Tripp & Lendemer • Molecular diagnoses
TAXON 63 (5) • October 2014: 969–971
POINT OF VIEW
Sleepless nights: When you can’t find anything to use but molecules to describe new taxa Erin A. Tripp1 & James C. Lendemer2 1 Museum of Natural History and Department of Ecology & Evolutionary Biology, N122 Ramaley Hall, University of Colorado, Boulder, Colorado 80309-0350, U.S.A. 2 Institute of Systematic Botany, The New York Botanical Garden, Bronx, New York 10458-5126, U.S.A. Authors for correspondence: Erin A. Tripp,
[email protected]; James C. Lendemer,
[email protected] DOI http://dx.doi.org/10.12705/635.1 Abstract A set of guidelines is proposed as a standard for authors who describe new taxa and affect other taxonomic revisions based solely on molecular characters. Keywords characters; code; delimitation; descriptions; diagnosis; guidelines; morphological; molecular; new species; nomenclature; recommendations; taxonomy; traits
INTRODUCTION Since the dawn of the molecular revolution, studies have increasingly used DNA sequence data for myriad applications including systematics and taxonomy, population genetics, and numerous other areas of ecology and evolutionary biology (Tripp & Hoagland, 2013). The vast majority of studies in systematic biology that have used DNA sequence data have done so in combination with data from other sources (e.g., morphology, anatomy, ecology, biochemistry, behavior) as a means of answering research questions via reciprocal illumination (Hennig, 1966). Among the types of data used by botanists and mycologists to date, morphology, anatomy, and to a lesser degree chemistry, have been paramount to taxonomic innovations such as the description of new species. Only recently have researchers begun to compose descriptions and diagnoses of new taxa based solely on molecular features. For example, Filipowicz & al. (2012) diagnosed the South American species Brunfelsia plowmaniana Filipowicz & M.Nee using data from the ndhF region; Leavitt & al. (2013) described new species in the lichen genus Rhizoplaca Zoph using characters derived from the nuclear internal transcribed spacer (ITS); and Shaw & al. (2010) re-circumscribed the bryophyte family Ambuchananiaceae Seppelt & H.A.Crum using data from rps4. While reviewing this literature, it became clear to us that the International Code of Nomenclature (ICN, McNeill & al., 2012) lacks adequate language regarding how new taxa based only on molecular characters should be validly described or diagnosed. We recognized this as a problem in Tripp & Lendemer (2012) in which we called into question the effective diagnosis and description of two fungal names introduced for taxa defined solely by molecular characters.
Although there exists a growing body of literature pertaining to the description of poorly differentiated taxa (referred to by many as “cryptic species”), we are at present unaware of any publication relevant to taxa covered by the ICN to recommend a comprehensive set of standard best practices for innovations based only on molecular data (but see excellent discussions in Fujita & al., 2012 and Jörger & Schrödl, 2013). As such, we developed the guidelines presented below. Our intention is that these guidelines serve as a starting point, recognizing that future authors may offer useful additions to or modifications of this list. Finally, we hope that these guidelines serve to motivate much needed discussions on potential additions to the Code regarding this topic at future International Botanical Congresses.
