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Estimating Mountain Goat Abundance using DNA from Fecal Pellets

Article  in  Journal of Wildlife Management · August 2011

DOI: 10.1002/jwmg.184

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The Journal of Wildlife Management 75(6):1527–1534; 2011; DOI: 10.1002/jwmg.184

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Estimating Mountain Goat Abundance

Using DNA From Fecal Pellets
KIM G. POOLE,1 Aurora Wildlife Research, 1918 Shannon Point Rd., Nelson, BC, Canada V1L 6K1
DARRYL M. REYNOLDS, British Columbia Ministry of Forests, Lands and Natural Resource Operations, P.O. Box 950 Stn. Prov. Govt.,
Sechelt, BC, Canada V0N 3A0
GARTH MOWAT, British Columbia Ministry of Forests, Lands and Natural Resource Operations, Suite 401, 333 Victoria St., Nelson, BC,
Canada V1L 4K3
DAVID PAETKAU, Wildlife Genetics International, P.O. Box 274, Nelson, BC, Canada V1L 5P9

ABSTRACT Non-invasive collection of tissue samples to obtain DNA for microsatellite genotyping required
to estimate population size has been used for many wildlife species but rarely for ungulates. We estimated
mountain goat (Oreamnos americanus) population size on a mountain complex in southwestern British
Columbia by identification of individuals using DNA obtained from fecal pellet and hair samples collected
during 3 sampling sessions. We identified 55 individuals from 170 samples that were successfully genotyped,
and estimated a population of 77 mountain goats (SE ¼ 7.4). Mean capture probability was 0.38
(SE ¼ 0.037) per session. Our technique provides one of the first statistically rigorous estimates of
abundance of an ungulate species using DNA derived primarily from fecal pellets. Our technique enables
managers to obtain minimum counts or population estimates of ungulates in areas of low sightability that can
be used for conservation and management. ß 2011 The Wildlife Society.

KEY WORDS abundance, British Columbia, DNA, fecal pellets, mark–recapture, mountain goats, Oreamnos
americanus.

Non-invasive collection of tissue samples to obtain DNA for
microsatellite genotyping required to identify individuals and
produce estimates of population size has been used for many
wildlife species, mainly carnivores (e.g., Woods et al. 1999,
Mowat and Paetkau 2002, Paetkau 2003). Non-invasive
DNA sampling of ungulate populations is uncommon
(Eggert et al. 2003, Piggott and Taylor 2003, Maudet
et al. 2004, Van Vliet et al. 2008). Ungulate tissue samples
obtained from carcasses have been used to examine genetic
diversity and population or subspecies questions (McFarlane
et al. 2009), and pellets collected in the field have contributed
to understanding of phylogenetics and population genetics
(Gebremedhin et al. 2009). Although population estimates
have been obtained from collection of carnivore scat
(Bellemain et al. 2005), only recently have pellets been
used to provide population estimates of ungulates using a
mark–recapture study design (Eggert et al. 2003, Valière
et al. 2007, Harris et al. 2010, Brinkman et al. 2011).
Most DNA studies have obtained DNA from hair collected
using barbed wire or glue. Collection of fecal pellet samples
(hereafter pellets) is attractive because of the ease of collec-
tion, potential for obtaining large sample sizes, and reduced
disturbance to the focal species. However, pellets may yield
low quality and quantity of DNA (Waits and Paetkau 2005,
Received: 22 April 2010; Accepted: 1 February 2011;
Published: 15 July 2011
1
E-mail: kpoole@aurorawildlife.com
Brinkman and Hundertmark 2009), in part a result of time
since deposition, sensitivity to weather factors, and DNA
contamination by micro-organisms (Maudet et al. 2004,
Piggot 2004, Murphy et al. 2007, Brinkman et al. 2009).
Mountain goats (Oreamnos americanus) are an important
species in British Columbia (BC), valued by First Nations
and recreational hunters and viewed as a symbol of rugged
mountains and true wilderness. Approximately half of the
world population occurs in the province (Festa-Bianchet and
Côté 2008). Periodic surveys are required to update popula-
tion estimates to ensure that harvests are sustainable; how-
ever, in many situations accurate estimates of mountain goat
populations are difficult to obtain. Helicopters are generally
used to conduct total counts of mountain goats, with sight-
ability correction applied afterwards for animals assumed
missed during the survey (Poole 2007). No measures of
variance are available with this technique. Other techniques
used to estimate population size are less developed (Poole
2007). Reliable mark–resight techniques have not been well
tested and tend to produce wide confidence limits (Smith
and Bovee 1984, Cichowski et al. 1994, Poole et al. 2000,
Pauley and Crenshaw 2006). Regression-based sightability
correction models have only recently begun to be developed
for mountain goats (Poole 2007, Rice et al. 2009), where
group size, terrain obstructions, and vegetation cover are
principle factors affecting sightability. Our objectives
were to demonstrate the utility of a method to produce a
DNA-based population estimate of mountain goats using

