Supplement 1: Cryptic genetic diversity and spatial patterns of admixture within Belizean marine reserves
C. C. D’Aloia, S. M. Bogdanowicz, R. G. Harrison, P. M. Buston
Tables
Table S1. Number of individuals collected and sequenced per site. The number of individuals collected per site reflectsthe number of individuals we could find in a standard dive. The number of individuals sequenced indicates the number of individuals with sequences retained after all quality filtering.
Site / # individuals collected / # individuals sequencedB1 / 15 / 15
B2 / 34 / 30
B3 / 32 / 31
B5 / 35 / 31
B6 / 35 / 31
B7 / 20 / 19
B8 / 35 / 31
B9 / 35 / 32
B10 / 21 / 21
B11 / 35 / 33
B12 / 35 / 30
B13 / 35 / 32
B14 / 31 / 31
B15 / 31 / 30
B16 / 34 / 29
B17 / 36 / 31
B18 / 31 / 31
B19 / 27 / 27
B20 / 33 / 31
B22 / 22 / 17
B23 / 24 / 24
B24 / 23 / 16
B25 / 31 / 21
T1 / 35 / 30
T2 / 35 / 32
T3 / 34 / 32
T4 / 35 / 30
T5 / 35 / 32
T6 / 35 / 32
G1 / 32 / 32
G2 / 32 / 30
G3 / 32 / 32
G4 / 33 / 32
G5 / 35 / 32
G6 / 31 / 30
L1 / 34 / 32
L4 / 35 / 32
L5 / 35 / 32
L6 / 31 / 30
Mean / 31.51 / 28.87
s.d. / 5.10 / 4.91
Table S2.List of primers forn=60 loci that successfully amplified across individuals in the multiplex PCR.
Locus Type / Locus ID / Forward Primer / Reverse PrimerAnonymous / G26 / ACAATGTGGACCGAGAGCTT / AAAGCTTTTAATCACGCTTAAATTAG
Anonymous / G32 / ACCTCCAGCAACAGGTAAACAG / TTGAAGCTTTATAACTGCAACATT
Anonymous / G43 / GCTGCTGTTGAAGAGCTTACC / CAGCAACAATTGGTCTTGTGTT
Anonymous / G52 / AGAACAACCAATCAGGGGAAAC / CCACAGACGGTGGAAACTTTTA
Anonymous / G53 / TCTCACAAAGAAAGGTCCCATTA / GATGAACATGTGCGAGTCGTAA
Anonymous / G55 / CCTAGCCTGCAGCTTGTAAAGT / TCCGGACTATAGATAGGTTTCCA
Anonymous / G56 / TAAATGCAGCAGTTCAGACGAT / GACTCTCTGCTCGTGAAGCTG
Anonymous / G59 / TCACACAATAAAACACTATAACATGC / TCCGAAAATGCAGTTTGCTT
Anonymous / G70 / AAATGCGATTGGAAAATTCTGT / TGTGCTGTTGTCAATTGTTGAT
Anonymous / G77 / ATTACAAACAGCTGAGGGCTGA / GGTGAACTTTAGTGATAAACTTTGTG
Anonymous / G83 / CAGAACTGGCATCTCTTGCTT / GTCTGCTCCGTCATGTTGAAT
Anonymous / G87 / CATACTGCCCAACAAAACAAAT / AGGACAGAGCTGGACCTCCT
Anonymous / G90 / TGGATATTCTTACGGGAATTTAGC / ATATTGTGACCGTCAGCGAAG
Anonymous / G92 / GCGCTGTAGACCTCCACATTAT / GGAATGTATTTCGATTCCATTTG
Anonymous / G93 / TCACGTCTCGTTACATCAAACA / AAAGCTCCCTCTAGTGGACAAA
Anonymous / G95 / GACGTCCAAGTCAAAGATGATTC / TTAAGAAACTGAAGAGGATTCTCCAT
Anonymous / G100 / AGTGTGTCCTTTCGAGTTTTGG / TCACAAACTATTGTTCGGGAAA
Anonymous / G107 / CCAGAATAATGATCTAAGTCTTCTCA / TGTGATGGTATTTCTTTACAGTTTGG
Anonymous / G112 / GAGGTCTTGCCTCTTCTTGG / CCATGGGTCTTAAAACAGGATAA
Anonymous / G113 / GGAAAGAAGCCTTAGAATTGTG / TCGATCCATACAACAGTCAACA
Anonymous / G124 / CTCAGTCTGATCTGAACCCTGA / GTCGTGCATTCTGTGAACTCTT
Anonymous / G141 / TCACCTCATTATGGAACACGTC / AGTGTAGGCCTTAAGTGCGAAG
Anonymous / G143 / CATCCGAGACATTTCCCTTTAC / CTTAGTCCAATTTCTCGGGTTG
