Effectiveness and Accuracy of Track Tubes for Detecting
Small-Mammal Species Occupancy in Southeastern
Herbaceous Wetlands and Meadows
Duston R. Duffie, Robert A. Gitzen, Nicholas W. Sharp, and Amy J. Turner
Southeastern Naturalist, Volume 18, Issue 1 (2019): 130–146
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2019 SOUTHEASTERN NATURALIST 18(1):130–146
Effectiveness and Accuracy of Track Tubes for Detecting
Small-Mammal Species Occupancy in Southeastern
Herbaceous Wetlands and Meadows
Duston R. Duffie1,2,*, Robert A. Gitzen2, Nicholas W. Sharp1, and Amy J. Turner3
Abstract - As a non-invasive approach for sampling small mammals, track tubes may be
especially useful in species occupancy studies that do not require marking of individuals.
However, such studies may involve significant uncertainty in identifying many tracks to
species. Using 37 study sites in eastern Alabama and Tennessee, we compared relative differences
in detection probabilities with track tubes vs. live traps for Peromyscus (deermice),
Oryzomys palustris (Marsh Rice Rat), and Sigmodon hispidus (Hispid Cotton Rat). In analyses
that ignored identification uncertainty or that used false-positive occupancy models
to address this uncertainty, track tubes and live traps had similar detection probabilities.
When uncertain detections were omitted from analysis, effective detectability was lower
with track tubes. False-positive occupancy modeling indicated that track-identification
uncertainty could not be ignored, as there was a non-zero probability of false-positive
detections. False-positive occupancy designs have high relevance to track-tube studies; in
addition, such studies should ensure that track identification is done under the oversight of
an experienced tracker.
Introduction
Although live traps are a highly useful approach for sampling wild small-mammal
populations, biologists have access to a rapidly expanding toolbox of potential
non-invasive alternatives, such as genetic sampling approaches (e.g., Russello et al.
2015), camera surveys (DeSa et al. 2012, McCleery et al. 2014), and hair sampling
with morphological species identification (e.g., Goldstein et al. 2014). Track tubes,
which are passive detection devices that record tracks of animals entering the tubes,
are a non-invasive alternative used effectively in many small-mammal field studies
(Drennan et al. 1998, Glennon et al. 2002, Nams and Gillis 2003). In contrast to
live trapping (Sikes et al. 2016), track tubes involve no risk of injury or death for
animals, a major advantage in studies of protected species (Pries et al. 2009, Stolen
et al. 2014, Wilkinson et al. 2012). This advantage is important throughout much
of the southeastern USA, given the high risk of predation by invasive Solenopsis
invicta (Buren) (Red Imported Fire Ants) on animals confined in live traps (Kraig
et al. 2010, Mabee 1998, Masser and Grant 1996).
1Alabama Department of Conservation and Natural Resources Division of Wildlife and
Freshwater Fisheries, 21453 Harris Station Road, Tanner, AL 35671. 2School of Forestry
and Wildlife Sciences, Auburn University, 602 Duncan Drive, Auburn, AL 36849. 3The University
of the South, 735 University Avenue, Sewanee, TN 37383. *Corresponding author
- drd0006@tigermail.auburn.edu.
Manuscript Editor: Brian Carver
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Conversely, direct capture allows biologists to obtain accurate morphological
identification of most species, facilitates collection of tissue and fecal samples, enables
determination of sex and reproductive status, and allows application of tags
or other marks for identifying recaptured individuals (Sheppe 1965, Sikes et al.
2016). However, these advantages of live traps may not be relevant to many studies
using occupancy-modeling approaches to assess patch-level species occurrence
(MacKenzie et al. 2002). The basic occupancy approach uses binary species-level detection
data (zero detections vs. at least 1 detection of the species during the survey)
from repeated surveys of sites to estimate the per-survey probability of detecting the
species at an occupied site. By incorporating detection probability into the statistical
model, occupancy modeling accounts for potential false absences (i.e., sites where
the target species was present but not detected) in making inference about occupancy
(MacKenzie et al. 2002). Achieving suitably precise estimates of occupancy parameters
requires using a method that produces high overall detection probabilities.