Poole et al.  Abundance of Mountain Goats Using DNA 1527

a mark–recapture study design and to compare these results
with an aerial survey.
STUDY AREA
We conducted our study on the Mt. Meager complex in the
Pacific ranges of the Coast Mountains in southwestern
British Columbia (508 370 N, 1238 330 W). Climate was of
the southern submaritime moisture regime (Green and
Klinka 1994). Potential summer goat habitat (approx.
90 km2, glaciers removed) primarily was made up of 2 bio-
geoclimatic zones: the Mountain Hemlock zone and the
Alpine Tundra zone above tree line. Tree line was generally
located at 1,600 m, with mountain peaks extending to
2,680 m. Glaciers covered approximately one-quarter of
the alpine area. July and January mean temperatures for
Whistler, 60 km southeast of the study area, were 15.98 C
and 3.08 C, respectively (Environment Canada 2010).
Whistler received an average of 1,230 mm of precipitation
annually including 410 cm of snowfall.
METHODS
Study design and methodology for the aerial survey generally
followed government standards (Resources Information
Standards Committee 2002, Poole 2007) and consisted of
a total count survey, with sightability correction subjectively
applied afterwards. On 21 July 2009 we surveyed an area of
potential goat habitat within alpine, open subalpine, and
forested cliff habitats, which generally included steep, cliff,
or open habitat above 1,550 m elevation. We used a Bell
206B Jet Ranger helicopter (Bell Helicopter Textron, Inc.,
Fort Worth, TX) with pilot, navigator, and 2 observers, and
we surveyed approximately 200–300 m in from the edge of
glaciers but not the ice mass centers. We flew roughly 150–
200-m contour lines at 80–120 km/hr, 75–100 m out from
the hillsides. Based on past experience with goat distribution
on the complex (D. Reynolds and S. Rochetta, BC Forests,
Lands and Natural Resource Operations, unpublished data),
we applied greater effort on the south side of the mountain
complex and less effort on the north side. We mapped
approximate flight lines and survey coverage on 1:50,000
scale topographical maps and calculated the survey area.
We recorded goat locations and helicopter flight tracks
with a hand-held Global Positioning System (GPS) unit
and later downloaded the data to a computer. We classified
goats only into kids and non-kids (yearlings and older;
hereafter adults) based on body size to minimize harassment
and because more detailed age and sex classification from the
air is not reliable (Smith 1988, Côté 1996, Gonzalez-Voyer
et al. 2001).
We conducted 3 1-day sessions of DNA sample collections.
Originally designed at 3-week intervals, weather delays for
session 2 resulted in 26 days and 16 days between sessions (22
Jul, 17 Aug, and 2 Sep 2009). We instructed the 25–30
volunteers per session on sampling protocols prior to deploy-
ment. We used a helicopter to place 12–16 crews of normally
2 individuals to cover all accessible goat habitat across the
mountain complex, primarily on ridgelines and adjacent to
escape terrain. Previous surveys and an aerial survey of the
1528
mountain conducted prior to the start of DNA collection
provided a broad indication where mountain goats could
occur (D. Reynolds, unpublished data). Our sampling effort
was systematic in that we sampled essentially all areas acces-
sible by humans. Although sampling was biased towards
potential goat habitat where a helicopter can land and
humans can walk safely, we assumed all individual goats
move through milder terrain at some point in their daily
and weekly movements (cf. Poole et al. 2009).
We instructed field crews to cover broad areas of potential
goat habitat or trails searching for pellets and hair, but we did
not give them instructions on what route to follow or specific
area to cover. We collected a GPS track file of movements
and sampling locations for each crew. Each crew walked up
to 5–6 km and covered up to 1–2 km2 of habitat. Samples
were most often collected along trails and near beds, which
were generally located in areas where goats had a clear view of
surrounding areas below them.
We emphasized collections of pellets, as preliminary testing
suggested that most hair observed in alpine areas at this time
of year was passively shed from the spring–summer molt,
with correspondingly lower success of DNA amplification
than plucked hair (Gagneux et al. 1997; D. Paetkau, Wildlife
Genetics International, unpublished data). Pellets can be
roughly aged by color and dryness (e.g., Prugh and
Ritland 2005, Brinkman et al. 2010). To maximize the
success of DNA extraction (Brinkman et al. 2009), we
instructed field personnel to attempt to collect only recently
deposited pellets (1–2 weeks of age). We termed pellets
‘‘fresh’’ if they were wet in appearance with a mucus sheen.
‘‘Recent’’ pellets in general appeared dark and shiny, but
lacked a wet appearance. We considered dull brown and
dried pellets, or those with mold or vegetation growth,
‘‘moderate,’’ ‘‘old,’’ or ‘‘dry’’ (collectively ‘‘older’’) and we
did not collect them unless younger pellets were not avail-
able. Generally we collected 4 pellets from each pellet pile
and placed them in a paper coin envelope, which we labeled
with crew information and the GPS waypoint. Because goats
tend to be in groups of >1 individuals and we had no reliable
way of subsampling for a single individual, we collected
samples from all fresh and recent pellet piles observed,
regardless of adjacency with other piles. We also collected
some hair samples, primarily in areas of fresh mountain goat
sign (tracks) but no pellets. We emphasized hair snagged on
alpine vegetation, hoping that hair pulled from an animal
would contain non-shed hair (with an attached root) and
would have greater success at DNA extraction than shed hair
on the ground (Gagneux et al. 1997). We collected 10 hairs
for a sample and often collected a full envelope.
We stored sample envelopes in paper bags and within 36 hr
of collection we dried them in a convection oven at approxi-
mately 65–708 C for 6–8 hr. We sent all samples to Wildlife
Genetics International (Nelson, BC, Canada) for microsat-
ellite genotyping. Samples were subjected to commercial
DNA extraction methods and then genotyped with an au-
tomated DNA sequencing machine using publicly available
microsatellite markers. We screened all samples for DNA
analysis, except samples from 1 ridge system during session 2,
The Journal of Wildlife Management  75(6)
which we randomly subsampled to reduce the sampling by
half as a cost-saving measure.
We extracted DNA using the DNeasy Blood and Tissue
Kit (Qiagen, Inc., Valencia, CA). For hair samples we
