Phylogeography and Demography of Common Plant Species from the Philippine Islands by Sandra L. Yap A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Ecology and Evolutionary Biology) in The University of Michigan 2010 Doctoral Committee: Associate Professor Robyn J. Burnham, Chair Assistant Professor Christopher W. Dick Assistant Professor Inés Ibáñez Research Scientist Anton Reznicek ! Sandra L. Yap 2010 I dedicate this dissertation to my family, Simplicio, Virgilia, Valerie, Sarah, Vivien, Vanessa, John Simon, and Vincent Rupert Yap !!" " Acknowledgements Finishing this dissertation would not have been possible without the unwavering support of my adviser, Robyn Burnham. Robyn helped me in countless ways from painstakingly reviewing my writing, to working out research problems by simply making me finish my thoughts out loud, and to giving me yoga advice so that I could relieve myself of stress. I’m even thankful for the Message Box. She truly went above and beyond, literally at 33,000 feet and figuratively. I’d also like to thank Chris Dick who generously shared his time, expertise, lab, and students to generate data, questions, and discussions. And to the other members of my thesis committee, Tony Reznicek and Ines Ibanez, thank you for asking me questions that helped refine my research. I am indebted to the Rackham Graduate School and the Ecology and Evolutionary Biology Department for furnishing me with grants to conduct my field research and molecular studies. I am also thankful for the support from the Barbour Scholarship allowing me time to focus on my dissertation. During the course of my time in Ann Arbor, I’ve made some incredible friends who’ve served as sounding boards, statistical consultants, editors, and most importantly, wonderful company at all times. My heartfelt thanks goes to Luis Fernando Chaves and Diego Alvarado Serrano who stuck it out with me until the very end; to Lan Nguyen, who made me follow the straight and narrow the first two years of graduate school; to Nicolas !!!" " Cabrera, who is still only a phone call away; to Susana Pereira for teaching me molecular techniques and sharing kartoffel- and Silvio’s pizza; the Burnham and Dick labs, Paul, Dave, Hope, Hoa, David, and others, for the daily company, lab meetings, and discussions; and to the multitude of people from LOTS and Beverly’s seminars through the years for cultivating a critical and inquisitive mind. I am also grateful to Leonard Co, who was the first to really introduce me to botany, ecology, and evolution. You are an inspiration. I thank my friend and colleague, Jean Molina, for the fun times in the field and for hashing out ideas; my friends, Mae, Hazel, Amber, for all the support through the years; my field assistant, Jun, for going where I went and doing the heavy lifting; and Dan, Jim, Stuart, and CI who all trusted that I could do my job, cheaply. Finally, I thank my family: my sister Vivien, for listening, commiserating, and believing in me; my parents, Virgilia and Simplicio Yap, for their unconditional support, prayers and sacrifice, and encouragement to pursue my interests even when those interests went beyond medicine; my other brothers and sisters Valerie, Sarah, Vanessa, Simon, and Vincent, also for their love, support, and constant phone calls; and, my cousins Marilyn, Ria, and Melissa Lim, for the fun, relaxing company during breaks from my research. "#! ! Table of Contents Dedication …………………………………………………………………………...….ii Acknowledgements …………………………………………………………………….iii List of Figures ……………………………………………………………………...….vi List of Tables ………………………………………………………………………......viii Abstract …………………………………………………………………………..…….x Introduction …………………………………………………………………………….1 Chapter 1. Origin, Evolution, and Future of the Philippine flora ……………………….14 2. Population genetics of endemic Philippine plants – patterns in Daemonorops mollis (Arecaceae) and Macaranga bicolor (Euphorbiaceae) ………………………………………………………..38 3. Hydrologic and topographic associations of a palm community in a lowland dipterocarp rainforest in the Philippines …………………73 4. Topography and species-habitat associations of the 30 dominant tree species in a tropical forest in the Philippines ……………………...103 5. Negative density dependence and dispersal limitation in dominant Philippine tree species……………………………………………………………...132 "! ! List of Figures Figure 1.1 Reconstruction of Southeast Asian geology at 50 Million years B.P. …………….30 1.2 Reconstruction of Southeast Asian geology at 45 Million years B.P. …………….30 1.3 Reconstruction of Southeast Asian geology at 25 Million years B.P. …………….31 1.4 Reconstruction of Southeast Asian geology at 5 Million years B.P. ……………...31 1.5 Present Day Southeast Asian geography. …………………………………………32 1.6 Wallace’s and Huxley’s Line ………………………………………….......