Table 1. Details of the ten microsatellite markers of Chromis margaritifer adults from Rowley Shoals and Scott Reef. Number of individuals genotyped at each site are given in brackets, along with the number of alleles (N and F
A
), the unbiased proportion of expected (H
E
) heterozygotes per locus and site,
IS
calculated for each locus and each site (numbers in bold indicate significant heterozygote
), average unbiased expected deficits). Also given are average number of alleles per locus (mean N
A heterozygosity (mean H private alleles (P
E
), the average (mean F
VA
) at each site.
IS
) for each loci across all sites, and the number of
Site Cm_A119 Cm_B007 Cm_B117 Cm_D006 Cm_A110 Cm_A115 Cm_A011 Cm_B102 Cm_D103 Cm_D114 P
VA
Rowley Shoals
RS1 (52) N
A
H
E
F
IS
RS2 (43) N
A
H
E
F
IS
RS3 (53) N
A
H
E
F
IS
RS4 (37) N
A
H
E
F
IS
RS5 (47) N
A
H
E
F
IS
RS6 (44) N
A
H
E
F
IS
Scott Reef
SL1 (49) N
A
H
E
F
IS
SL3 (41) N
A
H
E
F
IS
SL4 (50) N
A
H
E
F
IS
SS1 (49) N
A
H
E
F
SS2 (37) N
IS
A
H
E
F
IS
SS3 (32) N
A
H
E
F
IS
SS4 (45) N
A
H
E
F
IS
0.86
0.091
12
0.85
-0.079
12
0.83
0.065
13
0.87
0.009
11
0.82
0.126
13
0.86
0.009
11
0.85
0.084
10
0.86
0.021
12
0.84
-0.006
13
0.86
-0.022
13
0.86
-0.016
16
0.87
0.124
11
0.83
0.067
12
0.93
0.245
18
0.93
0.201
22
0.94
0.304
22
0.94
0.203
22
0.94
0.212
25
0.94
0.283
19
0.92
0.330
23
0.95
0.214
21
0.94
0.283
21
0.94
0.370
20
0.94
0.330
23
0.95
0.071
22
0.94
0.309
16
0.96
0.010
29
0.96
0.004
28
0.96
0.007
32
0.97
0.027
25
0.95
-0.026
30
0.96
0.037
28
0.95
0.035
29
0.96
0.152
27
0.96
0.075
31
0.96
0.003
27
0.96
0.014
28
0.96
0.063
30
0.96
0.065
26
0.94
-0.040
27
0.95
0.104
29
0.95
0.071
24
0.94
-0.006
25
0.94
-0.013
26
0.94
0.081
23
0.92
0.004
22
0.95
0.046
25
0.95
-0.008
26
0.94
0.027
22
0.93
0.067
25
0.95
0.096
25
0.95
0.099
24
0.25
0.018
2
0.26
0.171
3
0.21
-0.097
3
0.27
-0.160
4
0.27
0.039
4
0.13
-0.044
5
0.15
-0.075
5
0.36
0.034
2
0.20
-0.111
4
0.21
0.107
4
0.20
-0.086
2
0.17
0.155
5
0.32
0.297
2
0.76
0.292
13
0.80
0.211
14
0.73
0.287
16
0.83
0.398
15
0.76
0.114
16
0.83
0.249
11
0.80
0.157
13
0.76
0.390
17
0.84
0.223
12
0.77
0.394
15
0.80
0.333
15
0.82
0.297
16
0.77
0.257
14
0.84
0.227
10
0.82
0.068
9
0.83
0.015
10
0.82
0.061
11
0.82
0.066
11
0.80
-0.042
10
0.81
-0.073
8
0.78
-0.005
8
0.78
0.021
10
0.82
0.002
8
0.82
0.034
9
0.79
-0.010
9
0.78
0.004
9
0.64
-0.061
6
0.64
-0.061
7
0.64
-0.097
6
0.64
-0.051
7
0.68
-0.067
7
0.67
-0.092
5
0.66
0.096
5
0.64
0.128
6
0.67
0.059
5
0.53
-0.047
7
0.62
0.056
4
0.60
-0.005
7
0.62
-0.016
7
0.94
0.056
25
0.94
0.050
24
0.95
0.064
26
0.94
0.063
27
0.95
0.024
26
0.94
0.121
21
0.96
0.102
22
0.94
0.206
23
0.94
0.147
21
0.94
0.047
23
0.94
-0.035
24
0.94
0.066
23
0.94
0.048
26
0.96
0.098
33
0.95
0.175
35
0.95
0.165
34
0.95
0.176
35
0.96
0.057
36
0.96
0.118
32
0.97
0.194
28
0.96
0.251
29
0.96
0.320
31
0.96
0.147
28
0.94
0.154
36
0.96
0.101
33
0.96
0.131
29
8
3
3
6
2
6
4
3
3
5
4
1
2 mean N
A mean H
E mean F
IS
12
0.85
0.036
21
0.94
0.258
28
0.96
0.036
25
0.94
0.041
3
0.23
0.019
14
0.79
0.277
9
0.81
0.028
6
0.63
-0.012
24
0.94
0.074
32
0.96
0.161

Table 2. Details of the ten microsatellite markers from Chromis margaritifer recruits collected from
Rowley Shoals and Scott Reef. Number of individuals genotyped at each site are given in brackets, along with the number of alleles (N locus and site, and F
A
), the unbiased proportion of expected (H
E
) heterozygotes per
IS
calculated for each locus and each site (numbers in bold indicate significant heterozygote deficits). Also given are average number of alleles per locus (mean N unbiased expected heterozygosity (mean H
E
), the average (mean F
A
), average
IS
) for each loci across all sites.
