Ancient ‘quids’ reveal genetic information, clues into migration patterns of early Great Basin inhabitants

Ancient ‘quids’ reveal genetic information, clues into migration patterns of early Great Basin inhabitants

Above: Cave opening at the Mule Springs Rockshelter in southern Nevada’s Spring Mountain Range. Credit: Jeffrey Wedding, DRI.


 

Las Vegas, NV (April 24, 2018): If you want to know about your ancestors today, you can send a little saliva to a company where – for a fee – they will analyze your DNA and tell you where you come from. For scientists trying to find out about ancient peoples, however, the challenge is more complex.

Research published in the journal PLOS ONE by a team of archaeologists and microbiologists from Nevada’s Desert Research Institute (DRI) and Southern Illinois University Carbondale (SIU) showcases the use of modern research methods to uncover clues about the genetic ancestry of Native Americans who inhabited the Desert Southwest during the last thousand years.

“We were surprised by the consistency with which we were able to recover intact human DNA from a common type of plant-based artifact,” explained co-principal investigator Duane Moser, Ph.D., an associate research professor of microbiology at DRI and director of DRI’s Environmental Microbiology Laboratory.

During the Late Holocene Epoch, which began 12,000 to 11,500 years ago and continues through the present, occupants of the Mule Spring Rockshelter in the foothills of the Spring Mountains of southern Nevada commonly gathered agave and yucca plants for food. The artichoke-like hearts and inner leaves of the plants were roasted then chewed to consume the sweet fleshy pulp. This left wads of stringy fibers called ‘quids,’ which were spit out and left behind.

In the late 1960s, researchers from DRI and the University of Nevada, Las Vegas (UNLV) led by Richard Brooks, recovered thousands of quids at the rockshelter. Put into storage for half a century without any consideration for DNA preservation, a DRI-led research team decided to re-examine the quid specimens as possible repositories for ancient DNA.

“The quid’s coarse texture is excellent for capturing skin cells from the mouth, making them the equivalent of the modern-day cheek swab,” explained Susan Edwards, an associate research archaeologist at DRI and co-principal investigator who first thought of applying DNA extraction techniques to the quid samples.

A wad of stringy agave plant fibers commonly called ‘quids’.

A wad of stringy agave plant fibers commonly called ‘quids’. Credit: DRI

The research team used laboratory and computational resources at DRI’s Southern Nevada Science Center in Las Vegas, and later at SIU, to identify changes in the mitochondrial DNA sequences that are maintained in ancestrally related populations called haplogroups. These haplogroups can then be compared to Native American tribes and other ancient DNA lineages.

The study showed that the Mule Spring Rockshelter quid specimens ranged in age from about 350 to 980 years old. Because Mule Spring Rockshelter sits at a crossroads between the southern Great Basin, the Mojave Desert, and the Southwest Puebloan cultures, these results may provide a better timeline for an important but contentiously debated event in human history known as the Numic Spread.

Today’s Numic people contend they have always been here, a position some scientists readily support. However, some evidence suggests that Numic-speaking ancestors of contemporary native peoples spread from southern California throughout the Great Basin about 500 to 700 years ago; a date range which overlaps with the current study. Other studies suggest a much earlier arrival.

This research marks only the second time that scientists have been able to sequence human DNA from plant-based artifacts, expanding upon an approach utilized by Steven LeBlanc of Harvard University.

“Since these materials were also radiocarbon dated, in essence they provide a time-resolved hotel registry for this unique site over a period of hundreds of years,” added Moser.

As an added benefit of utilizing DNA from quid samples (rather than from more traditional sources such as bones or teeth), the research team found that they were able to obtain the information they needed while being respectful of cultural sensitivities.

“The distinct advantage of this genetic technique, is that it does not require the sampling of human remains” said Scott Hamilton-Brehm, lead author on the study and assistant professor of microbiology at SIU who completed his postdoctoral research at DRI.

In the future, the team hopes to continue this work by targeting additional quids from the Mule Spring Rockshelter collection, with the possibility of corroborating evidence of older dates for habitation of the site suggested by prior studies of more traditional cultural artifacts. Plans are in the works to perform similar studies on quids from other Great Basin sites to glean additional information about the movements of ancient peoples and utilize more powerful analytical approaches to obtain greater DNA sequence coverage than was obtained by this pilot study.

“We look forward to learning more about Native American presence in the Great Basin and Southwest area, and how the data compares over time,” added Lidia Hristova, a graduate of the UNLV Anthropology Program who conducted much of the hands-on DNA extraction from the samples while working as an undergraduate research assistant at DRI and studying at UNLV.

The full study, “Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA,” is available online from  PLOS ONE: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0194223 

Mule Spring Rockshelter is a protected cultural resource located on BLM-managed lands. DRI access to the Mule Spring collection was granted under permit and loan agreement. 

Tim Crosby, Communications and Marketing Strategist at SIU Carbondale contributed to this press release. 

Additional photos available upon request.  

