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Wildlife > eDNA - Midterm > Flashcards

eDNA - Midterm Flashcards

1
Q

Advantages of eDNA (state 5)

A
  • Non-invasive
  • More efficient (for aquatics) - highly accurate for species detection
  • More cost effective
  • Able to detect presence of pathogens and diseases
  • Minimizes risk of pathogen transfer between sites
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2
Q

What are the 7 major steps in eDNA analyses in order of their process?

A
  • Survey design
  • Sample collection
  • Sample filtration
  • Filter preservation
  • eDNA extraction
  • Analysis (qPCR)
  • Interpretation
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3
Q

What are 4 major limitations of eDNA?

A
  • Can not accurately quantify species abundance (only presence not detected)
  • Contamination can occur and cause a false positive
  • Interpretation requires the person to have knowledge of the 3 processes that influence detection
  • External sources of DNA can lead to false detection (like equipment)
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4
Q

What are the 3 factors to consider with eDNA?

A

Production
Transport
Degradation

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5
Q

In terms of PRODUCTION, what must be considered?

A
  • The rate of eDNA production release into the habitat varies across species, their life stage, and individuals
  • eDNA methods can not distinguish between different life stages
  • eDNA methods can not indicate abundance
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6
Q

In terms of TRANSPORT, what must be considered?

A
  • The rate of transport (spread/diffusion) of eDNA through water systems vary. This rate of transport is unknown for most species
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7
Q

In terms of DEGRADATION, what must be considered?

A
  • The rate of degradation strongly influences the amount of eDNA present in a sample
  • Life span of DNA in the environment depends several factors like water temp, pH levels, type of flow, etc.
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8
Q

How many days can eDNA persist in water source (general rule of thumb)?

A

7 - 21 Days after the removal of the organism from the system

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9
Q

Why must one carefully consider their study objective before using eDNA?

A
  • eDNA cannot determine a link to concentration of eDNA in a habitat to species abundance
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10
Q

When should you survey using eDNA?

A
  • When the timing is right (coincide with breeding season or biological timing windows)
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11
Q

What is an advantage of increasing survey effort?

A
  • yields high confidence in results
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12
Q

What is a disadvantage of increasing survey effort?

A
  • increases project labour and cost
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13
Q

What guides the level of sampling effort needed for both eDNA or traditional sampling methods?

A
  • OBJECTIVES!
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14
Q

What 4 factors influence the number of samples collected at a site?

A
  • Objectives
  • Budget
  • System (lotic or lentic)
  • Target species
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15
Q

What is the recommended number of samples for:

a) well studied high confidence species detection probabilities
b) Unknown detection probabilities
c) New species or practitioner

A

a) 1 sample sufficient
b) 3 samples recommended
c) 1 negative control sample per processing session is recommended

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16
Q

What is the recommended spacing for samples?

A
  • up to 50 m apart collected at locations where target species is likely to occur
17
Q

What is the recommended sample volume to be taken?

A
  • 1 L per sample, with 3 samples per site

- Should be consistent within study design for a single study when detection probabilities will be compared

18
Q

Where should sample be taken?

A
  • Surface water
  • Lotic sample collected from surface water in the thalweg
  • Multiple samples should be collected from same feature, in up stream manner to avoid contamination
19
Q

When sampling in multiple time periods, what pattern of sampling produces:

a) strong results
b) stronger results
c) strongest results

A

a) sampling across seasons within one time year
b) sampling in one season across multiple years
c) sampling across multiple seasons over multiple years

20
Q

What are the 2 methods for storage of field samples?

A
  • filters can be preserved and stored in molecular grade ethanol in the dark and remain viable for at least 6 months
  • samples can be folded inward and placed in coin envelope in a bag with self-indicating silica beads until desiccated
  • Once extracted, can be stored indefinitely
21
Q

When should you NOT collect samples in a lake/stream?

A
  • After or during high rainfall event or high flow events
22
Q

Provide 4 steps to avoid cross contamination

A
  • Do not leave sample gear unprotected/exposed
  • Do not enter water upstream of sample site, or within 3 m in lentic environment
  • Ensure sampling occurs before other field studies happen where personnel enter the water
  • Adhere to “hygiene protocols for amphibian field staff” to prevent spread of infectious diseases
23
Q

Describe the process of collecting water samples

A
  • LABEL lid and bottle with time, date, site, staff
  • CLEAN gloves, and refrain from touching anything other than bottle
  • Fill, shake, rinse bottle and empty away from site
  • RINSE x3 total
  • FILL sample bottles from surface water (typically 3 bottles, about 10 m apart)
  • Put samples in COOLER with ice
  • Collect water QUALITY with water quality meter
  • DECONTAMINATE clothing
24
Q

When should filtering occur?

A
  • Within 24 hours of sample collection
25
Q

What order should samples be filtered?

A
  • same order they were collected
26
Q

Where should filtering occur?

A
  • workspace dedicated to filtration
27
Q

How should samples be preserved?

A
  • cellulose membrane is filtered and the membrane is preserved in a vial with molecular grade ETHANOL or a coin-envelope stored in a bag with self indicating silica beads
28
Q

How should samples be labeled?

A
  • Ethanol resistant marker

- Project ID, site name, collection date, staff

29
Q

How should filter paper be handled once filtration is complete?

A
  • Using decontaminated forceps

- Never touched by hand!

30
Q

What are some cautions needed when interpreting positive results?

A
  • May represent true positive or false positive (Type 1 error)
  • For larger lentic or lotic water bodies, it is possible to have uneven distribution of target taxa eDNA
31
Q

What are some factors that may affect the reliability of eDNA results? (7 total)

A
  • eDNA may have been introduced through other means (feces)
  • May have been introduced by contamination
  • Environmental conditions
  • Low densities of target organisms in the habitat
  • Large distance from source organism
  • Suspended materials in samples causing reduced sensitivity
  • Timing of sample collection

Wildlife (14 decks)

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