Archaeological Recovery of Late Pleistocene Hair and Environmental DNA from Interior Alaska

ABSTRACT

Ancient hair and remnant plant DNA are important environmental proxies that preserve for millennia in specific archaeological contexts. However, recovery has been rare from late Pleistocene sites and more may be found if deliberately sought. Once discovered, singular hair fragments are not easily identified to taxa through comparative analyses and environmental DNA (eDNA) extraction can be difficult depending on preservation or contamination. In this paper, we present our methods for the combined recovery of ancient hair specimens and eDNA from sediments to improve our understanding of late Pleistocene environments from the Holzman site along Shaw Creek in interior Alaska. The approach serves as a useful case study for learning more about local environmental changes.

KEYWORDS:

• Late Pleistocene
• archaeology
• ancient hair
• environmental DNA
• field methods‌
• eastern Beringia
• peopling of the Americas‌

Acknowledgements

We recognise that this fieldwork occurred at Debedee Na’ (sheep horn creek) on ancestral Dene land. Funding for the Holzman archaeological project has been provided by Adelphi University in partnership with Shaw Creek Archaeological Research, LLC. Beth Shapiro received funding for eDNA processing from NSF ICER 1850949. We also thank all of the student researchers from around the world who assisted in the excavations of the Holzman site. Christina DeBlasio, Julio Ruiz Diaz, Alyssa Booth, and Ariel Barrera cataloged thousands of artifacts in the Adelphi Archaeology Lab. We thank Dan Werndly and Michael Bunce with the Trace and Ancient sedimentary DNA (TrEnD) Laboratory, Department of Environment and Agriculture at Curtin University in Perth, Australia for assistance with developing excavation protocols designed to reduce DNA contamination.

Disclosure Statement

No potential conflict of interest was reported by the author(s).

Notes

1 https://github.com/Paleogenomics/DNA-Post-Processing/blob/master/mito_assembly_pipeline.sh (Vershinina et al. 2020).

Additional information

Funding

This work was supported by Adelphi University and a National Science Foundation ICER grant [1850949] from Beth Shapiro at the University of California Santa Cruz Paleogenomics Laboratory.

Notes on contributors

Brian T. Wygal

Brian T. Wygal is an associate professor in the Department of Anthropology and the Director of Environmental Studies and Sciences at Adelphi University in New York. His research interests include environmental archaeology, deglaciation and human colonization, human ecology, and technological organization. He has a PhD in Anthropology from the University of Nevada, Reno.

Kathryn E. Krasinski

Kathryn E. Krasinski is an assistant professor in the Department of Anthropology at Adelphi University in New York. Her primary research interests include hunter-gatherer subsistence, human diasporas, Late Quaternary extinctions, community anthropology, zooarchaeology, and taphonomy. She has a PhD in Anthropology from the University of Nevada, Reno.

Jessica Z. Metcalfe

Jessica Z. Metcalfe is an assistant professor in the Department of Anthropology at Lakehead University in Thunder Bay, Ontario. Her research focuses on using terrestrial animal remains to reconstruct ancient environments and human activities. She earned a PhD from the University of Western Ontario, and held Killam and Banting postdoctoral fellowships at the University of British Columbia.

David McMahan

Dave McMahan received an MA from the University of Tennessee in 1983 with a specialty in paleoethnobotany. He had a long career as an archaeologist and forensic consultant in Alaska, and retired as Alaska State Archaeologist in 2013. He was trained in hair identification at McCrone Institute in Chicago, and cultivated an interest in archaeo-microscopy throughout his career.

Charles E. Holmes

Charles E. Holmes is an affiliate research professor at the University of Alaska Fairbanks and earned his PhD from Washington State University. His research interests include lithic technology, geoarchaeology, palaeo-environmental reconstruction, Beringian archaeology, and Alaska Native prehistory.

Barbara A. Crass

Barbara A. Crass is a research affiliate of the University of Alaska Museum of the North Archaeology Collection. She earned her PhD at the University of Wisconsin-Milwaukee with a specialty in Inuit mortuary analysis. Her research interests include Alaska Native prehistory, Beringian archaeology, bone as a fuel source, and hearth residues.

Teresa A. Wriston

Teresa Wriston is an assistant research professor and geoarchaeologist at the Desert Research Institute in Reno, Nevada. Since receiving her PhD from the University of Nevada, Reno, she has focused on understanding the complex history between humans and their changing environments and modeling differential archaeological site preservation.

Sabrina Shirazi

Sabrina Shirazi completed her PhD in Ecology and Evolutionary Biology at University of California Santa Cruz with a research focus on ancient and environmental DNA.

Alisa Vershinina

Alisa O. Vershinina is a postdoctoral scholar in the Ecology and Evolutionary Biology Department at the University of California Santa Cruz. She completed her PhD in Ecology and Evolutionary Biology from UC Santa Cruz and MS in Biology from St Petersburg State University, Russia. Her research focus is evolutionary history and population paleogenomics of Pleistocene megamammals.

Beth Shapiro

Beth Shapiro is an investigator with the Howard Hughes Medical Institute and professor of Ecology and Evolutionary Biology at the University of California Santa Cruz. Her research uses genetic data, including that recovered from the remains of long dead plants and animals, to better understand how species and populations evolve through time. She earned undergraduate and MS degrees from the University of Georgia and a DPhil from Oxford University.