An ancient DNA perspective on the prehistory of the Lower Illinois Valley PDF

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AN ANCIENT DNA PERSPECTIVE ON THE PREHISTORY OF THE LOWER ILLINOIS VALLEY Jennifer Anne Raff Submitted to the faculty of the University Graduate School in partial fulfillment of the requirements for the degree Doctor of Philosophy In the Departments of Biology and Anthropology Indiana University Oct...

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An ancient DNA perspective on the prehistory of the Lower Illinois Valley Jennifer Raff

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AN ANCIENT DNA PERSPECTIVE ON THE PREHISTORY OF THE LOWER ILLINOIS VALLEY

Jennifer Anne Raff

Submitted to the faculty of the University Graduate School in partial fulfillment of the requirements for the degree Doctor of Philosophy In the Departments of Biology and Anthropology Indiana University October 2008

Accepted by the Graduate Faculty, Indiana University, in partial fulfillment of the requirements for the degree of Doctor of Philosophy.

Doctoral Committee

_____________________________ (Frederika Kaestle, Ph.D.)

______________________________ (Susan Alt, Ph.D.)

______________________________ (Mark Braun, M.D.)

______________________________ (Della Cook, Ph.D.)

______________________________ (Armin Moczek, Ph.D.)

______________________________ (David Nelson, Ph.D.) (September 5, 2008)

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© (2008) (Jennifer Raff) ALL RIGHTS RESERVED

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Acknowledgements This research was facilitated by the efforts of many people. I am indebted first and foremost to my committee: Susan Alt, Mark Braun, Della Cook, Rika Kaestle, Armin Moczec, and David Nelson. My advisor, Rika Kaestle, has been wonderfully patient in helping me with my research and teaching, and I am grateful to her for the guidance, wisdom, and friendship that she has shared with me over the past few years. Della Cook has also been of tremendous help in my efforts to master the archaeological literature, and her advice and suggestions have played a critical role in shaping my development as a biological anthropologist. The faculty of both the Biology and Anthropology departments at Indiana University have been generous with their expertise, assisting me with research, writing, and teaching. In particular, I wish to thank José Bonner (who first put a pipette into my hands as a teenager), Susan Strome, Bill Saxton, Curt Lively, Linda Delph, Paul Jamison, and Kevin Hunt. Numerous additional people contributed to this work. I am grateful to Dennis O‘Rourke and Jake Enk at the University of Utah, and to Beth and Rudy Raff at Indiana University for encouragement and the generous contribution of reagents during the final stages of this research. Deborah Bolnick kindly provided her expertise and analysis on multiple projects. My graduate student colleagues were always enthusiastic about dissecting issues in research, teaching, and life, particularly Alison Doubleday, Georgia Millward, Allison Foley, Polly Husmann, Carlina De La Cova, and Charla McCormick. I am also grateful to Aaron Raff , Dwight and Stephanie Deckard, Jeremiah Bainbridge, Steve Tuttle, Patrick Kelly, Peter Bertermann, Kendra Mealy, Randy Pardue, Danielle Guevara, Josh Lester, Cassandra Burns, and Robene Bates, for their friendship and support over many years.

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My research received funding and support from the IU Department of Biology, the Institute of Molecular Biology, NSF IGERT, the Women in Science Program, and Skomp Research and Travel grants. I am indebted to the tireless support staff of both Biology and Anthropology departments, especially to Gretchen Clearwater. I am also grateful to the Native communities, both past and present, who have supported and been involved in this research. Finally, I also wish to particularly thank those individuals who have been my principle sources of support over the last few years. Laura Hohman shared friendship and many adventures with me (mostly involving bats), and was always available if I had questions or needed advice. Jeremy Jordan, my peerless (self-appointed) life-coach, kept me focused amid many distractions—an extremely difficult task for which his patience and sense of humor should be commended. Terri Jordan was always available to encourage, sympathize, advise and listen to me; I never ended a conversation with her without smiling. Jonas Schrodt helped me stay sane through a combination of terrible movies, terrible food, and the best company. Steve and Linda Scott, who have been the architects of an organization that has become my second family, served as both friends and parents to me during my years in Bloomington. Mick Williams helped me stay awake and amused on many long nights via texting, while I wrote and he kept the city safe. Jason Winkle, who is a constant source of inspiration in his approach toward life, is a model of the kind of teacher and friend that I aspire to be. This work, with great love, is dedicated to my family: Kathleen Burke, Dan Kedzie, Julie Kedzie, Greg Jackson, Beth Raff, and Rudy Raff. They have made my research possible in countless ways, but even more importantly, have shaped my development as a person and as a scientist.

