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The Use of DNA Characters in the Formal Naming of Species ∗ SUSANNE S

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The Use of DNA Characters in the Formal Naming of Species ∗ SUSANNE S Systematic Biology Advance Access published June 22, 2016 Points of View Syst. Biol. 0(0):1–11, 2016 © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: [email protected] DOI:10.1093/sysbio/syw032 A Return to Linnaeus’s Focus on Diagnosis, Not Description: The Use of DNA Characters in the Formal Naming of Species ∗ SUSANNE S. RENNER Systematic Botany and Mycology, University of Munich (LMU), Menzinger Street 67, 80638 Munich, Germany ∗ Correspondence to be sent to: Systematic Botany and Mycology, University of Munich (LMU), Menzinger Street 67, 80638 Munich, Germany; E-mail: [email protected] Received 12 September 2015; reviews returned 2 April 2016; accepted 5 April 2016 Downloaded from Associate Editor: Tiffani Williams Abstract.—Descriptions and diagnoses are alternative choices in all Codes of Nomenclature because Linnaeus relied on diagnoses, not descriptions, to name ca. 13,400 animals, plants, and fungi. A diagnosis names characters in which a new taxon differs from the most similar known taxon; a description mixes taxonomically informative and uninformative features, usually without indicating which is which. The first formal diagnoses of new taxa that included DNA-based characters http://sysbio.oxfordjournals.org/ came out in 2001, and by November 2015, at least 98 names of species of acoels, lichens, angiosperms, annelids, alveolates, arachnids, centipedes, turtles, fishes, butterflies, mollusks, nematodes, and pathogenic fungi have been published based on diagnostic mitochondrial, plastid, or nuclear DNA substitutions, indels, or rarely genetic distances, with or without additional morphological features. Authors have found diverse ways to specify the diagnostic traits (all published studies are here tabulated). While descriptions try to “cover” within-species variation, a goal rarely accomplished because of (i) the stochastic nature of specimen availability (thousands of species are known from single collections) and (ii) the subjective circumscription of species, the purpose of diagnoses was and is speedy identification. Linnaeus tried to achieve this by citing images, geographic occurrence, and previous literature. The renewed attention to sharp diagnosis now coincides with worldwide barcoding efforts, may speed up formal naming, and matches the increasing reliance on DNA for both classification and identification. I argue for DNA-based diagnoses of new species becoming a recommendation in all Codes, not just the bacterial code. [Codes of Nomenclature; description; diagnosis; DNA-based diagnosis; naming new species; nomenclature.] by Susanne Renner on August 3, 2016 “Descriptions cannot be made full enough Since about 2000, taxonomists have increasingly tried and accurate enough to satisfy later workers. to combine morphological and molecular data for Each generation of taxonomists must see the detecting and delimiting species (reviewed in Wheeler actual specimens used by earlier generations, 2008; Begerow et al. 2010; Hibbett and Taylor 2013; and I think the tendency now is, or should Vences et al. 2013), and since 2003, DNA barcoding has be, to make descriptions short, but of course become the method of choice for reliable identification, explicit and carefully calculated, and to make at least for insects, certain fungi, tropical trees, and many specimens widely available.” aquatic organisms (Hebert et al. 2003; Koljalg et al. 2013; Hausmann et al. 2013; Kress et al. 2015). Surprisingly, P.J. Darlington, Jr., 1971, p. 146 however, DNA characters have rarely been used in the formal description of species (Cook et al. 2010). Of 310 The naming of organisms following standardized barcoding publications surveyed by Kress et al. (2015) conventions is the basis for linking new information that led to the discovery of new species, only one (Félix to existing knowledge. It is also the basis for et al. 2014; Table 1) used DNA traits in species protologs. biological classification, effective communication, and Todate, two papers have discussed DNA-based formal extrapolation of findings about organisms. The mere diagnoses (Cook et al. 2010; Tripp and Lendemer 2014). accession numbers of DNA sequences (or other strings Both overlooked that the practice began 15 years ago of numbers lacking an agreed system of the numbers’ (Westheide and Hass-Cordes 2001), and they either innate significance) do not permit extrapolation of focused on a hypothetical example (Cook et al. 2010) information about morphological traits, biogeographic or examples from 2012 and 2013 (Tripp and Lendemer ranges, or sharing of published knowledge across 2014). Tripp and Lendemer (2012) also raised a potential disciplines, all of which is possible with a widely used problem with one type of DNA diagnosis, namely naming convention. Most researchers are using the genetic distances, which I take up in the “Discussion” conventions of the Linnaean system, with the fixed section. No previous paper has surveyed the conceptual starting points being Linnaeus’s treatments of plants and and factual history of DNA-based formal naming, and animals (1753, 1758; Persoon and Fries for certain fungi the absence of a review of how taxonomists have and the names of lichens). 