Disentangling the Coevolutionary Histories of Animal Gut Microbiomes The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Sanders, Jon G. 2015. Disentangling the Coevolutionary Histories of Animal Gut Microbiomes. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:17463127 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Disentangling the coevolutionary histories of animal gut microbiomes A dissertation presented by Jon Gregory Sanders to Te Department of Organismic and Evolutionary Biology in partial fulfllment of the requirements for the degree of Doctor of Philosophy in the subject of Organismic and Evolutionary Biology Harvard University Cambridge, Massachusetts April, 2015 ㏄ 2015 – Jon G. Sanders Tis work is licensed under a Creative Commons Attribution-NonCommercial- ShareAlike 4.0 International License. To view a copy of this license, visit http:// creativecommons.org/licenses/by-nc-sa/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. Professor Naomi E. Pierce Jon G. Sanders Professor Peter R. Girguis Disentangling the coevolutionary histories of animal gut microbiomes ABSTRACT Animals associate with microbes in complex interactions with profound ftness consequences. Tese interactions play an enormous role in the evolution of both partners, and recent advances in sequencing technology have allowed for unprecedented insight into the diversity and distribution of these associations. However, our understanding of the processes generating those patterns remains in its infancy. Here, I explore variation in microbiomes across two animal lineages—ants and mammals—to tease apart the role of these process in the evolution of gut microbiota. First, I explore patterns of phylogenetic correlation in gut microbiota of herbivorous Cephalotes ants and hominid apes. By examining the sensitivity of phylogenetic correlation to analytical parameters, I show that these outwardly similar patterns are likely to be the result of very different processes in each host lineage. Next, I examine in more depth the interacting effects of diet and phylogeny on the structure of baleen whale microbiomes. Whales consume a diet that differs dramatically from that of their closest extant relatives, the herbivorous artiodactyls. I use a combination of marker gene and shotgun metagenomic sequencing to show that a phylogentically conserved host trait, the multichambered gut, leads to functional and taxonomic similarities of whale gut microbiomes to those of their herbivorous ancestors via the fermentation of animal polysaccharides in the exoskeletons of their prey. Finally, I return to ants to examine how major shifs in the nature of gut microbial association correspond to host ecology. Using measures of absolute bacterial abundance, rather than iii diversity, I test the hypothesis that evolution of symbiosis with microbes has facilitated ants’ dominance of tropical rainforest canopies. Surprisingly, I fnd differences in the abundance of gut bacteria in different ant lineages that span many orders of magnitude, suggesting that evolutionary transitions in the functional role of symbiosis in this animal lineage correspond not only to changes in the diversity of these associations, but to changes in kind. Te results of these studies help to clarify the roles of history and selection in structuring animal gut microbiota, hinting that the interaction of these factors may fundamentally differ between animal lineages. iv Disentangling the coevolutionary histories of animal gut microbiomes TABLE OF CONTENTS Acknowledgments vi Introduction 1 Chapter 1 10 Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes 10 Chapter 2 41 Te whale gut microbiome digests animal prey using pathways common in terrestrial herbivores 41 Chapter 3 63 Gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants 63 Appendix 1 93 Chapter 1 Supplemental 93 Appendix 2 116 Chapter 2 Supplemental 116 Appendix 3 126 Chapter 3 Supplemental 126 Appendix 4 136 Cladescan: a program for automated phylogenetic sensitivity analysis 136 References 139 v ACKNOWLEDGMENTS Evolution is what happens. Tere is something profound in this, the accidental grace of happenstance, that I fnd unfailingly compelling. I had always intended this thesis to be a tribute to the serendipity of cooperation. Tat it be so as much in execution as in topic is ftting. It also means that I owe an enormous debt to a tremendous number of people. First and foremost to my coadvisors, Naomi Pierce and Peter Girguis, for having the unending faith in (and patience with) me to fnd my own way through this journey. You have given me the chance to explore quite literally the deepest depths and the darkest forests in the farthest corners of this incredible planet in search of my questions. You have been friends and