Comparisons of observed species richness, raw detection rates, and correlations
between track-tube indices and trapping-based population estimates suggest that
track tubes often may achieve equal or higher species-level detection probabilities
compared to live traps (Palma and Gurgel-Gonçalves 2007, Wiewel et al. 2007,
Wilkinson et al. 2012). However, except in studies of subspecies of Peromyscus
polionotus (Wagner) (Beach Mouse) in coastal dunes in the Southeast US (Pries et
al. 2009, Stolen et al. 2014) and an example analysis by Stanley and Royle (2005),
previous studies have not analyzed track-tube data with approaches that explicitly
incorporate individual or species-level detection probability. Biologists planning
small-mammal occupancy studies in the Southeast and other regions would benefit
from direct comparisons of detection probabilities between methods and a better
understanding of interspecific variation in their relative ef fectiveness.
Although identification of live animals based on morphology may be imperfect
for some small-mammal species, identification uncertainty is likely to be a more
frequent problem in track-tube studies given that identifications are based only
on track characteristics that can be highly similar among small-mammal species
(Elbroch 2003). Track-plate studies with larger taxa indicate that track identification
accuracy can vary significantly among observers, and experienced observers
usually are needed to ensure that tracks are identified to species correctly (Evans et
al. 2009, Stander et al. 1997, Zielinski and Schlexer 2009). Accurately discriminating
some small-mammal species may require fine-scale measurements from clear
tracks (Palma and Gurgel-Gonçalves 2007, Stolen et al. 2014). Yet, over-tracking,
moisture, and smudging from non-target animals often can hinder track clarity.
Except when focused on species assemblages in which the target species can be
identified with high confidence (Mills et al. 2016, Wilkinson et al. 2012), track-tube
studies frequently face uncertainty and potential mistakes in i dentifications.
To deal with identification uncertainty, some track tube studies have omitted
uncertain identifications from species-specific analyses or grouped identifications
of problematic species (Glennon et al. 2002, Wiewel et al. 2007). Other studies have
not explicitly discussed whether any identifications were uncertain. In occupancy
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modeling, even a low rate of false-presence observations (misidentifications leading
to mistakenly “detecting” a species at a site where it is not present) will cause
estimator bias (McClintock et al. 2010, Miller et al. 2011, Royle and Link 2006).
When data includes a mix of certain and uncertain identifications of a species or
supplemental information is available about probability of errors, approaches for
explicitly modeling probability of false-presence errors are now readily accessible
(Chambert et al. 2015, Ferguson et al. 2015, Miller et al. 2011; see Stolen et al.
2014 for a track-tube application with Peromyscus polionotus niveiventris (Chapman)
[Southeastern Beach Mouse]).
We compared the relative performance of track tubes vs. Sherman live traps
for assessing small-mammal occupancy in herbaceous wetlands and meadows in
the Southeast. As our primary comparison, we examined differences between the
2 methods in per-night detection probability for 3 widespread southeastern rodent
taxa. In addition, we examined between-observer consistency in track identification.
We implemented alternative strategies for dealing with uncertainty in track
identifications (false-positive models vs. omitting uncertain detections vs. ignoring
uncertainty) and examined whether estimates of detection probabilities from tracktube
sampling were sensitive to the choice among these strategi es.
Field-Site Description
Data for this study were collected as part of an assessment of current occurrence
of Zapus hudsonius (Zimmermann) (Meadow Jumping Mouse) in eastern
Alabama and at Arnold Air Force Base (AFB) in Tullahoma, Coffee, and Franklin
counties, TN. Sites were selected based on historical records and presence
of moist soils and dense cover of herbaceous or shrubby vegetation (Whitaker
1972). Therefore, our study focused on grassy meadows along marshes, ponds,
and streams, moist herbaceous areas with a forest overstory, and abandoned hayfields.
