Supplemental Information on Simulations
Data were simulated using the program PEDAGOG v1.24 (Coombs et al. 2010)
because of its ability to track individual pedigree and genotype information, allow for
manipulation of genetic, demographic, and error parameters, and automatically format
the simulation output into input files for pedigree reconstruction programs. The baseline
population was parameterized to have five age classes, a cohort size ultimately
determined by density dependent self-thinning with a 0.5 probability of being female.
Founding cohorts for each of the three populations were drawn from a population pool of
10,000 animals whose genotypes were assigned randomly from population-specific allele
frequencies for the set of eight primary loci.
Subsequent cohorts reproduced using a polygamous mating system where all
animals had an age-specific probability of maturing, mate number was drawn from a
Poisson distribution with mean and standard deviation of two, and males and females
within three generations of each other were allowed to mate. Fecundity was drawn from a
normal distribution with mean determined using the empirically derived function
F=0.00187*(LENGTH^2.190)(Letcher et al. 2007), and standard deviation equal to four.
For females mating with multiple males, the proportion of offspring sired was sizedominant with the largest male’s proportion drawn from a normal distribution with mean
of 0.8 and standard deviation of 0.05. Non-dominant males were assigned a randomly
generated proportion of the remaining offspring. Annual survival probabilities for age
classes zero through four were 0.10, 0.20, 0.20, 0.90, and 0.95, and were the same
regardless of sex or maturity status. The population was sampled after ten generations
with capture probabilities of 0.4 for age class zero animals, and 0.6 for the remaining age
classes. Sex of captured individuals was unknown. All simulations were replicated ten
times.
To allow direct comparison between the matched empirical and simulated data
sets, we performed an additional post-hoc step on each simulated population to equalize
number of families and family sizes. Simulated families were rank-ordered and
individuals within families were randomly trimmed to match the empirical results for
family sizes. We then directly assigned stream location information for simulated
individuals from the location of their empirical counterparts.
Literature Cited
Coombs JA, Letcher BH, Nislow KH (2010) PEDAGOG: Software for simulating ecoevolutionary population dynamics. Mol Ecol Resour, 10, 558-563.
Letcher BH, Nislow KH, Coombs JA, O'Donnell MJ, Dubreuil TL (2007) Population
response to habitat fragmentation in a stream-dwelling brook trout population.
PLoS ONE, 2, e1139. doi:1110.1371/journal.pone.0001139.