……....32 2.1.a Map of the Philippines …………………………………………….. …………….61 2.1.b Pleistocene island groups formed at the Last Glacial Maximum...... …………….61 2.2 Phylogenetic and phylogeographic relationships of D. mollis haplotypes based on cpDNA variation of 906bp from rpl16 …………………………………………62 2.3 Phylogenetic and phylogeographic relationships of M. bicolor haplotypes based on the ITS region ……………………………………………………………..……63 2.4 Phylogenetic and phylogeographic relationships of M. bicolor haplotypes based on the trnQ region ……………………………………….…………………………63 2.5 Phylogenetic and phylogeographic relationships of M. bicolor haplotypes based on the combined ITS and trnQ regions ……………………………….……………64 2.6 Isolation by distance in D. mollis determined between geographic distance and genetic distance using Slatkin’s linearized FST…………….……………………66 2.7. Isolation by distance in M. bicolor determined between geographic distance and genetic distance using Slatkin’s linearized FST …………………………………66 3.1 Study site. Palanan Forest Dynamics Plot in NE Luzon Island, Philippines ……….94 3.2 Distribution maps of the 5 palm species surveyed ………………………………….95 "#! ! 3.3 Test for dispersion using Morisita’s Index …………………………………………96 3.4 Distribution map of the four elevation habitats……….…………………………….97 3.5 Distribution map of the four slope habitats……….…………..…………………….97 3.6 Distribution map of the two stream habitats……….……..…..……….…………….97 4.1 Elevational map of the PFDP ………………………………………………………119 5.1.a Ripley’s K graph of Shorea negrosensis saplings ……………………………….,145 5.1.b Ripley’s K graph of Shorea guiso saplings ………………………….………..….145 5.2 Hot spot maps showing areas with high densities of individuals (in red) and area with fewer individuals than expected from random chance (in blue) ………….……146 "##! ! List of Tables Table 2.1 Macaranga bicolor and Daemonorops mollis samples …….. …………….……….61 2.2 Molecular markers tested for variability with corresponding length of the region amplified and no. of variable sites………………………………………………62 2.3 Pairwise FST values of D. mollis from all sites…………………………………...…64 2.4 Pairwise FST values of M. bicolor from all sites ……………………………………65 2.5. AMOVA of the chloroplast DNA sequence, rpl16, in D. mollis………………...…65 2.6. AMOVA of the combined ITS and trnQ sequences in M. bicolor ………….……..65 2.7. Group composition and FCT values detected by SAMOVA in 9 populations of D. mollis from 6 Philippine Islands based on the chloroplast region, rpl16 ………67 2.8. Group composition and FCT values detected by SAMOVA in 8 populations of M. bicolor from 5 Philippine Islands based on chloroplast and nuclear DNA regions ………………………………………………………………………….68 3.1 Palm species in the PFDP…………………………………………………………..94 3.2 Degree of aggregation in the three age classes of four palm species ………………96 3.3 Habitat associations of five palm species …………………………………………..98 4.1 Top 30 species listed in alphabetical order, ranked based on importance value ….120 4.2 Habitat associations of the 30 dominant species in the PFDP …………………….122 4.3 Summary of positive and negative association counts for the three topographic features (elevation, stream, and slope) according to the three life stages (saplings, juveniles, and adults), per-sepcies, and growth form …………...….124 5.1 Top 30 dominant species in the PFDP, ranked according to IV with corresponding number of stems in each sapling (SA), juvenile (JU), and adult (AD) size class, and maximum stem diameter ……………………………………………...…..144 "###! ! 5.2 Spatial scales where clustering is greatest saplings, juveniles, and adults for each of the 30 dominant tree species in the PFDP ……………………………147 5.3 Correlation coefficients of 30 dominant tree species in Palanan, Philippines ……148 "#! ! ABSTRACT Phylogeography and Demography of Common Plant Species from the Philippine Islands by Sandra L. Yap Chair: Robyn J. Burnham Effects of historical and current environmental conditions on plant populations from the Philippine Archipelago are investigated. The complex geologic history of the Philippines creating a diverse and highly endemic flora is reviewed. Apart from tectonic activity, the islands were subjected to changes in topography, temperature, and precipitation from Pleistocene glacial and interglacial periods (Heaney, 1991). Comparative phylogeography is used to determine the effects of Pleistocene events on the population genetic structure of two endemic species, Daemonorops mollis (Arecaceae) and Macaranga bicolor (Euphorbiaceae). Limited variation and the distribution of unique haplotypes in both species suggest that during periods of lowered sea levels, rainforest habitats were maintained as refugia throughout the archipelago. A land barrier between eastern and