Genetic Diversity and Phylogenetic Relationships of Ball Sea Cucumber (Phyllophorella kohkutiensis) in Thai Waters
Abstract
Ball sea cucumbers (Phyllophorella kohkutiensis) were originally found in Thailand. They have been increasingly fishing from both the Gulf of Thailand and the Andaman Sea. Nevertheless, basic knowledge essentially required for the species management has never been reported in Thailand. This study aimed to investigate genetic diversity, confirm the species identification and examine phylogenetic relationships of ball sea cucumbers in Thai waters, by analyzing DNA sequence variation at cytochrome c oxidase subunit I in mitochondrial DNA. The results suggested that ball sea cucumbers from Tumbon Koh Sarai, Amphur Muang, Satun Province (N = 15), Ban Don Bay, Amphur Tha Chang, Surat Thani Province (N = 15) and Koh Chang, Trat Province (N = 2) showed high haplotype diversity (h = 0.675 ± 0.089) but their nucleotide diversity was low (π = 0.00192 ± 0.00054). All ball sea cucumbers were the same species which was Phyllophorella kohkutiensis. Pairwise genetic distances between sea cucumber samples (distance measure = Kimura 2-parameter) were ranging from 0-1.07%. This is consistent with phylogenetic analysis between ball sea cucumbers and other sea cucumber species. Phylogenetic trees based on maximum parsimony and neighbor-joining methods showed that ball sea cucumbers were clustered within a single clade. Keywords : ball sea cucumber ; Phyllophorella kohkutiensis ; Thai waters ; COIReferences
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Arndt, A., Marquez, C., Lambert, P. & Smith, M. J. (1996). Molecular phylogeny of eastern Pacific sea cucumbers (Echinodermata: Holothuroidea) based on mitochondrial DNA sequence. Molecular Phylogenetics and Evolution, 6, 425-437.
Byrne, M., Rowe, F. & Uthicke, S. (2010). Molecular taxonomy, phylogeny and evolution in the family Stichopodidae (Aspidochirotida: Holothuroidea) based on COI and 16S mitochondrial DNA. Molecular Phylogenetics and Evolution, 56, 1068-1081.
Cherbonnier, G. (1961). Holothuries récoltées par A. Gallardo dans la Baie de Nha-Trang (Sud Viet-Nam) (suite). Bulletin Muséum National Histoire Naturelle Paris, 2 série, 32, 425-435.
Community Based Research Division. (2017). The villagers research in Ban Don Bay. Research Society Organization Journal, 99, 20. (in Thai)
Corstorphine, E. A. (2010). DNA barcoding of echinoderms: species diversity and patterns of molecular evolution. Master Thesis, University of Guelph, Ontario, Canada.
Davison, G. W. H., Ng, P. K. L. & Chew, H. H. (2008). The Singapore Red Data Book: Threatened plants and animals of Singapore. Singapore: Nature Society. 285 pp.
Department of Marine and Coastal Resources. (2020). DMCR News, November 16, 2019. Retrieved April 23, 2020, from https://www.dmcr.go.th/detailAll/36704/nws/22 (in Thai)
Donrung, P., Tunkijjanukij, S., Jarayabhand, P. & Poompuang, S. (2011). Spatial genetic structure of the surf clam Paphia undulata in Thailand waters. Zoological Studies, 50(2), 211-219.
Excoffier, L., Laval, G. & Schneider, S. (2005). Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47-50.
Hebert, P.D.N., Ratnasingham, S., & deWaard, J.R. (2003). Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London. Series B, Biological Sciences, 270, S96–S99.
Heding, S.G. & Panning, A. (1954). Phyllophoridae. Eine Bearbeitung der polytentaculaten dendrochiroten Holothurien des Zoologischen Museums in Kopenhagen. Spolia Zoologica Musei Hauniensis [=Skrifter udgivet af Universitetets Zoologiske Museum København], 13, 209 pp., 102 figs.
Huang, X. & Madan, A. (1999). CAP3: A DNA sequence assembly program. Genome Research, 9, 868-877.
Jussapalo, S. (2016). Potential of self-reliance community coastal fishery resources management in Tumbon Koh Sarai, Amphur Muang, Satun Province. Silpakorn University Journal, 36(1), 49-65. (in Thai)
Khamnamtong, B., Klinbunga, S. & Menasveta, P. (2009). Genetic diversity and geographic differentiation of the giant tiger shrimp (Penaeus monodon) in Thailand analyzed by mitochondrial COI sequences. Biochemical Genetics, 47, 42-55.
