Numbers in front of taxonomic names in first row correspond to numbers in the master model shown in Supplementary Figure S3.</p> <p><strong>- Supplementary_Table_S10.xlsx: </strong>Results of <em>MTNR1B</em> PAML dN/dS analyses for mammals. Refer to Table S7 caption for additional details. Numbers in front of taxonomic names in first row correspond to numbers in the master model shown in Supplementary Figure S4.</p> <p><strong>- Supplementary_Table_S11.xlsx: </strong>Results of PAML analyses for sauropsids.</p> <p><strong>- Supplementary_Table_S12.xlsx: </strong>Results of BLASTing and mapping short reads from <em>Alligator mississippiensis</em> RNA sequencing experiments.</p> <p><strong>- Supplementary_Table_S13.xlsx: </strong>Supporting data for validating putative inactivating mutations. Validating data came from four general sources of information: mutations shared by more than one species within a clade, mutations shared by two sources of sequencing data for the same species, mutations validated by coverage of mapped short reads and statistically elevated dN/dS ratio estimates. For additional details, see Supplementary Tables S2–S5 and S7–S10, as well as Figure 2 and Supplementary Figures S8–S18.</p> <p><strong>- Supplementary_Dataset_S1.txt:</strong><strong> </strong>Genomic alignments in fasta format used to determine the pseudogene/functional status of all four melatonin genes in different taxonomic groups.</p> <p><strong>- Supplementary_Dataset_S2.txt:</strong><strong> </strong>Alignment of <em>AANAT</em> in phylip format used in maximum likelihood phylogenetic reconstruction with RAxML. </p> <p><strong>- Supplementary_Dataset_S3.txt: </strong>Alignment of <em>ASMT</em> in phylip format used in maximum likelihood phylogenetic reconstruction with RAxML. </p> <p><strong>- Supplementary_Dataset_S4.txt: </strong>Alignment of <em>MTNR1A</em> and <em>MTNR1B</em> in phylip format used in maximum likelihood phylogenetic reconstruction with RAxML. </p> <p><strong>- Supplementary_Dataset_S5.txt:</strong><strong> </strong>Codon alignments of <em>AANAT</em> used in selection pressure analyses with PAML. </p> <p><strong>- Supplementary_Dataset_S6.txt: </strong>Codon alignments of <em>ASMT</em> used in selection pressure analyses with PAML.</p> <p><strong>- Supplementary_Dataset_S7.txt:</strong><strong> </strong>Codon alignments of <em>MTNR1A</em> used in selection pressure analyses with PAML.</p> <p><strong>- Supplementary_Dataset_S8.txt: </strong>Codon alignments of <em>MTNR1B</em> used in selection pressure analyses with PAML.</p> <p><strong>- Supplementary_Dataset_S9.txt: </strong>Tree topologies in newick format used in selection pressure analyses with PAML.</p>
An estimate of fitness reduction from mutation accumulation in a mammal allows assessment of the consequences of relaxed selection: Dataset
<p>Supplementary files (data and analysis) for "An estimate of fitness reduction from mutation accumulation in a mammal allows assessment of the consequences of relaxed selection"</p> <p>Supplementary File 1: C3H_pheno_fix_Jun7_2023_nolowmut.csv</p> <p>Data for all mice in MA experiment including: mouse ID, sire, dam, generation, mating ID, sex, weight at 3 weeks, weight at 6 weeks, tail length, litter size, litter ID, line ID</p> <p> </p> <p>Supplementary File 2: C3H_pheno_Kontrol_June2023.csv</p> <p>Data for all control mice including: mouse ID, sire, dam, generation, mating ID, sex, weight at 3 weeks, weight at 6 weeks, tail length, litter size, litter ID, line ID</p> <p> </p> <p>Supplementary File 3: C3H_birthdates.csv</p> <p>Data for all C3H mice including: mouse ID, birthdate</p> <p> </p> <p>Supplementary File 4: MA_pheno.R</p> <p>R code for visualising trait data, running linear regressions, and comparing control and MA experiment data</p> <p> </p> <p>Supplementary File 5: C3H_pheno_burnin20_Jun7_2023_nolowmut.csv</p> <p>Data for all mice in MA experiment including a 20 generation burn-in to simulate mutation-drift balance for Animal model analyses: mouse ID, sire, dam, generation, mating ID, sex, weight at 3 weeks, weight at 6 weeks, tail length, litter size, litter ID, line ID</p> <p> </p> <p>Supplementary File 6: asreml_C3H_ALL.R</p> <p>R code for estimating mutational heritabilities using mixed model analysis</p> <p> </p> <p>Supplementary File 7: C3H_ped_rekey_Jun2023.csv</p> <p>Pedigree data for all mice in MA experiment</p> <p> </p> <p>Supplementary File 8: C3H_ped_rekey_KEY.csv</p> <p>Key for pedigree data file</p> <p> </p> <p>Supplementary File 9: plot_pedigree_tree_MS_final.R</p> <p>R code for visualising pedigree of mice in MA experiment</p>
