Elucidation of fine-scale genetic structure of sandfish (Holothuria scabra) populations in Papua New Guinea and northern Australia
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- Ωρίων Δυοβουνιώτης
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1 Marine and Freshwater Research, 2017, 68, CSIRO 2017 Supplementary material Elucidation of fine-scale genetic structure of sandfish (Holothuria scabra) populations in Papua New Guinea and northern Australia Samantha J. Nowland A,C, Paul C. Southgate A,B, Rose K. Basiita A and Dean R. Jerry A A Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Qld 4811, Australia. B Present address: Australian Centre for Pacific Islands Research and Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Qld 4558, Australia. C Corresponding author. samantha.nowland@hotmail.com Page 1 of 6
2 Table S1. Summary of microsatellite marker suites, associated primers, relevant polymerase chain reaction (PCR) conditions, final primer concentrations and fluorescent labels utilised in the present study Markers with an asterisk were dropped from the analysis. Original source of primer sequences is Fitch et al. (2012) Locus Repeat motif Marker suite Final primer concentration (μm) Observed allele size range (bp) Primer sequence (5 3 ) and fluorescent tag used Lca1* (GT) 8 M F: NED CTTAGTCTGGTACGGTTGTCC R: GTTTACTAAGCAAGTGTCACAAAC Lca4 (GT) 11 M F: FAM AGAGCATGTATGTATCATCGAAACC R: AAACGGAACGGAACAAGCC Lca17 (AC) 11 M F: PET AGATTCATTTGGGAACTTTGGC R: AGGGTTGATGTAAGCTGCG Lca20 (AC) 12 M F: FAM TGCGTGTGGTGATTTTGAC R: ACCATTCTACAGCTCGTCCC Lca24 (AC) 18 M F: VIC TCCTTCGTCGCAGCATGAC R: TTCTTGTATTCCTTTGCAGGC Lca28* (GAT) 15 M F: PET TTCTGGTCTCGACTGGCAC R: TCAGTATCGGCTCCACAGG Lca31* (ATGT) 11 M F: VET TGTAGGTAGGTAGGTAGGTATGTATG R: CAGCAGTGGGTTTGGACAC Lca40 (ATGT) 13 M F: PET GCATTGATCATGTGGAATTTGCG R: CACCATAGACCTGGCTTGC Lca44 (AAAC) 9 M F: FAM GACGGTACGTCACCAGAGG R: TTCTTCGTCTTTTGGCGGG Lca48 (GT) 8 M F: VIC ACAATGCGGACGACAATGG R: ATCGTGTTTACAAGCGGGC Lca49 (ACAG) 8 M F: PET TGAGCACGGTGTATTGTCC R: TGATGTGAGCCACTGCG Lca54 (CTGT) 8 M F: FAM AGACAGTTGTGGGAAGGGC R: TGGATGGAATAACAATAGGTGTCC Lca59 (AC) 8 M F: FAM AGAGCACACGTATCCCCAC R: GGGGCAGGATAGAGCACATAG Lca42* (AC) 18 M F: NED TCCTTCGTCGCAGCATGAC R: TTCTTGTATTCCTTTGCAGGC Lca62* (AT) 8 M F: VIC AGCTAGCAGGGAAAAGAAGAAAG R: AGAGGCGGATGCTCTTACC Page 2 of 6
3 Table S2. Population by locus Oosterhout estimate of null alleles (Van Oosterhout et al. 2004) BE, Belifu; SI, Sivasat; UN, Ungakum; BA, Bangatang; LN, Limanak North; MB, Milne ; KB, Kimbe ; LS, Limanak South; MR, Manus Island Rambutyo; ML, Manus Island Loi; DW, Darwin (Australia); CY, Cape York (Australia) Locus BE SI UN BA LN MB KB LS MR ML DW CY Lca20A Lca49A Lca54A Lca59A Lca40A Lca4A Lca48A Lca24A Lca17A Lca44A Page 3 of 6