mentors, and will always remain an inspiration. I am incredibly grateful. To my committee members, Andrew Knoll and Eric Alm; and to previous committee members Chris Marx, Anne Pringle, and Peter Turnbaugh; for guidance, support, and direction. To a long list of collaborators and mentors at Stanford, Harvard, and elsewhere. I would not have made it here without rediscovering a love for biology at Hopkins Marine Station; thanks to Stephen Palumbi and George Somero, and the many other faculty, staff, and students there who started me on this road. I am incredibly fortunate to have shared an office with Daniel Kronauer, who shared with me the secrets of the Cephalotes phylogeny, as well as the secrets to taking their photographs. I must also thank Daniel for introducing me to Scott Powell, who has been an extraordinary friend, mentor, and guide to the wonderful world of turtle ants. For the gif of ants I also owe a profound debt to Jacob Russell and Corrie Moreau, whose work was an early inspiration, and who I am now lucky to call (along with their lab members Yi Hu, Piotr Lukasik, Ben Rubin) valued friends and collaborators. I am very, very grateful to have crossed paths with Megan vi Frederickson, who has been an invaluable source of insight and support over many years. Tanks especially to Annabel Beichman, to whom I owe an entire chapter of my thesis. Tanks also to John Wertz, Joe Roman, Colleen Cavanaugh, Margaret McFall-Ngai, Ned Ruby, Rob Knight, Lawrence David, and Heraldo Vasconcelos. To the fantastic members of the Pierce and Girguis labs, past and present. I have beneftted enormously from the friendship, intellectual stimulation, and moral support of both of these groups of people; I don’t know how most people get by with just one lab. I must especially thank Heather Olins, Kiana Frank, Jenny Delaney, Stephanie Hillsgrove, and Chris DiPerna of the Girguis lab; and Gabe Miller, Leonora Bittleston, James Crall, Sarah Kocher, Maggie Starvish, and Petra Kubikova of the Pierce lab. In particular, I am deeply grateful for the friendship and support of Roxanne Beinart and Chris Baker, each of whom has been a constant and invaluable presence in my life since I arrived here. To the many other people in OEB, the MCZ, and Harvard who have been sources of inspiration, assistance, and encouragement; especially Shane Campbell-Staton, Shelbi Russell, Stefan Cover, Jignasha Rana, and Chris Preheim. To Millstone Coop and the extraordinary people I met there; Alex, Chandra, Sara, Mary, Benny (and of course the chickens). To Wes, David, Megan, Anna, Gil, Darcy, Katy, Cara, Laure, and Danica, friends through so many miles and so many years. To Megan Jensen, my best friend of all. To Lina Arcila Hernandez, my incredible partner, who is the most tenacious, genuine, and kind person I have ever met. And of course, of course, to my family: Mom, Dad, Katie, Grandma Whiteman, and Grandma and Grandpa Watson. Tey have supported and encouraged me beyond what anyone could ever hope for or imagine. One cannot choose one’s family, but it is the greatest serendipity of all that I ended up with this one. vii INTRODUCTION It is now widely appreciated, in both the academy and the public consciousness, that we are not simply the unitary organisms encoded by our nuclear genomes (McFall- Ngai et al. 2013). For humans, it is estimated that less than one percent of the total gene diversity found in or on our physical corpus is encoded by one of our 23 nuclear chromosomes (Qin et al. 2010). Just one in ten of the cells in that corpus harbor our nuclear genome. Te vast majority of the remainder are bacteria, the bulk of them residing in the gut. We know that these symbiotic bacteria can have enormous effects on the phenotype of the host (McFall-Ngai et al. 2013)—and, consequently, on the realized ftness of those 23 human chromosomes. But while the patterns of inheritance of nuclear DNA through the animal germ line are generally well characterized, the rules governing the trans-generational association between animal cells and the overwhelming gene diversity encoded within bacterial cells remain poorly understood. Despite profound advances in the technology available to characterize diverse microbial communities, the patterns of diversity even among some of the best-characterized host-associated microbiota remain frustratingly subject to differences in interpretation (Ochman et al. 2010; Moeller et al. 2012; Degnan et al. 2012; Sanders et al. 2013). To truly understand the dance of these more and less intimately-associated genomes across millions of years, their effect on and how they are affected by evolution of the host organism—that is to say, us—we must frst learn how to interpret the patterns of their extant distributions with greater fdelity.