Graphic Illustration of Litsa Wooten's Talk: Visualizing Mongolian Mammal Specimens and their Parasites Through Time
<p><a href="https://lib.ku.edu/people/courtney-foat" target="_blank" rel="noopener">Courtney Foat</a>, Advisor for Strategic Initiatives & Organizational Engagement at the University of Kansas, graphically recorded this talk by Litsa Wooten at the Digital Data 2024 Conference in Lawrence, Kansas in May of 2024. We include this resource, with permission, because of its relevance to our NSF-supported Workshop: Digital Collections Data and Tracking Disease.</p>
Functional redundancy of non-volant small mammals increases in human-modified habitats
<p>This repository hosts all R codes, data and output supporting the findings of the study "Functional redundancy of non-volant small mammals increases in human-modified habitats", by André L. Luza (UFRGS, BR), Catherine H. Graham (WSL, CH), Sandra M. Hartz (UFRGS, BR), and Dirk, N. Karger (WSL, CH).</p> <p>The only data that are not here are the Ecoregions of WWF. These data can be found in the webpage of WWF.</p>
Small mammal survey in Narati (China) and Sary-Mogul (Kyrgyzstan)
<p>Field surveys were conducted in September 2006 at Narati (China) and September 2014 at Sary Mogul (Kyrgyzstan) using trapping and transect methods. See <a href="https://dataosu.obs-besancon.fr/FR-18008901306731-2015-08-06-20">dat@osu</a> for general metadata and Marston et al. (2022), cited below (submitted) for sampling details.</p> <p><a href="https://zenodo.org/record/7413284/files/Narati_transect.csv?download=1">Narati_transect.csv</a> : transects of over 41 km were surveyed in grassland areas between 1509-3335 m altitude. Each row corresponds to an approximatively 130 m segment, divided into 20 intervals of ten paces. Activity indicators identifiable to species or genus level (including foraging corridors, ground holes, earth tumuli and small mammal faeces) were recorded. The abundance index is the number of intervals where presence indicators were observed divided by the number of intervals walked (n = 20). The geographical coordinates are the centroïd of each segment.</p> <p><a href="https://zenodo.org/record/7413284/files/Narati_traplines.txt?download=1">Narati_traplines_rd.txt</a>: small mammal relative densities obtained using standard trapping as described in Marston et al. (2022).</p> <p><a href="https://zenodo.org/record/7413284/files/Sary_Mogul_transect.csv?download=1">Sary_Mogul_transect.csv</a>: For each transect, 20 intervals of 10 paces were surveyed with activity indicators identifiable to species or genus level (including foraging corridors, ground holes, earth tumuli and small mammal faeces) recorded. Relative density scores of small mammal presence (the number of intervals where presence indicators were observed) were produced for each species for each transect. In Sary Mogul, field surveys comprised 37 transects as described in <a href="https://doi.org/10.3390/rs11010039">Marston and Giraudoux (2019</a>)</p> <p><a href="https://zenodo.org/record/7413284/files/Sary_Mogul_traplines_rd.txt?download=1">Sary_Mogul_traplines_rd.txt</a>: small mammal relative densities obtained using standard trapping as described in Marston et al. (2022).</p>
Arctic specimens in the NHMO Mammal collection 2022
<p>All Arctic specimens in the NHMO Mammal collection as of August 2022. See Johannessen et al. 2023 "Arctic specimens in the zoological collections at the Natural History Museum, University of Oslo, Norway (NHMO)" for further details.</p>
Arctic specimens in the NHMO DNA bank Mammal collection 2022
<p>All Arctic specimens in the NHMO DNA bank Mammal collection as of August 2022. See Johannessen et al. 2023 "Arctic specimens in the zoological collections at the Natural History Museum, University of Oslo, Norway (NHMO)" for further details.</p>
Frugivoria: A trait database for birds and mammals exhibiting frugivory across contiguous Neotropical moist forests
Biodiversity in many areas is rapidly shifting and declining as a consequence of global change. As such, there is an urgent need for new tools and strategies to help identify, monitor, and conserve biodiversity hotspots. One way to identify these areas is by quantifying functional diversity, which measures the unique roles of species within a community and is valuable for conservation because of its relationship with ecosystem functioning. Unfortunately, the trait information required to evaluate functional diversity is often lacking and is difficult to harmonize across disparate data sources. Biodiversity hotspots are particularly lacking in this information. To address this knowledge gap, we compiled Frugivoria, a trait database