clipped roots from up to 10 hairs and then processed the
samples following standard protocols (Paetkau 2003). For
pellets we placed 1–6 pellets, depending on size, into a test
tube and covered them with Qiagen’s ATL digest buffer to
wash off the mucus containing intestinal cells. We agitated
these tubes by gentle swirling several times during incubation
and then removed the pellets after 1 hr. DNA purification
followed Qiagen’s protocol, with volumes of ethanol and
buffer AL scaled in proportion to the amount of ATL left
after pellet removal (generally 500 ml).
To identify individuals we used microsatellite markers
originally developed for cow (Bishop et al. 1994) and caribou
(Rangifer tarandus; Wilson et al. 1997) and selected from
preliminary work on mountain goats pellets from the Stikine
River area in northwestern British Columbia in 2005 (G.
Mowat, BC Forests, Lands and Natural Resource
Operations, unpublished data). We discontinued use of
marker Rt5 after session 1 because of low marker variability.
Amplified alleles not seen in goats identified samples origi-
nating from other species (e.g., moose [Alces alces]), which we
removed from further analysis. The genotyping process fol-
lowed the template of Paetkau (2003), except that we ana-
lyzed samples of intermediate quality 4 times at all markers.
To summarize, after the first attempt at multilocus micro-
satellite genotyping, we classified individual (single-locus)
genotypes as high or low confidence based on a series of
objective (signal strength) and subjective (appearance) traits,
after which we stratified both hair and pellet samples into 3
categories: 1) we culled samples with high confidence scores
for <3 markers, 2) we only reanalyzed high quality samples
with 1 low-confidence score at the low-confidence marker,
if any, and 3) we re-analyzed intermediate quality samples 3
more times at all markers and then used a quality index (sensu
Luikart et al. 2008) to cull lower quality samples. When
intermediate quality samples passed the specified quality
threshold, but had not yet produced 2 matching high-confi-
dence scores for each marker, we applied additional rounds of
single-locus analysis until this standard was satisfied for all
markers or we culled the sample. This effort is consistent
with the notion that error rates scale inversely with DNA
concentration (Taberlet et al. 1996) and supported our strat-
egy of focusing data replication efforts on lower quality
samples.
We conducted error checking by re-analysis of mismatch-
ing markers in pairs of genotypes that matched at all-but-one
or all-but-two markers (1MM- and 2MM-pairs, respective-
ly; Paetkau 2003). Genotyping errors normally create pairs of
genotypes that match at all markers but one (1MM-pairs)
and can therefore be corrected by re-analyzing the mismatch-
ing markers in such pairs (Kendall et al. 2009). This approach
has been shown capable of effectively preventing identifica-
tion of false individuals through genotyping error (Kendall
et al. 2009). Once individual identification was complete, we
selected one sample per individual for analysis of gender
Poole et al.  Abundance of Mountain Goats Using DNA
using the amelogenin marker also used for bears (Ursus
spp.; Ennis and Gallagher 1994).
We used closed mark–recapture models from software
Programs MARK and CAPTURE to estimate population
size (Otis et al. 1978, White and Burnham 1999, White
2008). We pooled multiple captures of individuals into 1
capture per session. Program MARK can be used to accom-
modate variation in capture probability among capture ses-
sions (time variation) explicitly and between sex cohorts via
the use of covariates. We fitted a series of models in MARK
that allowed various forms of time variation, including the
use of sex as a covariate. We fitted full-time models to allow
for variable capture probability among capture sessions,
which is a common result among field studies. We also fitted
reduced time models based on an examination of our capture
results, no time variation as a null model for comparison, and
we tested for variation in capture probability between sexes
given the variation in home range size and behavior between
sexes (Festa-Bianchet and Côté 2008). Each model gener-
ated a population estimate for each sex; we did not model one
population estimate in MARK because single estimate mod-
els assume equal population sizes for each sex, an unlikely
proposition (Festa-Bianchet and Côté 2008). Program
CAPTURE includes models that accommodate random
variation in capture probability among individuals (termed
heterogeneity) and also includes a model that accommodates
both heterogeneity and time variation. Time models are
negatively biased when heterogeneity among individuals is
measurable (Otis et al. 1978), hence we did not want to
exclude the use of the heterogeneity models in CAPTURE if
modeling of the sexes separately did not appear to capture
most of the heterogeneity in the data. We used Akaike’s
Information Criterion corrected for small sample size (AICc)
and model weights to aid in selection among plausible mod-
els in MARK to estimate population size. We used the
closure tests in the software Close Test (Stanley and
Burnham 1999) to test for losses or additions to the
population.
RESULTS
During the aerial survey we used 2.2 hr of helicopter time
and surveyed 90 km2. Overall survey intensity averaged
1.4 min/km2, with greater effort on the south side of the
mountain (1.7 min/km2) than on the north side (1.0 min/
km2). We observed 60 goats in 15 groups, including 18 kids
(30% of total goats). We observed no goats on the north side
of the mountain complex. Group size ranged from 1 to 11
goats and averaged 4.0  0.73 (x  SE). Based on other
research (summarized in Poole 2007, Rice et al. 2009) and
considering the survey effort and habitat, we subjectively
applied a sightability of 0.70 to derive an estimate of 86
goats (60 adults and 26 kids).
Field crews collected 490 samples; 91% were pellet samples.
One sample was not a mountain goat, 77 pellet samples
(16%) were not suitable for analysis (primarily crushed
or broken apart, or the inside exposed), 92 (19%) were
not analyzed (subsampling), and 150 (31%) failed during
genetic analysis, whereas 170 samples (35%) produced high-
1529
Table 1. Session effort and individual mountain goat captures as identified from DNA analysis, Mt. Meager complex, British Columbia, 2009.
New captures Males
Session No. pellet samples No. hair samples Captures No. % No. %
1 105 23 35 35 100 13 37
2 228 11 26 14 54 10 38
3 115 8 27 6 22 8 30
Total 448 42 88 55 22 40