PROPOSED GUIDELINES (1) The diagnoses and descriptions of taxa based solely on molecular characters should be undertaken only as a last resort, i.e., after detailed study has shown that non-molecular characters are unavailable or uninformative. (2) The diagnoses and descriptions of taxa based solely on molecular characters should: (a) include characters from multiple, preferably unlinked, loci; (b) include divergence calculation/s (based on one or more optimality criteria) from the closest known relative/s; and (c) still include a standard (e.g., morphological) description appropriate to the taxonomic group (in addition to a required molecular description). (3) Unique SNPs (single nucleotide polymorphisms), indels, or other categories of phylogenetically informative mutations should be specified in the diagnosis or description and: (a) preferably not be included within ambiguously aligned
Received: 3 Aug 2014 | returned for revision: 7 Aug 2014 | revision received: 11 Aug 2014 | accepted: 12 Aug 2014 | published online ahead of inclusion in print and online issues: 22 Aug 2014 || © International Association for Plant Taxonomy (IAPT) 2014
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regions; (b) be included in a differential diagnosis explaining in very specific terms how the new taxon differs from the closest known relative/s; (c) be indicated by reference to specific base positions in the nucleotide alignment used in circumscribing the new entity; (d) be translated to amino acids (if from coding regions) to ensure sites are not under strong selection and thus less likely to reflect molecular convergence; (e) secondary structure (when applicable) should be examined to determine whether phylogenetically informative mutations reflect compensatory substitutions, which would impact divergence calculations in 2b. (4) For taxa at the rank of species and below, the type specimen and additional representatives of the newly described entity, together with the type or, at minimum, topotypes of the closest known relative/s, should be included in the molecular sampling used for the study (see 7a and 7b below). (5) New taxa based solely on molecular characters should: (a) be recovered and strongly supported by multiple support criteria and methods of inference; (b) utilize genome-scale (i.e., multi-locus) data where available, together with appropriate methods of inference such as coalescence; and (c) reach or exceed an appropriate sequence divergence threshold based on available literature (e.g., Begerow & al., 2010 and Nilsson & al., 2008 for certain groups of fungi). (6) Studies in which new taxa based solely on molecular characters are introduced should: (a) include tests for possible rejection of monophyly of the newly proposed taxon/taxa (e.g., negative or reverse constraint topologies coupled with post hoc heuristic searches for best or most likely trees given the constraint), for individuals who feel monophyly is an important criterion for taxon delimitation; (b) include a taxonomic key based on molecular characters, preferably one in which various parts of the alignment (coding regions, etc.) and regions in which the phylogenetically informative mutations occur are clearly annotated; and (c) be published in the same publication as where the dataset and analyses used to delineate the new taxon/taxa are presented. (7) Taxon sampling for datasets used in studies that involve the description of new taxa based solely on molecular characters should: (a) include numerous (preferably > 10) sequenced vouchers of any new taxa, or a greater number appropriate to overcome sequencing error rates on the instrumentation used; (b) preferably include at least 15 of the closest relatives of the new taxon/taxa; (c) molecular sampling of the new taxa and their closest relatives should parallel or exceed the level of sampling undertaken by researchers when describing new taxa based on non-molecular characters; and (d) sampling within the new taxon and as well as within outgroups (the closest relatives of the new taxon) should be broad enough to encompass the phylogenetic, geographical, and ecological diversity within each taxon; natural variation present within a given taxon must be accounted for in the molecular diagnosis or description. (8) Prior to the date of effective publication, for any study in which new taxa based solely on molecular characters are introduced, the following materials should be placed in a public data repository where they are available for immediate use to anyone free of charge (i.e., materials should be open access): 970
(a) unedited, raw sequence reads (i.e., chromatograms with original base calls and ambiguities); (b) edited sequences; and (c) all alignments used in the study, including matrices with ambiguously aligned regions that were excluded from subsequent analysis. (9) Aliquots of DNA extractions produced from vouchers of the new taxon as well as those of other relatives used in the study should be deposited in a permanent DNA repository such as those available at K, NY, or US (or other suitable facilities). The repository, as well as any unique identifiers associated with the data, should be clearly indicated in the manuscript text. (10) The typification, effective diagnosis or description, and valid publication of the names of taxa (including those of hybrid origin) based solely on molecular characters must follow all Articles and Appendices included in the appropriate nomenclatural code (i.e., the names of algae, plants and fungi must comply with the International Code of Nomenclature).