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AN ANCIENT DNA PERSPECTIVE ON THE PREHISTORY OF THE LOWER ILLINOIS VALLEY

In this study I recover and analyze ancient DNA in order to identify prehistoric biological relationships on three different levels: between New World Midwestern precontact groups, between individuals buried together, and between ancient and modern strains of Mycobacterium tuberculosis complex (MTC) bacteria. Through this analysis, I attempt to shed light on aspects of the health and culture of the Schild people of the Lower Illinois Valley (LIV), a region peripheral to the Mississippian center of Cahokia. The appearance of Mississippian culture at Schild (including changes in material culture, settlement patterns, mortuary practices, and subsistence strategies) occurred approximately 100 years after the founding of Cahokia (ca A.D. 1050); mitochondrial DNA (mtDNA) haplogroup and haplotype distributions in LIV groups bracketing this transition indicates that low levels of gene flow coincided with this event. My analysis of the distribution of mtDNA lineages in Middle Woodland (ca B.C. 200A.D. 400), Late Woodland (ca A.D. 400-1000), and Mississippian (ca A.D. 1050-historic) period cemeteries from this region indicated that burial location was not determined by maternal relationships. On a larger scale, this analysis calls into question the ―Madonna and Child Trope‖: the common archaeological interpretation of woman-child co-burials as mothers and children. These results suggest that inferences regarding biological relationships in prehistoric cemeteries should be made with caution in the absence of morphological or genetic evidence.

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In molecular survey of the Schild burial series, I recovered DNA from eight individuals infected with tuberculosis. Phylogenetic analysis of portions of the gyrase B and 16S rRNA loci, and the presence of the MTC-specific insertion element IS6110, show that this ancient isolate belongs to the MTC, but is distinct from all modern members of the complex, suggesting a long evolutionary separation from Old World complex members. This ancient MTC strain exhibits non-typical skeletal pathology, in that bone lesions are more frequent than in human infections with any of the modern species. My evidence suggests that a previously uncharacterized strain of TB may have been present in American populations prior to European contact.

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Table of Contents Chapter 1. Introduction…………………………………………………………………………1 References………………………………………………………………………………………7 Chapter 2: Migration and the Mississippian Emergence in West-Central Illinois…………9 Abstract…………………………………………………………………………………………9 Introduction……………………………………………………………………………………..9 Materials and Methods………………………………………………………………………....16 Results……………………………………………………………………….............................20 Discussion……………………………………………………………………………………...22 Tables and Figures……………………………………………………………………………..27 Appendix I……………………………………………………………………………………..48 Literature Cited………………………………………………………………………………...50 Chapter 3: Native American kinship in the Eastern Woodlands: a review of the archaeological and ethnographic literature…………………………………………………...57 Abstract………………………………………………………………………………………...57 Introduction……………………………………………………………………………………57 Ethnographic background……………………………………………………………………...60 Kinship and the archaeological record………………………………………………………...65 Literature cited…………………………………………………………………………………77 Chapter 4: An examination of the association between biological relationships and differential mortuary treatment in the prehistoric Lower Illinois Valley…………………..83 Abstract………………………………………………………………………………………...83 Introduction…………………………………………………………………………………….83 Materials and Methods…………………………………………………………………………92 Results……………………………………………………………………………………….....94 Discussion……………………………………………………………………………………...98 Figures and Tables……………………………………………………………………………103 References……………………………………………………………………………………114 viii

