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Electronic Supplementary Material
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Effective number of breeders, effective population size and their relationship with census size in an
iteroparous species, Salvelinus fontinalis
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Daniel E Ruzzante1, Gregory McCracken1, Samantha Parmelee1, Kristen Hill1, Amelia Corrigan2, John
MacMillan2, Sandra J Walde1
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1
: Department of Biology, Dalhousie University, Halifax, NS, B3H4R2
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: Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture
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Table S1: Sample sizes used in the genetic analyses per sampling year and stream, mean (median) and
range in total length (cm). Stem length: Length of the main stem (km) over which there is no barrier to fish
movement. WF: waterfall present (Y) or absent (N) at stream outlet (preventing upstream migration from
the sea, or downstream of sample (for RCU and SBU). Note that 2013 sample sizes do not necessarily
coincide with sample sizes reported on Table 1; only individuals successfully genotyped at least at 7 out of
11 loci are indicated.
Stream #
1 (up)
1 (down)
2
Stream name
and code
Ross Creek
upstream (RCU)
Ross Creek
downstream
(RCD)
Woodworth
(WW)
Blackhole (BH)
3
4
Cobby Irving
(CY)
5
Chipman
(CH)
6
Church Vault
(CV)
7 (up)
Saunders
upstream (SBU)
8
Saunders
downstream
(SBD)
Turner
(TB)
9
Brown
(BN)
10
Robinson
(RB)
11
Healey
(HE)
12
Gaskill
(GK)
7 (down)
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2009
2012
2013
--
N=45
12.4 (12.9) 5.4 - 17.8
N=50
12.9 (13.0)
5.2 - 16.5
N=70
11.6 (13.2)
5.0 - 17.6
--
N=76
10.8 (12.0) 4.5 - 17.5
N=70
9.6 (10.5)
4.0 - 18.5
N=75
13.1 (13.0)
5.0 - 20.0
N=73
12.9 (13.0)
5.0 - 19.5
N=47
11.7 (12.0)
4.0 - 28.0
N=77
11.8 (12.0)
4.2 - 22.5
N=76
12.1 (12.0)
4.2 - 22.5
N=66
11.1 (11.5)
4.4 - 19.1
N=77
12.2 (12.4)
5.0 - 19.0
N=80
13.4 (14.2)
5.5 - 20.7
N=79
10.3 (10.4)
4.9 - 19.6
N=77
11.7 (11.2)
4.2 - 19.4
N=71
12.8 (12.3)
5.1 - 19.4
N=78
11.7 (12.0)
5.4 - 20.0
N=43
11.7 (11.3)
9.1 - 15.0
N=34
15.0 (14.9)
11.0 - 17.9
N=61
12.2 (12.1)
7.8 - 17.5
N=90
12.3 (12.4)
7.2 - 15.9
N=27
14.2 (14.2)
10.8 - 17.4
N=39
13.5 (13.3)
11.1 - 16.3
--
N=44
14.0 (13.8)
11.8 - 17.0
N=34
14.1 (14.2)
10.9 - 16.8
N=37
13.3 (13.7)
9.2 - 16.9
N=26
13.8 (13.9)
9.8 - 16.3
N=16
13.6 (13.5)
11.8 - 15.8
N=14
13.3 (12.7)
10.9-16.8
--
--
N=50
13.4 (13.1)
6.1 - 22.2
--
N=81
13.2 (13.3)
6.1 - 17.6
--
--
--
--
--
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Table S2. Mean length at age and annual mortality rate of brook trout from 14 sites on 12 streams North Mountain, Nova Scotia,
2013. Total sample sizes per site do not coincide with those indicated on Table 1 for 2013 which reports the number of individuals
successfully genotyped at at least 7 out of 11 loci.
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Site
Coordinates
Date
Lat. – Long.