confidence scores for all 7 remaining markers. Prior to re-
analysis in the context of error checking, the dataset con-
tained 11 1MM-pairs, all of which we found to be caused by
genotyping error (there were no 1MM-pairs in the final
dataset). The 6 2MM-pairs in the dataset were all replicated
during error checking, indicating that they were not created
by genotyping error.
We identified 55 individuals from 170 samples assigned
individual identifications (Table 1). For mark–recapture
analysis, we pooled data for individual captures for each
session, yielding 88 unique captures among sessions. The
largest number of individual captures occurred in session 1,
with smaller but similar numbers captured in sessions 2 and
3. Of the 27 individuals captured in session 3, 21 (78%) were
recaptures from sessions 1 and 2. Six individuals were cap-
tured in all 3 sessions. We detected each genotype an average
of 3.1 times (SE ¼ 0.31); 33% were captured only once
(Fig. 1). Males comprised 40% of the individuals we identi-
fied (Table 1). Based on the small size of some pellets, we
assumed 14 individuals were kids.
20
18
16
14
Frequency
Capture probability was highest in the first session and
detection of new individuals declined linearly (Table 1). Both
general closure tests suggested a closed population (P > 0.3).
Modeling results suggested that capture probability (p) was
detectably higher in session 1 (time1; pt1 ¼ 0.54,
SE ¼ 0.075) than sessions 2 (time2) and 3 (time3;
pt2¼t3 ¼ 0.41, SE ¼ 0.054) and that overall female capture
probability was higher than males (p(female) ¼ 0.52,
SE ¼ 0.062; p(male) ¼ 0.34, SE ¼ 0.082). None of these
effects was strong as shown by the similarity in model
weights. We estimated 40% of the population were males
(Model 1 in Table 2), the same ratio as observed in our
raw data. Mean capture probability was 0.38 per session
(SE ¼ 0.047; range 0.34–0.45).
The population estimate in the top time-varying model in
MARK was Nb ¼ 64 (SE ¼ 6.0, 95% CI 58–85, CV ¼ 9.3;
Model 1 in Table 2), although we believe this estimate was
conservative. The time varying model in CAPTURE (Mt)
produced an equally low estimate (Nb ¼ 65, SE ¼ 4.8, 95%
CI 60–79, CV ¼ 7.4). We were not convinced that the
above time models were able to model all sources of capture
variation; therefore we considered heterogeneity models
using CAPTURE. We selected the Jackknife heterogeneity
model (Mh-Jackknife) in CAPTURE to estimate population
size (Nb ¼ 77, SE ¼ 7.4, 95% CI 68–96, CV ¼ 9.6);