Chapter 5: Testing the Madonna and Child Trope…………………………………………116 Abstract……………………………………………………………………………………….116 Introduction…………………………………………………………………………………..116 Methods……………………………………………………………………………………....124 Results and Discussion……………………………………………………………………….126 References……………………………………………………………………………………132 Tables and Figures…………………………………………………………………………....137 Chapter 6: The evolution of the Mycobacterium tuberculosis complex and its origins on the American continent: a review of the literature……………………………………………...141 Abstract………………………………………………………………………………………141 Figures……………………………………………………………………………………......148 References……………………………………………………………………………………149 Chapter 7: Detection of Mycobacterium tuberculosis complex within a pre-contact New World population……………………………………………………………………………..154 Abstract……………………………………………………………………………………...154 Introduction………………………………………………………………………………….154 Methods……………………………………………………………………………………...159 Results and Discussion……………………………………………………………………….161 References…………………………………………………………………………………....162 Tables and Figures…………………………………………………………………………....167 Chapter 8: Ancient DNA evidence for a new strain of tuberculosis in pre-contact North America......................................................................................................................................169 Abstract………………………………………………………………………………………169 Introduction…………………………………………………………………………………..169 Results………………………………………………………………………………………..172 Discussion…………………………………………………………………………………….177 Materials and Methods……………………………………………………………………….182 Acknowledgements…………………………………………………………………………..186 Literature Cited……………………………………………………………………………….186 Figures…………………………………………………………………………………….......192 ix

Supplemental Information………………………………………………………………….193 Appendix 1: Description of sites utilized in this study……………………………………209 Appendix 2: Sequences of samples obtained in this study………………………………..211 Curriculum Vitae of Jennifer Raff

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Chapter 1 Introduction

Identifying biological relationships in prehistory is a crucial component of understanding human behavior and mortality. However, approaches to studying the relationship between biology and culture in past societies (including the analysis of languages, material culture, and skeletal material) can be frustratingly indirect. Moreover, when limitations of these approaches are not explicitly identified, components of material culture or languages can be conflated with concepts of ethnicity or biological populations. On a smaller scale, material culture is also frequently used as a proxy for ‗kinship‘, a term that could be applied to many different types of relationships in many different cultures. Defining kinship in past societies is regrettably problematic as genetic relationships may not be synonymous with kin relationships, nor readily identifiable in the archaeological record. However, identification of such relationships, as well as ethnicity in general, is the starting point for the study of the spread of prehistoric diseases, the effects (and causes) of prehistoric warfare, and for understanding discontinuities in material culture of past societies (i.e. did they result from population movement or from cultural diffusion?). Fundamentally, kinship (regardless of how it may be defined) is thought to be the core organizing principle of prehistoric societies. Without incorporating biological approaches into archaeological investigations, this important aspect of preliterate societies may be mischaracterized or unobservable. .

This research attempts, in part, to address some of these issues by utilizing ancient DNA

approaches to study a prehistoric North American burial group. Studies of living Native Americans have revealed five mitochondrial (and thus maternally-inherited) haplogroups (A, B, 1

C, D, and X) present in the Americas (Foster et al., 1998; Schurr et al., 1990), each of which is defined by mutations shared by its members. Within each haplogroup are subsumed numerous maternal lineages (haplotypes), each with unique mutations. Together, haplogroup and haplotype distributions in ancient and modern Native American populations serve as indications of genetic similarity or distance. The demographic history of the native peoples of America is reflected in the genetic profiles of both modern and ancient populations. In general, Native American mtDNA haplogroup frequencies have a strongly regional distribution in North America, suggesting ―geographic and temporal stability‖ between ancient and modern populations (O‘Rourke et al., 2000 p 231), with little evidence for genetic drift (Bolnick et al., 2005). One exception to this continuity, however, appears to have occurred in the Southeastern region of North America, where Muskogean-speaking populations exhibit strikingly different haplogroup frequencies from other Eastern North American groups, likely due to a genetic bottleneck resulting from population decimation subsequent to European contact. Complementing population-level analyses, aDNA research has also been used to identify founding lineages and number of migration events (e.g. Eschleman et al. 2003; Stone and Stoneking 1993, 1998), to reconstruct the prehistory and social structure of ancient populations (Stone and Stoneking 1998), as well as to trace individual genetic lineages present within a burial group through time and space (e.g. Mills 2003; Bolnick 2005; Kaestle and Smith 2001; Cabana et al., 2008). Although the majority of North American aDNA research has focused on western populations, a small number of studies on the genetic history of eastern North Americans have 2

