PHYLOGEOGRAPHIC STRUCTURE OF CO- DISTRIBUTED, UPLAND LINEAGES OF FROGS AND SNAKES ACROSS MOUNTAIN TOPS IN PENINSULAR MALAYSIA. EVAN QUAH SENG HUAT UNIVERSITI SAINS MALAYSIA 2016 PHYLOGEOGRAPHIC STRUCTURE OF CO-DISTRIBUTED, UPLAND LINEAGES OF FROGS AND SNAKES ACROSS MOUNTAIN TOPS IN PENINSULAR MALAYSIA. By EVAN QUAH SENG HUAT Thesis submitted for the fulfillment of the requirements of the degree of Doctor of Philosophy April 2016 ACKNOWLEDGEMENTS First and foremost I would like to express my deepest gratitude towards my supervisor Prof. Shahrul Anuar Mohd Sah for his unfaltering support during the course of this study. I am also indebted to my field supervisor Prof. L.L. Grismer for his continued guidance and companionship in the field. To my co-supervisor Prof. Siti Azizah Mohd Nor, thank you for your kind generosity by allowing me to work in your lab to complete the molecular portion of my dissertation. For assistance in the field I would to thank Mr. Yusof Omar, Mohd. Abdul Muin and other field assistants at USM as well as friends over at Herpetology Lab, La Sierra University, USA. To my fellow labmates at Lab 308, thank you for the assistance when I encountered issues with the lab work. I am particularly grateful to Perry L. Wood Jr. from Brigham Young University for assistance with analyses and the interpretation of the data. In addition I would like to thank the many friends and collaborators that generously loaned me material for comparison including Kelvin Lim of the Lee Kong Chian Natural History Museum, Singapore; Noel Thomas of National Parks, Singapore; Patrick Campbell of the Natural History Museum, London and Alan R. Resetar of the Field Museum, Chicago. Many friends contributed pictures that tremendously improved my thesis and I would like to thank Kurt Orion G, Rupert G. Lewis, Tom Charlton, Steven Wong, Peter Engelen, Matthew Sánchez, Jerome Chua, Nick Baker, Konrad Merbert, Robert F. Inger, Chris Hay, Neoh Siew Peng and Amirah Hurzaid. Last but not least I am grateful for the support of my family especially my parents who have supported me in my pursuit of this degree. ii TABLE OF CONTENTS Page ACKNOWLEDGEMENTS………………………….…….……………...……..…ii TABLE OF CONTENTS………………………………….……………….....……iii LIST OF TABLES…………………………………...………..…………….………x LIST OF FIGURES……………………………..………………………....………xii LIST OF ABBREVIATIONS………………………………………..…......……xxii ABSTRAK……………………………………………………….……………….xxiii ABSTRACT……………………………………………………………….…....…xxv CHAPTER 1. INTRODUCTION………………………………….……...……..…1 1.1. Brief overview of the study………………………………………………..…1 1.2. The rationale and importance of this study…………………………………..8 1.3. Hypotheses of the study………………………………………...…...…….…8 1.4. Objectives of the study……………………………………………………….9 CHAPTER 2. LITERATURE REVIEW……………………………………...….10 2.1. History of montane herpetology in Peninsular Malaysia…………………...10 2.2. Geographical history of Sundaland shaping upland habitats…………….....21 2.3. Brief introduction to the study taxa………………………..……………….27 2.3.1. Metaphrynella pollicaris…………………………….....…………....27 2.3.2. Philautus petersi………………………………………….....………27 2.3.3. Philautus vermiculatus…………………………………………..…..28 iii 2.3.4. Macrocalamus………………………………………...