Biodiversity in Forests of the Ancient Maya Lowlands and Genetic Variation in a Dominant Tree, Manilkara zapota (Sapotaceae): Ecological and Anthropogenic Implications by Kim M. Thompson B.A. Thomas More College M.Ed. University of Cincinnati A Dissertation submitted to the University of Cincinnati, Department of Biological Sciences McMicken College of Arts and Sciences for the degree of Doctor of Philosophy October 25, 2013 Committee Chair: David L. Lentz ABSTRACT The overall goal of this study was to determine if there are associations between silviculture practices of the ancient Maya and the biodiversity of the modern forest. This was accomplished by conducting paleoethnobotanical, ecological and genetic investigations at reforested but historically urbanized ancient Maya ceremonial centers. The first part of our investigation was conducted at Tikal National Park, where we surveyed the tree community of the modern forest and recovered preserved plant remains from ancient Maya archaeological contexts. The second set of investigations focused on genetic variation and structure in Manilkara zapota (L.) P. Royen, one of the dominant trees in both the modern forest and the paleoethnobotanical remains at Tikal. We hypothesized that the dominant trees at Tikal would be positively correlated with the most abundant ancient plant remains recovered from the site and that these trees would have higher economic value for contemporary Maya cultures than trees that were not dominant. We identified 124 species of trees and vines in 43 families. Moderate levels of evenness (J=0.69-0.80) were observed among tree species with shared levels of dominance (1-D=0.94). From the paleoethnobotanical remains, we identified a total of 77 morphospecies of woods representing at least 31 plant families with 38 identified to the species level. A significant proportion of trees used by the ancient Maya remain as dominant species in the forest today but no associations were detected based on economic value. Manilkara zapota was previously hypothesized to have been cultivated by the ancient Maya. We used seven original nuclear microsatellite markers as well as two primer sets identified in a related species to discern whether the influences of ancient Maya management were evident in ii modern populations. We characterized genetic variation and structure in populations of M. zapota from Tikal and from home gardens in Guatemala, as well as from two other ancient Maya sites in Belize (Chawak But′o′ob and La Milpa), and a group of clonally propagated cultivars. Levels of genetic variation were higher in forest and garden populations (HO=0.50) than in cultivated varieties of M. zapota (HO=0.40) and were more similar to Neotropical timber trees than Neotropical fruit trees. Excess homozygosity was detected, consistent with a history of inbreeding (f=0.118) and successive population bottlenecks. In contrast, low population sub- structuring (θ=0.007) was observed between sites 90 km apart, attributed in large part to high gene flow. We explored whether populations of M. zapota might be rebounding from historic bottlenecks in recently protected forest regions by examining changes in genetic variation and structure across multiple size classes, representing life history stages ranging from sapling to adult. No significant differences in genetic variation nor population differentiation were detected as a function of size classes within or among populations from the three ancient Maya sites. Overall patterns of heterozygote deficiency remained relatively consistent across all size classes. Parentage analyses supported the potential for high gene flow that had previously been indicated by low levels of population genetic structure and animal dispersal patterns. iii Copyright by Kim M. Thompson 2013 All Rights Reserved iv This dissertation is dedicated to my children: Erin Ruth Thompson Stanforth Benjamin Joseph Thompson Stanforth who are a continual source of inspiration and pride! Thank you for your support. Manilkara zapota on an ancient Maya house site at Tikal National Park, Guatemala. Photo by the author v vi ACKNOWLEDGEMENTS It takes a village to raise a dissertation from concept to completion. Those who contributed to my success include a stellar Research Advisory Committee (RAC), dedicated graduate and undergraduate students in Biology and Anthropology, generous faculty members outside of my RAC, international researchers studying the ancient Maya, seasoned professionals at herbaria and botanical gardens, and hard-working local assistants and friendly gardeners from Guatemala and Belize. I use the term “we” throughout this manuscript because of the many valuable contributions to this project, in the field, in the lab, with data analysis and in the editing process. Funding from organizations supporting student research was essential and special thanks go to The Garden Club of America and Botanical Society of America for external grants. Specific contributions to each part of the project are recognized