AsPac J. Mol. Biol. Biotechnol., Vol. 15 (1), 2007 Molecular Archeology 27 Asia Pacifc Journal of Molecular Biology and Biotechnology, 2007 Vol. 15 (1) : 27-31 *Author for Correspondence. Mailing address: School of Bioscience and Biotechnology, Faculty of Science and Technology 43600,Universiti Kebangsaan Malaysia, Selangor. Tel: 603-89213245 Email:hisham@cgat.ukm.my Molecular Archeology of Ancient Bone From 400 Year Old Shipwreck Shahrul Hisham Zainal Ariffn 1 , Rohaya Megat Abdul Wahab 3 , Zulkefie Zamrod 1 , Samsol Sahar 4 , Mohd Fauzi Abd Razak 1 , Eni Juliana Ariffn 1 And Sahidan Senaf 1 . 1 School of Bioscience and Biotechnology, Faculty of Science and Technology, UKM, Bangi, Selangor. 3 Department of Orthodontics, Faculty of Dentistry, UKM, Kuala Lumpur 4 Department of Museum and Antiquities Malaysia, Kuala Lumpur. Received 18 August 2006 / Accepted 14 December 2006 Abstract. Molecular archeology is a new frontier of ancient archeology. Studies involving molecular archeology can give extra information useful to interpret our past. Ancient DNA basically consists of small DNA fragments that survive for a very long period. This DNA can be used as a template to study molecular archeology. We were able to isolate ancient mitochondrial DNA (mtDNA) from bones that were recovered by the Department of Museum and Antiquity Malaysia during their Wanli’s shipwreck excavation project recently. The amount of recovered mtDNA was very small; extracted bone showed there was no DNA band after agarose electrophoresis. Amplifcation using PCR approach at D-loop I of human mitochondrial DNA was able to produce the amplifed DNA of 239bp in size. However, only 215 nucleic acids sequences were able to be confrmed when subjected to DNA sequencing procedures. Further analysis of the DNA sequenced of this amplifed DNA showed that 99% of the gener- ated sequenced was identical with D-loop region I of human mitochondrial DNA. The results showed that our procedure of DNA extraction although produces very low amount of DNA but yields pure DNA that can be used for further analysis such as PCR amplifcation and DNA sequencing. Keywords. ancient mitochondrial DNA, human bones, PCR amplifcation. IntrOductIOn Analysis of ancient DNA gives archeologists and anthropologists alternative and innovative ways to interpret and understand the past (Jones, 2003; Kaestle et al., 2002; O’Rourke et al., 2000.; Richards et al., 1995). The frst studies were done on Egyptian mummifed material by Paabo and colleagues in 1985 (Paabo, 1985). Molecular archeology has generated many new insights on important archeological and anthropological questions, encompassing human evolution, population affnities (Eshleman et al., 2003; Krings et al., 1997; Ovchinnikov et al., 2004; Stone et al., 1993) to domestication of animal and plant species (Brown et al., 1998; Vila et al., 2001). Two major hurdles in molecular archeology are the degradation of DNA over time and the contamination of ancient samples with modern DNA (Kaestle et al., 2002; Hofreiter et al., 2001; Taylor et al., 1996). Physical and chemical treatment during DNA extraction can further destroy DNA molecules that exist in the ancient remains. Therefore, the analysis of such DNA was not practical until the polymerase chain reaction (PCR) became available (Paabo, 1989). The PCR technique is essential for detecting ancient DNA molecules since the technique is extremely sensitive in detecting minute amounts of specifc DNA molecules and amplifying these molecules many times in a matter of hours (Innis et al., 1990; Yang and Watt, 2005). Damage of DNA templates and the presence of inhibitors may result in low effciencies or failure of the PCR amplifcation (Herrmann and Hummel, 1994; Yang et al., 2003). In order to overcome this problem, it is important to increase the effciency of PCR amplifcation. Yang et al. (1998) were able to amplify ancient mitochondrial DNA (mtDNA) from 2000 year old human skeletal remains from an Imperial Roman necropolis using hypersensitive PCR amplifcation, i.e. with a high number of PCR cycles. However, their approach utilized special DNA polymerase called AmpliTaq Gold TM making the procedure expensive (Yang et al., 1998). The Wanli was a trade ship believed to have sailed from China and sank in the 1630s during an attack by another trade ship. The shipwreck was discovered by Sten Sjostrand