We sampled 37 sites in 3 groups of surveys in 2015–2016 (Fig. 1). During
June–August 2015, we sampled 17 sites in Lee and Chambers counties in southeastern
Alabama (Alabama 2015 group). In July–August 2016, we sampled 11
sites in Jackson, Cherokee, De Kalb, and Lee counties; most of these sites were in
northeastern Alabama (Alabama 2016 group). We sampled a third group of 9 sites
at Arnold AFB during July 2016.
Methods
Field methods and track identification
At each site, we used folding Sherman live traps (7.62 cm x 8.89 cm x 22.86 cm,
Model LFA Folding Trap; H.B. Sherman Trap Inc., Tallahassee, FL) and track tubes
to sample small mammals. We built track tubes following a modified version of
Glennon et al.’s (2002) design, using two 30-cm sections of vinyl rain gutter taped
along one edge to form a tube. We capped one end of this tube using metal flashing
and duct tape to increase rain resistance (Fig. 2); this modification did not appear to
affect the detection of small or meso-sized mammals during informal comparisons
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of track tube designs We created the tracking substrate using a kerosene lantern to
soot ~12 cm of the end of the metal flashing lining the bottom of the tube that was
nearest the capped portion of the tube and a 15 cm x 7 cm strip of Contact© paper
shelf-liner (Kittrich Corporation, Pomona, CA) attached to the other end of the
metal flashing as a surface (track plate) for collecting tracks.
Each site was trapped with 24 live traps and 24 track tubes placed in a grid with
10 m between trap stations. Most sites were sampled with 3 x 16 or 4 x 12 grids;
several sites with narrow riparian corridors were sampled with 2 x 24 grids. One
trap (live trap or track tube) was placed at each station, with trap type alternating
between stations. Both trap types were baited with black oil sunflower seeds. To
reduce problems with Red Imported Fire Ants in Alabama sampling in 2015 and
at Arnold AFB, the area underneath each trap (approximately 15 cm x 36 cm) was
dusted with a layer of Sevin Dust © (Carboxyl 5%; Kraig et al. 2010).
We trapped each site for 1 session of 4 consecutive nights and checked live traps
and track tubes each morning. We removed the paper from track plates with track
detections and preserved them within clear plastic sheet protectors for later analysis.
We then placed new paper onto the track plate and reset the tube. We identified
Figure 1. Location of 37 study sites sampled for small mammals during 2015–2016 and
used for comparison of Sherman live traps and track tubes. Sampling occurred during
2015–2016 at Arnold Air Force Base in Tennessee (9 sites), northeast Alabama (11 sites),
and southeast Alabama (17 sites).
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captured animals to species, with hind-foot length, body length, and tail length
measured as necessary for identification.
We identified tracks to species or to the lowest taxonomic level possible with
a measure of high, medium, or low confidence of track identification at each
taxonomic level based on presence and clarity of diagnostic features. Diagnostic
Figure 2. Track-tube design used for sampling small mammals for comparison with Sherman
live trapping at 37 Alabama and Tennessee study sites, 2015–2016. Design was based
on Glennon et al. (2002) but modified to reduce effects of rain splatter and feeding debris
by capping one end with metal flashing and duct tape. Cotton Rat tracks are visible on the
track plate.
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characters were derived from our reference library of known tracks created from
live captures during this and previous studies and from multiple tracking publications
that described differences in foot morphology among species (Fig. 3; Elbroch
et al. 2012, Taylor and Raphael 1998, Van Apeldoorn et al. 1993). All tracks were
identified by one primary observer (D. Duffie) with 1 yr of track-identification
experience, who was trained by an experienced tracker (an individual trained and
experienced in the identification of tracks and sign; N. Sharp, 6.5 yrs experience;
certified Level III in the CyberTracker evaluation system [see Evans et al. 2009])
who also served as a secondary observer. A subset of 58 track plates from 1 trapping
group out of the total sample of 390 track plates was independently analyzed
by both observers to evaluate accuracy.
