Non-invasive DNA Sampling
1 WORKSHOP OUTLINE
I.
Introductions and Course Overview (10 min)
II.
Participants share their workshop goals and experience with non-invasive
techniques (15 min)
III.
DNA applications, types of non-invasive samples, and benefits of each (15 min)
a. Scat Samples
b. Hair Samples
c. Others
IV.
Research Examples (15 min)
a.
b.
c.
d.
e.
Bat feces
Fox feces
Coyote feces
Fisher hair
Otter feces
V.
Proper Handling and Storage of Samples (10 min)
VI.
Field Techniques and Sample Collection Demonstration (Outdoor) (1.25 hour)
a. Scat transects
b. Hair snares
c. GPS and data collection
VII.
Partnering strategies for DNA work (10 min)
VIII.
Integrating projects into courses (10 min)
IX.
Session wrap-up and questions (20 min)
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2 NON-INVASIVE DNA APPLICATIONS
The discovery of PCR and microsatellite primers has made non-invasive genetic sampling
feasible by allowing small amounts of DNA to be amplified and used for identification.
Mitochondrial DNA (mtDNA) is found in the mitochondria of a cell. It is unique in that it is only
passed to offspring from mothers. Mitochondrial DNA is less variable within species, but
variable between species, so it is used for species identification.
Nuclear DNA is obtained from the nucleus of the cell and is used for individual identification or
fine-scaled population genetics because it is more variable within a species.
Non-invasive genetic analysis can be applied to a wide-range of wildlife research:
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Species Determination
Sex Determination
Paternity and relatedness
Individual Identification
Estimation of Population Size and Sex Ratio
Management of Captive and Reintroduced Populations
Diet assessment
Hybridization and Inbreeding
Wildlife Forensics
Wildlife objectives related to ecology, management, and conservation:
Abundance and relative abundance
Occupancy
Species distribution and range
Sex-specific movements
Turnover rates and survival
Population genetics (study of the distribution and frequency of genes)
Population size, gene flow, mating systems, genetic diversity, relationships between
populations
Spatial organization
Landscape genetics
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3 PROPER HANDLING AND STORAGE OF SAMPLES
MOISTURE AND CONTAMINATION
Moisture is the enemy of DNA samples, causing the DNA to degrade quickly! Keep samples as dry as
possible by storing samples with a desiccant. Freezing is not a preferred method for wildlife samples.
Contamination with human DNA is not a huge concern with wildlife samples unless you are working with
primates. Microsatellite markers are species specific, and laboratories will use markers for the study
species that will not be confused with human DNA. Therefore, wearing gloves during sample collection
is not necessary to prevent contamination with human DNA, but should be used if contamination
between samples may occur, and to protect the safety of field personnel.
TYPES OF SAMPLES
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SCAT
Prey items in scat can sometimes be detected instead of the species depositing the scat. Take surface
rubs of fresh scat using absorbent swab (such as a Q-tip). Swabs can be stored in a breathable envelope,
or in a tube of desiccant.
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HAIR
DNA from hair is located in the hair follicles. Hair contains fewer chemical inhibitors than feces. When
collecting hairs, use devices that pluck hairs, rather than removing hairs that have already shed (hair
follicle may not be present). Store hairs in breathable (non-wax) envelopes.
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BONE AND ANTLERS
Bones and antlers can be a good source of DNA if they do not decompose when drying. Bone and antler
shavings can be stored dry in breathable paper envelopes.
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FEATHERS
Feathers can be an excellent source of DNA. Store feathers in breathable envelopes.
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EGGSHELLS
Eggshell membranes are a good source of DNA. Use cellophane tape on the outer side of the shell and
tape to a breathable envelope. Do not tape on the membrane side due to the risk of trapping moisture.
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URINE AND SALIVA
Urine and saliva are alternate sources of non-invasive DNA (urine in snow, scent posts). Check the
current literature for handling and storage.
LABELING SAMPLES
All samples should have a unique identification code. Include an electronic file with field data associated
with the sample (date of collection, location, etc.) when submitting samples to a laboratory.
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4 NON-INVASIVE DNA RESOURCES
BOOKS:
Non-invasive survey methods for carnivores. 2008. Robert A. Long, Paula MacKay, William J.
Zielinski, Justina C. Ray, editors. Island Press. 375 pp.
LABORATORIES:
Wildlife Genetics International, Inc.
http://www.wildlifegenetics.ca
P.O. Box 274
Nelson, BC V1L 5P9
877-352-3563
Northeast Wildlife DNA Laboratory
http://www4.esu.edu/academics/departments/biology/dna/services.cfm
East Stroudsburg University
Jane Huffman, Director
jhuffman@esu.edu
(570) 422-7891
LAB EQUIPMENT SUPPLIERS:
Qiagen – DNA Purification Kits
http://www.qiagen.com
Mo Bio – DNA Purification Kits
http://www.mobio.com/
Life Technologies – Invitrogen Custom DNA Primers and DNA Purification Kits
http://www.invitrogen.com/site/us/en/home/Products-and-Services/Product-Types/PrimersOligos-Nucleotides/invitrogen-custom-dna-oligos.html
Eurofins Operon – PCR Ready Primers
http://www.operon.com/products/pcr-primers/pcr-primer-overview.aspx?id=pcr
GENETIC DATABASES:
GenBank; National Center for Biotechnology Information
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