Ross Creek upstream (RCU)
Ross Creek downstream (RCD)
Woodworth Creek (WW)
Black Hole Brook (BH)
Cobby Irving Brook (CY)
Chipman Brook (CH)
Church Vault Brook (CV)
Saunders Brook upstream (SBU)
Saunders Brook downstream (SBD)
Turner Brook (TB)
Brown Brook (BN)
Robinson Brook (RB)
Healy Brook (HE)
Gaskill Brook (GK)
Summary
SD
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30
45 15.1
45 15.2
45 14.5
45 14.0
45 13.2
45 11.1
45 09.6
45 13.9
45 09.3
45 08.6
45 07.5
45 06.1
44 57.9
44 53.9
64 25.5
64 26.0
64 27.5
64 29.5
64 29.5
64 40.0
64 44.1
64 29.7
64 46.5
64 50.1
64 53.3
64 54.9
65 12.7
65 21.2
22-Jul
22-Jul
22-Jul
23-Jul
24-Jul
24-Jul
23-Jul
20-Aug
23-Jul
24-Jul
25-Jul
25-Jul
25-Jul
25-Jul
Young of year
1+ years
2+ years
3+ years
N
FL cm
N
FL cm
N
FL
N
20
32
14
4
17
25
10
22
5
14
21
14
4
15
217
5.2
5.1
6.4
5.8
5.7
6.2
5.6
6.1
5.2
5.9
6.1
5.7
5.9
6.1
5.8
0.4
45
43
48
40
33
33
35
26
37
28
47
42
53
43
553
11.3
11.1
13.0
11.6
11.4
12.0
10.8
10.8
10.7
12.3
10.8
10.9
11.7
11.5
11.4
0.7
19
18
16
23
24
12
28
28
29
34
10
15
15
16
287
14.8
14.7
18.2
14.2
14.6
15.5
13.8
14.2
13.6
16.3
14.4
14.9
15.4
14.9
15.0
1.2
2
1
3
14
7
11
8
5
10
5
3
9
9
7
94
FL
cm
17.5
18.5
19.7
16.6
17.9
19.4
19.9
17.6
17.4
19.4
18.2
17.8
18.2
18.1
18.3
Annual mortality rate
1+ years
0.58
0.58
0.67
0.43
0.27
0.64
0.20
-0.08
0.22
-0.21
0.79
0.64
0.72
0.63
0.43
0.3
2+ year
0.89
0.94
0.81
0.39
0.71
0.08
0.71
0.82
0.66
0.85
0.70
0.40
0.40
0.56
0.64
0.2
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Table S3(a). Proportion of mature brook trout by age class in three streams, North Mountain sampled on
Sep 16, 2014.
Age
YOY
1+
2+
Ross Creek Downstream
(RCD)
N
Mature
0
0
13
0.46
1
1.00
Woodworth
(WW)
N
Mature
8
0
11
0.91
7
1.00
Cobby Irving
(CY)
N
Mature
0
0
20
0.40
4
1.00
Mean
Mature
0
0.59
1.00
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We used the information in Table S3a above to estimate a weighted age at maturity (α) as follows:
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α = 2*0.59 + 3*(1-0.59) = 2.41
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Table S3(b). Proportion of mature brook trout by length and sex in three streams, North Mountain
sampled on Sep 16, 2014.
RCD
N
0
1
4
5
2
2
0
0
0
Fork length cm
8
9
10
11
12
13
14
15
16
WW
N
1
6
2
4
4
1
1
2
0
CY
N
0
1
5
4
5
5
3
4
1
Proportion mature
Male
Female
0
0
0
0
0.00
0.17
0.40
0.63
0.67
0.77
1.00
1.00
1.00
1.00
1.00
1.00
Total
0
0
0.09
0.54
0.73
1.00
1.00
1.00
1.00
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Table S3(c). Proportion of mature brook trout by age class and sex. Data for three North Mountain
streams sampled on Sep 16, 214 pooled.
.
Age
YOY
1+
2+
42
N
8
44
12
Immature
8
20
0
Male
N
0
8
8
Proportion
0.00
0.44
1.00
Female
Total
N Proportion
0
0.00
0
16
0.62
0.55
4
1.00
1.00
5
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44
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Table S4. Generation length estimated on the basis of the proportion of eggs contributed to the next
generation by females of age 1+ (up to 24 months), 2+ (up to 36 months), and 3+ (up to 48 months). N:
Total number of fish of different ages sampled over all streams in 2013.
