Environmental DNA (eDNA) from a Consultant's Perspectivechelbing/Hobbs-eDNA-consultant.pdf · •...

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Environmental DNA (eDNA) from a Consultant's Perspective By: Jared Hobbs, M.Sc., R.P.Bio., Senior Technical Expert / Biologist

Transcript of Environmental DNA (eDNA) from a Consultant's Perspectivechelbing/Hobbs-eDNA-consultant.pdf · •...

Page 1: Environmental DNA (eDNA) from a Consultant's Perspectivechelbing/Hobbs-eDNA-consultant.pdf · • Environmental DNA (eDNA) is a proven powerful and efficient method for conducting

Environmental DNA (eDNA) from a Consultant's Perspective

By: Jared Hobbs, M.Sc., R.P.Bio.,

Senior Technical Expert / Biologist

Page 2: Environmental DNA (eDNA) from a Consultant's Perspectivechelbing/Hobbs-eDNA-consultant.pdf · • Environmental DNA (eDNA) is a proven powerful and efficient method for conducting

Outline

1) Challenges and opportunities in Environmental Assessment Processes

2) The Importance of Rigour and Standards

3) Implementationa) Responsible Adoption

b) Proof of Concept

4) Looking Ahead

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Challenges and Opportunities in Environmental assessment Processes

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Conventional methods

• Environmental resource management requires accurate ecological information regarding the health of a given ecosystem and the distributions of the species that occupy it.

• Conventional survey techniques used to collect and analyze a species’ distribution are characterized as: labour intensive,

require skilled experts to design and lead the program,

susceptible to observer bias,

offer relatively limited capabilities to confirm species’ distributions

invasive to target taxa and / or destructive to their sensitive habitats

Page 5: Environmental DNA (eDNA) from a Consultant's Perspectivechelbing/Hobbs-eDNA-consultant.pdf · • Environmental DNA (eDNA) is a proven powerful and efficient method for conducting

PRAGMATIC ADVANTAGES OF eDNA

More accurate / sensitive and less subjective to bias Synchronous study of multiple species with less

restrictive timing windows Retro-active addition of focal taxa Less invasive to species and ecosystems, no risk of

pathogen transfer. Also safer for field staff. No permitting requirements

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When to use eDNA?

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Cost / Benefit Analysis (CBA)

• Cost Benefit Analysis (CBA): a systematic evaluation to comparatively asses the strengths and weaknesses associated with the application of eDNA vs. conventional methods.

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Cost / Benefit Analysis (CBA)

Vs.

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The Importance of Rigour and Standards

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Developing Lab Standards / Publishing Results• In collaboration with the University of

Victoria (Helbing Lab) we developed provincial standards for eDNA that set requirements for qPCR sample testing and assay development.

• Our methods were published in PLOS One.

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UVic / Maxxam Lab Standards for qPCR Analysis – A more rigorous approach

3 Runs

Most labs conduct 3 runs on each sample for the target taxa.

e”Target”

We also use plate controls: 2 pos/1 neg

8 technical replicates/sample

eTarget

Increased confidence in results (90-

100%)

4 technical replicates/sample

ePlant

Poor quality samplePerform inhibitor cleanup

&Retest with ePlant

UVic conduct 16 runs on each sample to control for false negatives

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Standardized Approach: MOE Standards

• We authored provincial MOE RISC standards that detail procedures for sample collection, filtration and preservation.

• We provide(d) internal training, through courses and collaborative project implementation, to facilitate consistency and rigour during application.

TRC Review Panel Feedback regarding the protocol? a. It seems to be thorough, and gives lots of

information in regards to what affects detection rates and common sources of contamination.

b. My overall impression is that it is a solid protocol that has had input from two strong labs (the Goldberg and Helbing labs) that are leading the way (with Hemmera) in eDNA research on the west coast.

2. Are the protocols technically sound? a. Yes, they are good. 3. Is the protocol easy to follow? a. Yes

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Implementation: Responsible Adoption

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We recognized the need to engage regulatory agencies first – if they didn’t adopt this method we couldn’t apply it to meet our clients needs.

We also needed to provide guidance to our staff to ensure rigour in our application: we developed an internal SOP; this later became a provincial standard.

