DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition

Bucklin, Ann; Hopcroft, Russell R.; Kosobokova, Ksenia; Nigro, Lisa M.; Ortman, Brian D.; Jennings, Robert M.; Sweetman, Christopher J.

doi:10.1016/j.dsr2.2009.08.005

Cited by 102 publications

(64 citation statements)

References 43 publications

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“…A number of recent studies (Saunders 2005;Bucklin et al 2007Bucklin et al , 2010Lorion et al 2009;Radulovici et al 2009;Steinke et al 2009) have confirmed the utility of COI for barcoding of marine organisms. However, the number of marine barcoding studies in the Arctic remains low; most work has focused on terrestrial groups in limited regions (Smith et al 2009;Zhou et al 2009).…”

Section: Molecular Taxonomy: Applications For Dna Barcoding In the Armentioning

confidence: 98%

Biodiversity and phylogeography of Arctic marine fauna: insights from molecular tools

et al. 2010

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The last decade has seen an increase in the frequency and breadth of application of molecular tools, many of which are beginning to shed light on long-standing questions in biogeography and evolutionary history of marine fauna. We explore new developments with respect to Arctic marine invertebrates, focusing on molecular taxonomy and phylogeography-two areas that have seen the most progress in the time-frame of the Census of Marine Life. International efforts to generate genetic 'barcodes' have yielded new taxonomic insights and applications ranging from diet analysis to identification of larval forms. Increasing availability of genetic data in public databases is also facilitating exploration of largescale patterns in Arctic marine populations. We present new case-studies in meta-population analysis of barcode data from polychaetes and echinoderms that demonstrate such phylogeographic applications. Emerging patterns from ours and other published studies include influences of a complex climatic and glacial history on genetic diversity and evolution in the Arctic, and contrasting patterns of both high gene flow and persistent biogeographic boundaries in contemporary populations.

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Section: Molecular Taxonomy: Applications For Dna Barcoding In the Armentioning

confidence: 98%

Biodiversity and phylogeography of Arctic marine fauna: insights from molecular tools

et al. 2010

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“…Unfortunately, research to test the performance of COI barcode data in marine invertebrate taxa has been limited (but see Radulovici et al 2010;Bucklin et al 2010Bucklin et al , 2011Blanco-Bercial et al 2014). Furthermore, studies investigating barcode performance often do so by comparing the relative performance of barcode data against morphologically identified specimens.…”

Section: Support For Rapid Species Delimitation For Hexanauplia Usingmentioning

confidence: 99%

“…Currently, it is challenging to use DNA barcode databases for identification of many marine species; most species remain to be described, and even known species often have little to no DNA barcode coverage (McManus and Katz 2009;Bucklin et al 2010;Blanco-Bercial et al 2014). Important first steps for enabling specimen identification using DNA barcodes are to investigate patterns of interspecific and intraspecific variation within target taxa and to determine the degree to which an integrative approach to species delimitation is necessary-as contrasted with more straightforward approaches using a single molecular marker Cruickshank 2013, 2014).…”

Section: Introductionmentioning

confidence: 99%

“…Despite these successes, establishing a robust system is still challenging. With 31 phyla-and with an estimated million species remaining to be discovered-the genetic variation within marine metazoans is not fully appreciated (Bucklin et al 2010). Earlier molecular approaches to specimen identification relied on the presence of low intraspecific genetic variation and larger interspecific divergence between species, i.e., the presence of a "barcoding gap" (discussed in Meyer and Paulay 2005).…”

Section: Introductionmentioning

confidence: 99%

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Barcode-based species delimitation in the marine realm: a test using Hexanauplia (Multicrustacea: Thecostraca and Copepoda)