ACKNOWLEDGMENTS We thank Dr. Joachim Kadereit, Dr. Bernard Goffinet, Dr. Steven Leavitt, Dr. Gerry Moore, Dr. Stacey D. Smith, and Evan Thomas for comments that improved this manuscript. This research was supported by NSF DEB-1354963 and NSF DEB-1355138 (to Erin Tripp & Lucinda McDade) as well as by NSF DEB-1145511 (to James Lendemer & Richard Harris). Finally, we thank an anonymous black bear (Roosevelt National Forest) whose destructive influences on the first author’s home prompted very late night development of the topics discussed herein.
LITERATURE CITED Begerow, D., Nilsson, H., Unterseher, M. & Maier, W. 2010. Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Appl. Microbiol. Biotechnol. 87: 99–108. http://dx.doi.org/10.1007/s00253-010-2585-4 Filipowicz, N., Nee, M.H. & Renner, S.S. 2012. Description and molecular diagnosis of a new species of Brunfelsia (Solanaceae) from the Bolivian and Argentinean Andes. Phytokeys 10: 83–94. http://dx.doi.org/10.3897/phytokeys.10.2558 Fujita, M.K., Leaché, A.D., Burbrink, F.T., McGuire, J.A. & Moritz, C. 2012. Coalescent-based species delimitation in an integrative taxonomy. Trends Ecol. Evol. 27: 480–488. http://dx.doi.org/10.1016/j.tree.2012.04.012 Hennig, W. 1966. Phylogenetic systematics, English ed., trans. by D.D. Davis & R. Zangerl. Urbana-Champaign: University of Illinois Press. Jörger, K. & Schrödl, M. 2013. How to describe cryptic species? Practical challenges of molecular taxonomy. Frontiers Zool. 10: 59. http://dx.doi.org/10.1186/1742-9994-10-59 Leavitt, S.D., Fernández-Mendozá, F., Pérez-Ortega, S., Sohrabi, M., Divakar, P.K., Lumbsch, H.T. & St. Clair, L.L. 2013. DNA barcode identification of lichen-forming fungal species in the Rhizocarpon melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species. MycoKeys 7: 1–22. http://dx.doi.org/10.3897/mycokeys.7.4508 McNeill, J., Barrie, F.R., Buck, W.R., Demoulin, V., Greuter, W., Hawksworth, D.L., Herendeen, P.S., Knapp, S., Marhold, K., Prado, J., Prud’homme van Reine, W.F., Smith, G.F.,
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Wiersema, J.G. & Turland, N.J. 2012. International Code of Nomenclature for algae, fungi, and plants (Melbourne Code). Regnum Vegetabile 154. Königstein: Koeltz Scientific Books. http://www.iapt-taxon.org/nomen/main.php Nilsson, R.H., Kristiansson, E., Ryberg, M., Hallenberg, N. & Larsson, K.H. 2008. Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol. Bioinform. Online 4: 193–201. http://dx.doi.org/10.4137/EBO.S653 Shaw, A.J., Cox, C.J., Buck, W.R., Devos, N., Buchanan, A.M., Cave, L., Seppelt, R., Shaw, B., Larraín, J., Andrus, R., Greilhuber J. & Temsch, E.M. 2010. Erratum [Newly resolved relationships
in an early land plant lineage: Bryophyta class Sphagnopsida (pear mosses)]. Amer. J. Bot. 97. http://www.amjbot.org/content/97/10/0.full Tripp, E.A. & Hoagland, K.E. 2013. Typifying an era in biology through synthesis of biodiversity information: Achievements and impediments. Taxon 62: 899–911. http://dx.doi.org/10.12705/625.14 Tripp, E.A. & Lendemer, J.C. 2012. (4–5) Request for binding decisions on the descriptive statements associated with Mortierella sigyensis (fungi: Mortierellaceae) and Piromyces cryptodigmaticus (fungi: Neocallimastigaceae). Taxon 61: 886–888. http://www.ingentaconnect.com/content/iapt/tax/2012/00000061/ 00000004/art00022
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