Identifying Canadian Freshwater Fishes through DNA Barcodes

By N. Hubert, Robert H. Hanner, E. Holm, N. Mandrak, E. Taylor, M. Burridge, D. Watkinson, P. Dumont, Allen Curry, P. Bentzen and 3 more. PLoS ONE, 2008

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Background DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5′ region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons. Methodology/Principal Findings We bi-directionally sequenced the standard 652 bp “barcode” region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species. Conclusions/Significance The present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics.

Subfields: Aquatic Science, Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/21ae002caa7e95215f1165d0ef413ea157f345d0

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Citations in the corpus

Italian market fish species identification and commercial frauds revealing by DNA sequencing (2014, methodology): “As genetic markers we employed COI e Cytb since these mitochondrial DNA sequences are the most widely used genetic markers for fish species identification (Hajibabaei et al., 2006; Hubert et al., 2008; Kochzius et al., 2010; Lakra et al., 2011; Steinke, Vences, Salzburger, & Meyer, 2005).”
A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System (2013, neutral): “5883/DS-FISHCAN1 [66]”
Evaluation of 10 plant barcodes in Bryophyta (Mosses) (2010, background): “For instance, the mitochondrial gene coxI (or COI) is accepted as a standard barcode in animals (e.g. Hebert et al., 2004; Hubert et al., 2008), although it is not universally successful in some groups such as Diptera (Meier et al., 2006) or corals (Shearer & Coffroth, 2008).”
DNA Barcoding, species delineation and taxonomy: a historical perspective (2015, neutral): “In this context, incorporating up to date taxonomic knowledge is a concern [12,20,51] and depositing voucher specimens in national repositories has been explicitly defined as a mandatory step to ensure accurate and up-to-date identifications by enabling taxonomists to validate or perform new…”
Biodiversity of arctic marine fishes: taxonomy and zoogeography (2011, background): “Conversely, within-species variation for most taxa was low (adjusted mean, 0.3%; range 0–3.5%), matching the lowest levels of conspecific variation reported in barcoding studies on fishes (Ward et al. 2005; Hubert et al. 2008; Steinke et al. 2009; Zemlak et al. 2009).”
Lampreys of the Iberian Peninsula: distribution, population status and conservation (2012, background): “…(e.g. Eneqvist 1937, McPhail & Lindsey 1970), and more recently, genetic studies using distinct molecular markers (especially mitochondrial DNA) failed to find genetic differences between lamprey species pairs (e.g. Docker et al. 1999, Espanhol et al. 2007, Blank et al. 2008, Hubert et al. 2008).”
DNA barcoding detects market substitution in North American seafood (2008, background): “This includes both freshwater (Hubert et al., 2008) and marine fishes (Rock et al.”
Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification (2012, background): “…taxonomic groups including butterflies (Hajibabaei et al. 2006; Lukhtanov et al. 2009; Dincă et al. 2011), birds (Kerr et al. 2009a, b, 2007; Johnsen et al. 2010), fishes (Ward et al. 2005; Hubert et al. 2008; Rasmussen et al. 2009; Wong et al. 2009; Steinke et al. 2009a,b) and bats…”
The campaign to DNA barcode all fishes, FISH-BOL. (2009, background): “fishes, the darters Etheostoma nigrum Rafinesque and Etheostoma olmstedi Storer (Hubert et al., 2008).”
Refined Global Analysis of Bemisia tabaci (Hemiptera: Sternorrhyncha: Aleyrodoidea: Aleyrodidae) Mitochondrial Cytochrome Oxidase 1 to Identify Species Level Genetic Boundaries (2010, neutral): “Phylogenetic analysis was performed using MrBayes (Huelsenbeck and Ronquist 2001).”
DNA barcoding is a useful tool for the identification of marine fishes from Japan (2011, background): “Mitochondrial COI gene, as an attractive “species barcode”, its high efficiency in species identification has been reported in Australia marine fishes (Ward et al., 2005), Canadian freshwater fishes (Hubert et al., 2008) and ornamental fishes in the market of North America (Steinke et al., 2009b).”
DNA barcoding of Pacific Canada’s fishes (2009, background): “Many studies have now shown the eVectiveness of a 650-bp fragment of the cytochrome c oxidase I (COI) gene for species identiWcation in varied animal lineages (Hebert et al. 2003a, b; Barrett and Hebert 2004; Hebert et al. 2004a, b; Hogg and Hebert 2004; Smith et al. 2005; Hajibabaei et al. 2006), i”