Electronic Supplementary Material:
Method S1:
Study Animal:
The house mouse, mus musculus, was chosen for this experiment as it is small, social and has
short gestation times, so multiple generations can be bred over a short period. It is also an
introduced species and very common, so it is easily attainable and there is no concern about
removing individuals from the wild. House mouse biology and husbandry is very well known
and similar to many native endangered rodents, thus results from this experiment may be
applicable to conservation efforts more broadly.
Trapping Mice:
Mice were caught using standard Elliott live mammal traps (Elliott Scientific Co., Upwey,
Victoria; size 90 mm × 100 mm × 330 mm) at Werribee Open Range Zoo. The traps were
baited with a combination of peanut butter, golden syrup and oats and the back sections were
filled with cotton wool to provide nest material and insulation. The traps were then wrapped
with plastic bags to keep any trapped mice dry. When catching the wild mice, up to 100 traps
were set amid dense vegetation along a fence line at Werribee Open Range Zoo each evening
and were then checked early in the morning. Any non-target animals (including native
reptiles) were immediately released at their point of capture.
Breeding Mice:
For the founding generation, 11 male and 9 female mice were caught and transported to
Melbourne Zoo where they were housed in individual plastic cages covered by wire tops (400
mm × 120 mm × 250 mm). Cages were lined with animal-safe wood shavings and contained
tissue paper and toilet rolls for bedding and cover. Food (Barastoc rat and mouse pellets and
fruit and vegetables) and water were provided ad libitum. The room was maintained at 22 ºC
± 2 ºC; natural light came through windows and high colour-rendering index artificial light
cycles were changed monthly to match natural photoperiod length. The cages were cleaned at
least once per week or more frequently as required. We applied outbreeding protocols to
minimize opportunities for progeny to become inbred through mating between relatives
across generation.
First generation (F1) offspring
During breeding, founder mice were housed so that males and females captured at different
trapping sites were mated, to ensure the greatest degree of genetic diversity. The parent
generations were housed with one male and one female in 40 x 12 x 25 plastic breeding cages
with wood shavings for bedding and tissue paper for nesting material. After young were born,
sires were removed from the breeding cages and housed in their original individual cages.
Offspring were housed with their mother until they were weaned at 21–25 days of age, then
at around 6 weeks of age they were sorted and housed with same-sex littermates (2–5 animals
per cage) in the same type of cages and with the same enrichment as in the breeding cages.
The environmental conditions (light, temperature) were the same as those for the founding
generation.
F2 and F3 generation offspring
F2 and F3 generation offspring were bred from first and second generation captive-born
individuals using the method described previously. Genealogical records were kept to ensure
related individuals were not mated and genetic diversity was maintained in the F2 and F3
generations.
Method S2: Testing for differences in inbreeding coefficients (F) netween captive and
wild mice.
Pairwise differences in average inbreeding coefficients among captive and wild mice were
tested using inbreeding coefficients estimates derived from the Lynch & Ritland method
using a bootstrapping procedure implemented in COANCESTRY. Individual multilocus
genotypes were drawn at random 10,000 times to form pairs of groups with the same number
of individuals as the original sampling groups. Inbreeding for each group was calculated and
the final distribution of the differences in average inbreeding between the two simulated
groups were compared to the observed difference in relatedness values to test for significance
between groups. The cumulative frequency of this comparison are plotted below and deptic
that the observed difference (solid black line) sits outside the 99% quantiles of the simulated
differences indicating a highly significant difference in the inbreeding coefficient between
captive and wild mice.
1
1% quantile
2.5% quantile
5% quantile
95% quantile
97.5% quantile
99% quantile
Observed
0.9
Cumulative Frequency
0.8
0.7
DPlot
Trial
Version
http://www.dplot.com
0.6
0.5
0.4
0.3
0.2
0.1
0
-0.11
-0.09
-0.07
-0.05
-0.03
0.00
0.02
0.04
0.06
0.08
0.10
Mean difference in inbreeding between groups (Estimator LynchRd)