Management and Conservation Article

Population Genetic Assignment of Confiscated

Gopher Tortoises
TONIA S. SCHWARTZ,1 Department of Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL 33620, USA
STEPHEN A. KARL,2 Hawaii Institute of Marine Biology, University of Hawaii, Manoa, P.O. Box 1346, Kaneohe, HI 96744, USA

ABSTRACT As gopher tortoises (Gopherus polyphemus) increasingly become threatened throughout their range in Florida, USA, the need
for management and conservation will intensify. Here we evaluate the forensic applicability of genetic assignment tests based on microsatellite
genotypic data to 1) accurately assign individuals in our genetic database to the sample location or population of origin and 2) determine the
origin of 6 confiscated tortoises. Overall, we could correctly assign 90% of the individuals in the database to their population of origin, but we
were unable to determine the source of the confiscated tortoises. However, these individuals are unlikely to have come from any of our sampled
sites and all 6 may have come from the same population. This approach can be used by law enforcement personnel to identify the origin of
confiscated tortoises as well as by developers and wildlife managers to determine the genetic appropriateness of potential recipient populations
when it is necessary to relocate individuals. (JOURNAL OF WILDLIFE MANAGEMENT 72(1):254–259; 2008)

DOI: 10.2193/2006-243

KEY WORDS Florida, forensic, genetic assignment, gopher tortoise, Gopherus polyphemus, Program STRUCTURE, relocation.

The gopher tortoise (Gopherus polyphemus) is found from the
extreme southern edge of South Carolina to the south-
eastern corner of Louisiana, and throughout most of
Florida, USA. Populations of gopher tortoises are becoming
increasingly threatened by extirpation throughout their
range (Auffenberg and Franz 1982, Diemer 1986, Bury
and Germano 1994), primarily due to real estate develop-
ment. As this trend likely will continue, the need for
conservation of this species will intensify. Presently, the
gopher tortoise is federally listed in Appendix II of the
Convention on International Trade in Endangered Species
of Wild Fauna and Flora (Inskipp and Gillett 2003), and at
the state level as Threatened in every state where it occurs
except in Florida, where it is listed as a Species of Special
Concern by the Florida Fish and Wildlife Conservation
Commission. Although recently, the gopher tortoise was
approved for Threatened status in Florida, contingent upon
a management plan being approved (Florida Fish and
Wildlife Conservation Commission 2006). Many technical
advances (Geographic Information Systems, spatial statis-
tics, DNA fingerprinting, etc.) now offer innovative ways of
assisting wildlife managers in the difficult task of assessing
and maintaining threatened populations. Particularly, ge-
netic data is useful in assessing the degree of population
subdivision in geographically widespread species (Avise
1994). These data also are useful in assessing the degree
of evolutionary distinctiveness of presumed isolated pop-
ulations or subspecies (Avise 2000). By accurately defining
evolutionary significant units, wildlife managers are better
able to apportion limited conservation resources to unique
and at-risk groups. Genetic approaches also can be used to
assign individuals to specific populations or population
subsegments in species that have genetically differentiated
and geographically localized population segments (Waser
1
Present address: 2012 Molecular Biology, Iowa State University,
Ames, IA 50011, USA
2
E-mail: skarl@hawaii.edu
and Stobeck 1998). From a management perspective, this is
particularly useful when it is necessary to relocate animals
with a desire to maintain the genetic architecture of a
species. From a law enforcement perspective, molecular
genetic techniques are powerful forensic tools for determin-
ing the species identity or source population for confiscated
individuals (Shivji et al. 2002, Cassidy and Gonzales 2005).
Highly variable nuclear microsatellites are successfully
used in the identification of individuals and populations
(Immel et al. 1999, Boyd et al. 2001). Assignment tests
designed for use with genetic data can identify unique
genetic signatures for each population (or sampling
location). Subsequently, individuals of unknown origin can
be assigned with specific probabilities to populations using a
genetic database (Pritchard et al. 2000). Analysis of
molecular variance approaches (AMOVA; Excoffier et al.
1992, Schneider et al. 2002) using estimates of population
genetic diversity can cluster groups in a hierarchical fashion,
thereby identifying genetically cohesive groups. Thus,
combining the 2 approaches allows the assignment of
individuals to local breeding groups, groups to populations,
and populations to species.
Our goals for this project were 2-fold. First, we wished to
determine how accurately assignment tests based on micro-
satellite data determine the location of origin of unknown
individuals. To do this, we tested how frequently individuals
in our database with known location information would be
successfully assigned to the correct sample. Second, we
wanted to apply this approach to determine the likely source
population of 6 tortoises confiscated from an individual
smuggler by agents of the South Carolina Department of
Natural Resources (SCDNR).
STUDY AREA
Gopher tortoises were collected from locations throughout
Florida (except the Panhandle) and in southern Georgia,
USA. Tortoises were captured in xeric scrub, longleaf pine

