Sains Malaysiana 40(2)(2011): 125–133


Molecular Phylogeny of Holothuria (Mertensiothuria) leucospilota (Brandt 1835) as Inferred from Cytochrome C Oxidase I Mitochondrial DNA Gene Sequences

Filogeni Molekul Holothuria (Mertensiothuria) leucospilota (Brandt 1835) Berdasarkan Penjujukan Gen Sitokrom C Oksidase I Mitokondria DNA


Kamarul Rahim Kamarudin1,*, ‘Aisyah Mohamed Rehan2, Ridzwan Hashim2, Gires Usup3,

Hajar Fauzanahmad2, Mohd Hanafi Anua2 & Mohd Yamanidris2


1School of Biological Sciences (SBS), The University of Auckland

Private Bag 92019, Auckland 1142, New Zealand


2Sea Cucumber (Echinodermata: Holothuroidea)

Research Group Institute of Oceanography & Maritime Studies (INOCEM)

Kulliyyah of Science, International Islamic University Malaysia (IIUM)

Jalan Istana, Bandar Indera Mahkota, 25200 Kuantan, Pahang Darul Makmur, Malaysia


3Marine Science Programme

School of Environmental & Natural Resource Sciences, Faculty of Science & Technology

Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor D.E., Malaysia


Received: 5 November 2009 / Accepted: 16 June 2010




Holothuria (Mertensiothuria) leucospilota (Brandt 1835), white threads fish or locally known as bat puntil is currently considered as the most abundant sea cucumber species in Malaysia. This study aimed to generate the genetic profile of H. leucospilota from Malaysia and then to determine the phylogenetic relationship between H. leucospilota and other members of genus Holothuria using partial sequences of cytochrome c oxidase I (COI) mitochondrial DNA (mtDNA) gene. In this study, specimens of H. leucospilota were collected from Intan Besar Island, Langkawi, Kedah Darul Aman in the west coast of Peninsular Malaysia. Three main methods namely neighbour joining, maximum parsimony and maximum likelihood were used for the phylogenetic tree reconstruction. Tree topologies showed that H. leucospilota has its own monophyletic clade clearly distinct from the other species. The pairwise genetic distance calculated further supported these findings. In addition, the results also should that the COI mtDNA gene is capable to unravel the phylogenetic relationship of H. leucospilota.


Keywords: Holothuria leucospilota; molecular systematics; partial sequences of cytochrome oxidase I gene; phylogeny tree




Holothuria (Mertensiothuria) leucospilota (Brandt 1835) atau nama tempatannya bat puntil kini dianggap sebagai spesies timun laut yang paling banyak taburannya di Malaysia. Kajian ini bertujuan untuk mendapatkan profil genetik H. leucospilota dan seterusnya menentukan perhubungan filogenetik antara H. leucospilota dari Malaysia dan ahli-ahli lain daripada genus Holothuria menggunakan jujukan separa gen sitokrom c oksidase I (COI) mitokondria DNA (mtDNA). Dalam kajian ini, spesimen H. leucospilota diperolehi dari Intan Besar Island, Langkawi, Kedah Darul Aman di pantai barat Semenanjung Malaysia. Tiga kaedah iaitu kaedah hubungkait jiran, parsimoni maksimum dan kaedah hubungkait maksimum telah digunakan untuk pembinaan pohon-pohon filogenetik Topologi pohon menunjukkan H. leucospilota mempunyai klusternya sendiri yang monofiletik yang jelas berbeza daripada spesies-spesies yang lain. Pengiraan jarak genetik secara berpasangan seterusnya telah menyokong keputusan-keputusan tersebut. Di samping itu, keputusan kini juga menunjukkan bahawa gen COI mtDNA mempunyai kapasiti untuk merungkaikan perhubungan filogenetik H. leucospilota.


Kata kunci: Sistematik molekul; Holothuria leucospilota; jujukan separa gen sitokrom c oksidase I mitokondria DNA, pohon filogen




Amos, B. & Hoelzel, A.R. 1992. Application of Molecular Genetic Techniques to The Conservation of small populations. Biological Conservation 61: 133-144.

Brandt, J.F. 1835. Prodromus descriptionis animalium ab H. Meriensio in orbis terrarium circumnavigatione observatorum. Fasc. 1. Petropoli: p. 11-75.

Felsenstein, J. 1984. Distance methods for inferrinf phylogenies: A justification. Evolution 38: 16-24.

Felsenstein, J. 2004. “PHYLIP”, Phylogeny Inference Package, version 3.6b (beta release). Seattle, WA: Department of Genome Sciences, University of Washington.

Hartl, D.L. & Clark, A.G. 1989. Principles of Population Genetics. 2nd ed. Massachusetts, USA: SinauerAssociates, Inc.

Hashim, R.B. 1993. Sumber Makanan Persisiran Laut Sabah. Kuala Lumpur: Dewan Bahasa dan Pustaka, p. 309.

Jaeger, G.F. 1833. De Holothuriis. Disssertatio Inauguralis. Turici: p. 1-40.

Kamarudin, K.R., Rehan, Lukman, A.L., Ahmad, H.F., Anua, M.H., Nordin, N.F.H., Hashim, R., Hussin, R. & Usup, G. 2009. Coral Reef Sea Cucumbers in Malaysia. Malaysian Journal of Science 28(2): 171-186.

Kamarudin, K.R., Hashim, R. & Usup, G. 2010. Phylogeny of Sea Cucumber (Echinodermata: Holothuroidea) as Inferred from 16S Mitochondri rRna Gene Sequences, Sains Malaysiana 39(2): 209-218.

Lambert, P. 1997. Sea Cucumbers of British Columbia, Southeast Alaska and Puget Sound. British Columbia: UBC Press.

Lesson, R.P. 1830. Centurie Zoologique on Choix D’animaux Rares, Nauveaux ou Inparfaitement Connus. Paris: Levrault, p. 1-244.

O’loughlin, P.M., Paulay, G., Vandenspiegel, D. & Samyn, Y. 2007. New Holothuria species from Australia (Echinodermata: Holothuroidea: Holothuriidae), with comments on the origin of deep and cool holothuriids. Memoirs of Museum Victoria 64: 35-52.

Page, R.D.M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358.

Palumbi, S., Martin, A., Romano, S., McMillan, W.O., Stice, L. & Grabowski, G. 1991. The Simple Fool’s Guide To PCR. Honolulu: Department of Zoology and Kewalo Marine Laboratory, Universiti of Hawaii.

Samyn, Y., VandenSpiegel, D. & Massin, C. 2006. Taxonomie des holothuries des Comores. Belgium: Abc Taxa, vol 1, i-iii, p. 130.

Semper, C. 1868. Reisen in Archipel der Philippinen, Holothurien. 2. Wissenschaftliche Resultate. Erster Band. Holothurien Heft iv. & V. Wilhelm engelmann. Leipzig: 1-288.

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 the quality analysis tools. Nucleic Acids Res. 24: 4876-4882.


*Corresponding author; email: