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.

Salmo macrostigma(Teleostei, Salmonidae): Nothing more than a brown trout (S. trutta) lineage?

“…Phylogenomic methods to delimit taxon boundaries are challenging but have greatly improved in the past few years. Such methods can distinguish between structure associated with intraspecific variation and introgression from that resulting from speciation (Baumsteiger et al ., ; Mutanen et al ., ; Wagner et al ., ; Zarza et al ., ) and sometimes allow for a deep taxonomic reassessment of evolutionary units in challenging taxa (Papakostas et al ., ), or even reconciliation of morphological and molecular taxonomies in integrative studies (Dejaco et al ., ; Morard et al ., ). The Salmo genus is certainly one interesting case to consider because large scale integrative taxonomic studies are currently lacking.…”

DNA Barcoding studies on Thrips in India: Cryptic species and Species complexes

“…These MOTUs picking methods implement different strategies and either underestimate or overestimate the taxa numbers. It is impossible to favor one method over another, and it is suggested to apply a wide range of species delimitation methods and choose the congruent results 51, 52 . Hence, we applied these different methods to compare the MOTUs number with our morphospecies and to verify the presence of cryptic species.…”

“…MOTU level-2 is the intermediate level most likely represents the level of biological species. MOTU level-3 is the lowest level corresponds to the basegroup and represents the genetic variability potentially observable at the level of a single individual 51 . This nomenclature of these MOTUs will set up a strong framework to study whether these MOTUs will gradually differentiate into a set of metapopulations into distinct morphospecies.…”

Range limits in sympatric cryptic species: a case study in Tetramorium pavement ants (Hymenoptera: Formicidae) across a biogeographical boundary

“…To overcome this challenge, at least partially, sampling should extend deep into the expected ranges on both sides of the biogeographical boundary, as well as through a diversity of environments spanning the habitat niche of the species of interest. Traditionally, species have been identified using morphological traits, but such characters may undergo convergent evolution under similar selective pressure, leading to underestimating the actual number of species and failing to identify cryptic species (Yang & Rannala, 2010;Morard et al, 2016). Cordes et al, 2017).…”