254 The Journal of Wildlife Management  72(1)

Table 1. Sample location, population association, sample size, the observed average heterozygosity (HO) and standard deviation over all loci, number of alleles
(A) and number of private alleles (a) over all loci, genetic differentiation (FST) between the aggregated confiscated individuals and the database sample
locations or populations over all loci, average assignment probability (Prob) and standard deviation, and percent of individuals correctly assigned with
Program STRUCTURE for gopher tortoises collected from throughout Florida and Georgia, USA, in 1999 to 2001.

Sample Population

Assignment Assignment

Collection location and sample abbreviationa n HO SD A a FST Prob SD % Location FST Prob SD %

GA
Savannah River Ecology Laboratory (SREL)b 17 0.27 0.23 19 0 0.488 0.88 0.14 100 SREL 0.488 0.90 0.13 100
Moody Air Force Base, Lowndes County (MB) 14 0.46 0.22 33 2 0.309 0.78 0.22 93 MB 0.309 0.81 0.20 93
Jones Research Center, Baker County ( JR) 20 0.53 0.22 30 2 0.336 0.90 0.05 100 JR 0.336 0.91 0.04 100
FL
Big Shoals State Park, Columbia County 10 0.56 0.25 35 3 0.197 0.33 0.29 20 North FL 0.156 0.71 0.26 85
Cedar Key Scrub Preserve, Levy County, and 12 0.51 0.30 36 3 0.224 0.52 0.33 67
Ichetucknee Springs State Park,
Columbia County
Ashton Biological Preserve, Alachua County 18 0.45 0.24 35 1 0.198 0.42 0.27 56
Goldhead Branch and Cecil Field state parks, Duval 13 0.40 0.21 35 2 0.126 0.57 0.34 69
and Clay counties
Brooker Creek Preserve and Fort Cooper State Park, 21 0.45 0.22 27 2 0.224 0.58 0.25 86 Middle FL 0.197 0.63 0.26 75
Hillsborough and Citrus counties
Lake Louisa State Park, Lake County 15 0.36 0.21 24 1 0.190 0.31 0.20 53
Highlands Hammock State Park, 19 0.41 0.19 23 0 0.266 0.47 0.28 68 South FL 0.277 0.74 0.21 93
Highlands County
Cayo Costa State Park, Lee County 21 0.34 0.17 22 0 0.327 0.69 0.22 90
Jonathan Dickenson State Park, Martin County ( JD) 20 0.45 0.27 39 7 0.152 0.82 0.12 100 JD 0.152 0.85 0.11 100
Totals or averages 200 0.43 0.08 77 23 0.63 0.30 77 0.76 0.23 90
a
Sample location abbreviations correspond to Schwartz and Karl (2005).
b
This population was originally collected from coastal GA (McIntosh County) and was relocated to Savannah River Ecology Laboratory, Aiken, SC, USA.

