Year of Award

2025

Document Type

Thesis

Degree Type

Master of Arts (MA)

Degree Name

Anthropology (Forensic and Biological Anthropology)

Department or School/College

Department of Anthropology

Committee Chair

Meradeth Snow

Commitee Members

Randal R. Skelton, Kristine Pilgrim

Keywords

West Mexico, Paleopathology, aDNA, Bioinformatics

Subject Categories

Biological and Physical Anthropology

Abstract

The application of metagenomic tools to further elucidate ancient DNA (aDNA) holds promise in paleopathology, particularly for inferring disease patterns in ancient populations, especially in those that are understudied. This study conducts a comparative analysis of the efficacy of taxonomic pipelines--Kraken 2, HOPS/MALT, and HAYSTAC--in detecting pathogens within highly degraded aDNA samples extracted from 22 Medio Period Paquimé individuals from the Casas Grandes archaeological site in Northwest Mexico. The taxonomic results from the pipelines are compared with contamination detection program mapDamage, although concerns arose about the latter program’s ability to work with prokaryotes. Additionally, the findings are compared against prior literature regarding health and ecology. This study tests three hypotheses: (1) that employing multiple taxonomic pipelines provides a cross-validation mechanism for identifying authentic reads in pathogen identification without predefined targets (i.e., a blind sweep); (2) that newer pipelines, specifically those that address the unique issues that arise with aDNA samples, will outperform older models in taxa identification; (3) that using these pipelines collectively will provide a foundation for future studies on the health and disease patterns of Casas Grandes. This study aims to better understand the implications of cross-validating taxonomic pipelines in paleogenomics and paleoepidemiology. It also seeks to address persistent limitations in these fields and improve methods for investigating disease in ancient populations. The project’s broader implications for improving pathogen detection and health history reconstruction in paleogenomics, especially for underrepresented populations in the literature. Initially, the authenticated aDNA reads generated in this analysis hoped to serve as preliminary data for future studies related to the genetic histories of the Casas Grandes peoples. However, in testing the three aforementioned taxonomic pipelines, it was found that only Kraken2 was successfully able to produce authentic reads from the aDNA samples. HOPS/ MALT was no longer available and HAYSTAC’s current system is not compatible with identification without predefined targets. What was found does provide some very minor avenues for futures investigations into agriculture-human interactions and the health of the Casas Grandes peoples; however, these avenues are only weakly supported. The study highlights the need for further research into methodologies in health studies and continued advancements in bioinformatics for aDNA.

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© Copyright 2025 Victoria Lynne Giovannangelo