emerged recently. The earliest and largest study of an ancient population in this region (Stone and Stoneking 1993, 1998) analyzed mtDNA recovered from 108 individuals of the Oneota Norris Farms cemetery from West-Central Illinois. This work established the first mitochondrial haplogroup profile of an ancient Eastern North American population, was used in further clarifying the peopling of the Americas, and was an early examination of the relationship between biological kinship and mortuary practices in North America. Subsequently, Napier (2000) reported the amplification of mitochondrial and Y chromosome DNA from 10 individuals buried in Cahokia‘s Mound 72. However, as the Y chromosome results were phylogenetically uninformative, and only 95 bp of mtDNA was amplified, these results were not included in any subsequent analyses (including the present study). Mills (2003) examined a Middle Woodland burial group from the Ohio Hopewell Mound Group, finding no evidence for matrilineal-based patterning of the burials. Bolnick (2005) analyzed mtDNA from Middle and Late Woodland burials at the Klunk cemetery in West-Central Illinois, finding evidence for migration and unidirectional gene flow (from Ohio to Illinois) during the Middle Woodland period, a lack of matrilineal-based cemetery structure, and also likely matrilocal post-marital residence (based on differential haplotype diversity levels in males vs. females). Shook and Smith (2008) contributed mitochondrial data from Morse and Orendorf Mississippian groups from the Central Illinois Valley, and Great Western Park and Glacial Kame individuals from Ontario. Despite these studies, the regional picture of the ancient Eastern New World genetic prehistory is still far from complete, and more studies of both ancient and modern populations are needed. This research utilizes ancient DNA analysis to address three themes in the prehistory of the Midwest. The cultural area that is discussed here, referred to as the ―Eastern Woodlands‖, is bounded on the west by the Mississippi River, on the north by the Great Lakes, and on the south 3

by the Gulf of Mexico. It therefore encompasses the geographic regions known as the ―Northeastern‖, and ―Southeastern‖ regions, which themselves are divided from each other by the Ohio River (Eggan 1952; Hudson 1976; Trigger 1978). Special emphasis is placed upon sites within the Midwest, particularly from the Lower Illinois Valley and American Bottom region within Illinois and Missouri. Temporally, this and subsequent chapters focus on the Middle Woodland (ca B.C. 200- A.D. 400), Late Woodland (ca A.D. 400-1000), and Mississippian (ca A.D. 1000-historic) periods. The first theme focuses on the development of Mississippian culture in the Lower Illinois Valley. The development of intensive maize agriculture was accompanied by profound changes in political systems, settlement patterns, technology, and mortuary practices. These changes originate at the site of Cahokia within the American Bottom, the largest settlement in North America until historic times, with a population in the tens of thousands (Milner 1998; Pauketat and Lopinot 1997). Archaeological analysis suggests that an exchange of technology, subsistence strategies, and culture (such as mortuary practice) from Cahokia to peripheral areas took place at the time of Mississippian Emergence. Through ancient DNA analyses of populations on the periphery of Cahokia that span the Mississippian Emergence (Chapter 2), I address the question: to what extent was the adoption of new practices accompanied by population movements? A second theme of this research (Chapters 3-5) examines the relationship among lineage, kinship, and burial treatment in Middle Woodland, Late Woodland and Mississippian sites from the Illinois River Valley using ancient DNA. Multiple changes in the treatment of the dead took place at the time of Mississippian Emergence, reflecting an important shift in religious beliefs, 4

social organization, and possibly in the concept of kinship as well. However, it is possible that concepts of kinship did not change at all, but were merely expressed in a different manner. Moreover, the mortuary practice variability observed in Mississippian cemeteries has been hypothesized to be indicative of the presence of several ethnic groups occupying the Cahokia hinterland (Milner 1984; Emerson and Hargrave 2000), who utilized mortuary practice as one means of reinforcing separate identities within a pluralistic society. In Chapter 3 I review the role and nature of kinship in Eastern North American societies, as observed in historic and living populations, and also as inferred from archaeological evidence in past societies. Chapter 4 tests the hypothesis that the structure of Mississippian cemeteries reflects maternal kinship groups. In Chapter 5, I address the assumption (frequent in archaeology) that women found associated with children in mortuary contexts are their m...