The Application of DNA Barcodes for the Identification of Marine Crustaceans from the North Sea and Adjacent Regions

Abstract

During the last years DNA barcoding has become a popular method of choice for molecular specimen identification. Here we present a comprehensive DNA barcode library of various crustacean taxa found in the North Sea, one of the most extensively studied marine regions of the world. Our data set includes 1,332 barcodes covering 205 species, including taxa of the Amphipoda, Copepoda, Decapoda, Isopoda, Thecostraca, and others. This dataset represents the most extensive DNA barcode library of the Crustacea in terms of species number to date. By using the Barcode of Life Data Systems (BOLD), unique BINs were identified for 198 (96.6%) of the analyzed species. Six species were characterized by two BINs (2.9%), and three BINs were found for the amphipod species Gammarus salinus Spooner, 1947 (0.4%). Intraspecific distances with values higher than 2.2% were revealed for 13 species (6.3%). Exceptionally high distances of up to 14.87% between two distinct but monophyletic clusters were found for the parasitic copepod Caligus elongatus Nordmann, 1832, supporting the results of previous studies that indicated the existence of an overlooked sea louse species. In contrast to these high distances, haplotype-sharing was observed for two decapod spider crab species, Macropodia parva Van Noort & Adema, 1985 and Macropodia rostrata (Linnaeus, 1761), underlining the need for a taxonomic revision of both species. Summarizing the results, our study confirms the application of DNA barcodes as highly effective identification system for the analyzed marine crustaceans of the North Sea and represents an important milestone for modern biodiversity assessment studies using barcode sequences.

A molecular phylogeny of Pseudocrangonyx from Japan, including a new subterranean species (Crustacea, Amphipoda, Pseudocrangonyctidae)

“…Primer sets for the PCR and cycle sequencing (CS) reactions used in this study were as follows: for 28S rRNA (28S), 28F and 28R (PCR and CS) (Hou et al 2007) with 28SF and 28SR (CS) (Tomikawa et al 2012) as internal primers; for histone H3 (H3), H3aF and H3bR (PCR and CS) (Colgan et al 1998); for cytochrome c oxidase subunit I (COI), LCO1490 and HCO2198 (PCR and CS) (Folmer et al 1994), or jgL-CO1490 and jgHCO2198 (Geller et al 2013), respectively, with M13F and M13R tails (Messing 1983), used for PCR, and then M13F and M13R used as primers for CS, followed Raupach et al (2015); for 16S rRNA (16S), 16STf (Macdonald III et al 2005) and 16Sbr (Palumbi 1996; modified to correspond with "Fruit Fly") (PCR and CS).…”

The life cycle of Huffmanela huffmani Moravec, 1987(Nematoda: Trichosomoididae), an endemic marine-relict parasite of Centrarchidae from a Central Texas spring

“…This suborder is extremely diverse and occurs in numerous benthic habitats across the oceans of the world (Raupach et al 2015). However, the two species of marine Huffmanela with strictly pelagic blue-water definitive hosts Campbell 1991, Moravec andGaribaldi 2000) are paradoxical, because these fishes are unlikely to come into contact with any benthic invertebrates.…”

A genetic fingerprint of Amphipoda from Icelandic waters – the baseline for further biodiversity and biogeography studies

“…The two MOTUs observed within the nominal A. manudens have different geographic and bathymetric distributions. The specimen from IceAGE was collected in the area of the Iceland-Faroe Ridge at 500 m depth, while the previously reported material came from a shallow station (50 m) in southeast North Sea (Raupach et al 2015). Further studies of voucher material should be conducted to assess the comparative morphology of the material and possibly that of type material.…”

“…The latter is commonly used for species delimitation in arthropods and particularly in Amphipoda (e.g. Hebert et al 2003, Costa et al 2007, 2009, Raupach et al 2015, Lobo et al 2017). Both uncorrected p-distance and K2P were used to calculate species distances.…”