Genetic diversity in a unique population of dugong (Dugong dugon) along the sea coasts of Thailand

Abstract

Dugong (Dugong dugon) populations have been shrinking globally, due in large part to habitat fragmentation, degradation and ocean pollution, and today are listed as Vulnerable by the IUCN. Thus, determining genetic diversity in the remaining populations is essential for conservation planning and protection. In this study, measures of inter-simple sequence repeat (ISSR) markers and mtDNA D-loop typing were used to evaluate the genetic diversity of 118 dugongs from skin samples of deceased dugongs collected in Thai waters over a 29-year period. Thirteen ISSR primers revealed that dugongs from the Andaman Sea and Gulf of Thailand exhibited more genetic variation in the first 12 years of the study (1990–2002) compared to the last decade (2009–2019). Dugongs from the Andaman Sea, Trang, Satun and some areas of Krabi province exhibited greater diversity compared to other coastal regions of Thailand. Eleven haplotypes were identified, and when compared to other parts of the world (235 sequences obtained from NCBI), five clades were apparent from a total 353 sequences. Moreover, dugongs from the Andaman Sea were genetically distinct, with a separate haplotype belonging to two clades found only in Thai waters that separated from other groups around 1.2 million years ago. Genetic diversity of dugongs in present times was less than that of past decades, likely due to increased population fragmentation. Because dugongs are difficult to keep and breed in captivity, improved in situ conservation actions are needed to sustain genetically healthy wild populations, and in particular, the specific genetic group found only in the Andaman Sea.

Microsatellite Polymorphism and the Population Structure of Dugongs (Dugong dugon) in Thailand

“…From this study, dugongs from the Andaman Sea were shown to have higher genetic diversity than those in the Gulf of Thailand, similar to data from previous inter-simple sequence repeat (ISSR) [32] and microsatellite [57] studies. In 2013, the first report of microsatellite markers (60 dugongs in the sea of Thailand between 1982-2007) found animals in the northern Andaman Sea had more genetic diversity than those in the Gulf of Thailand.…”

“…The samples were processed using DNA extraction kits according to manufacturer's instructions (DNeasy Blood & Tissue Kit, Qiagen, Germany) at the Faculty of Veterinary Medicine, Chiang Mai University [32], and the DNA measured qualitatively and quantitatively by agarose gel electrophoresis and spectrophotometry, respectively [4].…”

“…PCR amplifications were performed in PTC-200 at DNA EngineThermal Cycler (Bio-Rad Laboratories, Inc., CA, USA) under the following conditions: 95 • C for 5 min, followed by 40 cycles of 95 • C for 30 s, 50 • C for 45 s, and 72 • C for 1 min with a final extension step at 72 • C for 10 min. The PCR products were stained [32] by REDSAFE Nucleic acid staining solution (iNtRON Biotechnology, Gyeonggi-do, South Korea) and then separated electrophoretically on 2% agarose gel (PanReac AppliChem ITW companies, Darmstadt, Germany) by PowerPac 200 (Bio-Rad, Hercules, CA, USA) containing 1X Tris-acetate-ethylenediaminetetraacetate (TAE) buffer at 120 V for 30 min. The PCR products were then visualized by UV light under a GELMAX 125Imager (UVP, Cambridge, England) [32].…”

“…The PCR products were stained [32] by REDSAFE Nucleic acid staining solution (iNtRON Biotechnology, Gyeonggi-do, South Korea) and then separated electrophoretically on 2% agarose gel (PanReac AppliChem ITW companies, Darmstadt, Germany) by PowerPac 200 (Bio-Rad, Hercules, CA, USA) containing 1X Tris-acetate-ethylenediaminetetraacetate (TAE) buffer at 120 V for 30 min. The PCR products were then visualized by UV light under a GELMAX 125Imager (UVP, Cambridge, England) [32]. A fragment analysis platform was used (3730XL-96 genetic analyzer; Thermo Fisher Scientific, Foster, CA, USA), performed by Ward Medic Ltd. Vadhana, BKK, Thailand.…”

“…Using mitochondrial DNA (mtDNA) sequences, Plon et al [31] found a 355 bp sequence in the D-loop that matched dugongs from Australia and Indonesia, and revealed several new and divergent mtDNA lineages in the Indian Ocean. Recently, a study from our group reported a unique genetic structure in dugongs found only in the Andaman Sea of Thailand [32]. In this study, tissue samples from dugongs stranded off the coast of Thailand during 1994-2019 were analyzed using microsatellite markers to provide more information on genetic diversity and population structuring in the region.…”