Statistical analysis
To assess whether there were systematic differences in the number of species
detected by each method, we calculated the difference in the overall raw count of
rodent and shrew species detected with live traps vs. track tubes (high and medium
confidence detections pooled) for each site, and summarized the average
site-level difference. For this and subsequent analyses, we pooled all observations
of Peromyscus spp. (deermice) into a single category. Other species present in
our study region and potentially confused with Peromyscus, such as Ochrotomys
nuttalli (Harlan) (Golden Mouse) or Reithrodontomys humulis (Audubon and
Bachman) (Eastern Harvest Mouse), were not captured in live traps, and we were
Figure 3. Hind feet and example tracks from the 3 most commonly detected small-mammal
species at Alabama study and Tennessee study areas, 2015–2016 (pictures and tracks not
to scale). As shown, differences in foot morphology can be used to accurately distinguish
these species from tracks.
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confident that they could be distinguished from deermice based on differences in
foot morphology seen in our track library. Although we did not identify more than
1 deermouse species per site from live trap captures, we could not reliably identify
deermouse tracks to species across all sites. Detections of taxa other than rodents
and shrews were considered incidental and omitted from analysis .
We used single-season occupancy models (MacKenzie et al. 2002) to quantify
the relative effectiveness of track tubes vs. live traps for assessing occurrence of Sigmodon
hispidus (Say and Ord) (Hispid Cotton Rat, hereafter Cotton Rat), Oryzomys
palustris (Harlan) (Marsh Oryzomys or Marsh Rice Rat, hereafter Rice Rat), and
deermice in our study area. Because of our focus on site-level species occurrence, we
use the term “detection” to denote a trap night with at least 1 capture or track identification
of a species in at least 1 trap or tube in the array. For each study site, encounter
histories (combinations of binary values for each trap night indicating whether the
species was detected at the site) were compiled separately for track tubes and for
live-trap detections. An 8-digit encounter history was formed for each site by joining
the 4-night encounter histories from live traps with those from track tubes.
We performed one set of occupancy analyses that assumed no false-positive detections
in the track-tube encounter histories and examined whether our results were
sensitive to our confidence threshold of track identifications. We formed 3 alternative
detection histories: one incorporating all track tube detections of each species (high,
medium, low confidence pooled), one omitting low-confidence detections, and one
omitting low- and medium-confidence track detections. We analyzed each alternative
dataset separately using a multi-species Bayesian hierarchical occupancy model,
with posterior distributions for parameters estimated with program JAGS through the
"rjags" package (Plummer 2016) in program R (R Core Team 2016). We use Bayesian
modeling for all analyses because the incorporation of non-informative prior
distributions stabilized estimates of false-positive detection probabilities (sensu
Gelman et al. 2008) and increased modeling flexibility by allowing straightforward
incorporation of random effects. Fixed-effect parameters included species-specific,
study-wide occupancy probabilities, species-specific average study-wide detection
probabilities, and parameters allowing for a species-specific change in detectability
from the first trap night to the subsequent 3 trap nights of each trap session. We incorporated
an additional random effect to model heterogeneity among sites in detection
probability for each species (such as due to among-site variation in abundance). We
included a fixed-effect parameter to model the relative difference in detection probabilities
for track tubes vs. live traps for each species; detection probability was
modeled as an additive function of these parameters on the log-odds scale as in standard
logistic regression. We used non- or weakly informative prior distributions for
each parameter in the Bayesian analyses. Reported results are summaries of posterior
distributions estimated with 30,000 total samples per parameter (3 Markov chain
Monte Carlo chains of 50,000 samples each after chains converged satisfactorily,
with every 5th sample retained). We estimated posterior distributions for the speciesspecific
and overall average difference between methods on the odds-ratio scale
([odds of detection with track tubes] / [odds of detection with live traps]; odds ratio =
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1.0 if the 2 methods have identical detection probabilities). For all Bayesian analyses,
we examined alternative weakly informative prior distributions to confirm that our
results were not sensitive to such choices, and assumed adequate model fit based on
graphical examination of model residuals.
