Corresponding authors: Angela C Telfer (
Academic editor: Pavel Stoev
Comprehensive biotic surveys, or ‘all taxon biodiversity inventories’ (ATBI), have traditionally been limited in scale or scope due to the complications surrounding specimen sorting and species identification. To circumvent these issues, several ATBI projects have successfully integrated DNA barcoding into their identification procedures and witnessed acceleration in their surveys and subsequent increase in project scope and scale. The Biodiversity Institute of Ontario partnered with the
The existing species inventory for the
It is now universally accepted that we have entered a period of unprecedented global biodiversity loss (
Even prior to the concept’s introduction (
Following this model, the present study introduces DNA barcoding to a long-term biotic inventorying effort being conducted in a temperate nature reserve. The objective is to gauge the effect of adding this tool, in terms of both acceleration and increase of taxonomic scope, while concurrently constructing a reference DNA barcode library to facilitate future research and monitoring at this site. The existing inventory is expanded by employing two surveying strategies – a longer and comprehensive invertebrate trapping scheme, followed by a concentrated effort involving taxonomic experts in the form of a bioblitz (
The
Prior to this study, 2,246 species had been recorded at
Two strategies were employed in an effort to maximize the diversity of organisms inventoried. The first was a comprehensive collecting scheme executed over a period of approximately four months (May to August 2015). It involved a variety of targeted taxa and techniques, but heavily favoured the collection of terrestrial arthropods by passive trapping. Four Malaise traps were set up in various habitats around the
The second strategy for surveying the reserve was a more concentrated effort and involved taxonomic experts – the execution of a bioblitz (
Both surveying strategies provided a large number of specimens that were sorted and prepared for subsequent DNA barcode analyses at the Canadian Centre for DNA barcoding (CCDB;
One or more standard DNA barcode markers were targeted for each major group of organisms: for animals, the mitochondrial gene
For the sequences derived from animal specimens, the records were assigned operational taxonomic units (OTUs) called Barcode Index Numbers (BINs) by the Refined Single Linkage (RESL) algorithm implemented on BOLD (
For each specimen that was assigned an existing BIN, the record received the existing identification of the BIN to the lowest level that did not have taxonomic conflict. For each specimen assigned a new BIN for BOLD, the sequence was queried through the BOLD Identification Engine (BOLD-ID Engine;
Collection data, taxonomic assignment, sequence, electropherograms and primer details for each specimen record, and often a high resolution image, are available on BOLD in the public dataset, "
With the 'Data Spreadsheets' function in the BOLD workbench, the complete dataset was downloaded and reformatted into a Darwin Core Archive (Suppl. material
Telfer A, Young MR, Quinn J, Perez K, Sobel CN, Sones JE, Levesque-Beaudin V, Derbyshire R, Fernandez-Triana J, Rougerie R, Hebert PDN, deWaard JR and contributors* (2015+). Inventory and BioBlitz Records from
* See Suppl. material
or fraternus
subsp pedestris? No authorship found
/ flavofuscum
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or Ganoderma tsugae
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(Tyromyces albellus, Polyorus albellus
f. sorediata
/erinaceous
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Or euchlora
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X floribundum
or petiolata
X floribundum
or virgata
X piperita
or grandiflora
or tenuis
or spinulosa
or vulgare
The two surveying strategies – a four-month long terrestrial arthropod survey, followed by a concentrated bioblitz targeting a variety of taxa – resulted in 25,287 and 3,502 specimens barcoded, respectively, out of a total of 32,645 specimens collected. Observations of an additional 125 species and two higher taxa (for which no voucher specimen was kept) were recorded at the bioblitz (Suppl. material
The most diverse groups were
Combining all existing data results in a final tally of 3,348 species (Table
The present study has conducted an expansive biotic survey, released the data in several public biodiversity data repositories, and published the unique process and findings – all within a relatively modest timeframe. This model for rapid generation and dissemination of critical biodiversity data could be followed to conduct regional assessments of biodiversity status and change, and potentially aid in evaluating progress towards the Aichi Targets of the Strategic Plan for Biodiversity 2011–2020. To fully appreciate this approach, a closer look at four elements is presented: highlights of the biotic inventory, the multiple levels of acceleration, future improvements to the resource, and the utility of the resource going forward.
