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Phylogenetic Classification of Seed Plants of Taiwan

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Phylogenetic Classification of Seed Plants of Taiwan Lin and Chung Bot Stud (2017) 58:52 DOI 10.1186/s40529-017-0206-6 ORIGINAL ARTICLE Open Access Phylogenetic Classifcation of Seed Plants of Taiwan Cheng‑Tao Lin1 and Kuo‑Fang Chung2* Abstract Background: Biological classifcation, the hierarchical arrangement of scientifc names of organisms, constitutes the core infrastructure of biological databases. For an efcient management of biological databases, adopting a stable and universal biological classifcation system is crucial. Currently in Taiwan Biodiversity Information Facility (TaiBIF; http://taibif.tw/), the national portal website that integrates Taiwan’s biodiversity information databases, angiosperms are arranged according to Cronquist’s System of Classifcation, which is not compatible with current trend of the Angiosperm Phylogeny Group (APG) classifcation. To consolidate the function and management of the database, TaiBIF is moving to adopt the APG IV classifcation and Christenhusz et al. (Phytotaxa 19:55–70, 2011)’s classifcation of gymnosperms, which we summarize as the Phylogenetic Classifcation of Seed Plants of Taiwan. Results: The Phylogenetic Classifcation of Seed Plants of Taiwan places gymnosperms in fve families [vs. eight families in the Flora of Taiwan (FOT)] and angiosperms in 210 families (vs. 193 families in FOT). Three FOT gymnosperm families are synonymized in current treatment. Of the 210 APG IV families, familial circumscriptions of 114 families are identical with FOT and 50 families are recircumscription of FOT, with 46 families newly added. Of the 29 FOT families not included in current classifcation, two families are excluded and 27 families are synonymized. Conclusions: The adoption of the Phylogenetic Classifcation of Seed Plants of Taiwan in TaiBIF will provide better service and efcient management of the nation’s biodiversity information databases. Keywords: Angiosperm Phylogeny Group classifcation, APG IV, Big new biology, Data cleaning, Flowering plants, Gymnosperms, Spermatophytina, TaiBIF, TaiCOL Background 2013) through TaiCOL (Catalogue of Life in Taiwan; Biological classifcation, the hierarchical arrangement of http://col.taibif.tw/), TaiEOL (Taiwan Encyclopedia of scientifc names of organisms, provides keywords and Life; http://eol.taibif.tw/), TaiBOL (Cryobanking Pro- links to catalogue and organize biological information gram for Wildlife Genetic Material in Taiwan; http:// (Patterson et al. 2014). Biological classifcation consti- cryobank.museum.biodiv.tw/), and TELDAP (Taiwan tutes the core infrastructure of biological databases (Pat- e-Learning and Digital Archives Programs; http://core. terson et al. 2010, 2014). Adopting a stable and universal teldap.tw/). As an associate participant of GBIF (Global biological classifcation system not only is crucial for the Biodiversity Information Facility; http://www.gbif.org/), users but also fundamental for the efcient management TaiBIF also functions as a national node of GBIF (Shao of the databases. et al. 2013). Te initiation of TaiBIF started in 2003 with TaiBIF (Taiwan Biodiversity Information Facility; the establishment of TaiBNET (Taiwan Biodiversity http://taibif.tw/) is the national portal website that inte- National Information Network; http://taibnet.sinica. grates Taiwan’s biodiversity information (Shao et al. edu.tw), providing “Taiwan species checklist” and the list of local taxonomic experts (Shao et al. 2013). Cur- *Correspondence: [email protected] rently in TaiCOL, the successor of TaiBNET, the fower- 2 Research Museum and Herbarium (HAST), Biodiversity Research Center, ing plants are arranged according to Cronquist (1968)’s Academia Sinica, Taipei 11529, Taiwan System of Classifcation (Shao et al. 2008), replacing A. Full list of author information is available at the end of the article © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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. Lin and Chung Bot Stud (2017) 58:52 Page 2 of 14 Engler’s Syllabus der Pfanzenfamilien that was adopted as a basis for migrating process. Te migration process in the Flora of Taiwan (FOT), 2nd edition (Huang 1994). applied a ‘data cleaning framework’ to improve our data Although Cronquist’s System was highly infuential and set quality through diagnosing, detecting, and correcting had been followed by several major foras such as Flora procedures. Te data cleaning procedure included three of North America (Reveal 1993) and Flora of Australia major stages: (1) error type defning, (2) error instance (Kanis et al. 1999), much of the content