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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

Maximum statistical parsimony network of the three analyzed Macropodia species.Settings included a user specified maximum of connection steps at 25 and gaps treated as fifth state. Each line in the network represents a single mutational change; small black dots indicate missing haplotypes. The numbers of analyzed specimens (n) are listed, while the diameter of the circles is proportional to the number of haplotypes sampled (see given Open circles with numbers). Scale bars = 1 cm. Illustrations were taken and modified from a previous publication [81].
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pone.0139421.g006: Maximum statistical parsimony network of the three analyzed Macropodia species.Settings included a user specified maximum of connection steps at 25 and gaps treated as fifth state. Each line in the network represents a single mutational change; small black dots indicate missing haplotypes. The numbers of analyzed specimens (n) are listed, while the diameter of the circles is proportional to the number of haplotypes sampled (see given Open circles with numbers). Scale bars = 1 cm. Illustrations were taken and modified from a previous publication [81].

Mentions: The statistical maximum parsimony analysis also revealed multiple sharing of haplotypes for Macropodia parva (n = 9) and Macropodia rostrata (n = 7) (Fig 6). In total, seven haplotypes were identified for both species. Two haplotypes were shared by specimens of both species (h1 and h2), whereas the remaining five haplotypes were only scored in one specimen (singletons), with one haplotype found for Macropodia parva and four for Macropodia rostrata. K2P distances ranged from 0.48 to 1.12%. The nearest neighbor species was Macropodia tenuirostris (Leach, 1814) (n = 20, 7 haplotypes) with one dominant haplotype h1 (n = 14), separated by more than 20 additional mutational steps from the Macropodia parva/rostrata cluster. The minimum distance value between the Macropodia parva/rostrata cluster and Macropodia tenuirostris was 4.32%.


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)

Maximum statistical parsimony network of the three analyzed Macropodia species.Settings included a user specified maximum of connection steps at 25 and gaps treated as fifth state. Each line in the network represents a single mutational change; small black dots indicate missing haplotypes. The numbers of analyzed specimens (n) are listed, while the diameter of the circles is proportional to the number of haplotypes sampled (see given Open circles with numbers). Scale bars = 1 cm. Illustrations were taken and modified from a previous publication [81].
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139421.g006: Maximum statistical parsimony network of the three analyzed Macropodia species.Settings included a user specified maximum of connection steps at 25 and gaps treated as fifth state. Each line in the network represents a single mutational change; small black dots indicate missing haplotypes. The numbers of analyzed specimens (n) are listed, while the diameter of the circles is proportional to the number of haplotypes sampled (see given Open circles with numbers). Scale bars = 1 cm. Illustrations were taken and modified from a previous publication [81].
Mentions: The statistical maximum parsimony analysis also revealed multiple sharing of haplotypes for Macropodia parva (n = 9) and Macropodia rostrata (n = 7) (Fig 6). In total, seven haplotypes were identified for both species. Two haplotypes were shared by specimens of both species (h1 and h2), whereas the remaining five haplotypes were only scored in one specimen (singletons), with one haplotype found for Macropodia parva and four for Macropodia rostrata. K2P distances ranged from 0.48 to 1.12%. The nearest neighbor species was Macropodia tenuirostris (Leach, 1814) (n = 20, 7 haplotypes) with one dominant haplotype h1 (n = 14), separated by more than 20 additional mutational steps from the Macropodia parva/rostrata cluster. The minimum distance value between the Macropodia parva/rostrata cluster and Macropodia tenuirostris was 4.32%.

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