1 [17:49 8/6/2016 Sysbio-syw032.tex] Page: 1 1–11 [17:49 8/6/2016 Sysbio-syw032.tex] 2 TABLE 1. All studies published so far that have included DNA-based diagnoses in species protologs, that is, for the formal diagnosis of type material Taxon Number and geographic Type of molecular Morphological Deposition of Deposition of References region of new species diagnosis description type sequences or (yes/no); material alignment(s) Morphological (not always diagnosis the (yes/no) specimen from which DNA was isolated) Acoelomorpha 9 species of Specified Yes Yes Type material Sequences in Meyer-Wachsmuth (Platyhelminthes) Nemertinoides, substitutions in in a public GenBank et al. 2014 Nemertodermatida, worldwide in marine LSU and SSU collection Nemertodermatidae mesopsammon rRNA and histone 3 Alveolata 5 species of Alexandrium “The combined Yes Yes Holo- and Sequences in John et al. 2014 Dinophyceae nucleotide isotypes on GenBank sequences of the SEM stubs holotype strain …. and in The complete list formol in SYSTEMATIC BIOLOGY of diagnostic Senckenberg D1-D2 LSU, ITS herbarium (Iternal (FR) Transcribed Spacer)/5.8S and SSU Gen-Bank sequences which can be used as a genetic type for this species are reported in Supplementary Material.” Similarly for the other species Angiospermae 1 species of Brunfelsia Specified Yes No Type material Sequences in Filipowicz et al. Solanaceae from Brazil substitutions in in various GenBank 2012 the plastid ndhF herbaria gene and in nuclear ITS Angiospermae 3 species of Buxus from Specified Yes Yes Type material Sequences in González Gutiérrez Buxaceae Cuba substitutions in in various GenBank et al. 2013 the plastid matK herbaria gene and in coding region of trnL spacer Angiospermae 1 species of Rochefortia Specified Yes Yes Type material Sequences in Irimia and Ehretiaceae from Lesser Antilles substitutions in in various GenBank Gottschling 2016 the nuclear ITS1 herbaria region Page: 2 1–11 (continued) Downloaded from from Downloaded http://sysbio.oxfordjournals.org/ by Susanne Renner on August 3, 2016 3, August on Renner Susanne by [17:49 8/6/2016 Sysbio-syw032.tex] TABLE 1. Continued Annelida, Syllidae 1 species of Petitia Specified Yes No Holotype Several nuclear ITS Westheide and Bristle worms Seychelles substitutions in “used up,” seqs. in GenBank Hass-Cordes 2016 nuclear ITS and 8 three 2001 diagnositic RFLP syntypes in (Restriction Senckenberg Fragment Length Museum Polymorphism) fragments with specified primers Annelida, 1 species of Galeolaria, Specified Yes No Type material Sequences in Halt et al. 2009 Serpulidae Tube Australia substitutions in (Description in public GenBank worms mtDNA is called collection cytochrome b gene diagnosis) and nuclear ITS Arachnida, 2 species of Metasiro, Specified Yes No Type material Sequences in Clouse and Opiliones, South Carolina, USA substitutions in mt in a public GenBank Wheeler 2014 Cyphophthalmi: COI gene collection Neogoveidae Arthropoda, 1 species of Specified Yes Yes Type material Sequences in Edgecombe and Chilipoda, Craterostigmus,New substitutions in in a public GenBank Giribet 2008 Craterostigmidae Zealand nuclear 18S and collections Centipedes 28S rRNA, (including mitochondrial DNA (mt) 16S rRNA, voucher and the from protein-encoding holotype) cytochrome c POINT OF VIEW oxidase subunit I (COI) Ascomycota, 5 species of Rhizoplaca Unspecified No! No Type material Sequences in Leavitt et al. 2013 Lecanoraceae substitutions in in public GenBank Lichens nuclear ITS collection “Rhizoplaca and polymorpha MycoBank consists of specimens recovered within ‘clade IVc’ in Leavitt et al. (2011a), which is supported as a lineage distinct from all other populations according to coalescent-based genetic analysis of multiple genetic loci.” Ascomycota, 1 species of Lepraria Specified Yes No Type material Sequences in Lendemer 2011 Lecanoraceae substitutions in in public GenBank Lichens nuclear ITS (in collections Latin) Ascomycota, 1 species of Parmelia Specified No No Type material Sequences in Molina et al. 2011 Parmeliaceae Europe substitutions in a in public GenBank 3 Page: 3 1–11 Lichens group I intron and collections nuclear ITS (in Latin) Downloaded from from Downloaded http://sysbio.oxfordjournals.org/ by Susanne Renner
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