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Untangling Taxonomy: a DNA Barcode Reference Library for Canadian Spiders

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Untangling Taxonomy: a DNA Barcode Reference Library for Canadian Spiders Received Date : 14-Mar-2015 Revised Date : 30-Jun-2015 Accepted Date : 06-Jul-2015 Article type : Resource Article Untangling Taxonomy: A DNA Barcode Reference Library for Canadian Spiders Gergin A. Blagoev Jeremy R. deWaard* Sujeevan Ratnasingham Article Stephanie L. deWaard Liuqiong Lu James Robertson Angela C. Telfer Paul D. N. Hebert Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada * Corresponding author E-mail: [email protected] This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: Accepted 10.1111/1755-0998.12444 This article is protected by copyright. All rights reserved. Keywords: DNA barcoding, spiders, Araneae, species identification, Barcode Index Numbers, Operational Taxonomic Units Abstract Approximately 1460 species of spiders have been reported from Canada, 3% of the global fauna. This study provides a DNA barcode reference library for 1018 of these species based upon the analysis of more than 30,000 specimens. The sequence results show a clear barcode gap in most cases with a mean intraspecific divergence of 0.78% versus a minimum nearest-neighbour (NN) distance averaging 7.85%. The sequences were assigned to 1359 Barcode Index Numbers (BINs) with 1344 of these BINs composed of specimens belonging to a single currently recognized Article species. There was a perfect correspondence between BIN membership and a known species in 795 cases while another 197 species were assigned to two or more BINs (556 in total). A few other species (26) were involved in BIN merges or in a combination of merges and splits. There was only a weak relationship between the number of specimens analyzed for a species and its BIN count. However, three species were clear outliers with their specimens being placed in 11 to 22 BINs. Although all BIN splits need further study to clarify the taxonomic status of the entities involved, DNA barcodes discriminated 98% of the 1018 species. The present survey conservatively revealed 16 species new to science, 52 species new to Canada and major range extensions for 426 species. However, if most BIN splits detected in this study reflect cryptic taxa, the true species count for Canadian spiders could be 30–50% higher than currently recognized. Accepted This article is protected by copyright. All rights reserved. Introduction With 45,000 known species in 114 families, spiders are one of the most diverse orders of arthropods, a fact which stimulated the development of an on-line taxonomic catalogue (World Spider Catalog 2014). It now tracks the description of every new species, providing an authoritative resource for valid names. However, it does not simplify their identification. In common with other groups of arthropods, many species of spiders are difficult to identify, especially the juveniles that often dominate collections from seasonal environments (Foelix 2011). In fact, because most keys are only effective for adults and often just for males, many individuals cannot be identified to a species-level through morphological analysis. Because of Article this difficulty, biotic surveys frequently neglect spiders, despite their diversity and important role as predators in terrestrial ecosystems (Freitas et al. 2013). Studies over the past decade have revealed the efficacy of DNA barcoding, the analysis of sequence diversity in the 5’ region of the cytochrome c oxidase I gene, as a tool for the identification of animal species (Hebert et al. 2003). Insects have been the target for much of this work, especially members of the order Lepidoptera. These analyses have shown that 95–100% of the species in regional faunas can be discriminated (Hajibabaei et al. 2006; Hebert et al. 2009; Hausmann et al. 2011). Recent work has tested the impact on barcode resolution of expanding from a regional to continental scale. Barcodes discriminated all 75 Australian species in the family Sphingidae regardless of their collection site (Rougerie et al. 2014), while 1000 species of Lepidoptera showed only a small reduction in identification success in comparisons involving Austria and Finland (Huemer et al. 2014). Further studies have confirmed that DNA barcoding is effective in other insect orders. For example, the analysis of 1500 Finnish and 3500 German Accepted This article is protected by copyright. All rights reserved. species of Coleoptera revealed 99% success in their identification (Hendrich et al. 2014; Pentinsaari et al. 2014). The effectiveness of DNA barcoding as a tool for the identification of spiders has seen less evaluation. Barrett and Hebert (Barrett & Hebert 