(Pinus palustris), and sandhill habitat or where there is
sandy, well-drained soil. Scrub habitat is characterized by
low-growing shrubs (oaks [Quercus spp.], palmettos [Serenoa
repens], etc.) with or without a canopy of pine trees.
Longleaf pine and sandhill habitats are similar, except they
are dominated by tall longleaf pines and open, grassy
groundcover.
METHODS
Blood samples from 6 confiscated tortoises (referred to as
confiscated individuals 1 to 6) were sent to us from
SCDNR. We isolated DNA using a standard phenol and
chloroform technique (Herrmann and Frishchauf 1987, Karl
et al. 1992) and assayed the test individuals at the same 9
microsatellite loci used to develop our gopher tortoise
genetic database (Schwartz and Karl 2005). General
information on the number and frequency of alleles and
heterozygosity estimates for these loci is found in Schwartz
(2003) and Schwartz et al. (2003).
Gopher tortoises have been relocated extensively in certain
areas of Florida primarily for management purposes, and
some of our sample locations were known to be recipients of
relocated tortoises. As these relocation events can obscure
the true (historical) genetic signature of the populations, for
this exercise, we modified the original genetic database of
Schwartz and Karl (2005) by removing sample locations that
were demonstrated to be recipients of translocated individ-
uals (i.e., Wekiwa Springs State Park, Boyd Hill Nature
Park, Oldenburg Mitigation Park, and the University of
South Florida Eco Area; Schwartz and Karl 2005). We also
eliminated sample locations that had very small sample sizes
(i.e., Wakulla Springs State Park and Everglades National
Park; Schwartz and Karl 2005) and individuals that were
shown to be migrants that had moved or been moved by
humans into different populations (Schwartz and Karl
2005). Finally, we combined sampling locations that had
small sample sizes and were not statistically genetically
different: Brooker Creek Preserve and Fort Cooper State
Park, Hillsborough and Citrus counties, Florida; Goldhead
Branch and Cecil Field state parks, Duval and Clay
counties, Florida; and Ceder Key Scrub Preserve, Levy
County, and Ichetucknee Springs State Park, Columbia
County, Florida (Table 1). The final database consisted of
200 individuals from 12 sampling locations and is a subset of
individuals in the original database that provides a reliable
genetic signature of the population structure prior to human
disturbances (Schwartz and Karl 2005). We captured and
blood-sampled animals for this study under a Florida Fish
and Wildlife Service permit (WV01274) and The University
of South Florida Institute for Animal Care and Use permit
(1742).
We estimated pairwise FST values between all sample
locations and populations including a post hoc confiscated
group consisting of the 6 tortoises from SCDNR. We
verified that the hierarchical levels of genetic subdivision of
the modified database, based on FST estimates using an

