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TA B L E 2 Identified R packages useful for taxonomic name harmonization. Square brackets indicate supplementary references in Harmonizing taxon names in biodiversity data: A review of tools, databases and best practices
TA B L E 2 Identified R packages useful for taxonomic name harmonization. Square brackets indicate supplementary references
Lemur Database for Taxonomic Profiling (bacteria, archaea, fungi)
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Geographic range maps for Mammal Diversity Database v1.2 taxonomy from "Expert range maps of global mammal distributions harmonised to three taxonomic authorities"
<p>Data mirroring for long-term integrity of these critical geospatial resources. Included here are expert geographic range maps aligned to the taxonomy of the Mammal Diversity Database (MDD) version 1.2, which was published on 24 Sept 2020 https://zenodo.org/record/4139818. That taxonomy includes 6,485 total species, of which 103 are considered recently extinct, 20 are considered domestic extant, and 6,362 are considered wild extant (this corrects for 1 species, <em>Capra hircus</em>, that was incorrectly coded as 'domestic=0' rather than 'domestic=1' in the MDD v1.2). For this mapping project, only 6,362 species from MDD v1.2 have maps -- this total:</p> <ul> <li>excludes all extinct and domestic species;</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, have recent range information and were included in the MDD as extant.</li> </ul> <p><strong>### File inventory ###</strong></p> <ul> <li>Order-level zipped files (27 total), one for each extant order of mammals, unzips to geopackage (*.gpg) format;</li> <li>Mammalia-wide zipped file (1: "MDD_Mammalia.zip"), includes maps for all 27 orders, unzips to gpg format;</li> <li>Full taxonomy for MDD v1.2 (as published on https://zenodo.org/record/4139818) in csv format ("MDD_v1.2_all_6485species.csv"); and</li> <li>Subset of MDD v1.2 taxonomy for which range maps are here provided (6,362 species) in csv format ("mdd_spList_wFamilieswOrders_mapped_6362species.csv").</li> </ul> <p><br> <strong>### Full citation ###</strong></p> <p>Marsh, C.J., Sica, Y.V., Burgin, C.J., Dorman, W.A., Anderson, R.C., del Toro Mijares, I., Vigneron, J.G., Barve, V., Dombrowik, V.L., Duong, M., Guralnick, R., Hart, J.A., Maypole, J.K., McCall, K., Ranipeta, A., Schuerkmann, A., Torselli, M.A., Lacher Jr, T., Mittermeier, R.A., Rylands, A.B., Sechrest, W., Wilson, D.E., Abba, A.M., Aguirre, L.F., Arroyo-Cabrales, J., Astúa, D., Baker, A.M., Braulik, G., Braun, J.K., Brito, J., Busher, P.E., Burneo, S.F., Camacho, M.A., Cavallini, P., de Almeida Chiquito, E., Cook, J.A., Cserkész, T., Csorba, G., Cuéllar Soto, E., da Cunha Tavares, V., Davenport, T.R.B., Deméré, T., Denys, C., Dickman, C.R., Eldridge, M.D.B., Fernandez-Duque, E., Francis, C.M., Frankham, G., Franklin, W.L., Freitas, T., Friend, J.A., Gadsby, E.L., Garbino, G.S.T., Gaubert, P., Giannini, N., Giarla, T., Gilchrist, J.S., Gongora, J., Goodman, S.M., Gursky-Doyen, S., Hackländer, K., Hafner, M.S., Hawkins, M., Helgen, K.M., Heritage, S., Hinckley, A., Hintsche, S., Holden, M., Holekamp, K.E., Honeycutt, R.L., Huffman, B.A., Humle, T., Hutterer, R., Ibáñez Ulargui, C., Jackson, S.M., Janecka, J., Janecka, M., Jenkins, P., Juškaitis, R., Juste, J., Kays, R., Kilpatrick, C.W., Kingston, T., Koprowski, J.L., Kryštufek, B., Lavery, T., Lee Jr, T.E., Leite, Y.L.R., Novaes, R.L.M., Lim, B.K., Lissovsky, A., López-Antoñanzas, R., López-Baucells, A., MacLeod, C.D., Maisels, F.G., Mares, M.A., Marsh, H., Mattioli, S., Meijaard, E., Monadjem, A., Morton, F.B., Musser, G., Nadler, T., Norris, R.W., Ojeda, A., Ordóñez-Garza, N., Pardiñas, U.F.J., Patterson, B.D., Pavan, A., Pennay, M., Pereira, C., Prado, J., Queiroz, H.L., Richardson, M., Riley, E.P., Rossiter, S.J., Rubenstein, D.I., Ruelas, D., Salazar-Bravo, J., Schai-Braun, S., Schank, C.J., Schwitzer, C., Sheeran, L.K., Shekelle, M., Shenbrot, G., Soisook, P., Solari, S., Southgate, R., Superina, M., Taber, A.B., Talebi, M., Taylor, P., Vu Dinh, T., Ting, N., Tirira, D.G., Tsang, S., Turvey, S.T., Valdez, R., Van Cakenberghe, V., Veron, G., Wallis, J., Wells, R., Whittaker, D., Williamson, E.A., Wittemyer, G., Woinarski, J., Zinner, D., Upham, N.S., Jetz, W., 2022. Expert range maps of global mammal distributions harmonised to three taxonomic authorities. Journal of Biogeography 49 (5): 979-992. <a href="https://doi.org/10.1111/jbi.14330">https://doi.org/10.1111/jbi.14330</a><br> </p> <p><strong>###</strong><strong> Data downloads on Map of Life ###</strong></p> <p>All range maps for the three taxonomic sources are openly available for non-commercial use through https://mol.org/datasets or at species-level at https://mol.org/species, or for bulk download at https://doi.org/10.48600/mol-7r3j-8066 (HMW), https://doi.org/10.48600/mol-zzrs-q778 (CMW) and https://doi.org/10.48600/mol-48vz-p413 (MDD).