Looking at the Nudibranch Family Myrrhinidae (Gastropoda, Heterobranchia) from a Mitochondrial '2D Folding Structure' Point of View.

Giulia Furfaro,Paolo Mariottini

doi:10.3390/life11060583

Abstract

Integrative taxonomy is an evolving field of multidisciplinary studies often utilised to elucidate phylogenetic reconstructions that were poorly understood in the past. The systematics of many taxa have been resolved by combining data from different research approaches, i.e., molecular, ecological, behavioural, morphological and chemical. Regarding molecular analysis, there is currently a search for new genetic markers that could be diagnostic at different taxonomic levels and that can be added to the canonical ones. In marine Heterobranchia, the most widely used mitochondrial markers, COI and 16S, are usually analysed by comparing the primary sequence. The 16S rRNA molecule can be folded into a 2D secondary structure that has been poorly exploited in the past study of heterobranchs, despite 2D molecular analyses being sources of possible diagnostic characters. Comparison of the results from the phylogenetic analyses of a concatenated (the nuclear H3 and the mitochondrial COI and 16S markers) dataset (including 30 species belonging to eight accepted genera) and from the 2D folding structure analyses of the 16S rRNA from the type species of the genera investigated demonstrated the diagnostic power of this RNA molecule to reveal the systematics of four genera belonging to the family Myrrhinidae (Gastropoda, Heterobranchia). The “molecular morphological” approach to the 16S rRNA revealed to be a powerful tool to delimit at both species and genus taxonomic levels and to be a useful way of recovering information that is usually lost in phylogenetic analyses. While the validity of the genera Godiva, Hermissenda and Phyllodesmium are confirmed, a new genus is necessary and introduced for Dondice banyulensis, Nemesis gen. nov. and the monospecific genus Nanuca is here synonymised with Dondice, with Nanuca sebastiani transferred into Dondice as Dondice sebastiani comb. nov.

Highlights

The use of molecular techniques to investigate the evolutionary history of animal groups and to define monophyletic lineages expanded exponentially in the last few decades, becoming one of the essential steps to accomplish a good integrative taxonomy
We have extended the approach of 2D RNA-barcoding, investigating systematics at a taxonomic level higher than the species level
Results from Bayesian and Maximum Likelihood analyses yielded congruent topologies (Figure 1) both grouping all the Phyllodesmium species in a single and strongly supported (BI = 1; ML = 100) monophyletic clade, sister to Godiva quadricolor (BI = 1; ML = 100) with a low statistical support (BI = 75; ML = 45). These two clades are sister to another monophyletic group (BI = 1; ML = 81), which includes one monophyletic clade (BI = 1; ML = 100) that grouped species such as Dondice occidentalis and D. parguerensis (BI = 0.99; ML = 100) and D. trainitoi (BI = 1; ML = 97) sister to Nanuca sebastiani (BI = 1; ML = 100), and another monophyletic clade, which includes all the species belonging to the genus Hermissenda (BI = 1; ML = 100)

Summary

Introduction

The use of molecular techniques to investigate the evolutionary history of animal groups and to define monophyletic lineages expanded exponentially in the last few decades, becoming one of the essential steps to accomplish a good integrative taxonomy. Animal mitochondrial DNA is characterised by a high copy number, largely maternal inheritance, lack of recombination, and displays a higher mutation rate than the nuclear DNA It is affected by some constraints including retention of ancestral polymorphism, male-biased gene flow, selection on any mtDNA nucleotide, introgression following hybridisation and paralogy resulting from transfer of mtDNA gene copies to the nucleus [13,14,15,16]. To avoid these pitfalls, nuclear markers are usually added to the molecular analyses. This approach has been applied to marine Heterobranchia (Mollusca, Gastropoda) whose evolutionary history, when studied at family level, is reconstructed using mainly three molecular markers, the two mitochondrial genes, part of Cytochrome oxidase subunit

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Conclusion