containing dietary, life-history, morphological, and geographic traits, for mammals and birds exhibiting frugivory, which are important for seed dispersal, an essential ecosystem service. Accompanying Frugivoria is an open workflow that harmonizes trait and taxonomic data from disparate sources and enables users to analyze traits in space. This version of Frugivoria contains mammal and bird species found in contiguous moist montane forests and adjacent moist lowland forests of Central and South America– the latter specifically focusing on the Andean states. In total, Frugivoria includes 45,216 unique trait values, including new values and harmonized values from existing databases. Frugivoria adds 23,707 new trait values (8,709 for mammals and 14,999 for birds) for a total of 1,733 bird and mammal species. These traits include diet breadth, habitat breadth, habitat specialization, body size, sexual dimorphism, and range-based geographic traits including range size, average annual mean temperature and precipitation, and metrics of human impact calculated over the range. Frugivoria fills gaps in trait categories from other databases such as diet category, home range size, generation time, and longevity, and extends certain traits, once only a
Long-Term Studies of Huron Mountain Club Small Mammal Populations
These datasets include small mammal population data collected by Richard Manville (1940-1942), Phillip Myers (2003), and Allison Poor (2004-2005). Small mammal traps were initially placed in 8 locations throughout the Huron Mountains in Michigan's Upper Peninsula from 1940-1942 by Richard Manville. Small mammals present in the traps were recorded once each year and twice in 1941. This study was repeated by Phillip Myers and Allison Poor from 2003-2005.
SGS-LTER Long-Term Monitoring Project: Vegetation Cover on Small Mammal Trapping Webs on the Central Plains Experimental Range, Nunn, Colorado, USA 1999 -2006, ARS Study Number 118 (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/140/17. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Additional information and referenced materials can be found: http://hdl.handle.net/10217/83458. The abundance and diversity of small mammals in shortgrass steppe is strongly influenced by the structure and composition of vegetation. Vegetation structure provides cover from predators and harsh abiotic conditions. Plant species composition affects the types of seeds and herbaceous material available to granivores and herbivores, and influences arthropod populations, which are important prey for the omnivorous species that dominate in shortgrass steppe. Both vegetation structure and plant community composition are sensitive to the availability of precipitation as well as the activity of large mammalian herbivores. In 1999, we began measuring vegetation structure and plant community composition on the three grassland and three shrubland trapping webs where we live-trap small mammals
SGS-LTER Long-Term Montioring Project: Arthropod Pitfall Trapping on Small Mammal Trapping Webs on the Central Plains Experimental Range, Nunn, Colorado, USA 1998-2006, ARS Study Number 118 (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/134/17. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Additional information and referenced materials can be found: http://hdl.handle.net/10217/83450. With the exception of heteromyids, eg kangaroo rats and pocket mice, most small rodents in shortgrass steppe are omnivorous. Depending on season, arthropods (insects and arachnids) make up 40-85% of the diet of grasshopper mice and thirteen-lined ground squirrels, the most widespread rodents in northern shortgrass steppe. Small mammals are among the most important predators of ground-dwelling macroarthropods and herbivorous insects provide a direct resource link between weather and plant production. Understanding temporal variability in the abundance of arthropods is central to determining the mechanisms that drive small rodent populations. At present, there are no long-term studies of arthropods in shortgrass steppe, despite the important role that these taxa play in grassland food w