12 the Mh-Chao model produced a similar estimate

10 (Nb ¼ 74, SE ¼ 9.2). We rejected the Mth-Chao model,
8 which accommodates both heterogeneity and time variation
6 in captures, as it produced an estimate with 3 times greater
4 variance (Nb ¼ 84, SE ¼ 23.0).
2 Genotyping success was lower for hair samples (32%,
0 n ¼ 38) than for pellet samples (56%, n ¼ 282). We iden-
1 2 3 4 5 6 7 8 9 tified 9 individuals from 12 hair samples. Four of these
No. of captures individuals (3 M, 1 F) were only detected in hair samples
Figure 1. Frequency of number of captures for individual mountain goats
and only once each. For extracted pellet samples, field clas-
(n ¼ 55) identified through DNA samples, Mt. Meager complex, British sifications of fresh, recent, and older were associated with
Columbia, 2009. success rates of 91%, 67%, and 27%, respectively. Proportions

Table 2. Top ranked candidate closed time models from Program MARK fitted to mountain goat detection data from the Mt. Meager complex, British
Columbia, 2009, based on Akaike’s Information Criterion (AICc), model weights (wi), number of parameters (K), deviance, and their point estimates (sexes
combined) and standard errors. We modeled sex as a covariate of capture probability in models 2 and 5.
Modela DAICc wi K Deviance Point estimate SE
1. p(time1, time2 ¼ time3) 0.00 0.330 4 23.68 64 6.0
2. p(sex) 0.09 0.316 4 23.77 67 8.6
3. p(.) 0.91 0.210 3 26.69 65 6.2
4. p(time1, time2, time3) 2.10 0.116 5 23.65 64 6.0
5. p(time þ sex) 4.91 0.028 8 19.92 66 8.3

a
p, capture probability; time, capture probability was separate for each sampling session; time1, sampling session 1, etc.; (.), constant capture probability.

