DNA Barcoding of Marine Copepods: Assessment of Analytical Approaches to Species Identification

Abstract

More than 2,500 species of copepods (Class Maxillopoda; Subclass Copepoda) occur in the marine planktonic environment. The exceptional morphological conservation of the group, with numerous sibling species groups, makes the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of species based on DNA sequencing of single specimens and environmental samples. Despite the recent development of diverse genetic and genomic markers, the barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) gene remains a useful and – in some cases – unequaled diagnostic character for species-level identification of copepods. This study reports 800 new barcode sequences for 63 copepod species not included in any previous study and examines the reliability and resolution of diverse statistical approaches to species identification based upon a dataset of 1,381 barcode sequences for 195 copepod species. We explore the impact of missing data (i.e., species not represented in the barcode database) on the accuracy and reliability of species identifications. Among the tested approaches, the best close match analysis resulted in accurate identification of all individuals to species, with no errors (false positives), and out-performed automated tree-based or BLAST based analyses. This comparative analysis yields new understanding of the strengths and weaknesses of DNA barcoding and confirms the value of DNA barcodes for species identification of copepods, including both individual specimens and bulk samples. Continued integrative morphological-molecular taxonomic analysis is needed to produce a taxonomically-comprehensive database of barcode sequences for all species of marine copepods.

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

“…This range was chosen because it is expected to encompass the general transition between intraspecific and interspecific variation within our COI-5P data set (Blanco-Bercial et al 2014). For each program for which the user can specify the threshold (ABGD, jMOTU, Mothur, and UPARSE), the numbers of clusters generated at each p-distance were plotted, and the vertex point of the resulting curve was considered to represent the optimal threshold for clustering these data for that method (Handl et al 2005) (Fig.…”

“…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).…”

“…The success of DNA barcoding has been documented across a range of marine taxa (e.g., da Silva et al 2011;Blanco-Bercial et al 2014;and references therein). Despite these successes, establishing a robust system is still challenging.…”

“…Unfortunately, thresholds for species delimitation are often inappropriately chosen and simply based on past literature (Collins and Cruickshank 2013). Although there has been work developing methodologies to justify the selection of a molecular threshold (Lefébure et al 2006;Blanco-Bercial et al 2014), these methods rely solely on external comparisons, often only to taxonomic species identifications, which can vary widely depending on the identifier (Shen et al 2013). Nevertheless, once a well-defined and justified threshold is established, simple delimitation methods are advantageous for quickly and easily assessing potential biodiversity.…”

High diversity in Keratella cochlearis (Rotifera, Monogononta): morphological and genetic evidence

“…Similarly to GMYC, PTP assumes that there are less intraspecific substitutions than interspecific substitutions because they have less time to accumulate. This method does not require an ultrametric tree and has been shown to match other methods of species delimitation in rotifers (Tang et al, 2014) and copepods (Blanco-Bercial et al, 2014). Two types of PTP were used: ML (PTP-ML) approach and Bayesian approach (PTP-BA).…”