To explicitly account for and estimate the probability of site-level false-positive
detections with track tubes, we conducted a second analysis that integrated the
2 types of “site confirmation” (Chambert et al. 2015) false-positive occupancy
approaches outlined by Miller et al. (2011). Live-trap detections were treated as
certain detections with no chance of false-presence detections. Track-tube data
were treated as having 2 types of detections: certain detections, i.e., at least 1 highconfidence
identification of the species during the survey; and uncertain detections,
i.e., only medium- or low-confidence identifications recorded for that survey. Within
this framework, false-positive detections were possible at a site only if there were
no certain detections of the species from either method during the 4-night visit.
Adapting computer code from Chambert et al. (2015), we expanded the general
Bayesian model and JAGS code used for our first set of analyses by incorporating 2
additional sets of species-specific parameters: probability of a false-positive detection
and probability that a correctly identified track-tube detection at an occupied
site would be classified as certain (identified with high confidence). We modeled
both types of parameters as constant across all track-tube surveys and gave them
Uniform (0, 1) prior distributions.
Results
During 2015–2016, our total trap effort included 3168 trap nights (1584 live-trap
trap-nights and 1584 track-tube trap-nights) in the Alabama 2015 group of sites,
2112 trap nights (1056 live-trap trap-nights and 1056 track-tube trap-nights) in
the Alabama 2016 group, and 1728 trap-nights (864 live-trap trap-nights and 864
track-tube trap-nights) at Arnold AFB, with a nominal trap effort of 96 trap nights
per method per site (4 nights x 24 traps or track tubes per night). Across all sites,
we detected 6 species of rodents (Cotton Rat, Rice Rat, P. leucopus (Rafinesque)
[White-footed Deermouse], P. gossypinus (LeConte) [Cotton Deermouse], Neotoma
floridana (Ord) [Eastern Woodrat], and Microtus pinetorum (LeConte) [Woodland
Vole]) and 1 shrew that was not identified to species; we had no detections of
Meadow Jumping Mouse (Table 1). Track-tube results also recorded 3 identifications
of Sylvilagus sp. (rabbit) and incidental identifications of Procyon lotor (L.)
(Raccoon) and Didelphis virginiana (Kerr) (Virginia Opossum). At the site level,
there was no significant difference in the number of species detected by each trapping
method (average difference in species, live traps vs. track tubes: mean = 0.08
species; 95% CI = -0.14, 0.30; n = 37). For the most frequently captured species
(deermice and rats), across all sampling there were more total track-tube identifications
of each species than live-trap captures when all track confidence levels were
included (Table 1). However, when considering only high-confidence track-tube
detections, there were fewer track-tube identifications than live-trap captures for
Rice Rats and deermice.
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Of the subset of 58 track plates that were analyzed by a second observer, 35
contained small-mammal tracks. The 2 observers had 100% agreement on identifications
at the levels of mammalian order (rodents vs. shrew vs. each incidentally
detected order) and therefore to the level of family, as there were no orders for
which we detected multiple families. For 34 of the 35 plates, the observers’ identifications
were consistent to subfamily, which distinguished Neotominae (in our
study, deermice and Eastern Woodrat), Arvicolinae (voles), and Sigmodontinae
(Rice Rats and Cotton Rats). At the genus level, the 2 observers agreed on 16 of the
35 track plates with the same level of confidence and 17 track plates with different
levels of confidence, for an overall 94% agreement. To species, observers agreed
on 12 track plates with the same level of confidence and 14 track plates with different
levels of confidence. For 7 of the 9 plates for which observers did not agree
to species, the discrepancy was because the more experienced observer provided
a species identification while the second observer labeled the plate as providing
insufficient information.
