Supplementary Materials 1. Summary of the hierarchical STRUCTURE analysis including
the number of genetic clusters tested (K), likelihood means, and standard deviations
based on five different runs (reps) and deltaK, an estimator of the best K. Because the
deltaK method is not appropriate when the true K is 1, we verified whether the mean
lnP(k) was maximum for K = 1 in a first step to estimate K. Shade rows indicate best K for
the run.
K
Reps
All 11 localities
1
5
2
5
Mean lnP(K)
-7148.84
-5953.24
Stdev lnP(K)
0.27
0.50
3
5
-5662.78
14.83
4
5
-5405.08
42.80
5
5
-5180.26
41.28
6
5
-5116.24
2.23
7
5
-4990.92
1.28
8
5
-5046.00
71.77
9
5
-5124.90
52.59
10
5
-5148.86
74.24
11
5
-5189.02
65.55
12
5
-5260.52
42.31
Eastern localities (Abatescu, Rizzanese, Var, Fangu, and Golu)
1
5
-3170.14
0.21
2
5
-2895.78
2.04
3
5
-2685.84
0.40
4
5
-2647.68
8.89
5
5
-2705.38
15.11
6
5
-2807.86
23.29
Other eastern localities (Abatescu, Rizzanese, and Var)
1
5
-1905.98
0.64
2
5
-2073.30
300.52
3
5
-1971.40
11.94
deltaK
NA
1817.57
West and east
2.21
0.77
3.90
27.49
140.78
0.33
1.04
0.22
0.48
NA
NA
31.60
425.48
Fangu, Golu, and
other
10.78
2.96
NA
NA
0.90
13.27
(no regional
gradient was
observed in the
bar plot)
4
5
-2027.94
54.96
NA
Western localities (Boughzazene, Sègre, Fluvià, Tech, Annecy, and Bourget)
1
5
-2822.96
0.49
NA
2
5
-2454.20
0.20
1208.20
Rhône and other
3
5
-2327.08
0.40
248.09
4
5
-2298.26
0.56
140.28
5
5
-2347.92
73.45
1.25
6
5
-2305.50
9.36
10.80
7
5
-2364.18
13.60
NA
Rhône (Annecy and Bourget)
1
5
-735.94
0.34
NA
2
5
-743.52
4.75
1.03
3
5
-756.00
12.58
NA
Other western localities (Boughzazene, Sègre, Fluvià, and Tech)
1
5
-1696.54
0.40
NA
2
5
-1571.54
0.23
603.00
Boughzazene and
Pyrenees
3
5
-1585.36
25.07
1.45
4
5
-1562.72
3.85
29.12
5
5
-1652.26
8.02
NA
Pyrenees (Sègre, Fluvià, and Tech)
1
5
-1003.16
0.73
NA
2
5
-1035.44
13.60
1.33
3
5
-1085.78
24.90
2.99
4
5
-1061.66
60.03
NA
Supplementary Materials 2. Summary of the hierarchical FLOCK analysis including the
number of clusters tested (K), the plateau lengths found, the estimate of the best
number of clusters, and the decision flow resulting in this estimate (for more details on
the decision flow, see Duchesne and Turgeon 2012).
ALL 11 localities
K
Plateau lengths
2
3
4
5
6
7
8
9
10
11
50
3, 2, 2, 2, 2, 20, 2, 2, 2
2, 10, 2, 23, 3, 2
11, 13, 5, 8
3, 4, 13, 3, 5, 4, 3
12, 10, 2, 4
2
0
0
0
Estimate
STOP, K =2
(eastern vs. western localities)
EAST (Golu, Fangu, Rizzanese, Abatescu, and Var)
K
Plateau lengths
2
18, 29, 2
3
3, 3, 26, 5, 6, 2
4
5
44
2
Decision flow
1A, 2A
Estimate
Decision flow
STOP, K =4
(Golu, Fangu, Rizzanese, and Ligurian)
1A, 2A
LIGURIAN (Abatescu and Var)
K
Plateau lengths
Estimate
2
2, 2, 2
No estimate
3
0
4
0
5
0
6
0
STOP
WEST (Boughzazene, Annecy, Bourget, Tech, Fluvià, and Sègre)
K
Plateau lengths
Estimate
2
28, 22
STOP, K =3
3
49
(Boughzazene, Rhône, and Pyrenees)
4
3, 10, 2, 2, 2
Decision flow
2B
1B
Decision flow
1A, 2A
5
6
3
0
RHÔNE (Annecy, Bourget)
K
Plateau lengths
2
20, 3, 2, 2
3
2, 3
4
0
5
0
6
0
PYRENEES (Tech, Fluvià, and Sègre)
K
Plateau lengths
2
5, ,5, 2, 3, 4, 2
3
0
4
0
5
0
6
0
Estimate
K=2
(Annecy, Bourget)
Decision flow
STOP
1B
Estimate
No estimate
Decision flow
2B
STOP
2B