How to describe a cryptic species? Practical challenges of molecular taxonomy

Abstract

BackgroundMolecular methods of species delineation are rapidly developing and widely considered as fast and efficient means to discover species and face the 'taxonomic impediment’ in times of biodiversity crisis. So far, however, this form of DNA taxonomy frequently remains incomplete, lacking the final step of formal species description, thus enhancing rather than reducing impediments in taxonomy. DNA sequence information contributes valuable diagnostic characters and –at least for cryptic species – could even serve as the backbone of a taxonomic description. To this end solutions for a number of practical problems must be found, including a way in which molecular data can be presented to fulfill the formal requirements every description must meet. Multi-gene barcoding and a combined molecular species delineation approach recently revealed a radiation of at least 12 more or less cryptic species in the marine meiofaunal slug genus Pontohedyle (Acochlidia, Heterobranchia). All identified candidate species are well delimited by a consensus across different methods based on mitochondrial and nuclear markers.ResultsThe detailed microanatomical redescription of Pontohedyle verrucosa provided in the present paper does not reveal reliable characters for diagnosing even the two major clades identified within the genus on molecular data. We thus characterize three previously valid Pontohedyle species based on four genetic markers (mitochondrial cytochrome c oxidase subunit I, 16S rRNA, nuclear 28S and 18S rRNA) and formally describe nine cryptic new species (P. kepii sp. nov., P. joni sp. nov., P. neridae sp. nov., P. liliae sp. nov., P. wiggi sp. nov., P. wenzli sp. nov., P. peteryalli sp. nov., P. martynovi sp. nov., P. yurihookeri sp. nov.) applying molecular taxonomy, based on diagnostic nucleotides in DNA sequences of the four markers. Due to the minute size of the animals, entire specimens were used for extraction, consequently the holotype is a voucher of extracted DNA ('DNA-type’). We used the Character Attribute Organization System (CAOS) to determine diagnostic nucleotides, explore the dependence on input data and data processing, and aim for maximum traceability in our diagnoses for future research. Challenges, pitfalls and necessary considerations for applied DNA taxonomy are critically evaluated.ConclusionsTo describe cryptic species traditional lines of evidence in taxonomy need to be modified. DNA sequence information, for example, could even serve as the backbone of a taxonomic description. The present contribution demonstrates that few adaptations are needed to integrate into traditional taxonomy novel diagnoses based on molecular data. The taxonomic community is encouraged to join the discussion and develop a quality standard for molecular taxonomy, ideally in the form of an automated final step in molecular species delineation procedures.

Pseudamnicola Paulucci, 1878 (Caenogastropoda: Truncatelloidea) from the Aegean Islands: a long or short story?

“…Reliability of species delimitated by GMYC has also been discussed in the literature (e.g. Lohse 2009;Papadopoulou et al 2009b;Jörger et al 2012;Jörger and Schrödl 2013;Sauer and Hausdorf 2012), also with substantial criticism, and the method was further developed ). However, in our work, the GMYC results were confirmed by ABGD analysis.…”

“…According to the phylogenetic analysis and p-distance values for COI, the studied Pseudamnicola populations can be assigned to 16 clades, most of which are probably distinct species, according to the GMYC and ABGD analysis. The GMYC procedure has been applied in several previous studies Papadopoulou et al 2009a, b;Adolfsson et al 2010;Pagès et al 2010;Powell et al 2011;Vuataz et al 2011), including some on molluscs (Nekola et al 2009;Lorion et al 2010;Jörger et al 2012;Jörger and Schrödl 2013). Reliability of species delimitated by GMYC has also been discussed in the literature (e.g.…”

Life in the spray zone – overlooked diversity in West African torrent-frogs (Anura, Odontobatrachidae, Odontobatrachus)

“…In contrast to studies that predominantly rely on genetics in diagnoses of new species (Jörger and Schrödl 2013;Satler et al 2013;Petzold et al 2014), no taxonomic actions were conducted in the case of the Odontobatrachus natator-complex. Phylogeographic insights formed the basis for our assessment of morphological characters which led to the formal description of four new species with distinguishing morphological characters.…”

Nuclear and Mitochondrial Gene Data Support Recent Radiation within the Sea Spider Species Complex Pallenopsis patagonica

“…For all other clades, only a partial match between the different methods was observed. In such cases, Kekkonen and Hebert (2014) suggest to test whether (a) the resolved clades are monophyletic, (b) individuals are supported by diagnostic characters (nucleotide substitutions, insertions or deletions, see also Jörger and Schrödl, 2013), or (c) specimens of different clades occur in sympatry. All three criteria are based on species concepts.…”