Summary
Age class
0.0
1+ (2 years old)
2+ (3 years old)
3+ (4 years old)
Total
N
217
553
287
94
FL
5.8
11.4
14.9
18.3
eggs
0
20343
26140
13361
59844
Proportion eggs by
age
mx*lx
x • (lx • mx)
0.34
0.44
0.22
1 • 0.34
2 • 0.44
3 • 0.22
G= Sum[x • (lx • mx)]
1.88
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48
49
50
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We used the fecundity-length relationship described by Halfyard et al (2008) for brook trout in Nova
Scotia streams [i.e. fecundity= 0.003*(10*FL cm)2.2]. Specifically, for each 1 cm length category we
multiplied the proportion of mature female trout in our samples (Table S3) by the Nova Scotia fecundity
relationship to estimate the number of eggs contributed by each year class and site; we then summed by
year class over sites. The assumed sex ratio 1:1 was applied by reducing the total number of eggs by 0.50
and all trout (FL>12cm) were assumed to be mature. We assumed the populations are stable, i.e., Ro = 1.
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Reference
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Halfyard, E.A., J.L. MacMillan and R.J. Madden. 2008. Fecundity and Sexual Maturity in Select Nova
Scotia Trout Populations. Unpublished report. Inland Fisheries Division, Nova Scotia Department of
Fisheries and Aquaculture. Pictou, Nova Scotia.
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6
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60
61
62
63
64
65
66
67
68
69
70
71
72
73
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̂𝑐 , for the length of stream over which there is no barrier
Table S5. Estimates of census population size, 𝑁
to fish movement (i.e., no impassable waterfalls). Four streams (6 locations) were censed twice, first in
̂𝑐 for them. These were Ross Creek upstream
2014 and then again in 2015 and we provide 2 values of 𝑁
and downstream of waterfall (RCU and RCD), Woodworth (WW), Church Vault (CV), and Saunders
Brook upstream and downstream of waterfall (SBU, SBD). In 2014 all streams were censused by
extrapolating to the entire stream length, from a single electrofished section of stream. In 2015 we
electrofished the entire streambed (RCD) or 2 sections (SBU), 3 sections (RCU, WW, SBD), and 4
sections (CV) per stream, with the sections separated by between 500 m and 750 m from each other.
̂𝑒 / 𝑁
̂𝑐 (See Table 2).
When available, we used both estimates to calculate 𝑁
Stream
Local stream
length (m)
̂𝑐 (local
𝑁
stem length)
RCU
3615
3953 - 4680
RCD
WW
BH
CY
CH
CV
SBU
SBD
TB
BN
RB
HE
GK
900
2000
568
3000
6100
5900
3830
1870
2800
1300
6500
2303
2000
1369 - 690
1424 - 1800
854
2235
6139
12166-7500
5066-3850
2780-2000
5296
1417
10833
1878
1299
7
SFO112
SFOD91
SFO129
SFO75
SSA408
SFO88
SSA407
SFO113
SFO100
SFOB52
SFO115
73
90
91
74
87
101
101
86
91
99
95
146
180
182
148
174
202
202
172
182
198
190
0
1
6
3
1
4
5
2
8
0
0
0
0.6
3.3
2
0.6
2
2.5
1.2
4.4
0
0
Rate (%)
Table S6. Repeatability by locus
Repeatability
88
% Error
Scoring repeatability was examined by re-scoring 2 plates per locus. Repeatability ranged between 95.6%
for SFO100 and 100% for three of the 11 loci (Table S6). Average (median) repeatability over loci was
98.5% (98.8%).
