ANNUAL REPORT TO FLORIDA FISH AND WILDLIFE CONSERVATION

COMMISSION ON CONTRACT R112219563 WITH THE UNIVERSITY OF

TENNESSEE
Preliminary Estimates of Black Bear Population Size and Density in Apalachicola, Big
Cypress, and Eglin Study Areas, Florida 1
18 March 2016
JACOB HUMM, Department of Forestry, Wildlife and Fisheries, University of Tennessee, 274
Ellington Plant Sciences Building, Knoxville, TN 37996, USA.
J. WALTER McCOWN, Fish & Wildlife Research Institute, Florida Fish & Wildlife
Conservation Commission, 1105 S.W. Williston Rd., Gainesville, FL 32601-9044, USA.
BRIAN K. SCHEICK, Fish & Wildlife Research Institute, Florida Fish & Wildlife Conservation
Commission, 1105 S.W. Williston Rd., Gainesville, FL 32601-9044, USA.
JOSEPH D. CLARK, Principal Investigator, U.S. Geological Survey, Southern Appalachian
Research Branch, University of Tennessee, 274 Ellington Plant Sciences, Knoxville, TN
37996, USA
INTRODUCTION
In 2014, we initiated a 2-year study to estimate Florida black bear (Ursus americanus floridanus)
population sizes and density using spatially explicit capture recapture methods (Humm et al.,
2015). Plans were to estimate population parameters in Osceola and Ocala/St. Johns study areas
in 2014 and Apalachicola, Big Cypress, and Eglin study areas in 2015 (Fig. 1). In 2014, we
checked 83 hair traps on Osceola, 123 on Ocala, and 66 on St. Johns from 16 June to 24 July
2014. Based on the top model, bear density at Osceola averaged 0.104 bears/km2 (95% CI =
0.0630.180), or 615.8 bears (95% CI = 379.8998.5) when applied to the 5,295-km2 study area.
On Ocala/St. Johns, bear density averaged 0.100 (0.0830.120) bears/km2. When applied to the
13,025-km2 study area, the population estimate (expected N) was 1,225.6 bears (95% CI =
1,001.51,500.0). Those density estimates were amended slightly compared with the Humm et
al. (2015) report because expected N rather than realized N was most appropriate for our study
area because the former incorporates spatial process variance whereas the latter does not (Efford
and Fewster 2013).
METHODS
As in 2014, hair-sampling sites for Apalachicola, Big Cypress, and Eglin consisted of enclosures
comprised of 2 strands of barbed wire stretched around 35 trees. We positioned the 2 wires 35
40 and 6570 cm above the ground and blocked variations in the terrain (e.g., small gullies,
mounds) with vegetation to prevent bears from crossing over or under the wires. We hung bait
(bakery products) from a line that spanned the enclosure. We also used commercial bear lure
1

This report contains preliminary data that have not yet undergone scientific peer review and are thus not suitable
for citing.