Posterior median estimates of occupancy for the 3 most commonly detected
taxa did not show consistent differences among alternative approaches to handling
identification uncertainty, but precision was low (Fig. 4). Average per trap-night
true-positive detection probability with live traps was highest for Cotton Rat (estimates
from false-positive occupancy model: posterior median = 0.55; 95% credible
interval = 0.18, 0.83) compared to Rice Rat (median = 0.19; 95% CI = 0.06, 0.49)
and deermice (median = 0.27; 95% CI = 0.08, 0.59). When all tracks, regardless
Table 1. Live-trap captures and track-tube identifications by confidence level of small-mammal species
detected during sampling of 37 sites in Alabama and Tennessee, 2015–2016.
Track tube Track tube
Area Species Live trap (high confidence) (all confidence)
Alabama 2015
Shrew sp. 0 1 1
Deermouse sp. 0 4 13
Cotton Deermouse 4 0 0
Eastern Woodrat 1 1 1
Marsh Rice Rat 41 18 43
Cotton Rat 80 83 132
Alabama 2016
Deermouse sp. 2 9 13
Cotton Deermouse 7 0 0
Eastern Woodrat 0 1 1
Marsh Rice Rat 4 0 2
Cotton Rat 6 4 6
Arnold AFB
Deermouse sp. 0 34 47
White-footed Deermouse 40 0 0
Cotton Rat 3 4 6
Woodland Vole 1 0 0
Total 189 158 265
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of confidence level, were included in analyses that either ignored identification
uncertainty or used false-positive modeling, per trap-night odds of detection did
not differ between track tubes vs. live traps (Fig. 5). However, when low- or lowand
medium-confidence track-tube detections were omitted and all track detections
were assumed certain, odds of detection with track tubes on average were 55%
lower than odds with live traps. This difference was most pronounced with Rice
Rats (Fig. 5); they were detected only with live traps at 6 of the 19 sites where
Figure 4. Estimated posterior distribution, probability of occupancy, 2015–2016, using data
from sampling with Sherman live traps and track tubes at 37 sites in Alabama and Tennessee,
for deermice (PESP), Marsh Rice Rat (ORPA), and Cotton Rat (SIHI), by data set analyzed
(point = posterior median, error bars = 95% credible intervals). Data sets differed by how uncertainty
in track-tube detections was handled; live-trap detections were included in all data
sets. “LowMedHi” = all track-tube detections included; “MedHi” = low-confidence track-tube
detections omitted from analysis; “Hi” = low- and medium-confidence track-tube detections
omitted; “FP” = all track-tube detections included but with low- and medium-confidence detections
treated as uncertain and with some probability of being false-positive detections.
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Figure 5. Estimated posterior distribution for method odds ratio ([per-trap night odds of
detection with track tubes] / [odds of detection with live traps at an occupied site]), for deermice
(PESP), Marsh Rice Rat (ORPA), and Cotton Rat (SIHI), by data set analyzed (point
= posterior median, error bars = 95% credible intervals). Data are from sampling of 37 sites
in Alabama and Tennessee, 2015–2016. Odds ratio of 1.0 (horizontal reference line) equals
no difference in detection probability between methods; odds ratio < 1.0 = higher detection
probability with live traps; odds ratio > 1.0 = higher detection probability with track tubes.
See Figure 4 for additional information.
Table 2. Number of sites with at least 1 detection of each species categorized by method(s) of detection
and track identification confidence (n = 37 sites sampled in Alabama and Tennessee, 2015–2016).
Live Track tube only Track tube only Both trap types Both trap types
Species trap only (high confidence) (all confidence) (high confidence) (all confidence)
Deermouse sp. 3 4 10 8 9
Marsh Rice Rat 6 0 1 11 12
Cotton Rat 4 1 4 11 12
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observed, vs. no sites where they were detected only at a high confidence level
with track tubes (Table 2). Cotton Rat detectability varied little between methods.
