Electronic Supplementary Material:
AFLP datasets were generated by setting both loci and phenotype scoring thresholds to either 75or 100-rfu in AFLPSCORE v1.3b (Whitlock et al. 2008). ‘A’ indicates the original dataset
produced from AFLPSCORE consisting of all retained loci; ‘B’ indicates the original dataset
with singleton loci removed. The values reported in the body of the text are indicated in bold.
Table S1. Summary of the AFLP phenotype scoring results for all selective primer combinations
Selective primer
combination
EcoRI-AAC/MseI-CAC
EcoRI-AGC/MseI-CAC
EcoRI-AGC/MseI-CAT
EcoRI-AGC/MseI-CTT
EcoRI-AAG/MseI-CAA
Scoring Threshold
Locus
Phenotype
75
100
75
100
75
100
75
100
75
100
75
100
75
100
75
100
75
100
75
100
75
100
75
100
Mismatch
error rate %
1.46
1.43
1.77
1.74
1.71
1.68
1.30
1.28
1.71
1.63
1.59 (mean)
1.55 (mean)
Initial number
of loci
112
112
107
107
135
135
109
109
129
129
592 (total)
592 (total)
Number of
loci retained
99
94
101
93
117
112
95
80
117
109
529 (total)
488 (total)
1
Table S2. Within sub-population and global genetic diversity for the British Columbia population of Apodemia mormo. Global
measures are reported as mean values. All statistical analyses were performed using AFLP-SURV (Vekemans et al. 2002)
Site
N
W1
W2
W3
W4
W5
W6
W7
W8
C1
C2
E1
E2
N1
N2
All
45
39
19
38
44
41
15*
38
38
40
40
29
28
13*
467
75 rfu thresholds
A (526 loci)
PPL
He (±SE)
15.4
0.061 (0.006)
14.4
0.050 (0.005)
14.1
0.044 (0.005)
15.0
0.050 (0.005)
13.5
0.047 (0.005)
14.4
0.044 (0.005)
15.2
0.055 (0.006)
14.4
0.053 (0.005)
14.3
0.047 (0.005)
14.3
0.047 (0.005)
17.1
0.063 (0.006)
15.6
0.061 (0.006)
13.5
0.056 (0.005)
14.6
0.060 (0.006)
14.7
0.053 (0.005)
B (380 loci)
PPL
He (±SE)
21.3
0.083 (0.007)
20.0
0.069 (0.007)
19.5
0.060 (0.007)
20.8
0.069 (0.006)
18.7
0.064 (0.007)
20.0
0.061 (0.006)
21.1
0.075 (0.007)
20.0
0.073 (0.007)
19.7
0.064 (0.006)
19.7
0.064 (0.007)
23.7
0.086 (0.008)
21.6
0.083 (0.007)
18.7
0.077 (0.007)
20.3
0.081 (0.008)
20.4
0.072 (0.007)
100 rfu thresholds
A (484 loci)
PPL
He (±SE)
15.1
0.061 (0.006)
14.9
0.052 (0.005)
14.9
0.046 (0.005)
15.1
0.049 (0.005)
12.2
0.048 (0.005)
12.2
0.046 (0.005)
15.3
0.057 (0.006)
15.5
0.056 (0.006)
14.7
0.048 (0.005)
11.6
0.048 (0.005)
15.9
0.062 (0.006)
15.3
0.062 (0.006)
14.0
0.058 (0.006)
15.3
0.061 (0.006)
14.4
0.054 (0.009)
B (326 loci)
PPL
He (±SE)
22.4
0.088 (0.008)
22.1
0.077 (0.008)
22.1
0.068 (0.008)
22.4
0.072 (0.007)
18.1
0.071 (0.008)
18.1
0.068 (0.007)
22.7
0.083 (0.008)
23.0
0.082 (0.008)
21.8
0.070 (0.007)
17.2
0.070 (0.008)
23.6
0.090 (0.008)
22.7
0.090 (0.008)
20.9
0.085 (0.008)
22.7
0.087 (0.008)
21.4
0.079 (0.008)
N, number of analysed samples; PPL, proportion of polymorphic loci; He, expected heterozygosity
2
Table S3. Genetic structure summary for the British Columbian population of Apodemia mormo.
All statistical analyses were conducted using AFLP-SURV (Vekemans et al. 2002)
75
100
A
B
A
B
Ht
0.055
0.075
0.056
0.082
Hw (±SE)
0.053 (0.002)
0.072 (0.002)
0.054 (0.002)
0.079 (0.002)
Hb (±SE)
0.002 (0.0003)
0.003 (0.0003)
0.002 (0.0003)
0.004 (0.0004)
FST (±SE)
0.039 (0.113)*
0.039 (0.112)*
0.042 (0.107)*
0.043 (0.105)*
Ht, total gene diversity; Hw, average gene diversity within populations; Hb, average gene
diversity among populations in excess of that observed within populations; FST, proportion of the
total gene diversity that occurs among as opposed to within populations
*p < 0.00001
3
Table S4. Robustness of the genetic barriers identified by BARRIER v2.2 (Manni et al. 2004)
based on 100 permuted genetic distance matrices (FST). Barriers are listed in order of importance
(A, B, C, etc.), and are considered to possess high bootstrap support when bootstrap values are
greater than 50
Number of
barriers tested
for:
1 barrier
2 barriers
A
B
3 barriers
A
B
C
4 barriers
A
B
C
D
5 barriers
A
B
C
D
E
Scoring criteria
75-A
75-76
75-B
72
100-A
74-75
100-B
70-87
91-92
65
91
62
87-89
71
88-91
70
97-99
96
88
95-96
86
92
94-96
92
81
94-97
90
83
98-100
100
96
71
98-99
96
99
74
98-100
100
98
84
97-100
99
100
87
98-100
100
99
90
45
99-100
98
100
90
45
99-100
100
100
97
45
98-100
100
100
96
39-48
Table S5. Summary of the principal coordinate analysis (PCoA) of all studied sub-populations
performed in GENALEX v.6.0 (Peakall and Smouse 2006), based on a genetic distance matrix
(FST). The amount of variability that is accounted for by the first two coordinates is reported
Scoring
criteria
75
100
% of variation explained
A
B
A
B
Coordinate 1
45.26
45.11
45.78
45.59
Coordinate 2
24.47
24.50
23.95
23.95
4
Table S6. Summary of the mantel tests results examining the relationship between genetic
differentiation (Fst/ (1-Fst) and geographical distance (ln transformed) among all studied subpopulations (analysis performed using GENALEX v.6.0; Peakall and Smouse 2006). Geographic
distance was measured as both straight line distance between sites (Euclidean), and ‘adjusted’
distance between sites (based on constraining movement to valley bottoms)
Geographic
distance measure
Euclidean
Adjusted
Scoring
criteria
75
A
B
A
100
B
75
A
B
A
100
B
r2
P
0.144
0.147
0.179
0.182
0.206
0.209
0.242
0.247
0.005
0.005
0.002
0.002
0.001
0.001
<0.0001
<0.0001
α = 0.05
5