Schwartz and Karl  Assignment and Identification of Tortoises 255

AMOVA (Excoffier et al. 1992, Schneider et al. 2002), were
consistent with the population structure described in
Schwartz and Karl (2005).
We used Program STRUCTURE to assign individuals,
based on their genotype, to sample locations or populations
(Pritchard et al. 2000). Program STRUCTURE uses a
Bayesian approach to determine the prior probability of the
population(s) of origin for individuals. The approach assigns
individuals into groups such that all groups (i.e., sampling
locations or populations) have a minimum of Hardy–
Weinberg genotypic and inter-locus linkage disequilibrium
(Pritchard et al. 2000).
Our first goal was to do internal consistency tests to
determine how well Program STRUCTURE can assign
individuals in the database back to their correct group
(sample location or population depending on the analysis).
Unlike our previous analysis (Schwartz and Karl 2005) in
which all individuals were given a group affiliation, here one
individual from each sample location was defined as having
unknown group affiliation. We then used STRUCTURE to
assess the probability of assigning the individual to its true
source sample location (or population). For these analyses,
all 6 of the confiscated individuals also had unknown group
affiliation. STRUCTURE settings were as follows: use
population information, admixture ancestry model, corre-
lated allele frequency model, 100,000 burn-in replications,
and 500,000 Markov chain Monte Carlo replications. The
output of the analysis is the probability of membership in
each sample location (or population) for each individual
with unknown group affiliation. If the probability of
assignment to the group to which the individual belonged
was highest, we considered it a correct assignment. We
repeated this internal consistency test procedure until every
individual in the database had been tested (i.e., assigned as
having an unknown group affiliation).
After these internal consistency tests, we wanted to
determine if the 6 confiscated tortoises originated from
any of the sample locations (or populations) in our database,
or if they possibly all originated from a source not
represented in our database. To do this, we used
STRUCTURE to assign each of the 6 confiscated
individuals in 4 analyses: I) assignment to 1 of the 12
sample locations in the database, II) assignment to 1 of the 7
AMOVA-determined populations, III) assignment to 1 of
the 12 sample locations or to a thirteenth sample location
consisting of the other 5 confiscated individuals (referred to
as ‘‘own sample location’’), and IV) assignment to 1 of the 7
AMOVA populations or to an eighth population consisting
of the other 5 confiscated individuals (referred to as ‘‘own
population’’). In each of these analyses, we arbitrarily chose
one individual from each sample location in the database
and also defined it as having an unknown group affiliation
(as above). This allowed us to test to what degree
assignment to the confiscated (own) group might simply
be due to its small sample size. These analyses used the same
STRUCTURE settings as described above.
256
RESULTS
We grouped the sampling locations from the modified
database into 7 genetically differentiated populations con-
sistent with Schwartz and Karl (2005). All pairwise FST
values among populations in the modified database were
significantly different from zero (P  0.05) and ranged from
0.089 for Middle Florida versus South Florida to 0.488 for
Savannah River Ecology Laboratory versus confiscated
group (Table 1). FST values among sample locations in
the unmodified database can be found in Schwartz and Karl
(2005). There were 3 alleles found in the confiscated
tortoises that were not represented in the modified database.
The internal consistency tests in which we assigned
individuals of known origin back to the sample locations
and populations in the database had highly consistent
results for an individual over the multiple runs. Over 5
program runs with all individuals, the average standard
deviation of the probability of correct assignment was
60.014 and the modal standard deviation was 60.004.
Results were variable, however, among individuals, depend-
ing on which sample location the individual was from and
whether we were trying to assign it to a sample or to a
population (Table 1). The number of correct assignments at
the sample level was generally lower than at the population
level, and individuals from sample locations in the North
and Middle Florida populations proved to be the most
difficult to correctly assign. For some sample locations (e.g.,
Savannah River Ecology Laboratory, Moody Air Force
Base, and Jones Research Center, Baker County, GA,
Jonathan Dickenson State Park, Martin County, FL),
however, 90% of the individuals were correctly assigned
with high probability. Correctly assigning individuals to
populations was common with, on average, 90% of the
individuals being correctly placed with high probability
(0.76 6 0.23). There was clearly enough genetic informa-
tion provided in the database to assign confidently
individuals to genetic populations if not to sample location.
Attempts to assign individual confiscated tortoises to
sample locations or populations in the database (analyses I
or II) generally resulted in assignment to northern sampling
locations (mainly Goldhead Branch and Cecil Field state
parks, Duval and Clay counties, FL [GC]) or to a variety of
