Appendix D: Mark-recapture abundance of Presqu’ile

painted and snapping turtles

Road-effect mitigation promotes connectivity and reduces mortality at the population-level
Sean P Boyle, Matthew G Keevil, Jacqueline D Litzgus, Don Tyerman, David Lesbarrères

D.1 Analysis approach

We checked goodness-of-fit (GOF) of the capture-mark-recapture data from trapping surveys
(Table D.1) to fully-parameterized Cormack-Jolly-Seber (CJS) open population models using the
U-CARE approach (Choquet et al., 2005) as implemented in R version 4.0.2 (R Development
Core Team, 2020) by package R2ucare version 1.0.0 (Gimenez et al., 2017). We used median-c^
(Cooch and White, 2019a) to estimate overdispersion when GOF tests were not applicable.
We estimated model-averaged abundance at each occasion using the POPAN formulation of
Jolly-Seber (JS) open population models in Program MARK version 9.0 (White and Burnham,
1999) implemented in R (R Development Core Team, 2020) using package RMark version 2.2.7
(Laake, 2013). We then calculated mean abundance across all sampled years and quantified
uncertainty in this estimate using a bootstrapping approach (Madon et al., 2013).

Table D.1. Summary of turtle trapping surveys at Presq’ile Provincial Park.

Year
Species Quantity Total
2013 2014 2015 2016 2017
New caps. 11 12 10 6 5 44
Painted Turtles Recaps. 0 1 0 4 0 5
Total caps. 11 13 10 10 5 49
New caps. 46 54 28 27 9 164
Snapping Turtles Recaps. 0 13 23 21 7 64
Total caps. 46 67 51 48 16 228
Trap nights 576 688 864 744 784 3656
D.2 Goodness of fit (GOF)
The omnibus GOF test for snapping turtles did not indicate significant lack of fit at α =0.05 but
the p-value was marginal ( χ 2=14.7 , df = 8, P=0.066). Therefore, we also checked subtests to
assess specific assumptions. Subtests Test2.CT ( χ 2=2.7, df = 2, P=0.256) and Test2.CL (
χ =0.7, df = 1, P=0.4), which are sensitive to violations of assumptions due to trap dependence
2

or temporary emigration (Pradel, 1993), were not significant. Test3 subtests did not indicate
significant violations of survival assumptions (Test3.SR: χ 2=6.7, df = 3, P=0.083; Test3.SM:
χ =4.6, df = 2, P=0.102) but the p-values are low, which might suggest a pattern of transience
2

(Choquet et al., 2005). Transience manifests as a higher-than-expected frequency of individuals

that are only captured once resulting in lower apparent survival after the first occasion, which
could occur when non-resident individuals are captured while passing through the sampling area
(Pradel et al., 1997). To further investigate this possibility, we constructed a CJS candidate
model set that included transience models and compared them using an information theoretic
approach (Burnham and Anderson, 2002). Details of this analysis and results are included below.
Transience models were not supported by our model selection procedure, so we did not include a
transience effect in our abundance candidate model set for snapping turtles.
There were insufficient recaptures of painted turtles to test GOF. We proceeded to estimate
painted turtle abundance using a reduced set of plausible models, but we regard these estimates
as tentative. Because the GOF χ 2 statistic was not available for painted turtles, we estimated
overdispersion (c^ ) in MARK using and the the median-c^ approach (Cooch and White, 2019a).
However, the estimate had very low precision: median-c^ (95% CI) = 0.48 (-0.48–5.8).

