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Figure 7
Haplotype structure of D_ dentex samples with respect to nucleotide variation in the COI region
| Nucleotide positions in COI region | ||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Haplotype Number | Frequency | 19 | 20 | 37 | 47 | 54 | 65 | 80 | 98 | 111 | 126 | 129 | 131 | 150 | 165 | 171 | 192 | 238 | 247 | 284 | 342 | 398 | 399 | 406 | 407 | 441 | 447 | 455 |
| H 1 | 25 | T | A | G | A | A | T | A | C | T | T | A | A | C | T | T | G | T | A | A | A | C | T | T | C | T | T | G |
| H 2 | 1 | . | . | A | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| H 3 | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | C | . | . | . | . | . | . | . | C | . | . | . | . | . |
| H 4 | 1 | . | . | . | . | . | . | . | . | . | C | . | . | . | . | . | . | . | . | . | . | . | . | . | T | . | C | . |
| H 5 | 1 | . | . | . | . | . | . | . | A | C | C | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| H 6 | 1 | G | . | . | C | . | . | C | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| H 7 | 1 | G | C | A | C | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| H 8 | 1 | G | C | A | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | T | . | . | . | . | . | . | . |
| H 9 | 2 | . | . | . | . | . | G | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| H 10 | 1 | G | C | A | . | . | G | . | . | . | . | . | . | . | . | C | . | . | . | . | . | . | . | . | . | . | . | . |
| H 11 | 1 | G | C | A | C | . | G | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| H 12 | 1 | G | C | A | . | . | G | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| H 13 | 1 | G | C | A | . | G | G | . | . | . | . | . | . | . | . | . | . | . | . | C | . | . | . | . | . | . | . | . |
| H 14 | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | C | . | . | . | . | . |
| H 15 | 2 | G | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| H 16 | 2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | A | . | . | . | . | . | . | . | . | . | . | . |
| H 17 | 1 | G | . | A | . | . | G | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | G | . | . | . | . |
| H 18 | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | T | . | . | . | . | . | . |
| H 19 | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | C | . | . | . | . | . | . | . | . | . | . |
| H 20 | 1 | . | . | . | . | . | . | . | . | . | . | . | . | A | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| H 21 | 1 | . | . | . | . | . | . | . | A | . | . | . | . | . | . | . | . | . | C | . | . | . | . | G | . | . | . | . |
| H 22 | 1 | G | C | A | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| H 23 | 1 | . | . | . | . | . | . | . | A | . | . | . | . | . | . | . | . | . | . | . | . | . | . | G | . | . | . | . |
| H 24 | 1 | . | . | . | . | . | . | . | . | . | . | . | C | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| H 25 | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | A | . | . | . | . | . | . | . | . | A | . | C |
| H 26 | 1 | . | . | . | . | . | . | . | . | . | . | C | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
Sampling locations of common dentex and number of the samples per location
| No. | Sampling Location | Sample Code | Number of samples | |
|---|---|---|---|---|
| 1 | Karaburun- Natural | I-W | 9 | |
| 2 | Karaburun- Culture | I-C | 9 | |
| 3 | Çeşme-Natural | II-W | 5 | |
| 4 | Kuşadası-Natural | III-W | 10 | |
| 5 | Güllük-Natural | IV-W | 5 | |
| 6 | Bodrum-Natural | V-W | 4 | |
| 7 | Çanakkale-Natural | VI-W | 6 | |
| 8 | Antalya-Natural | VII-W | 5 | |
| TOTAL | 53 | |||
Haplotype groups and sample codes in the same haplotype group
| Haplotypes | Sample Code | ||
|---|---|---|---|
| H 1 | I-W-D.dentex-1, I-W-D.dentex-2, I-W-D.dentex-3, I-W-D.dentex-7, I-W-D.dentex-8, I-W-D.dentex-9, I-W-D.dentex-10, I-C-D.dentex-9, II-W-D.dentex-4, II-W-D.dentex-5, III-W-D. dentex-2, III-W-D.dentex-4, III-W-D.dentex-8, III-W-D.dentex-9, III-W-D.dentex-10, IV-W-D.dentex-2, IV-W-D.dentex-4, IV-W-D.dentex-5, IV-W-D.dentex-6, V-W-D.dentex-2, V-W-D. dentex-4, VI-W-D.dentex-2, VI-W-D.dentex-4, VI-W-D.dentex-5, VII-W-D.dentex-5 | ||
