Patterns of DNA Barcode Variation in Canadian Marine Molluscs

Abstract

BackgroundMolluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonstrated in other studies, this is the first effort to construct a DNA barcode registry for marine molluscs across such a large geographic area.Methodology/Principal FindingsThis study examines patterns of DNA barcode variation in 227 species of Canadian marine molluscs. Intraspecific sequence divergences ranged from 0–26.4% and a barcode gap existed for most taxa. Eleven cases of relatively deep (>2%) intraspecific divergence were detected, suggesting the possible presence of overlooked species. Structural variation was detected in COI with indels found in 37 species, mostly bivalves. Some indels were present in divergent lineages, primarily in the region of the first external loop, suggesting certain areas are hotspots for change. Lastly, mean GC content varied substantially among orders (24.5%–46.5%), and showed a significant positive correlation with nearest neighbour distances.Conclusions/SignificanceDNA barcoding is an effective tool for the identification of Canadian marine molluscs and for revealing possible cases of overlooked species. Some species with deep intraspecific divergence showed a biogeographic partition between lineages on the Atlantic, Arctic and Pacific coasts, suggesting the role of Pleistocene glaciations in the subdivision of their populations. Indels were prevalent in the barcode region of the COI gene in bivalves and gastropods. This study highlights the efficacy of DNA barcoding for providing insights into sequence variation across a broad taxonomic group on a large geographic scale.

Weird genotypes? Don't discard them, transmissible cancer could be an explanation

“…A phylogenic tree with all available M. trossuslus mtCOI sequences is shown in Figure 3. Two mtCOI sequences from the DNA barcode study of Layton, Martel, and Hebert (2014), and identified as M. trossulus , clustered with both ours and Metzger et al. (2016) leukemia cell sequences.…”

“…Sequences from chimeric French mussels are depicted with blue circles, neoplastic cell sequences (from Metzger et al., 2016) with red circles, nonneoplastic cell sequences (from Metzger et al., 2016) with black circles, sequences from GenBank with light gray diamonds and sequences from GenBank from Layton et al. (2014) in dark gray diamonds…”

Life history, patchy distribution, and patchy taxonomy in a shallow-water invertebrate (Mollusca: Polyplacophora: Lepidopleurida)

“…3). The study that originally published these sequence data used the name L. "alascensis" (Layton et al, 2014). This may in fact be the correct identification for those specimens.…”

Dna Barcodes to Study Diversity and Species Composition of Clams Found in and Around Mumbai Coast.

“…et al, 1975) such as cytochrome b oxidase (cyt-b) for tuna (Bartlett , 1991), 16S rRNA for holothurian species (Bergene et al, 1995), cytochrome c oxidase subunit I (COI) for three genera of planktonic copepods (Bucklin et al, 1999)), the ground breaking approach was brought by Hebert et al (2003) who proposed use of mitochondrial COI gene for species identification of animals and coined the term 'DNA barcoding'. This mitochondrial COI gene is used as standard DNA barcode for species identification as it shows higher interspecific distance than intraspecific divergence among and within species in addition to higher conserved amino acid sequence and possesses broad array of phylogenetic indications aiding in differentiation among less divergent species and phylogeographic clusters in single species (Brown et Later, this approach was widely followed by multiple researchers in the globe who tested this gene for its applicability for identification of marine fauna, Layton et al (2014) and Mikkelsen et al (2007) identified molluscs from Canada and four genera of Norwegian bivalves, respectively. However, since probabilities of contamination by mucopolysaccharides (Layton KKS et al, 2014;Skolov 2000) in marine clams are higher, this group of animals become quite complex for DNA barcode process and as a result, very less work has been done in molecular 1175 biodiversity of such species, particularly, in India.…”

“…This mitochondrial COI gene is used as standard DNA barcode for species identification as it shows higher interspecific distance than intraspecific divergence among and within species in addition to higher conserved amino acid sequence and possesses broad array of phylogenetic indications aiding in differentiation among less divergent species and phylogeographic clusters in single species (Brown et Later, this approach was widely followed by multiple researchers in the globe who tested this gene for its applicability for identification of marine fauna, Layton et al (2014) and Mikkelsen et al (2007) identified molluscs from Canada and four genera of Norwegian bivalves, respectively. However, since probabilities of contamination by mucopolysaccharides (Layton KKS et al, 2014;Skolov 2000) in marine clams are higher, this group of animals become quite complex for DNA barcode process and as a result, very less work has been done in molecular 1175 biodiversity of such species, particularly, in India. Moreover, difficulties in collection of these species exist due to marine habitats that are not easy to reach generating poor understanding of clam biodiversity around coastal region especially in India, although it has got ample coastal area of 7,516 km (Venkataraman and Wafar, 2005), no efficient initiative has been taken for identifying and analyzing clam biodiversity (Pawar, 2012) through DNA barcoding resulting into inadequate specimen and sequence data repository and lack of robust species level identification data along with genetic lineage studies leading to low scale scientific understanding of cryptic and endangered species.…”