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

Raupach MJ, Barco A, Steinke D, Beermann J, Laakmann S, Mohrbeck I, Neumann H, Kihara TC, Pointner K, Radulovici A, Segelken-Voigt A, Wesse C, Knebelsberger T - PLoS ONE (2015)

Bottom Line: 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.Six species were characterized by two BINs (2.9%), and three BINs were found for the amphipod species Gammarus salinus Spooner, 1947 (0.4%).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.

View Article: PubMed Central - PubMed

Affiliation: German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany.

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.

No MeSH data available.


Related in: MedlinePlus

Neighbor joining topology of the analyzed Copepoda based on Kimura 2-parameter distances.The number of analyzed specimens collapsed into a single node is provided following the species name. Triangles indicate the relative number of individual’s sampled (height) and sequence divergence (width). Blue triangles indicate species with intraspecific maximum pairwise distances >2.2%. Numbers next to nodes represent non-parametric bootstrap values >90% (1,000 replicates). Drawing of Caligus curtus O.F. Müller, 1789 is taken and modified from a previous publication [77].
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pone.0139421.g001: Neighbor joining topology of the analyzed Copepoda based on Kimura 2-parameter distances.The number of analyzed specimens collapsed into a single node is provided following the species name. Triangles indicate the relative number of individual’s sampled (height) and sequence divergence (width). Blue triangles indicate species with intraspecific maximum pairwise distances >2.2%. Numbers next to nodes represent non-parametric bootstrap values >90% (1,000 replicates). Drawing of Caligus curtus O.F. Müller, 1789 is taken and modified from a previous publication [77].

Mentions: Our NJ analyses based on K2P genetic distances revealed non-overlapping species clusters with bootstrap support values of 99 or 100% for all Copepoda (Fig 1), all Amphipoda (Fig 2), most Decapoda (Fig 3) as well as all Thecostraca, Isopoda, Cumacea, Diplostraca, Euphausiacea, Mysida and Stomatopoda (all in Fig 4). A NJ topology of all analyzed crustacean specimens based on K2P is presented in the supporting information (S2 Fig).


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

Raupach MJ, Barco A, Steinke D, Beermann J, Laakmann S, Mohrbeck I, Neumann H, Kihara TC, Pointner K, Radulovici A, Segelken-Voigt A, Wesse C, Knebelsberger T - PLoS ONE (2015)

Neighbor joining topology of the analyzed Copepoda based on Kimura 2-parameter distances.The number of analyzed specimens collapsed into a single node is provided following the species name. Triangles indicate the relative number of individual’s sampled (height) and sequence divergence (width). Blue triangles indicate species with intraspecific maximum pairwise distances >2.2%. Numbers next to nodes represent non-parametric bootstrap values >90% (1,000 replicates). Drawing of Caligus curtus O.F. Müller, 1789 is taken and modified from a previous publication [77].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4587929&req=5

pone.0139421.g001: Neighbor joining topology of the analyzed Copepoda based on Kimura 2-parameter distances.The number of analyzed specimens collapsed into a single node is provided following the species name. Triangles indicate the relative number of individual’s sampled (height) and sequence divergence (width). Blue triangles indicate species with intraspecific maximum pairwise distances >2.2%. Numbers next to nodes represent non-parametric bootstrap values >90% (1,000 replicates). Drawing of Caligus curtus O.F. Müller, 1789 is taken and modified from a previous publication [77].
Mentions: Our NJ analyses based on K2P genetic distances revealed non-overlapping species clusters with bootstrap support values of 99 or 100% for all Copepoda (Fig 1), all Amphipoda (Fig 2), most Decapoda (Fig 3) as well as all Thecostraca, Isopoda, Cumacea, Diplostraca, Euphausiacea, Mysida and Stomatopoda (all in Fig 4). A NJ topology of all analyzed crustacean specimens based on K2P is presented in the supporting information (S2 Fig).

Bottom Line: 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.Six species were characterized by two BINs (2.9%), and three BINs were found for the amphipod species Gammarus salinus Spooner, 1947 (0.4%).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.

View Article: PubMed Central - PubMed

Affiliation: German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany.

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.

No MeSH data available.


Related in: MedlinePlus