Anonymous / G151 / AGACGAGATGTTTTTCGCAGA / GGCTCTACTATAGGAAGGCCACA
Anonymous / G152 / GATCTGCTTGAGCTTCACCAC / TCACACTAAATCCCCCACTTTT
Anonymous / G153 / TGCATATAAATAGAAATTCATTCAGC / CTGCAACAAACACGTTCACCT
Anonymous / G166 / CAGTTGGTGCAGAAGGACTGTA / CACAGGATCTCCAAAAGCAGAC
Anonymous / G169 / TTATTCCGTTTCCTTTGTTGCT / CTGTCACACTCTCCTCCTCTCA
Anonymous / G170 / GGTAATCAGCTGAGGGATGAAG / TTTCCTTTGTTCAGGTTGTTGTT
Anonymous / G174 / CTCAAAATCATCGAGCAATCAA / TCATAAATCTCCCTGAGGCAAC
Anonymous / G177 / CCCCTGTACGTCTTCACATTAAC / GAACCAATTCATTTGCTGTGAG
Anonymous / G180 / TGATTACGCAGGGAAAAGGTAT / CATTTTGACATGAGGGCATTTA
Anonymous / G183 / GGCTCACTTTCCAAACTCAAAT / AAAACATAACACTGAGGTGGACTC
Anonymous / G186 / CTCCATGTAAGGATTGGTGCAT / CACAGAGCAGGAGTCTCTCTCA
Anonymous / G198 / ATTAAAACGAGGCACGTGATTT / CAGCTAACCCTAAAATGTGATGA
Anonymous / G202 / TTCTGTTTCTCTCTCAGTGAATGC / AACATGAAACGCGATCAAGAG
Anonymous / G205 / ATCTCCCAAAGACCAAAGTACG / TTACGACAATGAATGCTGTTTTT
Anonymous / G216 / TAAACCACGTTGGATCTGGAG / TCAGCTCCTATAAACAGAATGAGC
Anonymous / G228 / TTCATGAACCTCTGAGAGCAG / CCCATCCTCGCACCAAAG
Anonymous / G231 / AAGTTTTGGAGTGGACAGGGTA / TAAGAACTTGGAATGGCTCTCC
Anonymous / G237 / CATTAATTTGAGCACTGCTGCTT / GAACCGAGCTGAGTGTGAAG
Anonymous / G259 / CAGCCTCCACTCAACTCCAG / GAGCGAGGAGTAAGAACTGTCC
Anonymous / G260 / TCAGTCAATCCAACAAACCTATTG / CACATGTGAGCAGTGTTTTCAG
Anonymous / G266 / TCATTGAAATCTGGAAGGTTAAAA / AACGCCTTATACATAAAATGCTCTC
Anonymous / G270 / CAATTGCAACAAAACTCCTCCT / AGAAGAAATATGGGCTCTCTGC
Anonymous / G272 / GCGCTGTTTAAAGGTTCAATTA / AGCTGATCTATCCCAGGAACTG
Anonymous / G280 / GCAGGTGCAGAACATAGACG / TTCTTTTGTAGTGTTGGAGCTCAG
Anonymous / G285 / GCGAAAAGGAAGCCATAATACA / CACCAGATCTCTCAGACCAGTG
Anonymous / G287 / CATGCAGCTAAGGTCTACAACG / ACCTCTTTGGATAATGGCTTGA
Anonymous / G289 / GTATGAAAGCACTTGCTGTGGA / ATGCTGTACAATCTGCTCAACG
Anonymous / G291 / TGATCAAAAATACTGTTGCCAAA / GCATGTTAATAAAGAGGCATGGA
Anonymous / G294 / TGCTCTACAATATGGAACTCCTTG / CTGGGAGGTACTACCCCACTAC
Anonymous / G300 / GTAAGTCGTGTCCCTGGCTATG / ACCAGTACGTGAAAGAAAAGCA
Anonymous / G307 / ATGAACACTCACCAGCCTGATT / TGATGCTCTTTAATTTATGAACCAGA
Anonymous / G308 / TGCATATTCTAGTCAGCCTTCA / CTGGGATTGAAACGGCATTAT
Anonymous / G314 / GTTTGTTTACCCCAAGAAGCAG / AAAAATTGCGCAGTGTATTGTG
Anonymous / G336 / CAGATGAAGATGTCCCTCAGC / TGTTTGTAAGGTTGATTTTGTTCC
Anonymous / G340 / AGCTACACAGCACACAGGCTAA / TACTTCGACCACTGCAGGTATG
Anonymous / G342 / ATCCCAGGTTTCACACTGAGTC / GAACTGCACAAAACCCTCTGAT
mtDNA / Gcytb1 / GGCCGCCCTACGAAAAACCC / TAGAGGGAAAAAGGCCAAGAAAATAGAAA
Table S3. Per-site multilocus estimates of linkage disequilibrium based on n=57 ddRAD-derived anonymous loci. We present the index of association (IA) and a modification that corrects for sample size (d). The p-value is estimated based on 1,000 permutations and is equivalent for both statistics. Significant p-values are bolded.
