Pertanika J. Trop. Agric. Sci. 35 (3): 485 - 510 (2012) ISSN: 1511-3701 © Universiti Putra Malaysia Press TROPICAL AGRICULTURAL SCIENCE Journal homepage: http://www.pertanika.upm.edu.my/ Article history: Received: 20 May 2010 Accepted: 14 September 2011 ARTICLE INFO E-mail addresses: rchaya84@gmail.com (Tingga, R. C. T.), tabbulla@frst.unimas.my (Abdullah, M. T.) * Corresponding author Phylogeny and Phylogeography of Aethalops from Sundaland using Mitochondrial 12S rRNA Gene Tingga, R. C. T. 1, 2 * and Abdullah, M. T. 1 1 Molecular Ecology Laboratory, Department of Zoology, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia 2 Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia ABSTRACT One of the smallest fruit bats in Pteropodidae is Aethalops. This genus is known to be conined in montane forest, which is generally above 1000 meters above sea level (m.a.s.l.). Bornean Aethalops is generally known as Aethalops alecto in most previous literature. This study aimed at constructing the phylogenetic relationship of A. alecto and A. aequalis in Sundaland and determining gene low within Bornean A. aequalis using partial mitochondrial 12S rRNA gene. Seven populations of A. aequalis, representing Sabah and Sarawak and a single population from Kalimantan were observed, whereas A. alecto were represented by four populations from Indonesian islands. From the phylogenetic analyses and minimum spanning network, there were two major clusters within the genus, with Aethalops. A. aequalis in Borneo were clearly distinguished from A. alecto from the islands of Indonesia. However, phylogenetic analyses within A. aequalis were unresolved at the population levels in Sabah and Sarawak. Therefore, it can be concluded that A. aequalis is the species found only in Borneo. High genetic similarities were detected among the populations of A. aequalis in Sabah and Sarawak. Hypothetically, the Kalimantan harbors ancestral populations of A. aequalis in Borneo, with high genetic divergence from Sabah and Sarawak populations. Keywords: Aethalops, populations, phylogeny, phylogeography, Sundaland, 12S rRNA INTRODUCTION The montane bat Aethalops is among of the smallest Old World fruit bat (Pteropodidae), which is also known as Pigmy Fruit Bat or tailless fruit bat. Aethalops is conined in the montane forest above 1000 m (Payne et