2
(Code Blue Bear Magnet Raspberry Donut Attractant, Code Blue, Calera, Alabama, USA). We
placed the hair samples in coin envelopes, and stored them at room temperature prior to analysis.
We used a propane torch to burn any remaining hair off the barbs. We checked and rebaited all
hair-sampling sites weekly for 6 weeks, beginning in June.
The hair samples were shipped to Wildlife Genetics International (WGI; Nelson, British
Columbia, Canada) for genotyping. During weeks 16, we selected 2 samples per site per week
for genotyping to reduce the number of duplicate samples while maximizing the success rate.
Technicians at WGI randomized the samples within each site-week and selected the first sample
encountered containing >30 underfur or 5 guard hair roots. If none of the samples at a site-week
met this quality threshold, technicians chose the best available sample from the site, using a
minimum quality threshold of 1 guard hair root or 5 underfur hairs. If none of the samples met
this more lenient threshold, the site was left out of the analysis. Following standard protocols
(Woods et al. 1999, Paetkau 2003, Roon et al. 2005), DNA was extracted using QIAGEN
DNeasy Blood and Tissue spin columns. The analysis of individual identity was based on 8
markers, including a gender marker and 7 microsatellites. Mismatching markers in 1MM- and
2MM-pairs were reanalyzed and the errors corrected. This process effectively ensured that the
number of individuals identified in the dataset had not been inflated through undetected
genotyping error.
We used ver. 2.9.5 of the R package secr to estimate population parameters (Efford
2004, Efford et al. 2004, Borchers and Efford 2008, Efford 2012) within an information theoretic
model selection framework based on Akaikes Information Criterion adjusted for small sample
size (AICc, Burnham and Anderson 1998). We evaluated models whereby heterogeneity in
detection probabilities (g0) or a home range parameter () were explained by a sex covariate
(Pledger 2000) and whether detection probabilities of individual bears were affected by having
been previously detected at a specific site (bk). In addition, we evaluated percent forest cover as
a habitat covariate for density. First, we downloaded land cover data from the Florida Natural
Areas Inventory website (http://www.fnai.org/gisdata.cfm). In ArcGIS, we created a forest data
layer by reclassifying the fl_veg2014 data categories 1100 (Hardwood Forested Uplands), 1200
(High Pine and Scrub), 1310 (Dry Flatwoods), 1400 (Mixed Hardwood-Coniferous), 2200
(Freshwater Forested Wetlands), and 18333 (Tree Plantations) as forest (Redner and Srinivasan
2014). We then calculated mean percent forest using a moving window with a radius of 2,370 m
( for both sexes based on 2003 data). We estimated density and abundance within a 16-km
buffer area (the average distance between cluster centers) around the trap sites, excluding water
bodies, cities, etc. We used a 500-m mesh grid spacing for estimation in secr for Big Cypress
and Eglin but used 1,000 m for Apalachicola to reduce processing time.
RESULTS
We checked 324 hair traps on Apalachicola, 134 on Big Cypress, and 93 on Eglin from 15 June
to 1 August 2015. Based on our prescribed sampling protocol, we genotyped 683 of 4,027, 316
of 2,038 and 75 of 615 samples during weeks 16 on Apalachicola, Big Cypress, and Eglin,
respectively (Figs. 24). Hair sample quality control protocols removed 11 successful hair
snares in Apalachicola and 1 successful snare in Eglin prior to full genetic analysis. During the
6-week sampling period, 217 (124M:92F), 128 (81M:47F), and 22 (13M:9F) bears visited hair
traps 519, 258, and 49 times on Apalachicola, Big Cypress, and Eglin, respectively (Figs. 57).
On Apalachicola, the percent forest habitat covariate was supported but the effect was
negative ( = -1.185, 95% CI = -2.228-0.141), which we deemed to be biologically

