Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA

Scott D. Hamilton-Brehm, Lidia T. Hristova, Susan R. Edwards, Jeffrey R. Wedding, Meradeth Snow, Brittany R. Kruger, Duane P. Moser

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Chewed and expectorated quids, indigestible stringy fibers from the roasted inner pulp of agave or yucca root, have proven resilient over long periods of time in dry cave environments and correspondingly, although little studied, are common in archaeological archives. In the late 1960s, thousands of quids were recovered from Mule Spring Rockshelter (Nevada, USA) deposits and stored without consideration to DNA preservation in a museum collection, remaining unstudied for over fifty years. To assess the utility of these materials as repositories for genetic information about past inhabitants of the region and their movements, twenty-one quids were selected from arbitrary excavation depths for detailed analysis. Human mitochondrial DNA sequences from the quids were amplified by PCR and screened for diagnostic single nucleotide polymorphisms. Most detected single nucleotide polymorphisms were consistent with recognized Native American haplogroup subclades B2a5, B2i1, C1, C1c, C1c2, and D1; with the majority of the sample set consistent with subclades C1, C1c, and C1c2. In parallel with the DNA analysis, each quid was radiocarbon dated, revealing a time-resolved pattern of occupancy from 347 to 977 calibrated years before present. In particular, this dataset reveals strong evidence for the presence of haplogroup C1/C1c at the Southwestern edge of the US Great Basin from ~670 to 980 cal YBP, which may temporally correspond with the beginnings of the so-called Numic Spread into the region. The research described here demonstrates an approach which combines targeted DNA analysis with radiocarbon age dating; thus enabling the genetic analysis of archaeological materials of uncertain stratigraphic context. Here we present a survey of the maternal genetic profiles from people who used the Mule Spring Rockshelter and the historic timing of their utilization of a key natural resource.

Original languageEnglish
Article numbere0194223
JournalPLoS ONE
Issue number3
StatePublished - Mar 2018


This work received support from Frederick Lander Family Foundation, SE SH LH DM JW; Desert Research Institute salary support for DM, SH, and LH; and Southern Illinois University Carbondale, support for SH and MS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We are grateful to the Bureau of Land Management’s Nevada State and Las Vegas District Offices for their cooperation and permission to process samples from their Mule Spring Rockshelter collections. We thank Dr. Steven Leblanc for perceptive conversations, and Justin C. Tackney and Dr. Antonio Torroni for helpful discussions, and eight anonymous reviewers for helpful suggestion that improved the manuscript. Thank you to Rachel Summers for her aid in the aDNA laboratory. We also thank Dr. Christina Warinner for insights on molecular methods and Sophie Baker for editorial comments.

FundersFunder number
Desert Research Institute
Southern Illinois University


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