Differing Alleles
85
86
87
Number of
Overall, a total of N=1870 individuals were initially examined across all 11 loci. A total of 87 (4.65%) of
these exhibited fewer than 7 working loci and were therefore removed from the data set, thus leaving
N=1783 individuals for further analysis. Of these, 916 (51.37%), 431 (24.17%), 251 (14.08%) and 120
(6.73%) were successfully genotyped at all 11, 10, 9 and 8 loci, respectively, indicating that 96.35% of
the individuals with at least 7 loci, were successfully genotyped at a minimum of 8 loci. The remaining 65
individuals (3.65%) were successfully genotyped at 7 loci.
Alleles Counted
79
80
81
82
83
84
Number of
Polymorphism was examined at 11 PCR amplified microsatellite loci. These were: SfoC129, SfoC113,
SfoB52, SfoC88, SfoD75, SfoD91, SfoD100, SfoC115 (T. L. King, US Geological Survey, unpublished
data), Sfo112Lav (Perry et al., 2005), Ssa407UOS and Ssa408UOS (Cairney et al., 2000).
Working Individuals
76
77
78
Number Of
Microsatellite markers:
Marker
75
100
99.4
96.7
98
99.4
98
97.5
98.8
95.6
100
100
89
References
90
91
92
Cairney M, Taggart JB, Høyheim B. 2000 Characterization of microsatellite and minisatellite loci in
Atlantic salmon (Salmo salar L.) and cross-species amplification in other salmonids. Molecular Ecology
9, 2175–2178
93
94
95
Perry GML, King TL, St.-Cyr J, Valcourt M, Bernatchez L. 2005 Isolation and cross-familial
amplification of 41 microsatellites for the brook charr (Salvelinus fontinalis). Molecular Ecology Notes
5, 346–351
8
96
97
98
Table S7: Genetic diversity for brook trout populations based on 11 loci: Null Alleles, loci out of Hardy-Weinberg Equilibrium
(HWE) as assessed after Bonferroni correction within samples, loci in linkage disequilibrium (LD), average expected and observed
heterozygosities (He, Ho), number of private alleles, allelic richness (A).
Stream
Null alleles
2009/2010
2012
2013
RCU
RCD
100
NONE
115
112
NONE
WW
91/75
115
100, 112,
115, B52
BH
115
CY
CH
112, 113
407
CV
75,100, 407,88
NONE
100
113
TB
B52, 408
Ho
He
# private
alleles
Allelic
richness
2012
2013
100,408
115
115
112
NONE
91 - 407
100 - 112
0.498
0.539
0.534
0.568
4
1
5.20
5.62
112(mono),
115
112, 115
113-407, 88-91
0.546
0.609
2
5.54
100,115
NONE
52-112
0.401
0.410
1
3.4
115
129
100, 112
NONE
NONE
115
113-129, 113-408
0.447
0.503
0.485
0.550
1
4
4.34
4.76
91
75, 88, 115
NONE
-
0.485
0.516
4
4.43
468
91-88
0.360
0.366
2
3.37
113
-
0.496
0.557
4
4.83
NONE
88
75
SBD
Loci in LD
2009/2010
NONE
SBU
99
Loci out of HWE
75
100
115,407
115
100, 115
115
100, 115
-
0.388
0.402
1
4.2
BN
113, 408
115
NONE
75, 115
0.474
0.546
0
4.61
RB
NONE
112
NONE
129
88-B52, 115-B52,
88-115, 112-B52,
88-112
-
0.493
0.505
0
4.72
HE
91
B52,100,
408
91
B52, 88, 407,
408
100-115
0.513
0.612
3
5.91
GK
115
91,115,407
115
112, 115, 407
-
0.577
0.628
4
6.60
9
101
Table S8(a). FIS values per locus and population; all years pooled.