4 Table S3. Genetic-diversity summary statistics of sandfish (Holothuria scabra) populations, showing number of alleles (Na), allelic richness (Ar), observed heterozygosity (Ho), expected heterozygosity (He) and inbreeding coefficient (F IS) Departures from Hardy Weinberg expectations of heterozygosity (HWE) is indicated: sig, significant, P < 0.05; n.s., not significant. Underlined text indicates a different microsatellite locus Parameter Belifu Sivasat Ungakum Bangatan North Milne Kimbe South Rambutyo Loi Darwin Cape York Global n Lca17 Na ± 0.4 Ar ± 0.2 Ho ± 0.03 He ± 0.03 FIS ± 0.05 HWE n.s. sig sig n.s. sig sig sig sig sig sig sig sig Lca20 Na ± 0.7 Ar ± 0.5 Ho ± 0.04 He ± 0.01 FIS ± 0.04 HWE n.s. n.s. sig n.s. n.s. n.s. n.s. n.s. n.s. n.s. n.s. sig Lca24 Na ± 0.5 Ar ± 0.3 Ho ± 0.04 He ± 0.03 FIS ± 0.03 HWE n.s. sig n.s. n.s. n.s. n.s. n.s. n.s. n.s. sig n.s. n.s. Lca4 Na ± 0.7 Ar ± 0.4 Ho ± 0.04 He ± 0.02 FIS ± 0.05 HWE sig sig sig sig sig sig sig n.s. sig sig sig n.s. Page 4 of 6
5 Parameter Belifu Sivasat Ungakum Bangatan North Milne Kimbe South Rambutyo Loi Darwin Cape York Global Lca40 Na ± 1.1 Ar ± 0.2 Ho ± 0.02 He ± 0.00 FIS ± 0.02 HWE n.s. n.s. n.s. n.s. sig n.s. n.s. n.s. n.s. sig sig sig Lca44 Na ± 0.4 Ar ± 0.1 Ho ± 0.02 He ± 0.01 FIS ± 0.03 HWE n.s. n.s. n.s. n.s. n.s. n.s. n.s. n.s. n.s. n.s. sig n.s. Lca48 Na ± 0.7 Ar ± 0.4 Ho ± 0.04 He ± 0.02 FIS ± 0.06 HWE n.s. sig n.s. n.s. sig n.s. sig sig sig sig n.s. sig Lca49 Na ± 0.8 Ar ± 0.3 Ho ± 0.03 He ± 0.01 FIS ± 0.03 HWE sig sig n.s. n.s. n.s. n.s. n.s. n.s. n.s. n.s. n.s. n.s. Lca54 Na ± 0.4 Ar ± 0.3 Ho ± 0.03 He ± 0.04 FIS ± 0.03 HWE n.s. n.s. n.s. n.s. n.s. n.s. sig n.s. n.s. n.s. n.s. n.s. Page 5 of 6
6 Parameter Belifu Sivasat Ungakum Bangatan North Milne Kimbe South Rambutyo Loi Darwin Cape York Global Lca59 Na ± 0.5 Ar ± 0.3 Ho ± 0.03 He ± 0.01 FIS ± 0.03 HWE n.s. n.s. n.s. n.s. sig n.s. sig n.s. n.s. n.s. n.s. n.s. Pop. mean Na 10.7 ± ± ± ± ± ± ± ± ± ± ± ± ± 0.6 Ar 7.7 ± ± ± ± ± ± ± ± ± ± ± ± ± 0.3 Ho 0.59 ± ± ± ± ± ± ± ± ± ± ± ± ± 0.03 He 0.75 ± ± ± ± ± ± ± ± ± ± ± ± ± 0.02 FIS 0.24 ± ± ± ± ± ± ± ± ± ± ± ± ± 0.04 References Fitch, A. J., Leeworthy, G., Li, X., Bowman, W., Turner, L., and Gardner, M. G. (2012). Isolation and characterisation of eighteen microsatellite markers from the sea cucumber Holothuria scabra (Echinodermata: Holothuriidae). Australian Journal of Zoology 60, doi: /zo12114 Van Oosterhout, C., Hutchinson, W. F., Wills, D. P. M., and Shipley, P. (2004). Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4(3), doi: /j x Page 6 of 6
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