| The recovery and analysis of DNA from ancient plant remains has provided valuable insights about plant domestication, human subsistence patterns, trade and contact between past peoples, and other archaeological questions concerning past human-plant interactions. Although ancient DNA studies have been ongoing since the mid-1980s, high-throughput sequencing technologies now allow researchers to investigate ancient genomes more comprehensively than ever before. Instead of studying a few disparate genetic loci, entire genomes can be reconstructed, thereby identifying taxonomic affiliations of ancient specimens, revealing functional traits, and demystifying complex phylogenetic relationships with unprecedented analytical power. These "next-generation sequencing" platforms have been central in studies of ancient hominins and other extinct mammals, yet few geneticists have explored their use on archaeobotanical remains. This dissertation sets to rectify this shortcoming by discussing, exploring, and optimizing high-throughput sequencing of archaeobotanical remains. The first component of the dissertation is a standalone article which conveys important information about ancient DNA from archaeobotanical remains to the archaeological community, with synopses of laboratory methods written for those unfamiliar with molecular biology. In the second part of this manuscript, DNA extraction and amplification techniques are explored on ancient plant remains to determine the best ways to study ancient DNA from such sources. In the third section, a novel method to identify and quantify the relative amount of bacterial and fungal contamination in ancient plant samples is presented and verified on a collection of archaeobotanical remains. The final piece of the dissertation is a case study which demonstrates how these new technologies can be used to test ancient plant remains and shed light on past human behaviors. By way of targeted capture and cutting-edge sequencing technology, a majority of the chloroplast genome was recovered from ancient grape branches from Areni-1 Cave, Armenia. The genetic signatures of these samples suggest a different grape lineage may have been used to make wine in the Late Chalcolithic (∼4000 B.C.) than during the Middle Bronze Age or medieval period. |