Site
Rowley Shoals
RS3-R (30)
SL1-R (30)
SL3-R (22)
SS2-R (16)
H
E
F
IS
N
A
H
E
F
IS
N
A
H
E
F
IS
N
A
N
A
H
E
F
IS
Cm_A119
24
0.96
-0.019
25
0.96
0.050
24
0.96
0.080
17
0.96
-0.078
Cm_B007
11
0.87
0.060
13
0.86
0.097
10
0.86
-0.030
9
0.86
0.026
Cm_B117
20
0.95
0.106
17
0.92
0.229
18
0.94
0.209
12
0.93
0.235
Cm_D006
21
0.95
0.109
17
0.93
0.133
13
0.93
0.171
14
0.91
-0.067
Cm_A110
2
0.18
-0.111
3
0.16
-0.075
3
0.25
0.245
3
0.18
-0.079
Cm_A115
14
0.85
0.324
9
0.68
0.381
7
0.70
0.170
7
0.52
0.380
Cm_A011
9
0.84
-0.096
7
0.75
-0.038
8
0.80
0.302
6
0.73
0.028
Cm_B102
5
0.71
0.039
6
0.68
0.151
6
0.67
0.188
7
0.67
-0.153
Cm_D103
18
0.94
0.167
24
0.97
0.035
11
0.92
0.380
18
0.96
0.122
Cm_D114
27
0.95
0.178
31
0.97
0.092
19
0.94
0.209
15
0.92
0.300
mean N
A
23 11 17 16 3 9 8 6 18 23 mean H
E mean F
IS
0.96
0.008
0.86
0.038
0.93
0.195
0.93
0.087
0.19
-0.005
0.69
0.314
0.78
0.049
0.68
0.056
0.95
0.176
0.95
0.195
Table 3. Pairwise F
ST
(below diagonal) F’
ST
(above diagonal) estimates for Chromis margaritifer of adults samples collected from the Rowley Shoals and Scott Reef systems.
RS1 RS2
0.010
RS3
0.003
RS4
0.000
RS5
0.000
RS6
0.000
SL1
0.000
SL3
0.000
SL4
0.000
SS1
0.008
SS2
0.005
SS3
0.000
SS4
0.000
RS1
0.002
-
0.001
0.003
0.014
-
0.000
0.010
0.000
0.009
0.000
0.000
0.022
0.018
0.007
0.002
0.011
0.009
0.016
0.016
0.003
0.006
0.019
0.007
0.000
0.004
RS2
RS3
0.000
0.000
0.002
0.000
0.000
0.000
0.000
0.004
0.017
0.000
0.018
0.000
RS4
0.000
0.000
0.002
0.000
-
0.000
0.000
0.000
0.000
0.000
0.000
0.014
0.000
0.000
0.011
0.015
0.014
0.000
RS5
0.000
0.000
0.000
0.000
0.000
0.000
0.000
RS6
0.000
0.004
0.004
0.000
0.003
0.000
-
0.000
0.001
0.000
0.000
0.000
0.000
0.000
0.000
-
0.000
0.000
0.012
0.009
0.006
0.008
0.004
0.000
0.003
0.000
SL1
SL3
0.000
0.002
0.002
0.001
0.000
0.000
0.000
0.000
-
0.001
0.003
0.003
0.003
0.002
0.000
0.002
0.002
0.000
0.000
-
0.001
0.001
0.001
0.000
0.003
0.000
0.001
0.002
0.002
0.002
0.008
0.012
-
0.000
0.000
0.008
0.000
0.003
0.001
0.003
0.002
0.000
0.001
0.000
0.000
0.000
0.002
-
0.000
0.000
0.001
0.000
0.000
0.000
0.001
0.000
0.000
0.001
0.003
0.000
0.000
0.004
0.013
0.000
-
SL4
SS1
SS2
SS3
SS4
Table 4. Pairwise F’
ST
estimates for Chromis margaritifer of adults and recruits collected from sites at Rowley
Shoals and Scott Reef.