2005) found that DNA barcoding discriminated all 168 species of Canadian spiders that they examined, but their sample sizes were small. A subsequent study that analyzed nearly 3000 specimens from a site in the Canadian arctic indicated that each of the 198 species at this locality possessed a diagnostic array of barcode sequences (Blagoev et al. 2013). Similar results were obtained for 63 species of Alaskan spiders (Slowik & Blagoev 2012) and 361 species of Canadian spiders (Blagoev et al. 2009). Although these studies have established that DNA barcodes are very effective in identifying known Article species, they also revealed possible overlooked species, as evidenced by many cases of deep intraspecific divergence (Barrett & Hebert 2005; Blagoev et al. 2009). The spiders in other regions have seen less investigation. Astrin et al. (Astrin et al. 2006) reported the strong performance of DNA barcoding in identifying 52 European species in the family Pholcidae, while Miller et al. (Miller et al. 2013a) found that barcodes discriminated 31 species in the Netherlands. Candek and Kuntner (Čandek & Kuntner 2014) established that the effectiveness of DNA barcodes for identification was not impeded by geographic variation in a study on 20 species of spiders whose ranges span Europe and North America. These overall results have led to consensus that a comprehensive DNA barcode reference library will advance spider biology in important ways. For example, Miller et al. (Miller et al. 2013b) showed how it could provide new insights on the parasitoids which attack spiders. A well-parameterized library will also facilitate the use of next generation sequencing platforms to ascertain the species composition of mass collections (Hajibabaei et al. 2011; Yu et al. 2012; Ji et al. 2013). Because the latter Accepted This article is protected by copyright. All rights reserved. advance will enable the inclusion of spiders in large-scale biotic surveys, while the former will reveal new details on their ecological interactions (Wirta et al. 2014), there is a need for further library construction. This study reports progress toward the assembly of a DNA barcode reference library with 10X or higher coverage for all Canadian spiders. It represents a major taxonomic and geographic extension of earlier work which targeted a limited number of species and only examined them at a few localities. The goal of 10X coverage was established to permit the analysis of intraspecific variation in barcode sequences. Prior taxonomic studies have indicated the magnitude of the challenge – about 1460 species of spiders are known from Canada (Dondale 1979; Bennett 1999; Paquin et al. 2010; Dupérré 2013). These taxa include representatives from two of the three Article suborders and from 46 of the 114 families of spiders. Although the present study does not deliver a complete reference library for Canadian spiders, it does provide an average of 20X coverage for two-thirds of the fauna, including nearly all common species. As a result, it creates a highly functional identification system for this biotic assemblage. The study has also provided a better understanding of the importance of cryptic diversity in Canadian spiders by ascertaining the incidence of species which are assigned to two or more Barcode Index Numbers (Ratnasingham & Hebert 2013) and presents an inexpensive pathway that can speed the registration of new species. Accepted This article is protected by copyright. All rights reserved. Materials and Methods Specimen Collections Work began with the collection of spiders from sites across Canada. In contrast to many other groups of terrestrial arthropods where museum specimens are held dry on pins allowing barcode recovery for several decades (Hebert et al. 2013), spiders are typically stored in 70–80% alcohol at room temperature, conditions which lead to rapid DNA degradation (Vink et al. 2005). As a result, barcode recovery is difficult from specimens more than five years old, especially small- bodied species Miller et al. 2013a. Because most of its spiders were collected prior to 2000, the Article Canadian National Collection of Insects, Arachnids and Nematodes (Ottawa) contributed few records to the present study. However, collections at the Royal BC Museum (Victoria) and the Lyman Entomological Museum (Montreal) provided 8.3% and 0.7% of the specimens examined, reflecting their recent involvement in large-scale surveys. The remaining specimens (91%) were acquired through sampling programs led by the Biodiversity Institute of Ontario that employed diverse methods including hand collecting, sieving, sweep netting and trapping (Malaise, pan, pitfall, sticky) at sites across Canada (Fig. 1). Specimen Identifications All specimens
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