</p> <p> </p> <p><strong>###</strong><strong> Abstract ###</strong></p> <p><strong>Aim: </strong> Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroecology. We provide global range maps for the native ranges of all extant mammal species harmonised to the taxonomy of the Mammal Diversity Database (MDD) mobilised from two sources, the <em>Handbook of the Mammals of the World</em> (HMW) and the <em>Illustrated Checklist of the Mammals of the World</em> (CMW).</p> <p><strong>Location: </strong> Global.</p> <p><strong>Taxon: </strong> All extant mammal species.</p> <p><strong>Methods: </strong> Range maps were digitally interpreted, georeferenced, error-checked and subsequently taxonomically aligned between the HMW (6253 species), the CMW (6431 species) and the MDD taxonomies (6362 species).</p> <p><strong>Results: </strong> Range maps can be evaluated and visualised in an online map browser at Map of Life (mol.org) and accessed for individual or batch download for non-commercial use.</p> <p><strong>Main conclusion: </strong> Expert maps of species' global distributions are limited in their spatial detail and temporal specificity, but form a useful basis for broad-scale characterizations and model-based integration with other data. We provide georeferenced range maps for the native ranges of all extant mammal species as shapefiles, with species-level metadata and source information packaged together in geodatabase format. Across the three taxonomic sources our maps entail, there are 1784 taxonomic name differences compared to the maps currently available on the IUCN Red List website. The expert maps provided here are harmonised to the MDD taxonomic authority and linked to a community of online tools that will enable transparent future updates and version control.</p> <p><strong>Keywords: </strong> GIS; Mammalia; biodiversity; biogeography; conservation planning; mapping; species distributions.</p>
Figure 3 from: Desmet P, Brouilet L (2013) Database of Vascular Plants of Canada (VASCAN): a community contributed taxonomic checklist of all vascular plants of Canada, Saint Pierre and Miquelon, and Greenland. PhytoKeys 25: 55-67. https://doi.org/10.3897/phytokeys.25.3100
Figure 3 - The VASCAN Darwin Core Archive, structured following the GBIF GNA Profile. It is a compressed folder containing 4 text files with tab-seperated values and 2 xml files. Taxon and scientific name information is provided in taxon.txt, with one record for each taxon and child-parent-relationships representing the classification. Records in the extension files distribution.txt, vernacularname.txt and description.txt have a many-to-one relation with the records in taxon.txt and provide additional information for each taxon. The archive structure and term definitions are described in meta.xml. The dataset metadata are provided in eml.xml.
Figure 2 from: Desmet P, Brouilet L (2013) Database of Vascular Plants of Canada (VASCAN): a community contributed taxonomic checklist of all vascular plants of Canada, Saint Pierre and Miquelon, and Greenland. PhytoKeys 25: 55-67. https://doi.org/10.3897/phytokeys.25.3100
Figure 2 - Regional distribution of accepted species from the Database of Vascular Plants of Canada (VASCAN). For each region, the number of native, introduced and ephemeral species is shown, i.e. species with a confirmed presence in the region. The regions are ordered by total number of species.
Figure 1 from: Desmet P, Brouilet L (2013) Database of Vascular Plants of Canada (VASCAN): a community contributed taxonomic checklist of all vascular plants of Canada, Saint Pierre and Miquelon, and Greenland. PhytoKeys 25: 55-67. https://doi.org/10.3897/phytokeys.25.3100
Figure 1 - Taxonomic distribution of accepted species per family from the Database of Vascular Plants of Canada (VASCAN). The families are ordered by total number of species. Families with less than 80 species are grouped in 'Other families'.
