A new genetic comparison study between ancient people buried east of San Francisco Bay and modern members of California’s Muwekma Ohlone people supports the Tribe’s assertion – backed by family histories, government records and records from the Bay Area Spanish missions – that they and their ancestors have lived in this area longer than many archaeologists have estimated.

Archaeological excavations at Síi Túupentak. (Image credit: Courtesy of Far Western Anthropological Research Group)

In 2014, the San Francisco Public Utilities Commission proposed the creation of an educational facility near the Water Temple in Sunol, California. When it was determined that the site would likely uncover human remains, the Muwekma Ohlone tribe was contacted. The Tribal Council requested a study of two settlement sites found on the land, which date as far back as 490 BCE, or more than 2,500 years ago.

The Tribe brought in the Far Western Anthropological Research Group, with archaeology principal investigator Brian F. Byrd, to direct the archaeological excavations, analysis and reporting as a collaborative endeavor with the Tribe, and University of Illinois Urbana-Champaign anthropology Professor Ripan Malhi to design a genomic project on any remains identified there. Researchers from Stanford University also joined the collaboration to analyze the genomic data.

“It’s a project with the participation of both researchers and tribal leadership from beginning to end,” said Noah Rosenberg, the Stanford Professor in Population Genetics and Society in the School of Humanities and Sciences and co-author of the paper.

The results of that genomic analysis, published March 21 in Proceedings of the National Academy of Sciences, reveal a thread that connects the ancient genomes and genomes from modern-day Muwekma Ohlone. This continuity affirms beliefs held by the Tribe but was somewhat surprising from the point of view of the researchers, given the impacts of European colonization and what is currently hypothesized about the diversity and movement of populations of people who have lived in and around California throughout this time.

One site, which the Tribe has named Síi Túupentak (Place of the Water Round House Site – named after the Sunol Water Temple), dates from between 1345-1850 CE and 76 individuals were buried there. The second site, called Rummey Ta Kuččuwiš Tiprectak (Place of the Stream of the Lagoon Site), dates back 490 BCE-1775 CE and contained burials for 29 individuals.

Stanford News spoke with three of the co-authors of this paper: Rosenberg, Alissa Severson and Alan Leventhal. Severson was a doctoral student in Rosenberg’s lab during this work and is lead author of the paper. Leventhal is an emeritus lecturer in the Department of Anthropology at San Jose State University and an ethnohistorian and archaeologist for the Muwekma Ohlone tribe.

See also: Study ties present-day Native American tribe to ancestors in San Francisco Bay Area


Why did the Tribe initiate these genomic studies?

Leventhal: The recommendations for ancient DNA studies were part of the Tribe’s reclamation of their ancestral heritage sites, but also about having full oversight. So rather than being an afterthought, or rather than just being placed in the acknowledgments of the various publications, the Tribe was central to the research process.

Although left as a landless tribe, the Muwekma Ohlone have never abandoned their tribal relations or left their aboriginal homeland of the San Francisco Bay Area. This is supported by federal records, family histories and marriage, baptismal and death records from the three Bay Area missions – through which the lineages enrolled in the Tribe can trace their ancestry back to their aboriginal villages.

The biological continuity the Muwekma Ohlone are trying to demonstrate challenges what some archaeologists have been publishing without convincing evidence. For example, anthropologist Alfred Kroeber inaccurately declared the Tribe extinct in 1925. Then, more recently, the archaeological community published that there were no Ohlone in the Bay Area prior to 500 CE or, in some cases, prior to 1500 BCE. That murkiness raised the question: What evidence are they using? The Tribe asked me, as one of their archaeologists, how to address that and I told them we’d have to do destructive analysis for both dating and ancient DNA on ancestral remains.

So, having no control over what the results were, they were pleased with what we found. And, as a collaborating tribal entity, the Muwekma tribe is validating themselves in the eyes of the dominant society that practices the “politics of erasure.”

Rosenberg: One of the interesting aspects of this study is that it does have converging motivations. From the perspective of the genomics world, we’re now in an age where genomic analysis of ancient DNA is becoming increasingly feasible – with the potential to test hypotheses about ancient migrations and genetic continuity between ancient peoples and people alive today. The study advances methodology for looking at ancient and modern relationships beyond the specific implications for the Tribe itself.


What kinds of comparisons did you do?