……...……...29 2.3.5. Calamaria…...……………………………………..………...……...30 2.3.6. Popeia……………………………………………………..…...……31 CHAPTER 3. MATERIALS AND METHODS……………………………….....34 3.1. Sampling locations……………….…………………...………………….....34 3.1.1 Langkawi Island, Kedah….……………………………..…..……....34 3.1.2 Gunung Jerai, Kedah………………………...……………...….....…35 3.1.3 Penang Island, Penang………………………………………….…...36 3.1.4 Bukit Mertajam, Penang……………………………………..…...…38 3.1.5 Bukit Panchor, Penang……………………………………..……..…38 3.1.6 Sungai Enam, Belum, Perak………………………………..….……39 3.1.7 Bukit Larut, Perak………………………………………...……....…40 3.1.8 Cameron Highlands, Pahang………………………………...……....41 3.1.9 Fraser’s Hill, Pahang……………………………………...………....43 3.1.10 Genting Highlands, Pahang…………………………………..…......44 3.1.11 Gunung Ledang, Johor…………………………………...……...…..45 3.1.12 Gunung Stong, Kelantan………………………………...……...…...46 3.1.13 Gunung Tebu, Terengganu………………………………..……...…47 3.1.14 Tioman Island, Pahang………………………………………..…..…48 3.1.15 Republic of Singapore...……………………………………..………49 3.2. Field collections………….……………………………………...…….........49 3.3. Tissue extraction and preservation……......…………………………...…....51 3.4. DNA Extraction and Polymerase Chain Reactions (PCR) ………………...51 iv 3.4.1. DNA Extraction and PCR for cytochrome b gene (cyt b) in the snakes……………………………………………………………..…52 3.4.2. DNA Extraction and PCR for NADH dehydrogenase subunit 1 gene (ND1) in the frogs….………....………………………...…………...53 3.5. List of species used in the analyses….………………………..……..……...55 CHAPTER 4. PHYLOGENY OF THE FROGS METAPHRYNELLA POLLICARIS, PHILAUTUS VERMICULATUS AND P. PETERSI AS WELL AS SNAKES OF THE GENUS MACROCALAMUS, CALAMARIA AND POPEIA IN PENINSULAR MALAYSIA…………………………………….......74 4.1. Introduction…………………………………………….……………...……74 4.2. Materials and Methods………………………………………..…..……...…78 4.3. Results…………………………..…………………...…………………...…81 4.3.1. Molecular phylogeny of Metaphrynella………………………....….81 4.3.2. Molecular phylogeny of Philautus vermiculatus…….………....…...83 4.3.3. Molecular phylogeny of Philautus petersi…………...….....…..…....85 4.3.4. Molecular phylogeny of the genus Macrocalamus………...…..........87 4.3.5. Molecular phylogeny of the genus Calamaria…………………..….89 4.3.6. Molecular phylogeny of the genus Popeia………………….............92 4.4. Discussion………………………………………...………..………..…….95 4.4.1. Phylogeography of the frogs………………………………………...95 4.4.2. Phylogeography of the genus Macrocalamus……………………….96 4.4.3. Phylogeography of the genus Calamaria…………………………...99 4.4.4. Phylogeography of the genus Popeia……………………………...105 4.5. Affinities of unsampled taxa…………………..……………..…….........110 v 4.6. Taxonomic implications of genetic divergences, phylogenetic analyses and lineage divergence…………………..…….…………………………......112 4.7. Conclusion…………………..…………….……………………...……...113 CHAPTER 5. TAXONOMY, DISTRIBUTION AND NATURAL HISTORY OF THE FROGS METAPHRYNELLA POLLICARIS, PHILAUTUS VERMICULATUS AND P. PETERSI AS WELL AS SNAKES OF THE GENUS MACROCALAMUS, CALAMARIA AND POPEIA IN PENINSULAR MALAYSIA.…….……….…….………….……….…….………….……….…....114 5.1. Introduction………………….……………...…………………………......114 5.2. Materials and Methods………………….…………………………........…117 5.2.1. Morphological analysis……………………..