Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs

Abstract

BackgroundMany marine meiofaunal species are reported to have wide distributions, which creates a paradox considering their hypothesized low dispersal abilities. Correlated with this paradox is an especially high taxonomic deficit for meiofauna, partly related to a lower taxonomic effort and partly to a high number of putative cryptic species. Molecular-based species delineation and barcoding approaches have been advocated for meiofaunal biodiversity assessments to speed up description processes and uncover cryptic lineages. However, these approaches show sensitivity to sampling coverage (taxonomic and geographic) and the success rate has never been explored on mesopsammic Mollusca.ResultsWe collected the meiofaunal sea-slug Pontohedyle (Acochlidia, Heterobranchia) from 28 localities worldwide. With a traditional morphological approach, all specimens fall into two morphospecies. However, with a multi-marker genetic approach, we reveal multiple lineages that are reciprocally monophyletic on single and concatenated gene trees in phylogenetic analyses. These lineages are largely concordant with geographical and oceanographic parameters, leading to our primary species hypothesis (PSH). In parallel, we apply four independent methods of molecular based species delineation: General Mixed Yule Coalescent model (GMYC), statistical parsimony, Bayesian Species Delineation (BPP) and Automatic Barcode Gap Discovery (ABGD). The secondary species hypothesis (SSH) is gained by relying only on uncontradicted results of the different approaches (‘minimum consensus approach’), resulting in the discovery of a radiation of (at least) 12 mainly cryptic species, 9 of them new to science, some sympatric and some allopatric with respect to ocean boundaries. However, the meiofaunal paradox still persists in some Pontohedyle species identified here with wide coastal and trans-archipelago distributions.ConclusionsOur study confirms extensive, morphologically cryptic diversity among meiofauna and accentuates the taxonomic deficit that characterizes meiofauna research. We observe for Pontohedyle slugs a high degree of morphological simplicity and uniformity, which we expect might be a general rule for meiofauna. To tackle cryptic diversity in little explored and hard-to-sample invertebrate taxa, at present, a combined approach seems most promising, such as multi-marker-barcoding (i.e., molecular systematics using mitochondrial and nuclear markers and the criterion of reciprocal monophyly) combined with a minimum consensus approach across independent methods of molecular species delineation to define candidate species.

Persistent Gaps of Knowledge for Naming and Distinguishing Multiple Species of Crown-of-Thorns-Seastar in the Acanthaster planci Species Complex

“…Already somewhat foreshadowed by certain authors (e.g., [43]), they [44] also introduced the Barcode Identification Number (BIN) system as a third step. A website with a distinct BIN number is provided for clusters of sequences, where sophisticated statistical analyses (see [45] for a comparative evaluation) have provided evidence for intraspecific continuity versus interspecific discontinuity (the so-called barcoding gap, [46]). Meanwhile, the BIN-framework is well established and has already become an international standard for re-identification of still unnamed or undetermined species (e.g., [47]).…”

DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests

“…Lineages showing sequence divergence, often termed molecular operational taxonomic units (MOTUs) (Blaxter et al 2005), have been discriminated by analyzing sequence variation using distance analysis (Schloss and Handelsman 2005), neighborjoining clustering (Saitou and Nei 1987), phylogenetic trees (Zhang et al 2013), Bayesian inference (Yang and Rannala 1997), coalescence-based approach (Pons et al 2006;Fujisawa and Barraclough 2013), barcode-gap analysis (Puillandre et al 2012), and BINs (Ratnasingham and Hebert 2013). However, there is a growing trend to integrate multiple methods (Ashfaq et al 2015;Kekkonen et al 2015;Blagoev et al 2016) and multiple markers (Jörger et al 2012;Mrinalini et al 2015) to assess MOTU diversity. The results from such analyses have frequently been helpful in resolving taxonomic problems and in estimating species richness and abundance (Unterseher et al 2011;Mutanen et al 2013;Stahlhut et al 2013).…”

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

“…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.…”

“…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.…”