Abstract
Noninvasive DNA sampling from scats can provide powerful tools for wildlife research depending in large part on how scats are collected in the field. Preservation of scat in 95-100% ethanol can be highly effective, but not always practical. Use of swabs to sample the mucous layer from scats is a popular alternative, but has not been adequately tested in arid environments, where the mucous layer can rapidly desiccate. We conducted a paired comparison of methods, extraction from scats stored in ethanol ("direct method") versus from swabs ("swab method"), for carnivore scats collected under typical field conditions during May-September 2013 and January-February 2015 in northern California, USA. Direct quantification of DNA indicated that the extracts from ethanol-preserved direct-method samples contained, on average, an order of magnitude (14×) more target DNA than extracts from swab method (P < 0.03). For mitochondrial sequencing, which is typically used for species-typing, we obtained slightly higher success for the direct (81%) than the swab (73%) extracts, but not significantly so (P = 0.25, n = 104). Among 62 canid scats, microsatellite genotyping (typically used for individual identification) was much more successful for the direct extracts (74%) than the swab extracts (35%; P < 0.001, n = 62). Together, our findings indicated a substantial advantage of ethanol preservation followed by extraction directly from scats over swabbing in our arid study area. Our results apply most specifically to canids in the arid study environment; swabbing is potentially more effective in humid environments or in other carnivore species. Nevertheless, our findings highlight the importance of conducting pilot studies before committing to swabbing as a means of fecal DNA collection.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 797-803 |
| Number of pages | 7 |
| Journal | Wildlife Society Bulletin |
| Volume | 39 |
| Issue number | 4 |
| DOIs | |
| State | Published - Dec 1 2015 |
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Keywords
- DNA
- mesocarnivore
- microsatellites
- mitochondrial
- noninvasive genetics
- scat
- swab
ASJC Scopus subject areas
- Nature and Landscape Conservation
Cite this
A paired comparison of scat-collecting versus scat-swabbing methods for noninvasive recovery of mesocarnivore DNA from an arid environment. / Miles, Kathleen A.; Holtz, Michelle N.; Lounsberry, Zachary; Sacks, Benjamin.
In: Wildlife Society Bulletin, Vol. 39, No. 4, 01.12.2015, p. 797-803.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - A paired comparison of scat-collecting versus scat-swabbing methods for noninvasive recovery of mesocarnivore DNA from an arid environment
AU - Miles, Kathleen A.
AU - Holtz, Michelle N.
AU - Lounsberry, Zachary
AU - Sacks, Benjamin
PY - 2015/12/1
Y1 - 2015/12/1
N2 - Noninvasive DNA sampling from scats can provide powerful tools for wildlife research depending in large part on how scats are collected in the field. Preservation of scat in 95-100% ethanol can be highly effective, but not always practical. Use of swabs to sample the mucous layer from scats is a popular alternative, but has not been adequately tested in arid environments, where the mucous layer can rapidly desiccate. We conducted a paired comparison of methods, extraction from scats stored in ethanol ("direct method") versus from swabs ("swab method"), for carnivore scats collected under typical field conditions during May-September 2013 and January-February 2015 in northern California, USA. Direct quantification of DNA indicated that the extracts from ethanol-preserved direct-method samples contained, on average, an order of magnitude (14×) more target DNA than extracts from swab method (P < 0.03). For mitochondrial sequencing, which is typically used for species-typing, we obtained slightly higher success for the direct (81%) than the swab (73%) extracts, but not significantly so (P = 0.25, n = 104). Among 62 canid scats, microsatellite genotyping (typically used for individual identification) was much more successful for the direct extracts (74%) than the swab extracts (35%; P < 0.001, n = 62). Together, our findings indicated a substantial advantage of ethanol preservation followed by extraction directly from scats over swabbing in our arid study area. Our results apply most specifically to canids in the arid study environment; swabbing is potentially more effective in humid environments or in other carnivore species. Nevertheless, our findings highlight the importance of conducting pilot studies before committing to swabbing as a means of fecal DNA collection.
AB - Noninvasive DNA sampling from scats can provide powerful tools for wildlife research depending in large part on how scats are collected in the field. Preservation of scat in 95-100% ethanol can be highly effective, but not always practical. Use of swabs to sample the mucous layer from scats is a popular alternative, but has not been adequately tested in arid environments, where the mucous layer can rapidly desiccate. We conducted a paired comparison of methods, extraction from scats stored in ethanol ("direct method") versus from swabs ("swab method"), for carnivore scats collected under typical field conditions during May-September 2013 and January-February 2015 in northern California, USA. Direct quantification of DNA indicated that the extracts from ethanol-preserved direct-method samples contained, on average, an order of magnitude (14×) more target DNA than extracts from swab method (P < 0.03). For mitochondrial sequencing, which is typically used for species-typing, we obtained slightly higher success for the direct (81%) than the swab (73%) extracts, but not significantly so (P = 0.25, n = 104). Among 62 canid scats, microsatellite genotyping (typically used for individual identification) was much more successful for the direct extracts (74%) than the swab extracts (35%; P < 0.001, n = 62). Together, our findings indicated a substantial advantage of ethanol preservation followed by extraction directly from scats over swabbing in our arid study area. Our results apply most specifically to canids in the arid study environment; swabbing is potentially more effective in humid environments or in other carnivore species. Nevertheless, our findings highlight the importance of conducting pilot studies before committing to swabbing as a means of fecal DNA collection.
KW - DNA
KW - mesocarnivore
KW - microsatellites
KW - mitochondrial
KW - noninvasive genetics
KW - scat
KW - swab
UR - http://www.scopus.com/inward/record.url?scp=84962242121&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84962242121&partnerID=8YFLogxK
U2 - 10.1002/wsb.600
DO - 10.1002/wsb.600
M3 - Article
AN - SCOPUS:84962242121
VL - 39
SP - 797
EP - 803
JO - Wildlife Society Bulletin
JF - Wildlife Society Bulletin
SN - 0091-7648
IS - 4
ER -