The biotic inventory of
The rapidness of conducting this inventory was due to the acceleration of several steps that comprise the procedure. Firstly, several types of passive traps were employed to acquire large sample sizes for minimal collector effort. For instance, malaise traps often collect 2,000 specimens in a single week with only minutes of servicing time. Secondly, as discussed above, the addition of DNA barcoding streamlines sorting of the material, dividing the specimens into distinct units, minimizing the total number of specimens that require examination. Thirdly, in addition to the initial sorting, barcoding also provides nearly instant taxonomic assignment by querying against reference libraries using BOLD; the resolution of the assignment for queried records depends on the completeness of the reference library. Fourthly, the processing of the bioblitz material and analyses of the DNA barcode data were accelerated at all possible stages to test how quickly a large volume of specimens could proceed through all steps. The generation of data following the bioblitz was impressive: tissue sampling and lysis within 12 hours; DNA extraction and PCR within 24 h; cycle sequencing, cleanup and sequencer loading by 48 h; edited and validated sequences on BOLD by 72 h; taxonomic assignment, data release and manuscript presubmission by 96 h; final manuscript submission to BDJ by 108 h. The laboratory steps are mostly accelerated by automation, while data sharing is greatly facilitated by data release platforms such as BOLD and the Integrated Publishing Toolkit of Canadensys (
Many BINs are presently identified only to family, subfamily, or at most, genus level. It's important to note that the inventoried taxa that lack species-level determination, including intractable groups such as mites and midges, will be refined over time. Not only does DNA barcoding, empowered by the BIN system, roughly sort the material to direct and minimize the efforts of taxonomic experts (
In addition to this passive approach to refining the taxonomy of these specimens, we will be actively pursuing expert determinations for the unnamed BINs. For many groups, the experts among our coauthors will be able to provide species level resolution in a short period of time (e.g., J.F.-T. specializes in
When a significant number of species and other taxon categories become available, the refined dataset can be updated in the various data repositories and potentially in a second, updated version of the paper in BDJ. Any subsequent versions – each with a separate Digital Object Identifier (DOI) – would be linked to the original paper, allowing for continuing improvement and additions to the species list for the reserve. It is important to emphasize that the taxa awaiting species-level determination still have persistent identifiers as part of the BIN system; each BIN is assigned a BOLD-generated uniform resource identifier (URI) upon its establishment (e.g.
While the overarching objective of the study was to develop, assess and demonstrate a model for conducting and disseminating DNA barcode-assisted biotic surveys, a valuable resource was created in the process. The
Financial support was provided by the Ontario Ministry of Research and Innovation and by the government of Canada through Genome Canada and the Ontario Genomics Institute in support of the International Barcode of Life project. Anne McCain Evans and Chris Evans provided support for the BIObus program (
Author contributions: P.D.N.H. and J.R.D. designed the study; J.S., C.N.S. and M.R.Y. oversaw specimen and sequence analyses; A.C.T., J.R.D. and V.L.-B. conducted the analyses. J.M. and E.S. provided specimen images. All authors discussed the results and contributed to specimen collection, identifications, and to the manuscript, which was written by J.R.D., R.D., J.F.-T.
Map indicating habitat types and sampling sites for the 2015 biotic survey conducted at
Accumulation curves for singleton and total observed BINs for the 2015 survey of
Summary of species inventory for
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Earthworms | 0 | 2 | 2 | 2 |
Spiders and others | 0 | 198 | 198 | 198 | |
Crustaceans | 0 | 7 | 7 | 7 | |
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0 | 9 | 9 | 9 | |
Insects | 832 | 895 | 778 | 1,610 | |
Millipedes, Centipedes | 0 | 6 | 6 | 6 | |
Fishes | 28 | 14 | 3 | 31 | |
Amphibians | 13 | 2 | 0 | 13 | |
Birds | 231 | 87 | 0 | 231 | |
Mammals | 37 | 6 | 1 | 38 | |
Reptiles | 10 | 0 | 0 | 10 | |
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Fungus, Lichens | 191 | 84 | 60 | 251 |
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Snails, Clams | 0 | 18 | 18 | 18 |
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Plants, Mosses, Liverworts | 901 | 103 | 20 | 921 |
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Protozoans | 3 | 3 | 0 | 3 |
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2,246 | 1,433 | 1,102 | 3,348 |
Species inventory of rare prior to May 2015
checklist
Species inventory for
File: oo_55088.xlsx
Bat protocols
protocols
Protocols for the bat component of
File: oo_54234.pdf
Lysis, primer and marker details
laboratory
Details for laboratory work.
File: oo_54237.xlsx
Summary data for 2015 inventory
summary
Summary data for the 28,789 specimens collected for the 2015 inventory, including BIN assignments and locality
File: oo_55064.xlsx
Darwin core archive
occurrences
Darwin core archive of 2015
File: oo_55065.zip
Contributors list
authors
A list of all contributors who took part in the collection and identification of specimens collected as part of the 2015 inventory.
File: oo_54646.xls
Human observations during rare BioBlitz
occurrences
Human observations during
File: oo_55066.xlsx
BIN representative tree
tree
A neighbour-joining tree constructed from a single representative of each distinct BIN collected in
File: oo_55067.pdf
BIN image library
images
A collection of representative images of each BIN collected from the
File: oo_55068.pdf
Final combined inventory for rare Charitable Research Reserve
checklist
The final combined inventory for
File: oo_55089.xlsx
Raw data for accumulation curve
occurences
Lot and BIN data was downloaded for each specimen that received a BIN from BOLD Systems. It was formatted for input into EstimateS (Version 9.1.0) for creation of an accumulation curve.
File: oo_54647.xlsx
Sampling and new record images
images
Images of sampling sites, sampling techniques, specimen processing, and three new provincial spider reccords.
File: oo_54975.pdf