1530 The Journal of Wildlife Management  75(6)

of these categories differed among sessions, with 84% of
extracted samples from sessions 1 and 3 being classified fresh
or recent in the field, as compared to 17% of extracted
samples from session 2. This was reflected in session-specific
genotyping success rates of 68%, 31%, and 63%, respectively.
Heavy precipitation occurred in the week prior to session 2
collections (59 mm) compared to the week prior to sessions 1
and 3 (0–3 mm).
Heterozygosity of the 7 markers we used to identify indi-
viduals averaged 0.66 (excluding Rt5; Table 3). The proba-
bility that 2 randomly drawn, unrelated individuals would
share the same genotype (PID) was 1.78 106, and the
probability that full siblings would have identical genotypes
(PSIB) was 0.00315. Only 1 of 12 pellet samples collected on
snowfields and run for genetic analysis produced a viable
genotype.
The DNA-based estimate cost nearly 6 times more in base
costs than the aerial survey derived estimate (Table 4). The
cost difference would have been higher if volunteers had not
been used during the DNA inventory, but the pellet collec-
tion could not have been realistically conducted using only
agency personnel. In addition, use of volunteers increased
local engagement in wildlife management.
DISCUSSION
Non-invasive pellet and hair collections provided samples of
sufficient quality to identify individual mountain goats using
DNA and produce a statistically robust population estimate
for the Mt. Meager complex. Our study is one of the first
estimates of abundance of an ungulate species using DNA
derived from fecal pellets (Eggert et al. 2003, Valière et al.
2007, Harris et al. 2010, Brinkman et al. 2011) and suggests
the technique can be applied to other situations where direct
observation of individuals is difficult or estimates are impre-
cise. Our DNA-derived estimate was precise (CV ¼ 9.6), a
result of the 3-session design and high capture probabilities.
Precision of estimates will vary with population size, number
of sessions, and capture probability (Mulders et al. 2007) and
will likely be unique for most situations.
Our DNA-derived estimate was 28% higher than the raw
count we obtained during the aerial survey and 10% lower
than the corrected estimate based on 0.70 sightability. We
based the 0.70 sightability on past experience in similar
habitats (Poole 2007), but we admittedly subjectively select-
ed it. The DNA-derived estimate, which suggested sight-
ability of 0.78 during the aerial survey, appears reasonable
and has the advantage of providing a quantifiable level of
confidence.
Properly designed mark–recapture studies require that all
individuals in a population have a non-zero probability of
capture. If the pellets or hair of some individuals have no
probability of being collected, then population estimates
would be negatively biased. Sampling effectiveness also
requires that encounter rates with viable samples be maxi-
mized. Limitations on safe human travel resulted in a thor-
ough but comparatively small portion of the mountain
complex and potential mountain goat habitat being system-
atically sampled each session. However, given the time be-
tween sessions it seemed probable that most animals
potentially could have traveled to ridgelines or slopes where
sampling occurred. Examination of movements of GPS-
collared mountain goats over a 14-day period in August

Table 3. Measures of variability for 8 loci we used to genotype 55 mountain goats (33 for Rt5), Mt. Meager complex, British Columbia, 2009.
Locus HE HO A PID PSIB
a
BM1225 0.62 0.67 5 0.23 0.50
BM203a 0.76 0.75 6 0.11 0.40
BM4107a 0.64 0.60 5 0.21 0.49
BM4513a 0.75 0.76 6 0.11 0.40
BMC1009a 0.61 0.69 4 0.21 0.50
Rt1b 0.57 0.60 6 0.22 0.52
Rt27b 0.61 0.64 6 0.21 0.50
Rt5b 0.46 0.45 3 0.35 0.61
x 0.63 0.65 5.1
Overall probability of identity 1.78E06 0.00315

HE, expected heterozygosity; HO, observed heterozygosity; A, number of alleles; PID, probability of identity; PSIB, probability of sibling identity. Probability of
identity calculated using Kalinowski et al. (2007).
a
Bishop et al. (1994).
b
Wilson et al. (1997).

Table 4. Cost comparison (CDN$ in 2009) between aerial survey and DNA-based inventory of mountain goats on the Mt. Meager complex, British Columbia,
2009.
Aerial survey DNA inventory
Item Units Cost ($) Units Cost ($)
Helicopter costs ($1,000/hr) 5 hr 5,000 14 hr 14,000
Agency personnel and contractors ($500/day) 3 people 1,500 6 person-days 3,000
Volunteers 0 person-days 60 person-days
DNA supplies and laboratory costs 3 sessions 20,000
Total 6,500 37,000