…………..……...…..117 5.2.2. Designation of species-level lineages………………..……….…....119 5.3. Results………...…………….………………......…………………………120 5.3.1. Metaphrynella pollicaris (Boulenger)…..……………………...….120 5.3.2. Philautus vermiculatus (Boulenger)………………..……………...125 5.3.3. Philautus petersi (Boulenger)…..…………………….....................130 5.3.4. Snakes of the genus Collorhabdium, Macrocalamus and Oreocalamus (Squamata: Serpentes: Colubridae: Calamariinae) .……..……..….135 5.3.4.1. Oreocalamus hanitschi Boulenger….…………...…........…….135 5.3.4.2. Collorhabdium williamsoni Smedley.……..…………....…….139 5.3.4.3. Macrocalamus gentingensis Norsham & Lim.……..…….…...143 5.3.4.4. Macrocalamus jasoni Grandison.……..…………….......…….147 5.3.4.5. Macrocalamus lateralis Günther.……..………………...…….151 5.3.4.6. Macrocalamus schulzi Vogel & David.……..……………..….155 5.3.4.7. Macrocalamus tweediei Lim.……..………………...........……160 vi 5.3.4.8. Macrocalamus vogeli David & Pauwels.…….………...…..….164 5.3.4.9. Macrocalamus chanardi David & Pauwels.……..…………....167 5.3.4.10. Macrocalamus emas sp. nov. .……..…………………...….182 5.3.5. The reed snakes of the genus Calamaria (Squamata: Serpentes: Colubridae: Calamariinae) of Peninsular Malaysia …………….....199 5.3.5.1. Calamaria albiventer (Gray)………………………………….199 5.3.5.2. Calamaria ingeri Grismer, Kaiser & Norsham….…………....202 5.3.5.3. Calamaria lovii gimletti sensu lato Boulenger…….…..……...204 5.3.5.4. Calamaria lumbricoidea sensu lato Boie……...…….....…..…210 5.3.5.5. Calamaria pavimentata sensu lato Duméril, Bibron & Duméril. …..………..……..………………...……………………………217 5.3.5.6. Calamaria schlegeli sensu lato Duméril, Bibron & Duméril ………..…………..…………..……..…………………….........222 5.3.6. The pitvipers of the genus Popeia (Squamata: Serpentes: Viperidae: Crotalinae) of Peninsular Malaysia …………….……..………..….235 5.3.6.1. Popeia buniana Grismer, Grismer & Mcguire….……..…...…235 5.3.6.2. Popeia nebularis Vogel, David & Pauwels.……………......…238 5.3.6.3. Popeia fucata sensu lato Vogel, David & Pauwels.……….….244 5.4. Discussion…………………….………...……………….……………...…259 5.5. Conclusion…………………….…………………………..………………261 CHAPTER 6. BIOGEOGRAPHY OF THE FROGS METAPHRYNELLA POLLICARIS, PHILAUTUS VERMICULATUS AND P. PETERSI AS WELL AS SNAKES OF THE GENUS MACROCALAMUS, CALAMARIA AND POPEIA.. …..……………..…………..…………………………………………...263 6.1. Introduction………………..…………….…………………………….......263 vii 6.1.1. Geological and geomorphological influences of biogeography in Peninsular Malaysia………………..………...…………...……..…263 6.1.2. Historical biogeographical events influencing current biogeography………..…………..………….……………………....265 6.1.3. Climatic influences on biogeography………………………...........266 6.1.4. Structure of vegetation influencing biogeography.....……………...269 6.1.5. Anthropogenic impact on the environment influencing biogeography….…..………………..……………...……………….270 6.2. Materials and Methods...…….………………………………….…......…271 6.3. Results and Discussion…...…………….………………………..….…...271 6.3.1. Biogeography of the frogs…...……………..……………......…….271 6.3.2. Biogeography of the snakes of the genera Oreocalamus, Collorhabdium and Macrocalamus……………………....………..277 6.3.3. Biogeography of the genus Calamaria…...…………………..…....282