ASU ancient DNA lab reveals secrets in chimpanzee teeth

January 17, 2020

Dental plaque — the stuff that your hygienist is always scraping off your teeth — holds a treasure trove of your DNA and, if not cleaned off occasionally, will build up and remain on your teeth long after you are gone. This is why dental calculus, or plaque, is a rich source of ancient DNA in the archaeological record and has been used to answer many biological and anthropological questions about Neanderthal diet and behavior and patterns of ancient human migration.

So, when researchers were looking to understand the oral microbiome of our closest relative — chimpanzees — they turned to this record of biological information. chimpanzee tooth with dental plaque A chimpanzee tooth with dental plaque. Photo by Rebecca Nockerts Download Full Image

The study, led by Arizona State University genetic researchers Andrew Ozga and Regents Professor Anne Stone, found that there are core differences between chimpanzee and human oral bacteria. Surprisingly, no other research projects have focused on great ape oral ecosystems using dental calculus. Therefore, analyses of the results could only be compared against existing modern and prehistoric human samples.

From this first-of-its-kind investigation, researchers were able to assemble a full genome of a common pathogenic bacteria, P. gingivalis, from a single chimpanzee, and they found it is not too different from ones found in humans. Results also indicate that though there are many differences between chimpanzee and human oral bacteria, it is not clear if the differences are a result of diet, geography, host genomes or other unknown factors.

The paper, which was co-authored by ASU primatologist Associate Professor Ian Gilby, was published in Nature Scientific Reports and conducted in ASU’s ancient DNA lab, directed by Stone. Stone and Gilby are both research affiliates with the Institute of Human Origins and faculty in the School of Human Evolution and Social Change. Stone is also an associate director of the Center for Evolution and Medicine. Ozga is a former postdoctoral researcher with the ASU Center for Evolution and Medicine, now at Nova Southeastern University.

“Since we can’t go sticking our hands into the mouths of wild chimpanzees to sample oral bacteria, we thought it might be possible to use dental calculus recovered from chimpanzees at Gombe," said Ozga.

Gombe National Park, Tanzania, is the site of Jane Goodall’s long-term research on wild chimpanzees. The skeletal remains of chimpanzees have been retained since the 1960s, which is the source of the dental calculus in the study. Gilby is convener of the Gombe Chimpanzee Research Consortium and has worked in Gombe for more than 20 years.

Using ancient DNA laboratory methods, researchers examined dental calculus samples from 19 Gombe chimpanzees and used two sets of comparative data from prehistoric, historic and modern humans, plus Neanderthal calculus.

chimpanzee maxilla

Chimpanzee maxilla. Photo by Rebecca Nockerts

In addition to the comparative chimpanzee-human microbiome results, researchers wanted to see if the dental calculus preserves genetic material from plants or animals indicative of dietary habits. The Gombe chimpanzees have been observed for more than 50 years, and their diet is well documented. The results of this screening were not definitive, though some dietary DNA was evidenced in two samples.

“Due to the very nature of ancient and degraded historic DNA, we hesitate to conclude that the few DNA sequences we detected originated from the host’s diet,” said Stone.

This study does reveal an important new branch of study for the understanding of health and disease in human’s closest evolutionary cousin. Future research will investigate both wild and captive chimpanzees to see if there are differences between human and chimpanzee groups across different geographic regions and subspecies.

Julie Russ

Assistant director, Institute of Human Origins


Anthropology meets genetics to tell our collective story

ASU Regents' Professor Anne Stone talks about the the latest research in DNA and where it’s going in the future

April 23, 2019

We know that our DNA can tell us a lot about ourselves, from susceptibility to certain cancer types to biological relationships. With services like 23andMe growing in popularity, it seems we are also increasingly interested in what our genes can tell us about our past.

“People enjoy learning more about where they came from, and these kits are one way to do that,” said Anne Stone, a Regents’ Professor in the School of Human Evolution and Social Change and a research affiliate with the Institute of Human Origins at Arizona State University.  photo of Stone in her lab Regents' Professor Anne Stone in her lab. Photo courtesy of ASU Now

But unlike mail-in kits that only give insight into the individual, Stone, an anthropological geneticist, sees DNA’s larger potential for societal and historical revelations.

At her ASU-based Laboratory of Molecular Anthropology, she and her students examine a wide range of topics, from the population history of Peru and the Caribbean, to the microbes that live in the mouths of chimpanzees, humans and other primates.

In 2016, her work in health and populations earned her a place in the prestigious National Academy of Sciences.

Below, she answers questions about the latest research in her field and where it’s going in the future.

Answers have been edited for length and clarity.

Question: What is anthropological genetics?

Answer: Basically, we are using genetic analyses to address questions related to human or primate population history, adaptation or even community relationships. This gives us further insight into human variation and our fascinating past.

Q: How is the field not just answering questions about the past, but also helping make our lives better today and tomorrow?

A: There are several different projects currently in my laboratory that my graduate students and postdocs are working on — genetics is a team effort! — which could have implications for the future.

For example, we are analyzing ancient DNA to learn about the evolutionary history of M. tuberculosis (the pathogen causing tuberculosis) before and after the “Age of Discovery/Colonization.”

This helps us see how the pathogen changes over time and in different hosts, which can help us understand how this pathogen evolves even as it jumps from one host to another. This can provide insight into better ways to design drugs that don’t evolve resistant pathogens. It could also help assess how much of a threat pathogens in other organisms might be.

Another project is testing new forensic methods to extract and analyze DNA from degraded bones, which may lead to new methods to improve our ability to identify victims of forest fires or other disasters.

Q: What are some of the opportunities you see for future research in the field?

A: I think that the biggest changes are likely to be in terms of improving bioinformatics methods to analyze genomic data, which will help us understand more about the complex demographic history of humans and how we have adapted to different environments.

The strength of an anthropological approach is the cross-cultural and interdisciplinary perspective that we typically have. I am always inspired by my students; former undergraduate and graduate students from my lab are now working on a range of interesting projects, including growing bone stem cell “organoids” to understand how bone cells work and influence morphological traits, studying adaptation in tropical hunter-gatherers and comparing how the microbiomes among rural and urban populations differ to see how this might influence health.

More stories on the future of DNA

Mikala Kass

Communications Specialist, ASU Knowledge Enterprise