populations, but generally with low probabilities in both
cases (Table 2). When given the option of being assigned to
a group in the database or to their own group (analyses III
and IV), all confiscated tortoises, except individual 2,
assigned to their own group and generally with a high
probability (Table 2). Confiscated individual 2 was assigned
to the GC sample location in the North Florida population.
The individuals from the database that had their group
affiliation set as unknown in these analyses had assignments
consistent with the internal consistency tests (i.e., generally
assigning back to the source group with high probability),
except for 2 individuals from GC (out of a total of 72
individuals tested). One GC individual in analysis III
assigned to the confiscated sample, and this individual and
The Journal of Wildlife Management  72(1)
Table 2. Probability values of genetic assignment of 6 confiscated gopher tortoise individuals to a database of microsatellite genotypes of 200 individuals
collected from 12 sample locations in Georgia and Florida, USA, in 1999 to 2001.
Ia IIb
Confiscated
tortoise Samplee Probability Populatione Probability
1 GC 0.74 JD
2 GC, CK, RA 0.24 North FL
3 GC 0.55 JD
4 GC 0.61 SREL, JD
5 GC 0.45 Middle FL
6 GC 0.62 JD
a
Assignment was to sample location in the database.
b
Assignment was to population in the database.
c
Assignment was either to sample location in the database or to own sample consisting of the other 5 confiscated tortoises.
d
Assignment was either to population in the database or to own population consisting of the other 5 confiscated tortoises.
e
GC ¼ Goldhead Branch and Cecil Field state parks, Duval and Clay counties, FL; JD ¼ Jonathan Dickenson State Park, Martin County, FL; CK ¼
Cedar Key Scrub Preserve, Levy County, FL; RA ¼ Ashton Biological Preserve, Alachua County, FL; SREL ¼ Savannah River Ecology Laboratory, GA.
an additional individual from GC assigned to the con-
fiscated population in analysis IV.
DISCUSSION
In our evaluation of the forensic applicability of genetic
assignment tests based on microsatellite genotypic data, we
could correctly assign 90% of the individuals in the database
to their population of origin. We were, however, unable to
determine the source of the 6 confiscated tortoises. These
individuals, however, are unlikely to have come from any of
our sampled sites and all 6 may have come from the same
population. Based on the internal consistency tests, the
individuals in the database assign with high probability back
to their populations of origin and in many cases to specific
sample locations. From this, we are confident that the
assignment program can effectively distinguish the samples
and populations and would robustly assign the confiscated
individuals to the correct group if it were in the database.
The low probability of assignment of the confiscated
individuals to any group in the database indicates that their
true population of origin likely is not represented.
Consistently assigning confiscated tortoises to their own
population indicates that at least 5 of the 6 confiscated
tortoises are likely to have originated from a single
population somewhere out of the sampling range of this
database. This conclusion is further supported by the finding
of 3 alleles not represented in the modified database in 3 of
the 6 confiscated tortoises. With more samples from
throughout the range (i.e., more northern locations), we
probably could tell with confidence from where these
individuals were taken.
In analyses III and IV, the consistent assignment of the
known database individuals (who had their source informa-
tion set to unknown) to the correct group of origin indicates
that the small number of confiscated individuals did not
itself positively bias the assignment of the confiscated
individuals to their own population. If so, we would expect
that the known individuals also would have assigned to the
confiscated population as often as the confiscated individuals
Schwartz and Karl  Assignment and Identification of Tortoises
Analysis
IIIc IVd
Samplee Probability Population Probability
0.46 Own 0.43 Own 0.87
0.81 GC 0.21 North FL 0.78
0.48 Own 0.90 Own 0.93
0.42 Own 0.90 Own 0.92
0.30 Own 0.58 Own 0.68
0.76 Own 0.84 Own 0.90
did. The 2 out of the 72 known individuals tested that
assigned to the confiscated population were both from the
more northern GC sample location, which is consistent with
the general more northern association of the confiscated
individuals. Even so, when trying to assign individuals to
sample locations (i.e., analyses I and III), the estimated allele
frequencies in the database may not represent the true allele
frequencies in the sampling locations because of too few
individuals in the group. If our allele frequency estimates are
not accurate, the assignment probabilities for the confiscated
individuals may be over- or underestimates relative to the
probabilities if the true allele frequencies were known.
Although we were unable to confidently assign the
confiscated individuals to a sample or population, we can
draw some specific conclusions. First, assignment tests based
on genetic data from individuals included in this study are
robust, highly useful, and are likely to be beneficial for
gopher tortoise conservation as they have been for other
species (Vazquez-Dominguez et al. 2001, Guinand et al.
2004, Paetkau et al. 2004). Second, if the confiscated