D.3 Abundance estimation

The POPAN formulation of the JS model estimates four sets of real parameters: ϕ (apparent
survival), p (capture probability), N (superpopulation size), and b (probability of entry; often
abbreviated as pent). N and b are bookkeeping parameters that do not necessarily have a direct
biological interpretation (Schwarz and Arnason, 1996). Abundance estimates at each occasion (
^
N ) are estimated in MARK as derived parameters.
We estimated annual abundance of snapping turtles (Figure 5) using model averaging using
QAICc weights (Burnham and Anderson, 2002) (Table D.2). For painted turtles we averaged
annual abundance estimates (Figure 5) across a reduced candidate model set (Error: Reference
source not found). We weighted these models by unadjusted AICc rather than QAICc because
there was insufficient data to estimate a precise c^ value for painted turtles.
Table D.2. Candidate POPAN Jolly-Seber models for snapping turtle abundance. Quasi-
AICc values were used to score models by adjusting the overdispersion parameter (c^ )
estimated using the χ 2 statistic and degrees-of-freedom from the goodness-of-fit test for the
fully-parameterized Cormack-Jolly-Seber model: c^ = χ 2 /df =1.77 .
model npar QAICc QAICc weight QDeviance
(.)p(t)b(.) 8 208.9 0.0 0.36 -240.8
(t)p(trapN)b(.) 8 209.8 0.9 0.23 -239.9
(t)p(.)b(.) 7 211.5 2.6 0.10 -236.1
(t)p(.)b(t) 10 212.2 3.3 0.07 -241.8
(.)p(.)b(t) 7 212.2 3.3 0.07 -235.3
(.)p(t)b(t) 10 212.8 3.9 0.05 -241.2
(t)p(trapN)b(t) 11 213.1 4.2 0.04 -243.1
(t)p(t)b(.) 11 214.3 5.4 0.02 -241.9
(.)p(trapN)b(t) 8 214.4 5.5 0.02 -235.3
(t)p(t)b(t) 12 215.2 6.3 0.02 -243.3
(.)p(trapN)b(.) 5 218.6 9.7 0.00 -224.6
(.)p(.)b(.) 4 219.4 10.5 0.00 -221.8
 is apparent survival
p is recapture probability
b is probability of entry (see text)
(t) indicates parameter varies accross occasions/intervals
(.) indicates parameter is constant accross occasions/intervals
(trapN) indicates parameter varies according to annual total trap nights
In order to calculate confidence intervals for the model-averaged abundance estimates, we
followed the procedure outlined for post hoc CI calculation for close capture models in MARK
(Lukacs, 2019), which uses the unconditional (model-averaged) variance ( ^ ^ ; Buckland et
var ( θ)
al., 1997) computed by MARK for the log-normally distributed estimate of the number of
individuals not captured on an occasion, ^f 0 = N
^ t −nt . The 95% CI on N t was estimated as:
t

nt + f^ 0 /C , nt + ^f 0 C
t t

where C is:

( [( )] )
1/ 2
ar ( ^
v^ N)
C=exp 1.96 ln 1+ 2
f^ ❑ 0 t

Table D.3. Candidate POPAN Jolly-Seber models for painted turtle abundance. We used a
small set of reduced-parameter models that we deemed most appropriate a priori based on
our study design and the sparseness of the data. The ϕ (.) p (trapN )b( .) model has the fewest
parameters in the candidate set and we considered using only this model to estimate
abundance. However, simultaneously constraining both ϕ and b also constrains abundance
along a constant trajectory so we included models with time-dependence in one of those two
parameters in our model-averaged abundance estimates. AICc values were not adjusted for
overdispersion because the data were insufficient to obtain a precise estimate of the
overdispersion parameter (c^ ).
model npar AICc AICc weight Deviance
(.)p(trapN)b(.) 4 69.6 0.0 0.90 -106.8
(t)p(trapN)b(.) 7 75.0 5.4 0.06 -109.3
(.)p(trapN)b(t) 7 76.0 6.5 0.04 -108.2
 is apparent survival
p is recapture probability
b is probability of entry (see text)
(t) indicates parameter varies accross occasions/intervals
(.) indicates parameter is constant accross occasions/intervals
(trapN) indicates parameter varies according to annual total trap nights

D3.1 Mean abundance with bootstrapped confidence intervals

Mean snapping turtle estimated abundance over all sampled years was 117.4. Mean abundance is
not a standard component of Jolly-Seber abundance estimates, so we calculated it outside of the
model estimation procedure. Bootstrapping can be used to estimate uncertainty in post hoc
abundance estimates (Madon et al., 2013). Therefore, we estimated 95% confidence intervals for
mean abundance as 85.6–163 by resampling the encounter histories over 5000 bootstrapping
iterations. We followed the same procedure to estimate mean painted turtle abundance as 141.9
(95% CI: 9.3–347).
D.4 Snapping turtle transience and apparent survival
Transient individuals are non-residents that are only present in the study area for a brief time. A
substantial proportion of transients in a population manifests as a higher-than-expected
frequency of individuals that are only captured once resulting in lower apparent survival
following the occasion of first capture compared to subsequent captures (Pradel et al., 1997).
High proportions of transient individuals can cause abundance estimates to be inflated relative to
the resident population size (Madon et al., 2013). The low p-value of the U-CARE GOF subtest
Test3.SR (Choquet et al., 2005) is consistent with a pattern of transience in snapping turtles but
is not convincing at the α 0.05 level. We further investigated this possibility using Cormack-Jolly-
Seber (CJS) model set.
Unlike the JS models for abundance, the CJS likelihood conditions on first capture so that,
without the need to estimate abundance, there is no consideration of never-captured individuals
(Schwarz and Arnason, 1996). Therefore, it is more straight-forward to construct models that
depend on time-varying individual attributes such as time-since-marking models. We constructed
a CJS candidate model set that included time-since-marking transience models in which
survivorship over the interval following the occasion of first capture was independent of
(constant) survivorship over subsequent intervals (Cooch and White, 2019b). Candidate models
were compared using the same information theoretic approach that we applied to the POPAN JS
models.
Estimated apparent survival of snapping turtles was lower following initial capture than on
subsequent intervals in the top model with a transience effect (Error: Reference source not
found). However, there was no evidence favouring this model over other models lacking a
transience effect ( ΔQAIC <2 for five other models; Table D.4). The top transience model
ϕ (trans) p (t) differs from model ϕ (.) p (t) by only one additional parameter and ΔQAICc< 2 so
the additional transience parameter is not supported (Arnold, 2010).