102
103
104
RCU
RCD
WW
BH
CI
CH
CV
SBU
SBD
TB
BN
RB
HE
GK
SFO100
SfoB52
Sfo112
Sfo115
Sfo88
Sfo407
Sfo408
Sfo129
Sfo113
Sfo75
Sfo91
0.008
0.064
0.194
0.231
0.069
0.087
0.041
0.045
0.062
0.09
0.051
0.233
0.126
-0.009
0.316
-0.066
0.031
0.023
-0.09
0.078
0.051
-0.004
0.205
0.126
0.431
0.231
0.069
0.041
-0.015
-0.035
0.057
0.061
0.145
0.005
0.049
-0.017
0.272
0.021
-0.016
0.069
-0.004
-0.15
-0.015
-0.117
0.007
0.07
0.375
0.211
-0.01
0.143
0.017
-0.009
0.158
0.014
0.064
-0.003
0.062
-0.047
0.302
0.098
0.086
0.038
0.184
0.04
-0.095
0.2
0.188
0.125
0.155
0.096
0.154
0.091
0.01
-0.08
-0.068
0.018
0.035
0.012
0.112
-0.026
-0.014
0.139
-0.079
-0.177
-0.263
0.093
0.213
0.02
-0.012
0.137
0.045
0.121
0.077
0.023
0.085
-0.046
0.265
0.143
0.071
0.192
0.162
0.118
0.444
-0.121
-0.071
0.079
-0.072
-0.068
0.042
-0.022
0.062
0.758
0.028
0.277
0.344
-0.076
0.113
-0.218
0.093
0.006
-0.092
0.173
0.077
0.286
0.063
0.273
0.079
-0.035
-0.423
0.015
0.024
0.008
0.185
0.396
0.069
0.245
0.254
0.107
0.138
-0.036
-0.014
0.124
0.294
0.119
0.072
-0.122
0.342
0.096
0.128
-0.064
-0.023
-0.027
0.067
0.113
All
0.067
0.055
0.104
0.022
0.078
0.086
0.061
0.018
0.077
0.059
0.132
0.023
0.162
0.082
10
105
106
107
Table S8(b). Fis values per locus and population. Data for samples from 2009 and 2010.
Fis Per population :
SFO100
SfoB52
Sfo112
Sfo115
Sfo88
Sfo407
Sfo408
Sfo129
Sfo113
Sfo75
Sfo91
RCD
0.483
-0.029
-0.247
0.383
-0.19
0.141
-0.007
-0.07
0.146
-0.063
-0.12
WW
0.14
0.208
0.256
0.1
-0.052
0.037
0.099
-0.106
0.221
0.265
0.27
BH
0.076
-0.165
-0.034
0.377
0.058
-0.034
0.173
-0.081
-0.008
-0.022
-0.143
CI
0.053
0.045
0.365
0.095
0.028
0.128
0.12
-0.04
0.188
-0.007
0.06
CH
-0.039
-0.233
-0.191
0.051
0.26
0.203
0.092
-0.064
-0.19
0.013
0.344
CV
0.319
0.076
-0.104
-0.372
0.577
0.314
-0.006
-0.107
-0.272
0.259
-0.041
SBD
0.011
0.208
0.303
0.084
0.034
0.019
-0.128
-0.053
0.358
0.106
-0.021
TB
0.039
0.091
-0.091
0.452
0.028
-0.028
0.021
-0.16
-0.075
0.172
-0.009
BN
-0.059
-0.014
-0.003
-0.135
0.085
-0.114
0.253
-0.2
0.26
0.075
0.011
RB
NA
0.067
0.099
-0.091
0.371
0.014
-0.125
-0.589
0.075
-0.165
-0.073
HE
-0.154
0.272
0.344
0.286
0.104
0.122
0.061
-0.064
0.005
0.074
0.71
GK
0.103
0.139
-0.02
0.445
0.254
-0.075
-0.04
0.007
-0.263
-0.167
0.012
All
-0.01
0.135
0.055
0.083
0.049
0.045
0.07
0.041
0.04
-0.037
0.157
0.052
11
108
109
110
Table S8(c). Fis values per locus and population. Data for samples from 2012.
