Publications by authors named "Stephanie L Dewaard"

4 Publications

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A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples.

Sci Data 2019 12 6;6(1):308. Epub 2019 Dec 6.

Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.

The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet's land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.
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http://dx.doi.org/10.1038/s41597-019-0320-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6897906PMC
December 2019

Expedited assessment of terrestrial arthropod diversity by coupling Malaise traps with DNA barcoding .

Genome 2019 Mar 26;62(3):85-95. Epub 2018 Sep 26.

a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.

Monitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches. The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance. Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 21 194 specimens representing 2255 species. These protocols can support arthropod monitoring programs at regional, national, and continental scales.
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http://dx.doi.org/10.1139/gen-2018-0093DOI Listing
March 2019

Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada.

Appl Plant Sci 2017 Dec 22;5(12). Epub 2017 Dec 22.

Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.

Premise Of The Study: Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada.

Methods: Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recovered from the plastid loci and and from the nuclear ITS2 region. We used beta regression to quantify the effects of age, type of preservation, and taxonomic affiliation (family) on DNA sequence recovery.

Results: Specimen age and method of preservation had significant effects on sequence recovery for all markers, but influenced some families more (e.g., Boraginaceae) than others (e.g., Asteraceae).

Discussion: Our DNA barcode library represents an unparalleled resource for metagenomic and ecological genetic research working on temperate and arctic biomes. An observed decline in sequence recovery with specimen age may be associated with poor primer matches, intragenomic variation (for ITS2), or inhibitory secondary compounds in some taxa.
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http://dx.doi.org/10.3732/apps.1700079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749818PMC
December 2017

Untangling taxonomy: a DNA barcode reference library for Canadian spiders.

Mol Ecol Resour 2016 01 26;16(1):325-41. Epub 2015 Jul 26.

Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada.

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% vs. 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 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 analysed for a species and its BIN count. However, three species were clear outliers with their specimens being placed in 11-22 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.
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http://dx.doi.org/10.1111/1755-0998.12444DOI Listing
January 2016
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