individuals originated in Florida, they must be from an
unsampled population that is genetically quite different
from the 12 geographically widespread sample locations we
have assayed. We think that this is unlikely because our
geographic coverage of Florida is fairly complete (with the
exception of the Florida Panhandle area). These individuals
are probably not from Florida but come from the part of the
range that we have not sampled. Third, given the repeated
assignment of the confiscated individuals to the North
Florida population (particularly northeast locations), a
genetic survey of gopher tortoise populations along the east
coast likely would reveal the true population of origin. We
cannot, however, confidently extrapolate from these data to
predict more precisely where that population would be.
Finally, the biggest restriction to this study was the limited
reference genetic database with which to compare the
individuals of unknown origin. We think that expanding the
database to include the Florida Panhandle, more of the east
coast, and the remainder of the non-Florida range would
257
greatly enhance the applicability of this approach. Similar
studies also will be constrained according to the degree of
sampling coverage across the species’ range. The AMOVA
population results indicate that, at least for gopher tortoises,
a single sample location for every approximately 800,000 ha
of the range is likely to capture a majority of the genetic
diversity of the species and thus permit robust assignments
of individuals to genetically similar populations.
Unfortunately, we do not know of the ultimate fate of the
6 confiscated tortoises. In the absence of a clear location of
origin or a genetically compatible population, they likely
were placed in a rescue preserve (e.g., Oldenburg Mitigation
Park, Hernando County, FL). Given that tortoise smug-
gling is uncommon relative to relocations due to real estate
development, there would be minimal harm in this solution.
In general, however, how should managers interested, for
any reason, in moving or relocating tortoises proceed? We
believe that the following recommendation would minimize
disruption of any existing genetic architecture and is the
preferred solution. First, structure the database such that
there are increasingly dissimilar groupings. The first
grouping would be local breeding groups consisting of a
single geographic sample of individuals likely to be highly
similar (e.g., Brooker Creek Preserve sample). These are
then nested into more regional populations that have
experienced similar ecological and evolutionary pressures
and are interbreeding through migrating individuals (e.g.,
Middle Florida group). It is expected that these regional
populations are significantly genetically differentiated.
Relying on nongenetic data or more subjective criteria
(i.e., the magnitude of genetic distance), regional groups can
be clustered according to degree of ecological or genetic
distinctiveness (e.g., Middle and North Florida populations
could be combined into a Temperate Florida group for
ecological as well as genetic reasons). Larger divisions are
probably unnecessary and speciously designated. Individuals
to be moved (or of unknown origin) can be added to the
group for which they have the highest assignment
probability. In specific cases in which all groups are equally
improbable (similar to the case here), we recommend that, if
feasible, individuals be divided among groups to avoid
genetic swamping. Dispersing individuals into different
locations would mimic a small amount of gene flow, which
may slightly increase genetic diversity, but would not disrupt
locally adapted gene complexes (Lenormand 2002).
MANAGEMENT IMPLICATIONS
With a coordinated effort among state and regional
management agencies and conservation researchers to
increase the number of populations represented in the
genetic database, the approach outlined here could be an
extraordinarily useful tool in conservation of this species.
With mounting pressure from real estate development, the
frequency of relocation of tortoises is increasing. State
guidelines for moving tortoises prohibit the mixing of
genetic stocks. When it is necessary to relocate individuals,
this approach can be used to assess probabilistically the
258
genetic appropriateness of potential recipient populations. It
can also be used to identify the origin of confiscated tortoises
when poaching has occurred.
ACKNOWLEDGMENTS
R. Brachmann, C. Curtis, K. Hayes, C. Legler, K. Penney,
M. Smith, and D. Warner assisted in the collection of
samples. R. Ashton, R. Birkhead, T. Lamb, M. Lockhart,
E. McCoy, H. Mushinsky, M. Osentoski, S. Reidel, K.
Stiles, T. Tuberville, and L. Wendland generously provided
samples. B. Bowen, M. Craig, K. Ottewell, R. Toonen, the
members of ToBo laboratory, D. Warner, and 2 anonymous
reviewers provided helpful comments on the manuscript.
This project was funded in part by the Chelonian Research
Foundation Linnaeus Fund, Sigma Delta Xi Women in
Science, Eloise Gerry Fellowship, and a University of South
Florida Tharpe Fellowship to T. Schwartz, and by Arcadia
National Wildlife Inc. and National Science Foundation
Grant in Systematics DEB 98-06905 to S. A. Karl. This is
the School of Earth Science and Technology contribution
7086 and Hawaii Institute of Marine Biology contribution
1269.
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