Sains Malaysiana 46(12)(2017): 2251–2261

http://dx.doi.org/10.17576/jsm-2017-4612-01

 

Population Genetic Analysis of Oceanic Paddle Crab (Varuna litterata) in Thailand

(Analisis Populasi Genetik Ketam Meranduk Laut (Varuna litterata) di Thailand)

JUTHAMAS SUPPAPAN1, JAMJUN PECHSIRI1, SOMPONG O-THONG1, ARUNRAT VANICHANON1, PRADIT SANGTHONG2 & VERAKIAT SUPMEE3*

 

1Biotechnology Program, Faculty of Science, Thaksin University, Phattalung Campus

Phattalung 93100, Thailand

 

2Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand

 

3Department of Science, Faculty of Science and Technology, Rajamangala University of Technology Srivijaya, Nakhon Si Thammarat Campus, Nakhon Si Thammarat, 80110 Thailand

 

Received: 7 August 2016/Accepted: 22 May 2017

 

ABSTRACT

Population genetic structure of Varuna litterata living along the coast of Thailand were examined in this study. The samples were collected from 3 coastal regions: The Andaman sea (Satun, Trang, Phang Nga), the lower Gulf of Thailand (Pattani, Songkhla, Nakhon Si Thammarat) and the upper Gulf of Thailand (Petchburi, Samut Songkram, Rayong, Trat). Intraspecific variation was determined based on partial sequences of the cytochrome oxidase subunits I gene. A total of 182 samples were collected but only 32 haplotypes were obtained from these samples. An excess of rare haplotypes indicated that the female effective population size of V. litterata living along the coast of Thailand is large. Estimated values of haplotype diversity and nucleotide diversity were 0.790 and 0.003, respectively. The AMOVA (analysis of molecular variance) and phylogenetic analysis results showed that based on genetic variation, the population of this organism was found to have 2 genetically different populations: The Andaman sea population and the Gulf of Thailand population. Genetic exchange of V. litterata among populations inhabiting along the coast of Thailand could be described by the stepping stone model. The results of neutrality tests, both Tajima's D and Fu's Fs statistics, yielded negative values (-1.992 and -26.877, respectively) and statistically significant deviation from the neutrality, indicating that the V. litterata living along the Thailand coast had experienced population expansion. Mismatch distribution analysis indicated that a possible expansion occurred 211,428 years ago during the Pleistocene glaciations period.

 

Keywords: COI gene; genetic diversity; grapsid crab; mitochondrial DNA

 

ABSTRAK

 

Struktur populasi genetik Varuna litterata yang hidup di sepanjang pesisir pantai di Thailand telah dikaji. Sampel dikumpul daripada tiga rantau pesisir pantai: Laut Andaman (Satun, Trang, Phang Nga), bahagian bawah Teluk Thailand (Pattani, Songkhla, Nakhon Si Thammarat) dan di bahagian atas Teluk Thailand (Petchburi, Samut Songkram, Rayong, Trat). Variasi intraspesies ditentukan berdasarkan urutan separa subunit sitokrom oksidase gen I. Sejumlah 182 sampel telah diambil tetapi hanya 32 haplotip telah diperoleh daripada sampel tersebut. Lebihan haplotip langka menunjukkan saiz populasi betina V. litterata yang berkesan hidup di sepanjang Pantai di Thailand adalah besar. Anggaran nilai kepelbagaian haplotip dan kepelbagaian nukleotida masing-masing adalah 0.790 dan 0.003. Keputusan AMOVA (analisis molekul varians) dan analisis filogeni menunjukkan bahawa berdasarkan variasi genetik, populasi organisma ini didapati mempunyai dua populasi genetik berbeza: Populasi Laut Andaman dan Teluk Thailand. Pertukaran genetik V. litterataantara populasi yang mendiami di sepanjang Pantai Thailand dapat diterangkan dengan model batu loncatan. Ujian keputusan berkecuali, kedua-dua statistik D Tajima dan Fs Fu masing-masing menghasilkan nilai negatif (-1.992 dan -26.877) dan signifikan secara statistik sisihan daripada yang berkecuali, menunjukkan bahawa V. litteratayang hidup di sepanjang Pantai Thailand telah mengalami pengembangan populasi. Analisis pengagihan tak sepadan menunjukkan potensi pengembangan berlaku di 211,428 tahun yang lalu semasa tempoh Pleistocene glaciations.

 

Kata kunci: DNA mitokondrium; gen COI; kepelbagaian genetik; ketam grapsid

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*Corresponding author; email: audy422r@yahoo.com