APPENDIX
Hierarchical structure and diversity in a dendritic
lake trout (Salvelinus namaycush) system in
Northern Labrador
Gregory R. McCracken1, Robert Perry2, Donald Keefe2 and Daniel E. Ruzzante 1
1
Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, B3H
4R2, Canada; Gregory.mccracken@dal.ca
2
Newfoundland and Labrador Department of Environment and Conservation, 117 Brakes
Cove, Corner Brook, NL, A2H 7S1, Canada.
Table S1. Multiplex primer panel composition used for analysis of lake trout in the
Kogaluk River watershed in Newfoundland and Labrador, indicating loci dye label,
assigned panel number, and source authors. TA = primer annealing temperature.
Locus
SSA85
SCO215
SCO202
OGO1A
SNAMSU06
SNAMSU12
SFO334
OTSG253b
Primer
Panel
1
1
1
2
2
2
3
3
TA
Used
60
60
60
60
60
60
57
57
Label
Source
800
700
800
700
800
800
700
700
O'Reilly et al. 1996
Dehaan et al. 2005
Dehaan et al. 2005
Olsen et al. 1998
Rollins et al. 2009
Rollins et al. 2009
Perry et al. 2005
Williamson et al. 2002
Rollins et al. 2009
Sewall Young, personal
communication
4
57
700
Sewall Young, personal
SCO107
communication
*
52
700
Williamson et al. 2002
OTSG83b
*
62
700
Rexroad et al. 2002
OMM1105
*These primers were run individually, and not assigned to a multiplex panel as they
worked better by themselves.
SNAMSU02
SCO102
4
4
57
57
800
800
Table S2. Multiplex and single primer PCR reactions as well as reagent suppliers, used
for genetic analysis of lake trout in the Kogaluk River watershed in Newfoundland and
Labrador.
Multiplex PCR Reactions
2.5µL Qiagen Master Mix*
0.5µL Qiagen Q-solution
0.5µL RNAse free water
0.1-0.2µM fluorescently labeled forward
primer
0.1-0.2µM unlabelled reverse primer
50ng of DNA
Single Primer Reactions
2.35µL RNAse free water
0.5µL 10X reaction buffer **
0.5µL MgSO4 (20mM)
0.1µM fluorescently labeled forward primer
0.1µM unlabelled reverse primer
0.25U TSG Polymerase **
200µM dNTPs**
50ng of DNA
5µL Total volume
5µL Total volume
*(Qiagen Inc., United States); **(Bio Basic Inc., Markham, Ontario)
Table S3. Multiplex and single primer thermocycle conditions for PCR reactions used for
the genetic analysis of lake trout in the Kogaluk River watershed in Newfoundland and
Labrador.
Multiplex Thermocycle
Single Primer Thermocycle
95°C - 15 minutes
95°C - 3 minutes
94°C - 30 seconds
94°C - 30 seconds
X 35
Cycles Annealing - 1 minute*
Annealing - 1 minute*
72°C - 1 minute
72°C - 1 minute
60°C -30 minutes
72°C - 5 minutes
*Primer specific annealing temperatures
Table S4. Average slope measurements for all pairs of lakes sampled for lake trout (between 2006 and 2011) in the Kogaluk River
watershed in Newfoundland and Labrador.
Lake 1
Genetics H
Slushy
Esker
Strange
WP152
T-Bone
Cabot
Genetics B
Hawk
Lake 1
Genetics H
Slushy
Esker
Strange
Wp152
T-Bone
Cabot
Genetics B
Hawk
0.000
-0.858
-0.807
-1.852
-0.513
-0.934
-0.355
-3.314
-1.453
-0.283
0.858
0.000
-0.664
-1.706
-0.353
-0.814
-0.280
-3.298
-1.410
-0.225
0.807
0.664
0.000
-0.853
0.654
-0.258
0.027
-3.150
-1.218
0.010
1.852
1.706
0.853
0.000
1.507
0.402
0.337
-4.142
-1.314
0.222
0.513
0.353
-0.654
-1.507
0.000
-0.583
-0.129
-3.370
-1.353
-0.108
0.934
0.814
0.258
-0.402
0.583
0.000
0.209
-4.290
-1.408
0.133
0.355
0.280
0.027
0.337
-0.129
0.209
0.000
-4.066
-1.674
-0.014
3.314
3.298
3.150
-4.142
3.370
4.290
4.066
0.000
2.722
5.270
1.453
1.410
1.218
-1.314
1.353
1.408
1.674
-2.722
0.000
5.106
0.283
0.225
-0.010
-0.222
0.108
-0.133
0.014
-5.270
-5.106
0.000
Figure S1.
Delta K likelihood plots with regard to the STRUCTURE results in Figure 2 for lake trout sampled in the Kogaluk
River watershed in Newfoundland and Labrador, between 2006 and 2011. A) All 10 initial populations suggesting the most likely K
value at this initial hierarchical level is 2. B) The 6 populations north of the fjord suggesting little difference between K=2 and K=4.
We chose to use the smallest value, K=2, as it is more geographically intuitive (see Figure 2). C) The 4 populations south and west of
the fjord suggesting the most likely K value at initial hierarchical level is 4. D) Lakes Slushy, Strange, Esker, and WP152 whereby
K=2 and K=3 exhibited very similar delta K values suggesting only borderline genetic differences among at least some of the lake
trout populations. K=3 was chosen as it is more geographically intuitive than K=2.
Figure S2.
The relationship between elevation (meters above sea level) and mean estimates of effective population size of lake
trout for each of the 9 unique clusters identified with STRUCTURE found within the Kogaluk River watershed in Newfoundland and
Labrador. The correlation is non-significant (r2 = 0.0002, p > 0.97) suggesting that estimates of effective population size so are
independent of elevation, indicating that dispersal is unlikely to be directional in this system.
Figure S3.
The relationship between genetic cluster total lake area and mean estimates of effective population size of lake trout for
each of the 9 unique clusters identified with STRUCTURE found within the Kogaluk River watershed in Newfoundland and
Labrador. The correlation is significantly positive (r2 = 0.636, p < 0.02) suggesting that larger lakes contain larger effective population
sizes.
Figure S4.
The relationship between genetic cluster total lake area and mean estimates of effective population size of lake trout for
8 unique clusters, excluding the cluster containing lakes Esker and WP152, identified with STRUCTURE found within the Kogaluk
River watershed in Newfoundland and Labrador. The correlation is slightly positive; however, non-significant (r2 = 0.106, p > 0.4)
suggesting a non-significant relationship between habitat size and mean estimates of effective size once lakes Esker and WP152 (a
single cluster) are removed.