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
Diserahkan:
20 April 2015/Diterima: 30 Januari 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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*Pengarang
untuk surat-menyurat; email: physique481@yahoo.co.uk
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