Klinbunga, S., Siludjai, D., Wudthijinda, W., Tassanakajon, A., Jarayabhand, P. & Menasveta, P. (2001). Genetic heterogeneity of the giant tiger shrimp (Penaeus monodon) in Thailand revealed by RAPD and mitochondrial DNA RFLP analyses. Marine Biotechnology, 3, 428-438.
Laakmann, S., Boos, K., Knebelsberger, T., Raupach, M. J. & Neumann, H. (2016). Species identification of echinoderms from the North Sea by combing morphology and molecular data. Helgoland Marine Research, 70, 1-18.
Laxminarayana, A. (2005). Induced spawning and larval rearing of the sea cucumbers, Bohadschia marmorata and Holothuria atra in Mauritius. SPC Beche-de-mer Information Bulletins, 22, 48–52.
Liao, Y. & Pawson, D. L. (2001). Dendrochirote and dactylochirote sea cucumbers (Echinodermata: Holothuroidea) of China, with descriptions of eight new species. Proceedings of the Biological Society of Washington, 114(1), 58-90.
Madduppa, H., Taurusman, A. A., Subhan, B., Anggraini, N. P., Fadillah, R. & Tarman, K. (2017). Short Communication: DNA barcoding reveals vulnerable and not evaluated species of sea cucumbers (Holothuroidea and Stichopodidae) from Kepulauan Seribu reefs, Indonesia. Biodiversitas, 18(3),
893-898.
Michonneau, F. & Paulay, G. (2014). Revision of the genus Phyrella (Holothuroidea: Dendrochirotida) with the description of a new species from Guam. Zootaxa, 3760(2), 101-140.
Miller, A. K., Kerr, A. M., Paulay, G., Reich, M., Wilson, N. G., Carvajal, J. I. & Rouse, G. W. (2017). Molecular phylogeny of extant Holothuroidea (Echinodermata). Molecular Phylogenetics and Evolution, 111,
110-131.
Ong, J. Y., Wirawati, I. & Wong, H. P.-S. (2016). Sea cucumbers (Echinodermata: Holothuroidea) collected from the Singapore strait. Raffles Bulletin of Zoology, 34, 666-717.
Panithanarak, T., Karuwancharoen, R., Na-Nakorn, U. & Nguyen, T. T. T. (2010). Population genetics of the spotted seahorse (Hippocampus kuda) in Thai waters: implications for conservation. Zoological Studies, 49(4), 564-576.
Posada, D. & Crandall, K. A. (1998). MODELTEST: testing the model of DNA substitution. Bioinformatics, 14,
817-818.
Putchakarn, S., Mucharin, A., Komkham, P. & Pangsuk, B. (2017). Checklist of Echinoderms in Thailand. Bangkok: Office of Natural Resources and Environmental Policy and Planning. 150 pp. (in Thai)
Rodriguez, F., Oliver, J. L., Marin, A. & Medina, J. R. (1990). The general stochastic model of nucleotide substitution. Journal of Theoretical Biology, 142(4), 485-501.
Rozas, J., Ferrer-Mata, A., Sanchez-DelBarrio, J. C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S. & Sanchez-Gracia, A. (2017). DnaSP v6: DNA sequence polymorphism analysis of large datasets. Molecular Biology and Evolutions, 34, 3299-3302.
Skillings, D. J., Bird, C. E. & Toonen, R. J. (2014). Comparative population structure of two edible Indo-Pacific coral reef sea cucumbers (Echinodermata: Holothuroidea). Bulletin of Marine Science, 90(1), 359-378.
Soliman, T., Fernandez-Silva, I. & Reimer, J. D. (2016). Genetic population structure and low genetic diversity in the over-exploited sea cucumber Holothuria edulis Lesson, 1830 (Echinodermata: Holothuroidea) in Okinawa Island. Conservation Genetics, 17, 811-821.
Swofford, D. L. (2002). PAUP*-phylogenetic analysis using parsimony (*and other methods), Version 4.0b10. Sunderland, MA: Sinauer Associates.
Tamura, K. & Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512-526.
Tassanakajon, A. (2003). Genetic diversity and population structure of the black tiger shrimp, Penaeus monodon, in Thailand revealed by microsatellite markers. Journal of Research Methodology, 16(3), 359-373.
(in Thai)
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 24, 4876-4882.