Fis Per population :
SFO100
SfoB52
Sfo112
Sfo115
Sfo88
Sfo407
Sfo408
Sfo129
Sfo113
Sfo75
Sfo91
RCU
-0.076
-0.175
-0.083
0.343
-0.01
0.014
0.019
-0.02
0.079
0.105
0.081
RCD
-0.009
-0.019
-0.065
0.42
0.023
-0.016
-0.04
-0.145
0.033
0.137
0.119
WW
0.104
-0.234
NA
0.177
0.134
0.098
-0.05
-0.206
-0.102
-0.041
0.116
CV
0.129
0.13
0.059
0.216
0.187
-0.11
-0.132
-0.289
-0.054
-0.125
-0.186
SBD
-0.075
0.175
-0.182
0.11
0.054
0.14
0.236
-0.14
-0.057
0.055
0.062
All
0.024
0.034
0.011
-0.015
0.052
12
111
Table S8(d). Fis values per locus and population. Data for samples from 2013.
112
113
Fis Per
population :
SFO100
SfoB52
Sfo112
Sfo115
Sfo88
Sfo407
Sfo408
Sfo129
Sfo113
Sfo75
Sfo91
RCU
RCD
WW
BH
CI
CH
CV
SBU
SBD
TB
BN
RB
HE
GK
0.034
0.165
0.488
-0.024
0.116
0.069
0.056
0.082
0.012
0.077
0.023
0.097
0.006
0.156
0.181
-0.089
-0.017
0.036
-0.065
0.012
0.07
-0.017
0.238
0.286
0.535
0.282
0.061
-0.034
-0.038
0.144
0.012
0.05
0.07
-0.078
0.16
NA
0.143
-0.036
0.004
-0.019
0.058
-0.277
-0.007
-0.095
-0.088
0.133
0.378
0.35
-0.095
0.127
-0.229
0.055
0.098
0.035
0.036
0.009
0.174
-0.001
-0.038
0.008
0.041
0.019
0.278
0.174
-0.154
0.154
0.161
0.132
0.247
0.118
-0.094
0.028
0.103
0.059
0.051
-0.026
0.188
0.012
0.112
-0.026
-0.014
0.139
-0.079
-0.177
-0.263
0.093
0.213
0.02
0.025
0.068
0.032
0.138
0.086
-0.111
0.04
0.042
0.234
0.229
0.132
0.274
0.152
0.382
0.427
-0.181
-0.092
0.083
-0.038
-0.095
-0.032
-0.023
0.133
0.127
-0.012
0.328
0.068
-0.066
0.051
-0.22
-0.004
-0.023
-0.154
0.126
0.088
0.393
0.116
0.053
0.107
-0.008
-0.366
-0.039
0.086
0.031
0.227
0.398
-0.018
0.159
0.159
0.093
0.158
-0.144
-0.061
0.123
0
0.123
0.052
-0.156
0.28
0.066
0.142
-0.067
-0.028
0.032
0.102
0.13
All
0.072
0.022
0.107
-0.02
0.045
0.048
0.089
0.018
0.086
0.055
0.007
0.031
0.113
0.078
13
114
Table S9. Pairwise FST values, estimated with all sampled individuals.
115
RCU
RCD
WW
BH
CY
CH
Ross Creek Up (RCU)
Ross Creek Down (RCD)
Woodworth (WW)
Black Hole (BH)
Cobby Irving (CY)
Chipman (CH)
0.000
0.008
0.063
0.160
0.089
0.133
0.000
0.047
0.162
0.078
0.129
0.000
0.127
0.077
0.089
0.000
0.160
0.119
0.000
0.133
0.000
Church Vault (CV)
Saunders Brook Up (SBU)
Saunders Brook Down (SBD)
Turner Brook (TB)
Brown (BN)
Robinson (RB)
0.129
0.166
0.134
0.175
0.121
0.095
0.115
0.166
0.123
0.173
0.116
0.095
0.081
0.170
0.098
0.128
0.077
0.092
0.175
0.194
