Assessing the preservation of cytosine methylation in ancient DNA from five prehistoric Native American populations

textCytosine methylation of CpG dinucleotides is an important epigenetic mark that regulates gene expression in humans. While methylation patterns in extant populations have been widely studied, few studies have attempted to analyze methylation in ancient DNA. Indeed, it was only recently shown that methyl groups can be preserved in ancient DNA. However, it is unknown how often methylation patterns can be recovered from ancient samples with preserved nuclear DNA. If they are frequently preserved, it may ultimately be possible to infer patterns of gene activity at the population level in ancient times. In this study, I assessed the preservation of cytosine methylation in ancient DNA from the remains of 30 prehistoric Native Americans from California, Illinois, Kentucky, and Mexico. These samples were previously shown to contain endogenous mitochondrial and nuclear DNA. I analyzed the cytosine methylation states of CpG-rich retrotransposons, which are epigenetically inactivated by cytosine methylation in humans. Unmethylated cytosines were converted to uracils by treatment with sodium bisulfite. Bisulfite products were pyrosequenced, and C-to-T conversions at potentially methylated CpG dinucleotides were quantified. I found that cytosine methylation is readily recoverable from human remains with preserved nuclear DNA from various localities over the time depth tested (~6000 years). This study presents the first direct evidence of cytosine methylation in ancient human remains, and suggests that it may be possible to analyze patterns of gene activity in ancient populations.Anthropolog

What remains : genetic and epigenetic correlates of sociopolitical change and the ulterior traces of power

Recent developments in queer and feminist materialisms have offered productive ways to rethink the connections between nature and culture, and how these forces are mutually entailed in the constitution of bodies. These insights hold radical potentials for reconfiguring what science can mean and for remaking the worlds it helps to materialize. However, such perspectives are rarely taken as entry points for the production of scientific knowledge. Drawing upon emerging scholarship from queer, feminist, and indigenous theorists, this dissertation aims to take on the genetics lab as a site of political transformation. Here, I develop and apply new approaches for recovering the genetic and epigenetic correlates of sociopolitical change, showing that bodies are a “shifting entanglement of relations” (Barad 2007) between sociopolitical and material forces. I begin by evaluating the boundary-making practices and conditions of possibility through which the field of population genetics has materialized certain indigenous bodies and histories to the exclusion of others. This research demonstrates how conventional population genetic research in North America, long predicated on notions of “biological purity”, has helped to maintain the sociopolitical conditions of the settler state. Working from tribal and First Nations self-definitions, this research brings attention to histories that have been hidden in previous population genetic studies in the Americas. This work further destabilizes notions of “indigenous DNA” as the sole criteria for indigenous belonging, through which settler claims to indigenous bodies and cultural heritage have unfolded in recent decades (TallBear 2013). Next, I developed and evaluated methods for reconstructing chemical modifications to DNA, known as cytosine methylation, in five ancient genomes. Because changes in methylation can be shaped by social and environmental factors, reconstructing cytosine methylation in DNA from ancient people could help recover aspects of their lived experiences, shedding new light on past lifeways. I applied paleoepigenetic approaches to evaluate archaeologically-informed questions about the Wari society, the first expansive state in the central Peruvian Andes. By reconstructing ancient methylation patterns from 14 individuals who lived before and after the decline of the Wari state, I show that changes in DNA methylation trace sociopolitical and environmental changes in the ancient world.Anthropolog