Uthicke, S., Schaffelke, B. & Byrne, M. (2009). A boom–bust phylum? Ecological and evolutionary consequences of density variations in echinoderms. Ecological Monographs, 79, 3–24.
Wanna, W., Rolland, J.-L., Bonhomme, F. & Phongdara, A. (2004). Population genetic structure of Penaeus merguiensis in Thailand based on nuclear DNA variation. Journal of Experimental Marine Biology and Ecology, 311, 63-78.
Ward, R. D., Holmes, B. H. & O’ Hara, T. D. (2008). DNA barcoding discriminates echinoderm species. Molecular Ecology Resources, 8, 1202–1211.
Wen, J., Hu, C., Zhang, L. & Fan, S. (2011). Genetic identification of global commercial seacucumber species on the basis of mitochondrial DNA sequences. Food Control, 22, 72-77.
Arndt, A., Marquez, C., Lambert, P. & Smith, M. J. (1996). Molecular phylogeny of eastern Pacific sea cucumbers (Echinodermata: Holothuroidea) based on mitochondrial DNA sequence. Molecular Phylogenetics and Evolution, 6, 425-437.
Byrne, M., Rowe, F. & Uthicke, S. (2010). Molecular taxonomy, phylogeny and evolution in the family Stichopodidae (Aspidochirotida: Holothuroidea) based on COI and 16S mitochondrial DNA. Molecular Phylogenetics and Evolution, 56, 1068-1081.
Cherbonnier, G. (1961). Holothuries récoltées par A. Gallardo dans la Baie de Nha-Trang (Sud Viet-Nam) (suite). Bulletin Muséum National Histoire Naturelle Paris, 2 série, 32, 425-435.
Community Based Research Division. (2017). The villagers research in Ban Don Bay. Research Society Organization Journal, 99, 20. (in Thai)
Corstorphine, E. A. (2010). DNA barcoding of echinoderms: species diversity and patterns of molecular evolution. Master Thesis, University of Guelph, Ontario, Canada.
Davison, G. W. H., Ng, P. K. L. & Chew, H. H. (2008). The Singapore Red Data Book: Threatened plants and animals of Singapore. Singapore: Nature Society. 285 pp.
Department of Marine and Coastal Resources. (2020). DMCR News, November 16, 2019. Retrieved April 23, 2020, from https://www.dmcr.go.th/detailAll/36704/nws/22 (in Thai)
Donrung, P., Tunkijjanukij, S., Jarayabhand, P. & Poompuang, S. (2011). Spatial genetic structure of the surf clam Paphia undulata in Thailand waters. Zoological Studies, 50(2), 211-219.
Excoffier, L., Laval, G. & Schneider, S. (2005). Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47-50.
Hebert, P.D.N., Ratnasingham, S., & deWaard, J.R. (2003). Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London. Series B, Biological Sciences, 270, S96–S99.
Heding, S.G. & Panning, A. (1954). Phyllophoridae. Eine Bearbeitung der polytentaculaten dendrochiroten Holothurien des Zoologischen Museums in Kopenhagen. Spolia Zoologica Musei Hauniensis [=Skrifter udgivet af Universitetets Zoologiske Museum København], 13, 209 pp., 102 figs.
Huang, X. & Madan, A. (1999). CAP3: A DNA sequence assembly program. Genome Research, 9, 868-877.
Jussapalo, S. (2016). Potential of self-reliance community coastal fishery resources management in Tumbon Koh Sarai, Amphur Muang, Satun Province. Silpakorn University Journal, 36(1), 49-65. (in Thai)
Khamnamtong, B., Klinbunga, S. & Menasveta, P. (2009). Genetic diversity and geographic differentiation of the giant tiger shrimp (Penaeus monodon) in Thailand analyzed by mitochondrial COI sequences. Biochemical Genetics, 47, 42-55.
Klinbunga, S., Siludjai, D., Wudthijinda, W., Tassanakajon, A., Jarayabhand, P. & Menasveta, P. (2001). Genetic heterogeneity of the giant tiger shrimp (Penaeus monodon) in Thailand revealed by RAPD and mitochondrial DNA RFLP analyses. Marine Biotechnology, 3, 428-438.
Laakmann, S., Boos, K., Knebelsberger, T., Raupach, M. J. & Neumann, H. (2016). Species identification of echinoderms from the North Sea by combing morphology and molecular data. Helgoland Marine Research, 70, 1-18.
Laxminarayana, A. (2005). Induced spawning and larval rearing of the sea cucumbers, Bohadschia marmorata and Holothuria atra in Mauritius. SPC Beche-de-mer Information Bulletins, 22, 48–52.