Poole et al.  Abundance of Mountain Goats Using DNA 1531

from a southeastern British Columbia dataset (Poole et al.
2009) suggested most animals traveled over a 2-km-wide
area, and some up to 7 km. No areas of alpine habitat
(glaciers excluded) on the southern slopes of the mountain
complex where most mountain goats were known to occur
were >1 km from an area sampled by a crew. We captured
Mt. Meager complex mountain goats detected more than
once during the study an average of 1.0 km (SE ¼ 0.15;
range 0.01–3.5 km) apart at the most distant locations.
Given the high capture probability (0.38), we assumed
most individuals in the population traveled to areas where
sampling could be safely conducted at least some time during
the capture sessions.
During the aerial survey conducted prior to the DNA
study, 3 groups accounted for 43% of the animals observed
(7–11 individuals/group). The gregarious nature of moun-
tain goats and tendency for nursery groups (females with
young) to be larger than bachelor groups during summer
(Festa-Bianchet and Côté 2008) suggests that grouping may
influence population estimates because of clumped distribu-
tion. However, in the central portion of the sampling area,
we captured 43 goats at least once among the 3 sessions, but
only 6 individuals were captured in every session. Movements
of groups and changes in mean group size occur over summer
(Festa-Bianchet and Côté 2008), which would tend to alter
group composition and dynamics. Thus, group movements,
dynamics, and mixing of individuals during a summer may
have been large enough to minimize potential bias.
Adult males tend to be more sedentary and make larger use
of forested habitats than nursery groups during summer in
some populations (Festa-Bianchet and Côté 2008). Our
sampling would not have detected bachelor groups if they
had been localized in areas not covered by sampling crews.
However, 40% of the genotyped individuals in our study
were males, similar to the average 38% adult males compared
to all adults in the Caw Ridge, Alberta, population between
1999 and 2003 (Festa-Bianchet and Côté 2008). In addition,
we detected only a male in 2 areas of sampling, and 2 out of 3
individuals identified in a third area were males, suggesting
we sampled at least some bachelor groups. Thus it is unlikely
that we missed a significant segment of the male population
because of behavioral isolation. Similarly, we believe 14 of
the individuals we sampled were kids (based on small pellet
size), which is only slightly lower than the 18 kids we
observed during the aerial survey, again suggesting no major
bias in DNA sampling.
We suggest that our model selection was robust. The
passive nature of sample collection and the approximately
systematic sampling effort negated either form of behavior
response (trap-happy or trap-shy), and therefore we did not
consider behavior models during model choice (Harris et al.
2010). Although we used individuals identified from both
hair and pellet samples, our emphasis on collection of pellet
samples would probably have helped to overcome any het-
erogeneity in detection as a result of sex or age differences in
the timing of shedding of hair (Côté and Festa-Bianchet
2003). Kids do not shed in their first year and would gener-
ally be missed in hair collections, but we frequently collected
1532
small pellets that likely originated from kids. Sample effort
was similar among sessions and the risk of a behavioral
response very small, so the most likely form of variation
was heterogeneity. Heterogeneity was likely, given the vari-
ation in range size and movements among age and sex classes
and random influences such as non-systematic field sampling
and variation in genotyping success.
Geographic closure, an important assumption of mark–
recapture models, is violated if there is movement of indi-
viduals on and off the study area among capture sessions
(White et al. 1982). Tests indicate population closure during
our study. The Mt. Meager complex is a block of habitat
surrounded on 3 sides by deep, forested valleys. High-eleva-
tion connections exist only to the southwest. Biologists
knowledgeable with the area have not detected mountain
goats in the area immediately adjacent to the Mt. Meager
complex (D. Reynolds and S. Rochetta, unpublished data).
Mountain goats residing on the mountain during the sum-
mer may remain there year round, but the degree of seasonal
interchange or dispersal between adjacent areas is not known.
Dispersal is most common with sub-adult males during late
summer (Festa-Bianchet and Côté 2008).
As expected (Gagneux et al. 1997; D. Paetkau, unpublished
data), genotyping success from pellets (56%) was higher than
from hair samples (32%), confirming that mountain goat
sampling should concentrate on pellet collection during
summer. However, we detected 4 of the 55 individuals
identified (3 M, 1 F) only in hair samples, suggesting that
hair sampling can beneficially supplement pellet collections.
G. Mowat (unpublished data) obtained 33% genotyping
success for analysis of mountain goat pellets conducted in
2005. As shown by Brinkman et al. (2010), advances in DNA
extraction laboratory protocols for pellets likely contributed
to our high genotyping success. In addition, differences in
genotyping success among pellets classified by age clearly
demonstrate that DNA quality can be assessed in the field to
optimize laboratory costs and effectiveness. Brinkman et al.
(2010) found similar results for decreased genotyping success
over time and recommended field classification of Sitka
