Centre for Biodiversity Genomics - Canadian Specimens

Study Extent

Sampling frequency varies according to project, year and location of collection. Please see individual data records for complete collection details.

Sampling

Please see individual data records for complete collection details.

Quality Control

All specimens are visible on BOLD (www.boldsystems.org). Through comparison with other specimens using their DNA barcode sequences, contaminated specimens and misidentifications were discovered and fixed where possible. All fields underwent a data cleansing process to ensure data were entered in a standardized matter.

Method steps

1. Please see individual data records for complete collection details.

Specimens were identified to species where possible by taxonomic experts. As we operate a high-throughput facility with an influx of approximately 1 million specimens every year, we also rely on semi-automated and automated methods of assigning taxonomy to specimens. Using DNA barcode sequences from BOLD Systems (BOLD; www.boldsystems.org), these remaining specimens were assigned a taxonomic name based on sequence similarity to named specimens. Two different procedures were used to assign names based on DNA barcode sequences: 1)CollectionsID - Taxonomic names were assigned to all specimens found in the same Barcode Index Number (BIN). An advanced algorithm is used to cluster BINs based on sequence similarity and BINs show high concordance with species (see Ratnasingham and Hebert 2013 https://doi.org/10.1371/journal.pone.0066213). CollectionsID scans the existing database of named specimens, and assigns taxonomic information whenever a BIN match is found. Applies to : Phylum- Species level ID 2)BOLD ID Engine (Manual) – BOLD stores sequence information for every barcoded organism. The BOLD ID Engine compares the sequence similarity of your chosen specimen against the other sequences in the database, and returns the taxonomic information for the best matches. We then assign taxonomy based on the following rule set: a.Order to Family identification: Assigned when class, order, or family name has greater than 80% sequence similarity to listed results b.Genus identification: Assigned when genus name has greater than 95% sequence similarity to listed results c.Species identification: Assigned when species name has greater than 98% sequence similarity to listed results (indicating specimens are from the same BIN) If there are conflicts present in the result (i.e. more than one family name present and having greater than 80% sequence similarity), we assign names when it is overwhelmingly clear one name is more prevalent and is likely the correct taxonomic name (i.e. 20 Tipulidae listed, 1 Limoniidae, we would assign Tipulidae). This is a judgment call made by trained senior staff of the CBG Collections Unit.

1. Arthropoda
   rank: phylum
2. Chordata
   rank: phylum
3. Annelida
   rank: phylum
4. Mollusca
   rank: phylum
5. Cnidaria
   rank: phylum
6. Platyhelminthes
   rank: phylum
7. Brachiopoda
   rank: phylum
8. Bryozoa
   rank: phylum
9. Echinodermata
   rank: phylum
10. Hemichordata
    rank: phylum
11. Nematoda
    rank: phylum
12. Nemertea
    rank: phylum
13. Porifera
    rank: phylum
14. Priapulida
    rank: phylum
15. Rhodophyta
    rank: phylum
16. Tardigrada
    rank: phylum

These specimens derive from Canada, stemming primarily from collections made by the CBG at 159 sites since 2008 including 45 national parks, 65 provincial parks and 49 other protected or private areas.