Supplemental Tables
Table S1: Pairwise F st
values between the four species present in the ‘Founders’ training set.
The red wolf population for this comparison is represented by the original founders of the wild population.
Table S2: Measures of average allelic richness, H
0
, F
IS
, and private alleles across all loci for the four species incorporated in the ‘Founders’ training set. The red wolf population for this comparison is represented by the original founders of the wild population.
Table S3: Correlation values (r) between known red wolf ancestry and estimated red wolf ancestry using the different loci subsets. The columns depict the values produced by the two
Bayesian clustering programs. For this loci comparison, we used the training set option in both programs and used the ‘Founders’ training set. Note: for all correlations, p<0.001.
Table S4: Number of individuals assigned to each category of red wolf ancestry from 1987-
2008. “Pure RW” refers to individuals that have 100% red wolf ancestry using the pedigree.
“RW backcross” covers animals between 87.5-99.9% red wolf ancestry. “RWxF1 backcross” refers backcross hybrids between red wolves and F1 hybrids. “F1 hybrids” are first-generation hybrids between red wolves and coyotes. The “Coyote/Unassigned” column refers to individuals that either could not be classified into the pedigree or were determined to be coyotes using the
CAT.

Supplemental Figures
Figure S1 : Changes in pairwise F st over time between red wolves and the other canid species using the A. ‘Update’ training set and B. ‘12 years’ training set
Figure S2
: Change in allelic richness for the ‘pure’ (i.e. 100%) red wolf population over time.
Each year represents the values for the individuals that were included in the training set ‘12 years’ scenario for that year. The initial value represents the allelic richness of the founder red wolves. Allelic richness was averaged across all loci.
Figure S3 : Change in observed heterozygosity (H
0
) for the ‘pure’ red wolf population over time.
Each year represents the values for individuals present training set ‘12 years’. The initial value represents the H
0
of the founder red wolves.
Figure S4 : Average absolute difference between real and estimated ancestry values using A.
STRUCTURE and B.
BAPS for each loci subset. The difference between these values was averaged for each known level of red wolf ancestry. Each set of loci is indicated by a separate line: the full suite included 17 loci.
Figure S5 : Misclassification rate of individuals by BAPS using different sets of loci. Individuals are grouped according to the four red wolf ancestry classes and misclassification rate refers to the percentage of individuals in that ancestry class that were misclassified. For ‘Pure’ and
‘Backcross’ red wolves, misclassification means they were classified as hybrids (<87.5%) by
BAPS. For ‘F1 x red wolf backcrosses’ and ‘F1 hybrids’, misclassification means they were classified as legal red wolves (>87.5%) by BAPS.
Figure S6 : Misclassification rate of individuals by STRUCTURE using different sets of loci.
Individuals are grouped according to the four red wolf ancestry classes and misclassification rate refers to the percentage of individuals in that ancestry class that were misclassified. For ‘Pure’

and ‘Backcross’ red wolves, misclassification means they were classified as hybrids (<87.5%) by
STRUCTURE. For ‘F1 x red wolf backcrosses’ and ‘F1 hybrids’, misclassification means they were classified as legal red wolves (>87.5%) by STRUCTURE.

Table S1
Coyote
Gray wolf
Domestic dog
Gray wolf
0.1274
Domestic Dog
0.1087
0.1016
Red wolf
0.1404
0.1699
0.1664

Table S2
Coyote
Gray wolf
Domestic dog
Red wolf
Allelic richness
7.312
5.0
5.847
4.606
H
0
0.770
0.585
0.589
0.672
F
IS
0.046
0.133
0.166
-0.061
Private alleles
31
3
5
3

6 loci
Table S3
17 loci
15 loci
12 loci
9 loci
STRUCTURE
0.917
0.919
0.913
0.887
0.872
BAPS
0.834
0.839
0.841
0.845
0.826

1991
1992
1993
1994
1995
1987
1988
1989
1990
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
Table S4
Pure RW RW backcross
1
2
1
12
7
16
30
28
46
27
12
5
15
17
7
22
17
20
17
8
14
12
11
16
13
6
12
11
8
RWxF1 backcross
8
3
2
1
1
3
6
3
1
4
1
F1 hybrid Coyote/Unassigned
5
2
19
1
4
1
1
15
20
7
15
9
1
8
10
1
8
10
15
1

2006
2007
2008
32
3
9
20
28
44
50
2
37

Figure S1
A 0,3
0,28
0,26
0,24
0,22
0,2
0,18
0,16
0,14
B 0,32
0,3
0,28
0,26
0,24
0,22
0,2
0,18
0,16
0,14
Year
Year
Coyote
Gray wolf
Dog
Coyote
Gray wolf
Dog

Figure S2
4,8
4,6
4,4
4,2
4
3,8
3,6
3,4
3,2
3
Year

Figure S3
0,7
0,65
0,6
0,55
0,5
0,45
Year

B 60
50
40
30
20
10
0
Figure S4
A 30
25
20
15
10
5
0
Percent red wolf ancestry
Percent known red wolf ancestry
17 loci
15 loci
12 loci
9 loci
6 loci
17 loci
15 loci
12 loci
9 loci
6 loci

Figure S5
100
90
80
70
60
50
40
30
20
10
0
17 loci 15 loci 12 loci 9 loci 6 loci
Number of loci
Pure RW
Backcross RW
F1 x RW backcross

Figure S6
15
10
5
0
30
25
20
45
40
35
17 loci 15 loci 12 loci 9 loci 6 loci
Number of loci
Pure RW
Backcross RW
F1 x RW backcross