SUPPORTING INFORMATION
Two seas, two lineages. How genetic diversity is structured in Atlantic and Mediterranean greater amberjack Seriola dumerili and longfin yellowtail Seriola rivoliana (Perciformes, Carangidae)
Tanja Šegvić-Bubić, Federico Marrone, Leon Grubišić, David Izquierdo-Gomez, Ivan Katavić, Marco Arculeo, and Sabrina Lo Brutto
Appendix A: Supplementary Tables and Figures
Supplemental Table 1 Origin of the studied samples, or GenBank accession number, of Seriola dumerili, Seriola rivoliana, Seriola quinqueradiata, Seriola lalandi, and corresponding number of specimens amplified with the different markers and included in the analyses.
Sea / Reference Harbour / Region, Country / Locality Code / 16S&Cyt-b / D-Loop / MicrosatellitesSeriola dumerili
N-E Atlantic / Santa Cruz de Tenerife / Canary Islands, Spain / ATL-TE / 5 / 8 / 20
Mediterranean / Alicante / Costa Blanca, Spain / MED-AL / - / - / 52
Mediterranean / Castellammare del Golfo / Sicily, Italy / MED-CA / 2 / 11 / 20
Mediterranean / Porticello / Sicily, Italy / MED-PO / - / 11 / 20
Mediterranean / Sant’Agata di Militello / Sicily, Italy / MED-SA / 1 / 10 / 20
Mediterranean / Selinunte / Sicily, Italy / MED-SE / 2 / 10 / 20
Mediterranean / Scoglitti / Sicily, Italy / MED-SC / 1 / 10 / 14
Mediterranean / Siracusa / Sicily, Italy / MED-SR / 2 / 10 / 16
Mediterranean / Catania / Sicily, Italy / MED-CT / 1 / 8 / 20
Mediterranean / Tunis / Gulf de Tunis, Tunisia / MED-TU / 1 / 10 / -
Mediterranean / Split / Adriatic, Croatia / MED-MAD / - / - / 57
Mediterranean / Dubrovnik / Adriatic, Croatia / MED-SAD / - / - / 30
NC_016870 / Japan / 1 / - / -
Seriola rivoliana
N-E Atlantic / Azores / Azores, Portugal / ATL-AZ / 11 / 13 / 11
Mediterranean / Lampedusa / Sicily, Italy / MED-LA / 2 / 2 / -
Seriola lalandi
NC_016869 / Japan / 1 / - / -
Seriola quinqueradiata
NC_016868 / Japan / 1 / - / -
AB517559 / Japan / - / 1 / -
Supplemental Table 2. MtDNA primer pairs used in the study.
Gene / Primer pairs (5’ – 3’) / References16S / H16: 5’ - CG GTC TGA ATG TCT GAG ATT G – 3’
L16: 5’ – CGC CTG TTT AAC AAA AAC A – 3’ / Bouchon et al.,, 1994
Cyt-b / 28For: 5’ – CGA ACG TTG ATA TGA AAA CCA TCG TTG – 3’
34Rev: 5’ –AAC TGC AGC CCC TCA GAA TGA TAT TTG TCC TCA – 3’ / Kocher et al.,, 1989
Meyer et al.,, 1990
D-Loop / SerCR_H: 5’ – CGA TTT CTG TCC CTG ACC AT – 3’
SerCR_L: 5’ – CCT ACC CCT AGC TCC CAA AG – 3’ / Developed in this paper
References
Bouchon, D., Souty-Grosset, C., Raimond, R., 1994. Mitochondrial DNA variation and markers of species identity in two penaeid shrimp species: Penaeus monodon (Fabricius) and P. japonicus (Bate). Aquaculture 127, 131–144.
Kocher, T.D., Meyer, T.W., Edwards, S.V., Paabo, S.F., Villablanca, F.X., Wilson, A.C., 1989. Dynamics of mtDNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences of the USA 86, 6196–6200.
Meyer, A., Kocher, T., Basasibwaki, P., Wilson, A.C., 1990. Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences. Nature 347, 550–553.
Supplemental Table 3. MtDNA: descriptive statistics of genetic diversity of Seriola dumerili sampled from the western-central Mediterranean and from the eastern Atlantic Ocean based on D-Loop sequence data.