3
unreasonable, so we excluded that model from the analysis. Other model selection results in secr
suggested that there was a strong sex effect on ( = 0.879, 95% CI = 0.6351.122) and g0 ( = 0.658, 95% CI = -1.145-0.171) and site-specific behavioral effects (bk) on g0 ( = 2.980, 95%
CI = 2.6463.332, Table 1). Based on the top model, bear density at Apalachicola averaged
0.082 bears/km2 (95% CI = 0.0630.105; Table 2). When applied to the 13,193-km2 study area,
the population estimate (expected N) was 1,076.0 bears (95% CI = 833.31,384.4).
On Big Cypress, the percent forest habitat covariate was not supported ( = 0.172, 95%
CI = -0.6571.000) but there was a strong sex effect on ( = 0.880, 95% CI = 0.5291.231) and
g0 ( = -1.958, 95% CI = -2.618-1.297) as were site-specific behavioral effects (bk) on g0 ( =
1.899, 95% CI = 1.3362.461, Table 1). Based on the top model, bear density at Big Cypress
averaged 0.144 bears/km2 (95% CI = 0.1040.201, Table 2). When applied to the 7,983-km2
study area, the population estimate (expected N) was 1,152.0 bears (95% CI = 829.11,600.8).
On Eglin, the percent forest habitat covariate was not supported ( = -1.997, 95% CI = 7.1383.145) but there was a strong sex effect on ( = 1.500, 95% CI = 0.7132.287) and g0 (
= -1.672, 95% CI = -3.258-0.086) as were site-specific behavioral effects (bk) on g0 ( = 2.325,
95% CI = 1.1443.506, Table 1). Based on the top model, bear density at Eglin averaged 0.029
bears/km2 (95% CI = 0.0120.066, Table 2). When applied to the 4,854-km2 study area, the
population estimate (expected N) was 139.3 bears (95% CI = 60.1322.7).
DISCUSSION
As with the estimates from Osceola and Ocala/St. Johns in 2014, the overall density estimates
from Apalachicola, Big Cypress, and Eglin were low when compared with density estimates
from other bear populations in the Southeast (Table 3). Densities reported in Table 3 are
typically for small areas where bear habitat is good and densities are greater than the surrounding
area. Therefore, it is perhaps not surprising that the Florida estimates, which depict more
extensive and variable bear populations, were lower. Density estimates reported by Simek et al.
(2005) in 2002 were similar to our density estimates. However, our estimates included larger
areas than surveyed by Simek et al. (2005) and represents both good and moderate habitat
quality. Consequently, our abundance estimates generally were higher. For example, Simek et
al. (2005) estimated about 438695 bears on a 9,524-km2 on their Apalachicola study area in
2002 compared with our estimate of 833.31,384.4 on 13,193-km2. Likewise, Simek et al.
(2005) reported a population size at Big Cypress of 516878 bears on 5,324 km2, compared with
our estimate of 829.11,600.8 on 7,983 km2. Our estimates at Eglin (60.1322.7 on 4,854 km2)
were similar to those reported by Simek et al. (2005, 63101 bears on 1,979 km2) though our
confidence intervals were wider. We point out that direct comparisons of density and abundance
estimates between studies should be made cautiously because methodologies differed. Our
spatially explicit estimates have the advantage of estimating density directly and explicitly
incorporating the effects of spatial heterogeneity into the estimate (Royle et al. 2014), techniques
that were not available to Simek et al. (2005).
The percent forest cover variable did not perform as expected. On Apalachicola, the
slope was negative, suggesting increasing bear densities as percent forest cover decreased. The
overall effect of the covariate on the abundance estimate was minor, however, as the estimate
with percent forest as a covariate was 1,132.3 compared with the estimate of 1,076.0 without it.
For purposes of this analysis, we grouped all forest cover types into one category. That may
have been overly simplistic because different forest cover types (e.g., pine versus hardwood) do

4
not affect bear densities in the same way. We plan to evaluate other site-specific covariates as
data analysis continues.
ACKNOWLEDGEMENTS
We would like to thank the Florida Fish and Wildlife Conservation Commission and the U.S.
Geological Survey for funding this study. We are grateful for the many personnel from FWC,
other agencies, and volunteers who helped during this study and without whom it would not have
been possible including D. Hardeman, Jr., V. Deem, J. Reha, L. Perrin, K. Kallies, C. Smith, and
S. Christman who conducted much of the field work. We thank M. Pollock, B. Sermons, B.
Almario, P. Manor, D. Alix, S. Hester, M. Smith, D. Mitchell, D. Onorato, and M. Lotz of FWC
for invaluable assistance. We thank M. Beard, J. Dunlap, and A. Smith of Apalachicola National
Forest, J.D. Lee, R. Clark, D. Jansen, S. Schulze, and the Mud Lake Fire Complex Incident
Management Team of Big Cypress National Preserve. We thank B. Hagedorn, J. Preston, and J.
Johnson of Eglin AFB, and D. Jenkins, and J. Jennings of Tyndall AFB. We thank B.
Nottingham, M. Danaher, and K. Godsea of Florida Panther NWR and T. Peacock and J.
Reinman of St Marks NWR. We thank B. Camposano, D. Young, S. Allen, H. Ferrand, D.
Sowell, M. de la Vega, and C. Schmiege of Florida Forest Service. We thank K. Wilson of
Florida DEP and J. Bozzo of SFWMD. We would like to thank the landowners and managers of
JB Ranch and Green Glades West Ranch. We thank T. Fiore of Collier Enterprises, J.
deBrauwere of Profundus Corp., P. McMillan, and M. Stokes of Neal Land and Timber, R.
Batillo of Foley Land and Timber, R. Long of Holland Ware Foundation, R. Sharpe of Bear
Creek Timber, J. Meares of Westervelt Co., and B. McLeod of Avalon Plantation. We would like
to thank D. Paetkau of WGI for conducting the genotyping. Lastly, we wish to thank S. Simek
for her earlier efforts from 20012003, upon which much of our study relies. Any use of trade,
firm, or product names is for descriptive purposes only and does not imply endorsement by the
U.S. Government. These are preliminary data and have not undergone scientific peer review at
the time of this writing.
LITERATURE CITED
Borchers, D. L., and M. Efford. 2008. Spatially explicit maximum likelihood methods for
capturerecapture studies. Biometrics 64:377385.
Burnham, K. P., and D. R. Anderson. 1998. Model selection and inference: a practical
information-theoretic approach. Springer-Verlag, New York, New York, USA.
Efford, M. G. 2004. Density estimation in live-trapping studies. Oikos 106:598610.
Efford, M. G. 2012. Secr: spatially explicit capture-recapture models. _R package ver. 2.9.5
http://CRAN.R-project.org/package=secr. Accessed 12 March 2016.
Efford, M. G., D. K. Dawson, and C. S. Robbins. 2004. DENSITY: software for analyzing
capture-recapture data from passive detector arrays. Animal Biodiversity and
Conservation 27:217228.
Efford, M. G., and R. M. Fewster. 2013. Estimating population size by spatially explicit
capture-recapture. Oikos 122:918928.
Humm, J., J. W. McCown, B. K. Scheick, and J. D. Clark. 2015. Black bear population size and
density in Osceola and Ocala/St. Johns Study Areas, Florida. Annual Report to Florida
Fish and Wildlife Conservation Commission on Contract R112219563 with the
University of Tennessee. Tallahassee, Florida.