0.152
0.100
0.100
0.157
0.143
0.172
0.159
0.177
0.139
0.153
Healey (HE)
Gaskill (GK)
0.132
0.094
0.116
0.094
0.095
0.074
0.194
0.096
0.171
0.127
116
117
CV
SBU
SBD
TB
BN
RB
0.109
0.151
0.087
0.087
0.084
0.122
0.000
0.093
0.037
0.152
0.085
0.145
0.000
0.061
0.192
0.157
0.182
0.000
0.112
0.074
0.130
0.000
0.071
0.145
0.000
0.082
0.000
0.145
0.053
0.150
0.091
0.214
0.117
0.135
0.062
0.179
0.081
0.123
0.050
0.097
0.062
HE
GK
0.000
0.097
0.000
14
118
119
120
121
122
123
124
125
̂𝑒(𝐿𝐷) ) and on drift
Table S10: Effective population size estimates (95% confidence intervals) based on linkage disequilibrium (𝑁
̂𝑒(𝑀𝐿𝑁𝑒) ) for samples (mixed ages) obtained in years 2009-2010 (12 streams), 2012 (4 streams), and 2013
using temporal samples (𝑁
(12 streams). SS: Sample size. Harmonic mean (across loci) sample size. Pcrit: Critical P-value used in LDNe. Mean
̂𝑒(𝑚𝑖𝑥𝑒𝑑 𝑎𝑔𝑒𝑠) ): weighted harmonic mean 𝑁
̂𝑒 (and CI) among estimates. NA: Sample not available. Generations: number of
(𝑁
generations assumed to have passed between samples from to and t1 in temporal method. to: samples collected in 2013; t1: samples
collected in 2009-2010, except for RCU which was collected in 2012. Average 𝑁̂𝑒 across methods: Arithmetic Average 𝑁̂𝑒 across methods,
̂𝑒(𝑀𝐿𝑁𝑒).
̂ 𝒆(𝒎𝒊𝒙𝒆𝒅 𝒂𝒈𝒆𝒔) ) and 𝑁
i.e., between Mean (𝑵
89.35
0.006
CH
27
26.53
0.019
CV
39
35.53
0.013
SBU
NA
SBD
44
43.91
0.011
TB
34
33.81
0.015
BN
37
36.36
0.014
RB
26
25.54
0.020
HE
16
15.81
0.032
GK
14
13.53
0.037
126
50
46.43
0.011
70
61.5
0.008
70
63.56
0.008
75
70.3
0.007
NA
73
67.7
0.007
NA
47
43.3
0.012
NA
77
68.9
0.007
76
66.5
0.008
66
55.6
0.009
77
67.3
0.007
NA
80
73.6
0.007
NA
79
70.1
0.007
NA
77
67.1
0.007
NA
71
63.2
0.008
NA
78
73.4
0.007
51
44.15
0.011
99
(30-∞)
NA
∞
(117-∞)
∞
(93-∞)
∞
(122-∞)
∞
(56-∞)
75
(19-∞)
72
(25-∞)
81
72.53
0.007
140
(58-∞)
80
(30-∞)
6724
(161-∞)
181
(69-∞)
364
(35-∞)
∞
(59-∞)
331
(91-∞)
151
(47-∞)
595
(32-∞)
107
(53-543)
∞
(116-∞)
∞
(205-∞)
∞
(207-∞)
45
(30-75)
111
(60-352)
127.3
(41 - ∞)
235.0
(72 - ∞)
124.6
(58 - ∞)
151.3
(36 - ∞)
135.4
(55 - ∞)
446.5
(80 - ∞)
141.6
(40 - ∞)
595
(32-∞)
155.5
(63 - ∞)
(108 - ∞)
(168 - ∞)
(123 - ∞)
48.6
(27 - ∞)
102.5
(49 - ∞)
1
2
2
2
2
2
2
2
2
2
2
2
2
40.8
(28 – 68)
32.8
(25 – 44)
27.2
(21 – 36)
114.0
(62 – 341)
50.1
(35 – 79)
24.4
(18 – 34)
46.4
(33 – 70)
72.4
(47 – 133)
47.4
(31 – 81)
15.0