SGS-LTER Long-Term Monitoring Project: Small Mammals on Trapping Webs on the Central Plains Experimental Range, Nunn, Colorado, USA 1994 -2006, ARS Study Number 118 (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/137/17. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Additional information and referenced materials can be found: http://hdl.handle.net/10217/83452. Small mammals (rabbits, rodents) are integral components of semiarid ecosystems because of their roles as consumers of plants, seeds and arthropods, as soil disturbance agents, and as food for raptors, snakes and mammalian carnivores. Because of their vagility and intermediate trophic position, populations of small mammals may track changes in vegetation and the abiotic environment that may result from shifts in land-use and other anthropogenic disturbances. However, these populations are variable over space and time, and their response to environmental changes may not be immediately apparent given their behavioral flexibility and relatively long life-spans and generation times. Patterns in the distribution and abundance of small mammals thus may simultaneously reflect and affect the
Small mammal structure cover collected at Team Vole fences near Nome, Toolik Lake, and Utqaigvik, Alaska, summer 2019
Percent cover of tundra vole and brown lemming structures collected from within the Team Vole enclosure/exclosure fences near Nome, Toolik, Utqiagvik, AK 2019.
Mammal occurrence data derived from camera traps in grassland-shrubland ecotones at 24 sites in the Jornada Basin, southern New Mexico, USA, 2014-ongoing
The objective of this ongoing study is to investigate how abundance, distribution, and activity of mammals (>= 1 kg) vary across grassland to shrubland ecotones in the northern Chihuahuan Desert. This dataset includes animal occurrence data derived from camera trap images captured in 24 grassland-to-shrubland ecotone sites in the Jornada Basin, Dona Ana County, New Mexico, USA. The data set contains occurrence records from 14 mammal species with the date and time a species was detected. Also included are the number of individuals in a photo, operational dates and number of functional camera days for cameras, total number of trap nights a camera was active, and geographical coordinates of camera trap locations. Sampling is ongoing and occurs during the monsoon season from July-November. Sampling has occurred annually since 2014.
CSM06 Seasonal summary of numbers of small mammals on miscellaneous traplines in prairie habitats that were trapped from 1 to 11 years at Konza Prairie
Data set contains seasonal summaries (spring, summer and autumn) of the number of individuals of each species of small mammal captured (relative abundance) on each prairie trapline. Each record contains year, season, trapline and number of individuals captured of each species. These live trap records are based on daily captures during 4-day trapping periods in spring (early March to early April), summer (late June to late July) and autumn (early October to mid-November) for each permanent trapline (two traplines per treatment). These treatments include annual burns, 2-year burns, 4-year burns and 10-year burns; none were grazed by bison. This data set includes 14 traplines sampled in autumn and spring and 30 traplines in summer.
CSM05 Seasonal summary of numbers of small mammals on the six LTER traplines in prairie habitats on which fire regime has been reversed at Konza Prairie
Data set contains seasonal summaries (spring and autumn) of the number of individuals of each species of small mammal captured (relative abundance) on each grassland trapline. Each record contains year, season, trapline and number of individuals captured of each species. These live trap records are based on daily captures during a single 4-day trapping period in spring (mid-March to early April) and autumn (late October to early December) for each of six permanent traplines established on two fire treatments (three traplines per treatment). These two fire treatments include one treatment that was changed from a 20-year burn to an annual burn and one that was changed from an annual burn to 20 years between fires. Bison do not graze these two habitat types.
CSM03 Seasonal summary of numbers of small mammals on the two LTER traplines in planted grassland (Brome fields) habitats at Konza Prairie
Data set contains seasonal summaries (spring, summer and autumn) of the number of individuals of each species of small mammal captured (relative abundance) on each woodland trapline. Each record contains year, season, trapline and number of individuals captured of each species. These live trap records are based on daily captures during a single 4-day trapping period in spring (early March to early April), summer (early July to late July) and autumn (mid-October to early December) for each of four permanent traplines established in two habitats (two traplines in gallery forest and two on limestone ledges). Bison did not graze any of the treatment units during the period of study.
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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.