Copyright by Jaime Mata-Míguez 2016 The Dissertation Committee for Jaime Mata-Miguez Certifies that this is the approved version of the following dissertation: Assessing the Demographic and Genetic Impact of State Expansion in Pre-Hispanic and Colonial Mexico Committee: Deborah A. Bolnick, Supervisor Enrique Rodriguez-Alegria Anthony Di Fiore Brian M. Kemp Christopher C. Nice Assessing the Demographic and Genetic Impact of State Expansion in Pre-Hispanic and Colonial Mexico by Jaime Mata-Miguez, B.S.; B.S.; M.A. Dissertation Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy The University of Texas at Austin August 2016 Assessing the Demographic and Genetic Impact of State Expansion in Pre-Hispanic and Colonial Mexico Jaime Mata-Miguez, PhD The University of Texas at Austin, 2016 Supervisor: Deborah A. Bolnick Political expansions in Mexico may have had important demographic effects. However, these demographic effects remain unclear. In Xaltocan, a native town in central Mexico founded by Otomi-speaking people in AD 900, archaeological and historical evidence provide somewhat contradictory accounts of such effects. When Xaltocan expanded during the 10-13th centuries, two culturally distinct groups inhabited this town. Archaeologists hypothesize that one group comprised newcomers who settled on the periphery of Xaltocan and were unrelated to the Otomis in the interior, but this scenario remains unclear. In 1395, the Tepanec state conquered Xaltocan, and this town was incorporated into the Aztec state in 1428. Historical documents assert that the Otomis abandoned Xaltocan following the Tepanec conquest and the Aztec state repopulated this town in 1435. However, archaeological evidence of cultural continuity through this time suggests that some Otomis remained at Xaltocan after the Tepanec and Aztec conquests, so the demographic consequences of these events iv remain unsolved. After the Spanish conquest in 1521, the native residents adopted Spanish material culture, but historical documents point to infrequent contact with Spaniards. Archaeological and historical evidence also suggest that political reorganizations and trade stimulated immigration from other native populations. However, whether this immigration increased in colonial times or not is unclear. To clarify these demographic effects, I analyzed DNA from ancient and modern Xaltocan residents. Mitochondrial DNA (mtDNA) indicates that the periphery residents during the 10-13th centuries were maternally unrelated to the Otomis, as archaeologists suggest. However, mtDNA, Y-chromosome, and autosomal DNA reveal genetic discontinuities associated with the Tepanec and Aztec conquests, revealing important demographic consequences unidentified in the archaeological record. Furthermore, in colonial times, mtDNA, Y-chromosome DNA, and genome-wide single nucleotide polymorphisms indicate very little (or perhaps non-existent) admixture, which is consistent with infrequent contact with Spaniards during this period. Finally, temporal changes of mtDNA diversity in colonial times were largely due to immigration from other native populations, as archaeological and historical evidence suggests. Thus, this dissertation illustrates how anthropologists can integrate archaeological, historical, and genetic evidence to study the demographic effects of political expansions. v Table of Contents List of Tables ......................................................................................................... ix List of Figures ........................................................................................................ xi Introduction ..............................................................................................................1 Chapter 1: The Genetic and Demographic Impact of Political Expansions in Pre- Hispanic Mexico: Evidence from Ancient DNA ............................................7 Introduction .....................................................................................................7 Materials and Methods ..................................................................................14 Samples ................................................................................................14 Dating and Temporal Classification of Samples .................................15 DNA Extraction and Genetic Analysis ................................................16 Statistical Analyses ..............................................................................17 Results and Discussion .................................................................................19 Ancient DNA Analysis ........................................................................19 Immigration and Population Expansion Before 1395 ..........................20 Kin Burials Within Pre-1395 Interior and Periphery Xaltocan ...........22 Genetic and Demographic Impacts of the Tepanec Conquest .............23 Population Changes at Xaltocan Following the Aztec Conquest ........27 Kin Burials Within Tepanec and Aztec Houses ..................................28 Modeling Demographic and Genetic Changes in Pre-Hispanic Xaltocan .....................................................................................................31 Supplementary Information ..........................................................................43 Samples ................................................................................................43 Genetic Analyses .................................................................................43 Mitochondrial DNA Analyses ....................................................43 Autosomal DNA Analyses and Molecular Sex Determination ..44 Y-Chromosome DNA Analyses .................................................45 Contamination Controls ..............................................................47 Statistical Analyses ..............................................................................49 vi Chapter 2: A Genetic Test of Historical and Archaeological Hypotheses on the Effects of Spanish Colonialism in Mexico ...................................................78 Abstract .........................................................................................................78 Introduction ...................................................................................................79 Spanish Colonialism in Mexico ...........................................................80 Migration from Europe and Africa: Patterns and Consequences 81 Political Reorganizations and Changing Patterns of Regional Trade ............................................................................................85 Previous Genetic Research .........................................................88 Methods.........................................................................................................90 Samples ................................................................................................90 DNA Extraction and Genotyping.........................................................92 Statistical Analyses ..............................................................................93 Results and Discussion .................................................................................98 Gene Flow from Europe and Africa.....................................................99 Gene Flow Between Xaltocan and Other Native Populations in Mexico100 Conclusion ..................................................................................................102 Chapter 3: A Genetic Test of Historically-Based and Archaeological Hypotheses on the Effects of Spanish Colonialism: Genome-Wide DNA Evidence from Xaltocan, Mexico ........................................................................................133 Abstract .......................................................................................................133 Introduction .................................................................................................134 Previous Genetic Research .........................................................................135 Methods.......................................................................................................138 Samples ..............................................................................................138 SNP Genotyping ................................................................................138 Comparative SNP Data ......................................................................138 Data Curation .....................................................................................139 Data Analysis .....................................................................................139 Results and Discussion ...............................................................................140 vii Conclusion ...........................................................................................................151 References ............................................................................................................162 Chapter 1 .....................................................................................................162 Supplementary Information ...............................................................166 Chapter 2 .....................................................................................................174