Conspicuous genetic structure belies recent dispersal in an endangered
beach mouse (Peromyscus polionotus trissyllepsis)
James D. Austin, Jeffery A. Gore, Daniel U. Greene, Cecile Gotteland
Supplemental methods
Sampling
On 25-26 March 2010, 48 captive born PKBM were released at GSP. Tail clips from
27 of the released mice were available for genetic study. We subsequently
exhaustively live-trapped (see Fig. S1) at GSP at intervals of 2, 4, 8, 12, 24, and 52
weeks, post-release. Each period consisted of 3 trap nights, except the 52-week that
covered 5 nights. We obtained tissue from all newly trapped mice for genetic study.
We also sampled mice trapped in 16 grids across PKSP in May 2010 (1920 trap
nights), and at 19 grids in GINS in March 2010 (2,280 trap nights). In May 2012, GSP
(1,220 trap nights) and PKSP (10 of the original 16 grids and 648 trap nights) were
re-sampled, and in July 2012 GINS was re-sampled (16 of 19 grids and 394 trap
nights; Fig. S1). Trapping at frontal dune locations interspersed between the parks
was haphazard, and varied from 10-20 traps and 1-5 nights per location (depending
on availability) for a total of 310 trap nights. Mice were trapped in 5 x 6 x 16 cm livetraps (H. B. Sherman Traps Inc., Tallahassee, Florida). Grids used in PKSP and GINS
consisted of 4 rows of 8 traps that were spaced 15 m apart. Traps contained cotton
(Ancare, Bellemore, NY) and were baited with seeds. Traps were opened before
sunset each day and checked beginning at midnight. Mice were uniquely ear-tagged,
weighed, sexed, and tissue sampled (dorsal tip of pinna) before being released at the
capture site.
Spatial analysis and genetic structure
Bayesian clustering using STRUCTURE included a correlated allele admixture model
that assumes clusters diverged from a common ancestor and that genetic drift has
played a major role in determining allele frequencies. We tested the fit of models K
= 1 to K = 10. Each run proceeded with 50,000 MCMC iterations as “burn-in”,
followed by 100,000 iterations. Each K was examined across 20 independent runs.
Results were plotted using StructureHarvester
(http://taylor0.biology.ucla.edu/structureHarvester/; accessed Aug. 2013). We
replicated these analyses using sample location (GSP, PKSP, and GINS) as a prior
using “USEPOPINFO” flag. Runs were post-processed using CLUMPP version 1.1
(Jakobsson and Rosenberg 2007) and Distruct (Rosenberg 2004).
Hybrid assignments
Before running NEWHYBRID on the empirical data, we took a simulation approach to
evaluate the statistical power of our population allele frequencies to detect hybrids
between GSP and PKSP, and between PKSP and GINS. To conservatively estimate
allele frequencies of residents (more likely to be identical by descent, rather than
immigrants or recent immigrate ancestry) at each location we first identified “pure”
individuals from each population based on the following criteria: 1) A minimum Q
values of 0.98 assignment to either parental population based on the averaged 20
replicates from the best-fit Structure model, and 2) those individuals had no missing
genotyped loci. We first simulated new parental populations using the allele
frequencies from the pure genotypes selected as above, generating 100 new pure
parents for each location by randomly drawing alleles from the empirical
frequencies of the pure representatives. From these randomly generated parental
genotypes we then simulated 100 each of F1 between neighboring locations and
parental populations backcrossed to F1.These genotypes were simulated in
HYBRIDLAB version 1.1 (Nielson et al. 2006). Simulated genotypes were then
analyzed using NEWHYBRID. We subsequently estimated the power of the allele
frequencies at the 16 loci to correctly assign simulated genotypes to their category
(pure, F1, backcrossed) as the ratio of correctly identified to the 100 simulated
individuals of the same category. Accuracy of assignment to a category was
evaluated as the number of correctly identified individuals for a category over the
total number of individuals assigned to that category for a given threshold of
acceptance of assignment (TQ). We evaluated TQ values of 0.7, 0.8 and 0.9.
Supplemental citations
Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation
program for dealing with label switching and multimodality in analysis of
population structure. Bioinformatics 23:1801–1806
Nielson E, Bach LA, Kotlicki P (2006) Hybridlab (version 1.0): a computer program
for generating simulated hybrids from population samples. Mol Ecol
Resources 6:971–973
Rosenberg NA (2004) Distruct: a program for the graphical display of population
structure. Mol Ecol Notes 4:137–138