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      Towards a dynamic list of Amazonian tree species

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          Abstract

          To provide an empirical foundation for estimates of the Amazonian tree diversity, we recently published a checklist of 11,675 tree species recorded to date in the region (ter Steege H, et al. (2016) The discovery of the Amazonian tree flora with an updated checklist of all known tree taxa. Scientific Reports 6:29549). From this total of plant records compiled from public databases and literature, widely used in studies on the Amazonian plant diversity, only 6,727 tree species belong to the first taxonomically-vetted checklist published for the region (Cardoso D, et al. (2017) Amazon plant diversity revealed by a taxonomically verified species list. PNAS 114:10695-10700). The striking difference in these two numbers spurred us to evaluate both lists, in order to release an improved Amazonian tree list; to discuss species inclusion criteria; and to highlight the ecological importance of verifying the occurrence of “non-Amazonian” trees in the region through the localization and identification of specimens. A number of species in the 2016 checklist that are not trees, non-native, synonyms, or misspellings were removed and corresponded to about 23% of the names. Species not included in the taxonomically-vetted checklist but verified by taxonomists to occur in Amazonia as trees were retained. Further, the inclusion of recently recorded/new species (after 2016), and recent taxonomic changes added up to an updated checklist including 10,071 species recorded for the Amazon region and shows the dynamic nature of establishing an authoritative checklist of Amazonian tree species. Completing and improving this list is a long-term, high-value commitment that will require a collaborative approach involving ecologists, taxonomists, and practitioners.

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          Hyperdominance in the Amazonian tree flora.

          The vast extent of the Amazon Basin has historically restricted the study of its tree communities to the local and regional scales. Here, we provide empirical data on the commonness, rarity, and richness of lowland tree species across the entire Amazon Basin and Guiana Shield (Amazonia), collected in 1170 tree plots in all major forest types. Extrapolations suggest that Amazonia harbors roughly 16,000 tree species, of which just 227 (1.4%) account for half of all trees. Most of these are habitat specialists and only dominant in one or two regions of the basin. We discuss some implications of the finding that a small group of species--less diverse than the North American tree flora--accounts for half of the world's most diverse tree community.
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            Taxonomic inflation: its influence on macroecology and conservation.

            Species numbers are increasing rapidly. This is due mostly to taxonomic inflation, where known subspecies are raised to species as a result in a change in species concept, rather than to new discoveries. Yet macroecologists and conservation biologists depend heavily on species lists, treating them as accurate and stable measures of biodiversity. Deciding on a standardized, universal species list might ameliorate the mismatch between taxonomy and the uses to which it is put. However, taxonomic uncertainty is ultimately due to the evolutionary nature of species, and is unlikely to be solved completely by standardization. For the moment, at least, users must acknowledge the limitations of taxonomic species and avoid unrealistic expectations of species lists.
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              The taxonomic name resolution service: an online tool for automated standardization of plant names

              Background The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science. Results The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets. Conclusions We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/.
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                Author and article information

                Contributors
                hans.tersteege@naturalis.nl
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                5 March 2019
                5 March 2019
                2019
                : 9
                : 3501
                Affiliations
                [1 ]ISNI 0000 0001 2159 802X, GRID grid.425948.6, Naturalis Biodiversity Center, ; Vondellaan 55, Postbus 9517, 2300 RA Leiden, The Netherlands
                [2 ]ISNI 0000 0001 2175 1274, GRID grid.452671.3, Coordenação de Botânica, , Museu Paraense Emílio Goeldi, ; Av. Magalhães Barata 376, C.P. 399, Belém, PA 66040–170 Brazil
                [3 ]ISNI 0000 0004 1754 9227, GRID grid.12380.38, Systems Ecology, , Free University Amsterdam, ; Amsterdam, The Netherlands
                [4 ]ISNI 0000 0001 0476 8496, GRID grid.299784.9, Science and Education, , The Field Museum, ; 1400S. Lake Shore Drive, Chicago, IL 60605–2496 USA
                [5 ]ISNI 0000 0001 2112 9282, GRID grid.4444.0, AMAP, IRD, CIRAD, CNRS, Université de Montpellier, INRA, Boulevard de la Lironde, TA A-51/PS2, ; F-34398 Montpellier Cedex, France
                [6 ]ISNI 0000 0000 9919 9582, GRID grid.8761.8, Department of Biological and Environmental Sciences, , University of Gothenburg, ; Box 461, SE-405 30, Göteborg, Sweden
                [7 ]Gothenburg Botanical Garden, Carl Skottsbergsgata 22A, SE-413 19 Göteborg, Sweden
                [8 ]Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
                [9 ]ISNI 000000041936754X, GRID grid.38142.3c, Department of Organismic and Evolutionary Biology, , Harvard University, ; 26 Oxford St., Cambridge, MA 02138 USA
                [10 ]Yachay Tech, School of Biological Sciences, Hacienda San José s/n, San Miguel de Urcuquí, Ibarra, Ecuador
                [11 ]Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud-BIOMAS- Universidad de las Américas, Campus Queri, Quito, Ecuador
                [12 ]UNELLEZ-Guanare, Programa de Ciencias del Agro y el Mar, Herbario Universitario (PORT), Mesa de Cavacas, Estado Portuguesa, 3350 Venezuela
                [13 ]Present Address: Compensation International Progress S.A., P.O. Box 260161 Bogotá, D. C. Colombia
                [14 ]GRID grid.440587.a, Programa Professor Visitante Nacional Sênior na Amazônia – CAPES, , Universidade Federal Rural da Amazônia, Av. Perimetral, s/n, ; Belém, PA Brazil
                Author information
                http://orcid.org/0000-0002-8738-2659
                http://orcid.org/0000-0002-1440-9718
                http://orcid.org/0000-0002-9211-2880
                http://orcid.org/0000-0003-0883-1530
                http://orcid.org/0000-0003-1842-9297
                Article
                40101
                10.1038/s41598-019-40101-y
                6401171
                30837572
                053fa80a-e368-459b-9ec8-57bd0bf56857
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 26 July 2018
                : 11 February 2019
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