Species identification of echinoderms from the North Sea by combining morphology and molecular data

Abstract

Background: Taxonomic uncertainties in the morphological species identification and taxonomic revisions in individual groups are known for all echinoderm classes. These uncertainties in morphological species identification and discrimination have spawned the application of molecular genetic identification techniques. However, as the fundamental step to allow and ensure future molecular species identification, valid and comprehensive reference library entries comprising morphological and molecular species information together with various metadata are essentially needed. In our study we compare morphological and molecular genetic species identification techniques for representatives of North Sea echinoderm classes, i.e. the Asteroidea, Ophiuroidea, Echinoidea and Holothuroidea.Methods: Individuals were sampled during different surveys in different regions of the North Sea, identified to species level based on morphological diagnostic features, and were genetically analysed using a fragment of the mitochondrial cytochrome c oxidase subunit I (COI). Results and Discussion:The morphological determination revealed 32 species including one taxon determined only to genus level. In contrast to this, the COI analysis supported 34 monophyletic clades with pronounced differences between the intra-and the inter-specific genetic variability (a barcoding gap of 4.93 %) with highest intra-specific variabilities found in the ophiuroid species Amphiura filiformis, A. chiajei and Ophiura sarsii. In 94 % of the investigated species, morphological identification and COI sequence clusters were congruent whereas for two asteroid species we found an underestimated diversity. For Astropecten irregularis, one of the most common starfish species of the North Sea, we found two distinct and possibly depth-related clades, probably sibling species, differing by 11.1-11.9 % sequence divergences (p-distances). For two starfish individuals, morphologically identified as Henricia sanguinolenta, the COI analysis revealed two monophyletic clades, of which one was classified as H. cf. oculata by comparison to published sequences. Conclusions:This newly established sequence reference library for the North Sea Echinodermata allows and ensures future molecular species identification for various life-cycle stages including juveniles and meroplanktonic larvae and provides sequences for phylogeographic studies and the detection of sibling as well as cryptic species.

Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes

“…Most of these sequences are accessible on the Barcode of Life Data system (BOLD, http://www.boldsystems.org ) under the following projects: Barcoding North Fish I (BNSFI), Barcoding North Sea Decapoda (BNAGB), Barcoding Gobiidae from the North Sea and the Baltic Sea (BGNBS), Barcoding Northeast Atlantic Cephalopoda (BNEAC), Barcoding Northeast Atlantic Gastropods and Bivalves (BNAGB), North Sea Echinodermata (DS-NSECH), Barcoding North Sea Cirripedia (BNSCI), Barcoding North Sea Isopoda (BNSIS), Barcoding North Sea Amphipoda (BNSA), Barcoding North Sea Copepoda (BNSCP), and Barcoding North Sea Crustacea (BNSC). The majority of the sequences are published, partially on NCBI 1 , 2 , 34 – 43 . The sequence reference library also includes some unpublished data on Cnidaria, Copepoda, and Polychaeta.…”

“…For taxonomic validation of eDNA analysis results, a reliable DNA sequence reference library is essential. From 2010 through 2016, a DNA barcode (COI) reference library was produced for North Sea metazoans at the Senckenberg Institute in Wilhelmshaven 1 , 2 , 34 – 43 . Species material, including the morphological species description came from the Long-term Ecological Research (LTER) sites as “North Sea Benthos Observatory” and the “Helgoland Roads” (for more information see: https://deims.org/network/germany-lter-d and https://deims.org/1e96ef9b-0915-4661-849f-b3a72f5aa9b1 ), ensuring high taxonomic quality of that DNA reference library.…”

Unexpected high abyssal ophiuroid diversity in polymetallic nodule fields of the Northeast Pacific Ocean, and implications for conservation

“…Noticeably, the BIN method in BOLD recovered a higher number of species than all other approaches. BOLD and specifically BINs can greatly improve the Linnaean taxonomic assignment in many animal groups, including echinoderms (Layton et al, 2016;Laakman et al, 2016). The low intra-cluster divergence (2.2%) at the initial cluster step of RESL methodology (Ratnasingham and Hebert, 2013;Song et al, 2018) could be the reason why, in some cases the BIN method overestimated species number, especially since there appears a small overlap between intraspecific and interspecific distance in our data (Fig.…”

“…The results obtained here were consistent with many other studies showing that different species delimitation methods can produce different delimitation scenarios when employing single-locus data (Hofmann et al, 2019). The single-locus species delimitation methods tested here, although they are extensively used throughout the literature, including for the Ophiuroidea (Khodami et al, 2014;Laakman et al, 2016;Boissin et al, 2017), are each subject to potential biases and differing https://doi.org/10.5194/bg-2019-360 Preprint. Discussion started: 26 November 2019 c Author(s) 2019.…”

A DNA barcode library for ground beetles of Germany: the genus Pterostichus Bonelli, 1810 and allied taxa (Insecta, Coleoptera, Carabidae)

“…Despite the fact that various effects may limit the efficiency of a successful species identification, for example recent or ongoing hybridization events (e.g., Rougerie et al 2012;Mutanen et al 2016;Havemann et al 2018), mitochondrial DNA-like sequences in the nucleus (numts) (e.g., Rogers and Griffiths-Jones 2012;Jordal and Kambestand 2014), or effects of Wolbachia infections (e.g., Smith et al 2012;Klopfstein et al 2016;Kolasa et al 2018;Kajtoch et al 2019), DNA barcoding has become the method of choice in terms of modern molecular species identification, including the identification of single specimens as well as metabarcoding of bulk samples (e.g., Casiraghi et al 2010;Brandon-Mong et al 2015). In recent years, various barcode libraries for numerous animal groups of Germany were established, including both marine and freshwater fish (Knebelsberger et al 2014;Knebelsberger et al 2015), amphibians and reptiles (Hawlitschek et al 2016), echinoderms (Laakmann et al 2017), molluscs (Gebhardt and Knebelsberger 2015;Barco et al 2016), crustaceans (Raupach et al 2015), spiders (Astrin et al 2016), myriapods (Spelda et al 2011), and numerous insect taxa, e.g., Coleoptera (Hendrich et al 2015), Ephemeroptera, Plecoptera, Trichoptera (Morinière et al 2017), Heteroptera (Raupach et al 2014;Havemann et al 2018), Hymenoptera (Schmidt et al 2015;Schmidt et al 2017;Schmid-Egger et al 2019), Lepidoptera (Hausmann et al 2011), Neuroptera (Morinière et al 2014), and Orthoptera (Hawlitschek et al 2017). Previous studies also laid the groundwork of a comprehensive DNA barcode library for the ground beetles (Coleoptera: Carabidae) of Germany (Raupach et al 2010;Raupach et al 2011;…”