Of the 20 sites at which Cotton Rats were detected, they were detected with both
methods at 12 sites, while they were detected only with live traps at 4 sites and
only with track tubes at 4 sites (Table 2). However, of the 22 sites where deermice
were detected, they were recorded only with track tubes at 10 sites (including 7 of
8 Alabama sites in 2015), vs. 3 sites where they were detected only with live traps.
False-positive occupancy modeling indicated that misidentification and potential
false-presence observations were a concern for deermice (posterior median
probability of false-positive detection = 0.11 [0.04, 0.30]) and Cotton Rats (0.05
[0.01, 0.21]). By definition, false-positive detections were possible only at sites
where no certain detections were obtained. For deermice, there were 6 sites where
the only detections recorded were uncertain (medium- or low-confidence track
identifications), while for Cotton Rats, there were 3 sites where only uncertain
detections were recorded. However, for Rice Rats, except for 1 site with only an
uncertain detection, at all other sites at least one certain detection (trap capture or
high-confidence track identification) was recorded. The data did not provide useful
information about the probability of false-positive detections of Rice Rats (posterior
median = 0.07 [0.002, 0.91]). The estimated probability that a true-positive track
detection would be classified as certain (high confidence) was highest for Cotton
Rats (0.82 [0.68, 0.92]), intermediate for deermice (0.73 [0.56, 0.87]), and lowest
for Rice Rats (0.52 [0.35, 0.70]).
Discussion
In our sampling, track tubes detected similar numbers of species per site compared
to live traps. When uncertainty in track identifications either was ignored
or was explicitly addressed with false-positive models, per-trap-night odds of
detection were similar between methods. This result indicates that track tubes are
an effective and viable alternative to live trapping for occupancy studies of mice
and rats in our study system, particularly given other advantages of track tubes.
They eliminate meaningful risk to animals, reduce some study costs significantly
(e.g., our costs were ~$5 US per track tube for supplies and building time versus
purchasing Sherman live traps currently priced $20 US per trap), and offer greater
flexibility in frequency and timing of field checks compared to live traps (e.g.,
Nams and Gillis 2003). In our preliminary sampling, sooted track tubes were a reliable
detection method during dry weather for up to 6 trap nights before track plates
needed replacement. However, in our wet-meadow study sites, daily track-plate
replacement was required during periods of heavy rainfall. In wetland areas where
traps are consistently exposed to water, track tubes may not be a useful technique
(DeSa et al. 2012).
A more general issue raised in our study is track identification uncertainty. The
utility of track tubes depends on whether or not tracks can be reliably identified to
the taxonomic level needed by the study and whether the study uses appropriate
approaches for addressing identification uncertainty when present. Experienced and
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well-trained observers, a reference library of known tracks, and accurate diagnostic
criteria (e.g., unique track morphology) usually are needed to identify tracks to
species (DeSa et al. 2012, Evans et al. 2009, Zielinski and Schlexer 2009). Qualitycontrol
strategies such as repeated accuracy checks and tests of among-observer
agreement are recommended whenever a track-tube study faces identification
uncertainty. Because of the importance of observer experience for accurate track
identification, track tube studies should report the experience level of personnel
overseeing track identification, ideally using tracker-certification levels (Evans et
al. 2009).
Even for experienced observers, tracks of some species may be too similar to
distinguish with certainty, and some tracks will be incomplete or have imperfect
clarity. Therefore, besides attempting to maximize accuracy of identifications,
track-tube studies also need strategies for dealing with unresolved uncertainty.
Based on our estimates of the per-survey probabilities of false-positive detections
for deermice and Cotton Rats, ignoring uncertainty in identifications would not
be justified in our study system because standard occupancy estimators would be
biased (Royle and Link 2006, McClintock et al. 2010, Miller et al. 2011). Simply
omitting uncertain track identifications is a suboptimal approach if it lowers effective
detection probabilities substantially (Miller et al. 2011), as was observed with
our data (Fig. 4). This reduction in detection probability for track tubes would lead
to a need for more survey nights per site to maintain precision of occupancy estimates
(MacKenzie et al. 2002). In contrast, in the false-positive analysis, which did
not discard uncertain identifications but did address uncertainty, there was no loss
of effectiveness with track tubes relative to detection probabilitie s of live traps.
