The Creation of Metropolitan Amazonia: Genetic Consequences of Migration and Urbanization By Randy E. David M.A., State University of New York at Binghamton, Binghamton, NY, 2011 Graduate Certificate, State University of New York at Binghamton, Binghamton, NY, 2011 B.S., State University of New York at Binghamton, Binghamton, NY, 2009 2019 Submitted to the Graduate Degree Program in Biological Anthropology and the Faculty of the Graduate School of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy. ____________________________________________________ Chairperson: Michael H. Crawford, Ph.D. ____________________________________________________ Bartholomew Dean, Ph.D. ____________________________________________________ Dennis H. O’Rourke, Ph.D. ____________________________________________________ Maria E. Orive, Ph.D. ____________________________________________________ Jennifer Raff, Ph.D. Date of Defense: July 22, 2019 ii The dissertation committee for Randy E. David certifies that this is the approved version of the following dissertation: The Creation of Metropolitan Amazonia: Genetic Consequences of Migration and Urbanization ____________________________________________________ Chairperson: Michael H. Crawford, Ph.D. Date Approved: September 3, 2019 iii Abstract Uniparental genetic markers were analyzed in a sample of 182 individuals from the Peruvian Amazonian city of Yurimaguas. The site of extensive pre-Columbian and modern migratory fluctuation, contemporary Yurimaguas is characterized by considerable population diversity. Individually unique migratory and demographic profiles were combined with population genetic methodology to cultivate a co-constitutive view of the establishment of a modern Amazonian urban center. Yurimaguas, like many cities in the Global South, continues to experience the multifarious effects of accelerated migration and urbanization on population architecture. Biodemography and population genetics are used to assess consequences and evaluate potential contributing environments and events. A nuanced, interdisciplinary perspective through both a populational and molecular lens on the creation of today’s urban populations is critical to informing the following: (1) our evolutionary development, historical interactions, and prior movements, (2) the relationship between genetic diversity and the evolutionary forces of gene flow, genetic drift, and natural selection, and (3) human migratory and mating behavior. Key Terms: Ancestry-Informing Markers (AIMs), Biodemography, Human Migration, Non- Recombining DNA, Peruvian Amazon, Population Genetics, Urbanization iv This dissertation is dedicated to my family, a reservoir of infinite encouragement, support, and love. v Acknowledgements I am eternally obliged to Dr. Michael H. Crawford for his unwavering leadership and character. I am most grateful to Dr. Bartholomew Dean for his humanity and devotion. I would like to thank Dr. Dennis H. O’Rourke for his generosity. I am appreciative of the assistance of Drs. Maria E. Orive, Jennifer Raff, and Justin Tackney. Colleagues and friends Akbar Amat, Cyrus Azizi, Dr. Kristine Beaty, Dr. Melody Ratliff-Wood, Dr. Norberto Baldi-Salas, Dr. Fazel Hadadifard, Dr. Abdelmajid Hannoum, Dr. Joshua Homan, and Dr. Gabriel de Oliveira have made my time at the University of Kansas an inspiring period of scholarship and growth. I would like to thank my support system dating back to my first day in higher education, including: Emily Barile, Dr. Nicole Barile, Ezechiel Bly, Paul Choe, William Farber, David Fong, Valbona Gashi, Dr. Ronald Gomez, Dr. Amelia Harris, Kyle Hoellger, John Keith Keaveny, Jonathan Kim, Dr. Zachary Logozio, Max Mileaf, Dr. Tyler J. Miranda, Craig Morgan, Dr. Deanna Scoca, Aryssa Wernle, Kymel Yard, and Dr. Daniel Zheng. Lastly, I would like to thank the people of Yurimaguas, Peru for their acceptance, sincerity, and patience. This dissertation was completed thanks to the generous support of the following: • Carol Clark Grant, University of Kansas • Dean’s Office Research Excellence Fund, Graduate Student and Postdoctoral Fund Award, University of Kansas • GENO 2.0 (Genographic Project) Grant, National Geographic Society • Graduate Studies Research Support Award, University of Kansas • Graduate Studies Summer Fellowship, University of Kansas • Program in Biological Anthropology, University of Kansas • University of Kansas Institute for Policy and Social Research, Center for Migration Research, Graduate Student Grant Program • University of Kansas Institute for Policy and Social Research, Center for Migration Research, Seed Grant Program vi Table of Contents Abstract ............................................................................................................................................ iii Acknowledgements ...........................................................................................................................v List of Figures ................................................................................................................................. viii List of Tables .....................................................................................................................................x Chapter I: Introduction ...................................................................................................................... 1 Chapter II: Historical Background .................................................................................................... 7 Geography ........................................................................................................................... 7 The Amazon Basin The Lower Huallaga River Valley Pre-Columbian Period ......................................................................................................... 9 Arrival in Lowland South America Language Early “Selva Baja” Culture From a Colony to an Independent Republic ..................................................................... 11 European Exploration of the Upper Amazon The Extraction of Native Labor Power, and Mission Life The Spread of Disease The Political and Economic Foundation of Loreto Region The Rubber Boom The Modern Era (Mid-20th Century to Present)................................................................. 19 Loreto Region and the City of Yurimaguas, Today ........................................................... 21 Chapter III: Scientific Literature Review ......................................................................................... 29 Conducting Research in the Lower Huallaga River Valley ............................................... 32 Genetic Consequences of Migration and Urbanization in Peruvian Amazonia ................ 33 Chapter IV: Methods and Materials ................................................................................................ 42 Collection of Data and DNA Samples ............................................................................... 42 Laboratory Methodology ................................................................................................... 44 DNA Extraction and Purification Mitochondrial DNA Non-Recombining, Y-Chromosomal DNA Software-Based Genetic Analyses.................................................................................... 52 Mitochondrial DNA Non-Recombining, Y-Chromosomal DNA Statistical Analyses ........................................................................................................... 57 Demographic and Migratory Trends in the Yurimaguas Sample Research Question 1 Research Question 2 Research Question 3 Research Question 4 Research Question 5 Research Question 6 Storage of Genetic Data .................................................................................................... 71 Chapter V: Results ......................................................................................................................... 73 vii Demographic and Migratory Trends in the Yurimaguas Sample ...................................... 73 Research Question 1......................................................................................................... 96 Research Question 2....................................................................................................... 103 Research Question 3....................................................................................................... 108 Research Question 4....................................................................................................... 111 Research Question 5....................................................................................................... 117 Research Question 6....................................................................................................... 121 Chapter VI: Discussion ................................................................................................................. 128 Demography .................................................................................................................... 128 Population Genetics ........................................................................................................ 133 Chapter VII: Conclusions .............................................................................................................. 148 Works Cited .................................................................................................................................