Population / N / H / S / h / πATL-TE / 8 / 6 / 27 / 0.893 ± 0.111 / 0.02919 ± 0.008
MED-CA / 11 / 6 / 25 / 0.836 ± 0.089 / 0.01347 ± 0.007
MED-PO / 11 / 7 / 25 / 0.873 ± 0.089 / 0.02021 ± 0.008
MED-SA / 10 / 6 / 7 / 0.778 ± 0.137 / 0.00434 ± 0.002
MED-SE / 10 / 8 / 27 / 0.933 ± 0.077 / 0.01489 ± 0.007
MED-SC / 10 / 5 / 24 / 0.756 ± 0.130 / 0.02651 ± 0.007
MED-SR / 10 / 5 / 21 / 0.822 ± 0.097 / 0.01997 ± 0.008
MED-CT / 8 / 5 / 23 / 0.857 ± 0.011 / 0.02438 ± 0.008
MED-TU / 10 / 4 / 22 / 0.533 ± 0.180 / 0.01156 ± 0.008
Overall / 88 / 28 / 45 / 0.824 ± 0.038 / 0.02009 ± 0.003
N, sample size; H, number of haplotypes; S, number of segregating sites; h, haplotype diversity (±S.D.); π, nucleotide diversity (±S.D.)
Supplemental Table 4. MtDNA: number of the D-Loop haplotypes obtained in Seriola dumerili populations sampled from the western-central Mediterranean and from the eastern Atlantic Ocean
ATL-TE / MED-CA / MED-PO / MED-SA / MED-SE / MED-SC / MED-SR / MED-CT / MED-TUHaplotypes / 6 / 6 / 7 / 6 / 8 / 5 / 5 / 5 / 4
Hap1 / 1
Hap2 / 3
Hap3 / 1
Hap4 / 1
Hap5 / 1
Hap6 / 1
Hap7 / 1
Hap8 / 1
Hap9 / 4 / 4 / 5 / 3 / 5 / 4 / 3 / 7
Hap10 / 1 / 1 / 2 / 2 / 2 / 1
Hap11 / 1 / 1 / 1
Hap12 / 1 / 1
Hap13 / 1 / 1 / 1 / 1 / 1
Hap14 / 1
Hap15 / 1
Hap16 / 1
Hap17 / 1 / 1 / 1
Hap18 / 3 / 1 / 1 / 2
Hap19 / 1
Hap20 / 1
Hap21 / 1
Hap22 / 2
Hap23 / 1
Hap24 / 1
Hap25 / 1
Hap26 / 1
Hap27 / 1
Hap28 / 1
Supplemental Table 4. Microsatellites: size range of microsatellite loci (Renshaw et al., 2006, 2007) used in the present study for twelve populations of the greater amberjack and longfin yellowtail (Seriola dumerili and S. rivoliana) sampled in the western-central Mediterranean area and eastern Atlantic.
Size range (bp) for each locusPopulations / Sdu44
(114-124) / Sdu39
(154-180) / Sdu19
(236-272) / Sdu10
(295-346) / Sdu31
(84-98) / Sdu36
(200-226) / Sdu41
(96-130) / Sdu46
(217-259)
Seriola dumerili
ATL-TE / 115-123 / 148-166 / 232-264 / 295-337 / 84-94 / 206-214 / 94-124 / 217-245
MED-AL / 115-125 / 148-178 / 236-268 / 295-340 / 80-94 / 200-226 / 94-124 / 217-245
MED-CA / 115-129 / 142-180 / 236-264 / 295-337 / 80-94 / 198-226 / 100-112 / 217-251
MED-PO / 115-125 / 148-178 / 236-268 / 295-334 / 84-94 / 200-214 / 94-124 / 217-245
MED-SA / 115-129 / 148-182 / 236-264 / 295-337 / 84-94 / 200-214 / 94-124 / 217-245
MED-SE / 115-125 / 148-178 / 236-264 / 295-337 / 84-94 / 200-214 / 94-106 / 217-245
MED-SC / 115-125 / 148-178 / 236-268 / 301-334 / 84-94 / 200-214 / 94-100 / 217-245
MED-SR / 115-125 / 142-180 / 236-264 / 295-337 / 80-94 / 200-216 / 94-112 / 217-251
MED-CT / 115-123 / 156-180 / 236-268 / 295-337 / 84-94 / 200-214 / 94-106 / 217-245
MED-MAD / 115-129 / 142-182 / 236-264 / 295-337 / 80-94 / 200-226 / 94-124 / 217-245
MED-SAD
/ 115-129 / 148-180 / 236-268 / 295-334 / 80-94 / 200-226 / 94-106 / 217-245
Seriola rivoliana
ATL-AZ / 117 / 142-146 / 232-252 / 286-313 / 114-164 / 200-244 / 118-154 / 210-231
In bold, size range published by Renshaw et al., 2006, 2007
References
Renshaw, M.A., Patton, J.C., Rexroad III, C.E., Gold, J.R., 2006. PCR primers for trinucleotide and tetranucleotide microsatellites in greater amberjack, Seriola dumerili. Molecular Ecology Notes 6, 1162–1164.
Renshaw, M.A., Patton, J.C., Rexroad III, C.E., Gold, J.R., 2007. Isolation and characterization of dinucleotide microsatellites in greater amberjack, Seriola dumerili. Conservation Genetics 8, 1009-1011.
