Phylogenetic History of the AMY Gene Cluster in Catarrhines
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City University of New York (CUNY) CUNY Academic Works School of Arts & Sciences Theses Hunter College 2-1-2019 Phylogenetic History of the AMY Gene Cluster in Catarrhines Christian M. Gagnon CUNY Hunter College How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/hc_sas_etds/377 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Phylogenetic History of the AMY Gene Cluster in Catarrhines By Christian Gagnon Submitted in partial fulfillment of the requirements for the degree of Master of Arts in Anthropology, Hunter College of the City University of New York 2018 Thesis Sponsor: _____01/02/2019_____ _____________________________ Date Signature Dr. Michael E. Steiper _____01/02/2019_____ _____________________________ Date Signature of Second Reader Dr. Jessica Rothman 1 Acknowledgements: I owe a great debt of gratitude to my academic advisor, Dr. Michael E. Steiper, whose efforts and cooperation made this project possible. Furthermore, Dr. Steiper’s encouragement and support have been instrumental in my development as both an undergraduate and graduate student, I feel fortunate to have benefitted from his knowledge and guidance over these past several years. I thank my second reader Dr. Jessica Rothman for her invaluable expertise in the fields of primatology, ecology, and nutrition without which the completion of this project would have been much more difficult. I am also grateful to Dr. George Perry of Penn State University for his support and input in the development of this project. I would also like to thank the developers of the many tools necessary for a project of this scope to be undertaken, including the creators of MAFFT, PAML, Mega, and Datamonkey, Special thanks to my lab mate, Natalia Grube, for always being a sounding board for my ideas and her unwavering support. I also would like to recognize Caley Johnson for her contributions to the project. Her insights into primate nutritional ecology were a valuable resource. Thank you to the faculty and Graduate Students of the Hunter College Anthropology Department and the New York Consortium of Evolutionary Primatology for providing a stimulating learning environment conducive to my success. 2 Table of Contents I. List of Figures ........................................................................................................................ 4 II. List of Tables ........................................................................................................................ 4 III. Abstract ............................................................................................................................... 4 IV. Introduction: AMY and Its Relevance to Human Evolution ........................................... 5 V. Materials and Methods ..................................................................................................... 14 A. Methods Summary ......................................................................................................... 14 B. Genomic Sequences ........................................................................................................ 15 C. Coding DNA Sequences ................................................................................................. 18 D. Genomic Sequence Alignment (MAFFT) ...................................................................... 19 E. Adaptive Branch-Site Rel Test (aBSREL) .................................................................... 20 F. Gene Conversion Analysis (GENECONV) .................................................................... 20 G. Phylogenetic Analysis (RAXML) .................................................................................. 21 VI. Results ............................................................................................................................... 21 A. Sequence Alignment ...................................................................................................... 22 B. GENECONV Results ..................................................................................................... 22 C. Phylogenetic Results ...................................................................................................... 26 D. aBSREL Results ............................................................................................................. 29 VII. Discussion ........................................................................................................................ 32 VIII. References ...................................................................................................................... 36 IX. Appendix ........................................................................................................................... 41 3 I. List of Figures Figure 1. Human AMY gene positions Pg. 10 Figure 2. Phylogenetic Tree (Whole Gene) Pg. 27 Figure 3. Phylogenetic Tree (Coding Regions Only) Pg. 28 Figure 4. aBSREL Tree Pg. 30 Figure 5. Phylogenetic Analysis Summary Pg. 33 II. List of Tables Table 1. Genome Coordinates for AMY Orthologs Pg. 16 Table 2. Coding Region Coordinates for Human AMY1A Pg. 19 Table 3. Gene Conversion Sites Pg. 24 Table 4. aBSREL Tree Summary Pg. 31 Table 5. aBSREL Positively-Selected Branches Pg. 31 III. Abstract The AMY gene family plays an essential role in the expression of ⍺-amylase, an enzyme critical to starch digestion. The importance of dietary starch in the evolution of human traits such as the brain is an ongoing point of debate in evolutionary biology because many studies have focused on the increase in animal proteins in hominin diets as the catalyst that made its expansion possible. Levels of amylase expression vary among primates, and although the regulatory mechanism is mostly unknown, evidence suggests that gene copy number variation (CNV) plays a role in humans (Perry et al., 2007). Previous studies indicate that humans who have traditionally 4 consumed high starch diets possess an increased number of AMY gene copies which correlated with increased amylase protein expression in saliva. However, it is important to note that Papio hamadryas and Theropithecus gelada show higher salivary amylase expression than Homo sapiens and Pan troglodytes despite having fewer gene copies. The finding that these primates have higher amylase expression in saliva suggests CNV cannot fully explain its regulation. In this study, I mined and phylogenetically analyzed 30 AMY-related genes from 11 species of haplorrhines. My research sheds light on the complex evolutionary history of this gene family in humans and other primates to further our understanding of our ecological past and the evolutionary pressures that drove these adaptive changes. These findings show that the ancestor of all anthropoids likely had a single AMY-like gene. This gene duplicated independently in New World monkeys and Old World monkeys. Assuming that the gibbon lost its “AMY1 like” gene, in the ancestor of the apes, there was a single AMY that duplicated into the AMY1 and AMY2 like genes. This AMY2 gene then duplicated into AMY2a and AMY2b. All apes have these three orthologs, but gibbons lost their AMY1. In gorillas, AMY2b duplicated again. In humans, AMY1 duplicated further resulting in a three salivary orthologs 1a, 1b, and 1c. These results suggest that the gradual expansion was driven by selective forces to allow humans and other primates to adapt to various ecological landscapes and maximize energy intake from starch-rich foods in periods of food scarcity or in some cases, a staple of their diet. IV. Introduction AMY and its Relevance to Human Evolution 5 There is an ongoing debate among evolutionary theorists regarding the relative importance of proteins derived from meat-based diets versus starch, a form of carbohydrates, from plant foods in the evolution of enlarged primate brains. Although there is support for the idea that the shift from a more plant-rich diet to a meat-rich diet drove the expansion of the primate brain (Aiello & Wheeler, 1995; Milton, 2003), others argued that digestible carbohydrates and cooking may have played equally important roles (Hardy et al., 2015; Wrangham, 2009). Glycogen production in the liver and muscle tissues, the result of glucose intake from carbohydrates, including dietary starch, is essential to human cognitive abilities (Suzuki et al., 2011). Human brains require a steady and reliable source of glycemic carbohydrates to maintain healthy brain function, which accounts for nearly 25% of our basal metabolic spending (Fonseca-Azevedo & Herculano-Houzel, 2012). Based on isotopic and craniodental fossil evidence, several studies suggest that the transition to open habitats led to a possible increase in starch-rich foods from underground storage organs (i.e. tubers, corms, roots and bulbs) and allow early hominins to optimize energy intake from their diet (Codron et al., 2007; Dominy et al., 2008; Laden & Wrangham, 2005; Sponheimer et al., 2013). Many living primate populations inhabit open habitats, and as research has shown, they consume these critical food sources. Savannah dwelling chimpanzees in Ugalla (Tanzania), use tools to uncover underground storage organs (USOs) during the rainy season when food is more abundant (Constantino & Wright, 2009; Hernandez-Aguilar et al., 2007). This evidence of tool use is in contrast some fallback