D.5 Discussion
Mortality and permanent emigration are confounded in live encounter models such as CJS and
JS, so apparent survivorship cannot be assumed to represent true survivorship. The apparent
survival values that we estimated are much lower than typical long term survivorship estimates
obtained for snapping turtles using mark-recapture (e.g., Keevil et al., 2018; Congdon et al.,
1994; Flaherty et al., 2008) or telemetry surveys (Paisley et al., 2009). Therefore, we attribute the
population dynamics that we observed primarily to movement of individuals into, and out of, the
study site, which was a trapping grid situated in a marshy embayment contiguous with other
habitat along a much longer shoreline. These dynamics do not necessarily entail serious
violations of JS assumptions involved in estimating the abundance of individuals available for
capture at the sampling site on particular occasions. Temporary emigration (TE), where
individuals leave the study site and return (or are otherwise temporarily unavailable for capture),
does violate JS assumptions and has been detected over much longer time frames in snapping
turtles (Keevil et al., 2018). However, no indication of TE was detected by the GOF tests that we
applied and any potential TE effect appears to be negligible over the limited time span covered
by our analysis. There was also no evidence to support a specific transience effect.
More generally, we accounted for potential lack of fit due to assumption violations by adjusting
for overdispersion in our snapping turtle analysis. For both species, the limitations of our study
design and sample size suggest that the abundance estimates should be interpreted cautiously.
This is especially true in the case of painted turtles in which there was insufficient data to test
GOF. Nevertheless, these results help to establish context for our broader investigation into the
impacts of road mortality and mitigation at the study site.

Table D.4. Candidate Cormack-Jolly-Seber models for snapping turtle apparent survival and
recapture. Models accounting for transience allow apparent survivorship to vary between the
interval following first capture and subsequent intervals. Quasi-AICc values were used to
score models by adjusting the overdispersion parameter (c^ ) estimated using the χ 2 statistic
and degrees-of-freedom from the goodness-of-fit test for the fully-parameterized model:
2
c^ = χ /df =1.77 .
model npar QAICc QAICc weight QDeviance
(trans)p(t) 6 186.6 0.0 0.24 15.1
(t)p(.) 5 187.5 0.8 0.16 18.0
(.)p(.) 2 187.8 1.1 0.14 24.6
(.)p(t) 5 188.1 1.4 0.12 18.6
(t)p(trapN) 6 188.2 1.5 0.11 16.6
(trans)p(.) 3 188.3 1.7 0.10 23.1
(.)p(trapN) 3 189.8 3.2 0.05 24.6
(t)p(t) 7 190.2 3.6 0.04 16.5
(trans)p(trapN) 4 190.3 3.7 0.04 23.0
 is apparent survival
p is recapture probability
(t) indicates parameter varies accross occasions/intervals
(.) indicates parameter is constant accross occasions/intervals
(trapN) indicates parameter varies according to annual total trap nights
(trans) indicates transience effect
 Table D.5. Parameter estimates for the two highest scoring CJS models for snapping turtles
in Presqu’ile Provincial Park. Parameter indices refer to year (of occasions for p; at the start
of intervals for ϕ ). For the transience model (ϕ (trans) p (t)), subscripts on apparent survival
refer to the interval following first capture (ϕ 1) or all subsequent intervals (ϕ 2+ ¿¿). Standard
error (SE) and 95% CLs (LCL and UCL) were adjusted for overdispersion.
model param. Estimate SE LCL UCL
(trans)p(t) 1 0.433 0.090 0.271 0.611
(trans)p(t) 2+ 0.766 0.150 0.390 0.944
(trans)p(t) p2014 0.563 0.156 0.272 0.817
(trans)p(t) p2015 0.607 0.154 0.304 0.845
(trans)p(t) p2016 0.507 0.169 0.214 0.795
(trans)p(t) p2017 0.162 0.095 0.047 0.431
(t)p(.) 2013 0.665 0.174 0.301 0.902
(t)p(.) 2014 0.503 0.121 0.281 0.723
(t)p(.) 2015 0.639 0.174 0.288 0.886
(t)p(.) 2016 0.201 0.101 0.068 0.465
(t)p(.) p 0.482 0.108 0.285 0.685

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