Severson: The oldest site, Rummey Ta Kuččuwiš Tiprectak, had four individuals that we ended up using in the comparison. The more recent site, Síi Túupentak site had eight individuals. The most ancient individual we included in the genomic analysis was dated to the 1st century CE and the most recent to the 1700s. And eight modern individuals participated. That gives us this whole time transect through the region.

First, we tried to assemble whatever publicly available genetic information there was from other ancient and modern Indigenous communities throughout North and South America. That helped for asking the big picture question about where our three sets of individuals fall in relation to all these other populations.

The second set of studies focused on the individuals that we sequenced and the previously reported individuals from the closest regions of Nevada, Southern California, Mexico and the Pacific Northwest. That allowed us to ask more fine-scale questions about relationships. The last piece was to dive into comparisons between the two ancient sites and the modern Muwekma Ohlone.


What did you find?

Severson: When we were looking at the large-scale picture, we found that newly sequenced ancient individuals from the Bay Area clustered most closely with the ancient individuals from Southern California and Nevada.

Then, when we delved in a little bit deeper, we started to see that individuals from Nevada, individuals from Southern California, and individuals from the Bay Area all clustered separately. The fact that we saw this kind of separate clustering that held up over time suggested that these were distinct genetic groups.

Rosenberg: In the most fine-scale analysis, we saw a component of ancestry that was shared between the two ancient sites – one much older than the other – and then we observed that same component of ancestry was present in the present-day Muwekma Ohlone individuals. The component does also exist in other present-day people, but it’s at a much higher proportion of ancestry in the Muwekma Ohlone than in, say, populations from Mexico or the Southwest United States. So that’s suggestive of continuity of that portion of the genetic ancestry from one ancient site to the next and between both ancient sites and the present day.


How do these findings challenge assumptions that researchers might have had about the continuity of Muwekma Ohlone in this area?

Rosenberg: From the tribal oral histories and their understanding of their relationship to this location, the sense is that their ancestors were in this place for a very long time. But because of the disruption of the mission period, as well as many other migrations that took place around California and the West, there are many possible outcomes that could have occurred in the genomic analysis.

Linguistically, the Muwekma Ohlone fall into the Penutian language group, which is dispersed over a wide geographic area in California, the Great Basin and the Pacific Northwest. But in our analysis, we found that the Muwekma Ohlone do not group with other Penutian speakers to a greater extent than one might expect based on geography, and that, in fact, some of the closer samples to the Muwekma Ohlone were from Southern California, where the Penutian family is absent.


Beyond the specific results, what else do you want people to understand about this research and the broader project that encompasses it?

Leventhal: Because the ontogeny of the request came from the Tribe, this is couched in an ethical framework. It’s not anthropologists or biologists looking at Native Americans as objects of study. It’s an attempt for the Tribe to have ownership of their history and heritage and biology. For example, the Tribe can build on this work to recover their ancestral remains from other sites, which is of great significance to them.

Hopefully, it would serve as a model to which other tribal communities, under the appropriate circumstances, can feel comfortable in establishing these collaborations with various scholars whom they trust.

Rosenberg: From the genomics perspective, we’re hoping to take the combination of the scientific approach and the collaborative approach into other projects that involve other tribal collaborators. That’s work with Ripan Malhi, who specializes at this intersection of developing collaborations between genomics researchers and indigenous groups.

Severson: When you’re a student doing the work, it’s not common to have this kind of direct connection to the people who are “the data” that you’re working with. We got to have that dialogue, where we could discuss what we’re doing and what we found, and how that makes sense with their history. I felt very lucky to be working on this project. It felt like what we should be doing.

Additional co-authors of this work are affiliated with Far Western Anthropological Research Group, Northwestern University, University of Illinois at Urbana-Champaign, Florida Atlantic University, the Muwekma Ohlone tribe of the San Francisco Bay Area, and San Jose State University. Rosenberg is also a member of Stanford Bio-X and the Institute for Computational and Mathematical Engineering (ICME).

This research was funded by the National Science Foundation.

To read all stories about Stanford science, subscribe to the biweekly Stanford Science Digest.

Media Contacts

Taylor Kubota, Stanford News Service: (650) 724-7707; tkubota@stanford.edu

Diana Yates, University of Illinois Urbana-Champaign News Bureau: diya@illinois.edu