5
Paetkau, D. 2003. An empirical exploration of data quality in DNA-based population
inventories. Molecular Ecology 12:13751387.
Pledger, S. 2000. Unified maximum likelihood estimates for closed capturerecapture models
using mixtures. Biometrics 56:434442.
Redner, J., and S. Srinivasan. 2014. Florida vegetation and land cover 2014. Final Report,
Center for Statistical Analysis, Florida Fish and Wildlife Conservation Commission,
Tallahassee, Florida, USA.
Roon, D. A., L. P. Waits, and K. C. Kendall. 2005. A simulation test of the effectiveness of
several methods for error-checking non-invasive genetic data. Animal Conservation
8:203215.
Royle, J. A., R. B. Chandler, R. Sollmann, and B. Gardner. 2014. Spatial capture-recapture.
Academic Press, Amsterdam, The Netherlands.
Simek, S. L., S. A. Jonker, B. K. Scheick, M. J. Endries, and T. H. Eason. 2005. Statewide
assessment of road impacts on bears in six study areas in Florida from May 2001
September 2003. Final Report Contract BC-972, completed for the Florida Department
of Transportation and Florida Fish and Wildlife Conservation Commission.
Woods, J. G., D. Paetkau, D. Lewis, B. N. McLellan, M. Proctor, and C. Strobeck. 1999.
Genetic tagging of free-ranging black and brown bears. Wildlife Society Bulletin
27:616627.

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Table 1. Model selection results from secr for estimating density of bears at Apalachicola, Big Cypress, and Eglin study areas, 2015.
D is density, h2 is a heterogeneous sex effect, g0 is the detection rate, bk is a site-specific behavioral bias, is a home range
parameter, and percentfor is the percent forest.
__________________________________________________________________________________________________________
Model

No. par.

Log likelihood

AICc

AICc

Weight

__________________________________________________________________________________________________________
Apalachicola
1
D~percentfor, g0~h2+bk, ~h2
D~1, g0~h2+bk, ~h2
D~1, g0~1, ~1

8
7
4

-1753.345
-1755.489
-1969.321

3523.383
3525.514
3946.831

0.000
2.131
423.448

0.7437
0.2563
0.0000

Big Cypress
D~1, g0~h2+bk, ~h2
D~percentfor, g0~h2+bk, ~h2
D~1, g0~1, ~1

7
8
4

-940.718
-940.635
-994.471

1896.369
1898.481
1997.267

0.000
2.112
100.898

0.7419
0.2581
0.0000

Eglin
D~1, g0~h2+bk, ~h2
7
-195.946
413.892
0.000
0.9093
8
-195.713
418.502
4.610
0.0907
D~percentfor, g0~h2+bk, ~h2
D~1, g0~1, ~1
4
-219.021
448.395
34.503 0.0000
__________________________________________________________________________________________________________

Slope of percentfor parameter estimate was deemed to be biologically unreasonable so this model was not selected.