2014 (8 projects)GMT eDNA Assessment 2014

SFPR eDNA Assessment 2014

Spadefoot and Tiger Salamander

Rocky Mountain Tailed Frog-Flathead 2014

Pacific Water Shrew eDNA

Giant Salamander Sunshine Coast PWS and ASTR eDNA

Woodfibre LNG

eDNA in BC: Year One - 2014

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eDNA in BC: Year Two - 2015

We expanded our application to Yukon, engaged more deeply with more academic labs (Yukon College, Helbing Lab-UVic and Montana).

We also expanded focus to additional target taxa and environments.

2015 (8 projects)GMT eDNA Assessment 2015SFPR eDNA Assessment 2015

Port Metro Vancouver S@Risk InventoryColony Farms eDNA Assessment

Rocky Mountain Tailed Frog-wigwam

CDC Yukon eDNA for Western Toad and Columbia Spotted Frog

CDC Yukon Pathogen assessment

eDNA Standards DevelopmentYukon SIF (salmon project with Yukon college)

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eDNA in BC: Year Three - 2016

We continued to expand focus on new species, in new geographies, for new clients and with new partnerships.

2016 (8 projects)Arctic Greyling

MLNG eDNA (amphib's at risk)

SFPR/GMT eDNA Assessment 2016

FWCP coastal tailed frog - Lillooet

Rocky Mountain Tailed Frog-Yahk

CDC Pathogens/Training

Creston Bullfrog

HCTF Red-legged frog

In 2016, we also began to develop fish primers!

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eDNA in BC: Year Four - 2017

2017 (21 projects)Yukon Grayling and Chinook (3 collections in 2017)

Stave eDNA

Carmanah / Walbran lentic eDNA

CRD Bullfrog Assessment

HCTF Oregon spotted frog/Cascades frog (year 2)

Yukon Env. Western Toad (Watson Lake)

Atlin Western Toad

Okanagan Invasive Species-Sampling

PMV Sp@Risk

SRWS Chinook Barrier Assessment

Bayonne Creek Mine SAR assessment

Stulkawhits coastal tailed frog assessment

Fraser Leachate Lagoons eDNA assessment

Dollarton Pacific water shrew/coastal tailed frog eDNA

Prince Rupert Port Authority South Kaien Island

Rocky Mountain Tailed Frog-Yahk

Kitimat coastal tailed frog and efish

Rivers Inlet Salmon and coastal tailed frog

BCIC Ignite provides funding to Hemmera/Uvic to accelerate commercialization of new technologies and innovations in the natural resources and applied sciences in British Columbia. Awarded $188K of funding to support development and research of eDNA.

Hemmera was awarded recognition, at RemTech 2017, for leadership in “innovation” for our work with eDNA development.

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Implementation: Proof of Concept

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eDNA Projects: BC and Beyond

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Tailed Frog: Two examples

• Occur in cool, permanent well oxygenated mountain streams with a step-pool morphology

• Prefer cobble substrate with lots of interstitial spaces; low tolerance for sedimentation.

• Adults use riparian habitats for terrestrial foraging.

• Eggs laid under large rocks in the thalwag.

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Coastal Tailed Frog: Distribution

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Coastal Tailed Frog: 2016 eDNA Project

• In 2016 we used eDNA to survey suitable habitats in the Cascades, along the eastern limit of the species’ range in British Columbia.

List Status

BC CDC Blue listed

COSEWIC Threatened

SARA Endangered S.1

2016 FWCP Project location

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Coastal Tailed Frog

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Coastal Tailed Frog

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Rocky Mountain Tailed Frog: Distribution

• Global distribution from BC, Montana, Idaho, Washington and Oregon

• Two geographically disparate populations in BC; Yahk & Flathead Rivers; in 39 stream reaches.

List Status

BC CDC Red listed

COSEWIC Endangered

SARA Endangered S.1

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Previous Inventory Results

Study YearTotal TCS

SitesPositive

Detections

1996-1998 239 19

2001 220 79

2003 204 63

2004 50 0

Total 713 161

Page 27: Environmental DNA (eDNA) from a Consultant's Perspectivechelbing/Hobbs-eDNA-consultant.pdf · • Environmental DNA (eDNA) is a proven powerful and efficient method for conducting

(Previous) Canadian Distribution

Yahk Flathead

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eDNA Results

Yahk

Flathead

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Current Canadian Distribution

YahkFlathead

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Tiger Salamander - Okanagan

• Extralimital site at Ritchie Lake tested positive in 2014 however eDNA was new, so there was some skepticism and reticence to trust the result.

