Sains Malaysiana 39(2)(2010): 209–218

Phylogeny of Sea Cucumber (Echinodermata: Holothuroidea) as Inferred from 16S Mitochondrial rrna Gene Sequences

(Filogeni Timun Laut (Echinodermata: Holothuroidea) Berdasarkan Jujukan Gen 16S Mitokondria rRNA)

Kamarul Rahim Kamarudin* & Ridzwan Hashim

Sea 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

Gires Usup

Marine Science Programme

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

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

Received: 13 October 2008 / Accepted: 4 September 2009

ABSTRACT

This study aimed to determine phylogenetic relationship between and among selected species of sea cucumbers (Echinodermata: Holothuroidea) using 16S mitochondrial ribosomal RNA (rRNA) gene. Phylogenetic analyses of 37 partial sequences of 16S mitochondrial rRNA gene using three main methods namely neighbour joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) showed the presence of five main genera of sea cucumbers: Molpadia from order Molpadiida and four genera of order Aspidochirotida namely Holothuria, Stichopus, Bohadschia and Actinopyga. All of the 17 species obtained from Malaysia distributed among the main genera except within Interestingly, Holothuria excellens was out of Holothuria group causing Holothuria to be paraphyletic. High bootstrap value and consistent clustering made Molpadia, Stichopus, Bohadschia and Actinopyga monophyletic. The relationship of with the other genera was unclarified and Stichopus was sister to Molpadia. The latter finding caused the resolution at order level unclear. The pairwise genetic distance calculated using Kimura 2-parameter model further supported and verified findings from the phylogenetic trees. Further studies with more samples and different mitochondrial DNA genes need to be done to get a better view and verification on the molecular phylogeny of sea cucumbers.

Keywords: Phylogenetic relationship; partial sequences of 16S mitochondrial ribosomal RNA gene; sea cucumbers

ABSTRAK

Kajian ini bertujuan untuk menentukan perhubungan filogenetik antara spesies-spesies terpilih timun laut (Echinodermata: Holothuroidea) dengan menggunakan gen subunit 16S mitokondria ribosom RNA (rRNA). Analisis filogenetik melibatkan 37 separa jujukan gen 16S mitokondria ribosom RNA yang menggunakan tiga kaedah utama iaitu kaedah hubung kait jiran (NJ), parsimoni maksimum (MP) dan kaedah hubung kait maksimum (ML) telah menunjukan kehadiran lima kumpulan utama timun laut iaitu Molpadia daripada order Molpadiida dan empat genus daripada order Aspidochirotida iaitu Holothuria, Stichopus, Bohadschia dan Actinopyga. Semua 17 spesies yang diperolehi dari Malaysia tergolong dalam kumpulan-kumpulan utama tersebut kecuali dalam kumpulan Penemuan paling menarik adalah Holothuria excellens tidak tergolong dalam kumpulan Holothuria menyebabkan Holothuria bersifat parafiletik. Nilai bootstrap yang tinggi dan pengkelasan yang konsisten menyebabkan Molpadia, Stichopus, Bohadschia dan Actinopyga bersifat monofiletik. Perhubungan genetik antara dengan genus yang lain tidak dapat diklarifikasikan dan Stichopus pula mempunyai hubungan genetik yang rapat dengan Molpadia dari order Molpadiida. Perhubungan kedua tersebut menyebabkan resolusi pada peringkat order adalah tidak jelas. Pengiraan jarak genetik secara berpasangan menggunakan model Kimura 2-parameter seterusnya telah menyokong dan mengesahkan keputusan-keputusan yang diperolehi daripada pokok-pokok filogenetik yang diperolehi. Kajian lanjut melibatkan bilangan sampel yang lebih banyak serta gen mitokondria DNA yang berbeza perlu dilakukan untuk mendapatkan gambaran serta pengesahan yang lebih baik terhadap filogeni molekul timun laut.

Kata kunci: Perhubungan filogenetik; separa jujukan gen 16S mitokondria ribosom RNA; timun laut

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*Corresponding author; email: physique481@yahoo.co.uk@yahoo.com