Figure 2 from: Lepage D, Vaidya G, Guralnick R (2014) Avibase – a database system for managing and organizing taxonomic concepts. ZooKeys 420: 117-135. https://doi.org/10.3897/zookeys.420.7089
Figure 2 - The relationships between the taxonomic entities related to the Vireo solitarius superspecies. Numbers under each name refer to Avibase IDs. The concept for the nominal plumbeus sec. Oberholser, 1974 is therefore distinct from the concept for the nominal subspecies plumbeus when jacksoni is subsumed. It is worth noting however that the recognition or not of jacksoni does not affect the higher related concepts, such as the plumbeus species, any of its other subspecies, or the rest of the Vireo solitarius complex because they are either orthogonal to those alternative arrangements or they completely include both. In the database model (Fig. 1), these trees are maintained with the parent-child relationship table in which each Avibase ID only needs to identify its immediate parent, while other relationships can be calculated programmatically.
Figure 1 from: Lepage D, Vaidya G, Guralnick R (2014) Avibase – a database system for managing and organizing taxonomic concepts. ZooKeys 420: 117-135. https://doi.org/10.3897/zookeys.420.7089
Figure 1 - Simplified schema of Avibase primary tables, The Avibase ID table is the central element of Avibase, to which all other concepts are related, and which aims to represent all distinct taxonomic concepts ever published for birds. Published taxonomic concepts (species and subspecies, as well as subspecies groups in some cases), along with their scientific and common names as recognized in the publication, are each mapped to a single Avibase ID. A table of parent-child relationships is used to describe relationships between different Avibase IDs. Because all taxonomic concepts are congruent with Avibase IDs, relationships among taxonomic concepts themselves are not needed. Biological properties (geographic range, life-history, etc.) are linked directly to Avibase ID, as are synonyms, a table that partly overlaps with the names used by taxonomic concepts, but that can also extend to vernacular names in multiple languages. Name concepts, which relate to names attached to original type specimens, are a property of taxonomic concepts, and can themselves be linked to ITIS Taxonomic Serial Number (TSN) identifiers.
Figure 4 from: Lepage D, Vaidya G, Guralnick R (2014) Avibase – a database system for managing and organizing taxonomic concepts. ZooKeys 420: 117-135. https://doi.org/10.3897/zookeys.420.7089
Figure 4 - Fractional weights (w) can be used to validate the taxonomic arrangements within a particular authority. In this example, in any valid listing of the concepts within an authority, the sum of all taxonomic concepts related to the superspecies Vireo solitarius should add up to 1.0 at both the species and the subspecies levels.
Figure 3 from: Lepage D, Vaidya G, Guralnick R (2014) Avibase – a database system for managing and organizing taxonomic concepts. ZooKeys 420: 117-135. https://doi.org/10.3897/zookeys.420.7089
Figure 3 - The relationships between Pterodroma arminjoniana, Pterodroma heraldica and Pterodroma atrata, with two alternative arrangements (A and B) of biological concepts found in taxonomic authorities. Concepts with the same lowercase letters in brackets in the two diagrams represent congruent circumscriptions.
Diamond formatted protein database for taxonomic classification
<p>This is a diamond formatted database (diamond version 0.9.22) built on December 14th 2018.</p> <p>The database contains a total of 17,694,143 sequences:</p> <ul> <li>2,708,401 protein sequences from the <a href="https://bitbucket.org/dbeisser/taxmapper_supplement/src/master/">taxmapper database</a> (commit 450d337), containing 121 unique taxa.</li> <li>14,976,193 protein sequences from 1055 unique fungal taxa (downloaded from <a href="https://genome.jgi.doe.gov/1000_fungi_project">JGI 1000 fungi project</a> on November 23 2018).</li> <li>9,549 protein sequences from the <em>Hygrophorus russula</em> genome obtained from Genbank (accession GCA_003314125.1) on November 28 2018.</li> </ul> <p>The <em>Hygrophorus russula</em> protein sequences were obtained by running Augustus (v. 3.2.3) gene caller on the genomic fasta file using the laccaria_bicolor gene model.</p> <p>Taxonomic information was built into the diamond database by running:</p> <pre><code class="language-bash">zcat fasta.gz | diamond makedb -d diamond -p 4 --taxonmap taxonmap.gz --taxonnodes nodes.dmp</code></pre> <p>The nodes.dmp file was obtained from the <a>taxdump.tar.gz</a> file on December 11 2018.</p>
FIGURE 2 in The Wild Silkmoths (Lepidoptera: Bombycoidea: Saturniidae) of Colombia: a database of occurrence points and taxonomic checklist
FIGURE 2. Distribution of surveyed Colombian Saturniidae voucher specimens, including type specimens (i.e., holotypes, paratypes, and lectotypes), in 13 national (grey) and 18 international (black) biological collections examined in this study (Table S1).
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