Supplemental Table 5. Microsatellites: pairwise FST values (below diagonal) and Cavalli-Sforza and Edwards chord distance (above diagonal) among the twelve populations of greater amberjack and longfin yellowtail (Seriola dumerili and S. rivoliana ATL-AZ) from the western-central Mediterranean area and from the eastern Atlantic Ocean.
MED-CA / MED-PO / MED-SA / MED-AL / MED-
SC / MED-
SR / MED-
CT / MED-
SE / MED-MAD / MED-SAD / ATL-
TE / ATL-
AZ
MED-CA / 0.0163 / 0.020 / 0.018 / 0.020 / 0.023 / 0.027 / 0.018 / 0.013 / 0.016 / 0.067 / 0.317
MED-PO / -0.012 / 0.014 / 0.024 / 0.017 / 0.019 / 0.022 / 0.014 / 0.012 / 0.017 / 0.061 / 0.320
MED-SA / -0.011 / -0.007 / 0.021 / 0.014 / 0.019 / 0.020 / 0.012 / 0.013 / 0.016 / 0.059 / 0.315
MED-AL / 0.001 / 0.002 / -0.005 / 0.012 / 0.023 / 0.035 / 0.013 / 0.017 / 0.022 / 0.058 / 0.306
MED-SC / -0.002 / 0.002 / -0.004 / 0.011 / 0.013 / 0.027 / 0.009 / 0.011 / 0.015 / 0.052 / 0.313
MED-SR / -0.008 / 0.003 / -0.004 / -0.010 / 0.013 / 0.033 / 0.015 / 0.018 / 0.019 / 0.058 / 0.316
MED-CT / -0.008 / -0.003 / -0.004 / 0.004 / 0.007 / -0.009 / 0.022 / 0.023 / 0.022 / 0.067 / 0.324
MED-SE / -0.006 / 0.003 / -0.001 / -0.003 / 0.008 / -0.016 / -0.012 / 0.009 / 0.014 / 0.052 / 0.309
MED-MAD / -0.005 / 0.001 / -0.002 / 0.003 / 0.000 / 0.004 / 0.003 / -0.002 / 0.015 / 0.055 / 0.309
MED-SAD / -0.005 / 0.008 / -0.001 / 0.005 / 0.007 / -0.000 / 0.008 / 0.000 / 0.009 / 0.060 / 0.320
ATL-TE / 0.059* / 0.058* / 0.061* / 0.052* / 0.064* / 0.049* / 0.050* / 0.043* / 0.049* / 0.075* / 0.321
ATL-AZ / 0.336* / 0.354* / 0.339* / 0.325* / 0.335* / 0.320* / 0.351* / 0.346* / 0.340* / 0.370* / 0.361*
For locations codes refer to Suppl. Table 1. * = significantly different at the p < 0.001 alpha-level after Bonferroni correction.
Supplemental Figure 1.
Supplemental Figure 1 Microsatellites: NJ tree of chord genetic distances for population samples of Seriola dumerili and Seriola rivoliana (ATL-AZ). Values on nodes represent percentage bootstrap support after 1000 replicates, only values greater than 50% are shown
Appendix B: Running parameters for Bayesian-clustering programs
In Structure, for each K (ranging from 1 to 11), 20 replicates with a burn-in of 50,000 followed by 500,000 MCMC iterations were computed using the admixture model with correlated allele frequencies. To assess the most likely number of clusters, ∆K values were estimated using the ad hoc approach of Evanno et al. (2005) implemented in Structure Harvester v. 0.6.93 (Earl and von Holdt, 2011). The average pairwise similarity of runs was assessed with the CLUMPP v. 1.1.2 program (Jakobsson and Rosenberg, 2007), with the ‘FullSearch’ algorithm, 10,000 random input orders, and 10,000 repeats. The run with the highest ∆K was used to construct the dendrogram, which was visualized with the Distruct v. 1.1 program (Rosenberg, 2004). For the spatial cluster model implemented in the Geneland package, Markov chain Monte Carlo (MCMC) repetitions were set at 100,000, thinning was set at 100, and the burn-in period was set at 200. The number of groups (K) to be tested was set at 1–11. All individuals were assigned to K populations based on their multilocus genotype and the spatial coordinates. To ensure that the run was sufficiently long, 20 different runs were preformed and estimated parameters were compared (K, individual population membership, maps). The best result was chosen based on the highest average posterior probability.
References
Earl, D.A. and von Holdt, B.M., 2011. STRUCTURE HARVESTER: a website and program for visualizing Structure output and implementing the Evanno method. Conservation Genetics Resources 4, 359–361.
Evanno, G., Regnaut, S., Goudet, J., 2005. Detecting the number of clusters of individuals using the software Structure: a simulation study. Molecular Ecology 14, 2611-2620.
Jakobsson, M., Rosenberg, N., 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 1801–1806.
Rosenberg, N.A., 2004. Distruct: a program for the graphical display of population structure. Molecular Ecology Notes 4, 137–138.