• Three years later a govt biologist found, photographed and reported a tiger salamander at Ritchie Lake!

• Objective: to assess presence of tiger salamander in the Okanagan Valley, BC.

• 2014: 35 sites sampled, 11 positive

• 2017: 19 sites sampled, 10 positive

Email from Bryn White (BC MOE)April 16, 2018“Hi Jared - look at this fat little beauty I found at Ritchie Lake in Garnet Valley north of Summerland (we fenced it) -that was the one that you tested with E DNA and came up positive for SPIN and AMTI. “

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Tiger Salamander -Okanagan

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Invasive Species Applications: American Bullfrog

• Objective: to assess presence of American bullfrog in the Okanagan Valley, BC.

• 2017: 10 sites sampled, 1 positive & 1 suspected

• This result was after an intensive multi-year eradication program that was purported to have eliminated American bullfrog from the Okanagan

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Looking Forward: The Path Ahead

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Application Opportunities

UVic and Hemmera have made important technical advancements to mitigate type one and type two errors?With our advancements in application of this method eDNA now provides a potentially powerful solution to more confidently inform many of the challenges faced by environmental professionals:

Better inform operational designs

Create efficiencies in compliance monitoring to assess effectiveness of mitigation activities

Identify appropriate compensatory habitat

Efficiently inform effectiveness assessment of site reclamation and functional restoration efforts

Facilitate broad scale inventory to better understand species distribution, and inform risk assessment to wildlife at a population level, or landscape scale

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How can eDNA be applied to realize efficiencies in new geographies? Can we help proponents

understand the advantages conferred by eDNA ?

Can we help proponents, and their QEPs, identify opportunities for more efficient and cost effective solutions?

Collaborative Engagement

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Sharing our Advances: Training

Training is provided, through NRTG , to Environmental practitioners, regulatory agencies and clients to ensure rigorous, accurate and cost-effective application of eDNA methods.

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Recognizing Opportunities to Support

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Who’s interested in eDNA?

Really? Who’s not???

• Regulators (gain improved understanding, using potentially the most cost-effective, non-detrimental methods available)

• Resource managers who want to ensure rigor in baseline studies and are looking for cost-effective methods.

• Practitioners with interests in applied conservation and research

• Academic institutions

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eDNA Methods in BC: A Summary

• Environmental DNA (eDNA) is a proven powerful and efficient method for conducting aquatic survey for species of management concern (e.g. species at risk, introduced species, wildlife pathogens).

• Hemmera (working with C. Helbing and C. Goldberg) was the first to apply eDNA in a commercial (non-academic) setting in western Canada. We’re excited by its potential to:

greatly enhance knowledge to conserve (aquatic) species at risk

assess restoration program effectiveness

support environmental assessment processes

assess invasive species control programs

support development of monitoring programs for management purposes

Page 40: Environmental DNA (eDNA) from a Consultant's Perspectivechelbing/Hobbs-eDNA-consultant.pdf · • Environmental DNA (eDNA) is a proven powerful and efficient method for conducting

Available eDNA PrimersSpecies Common Name

Anaxyrus (Bufo) boreas Western toad

Ascaphus montanus Rocky mountain tailed frog

Ascaphus truei Pacific (Coastal) tailed frog

Lithobates (Rana) catesbeiana North American bullfrog

Lithobates (Rana) pipiens Northern leopard frog

Oncorhynchus kisutch Coho salmon

Oncorhynchus tschawytscha Chinook salmonRana aurora Northern red-legged frog

Rana cascadae Cascades frog

Rana luteiventris Columbia spotted frog

Rana pretiosa Oregon spotted frog

Sorex bendirii Pacific water shrew

Thymallus arcticus Arctic Grayling

eFish FisheFrog Frog

eMammal Mammal

ePlant Plant

Spea intermontana Great Basin spadefoot

Ambystoma mavortium Tiger Salamander

Oncorhynchus clarkii Cutthroat trout

Oncorhynchus mykiss Rainbow trout

Oncorhynchus nerka Sockeye Salmon

Page 41: Environmental DNA (eDNA) from a Consultant's Perspectivechelbing/Hobbs-eDNA-consultant.pdf · • Environmental DNA (eDNA) is a proven powerful and efficient method for conducting

Contact Us

Jared Hobbs

Hemmera Envirochem Inc.18th Floor, 4730 Kingsway Burnaby, BCT: [email protected]

Thank you