Our results reinforce the potential utility of false-positive models for occupancy
studies using track tubes (Stolen et al. 2014). Although the primary purpose of these
models is to reduce estimator bias for inference about occupancy, they also produce
quantitative measures of identification uncertainty (false-positive detection
probabilities and related parameters) that integrate observer accuracy and inherent
biological constraints on accuracy (e.g., due to species overlap in key track characteristics).
In our study, the estimated probability of identifying a true-positive
detection with certainty was much lower for Rice Rats than Cotton Rats, despite
general similarity in tracks of these 2 species. This finding may be a function of the
higher relative abundance of Cotton Rats in our study, as more tracks per survey
equals higher probability of obtaining at least one high-confidence detection. Along
with this, Cotton Rats are more easily identified due to their prominent, paired
metatarsal pads.
Biologists considering use of track tubes in small-mammal occupancy studies
should carefully review available study-design guidance related to false-positive
approaches, as the choice of approach and allocation of field effort depends on
the specific details of each study situation (Chambert et al. 2015, Clement 2016,
Miller et al. 2011). For example, using a combination of track tubes and direct
capture could seem like a sensible approach when there is concern about accuracy
of track misidentification. However, combining methods would be redundant if
many track identifications for a given species are certain. Even when that is not the
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case, optimal allocation of effort between sampling methods could favor using both
methods, only track tubes, or only live traps, depending on expected probabilities of
occupancy, true-positive detections, and false-positive detection (Clement 2016).
Intuitively, incorporating track tubes into occupancy studies along with or in place
of direct-capture methods would seem to have utility mainly when tracks of all
potentially present taxa of interest can be identified with relatively low probability
of false-positive identifications. For example, even in single-species scenarios,
optimal allocation would favor putting all effort into direct-capture surveys when
per-survey false-positive detection probability is >0.01 if per-survey probability
of true-positive detection is less than 0.4, direct-capture and track-tube costs per survey
are similar, and direct-capture surveys have no chance of species misidentification
(Clement 2016).
Several potential extensions discussed by Miller et al. (2011) and Chambert et
al. (2015) for false-positive analyses would be applicable for studies such as ours.
The basic false-positive occupancy model could be expanded to allow multiple categories
of uncertainty, to model individual track identifications rather than binning
them into a single detection state for each survey, and to consider other aspects of
potential identification errors. In our study, nearly all uncertain detections of Rice
Rats and Cotton Rats were identified with certainty to subfamily level. We could
be certain, for example, that an uncertain identification of a Rice Rat was either a
correct identification of a Rice Rat or a misidentification of a Cotton Rat. Incorporating
this reciprocal misidentification constraint with such co-occurring species
pairs would have utility in track-tube studies as well as direct-capture studies dealing
with identification uncertainty (e.g., Cotton Mouse vs. White-footed Mouse;
Fernandes et al. 2010).
Conclusions
Track tubes are a useful non-invasive approach in occupancy studies of small
mammals in the Southeast. However, their utility depends on whether taxa can be
identified accurately to the level needed by the study and whether identification
uncertainty can be handled appropriately. Extensions to existing false-positive
occupancy models are an area of active research (Chambert et al. 2015), and studies
utilizing track tubes will benefit from these developments. Still, it will remain
important to minimize uncertainty by using study protocols that produce high
detection probabilities and high-quality species identifications. To ensure suitable
accuracy in any track-tube study, track identification should be done under the
training and oversight of an experienced tracker and with appropriate checks of
observer accuracy. We recommend that tracking studies document the experience
level of key project personnel, the degree of identification uncertainty present in
their study, and the steps taken to address that uncertainty .
Acknowledgments
The Alabama Division of Wildlife and Freshwater Fisheries sampled Alabama study
sites. Shannon Allen facilitated protocol consistency and data collection at Arnold Air Force
Southeastern Naturalist
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Base. Chelsea Warner, Morgan Allen, Kevin Ryer, Alisia Diamond, and other technicians
collected field data. The School of Forestry and Wildlife Sciences, Auburn University, provided
support for manuscript preparation.
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