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Table 2. Parameter estimates of bears at Apalachicola, Big Cypress, and Eglin study areas, 2015
from whereby N is expected abundance, g0 is the detection rate, and is a home range parameter.
____________________________________________________________________________
Parameter
Estimate
SE
LCL
UCL
____________________________________________________________________________
Apalachicola
Density
N
Female
g0 (mixture = 68.2%)
(mixture = 68.2%)
Male
g0 (mixture = 31.8%)
(mixture = 31.8%)
Big Cypress
Density
N
Female
g0 (mixture = 44.4%)
(mixture = 44.4%)
Male
g0 (mixture = 55.6%)
(mixture = 55.6%)

0.082
1,076.0

0.011
140.9

0.063
833.3

0.105
1,389.4

0.081
1,616.0

0.017
176.1

0.054
1,306.1

0.121
1,999.6

0.044
3,890.9

0.007
257.1

0.033
3,418.7

0.059
4,428.3

0.144
1,152.0

0.024
194.7

0.104
829.1

0.201
1,600.8

0.213
1,105

0.053
120.0

0.127
893.8

0.335
1,366.4

0.037
2,664.8

0.010
416.6

0.022
1,965.1

0.062
3,613.5

0.029
139.3

0.013
62.6

0.012
60.1

0.066
322.7

0.148
1,144.8

0.109
449.4

0.031
545.1

0.488
2,404.3

0.032
5,131.3

0.015
1,004.3

0.012
3,509.1

0.079
5,606.2

Eglin
Density
N
Female
g0 (mixture = 74.3%)
(mixture = 74.3%)
Male
g0 (mixture = 25.7%)
(mixture = 25.7%)

____________________________________________________________________________

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Table 3: Reported population densities (bear/km2) of select black bear populations in the
southeastern United States (adapted from Murphy [2011]) based on spatially explicit capture
recapture methods.
_____________________________________________________________________________
Location
Bear/km2
Reference
_____________________________________________________________________________
Eglin
0.029
This study
McCreary County, KY
0.03
Murphy (2011)
Eglin
0.0320.051
Simek et al. (2005)
Carvers Bay, SC
0.04
Drewry (2010)
Apalachicola
0.0460.073
Simek et al. (2005)
St. Johns
0.0480.085
Simek et al. (2005)
Apalachicola
0.082
This study
Ocala/St. Johns
0.100
Humm et al. (2015)
Osceola
0.104
Humm et al. (2015)
Osceola
0.1090.171
Simek et al. (2005)
Big Cypress
0.0970.165
Simek et al. (2005)
Big Cypress
0.144
This study
Upper Atchafalaya River Basin, LA
0.150.18
Lowe (2011)
Big South Fork NRRA, TN
0.22
unpublished
White River National Wildlife Refuge, AR
0.220.25
Clark et al. (2010)
Ocala
0.1960.284
Simek et al. (2005)
Lewis Ocean Bay, SC
0.31
Drewry (2010)
Tensas River Basin, LA
0.66
Hooker (2010)
_____________________________________________________________________________

Osceola

Osceola
Eglin
Apalachicola

Ocala/Ocala/St.
St. Johns
Johns

Big Cypress

Figure 1. Site locations for hair sampling in Florida, 201415. The translucent boundaries
represent the study areas for which density and abundance were estimated. The green shading is
forest cover.

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Figure 2. Trap sites and activity in Apalachicola study area, Florida, 2015. The circles indicate the total number of hair samples collected
at each trap, 2015.

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Figure 3. Trap sites and activity in Big Cypress study area, Florida, 2015. The circles indicate the total number of hair samples collected
at each trap, 2015.

12

Figure 4. Trap sites and activity in Eglin study area, Florida, 2015. The circles indicate the total number of hair samples collected at each
trap, 2015.

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Figure 5. Trap sites and activity in Apalachicola study area, Florida, 2015. The crosses
represent hair traps and the colored points within each trap cluster represent a different bear.
Points connected by a line represent the same bear.

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Figure 6. Trap sites and activity in Big Cypress study area, Florida, 2015. The crosses represent
hair traps and the colored points within each trap cluster represent a different bear. Points
connected by a line represent the same bear.

15

Figure 7. Trap sites and activity in Eglin study area, Florida, 2015. The crosses represent hair
traps and the colored points within each trap cluster represent a different bear. Points connected
by a line represent the same bear.