DNA barcoding and Malaise traps capture the remarkable diversity in Canada’s National Parks

Posted on January 13, 2016 by Kate Perez

Hi everyone!

As some of you may know, we here at BIO spend a great deal of our field work sampling in Canada’s beautiful National Parks. In fact, from 2012 to 2014, BIO and Parks Canada partnered up to complete a massive national barcoding project that aimed to map out the country’s arthropod biodiversity: the Canadian National Parks (CNP) Malaise Program. I spent a lot of time planning, organizing, and coordinating this project and am thrilled to finally have results!

To recap, our favourite insect-collecting method is the Malaise trap; a tent-like structure that is effective at capturing various kinds of flying insects. These traps are cost-effective and easily deployed, so BIO provided Malaise trapping kits to Parks Canada staff who executed the insect collection effort in their park throughout the snow-free seasons. Various habitats were sampled from all over the country; including the temperate rainforests of the western Vancouver coast, the Rocky Mountains of British Columbia and Alberta, the prairies of southern Saskatchewan, boreal forests across the country, and the Atlantic Maritimes. Multiple tundra habitats were also sampled in all three Canadian territories including two sites in Quttinirpaaq, Canada’s northern-most park. The program also included two island parks; one in the Pacific (Gwaii Haanas) and one in the Atlantic (Sable Island).

CNP 2012-2014 map legend — Map of Canada indicating CNP Malaise Program sampling sites from 2012-2014.

In 2014, after completing the sampling in all 43 of Canada’s accessible National Parks, staff at BIO spent the next year and a half processing the samples, and completed their analysis in late 2015. Final reports for the 23 parks sampled in 2014, and all the reports compiled from previous years, can be found on our Reports page.

Over just three years the CNP Malaise Program has collected more arthropod species than ever recorded in the history of Canadian biodiversity! We collected a staggering 725K arthropod specimens of which nearly 620K received a DNA barcode resulting in a total of 36,423 distinct ‘barcode clusters’ or presumed species. This represents 13% more species than previously recorded in Canada (32,045 arthropod species as reported by Mosquin et al. 1995). It’s estimated that the total number of known and unknown arthropod species in Canada is 63,643 (Mosquin et al. 1995), and we’ve documented nearly 60% of that potential diversity. The efforts of this program truly highlight the impressive amount of diversity that can be captured using Malaise traps in combination with DNA barcoding for species differentiation.

CNP 2012-2014 MT composite_Page_4 — Images of trap sites from different parks across the country.

An average of 2,000 species was collected from each of the national parks sampled. After two sampling seasons (2012 and 2014), the southern Ontario park, Thousand Islands, had the highest arthropod diversity with 5,244 species gathered. Forillon in Quebec’s Gaspé Peninsula had the second highest species diversity (3,956) followed by the prairie park, Grasslands (3,404), in Saskatchewan. The most commonly encountered species was Smittia sp. – a non-biting midge belonging to the family Chironomidae – with 7,243 individuals barcoded. Despite the huge amount of species diversity we have gathered, there is still much more to be discovered.

Of the 36K species captured, more than half (21K) were unique to a single collection site; meaning they were only detected in one of the 43 parks. In contrast, only 120 species were found in 20 or more parks; the most widespread species was Scatopsciara atomaria (a type of fungus gnat, which you may recognize as the small black flies that appear in your house from potting soil!). This species was found in 36 of the 43 parks. Furthermore, nearly half the species in each park (48%) were represented by only one individual. These observations suggest that we’re nowhere close to collecting all the insects in Canada.

Nevertheless, the CNP Malaise Program has gathered a substantial amount of arthropod diversity data throughout the country. BIO has begun the long process of constructing a real-world “Pokédex” (for those familiar with Pokémon): a comprehensive digital reference including a complete species inventory and barcode library for arthropods in our National Parks. The completion of this extensive 3-year project demonstrates the power of DNA barcoding to help us understand the diversity around us, especially when coupled with this time- and cost-efficient approach for capturing biodiversity using Malaise traps. Ultimately, this study brings us closer to creating a complete DNA barcode library for all species that occur in Canada.

