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

Abstract

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.

Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities

“…Furthermore, we experienced difficulty amplifying the COI marker for crustacean groups such as Calanus, Oithona, and Pseudocalanus . These groups were also reported as problematic for amplification in Young, Abbott, Therriault, and Adamowicz (). No major difficulties were encountered when assigning COI reads to the corresponding species, and we were able to distinguish closely related species from the same genus.…”

eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity

“…The primer sequences and sequence databases were also evaluated in silico for their ability to detect native and potential nonindigenous Arctic metazoans. A list of recorded coastal Arctic metazoans was obtained by pooling all Arctic species databases that we had access to ( N total = 897 metazoan identified at the species level; Fisheries and Oceans Canada Arctic Marine Invertebrate Database (Supporting Information Appendix ), Archambault unpublished data, Cusson, Archambault, and Aitken (), Goldsmit, ; Goldsmit, Howland, & Archambault, ; K. Howland, P. Archambault, N. Simard and R Young, unpublished data, Piepenburg et al., ; Link, Piepenburg, & Archambault, ; López, Olivier, Grant, & Archambault, ; Olivier, San Martín, & Archambault, ; Roy, Iken, & Archambault, ; Young, Abbott, Therriault, & Adamowicz, ). Potential NIS invaders ( N = 130 species) were targeted based on (1) screening level risk assessments and predictive species distribution models indicating they were high risk (Goldsmit et al., ), (2) their presence in ports connected to the Canadian Arctic, and/or (3) their presence in ballast waters and hulls of ships based on monitoring at Canadian Arctic ports (Chan, MacIsaac, & Bailey, ; Chan et al., ).…”

Species identification and connectivity of marine amphipods in Canada’s three oceans

“…Several methods have been developed to delimitate species using single locus data such as the barcode gap detection [ 5 , 10 , 11 ] or based on phylogenetic trees [ 12 , 13 ]. These methods have been successfully used in the exploration of biodiversity in insects [ 12 ], in crustaceans [ 10 , 14 , 15 ], in polychaetes [ 16 ], in echinoderms [ 17 ]. However, the delimitation of species based on a single locus can be problematic due to incomplete lineage sorting, heteroplasmy, introgression, young species showing no variation at COI or because it relies on taxonomic data [ 18 – 20 ].…”