Young

Abbott

Therriault

et al. 2017

Genome

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DNA barcoding has been used successfully for identifying specimens belonging to marine planktonic groups. However, the ability to delineate species within taxonomically diverse and widely distributed marine groups, such as the Copepoda and Thecostraca, remains largely untested. We investigate whether a cytochrome c oxidase subunit I (COI-5P) global pairwise sequence divergence threshold exists between intraspecific and interspecific divergences in the copepods plus the thecostracans (barnacles and allies). Using publicly accessible sequence data, we applied a graphical method to determine an optimal threshold value. With these thresholds, and using a newly generated planktonic marine data set, we quantify the degree of concordance using a bidirectional analysis and discuss different analytical methods for sequence-based species delimitation (e.g., BIN, ABGD, jMOTU, UPARSE, Mothur, PTP, and GMYC). Our results support a COI-5P threshold between 2.1% and 2.6% p-distance across methods for these crustacean taxa, yielding molecular groupings largely concordant with traditional, morphologically defined species. The adoption of internal methods for clustering verification enables rapid biodiversity studies and the exploration of unknown faunas using DNA barcoding. The approaches taken here for concordance assessment also provide a more quantitative comparison of clustering results (as contrasted with "success/failure" of barcoding), and we recommend their further consideration for barcoding studies.

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“…The COI mtDNA region has been shown to be a good marker for crustacean species (Costa et al, 2007). Importantly, mtCOI is sufficiently variable to be useful in identifying and discriminating even the most closely related species (Lefébure et al, 2006;Bucklin et al, 2007Bucklin et al, , 2009Darling and Tepolt, 2008). Sotelo et al (2008) reported that the COI region displays diagnostic differences between species of the genus Maja; divergence between species was much higher than within them.…”

Section: Discussionmentioning

confidence: 99%

Identification of European species of <i>Maja</i> (Decapoda: Brachyura: Majidae): RFLP analyses of COI mtDNA and morphological considerations

Guerao¹,

Andrée²,

Froglia

et al. 2011

Sci. Mar.

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SUMMARY: Four species of crabs of the genus Maja have been described along the European coast: M. brachydactyla, M. squinado, M. goltziana and M. crispata. The commercially important species M. brachydactyla and M. squinado achieve the largest body sizes and are the most similar in morphology, and are therefore easily confused. The four species of Maja were identified using a novel morphometric index and a polymerase chain reaction followed by restriction fragment length polymorphism analysis (RFLP). The relationship between carapace length and the distance between the tips of antorbital spines was used to distinguish adults of M. brachydactyla and M. squinado. PCR-RFLP analysis of a partial sequence of the mitochondrial cytochrome oxidase type I (COI) revealed that the four species of the genus Maja can be unambiguously discriminated using the combination of restriction endonucleases enzymes HpyCH4V and Ase I. The molecular identification may be particularly useful in larvae, juvenile and young crabs, when the morphological differences found in adults are not applicable.Keywords: Maja, M. squinado, M. brachydactyla, molecular identification, morfometry, COI, RFLP. RESUMEN: Identificación de las especies europeas del género Maja (Decapoda: Brachyura: Majidae): análisis de PCR-RFLP de una región del mtADN COI y consideraciones morfológicas. -Cuatro especies del género Maja han sido descritas en las costas europeas: M. brachydactyla, M. squinado, M. goltziana y M. crispata. Las especies M. brachydactyla y M. squinado, que tienen importancia comercial, alcanzan los tamaños más grandes y son morfológicamente muy similares, siendo muy fácil confundirlas. La identificación de las cuatro especies se ha realizado utilizando un nuevo índice morfométrico y un análisis de polimorfismos de fragmentos de restricción (RFLP). La relación entre la longitud del cefalotórax y la distancia entre los extremos distales de las espinas antorbitales se ha utilizado para la diferenciación de los adultos de M. brachydactyla y M. squinado. El análisis PCR-RFLP de una secuencia parcial de la citocromo oxidasa tipo I mitocondrial (COI) indica que las cuatro especies del género Maja pueden ser discriminadas usando una combinación de las endonucleasas HpyCH4V y Ase I. La identificación molecular puede ser particularmente útil en las larvas, juveniles y cangrejos jóvenes, cuando las diferencias morfológicas encontradas en los adultos no son aplicables.Palabras clave: Maja, M. squinado, M. brachydactyla, identificación molecular, morfometría, COI, RFLP.

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DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition

Cited by 102 publications

References 43 publications

Biodiversity and phylogeography of Arctic marine fauna: insights from molecular tools

Biodiversity and phylogeography of Arctic marine fauna: insights from molecular tools

Barcode-based species delimitation in the marine realm: a test using Hexanauplia (Multicrustacea: Thecostraca and Copepoda)

Identification of European species of <i>Maja</i> (Decapoda: Brachyura: Majidae): RFLP analyses of COI mtDNA and morphological considerations

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