Mosquin, T., Whiting, P.G. and McAllister, D.E. 1995. Canada’s biodiversity: the variety of life, its status, economic benefits, conservation costs and unmet needs. Canadian Centre for Biodiversity, Canadian Museum of Nature. Ottawa, ON. xxiv + 293 p.

The Moss Bosses

Posted on January 3, 2016January 13, 2016 by Liz Darling (Sears)

By Liz Darling (Sears) and Jesse Sills

Hi everyone! Now that the vascular plants of Canada DNA barcoding project is all finished (Read about it here), the team here at the Centre for Biodiversity Genomics has moved on to another group of plants: the Bryophytes. This term broadly encompasses all land plants that do not have any true vascular tissue, which includes the mosses, liverworts and hornworts.

No rolling stones, we can’t seem to stop gathering moss! Liz and Jesse pose with the boxes of specimens

For the first two weeks of February, Jesse Sills, Masha Kuzmina and Liz Darling (Sears) headed off to the capital of Canada to collect mosses from the Canadian Museum of Nature. We were working out of their herbarium, which is located in the secondary collections building, rather than the main building that is accessible to the public (and contains many amazing exhibits!). When creating a reference database, it is incredibly useful to have access to well-curated collections such as this one in order to allow us to take samples from species that have been examined and identified by multiple experts. The idea is basically to collect roughly three specimens of each species available, preferably as widely spread across Canada as possible. This allows us to curate a database of DNA from not only as many species as possible, but also try to investigate whether a species experiences genetic drift when separated by thousands of kilometers. By collecting and barcoding these known species, we can then form a basis to identify unknown species by comparing to the reference database.

There is a plethora of striking similarities between sampling vascular plants and mosses, but several differences actually make sampling the bryophytes significantly more difficult. Firstly, instead of being mounted on herbarium sheets like vascular plants, mosses are stored in envelopes.

The envelopes of mosses are stored upright in boxes within the herbarium cabinets

Although this doesn’t sound like a big difference, having to open and close each envelope to be able to look at the specimens drastically slows down the process. Secondly, mosses are generally a lot smaller than vascular plants, making sampling under a microscope necessary.

Masha peers through the microscope, carefully choosing the material to sample

Jesse sampling at the second microscope station

Thirdly, mosses have a most inconvenient habit of growing in groups with many other species, often closely related to them. This can make it quite difficult to determine which species in the moss clump is the one you are trying to collect. Microscopes and identification books quickly became our best friends when it came to sampling these tiny plants. The museum envelopes can vary from containing a large rock with a small speck of moss on it, to a handful of dirt with some small pieces of moss to a huge piece of moss containing up to 7 different species.

An example of a messy sample, this envelope was mostly gravel and dirt (CCDB-28007-C02)

Some of the specimens were in absolutely beautiful condition (CCDB-28051-B09)

An example of a specimen with multiple species present. Each arrow points to another species – the red one even points to a mollusk! (CCDB-28095-B02) — An example of a specimen with multiple species present. Each arrow points to another species – the red one even points to a mollusc! (CCDB-28095-B02)

We also took images of each specimen using scanners and a camera. Impressively, over the span of 8 days we managed to sample all of the green mosses in the collection – a total of 1805 specimens! This brings the total for the project up to 1981 specimens representing 792 different species of moss.

Setting up the specimens to be imaged involves laying them out on white cardstock with all possible identification sheets easily legible

Liz taking high resolution scans of the specimens

As a relatively poorly studied group of plants, it is not really known how many species of moss there are in Canada, with estimates ranging from 1100 – 2400 species. Wherever the true number lies, it is definitely much higher than we have currently collected, which means we still have a lot of work to do! It just might be that our work helps to uncover some of the mysteries of this microscopic world!

-Liz & Jesse

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