in the acknowledgments at the ends of Chapters 2 and 3. My Research Advisory Committee included David Lentz, Theresa Culley, Vernon Scarborough, Nicholas Dunning, Steven Rogstad and Regina Baucom. I am grateful for the knowledge that each of them shared and challenges they presented to facilitate my training as a scientist. There were a few disappointments along the way, including never receiving the long anticipated 450 samples that were collected for me in Calakmul, monomorphic chloroplast markers, and poor extraction from seeds after spending long and late hours in the lab. But problems seem to be an inevitable part of the process and my RAC helped me to weather these and appreciate what I had accomplished. I am grateful to David for involving me in the international project at Tikal, giving me many opportunities for professional growth, providing the training I needed to succeed, and celebrating my accomplishments. His flexibility in letting me work outside of his lab to take on a vii genetic study furthered my skills as a botanist as well as our understanding of the issues presented here. David also gave me the idea to work on Manilkara zapota, a tree for which I now have great appreciation. Theresa has been a valued mentor since my undergraduate studies and has been incredibly generous in her support of my genetic work in an already very busy lab. She also trusted me to take over her Medical Botany course for a quarter because she knew teaching was important to me. Her guidance, training, support and friendship have been invaluable to my success in this program. Vern Scarborough was instrumental in obtaining funding so that graduate students could stay involved in the Tikal project during a second field season and has always championed my research efforts. Nick Dunning first demonstrated the sounds of a howler monkey, as we traveled to Guatemala, so that I would be well informed in the field. He has been generous with sharing his resources on ancient Maya agriculture. Steve Rogstad’s classes gave me a solid background in botany and tropical ecology and I valued his insights when we met to discuss questions I had regarding my project. Gina Baucom gave valuable feedback on the written portion of my candidacy exam, which guided future efforts in presenting my project, and assured me that I had enough data to finish this dissertation. I have appreciated the collaborative environment of scientists at the University of Cincinnati as I worked through this process of earning a PhD. Brian Kinkle was the Graduate Director when I started at UC and he continued to offer helpful advice and support throughout my tenure here. Steve Matter was available whenever I needed assistance in talking through statistical issues. Dennis Grogan and Julie Stacey generously helped me to create an exciting lab on Microbiology for a Summer Bridge course. There have many graduate students who shared this experience with me but I especially want to thank Angie Hood, Susan Jaconis and Brian Lane who shared field work as well as friendship and Megan Philpott, my first undergraduate mentee who later joined viii the Culley lab. Thanks also to Dana Cavallero who helped with identifying and mounting for SEM the paleoethnobotanical remains and to Michael Hickey for continuing the wetland project I initiated in my undergraduate research with Theresa Culley and Mike Miller. To all the members of the Culley lab who offered me advice and support throughout my genetics project, I offer my thanks. Undergraduate researchers have been instrumental in bringing this project to completion and each of these enthusiastic workers are recognized at the end of the chapters to which they contributed. I feel privileged to have joined a vibrant community of scientists, botanists and educators, from the people I met at conferences who generously shared their insights and ideas to those who shared work in the field and lab. Special thanks to an extraordinary archaeologist, Liwy Grazioso, my roommate in Guatemala who became a friend and colleague. Meeting Nick Brokaw in Belize was a blessing as he included me in his trips to Chawak But′o′ob and offered valuable insights on the ecology of the region. Fred Valdez ensured my success in collecting leaves in Belize by recommending me for funding, procuring a place for me at the Richard E.W. Adams Research Facility, operated by the Programme for Belize Archaeology Project (PfBAP), and coordinating assistance in the field. Finally, I thank the many friends and family members whose loving support ensured my success. Deb Westheimer, Debbie Frankenhoff, John Brockman, Dianne Frick, Susan and Jim Vogt, Rhonda Whitten, Sylvia Hadley, and Cliff Steele have seen me through many changes, offered a sympathetic ear, expressed genuine interest in my work, and provided practical support when I most needed it; their friendship has meant the world to me. My father, John Thompson, instilled in me a strong respect for education and he and his wife, Mary, have cheered me on in this endeavor.