title: Nomenclature for the Nameless: A Proposal for an Integrative Molecular Taxonomy of Cryptic Diversity Exemplified by Planktonic Foraminifera.
abstract: Investigations of biodiversity, biogeography, and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morphotaxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many groups of organisms, morphologically defined species often disguise considerable genetic diversity, which may be indicative of the existence of cryptic species. The diversity hidden by morphological species can be disentangled through genetic surveys, which also provide access to data on the ecological distribution of genetically circumscribed units. These units can be identified by unique DNA sequence motifs and allow studies of evolutionary and ecological processes at different levels of divergence. However, the nomenclature of genetically circumscribed units within morphological species is not regulated and lacks stability. This represents a major obstacle to efforts to synthesize and communicate data on genetic diversity for multiple stakeholders. We have been confronted with such an obstacle in our work on planktonic foraminifera, where the stakeholder community is particularly diverse, involving geochemists, paleoceanographers, paleontologists, and biologists, and the lack of stable nomenclature beyond the level of formal morphospecies prevents effective transfer of knowledge. To circumvent this problem, we have designed a stable, reproducible, and flexible nomenclature system for genetically circumscribed units, analogous to the principles of a formal nomenclature system. Our system is based on the definition of unique DNA sequence motifs collocated within an individual, their typification (in analogy with holotypes), utilization of their hierarchical phylogenetic structure to define levels of divergence below that of the morphospecies, and a set of nomenclature rules assuring stability. The resulting molecular operational taxonomic units remain outside the domain of current nomenclature codes, but are linked to formal morphospecies as regulated by the codes. Subsequently, we show how this system can be applied to classify genetically defined units using the SSU rDNA marker in planktonic foraminifera and we highlight its potential use for other groups of organisms where similarly high levels of connectivity between molecular and formal taxonomies can be achieved.
authors.affiliation: MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany, rmorard@marum.de.
authors.forename: Raphaël
authors.initials: R
authors.lastname: Morard
authors.affiliation: Université de Lyon; UMR5023 Ecologie des Hydrosystémes Naturels et Anthropisés; Universiteì Lyon 1; ENTPE; CNRS; 6 rue Raphaël Dubois, 69622 Villeurbanne, France.
authors.forename: Gilles
authors.initials: G
authors.lastname: Escarguel
authors.affiliation: MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany, Japan Agency for Marine Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Kanagawa, Japan.
authors.forename: Agnes K M
authors.initials: AK
authors.lastname: Weiner
authors.affiliation: Université de Reims-Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Campus Moulin de la Housse, Batiment 18, 51100 REIMS, France.
authors.forename: Aurore
authors.initials: A
authors.lastname: André
authors.affiliation: Université de Lyon; UMR5023 Ecologie des Hydrosystémes Naturels et Anthropisés; Universiteì Lyon 1; ENTPE; CNRS; 6 rue Raphaël Dubois, 69622 Villeurbanne, France, Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France.
authors.forename: Christophe J
authors.initials: CJ
authors.lastname: Douady
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Wade
authors.affiliation: School of GeoSciences, University of Edinburgh, Edinburgh EH9 3JW, UK, School of Geography and GeoSciences, University of St Andrews, Fife KY16 9AL, UK.
authors.forename: Kate F
authors.initials: KF
authors.lastname: Darling
authors.affiliation: Department of Biology, Shinshu University, Asahi3-1-1, Matsumoto, Nagano 390-8621, Japan.
authors.forename: Yurika
authors.initials: Y
authors.lastname: Ujiié
authors.affiliation: Department of Biology, Gilmer Hall, University of Virginia, 485 McCormick Road, Charlottesville, VA 22904, USA.
authors.forename: Heidi A
authors.initials: HA
authors.lastname: Seears
authors.affiliation: Univ Lyon, Université Lyon 1, ENS de Lyon, CNRS, UMR 5276 LGL-TPE, F-69622 Villeurbanne, France;
authors.forename: Frédéric
authors.initials: F
authors.lastname: Quillévéré
authors.affiliation: Centre Européen de Recherche et d'Enseignement de Géosciences de l'Environnement, Centre National de la Recherche Scientifique, et Aix-Marseille Université, Aix-en-Provence, France.
authors.forename: Thibault
authors.initials: T
authors.lastname: de Garidel-Thoron
authors.affiliation: Centre National de la Recherche Scientifique, UMR 7144, EPEP, Station Biologique de Roscoff, 29680 Roscoff, France, and Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, 29680 Roscoff, France.
authors.forename: Colomban
authors.initials: C
authors.lastname: de Vargas
authors.affiliation: MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany.
authors.forename: Michal
authors.initials: M
authors.lastname: Kucera
mesh_terms: D044822:Biodiversity; D002965:Classification / Q000379:methods*; D004275:DNA, Ribosomal; D056908:Foraminifera / Q000145:classification*; D014644:Genetic Variation; D010802:Phylogeny; D010933:Plankton / Q000145:classification
chemical_list: D004275:DNA, Ribosomal
keywords: Cryptic species; MOTUs; genetic diversity; molecular nomenclature; planktonic foraminifera