Liao, Y. & Pawson, D. L. (2001). Dendrochirote and dactylochirote sea cucumbers (Echinodermata: Holothuroidea) of China, with descriptions of eight new species. Proceedings of the Biological Society of Washington, 114(1), 58-90.
Madduppa, H., Taurusman, A. A., Subhan, B., Anggraini, N. P., Fadillah, R. & Tarman, K. (2017). Short Communication: DNA barcoding reveals vulnerable and not evaluated species of sea cucumbers (Holothuroidea and Stichopodidae) from Kepulauan Seribu reefs, Indonesia. Biodiversitas, 18(3),
893-898.
Michonneau, F. & Paulay, G. (2014). Revision of the genus Phyrella (Holothuroidea: Dendrochirotida) with the description of a new species from Guam. Zootaxa, 3760(2), 101-140.
Miller, A. K., Kerr, A. M., Paulay, G., Reich, M., Wilson, N. G., Carvajal, J. I. & Rouse, G. W. (2017). Molecular phylogeny of extant Holothuroidea (Echinodermata). Molecular Phylogenetics and Evolution, 111,
110-131.
Ong, J. Y., Wirawati, I. & Wong, H. P.-S. (2016). Sea cucumbers (Echinodermata: Holothuroidea) collected from the Singapore strait. Raffles Bulletin of Zoology, 34, 666-717.
Panithanarak, T., Karuwancharoen, R., Na-Nakorn, U. & Nguyen, T. T. T. (2010). Population genetics of the spotted seahorse (Hippocampus kuda) in Thai waters: implications for conservation. Zoological Studies, 49(4), 564-576.
Posada, D. & Crandall, K. A. (1998). MODELTEST: testing the model of DNA substitution. Bioinformatics, 14,
817-818.
Putchakarn, S., Mucharin, A., Komkham, P. & Pangsuk, B. (2017). Checklist of Echinoderms in Thailand. Bangkok: Office of Natural Resources and Environmental Policy and Planning. 150 pp. (in Thai)
Rodriguez, F., Oliver, J. L., Marin, A. & Medina, J. R. (1990). The general stochastic model of nucleotide substitution. Journal of Theoretical Biology, 142(4), 485-501.
Rozas, J., Ferrer-Mata, A., Sanchez-DelBarrio, J. C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S. & Sanchez-Gracia, A. (2017). DnaSP v6: DNA sequence polymorphism analysis of large datasets. Molecular Biology and Evolutions, 34, 3299-3302.
Skillings, D. J., Bird, C. E. & Toonen, R. J. (2014). Comparative population structure of two edible Indo-Pacific coral reef sea cucumbers (Echinodermata: Holothuroidea). Bulletin of Marine Science, 90(1), 359-378.
Soliman, T., Fernandez-Silva, I. & Reimer, J. D. (2016). Genetic population structure and low genetic diversity in the over-exploited sea cucumber Holothuria edulis Lesson, 1830 (Echinodermata: Holothuroidea) in Okinawa Island. Conservation Genetics, 17, 811-821.
Swofford, D. L. (2002). PAUP*-phylogenetic analysis using parsimony (*and other methods), Version 4.0b10. Sunderland, MA: Sinauer Associates.
Tamura, K. & Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512-526.
Tassanakajon, A. (2003). Genetic diversity and population structure of the black tiger shrimp, Penaeus monodon, in Thailand revealed by microsatellite markers. Journal of Research Methodology, 16(3), 359-373.
(in Thai)
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 24, 4876-4882.
Uthicke, S., Schaffelke, B. & Byrne, M. (2009). A boom–bust phylum? Ecological and evolutionary consequences of density variations in echinoderms. Ecological Monographs, 79, 3–24.
Wanna, W., Rolland, J.-L., Bonhomme, F. & Phongdara, A. (2004). Population genetic structure of Penaeus merguiensis in Thailand based on nuclear DNA variation. Journal of Experimental Marine Biology and Ecology, 311, 63-78.
Ward, R. D., Holmes, B. H. & O’ Hara, T. D. (2008). DNA barcoding discriminates echinoderm species. Molecular Ecology Resources, 8, 1202–1211.
Wen, J., Hu, C., Zhang, L. & Fan, S. (2011). Genetic identification of global commercial seacucumber species on the basis of mitochondrial DNA sequences. Food Control, 22, 72-77.
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2021-05-05
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