BIODIVERSITAS ISSN: 1412-033X Volume 20, Number 11, November 2019 E-ISSN: 2085-4722 Pages: 3352-3357 DOI: 10.13057/biodiv/d201131 Phylogenetic position of Javan banteng (Bos javanicus javanicus) from conservation area in Java base on mtDNA analysis MARYATUL QIPTIYAH 1,2, , SATYAWAN PUDYATMOKO 2, , AYPBC WIDYATMOKO 2 , ILG NURTJAHJANINGSIH 2 , MUHAMMAD ALI IMRON 2 1 Faculty of Forestry, Universitas Gadjah Mada University. Jl Agro No.1, Bulaksumur, Sleman 55281, Yogyakarta, Indonesia. Tel.: +62-274- 550541,  email: maryatulqiptiyah@biotifor.or.id;  spudyatmoko@ugm.ac.id 2 Center for Biotechnology and Tree Improvement Research and Development. Jl. Palagan Tentara Pelajar Km 15, Purwobinangun, Pakem, Sleman 55582, Yogyakarta, Indonesia Manuscript received: 2 September 2019. Revision accepted: 28 October 2019. Abstract. Qiptiyah M, Pudyatmoko S, Widyatmoko AYPBC, Nurtjahjaningsih ILG, Imron MA. 2019. Phylogenetic position of Javan banteng (Bos javanicus javanicus) from conservation area in Java base on mtDNA analysis. Biodiversitas 20: 3352-3357. Two of three subspecies of banteng (B. javanicus) can be found in Indonesia, namely B. j. lowi and B. j. javanicus. The taxonomic assignment of the two subspecies is still in the discussion researchers currently. One of the reproductive characters of members the Bovidae family, including the banteng, is known to have interbreeding ability between species and can produce fertile offspring. In some places, there exist grazing cattle near or in the banteng’s natural habitat. This phenomenon aimed to provide banteng mates with cows, which later they will breed high-quality offsprings. Regarding interbreeding capability, this condition can be a threat to the genetic purity of wild banteng. The main objectives of this study were to identify the phylogenetic position of Javan banteng from conservation areas in Java in relation to the other taxon and detect their genetic purity. We analyzed 28 cytochrome b and d-loop region sequences of Javan banteng from feces materials of four conservation areas (Ujung Kulon National Park, Alas Purwo National Park, Meru Betiri National Park, and Baluran National Park). We compared our data with reference sequences data of the other Bovidae species and Capra hircus as outgroup. The reference data was taken from NCBI, and they were analyzed using maximum likelihood. The results showed that Javan banteng was in a different group from other taxa. Separation of subspecies B. j. javanicus and B. j. lowi occurred circa 1.25 mya. The results from this study suggested that there is no indication of genetic introgression between Javan banteng and the (domesticated) cattle. Keywords: Bovidae, cytochrome b, d-loop, Javan banteng INTRODUCTION Banteng (Bos javanicus d’Alton, 1826) is divided into three subspecies, namely, Bos javanicus birmanicus that is found in mainland of Asia; Bos javanicus lowi which is scattered in many parts of Kalimantan mainland; and Bos javanicus javanicus which is found in some locations in Java island (Hogerwerf 1970; Gardner et al. 2014; Castello 2016). The current distribution of Javan banteng (B. j. javanicus) in the Java island can be grouped into two regions, namely, in the western region of Java, i.e., Ujung Kulon National Park (UKNP) and the eastern region, i.e., Meru Betiri National Park (MBNP), Baluran National Park (BNP) and Alas Purwo National Park (APNP) (Hakim et al. 2015). The Bornean banteng (B. j. lowi) spread mostly in Kutai NP and Kayan Mentarang NP. In general, wild banteng is often found in semi-open forests with grasslands (Garsetiasih 2013; Matsubayashi et al. 2014; Gardner et al. 2014) and mineral source such as shoreline or saltlick sources area (Hoogerwerf 1970; Whitten et al. 1996; Hedges and Meijaard 1999; Imron et al. 2016). The taxonomic position of two banteng groups (B. j. javanicus and B. j. lowi) from Indonesia is still unclear (Timmins et al. 2008). Based on morphological characters, the body size of the Bornean banteng was smaller than the other subspecies (Hogerwerf 1970; Matsubayashi et al. 2014; Castello 2016). Several habitats of banteng in conservation areas in the Java island has a serious threat, such as, the existence of settlements that are too close to the protected area (Sutarno and Setyawan 2016). Such situations occur in Meru Betiri NP, which has plantation areas and settlements within (enclaves), and it is also used as a Javan banteng habitat (Garsetiasih 2012). In BNP there are some people raising livestock without cage and using grazing areas in the territory of the national park (Pudyatmoko et al. 2018). Subspecies B. j. birmanicus are found to lived sympatrically with gaur (B. frontalis) and kouprey (B. sauveli) groups in Cambodia (Hassanin and Ropiquet 2007). Indonesia’s Bornean banteng (B. j. lowi) in feeding ground of Long Tua, Kayan Mentarang NP, North Kalimantan, have been reported to live with cattle until 1992 (Hedges and Meijard 1999). Such condition of wild banteng habitats that were being too close to feral herd domestic cattle raises a concern about the genetic purity of banteng. This concern is supported by the fact that the Bovidae group has excellent potential for interbreeding between species in the same genus (Martojo 2012). The Cambodian banteng (B. j. birmanicus) have interbred with domesticated cattle around the area, and it resulted in