Sains Malaysiana 45(7)(2016): 1079–1087

Phylogenetic Relationships within the Genus Holothuria Inferred from 16S Mitochondiral rRNA Gene Sequences

(Hubungan Filogenetik dalam Genus Holothuria berdasarkan

Jujukan Gen 16S Mitokondria rRNA)

KAMARUL RAHIM KAMARUDIN¹*, 'AISYAH MOHAMED REHAN², RIDZWAN HASHIM³,

GIRES USUP⁴ & MARYAM MOHAMED REHAN¹

¹Food Biotechnology, Faculty of Science and Technology, Universiti Sains Islam Malaysia (USIM), Bandar Baru Nilai, 71800 Nilai, Negeri Sembilan Darul Khusus, Malaysia

²Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Jalan Istana, Bandar Indera Mahkota, 25200 Kuantan, Pahang Darul Makmur, Malaysia

³Department of Biomedical Science, Kulliyyah of Allied Health Sciences, International Islamic University Malaysia (IIUM), Jalan Istana, Bandar Indera Mahkota, 25200 Kuantan,

Pahang Darul Makmur, Malaysia

⁴Marine Science Programme, School of Environmental & Natural Resource Sciences, Faculty of Science & Technology, Universiti Kebangsaan Malaysia (UKM), 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

Received: 20 April 2015/Accepted: 30 January 2016

ABSTRACT

This study aimed to resolve the taxonomic status of a morphologically undetermined sea cucumber species of order Apodida from Malaysia (GenBank accession no.: FJ223867) using partial 16S mitochondrial rRNA gene sequences and subsequently to determine the validity of morphological taxonomy of Holothuria species into its current subgenera. The undetermined species clustered with all taxa of Holothuria in previous study. Phylogenetic analyses using maximum parsimony and Bayesian methods suggest that the undetermined species was genetically closer to Holothuria (Lessonothuria) pardalis and Holothuria (Acanthotrapeza) coluber; and its position in both phylogenetic trees further suggests its status as a Holothuria taxon. Subgenera of Holothuria, Merthensiothuria and Metriatyla are monophyletic with strong bootstrap supports and posterior probabilities of clades, thus strengthening their morphological taxonomies. Nonetheless, the non-monophyly of subgenera of Halodeima, Microthele and Platyperona suggests a requirement for their taxonomic revisions using integrative taxonomy. The status of Holothuria (Halodeima) edulis subgroups in the maximum parsimony and Bayesian trees is indistinct and further taxonomic revisions are necessary. In terms of sister relationship, both phylogenetic trees suggest that subgenus Holothuria is a sister taxon of subgenus Roweothuria while the other sister relationships were unclear due to the undetermined species, paraphyly and polyphyly of a number of subgenera. Further studies with more specimens of genus Holothuria from broader geographical locations and various mtDNA genes along with morphological approaches may facilitate to provide better insights into the molecular phylogeny of subgenera of Holothuria.

Keywords: Bayesian inference; Holothuria; partial sequences of 16S mitochondrial ribosomal RNA gene; phylogenetic relationship

ABSTRAK

Kajian ini bertujuan untuk merungkai status taksonomi satu spesies timun laut daripada order Apodida dari Malaysia yang tidak dapat ditentukan status spesiesnya secara morfologi (no akses GenBank: FJ223867) menggunakan jujukan separa gen 16S mitokondria ribosom RNA dan menentukan kelangsungan taksonomi morfologi spesis Holothuria ke subgenus semasanya. Kajian sebelum ini menunjukkan timun laut daripada order Apodida membentuk kluster bersama-sama dengan takson genus Holothuria. Analisis filogenetik menggunakan kaedah hubung kait maksimum dan Bayes mencadangkan spesies timun laut daripada order Apodida yang tidak dapat ditentukan spesiesnya adalah amat rapat secara genetik dengan Holothuria (Lessonothuria) pardalis and Holothuria (Acanthotrapeza) coluber; dan kedudukannya dalam kedua-dua pohon filogeni tersebut selanjutnya mencadangkan statusnya sebagai takson Holothuria. Subgenus Holothuria, Merthensiothuria dan Metriatyla adalah monofiletik dengan sokongan ikatan but yang kuat, seterusnya menyokong kuat pengelasan taksonomi subgenus berdasarkan morfologi. Walau bagaimanapun, ketidakmonofili subgenus Halodeima, Microthele dan Platyperona mencadangkan perlunya semakan taksonomi menggunakan taksonomi berintegratif. Status subkumpulan Holothuria (Halodeima) edulis yang tidak jelas pada pohon-pohon filogenetik hubung kait maksimum dan Bayes memerlukan semakan taksonomi lanjutan. Berdasarkan perhubungan rapat, kedua-dua pohon filogenetik mencadangkan subgenus Holothuria adalah amat rapat secara genetik kepada subgenus Roweothuria sementara perhubungan yang lain adalah tidak jelas disebabkan spesies yang tidak dapat ditentukan status taksonomi, parafili dan polifili beberapa subgenus. Kajian lanjut melibatkan lebih banyak specimen Holothuria dari lokasi geografi lebih luas dan pelbagai gen mitokondria DNA selari dengan pendekatan morfologi mungkin boleh membantu memberikan gambaran lebih jelas tentang filogeni molekul subgenus Holothuria.

Kata kunci: Holothuria; pendekatan Bayes; perhubungan filogenetik; separa jujukan gen 16S mitokondria ribosom RNA

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