of Cronquist Sys- identifying, and (3) error correcting (Maletic and Mar- tem is not compatible to the current trend of the APG cus 2000). Furthermore, we followed the data cleaning classifcation. principles and methods suggested by Chapman (2005) Te Angiosperm Phylogeny Group (APG) classifcation when processing nomenclature data. In the initial stage of the orders and families of fowering plants, now in its of migration, instead of constructing a name-based data- fourth edition (APG IV), is a collaborative efort of plant base, a taxon-based database, which includes a unique molecular systematic community worldwide (Te Angi- taxonomy identifer (taxon ID) and several attributes osperm Phylogeny Group 1998, 2003, 2009, 2016), pro- such as family, genus, scientifc names and vernacu- viding the greatest stability and predictability regarding lar names, etc., was constructed. In order to reduce the biodiversity information of fowering plants (Mayr 1981; redundancy of the database and improve the data qual- Wearn et al. 2013). Although APG classifcation has not ity and integrity, we adopted relational database normali- been adopted ofcially in Taiwan, families circumscribed zation to parse the raw data table into a second normal by molecular phylogenetic studies and summarized by form schema. Trough the normalization process, poten- APG have been increasingly accepted by both academic tial errors such as duplicate entries, misplaced taxa, etc., (Hsu et al. 2011, 2016a, b; Wu et al. 2015) and citizen could be eliminated efciently. In the second stage, we scientists (e.g., Nature Campus http://nc.biodiv.tw/bbs/ automated a python script to cross-validate our data index.php). base with Missouri Botanical Garden’s Tropicos (http:// As an ofcial provider of biodiversity information of www.tropicos.org/) and International Plant Names the country, the classifcation systems followed by Tai- Index (IPNI, http://ipni.org), identifying unmatched or COL has deep and profound infuences. In an efort to unfound names for manual checking. In the third stage, consolidate the function and management of TaiBIF that three major possible errors or problems: (1) illegitimate shall result in stable and better services of the websites, or invalid names, (2) misspelled names, (3) diferent taxo- it is inevitable for TaiCOL to adopt classifcation systems nomic treatment, were corrected after cross-validation. that are constructed based on results of robust molecular We adopted Ruggiero et al. (2015) for the higher level phylogenetic analyses. Tis article outlines phylogenetic classifcation of seed plants (Subphylum Spermatophy- classifcation of families of the seed plants of Taiwan tina and above). For gymnosperms (Superclass Gymno- summarized based on Christenhusz et al. (2011)’s clas- spermae), Christenhusz et al. (2011)’s classifcation was sifcation of gymnosperms, APG IV, and subsequent followed, though caution was taken for the uncertainty studies. To facilitate the transition toward APG IV, we of the phylogenetic position of gnetophytes (Lu et al. also provide the spreadsheet of the classifcation schema 2014; Wang and Ran 2014). For angiosperms (Superclass for all seed plant genera that will be adopted by TaiCOL Angiospermae), major clades recognized as superorders (Additional fle 1: Appendix S1). Tis spreadsheet will be in Chase and Reveal (2009) and the classifcation of Te updated constantly and can be downloaded through Tai- Angiosperm Phylogeny Group (2016) was adopted, with COL. A brief note is provided for families of which cir- the exception of Boraginales in which Luebert et al. cumscription has been changed between the treatment of (2016)’s new familial classifcation was followed. For FOT and APG IV classifcation. orders and families of which vernacular names are lack- ing in the current literature of the fora of Taiwan, the Methods names proposed by Liu et al. (2015) were followed. Te database of seed plants of Taiwan was compiled from “a checklist of the vascular plants of Taiwan” of the Results and discussion Flora of Taiwan (Bouford et al. 2003), “Illustrated Guide Based on Christenhusz et al. (2011), APG IV (2016), and to Aquatic Plants of Taiwan” (Yang et al. 2001), Wu et al. Luebert et al. (2016)’s familial classifcation of Boragina- (2010) that summarized naturalized and invasive fora, les, the “Phylogenetic Classifcation of Seed Plants of Tai- subsequently published native (e.g., Hsu et al. 2011; Wu wan” is presented below. Of the four classes (I–IV), eight et al. 2015) and naturalized (e.g., Liang et al. 2011; Wang orders (A–H), and 12 families of gymnosperms in Chris- et al. 2016) species, and the fora of Tongsha (Pratas) tenhusz et al. (2011)’s
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