Comparison of molecular species identification for North Sea calanoid copepods (Crustacea) using proteome fingerprints and DNA sequences

• Published in: Molecular ecology resources Vol. 13; no. 5; pp. 862 - 876
• Main Authors: Laakmann, S., Gerdts, G., Erler, R., Knebelsberger, T., Martínez Arbizu, P., Raupach, M.J.
• Format: Journal Article
• Language: English
• Published: Oxford Blackwell Publishing Ltd 01.09.2013; Blackwell; Wiley Subscription Services, Inc
• Subjects: 18S rDNA; adults; Animal and plant ecology; Animal, plant and microbial ecology; Animals; Aquatic habitats; Biological and medical sciences; COI; Copepoda; Copepoda - chemistry; Copepoda - classification; Copepoda - genetics; cost effectiveness; Crustacea; Cryptic species; cytochrome-c oxidase; Desorption; Developmental stages; DNA, Mitochondrial - chemistry; DNA, Mitochondrial - genetics; DNA, Ribosomal - chemistry; DNA, Ribosomal - genetics; Ecological studies; ecosystems; Electron Transport Complex IV - genetics; Fundamental and applied biological sciences. Psychology; General aspects; Genetics of eukaryotes. Biological and molecular evolution; habitats; interspecific variation; intraspecific variation; Invertebrates; Ionization; Ions; Lasers; Life history; MALDI-TOF MS; Marine; mass; Mass spectra; Mass spectrometry; Metazoa; mitochondria; Molecular Sequence Data; North Sea; nucleotide sequences; organisms; Population genetics, reproduction patterns; proteome; Proteome - analysis; proteomic fingerprinting; proteomics; Pseudocalanus; Pseudocalanus moultoni; RNA, Ribosomal, 18S - genetics; Sample preparation; sampling; sequence analysis; Sequence Analysis, DNA; species identification; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods; Synecology; technology; zooplankton; Atlantic Ocean; North Atlantic; North Sea; ANE, North Sea; proteomic fingerprinting; Proteome; 18S rDNA; Calanoidea; Crustacea; MALDI-TOF MS; Arthropoda; DNA; Fingerprint method; Proteomics; Copepoda; Genetic identification; Invertebrata; COI; Zooplankton; Species identification; species identification; zooplankton
• ISSN: 1755-098X; 1755-0998; 1755-0998
• DOI: 10.1111/1755-0998.12139

Calanoid copepods play an important role in the pelagic ecosystem making them subject to various taxonomic and ecological studies, as well as indicators for detecting changes in the marine habitat. For all these investigations, valid identification, mainly of sibling and cryptic species as well as early life history stages, represents a central issue. In this study, we compare species identification methods for pelagic calanoid copepod species from the North Sea and adjacent regions in a total of 333 specimens. Morphologically identified specimens were analysed on the basis of nucleotide sequences (i.e. partial mitochondrial cytochrome c oxidase subunit I (COI) and complete 18S rDNA) and on proteome fingerprints using the technology of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS). On all three molecular approaches, all specimens were classified to species level indicated by low intraspecific and high interspecific variability. Sequence divergences in both markers revealed a second Pseudocalanus species for the southern North Sea identified as Pseudocalanus moultoni by COI sequence comparisons to GenBank. Proteome fingerprints were valid for species clusters irrespective of high intraspecific variability, including significant differences between early developmental stages and adults. There was no effect of sampling region or time; thus, trophic effect, when analysing the whole organisms, was observed in species‐specific protein mass spectra, underlining the power of this tool in the application on metazoan species identification. Because of less sample preparation steps, we recommend proteomic fingerprinting using the MALDI‐TOF MS as an alternative or supplementary approach for rapid, cost‐effective species identification.