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The Desert Research Institute (DRI) is a recognized world leader in investigating the effects of natural and human-induced environmental change and advancing technologies aimed at assessing a changing planet. For more than 50 years DRI research faculty, students, and staff have applied scientific understanding to support the effective management of natural resources while meeting Nevada’s needs for economic diversification and science-based educational opportunities. With campuses in Reno and Las Vegas, DRI serves as the non-profit environmental research arm of the Nevada System of Higher Education. For more information, please visit  www.dri.edu.

New research improves prospects for imperiled Devils Hole Pupfish in captivity

New research improves prospects for imperiled Devils Hole Pupfish in captivity

Above: Researchers Joshua Sackett (left) and Duane Moser (right) of DRI help National Park Service officials move scaffolding infrastructure during a routine sampling visit to Devils Hole on December 13, 2014. Credit: Jonathan Eisen.


DRI study finds key differences between artificial habitat and the real Devils Hole

Las Vegas, NV (Tuesday, March 20, 2018): In a first-of-its kind study of comparing the microbiology of Devils Hole with that of a constructed scale replica at the Ash Meadows Fish Conservation Facility (AMFCF), a team of scientists from the Desert Research Institute (DRI) in Las Vegas discovered key differences in nutrient levels and species composition that may be impacting the ability of the highly endangered Devils Hole Pupfish (Cyprinodon diabolis) to survive in captivity.

“We were interested in taking a closer look at the chemical and biological factors that control productivity at both sites,” said Duane Moser, Ph.D., an associate research professor of microbiology at DRI who has been involved with research at Devils Hole since 2008. “In studying both, we could gain some insights into how well the artificial refuge actually replicates Devils Hole, and in turn, offer recommendations for ways to make the refuge a better habitat for the pupfish.”

Devils Hole Pupfish (population 115 in autumn 2017) are an iridescent blue, one-inch-long pupfish. They are native only to Devils Hole, an isolated water-filled cavern of unknown depth located in a detached unit of Death Valley National Park within the Ash Meadows National Wildlife Refuge in Amargosa Valley, Nevada. Devils Hole is an extreme environment, with water temperatures and dissolved oxygen concentrations near their lethal limits for most fishes.

Since 2013, scientists have been trying to establish a backup population of these endangered fish in a constructed tank at the AMFCF, which is located a short distance west of Devils Hole. Although the facility was designed to match the climate, water chemistry and physical dimensions of an area of shallow shelf habitat in Devils Hole, the pupfish have had only limited success reproducing and surviving in this artificial environment.

In 2015, Moser and a team of researchers from DRI set out to learn if there were other factors that might be impacting the success of these fish. Their new study, published in the March edition of PLOS One, characterizes and compares water chemistry and microbial communities between Devils Hole and the AMFCF.

Although water temperature and dissolved oxygen at the AMFCF are intentionally maintained at values that are slightly lower and higher, respectively, from those of Devils Hole, this work shows that the nutrient balance between the two sites is also very different, with AMFCF being strongly nitrogen limited – about five times lower than that of Devils Hole.

In the microbial communities, which contribute to the distribution and availability of dissolved nutrients in the water and are also a food source for the pupfish, the research team discovered more than 2,000 microbial species from 44 distinct phyla present in the water at Devils Hole. They detected similar levels of species diversity at AMFCF, but found that different bacterial phyla were dominant at each site. These differences may relate to the observed differences in nitrogen concentrations.

“Nitrogen levels have an effect on the types of organisms that you’ll find, and the types of metabolisms that they have,” said Joshua Sackett, a graduate research assistant with the Desert Research Institute and doctoral student in the School of Life Sciences at the University of Nevada, Las Vegas. “We found a lot fewer of at least one major category of primary producers – the cyanobacteria – in the AMFCF compared to Devils Hole, and we think that’s due to differences in nutrient concentration.”

One of the strengths of the comparative power of this study is that the data from each site were gathered on the same day. This study highlights the potential importance of considering water chemistry and microbiology when constructing artificial fish habitats – and the team hopes that the information will provide a valuable contribution to the continued survival of the Devils Hole Pupfish in captivity.

“This work revealed very different microbial populations, which we infer might correspond to large differences in nutrient dynamics between the sites – especially in terms of nitrogen,” Moser said. “Consequently, some relatively modest tweaks in how the refuge is operated could potentially improve the prospects for continued survival of one of Earth’s most imperiled fishes.”

The full version of the study – A comparative study of prokaryotic diversity and physicochemical characteristics of Devils Hole and the Ash Meadows Fish Conservation Facility, a constructed analog – is available online: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0194404

For more information about DRI, visit www.dri.edu

Photo caption: Researchers Joshua Sackett (left) and Duane Moser (right) of DRI help National Park Service officials move scaffolding infrastructure during a routine sampling visit to Devils Hole on December 13, 2014. Credit: Jonathan Eisen.

Additional photos are available upon request.

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The Desert Research Institute (DRI) is a recognized world leader in investigating the effects of natural and human-induced environmental change and advancing technologies aimed at assessing a changing planet. For more than 50 years DRI research faculty, students, and staff have applied scientific understanding to support the effective management of natural resources while meeting Nevada’s needs for economic diversification and science-based educational opportunities. With campuses in Reno and Las Vegas, DRI serves as the non-profit environmental research arm of the Nevada System of Higher Education. For more information, please visit www.dri.edu.