(12 – 17)
37.3
(25 – 63)
18.8
(15 – 25)
57.4
(36 – 111)
̂𝑒
Average 𝑁
across methods
90
0.007
̂𝑒(𝑀𝐿𝑁𝑒)
𝑁
(95% CI)
CY
68.3
Generations
0.008
76
̂ 𝒆(𝒎𝒊𝒙𝒆𝒅 𝒂𝒈𝒆𝒔) )
(𝑵
60.91
∞
(103-∞)
84
(43-353)
223
(80-∞)
Mean
61
0.012
̂ 𝒆(𝑳𝑫)
𝑵
(95% CI)
BH
Pcrit
0.015
Harmonic mean
SS 2013
33.34
SS 2013
34
(95% CI)
WW
737
(65-∞)
48
(30-96)
89
(37-4300)
89
(53-194)
∞
(59-∞)
254
(45-∞)
40.42
̂ 𝒆(𝑳𝑫)
𝑵
0.012
Pcrit
42.17
Harmonic mean
SS 2012
43
45
SS 2012
RCD
(95% CI)
NA
̂ 𝒆(𝑳𝑫)
𝑵
SS 2009-2010
RCU
Pcrit
Stream
Harmonic mean
SS 2009-2010
15
85
(34 - ∞)
138
(48 - ∞)
76
(39 - ∞)
133
(49 -∞)
93
(45 - ∞)
235
(49 - ∞)
94
(36 - ∞)
595
(32 - ∞)
114
(55 - ∞)
47.4
(31 – 81)
15.0
(12 – 17)
37.3
(25 – 63)
33.7
(21 - ∞)
80
(42 - ∞)
16
127
128
129
130
̂ 𝒃(𝑳𝑫) ) obtained with
Table S11: Estimates (95% CI) of the effective number of breeders (𝑵
̂𝑏(𝑎𝑑𝑗2) and 𝑁
̂𝑒(𝑎𝑑𝑗2) are given for
individuals of age cohort 1+ (2013 collections). Estimates of 𝑁
AL=1.59 and α=2.41. SS: Sample size. Harmonic mean SS: harmonic mean sample size over
successfully scored loci.
131
RCU
27
23.83
75.5
(22 - ∞)
RCD
27
23.69
WW
45
41.57
BH
34
30.95
CY
24
21.81
(26 - ∞)
258.1
(21 - ∞)
CH
26
22.51
∞
CV
33
27.99
SBU
12
9.74
SBD
54
47.05
TB
20
17.96
BN
45
39.86
∞
(63 - ∞)
145
(44 - ∞)
∞
(36 – ∞)
39.3
(30 - ∞)
∞
(19 - ∞)
∞
(142 - ∞)
29.4
(9 – ∞)
∞
(78 -∞)
RB
34
29
HE
44
38.02
GK
37
34.48
∞
(-2035 - ∞)
35.5
(20 - 85)
49.9
(30 – 115)
65.8
(19 - ∞)
(55 - ∞)
126.4
(38 - ∞)
(23 - ∞)
225.0
(18 - ∞)
(31 - ∞)
34.3
(26 - ∞)
(17 - ∞)
(124 - ∞)
25.6
(8 - ∞)
(68 - ∞)
30.9
(17 - 244)
43.5
(26 – 330)
̂𝑒(𝑎𝑑𝑗2)
𝑁
̂𝑏(𝑎𝑑𝑗2)
𝑁
̂ 𝒃(𝑳𝑫)
𝑵
(95% CI)
Harmonic mean
SS
SS
133
134
Stream
132
189.1
(55 - ∞)
(158 - ∞)
363.1
(109 - ∞)
(66 - ∞)
646.3
(52 - ∞)
(89 - ∞)
98.4
(75 - ∞)
(48 - ∞)
356 - ∞)
73.6
(23 - ∞)
(195 - ∞)
88.9
(49 – 701)
124.9
(75 – 949)
17
135
136
137
138
139
140
141
Fig. S1. Hierarchical population STRUCTURE analyses based on 11 loci for brook trout populations collected from 12 streams (14
sites) from the North Mountain, NS in 2009, 2012 and 2013. The first analysis revealed two clusters (K=2). Analyses of each cluster
separately uncovered further levels of hierarchical structure with all populations including Saunders Brook Upstream and downstream
of a waterfall (SBU and SBD) eventually differing from each other with one exception: RCU and RCD were indistinguishable.