Paleogenomic Analyses of Demographic Change and Adaptation in the Evolutionary Histories of Human Populations in the Andes Restricted; Files Only

Abstract

Studies of Indigenous ancestry and lifeways have remained underrepresented in the field of population genomics. Accordingly, the objective of this dissertation was to gain a better understanding of the ancient history of the Americas, particularly in the Central Andes. Studies employing whole genomes, both ancient and modern, can access a wealth of ancestral information coded within the genome. Through population genomic research and collaboration, this dissertation investigated the genetic history of the Central Andes region of South America, in what is today Peru and Ecuador, over periods including the transition from hunter-gatherer economies to agricultural civilizations. This dissertation comprises three published, peer-reviewed papers: (1) A review of current understandings of pathogenic disease as an evolutionary pressure in the Americas, (2) Tuberculosis immunity and high altitude adaptation in two modern-day Ecuadorian populations living at high altitude, and (3) Paleogenomic insights into cooperation in the ancient Andes from positive selection on oxytocin pathway genes. Collectively, this work suggests different population dynamics exist across the Central Andes, necessitating nuanced analyses of fine-scale regional patterns of demographic change and adaptation, as well as collaboration with local populations and researchers to drive increased representation of the peoples living across this diverse region.

Table of Contents

CHAPTER 1: INTRODUCTION

1.1 Aims of the Dissertation

1.2 13,000 Years of Human History in South America

1.3 Understanding Ancient Life Using Genomics

1.4 Population Genomics and Recent Human Evolution

1.5 Chapter Summaries

1.6 Introductory References

CHAPTER 2: A REVIEW OF THE EVOLUTIONARY HISTORY OF INFECTIOUS DISEASE IN THE ANCIENT AMERICAS

2.1 Abstract

2.2 Introduction

2.3 Tuberculosis

2.4 Malaria

2.5 Syphilis, Yaws, and Bejel

2.6 Chagas Disease

2.7 Bias in Characterization of Diseases in the Americas: The Case of Yellow Fever and the Panama Canal Project

2.8 Discussion

2.9 References

CHAPTER 3: GENOMIC EVIDENCE FOR ADAPTATION TO HIGH ALTITUDE AND TUBERCULOSIS IMMUNITY IN THE ANDES BEFORE EUROPEAN CONTACT

3.1 Abstract

3.2 Introduction

3.3 Results

3.4 Discussion

3.5 Limitations of Study

3.6 Methods: Community Engagement and Sample Collection

3.7 Methods: DNA Extraction

3.8 Methods: Data Processing, Alignments, and Phasing

3.9 Methods: Demographic Analyses

3.10 Methods: Selection Scans

3.11 References

CHAPTER 4: PALEOGENOMIC INSIGHTS INTO COOPERATION IN THE ANCIENT ANDES FROM POSITIVE SELECTION ON OXYTOCIN PATHWAY GENES

4.1 Abstract

4.2 The Oxytocin System and Cooperation

4.3 Cooperation and Socioeconomic Change in the Ancient Andean Highlands

4.4 Results

4.5 Discussion

4.6 Methods

4.7 References

CHAPTER 5: CONCLUSION

APPENDIX A: CHAPTER 2 SUPPLEMENTARY INFORMATION

APPENDIX B: CHAPTER 3 SUPPLEMENTARY INFORMATION

APPENDIX C: CHAPTER 4 SUPPLEMENTARY INFORMATION

About this Dissertation

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School	Laney Graduate School
Department	Anthropology
Degree	Ph.D.
Submission	Dissertation
Language	English
Research Field	Anthropology, Physical
Mot-clé	Demography Andes Ancient DNA Population Genomics Natural Selection
Committee Chair / Thesis Advisor	John Lindo, Emory University
Committee Members	Carmen J. Marsit, Emory University Marcela E. Benitez, Emory University

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