Mammal Diversity Database - Upham, Nathan; Burgin, Connor; Widness, Jane; Liphardt, Schuyler; Parker, Camila; Becker, Madeleine; Rochon, Ingrid; Huckaby, David; Mammal Diversity Database (Zenodo, 2023)
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 Mammal Species of the World (MSW) series. Here, we present the Mammal Diversity Database (MDD), a digital, publically accessible, and updateable list of all mammalian species, now available online: https://mammaldiversity.org. 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 American Society of Mammalogists (ASM; 2017-present), with initial logistical and planning support (2017-2019) provided by the NSF Vertlife Terrestrial grant. Logistical support is now also being provided by the Biodiversity Knowledge Integration Center at Arizona State University. The ASM Biodiversity Committee 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. A new section on Subjective Decisions has been added to the MDD About page 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 IUCN SSC Bat Specialist Group 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 2023. Version 1.11 (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 holotypeVoucher 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 Tracked Differences 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: Bos domesticus into Bos javanicus, and Bos indicus into Bos taurus), 1 species removal (Makalata obscura, now considered nomen dubium), 36 species with genus name changes, 5 genus additions (Otohylomys, Baeodon, Neusticomys, Poecilictis, and Parachoerus) and 7 genus lumps (Crossogale, Aeorestes, Dasypterus, Koopmania, Pediolagus, Petropseudes, Catagonus), 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. Version 1.10 (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 Dromiciops mondaca, which was synonymized under D. gliroides). The holotypeVoucher 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 Tracked Differences 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 Lissonycteris -> Myonycteris, Aonyx/Lutrogale -> Lutra, Eothenomys -> Anteliomys, Ellobius -> Bramus, Proedromys -> Mictomicrotus, Lasiopodomys back to Stenocranius, and Cephalophus -> Cephalophorus), 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 Capra hircus to domestic status as the domestic form of C. aegagrus. In total, there was a net increase of 19 species and 5 genera of recognized extant or recently extinct mammals since MDD v1.9. Version 1.9.1 (29 Jun 2022). This is a patch release that adds the field 'holotypeVoucherURIs' 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). Version 1.9 (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 Lagenorhynchus dolphins, along with the previous inclusion of some Cebus species). The holotypeVoucher 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 Tracked Differences 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 (Brachylagus idahoensis to Sylvilagus idahoensis and Nycticebus pygmaeus to Xanthonycticebus pygmaeus), and 1 range extension (for Marmosa alstoni 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. Version 1.8 (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 holotypeVoucher 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 Tracked Differences 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. Version 1.7 (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 holotypeVoucher 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 Tracked Differences 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 Gazella bilkis synonymized under extant Gazella arabica following Bärmann et al. 2013; extinct Pseudomys gouldii changed to extant since extant Pseudomys fieldi 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. Version 1.6 (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 holotypeVoucher field is now filled for 2,548 accepted species thanks to the continued efforts of Ingrid Rochon. The Tracked Differences 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 (Dryomys yarkandensis invalid while in pre-print), and 18 genus changes. Version 1.5 (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 holotypeVoucher field, which now filled for 2,459 accepted species thanks to the continued efforts of Ingrid Rochon. We also continue to maintain the Tracked Differences 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. Version 1.4 (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 holotypeVoucher 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 Tracked Differences 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 (taxonomyNotes) 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. Version 1.3.1 (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 per-species notes 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. Version 1.3 (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 per-species notes, 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. Version 1.2 (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 Handbook of the Mammals of the World 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 Ungulate Taxonomy. 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 species-level geographic range maps for 6,362 species, available at https://doi.org/10.5281/zenodo.6644198 as mirrored from the data publication of Marsh et al. 2022 (https://doi.org/10.1111/jbi.14330). This range map data set differs from the 6,485 total species in MDD v1.2, as follows: excludes all recently extinct (103) and domestic species (20; correcting for Capra hircus that was coded as 'domestic=0' rather than 'domestic=1' originally); excludes 2 species for which no spatial information was available (Nycticeius aenobarbus and Phoniscus aerosus); and includes 2 species (Elaphurus davidianus and Oryx dammah) that are extinct in the wild (EW) in IUCN, but which have recent range information and were coded in the MDD as extant. Version 1.1 (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). Version 1.0 (1 Feb 2018; described in https://doi.org/10.1093/jmammal/gyx147). 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/km2), followed by Australasia-Oceania (90.6) and the Neotropics (85.1). References 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. GROVES, C., AND P. GRUBB. 2011. Ungulate Taxonomy. JHU Press. 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. HOLBROOK, L. T. 2013. Taxonomy Interrupted. Journal of Mammalian Evolution 20:153–154. 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.
This is a real-time upload of the MDD v.1.11 taxonomy published 15 April 2023 on the mammaldiversity.org website. Funded by the American Society of Mammalogists and NIH 1R21AI164268-01 Intelligently predicting viral spillover risks from bats and other wild mammals (https://reporter.nih.gov/search/jHonNExiyEulTWBDs1zc-Q/project-details/10289637)
Collaborative Research: VertLife Terrestrial: A complete, global assembly of phylogenetic, trait, spatial and environment characteristics for a model clade
Keywords: cc-by-4.0; Mammalia; Species; Diversity; Checklist; Rodentia; Chiroptera; Artiodactyla; Richness; Evolution; Ecology; Conservation