Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes

Abstract

BackgroundThe identification of vast numbers of unknown organisms using DNA sequences becomes more and more important in ecological and biodiversity studies. In this context, a fragment of the mitochondrial cytochrome c oxidase I (COI) gene has been proposed as standard DNA barcoding marker for the identification of organisms. Limitations of the COI barcoding approach can arise from its single-locus identification system, the effect of introgression events, incomplete lineage sorting, numts, heteroplasmy and maternal inheritance of intracellular endosymbionts. Consequently, the analysis of a supplementary nuclear marker system could be advantageous.ResultsWe tested the effectiveness of the COI barcoding region and of three nuclear ribosomal expansion segments in discriminating ground beetles of Central Europe, a diverse and well-studied invertebrate taxon. As nuclear markers we determined the 18S rDNA: V4, 18S rDNA: V7 and 28S rDNA: D3 expansion segments for 344 specimens of 75 species. Seventy-three species (97%) of the analysed species could be accurately identified using COI, while the combined approach of all three nuclear markers provided resolution among 71 (95%) of the studied Carabidae.ConclusionOur results confirm that the analysed nuclear ribosomal expansion segments in combination constitute a valuable and efficient supplement for classical DNA barcoding to avoid potential pitfalls when only mitochondrial data are being used. We also demonstrate the high potential of COI barcodes for the identification of even closely related carabid species.

Lyrodus mersinensis sp. nov. (Bivalvia: Teredinidae) another cryptic species in the Lyrodus pedicellatus (Quatrefages, 1849) complex

“…nov. and L. pedicellatus. This was to be expected because substitution rates in nucleotides in mitochondrial genes are, in general, higher than those in nuclear rRNA genes (Raupach et al 2010). Nevertheless, 28S sequences also contain unique diagnostic characters to distinguish between the two cryptic species which confirms previous results that the 28S rRNA gene is a good marker to discriminate species in the Teredinidae (Taylor et al 2007;Distel et al 2011;Weigelt et al 2016).…”

Infestation ofLernaea cyprinacea(Copepoda: Lernaeidae) in two invasive fish species in Romania,Lepomis gibbosusandPseudorasbora parva

“…Given this controversy, we used a fragment of the hypervariable region D1-D2 of the 28S rRNA to confirm that the copepod specimens collected on both host species in our study are indeed conspecific. The hypervariable regions of 28S rRNA have been used by other authors as species diagnostic markers in arthropods, annelids and mollusks (Markmann and Tautz, 2005;Raupach et al, 2010;Song et al, 2008). All eight examined sequences (from two host species) were identical.…”

Identification of cephalopod species from the North and Baltic Seas using morphology, COI and 18S rDNA sequences

“…A promising candidate is the 18S rDNA gene. Although 18S is one of the most frequently used markers in phylogenetic studies (e.g., Field et al 1988;Aguinaldo et al 1997;Halanych 2004;Telford et al 2005), it is also useful for species identification purposes (Raupach et al 2010). The high amount of 18S rDNA in eukaryotic cells and the highly conserved flanking regions, that allow the use of universal primers, make it relatively easy to amplify (Hillis and Dixon 1991).…”