Site / IA / d / p-valueB1 / 1.829689 / 0.034538 / 0.35
B2 / 0.106576 / 0.001933 / 0.75
B3 / 0.382379 / 0.00694 / 0.01
B5 / -0.08142 / -0.00148 / 0.76
B6 / -0.00038 / -6.86E-06 / 0.49
B7 / -0.07476 / -0.00136 / 0.63
B8 / 0.047512 / 0.000861 / 0.83
B9 / 0.54044 / 0.00979 / 0.41
B10 / 0.779436 / 0.014196 / 0.56
B11 / 0.269362 / 0.004879 / 0.75
B12 / 0.598777 / 0.010927 / 0.86
B13 / -0.00368 / -6.65E-05 / 0.52
B14 / -0.03796 / -0.00069 / 0.61
B15 / -0.15355 / -0.00279 / 0.96
B16 / 0.27951 / 0.005086 / 0.55
B17 / 0.0229 / 0.000416 / 0.60
B18 / -0.10285 / -0.00187 / 0.93
B19 / -0.0133 / -0.00024 / 0.66
B20 / 0.219235 / 0.003961 / 0.12
B22 / 0.326803 / 0.005959 / 0.05
B23 / 0.435416 / 0.00795 / 0.20
B24 / -0.18886 / -0.00352 / 0.85
B25 / -0.20654 / -0.00381 / 0.93
T1 / 0.097509 / 0.001769 / 0.92
T2 / 7.27E-05 / 1.32E-06 / 0.48
T3 / 0.04153 / 0.000751 / 0.91
T4 / 0.453462 / 0.008274 / 0.98
T5 / 0.172668 / 0.003151 / 0.28
T6 / -0.17322 / -0.00312 / 0.96
G1 / 0.198257 / 0.003614 / 0.07
G2 / 0.505175 / 0.00929 / 0.26
G3 / 0.403944 / 0.00757 / 0.52
G4 / 0.901724 / 0.016554 / 0.55
G5 / 1.223975 / 0.02266 / 0.14
G6 / 0.218703 / 0.003988 / 0.05
L1 / -0.23185 / -0.00423 / 0.99
L4 / 0.750458 / 0.013699 / 0.98
L5 / 2.205021 / 0.040415 / 0.89
L6 / 0.830703 / 0.01518 / 0.37
Figures
Fig. S1. HWE per locus per sampling site. Significant p-valuesafter a Bonferroni correction for multiple comparisons are shown by the gray shading.
Fig. S2.Pairwise tests of linkage disequilibrium (LD) at site B3, which was the only site with evidence of significant multilocus LD. Here, loci are on the x- and –y axes and the matrix is populated with pairwisedvalues shown by a color gradient.
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Fig. S3. Structure analyses of k=4 clusters for individuals within the northern/atoll cluster, based on 57 anonymous ddRAD-derived loci. To directly compare results with the pilot study of population structure within the same sub-region, methods were replicated from that study(D’Aloia et al. 2014). The results are temporally consistent: the northern-central barrier reef shows a mix of yellow and blue clusters (B1-B20); Glover’s Atoll (G1-G6) is nearly completely pink; Lighthouse Atoll (L1-L6) is nearly completely green; and Turneffe is predominantly yellow, but shows substantial evidence of mixing.
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Fig. S4. Additional DAPC analyses show that the reduced sample size in the South is driving the difference in density peaks. In (a) all admixed individuals (n = 77 total) were dropped from the dataset. There were relatively more admixed individuals in the South compared to the North, but dropping them did not substantially change the density peaks. However, in (b) we corrected for unequal sample sized between the two clusters by randomly sampling the same number of individuals in the North that are found in the South (n = 78 individuals/cluster). When both clusters are sampled evenly, the density peaks are similar in magnitude. Note that the order of clusters along the first axis differs in the main text.
References:
D'Aloia CC, BogdanowiczSM, Harrison RG, Buston PM (2014) Seascape continuity plays an important role in determining patterns of spatial genetic structure in a coral reef fish.Mol Ecol23:2902–2913
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