black-tailed deer (Odocoileus hemionus) pellets in coastal
Alaska. We were unable to quantify actual pellet age with
age category, and DNA degradation will vary with exposure
and environmental conditions, but it is likely that most
successful samples were <2 weeks of age (Brinkman et al.
2009).
Genotyping success during session 2 (31%) was far lower
than in sessions 1 and 3 (63–68%). It is likely that heavy rain
events in the week prior to collection in session 2 resulted in
rain washing off some of the mucus, which contains the
epithelial cell DNA from the outside of pellets, or increased
DNA degradation rates (Brinkman et al. 2009). Almost all of
the pellets collected on snowfields failed during genotyping
procedures, which was surprising, as we believed that cooler
conditions would slow DNA degradation and increase gen-
otyping success rates (Belant et al. 2007, Harris et al. 2010).
Maudet et al. (2004) found much lower genotyping error
rates in wild ungulate feces sampled in winter compared to
spring but attributed the difference to diet resulting in lower
The Journal of Wildlife Management  75(6)
DNA content during spring compared with winter.
Although we had greater difficulty aging pellets on snow-
fields, our low success may be related to the high moisture
encountered on snowfields during summer temperatures
with melting conditions that degraded the DNA or rinsed
the mucus coating from pellets.
Aerial surveys of ungulates provide minimum counts to
which sightability correction factors can be applied to ac-
count for animals assumed missed; no variance can be asso-
ciated with the count unless repeat surveys are conducted.
Accuracy of aerial surveys for mountain goats is known to
vary among surveys, likely related to changes in sightability
(Gonzalez-Voyer et al. 2001). Differences in habitat, topog-
raphy, and animal behavior may also influence sightability
among areas (Poole 2007). However, although costs were
roughly 6 times greater, non-invasive sample collection and
DNA genotyping in a mark–recapture design produced a
statistically rigorous estimate with a quantifiable level of
confidence around the estimate. Situations where aerial in-
ventories are not practical because of low sightability or small
population size may be more appropriate for a DNA-based
methodology to estimate population size. Examples of ap-
plicable situations may include mountain goats living in
forested river or canyon habitats, small populations of goats
in low-elevation winter range within the forest matrix, or a
population of woodland caribou existing at low densities in a
forested area where sampling can be done rapidly and
effectively.
Management Implications
Our methodology can contribute to long-term monitoring
and management of mountain goats and other ungulates, and
can be used to support current harvest management strate-
gies. DNA sampling provided a rigorous population estimate
with a quantifiable level of confidence, as opposed to a
minimum count from an aerial survey, to which a subjective
sightability correction can be applied (Poole 2007). DNA
sampling of ungulates can be applied to many situations, for
example where ungulates occupy an area with low sightability
(such as in heavily forested areas; Brinkman et al. 2011) and
reasonable access. Identification of individuals can provide
minimum population counts or, with proper design and
multiple capture sessions, be used to develop a population
estimate. Sampling in winter prior to spring melt conditions
may extend the viable life of usable samples; we do not
recommend sampling on snowfields during summer because
of low genotyping success. Classifying pellets by age in the
field facilitates cost-effective extractions in the laboratory. To
minimize the likelihood of resample, remaining pellet groups
in the field could be scuffed out.
We suggest that during summer managers and researchers
concentrate on pellet collections for ungulates because of the
higher genotyping success from pellets as compared to hair,
which may be primarily shed. Based on studies of genotyping
success over time since deposition, 14–21 days between
sampling sessions appears to be a reasonable period to maxi-
mize pellet deposition and capture probabilities and maxi-
mize genotyping success, while minimizing the risk of repeat
Poole et al.  Abundance of Mountain Goats Using DNA
sampling of the same pellet groups and movement into and
out of the study area. Given the apparent reduction in
genotyping success following heavy rain events, it may be
prudent to delay collections to allow sufficient deposition of
pellets with quality DNA.
Acknowledgments
Peter Kiewit Sons Co. provided funding for this project by
donation to British Columbia Conservation Foundation,
who administered the project under the guidance of J.
Neilson. Blackcomb Helicopters provided safe flying to
and from the mountain. We thank the approximately 55
volunteers, primarily associated with the Pemberton Wildlife
Association and BC Forests, Lands and Natural Resource
Operations, who enthusiastically participated in the field
study. We especially thank A. Mitchell for logistics and
A. McEwan for organizing so many keen volunteers. We
are grateful to J. Benson, Wildlife Genetics International, for
her interest and diligence with this project. M. Festa-
Bianchet, D. Forsyth, G. Kuzyk, and 2 anonymous reviewers
provided helpful comments on earlier drafts of the
manuscript.
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The Journal of Wildlife Management  75(6)