RS1 RS2 RS3 RS4 RS5 RS6 SL1
-
SL3 SL4 SS1 SS2 SS3 SS4
RS1
0.050
RS2
0.042
0.058
RS3
0.044
0.044
0.057
RS4
0.039
0.047
0.053
0.051
RS5
0.037
0.042
0.037
0.051
0.049
0.037
0.040
0.055
0.056
0.054
0.049
0.046
0.055
0.052
0.047
-
0.041
0.042
-
0.044
-
0.038
0.054
0.048
0.053
0.044
0.043
0.038
0.041
-
0.049
0.058
0.055
0.065
0.055
0.047
0.051
0.056
0.040
-
0.047
0.055
0.054
0.051
0.062
0.043
0.050
0.061
0.053
0.058
-
0.059
0.080
0.064
0.084
0.075
0.062
0.057
0.062
0.056
0.056
0.072
-
0.043
0.049
0.049
0.055
0.049
0.044
0.046
0.046
0.040
0.049
0.064
0.059
-
RS6
SL1
SL3
SL4
SS1
SS2
SS3
SS4

First, we explored the propensity of damselfish larvae to self-recruit back to their natal reef within each atoll system by employing a spatial autocorrelation analysis to assess the extent of genetic affinity among geographically proximate fish (conducted in GenAlEx v6.3 Peakall & Smouse 2006). To test statistical significance of r at each distance class, the upper and lower bounds of the 95% confidence interval were defined by 1000 random permutations and if r was located within this confidence belt, the null hypothesis of no spatial genetic structure was accepted. Despite the large number of pairwise comparisons at each distance class (min n = 1227, max n = 14748), and the high power of the permutational test (Double et al. 2005), the autocorrelation coefficient did not fall outside the 95% confidence belt at any distance class at either atoll system, providing evidence that genetic relatedness between individual damselfish was not due to the geographic distance within the atoll systems of Rowley Shoals and Scott Reef (Fig. 1).
Figure 1 Spatial autocorrelation analyses of the genetic correlation coefficient (r) as a function of distance for
Chromis margaritifer at Scott Reef and Rowley Shoals in NWA calculated with GenAlEx v6. Dotted lines indicate the upper and lower bounds of the 95% confidence interval defined by 1000 random permutations.
Scott Reef r
0.008
0.006
0.004
0.002
0
-0.002
-0.004
-0.006
-0.008
0.05
0.25
5 12.5
25
Distance Class (km)
50 75 100 r
0.008
0.006
0.004
0.002
0
-0.002
-0.004
-0.006
-0.008
0.05
Rowley Shoals
0.25
5 12.5
25 50 75 100
Distance Class (km)
Second, we explored utility of a parentage analysis (with the method of Christie et al. 2010), but did not detect any parent/offspring pairs. This was not surprising, since applicability of parentage analysis relies heavily on the fraction of potential parents sampled, and therefore in our study system with large population sizes it is a practical challenge to sample more than a tiny fraction of parents (Saenz-Agudelo et al. 2009).
Third, we used the Bayesian programs STRUCTURE 2.3 (Pritchard et al. 2000) to estimate the true number of populations without providing geographic information on collection location of each fish, and GENECLASS v2
(Piry et al. 2004) to assign recruits to adult sites. As expected from the low levels of subdivision, there was not enough information in the data for STRUCTURE to identify more than one population, nor GENECLASS to confidently (<95% probability) assign recruits to populations (sites) sites of origin regardless of parameter selections.

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Double MC, Peakall R, Beck NR, Cockburn A (2005) Dispersal, philopatry, and infidelity: dissecting local genetic structure in superb fairy-wrens (Malurus cyaneus). Evolution, 59, 625-635.
Peakall R, Smouse PE (2006) GenAlEx 6: Genetic Analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288-295.
Piry S, Alapetite A, Cornuet JM, et al. (2004) GENECLASS 2: A software for Genetic Assignment and
First-Generation Migrant Detection. Journal of Heredity, 95, 536-539.
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
Saenz-Agudelo P, Jones GP, Thorrold SR, Planes S (2009) Estimating connectivity in marine populations: an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios. Molecular Ecology, 18, 1765-1776.