| H 2 | I-W-D.dentex-4 | H 15 | III-W-D.dentex-1, III-W-D.dentex-5 |
| H 3 | I-W-D.dentex-5 | H 16 | III-W-D.dentex-3, VI-W-D.dentex-3 |
| H 4 | I-C-D.dentex-1 | H 17 | III-W-D.dentex-6 |
| H 5 | I-C-D.dentex-2 | H 18 | III-W-D.dentex-7 |
| H 6 | I-C-D.dentex-3 | H 19 | V-W-D.dentex-1 |
| H 7 | I-C-D.dentex-4 | H 20 | V-W-D.dentex-3 |
| H 8 | I-C-D.dentex-5 | H 21 | VI-W-D.dentex-1 |
| H 9 | I-C-D.dentex-7, IV-W-D.dentex-1 | H 22 | VI-W-D.dentex-6 |
| H 10 | I-C-D.dentex-8 | H 23 | VII-W-D.dentex-1 |
| H 11 | I-C-D.dentex-10 | H 24 | VII-W-D.dentex-2 |
| H 12 | II-W-D.dentex-1 | H 25 | VII-W-D.dentex-3 |
| H 13 | II-W-D.dentex-2 | H 26 | VII-W-D.dentex-4 |
| H 14 | II-W-D.dentex-3 | ||
Genetic diversity and neutrality tests of the D_dentex populations with respect to locations
| Population | Sample size (n) | N Haplotype number | Haplotype Diversity (h) | PS | PIR | Nucleotide diversity (π) | Taijm’a’s D | Fu’s Fs |
|---|---|---|---|---|---|---|---|---|
| I-C. D.dentex | 9 | 9 | 1.000 | 6 | 13 | 0.0097(± 0.0012) | −1.513 | −0.380 |
| I-W. D.dentex | 9 | 3 | 0.417 | 4 | 7 | 0.0014 (± 0.0007) | −0.176 | −5.174** |
| II-W. D.dentex | 5 | 4 | 0.900 | 1 | 6 | 0.0076 (± 0.0022) | 0.498 | −0.036 |
| III-W. D.dentex | 10 | 5 | 0.756 | 0 | 1 | 0.0031 (± 0.0005) | −1.276 | −1.320 |
| IV-W. D.dentex | 5 | 2 | 0.400 | 0 | 2 | 0.0008 (± 0.0007) | −0.817 | 0.090 |
| V-W. D.dentex | 4 | 3 | 0.833 | 0 | 7 | 0.0021 (± 0.0007) | −0.710 | −0.887 |
| VI-W. D.dentex | 6 | 4 | 0.800 | 0 | 7 | 0.0049 (± 0.0014) | −1.390* | −0.219 |
| VII-W. D.dentex | 5 | 5 | 1.000 | 0 | 3 | 0.0059 (± 0.0014) | −1.162 | −2.371* |
Genetic distance calculation of D_ dentex populations with respect to where the stations’ samples were collected from (Nei’s dxy and Da method)
| Da | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| I-C | I-W | II-W | III-W | IV-W | V-W | VI-W | VII-W | ||
| Dxy* | |||||||||
| Karaburun I-C | 0 | 0.00148 | −0.00045 | 0.00080 | 0.00141 | 0.00169 | 0.00060 | 0.00160 | |
| Karaburun I-W | 0.00701 | 0 | 0.00056 | 0.00009 | 0.00000 | 0.00000 | −0.00008 | 0.00000 | |
| Çeşme II-W | 0.00815 | 0.00503 | 0 | 0.00014 | 0.00050 | 0.00084 | 0.00000 | 0.00084 | |
| Kuşadası III-W | 0.00717 | 0.00233 | 0.00545 | 0 | 0.00006 | 0.00014 | −0.00028 | −0.00004 | |
| Güllük IV-W | 0.00666 | 0.00112 | 0.00470 | 0.00201 | 0 | 0.00000 | 0.00000 | 0.00000 | |
| Bodrum V-W | 0.00757 | 0.00175 | 0.00566 | 0.00273 | 0.00147 | 0 | 0.00000 | 0.00000 | |
| Çanakkale VI-W | 0.00788 | 0.00307 | 0.00622 | 0.00370 | 0.00287 | 0.00349 | 0 | −0.00042 | |
| Antalya VII-W | 0.00936 | 0.00363 | 0.00755 | 0.00444 | 0.00335 | 0.00398 | 0.00496 | 0 | |
Distance matrix obtained according to Wright’s F statistics for the Common Dentex (Dentex dentex) sample at the stations in the study
| I-C | I-W | II-W | III-W | IV-W | V- W | VI-W | VII-W | ||
|---|---|---|---|---|---|---|---|---|---|
| Karaburun I-C | 0.00000 | ||||||||
| Karaburun I-W | 0.22466* | 0.00000 | |||||||
| Çeşme II-W | 0.08522 | 0.00077 | 0.00000 | ||||||
| Kuşadası III-W | 0.03716 | 0.07255 | −0.02564 | 0.00000 | |||||
| Güllük IV-W | −0.08257 | 0.16667 | 0.04412 | 0.00474 | 0.00000 | ||||
| Bodrum V-W | 0.21178 | −0.02273 | −0.03261 | 0.04085 | 0.16667 | 0.00000 | |||
| Çanakkale VI-W | 0.03226 | 0.01562 | −0.08541 | −0.05174 | −0.00737 | −0.02362 | 0.00000 | ||
| Antalya VII-W | 0.02463 | 0.04000 | −0.06047 | −0.05882 | −0.01205 | 0.00415 | −0.08711 | 0.00000 |
Map coordinates of the stations where common dentex samples were obtained
| Stations | Common Dentex Natural | Common Dentex Culture | |
|---|---|---|---|
| (I) Karaburun | Foça offshore | Akvatur Fish Farm | |
| (II) Çeşme* | Çeşme fish pond | ||
| (III) Kuşadası** | Çağlar fishery agency | ||
| (IV) Güllük | Güllük Gulf | ||
| (V) Bodrum | Bodrum Şenol Fishery | ||
| (VI) Çanakkale | Engin Fishery | ||
| (VII) Antalya | Antalya offshore |