Archaeogenomics is the name of the group that molecular biologist Vanessa Villalba Mouco has been leading for a few months at the Institute of Evolutionary Biology (IBE-CSIC-UPF), a joint center of the Spanish National Research Council (CSIC) and Pompeu Fabra University (UPF) in Barcelona. It refers to a discipline capable of integrating genomic and archaeological analyses to shed light on hypotheses posed by archaeological remains and written documents.

She already knows this institute well, having completed her postdoctoral stage there, during which she studied the impact of the last Ice Age on the Iberian Peninsula, between approximately 25,000 and 20,000 years ago. Now, she has returned to focus on studying the social organization of al-Andalus in medieval Iberia using genomic data. In this interview, the researcher expresses her desire to “act as a bridge” between the two worlds—genomics and archaeology—so that her students “learn what is necessary to do archaeogenomics in a truly collaborative way.”

Q: You’ve recently arrived at IBE, and it’s early to ask about results, but what are the questions you aim to answer in the two projects on al-Andalus in medieval Iberia that you’re leading?
A: We’re interested in studying the impact of the arrival of Islam in the Iberian Peninsula, focusing on the northeastern region—Navarre, Aragon, and Catalonia. We want to try to understand everyday life stories through the study of Islamic-era necropolises, which in the Iberian Peninsula spanned from the 8th to the 15th centuries, but also late Roman, Visigothic, and Carolingian ones, which could be Christian, Jewish, or Muslim. When people died, they were buried according to their culture, but what were their interactions in life? By studying kinship between necropolises through genomics, we might find that these interactions were more frequent than we thought.

Q: In other IBE groups, genomics is used to understand the evolutionary tree on a scale of millions of years. However, with you, we’re talking about the history of our species, which is very recent on an evolutionary scale, right?
A: On the timeline I work with, evolutionary changes have virtually no significance. Archaeogenomics studies changes in human populations and their correlation with what is inferred from written documents or archaeological excavations. Often, we base our work on hypotheses already proposed by archaeology and try to bring clarity through genomic analysis—for example, deciphering whether people buried together in a necropolis belonged to the same family unit or not.

Q: What can kinship relationships among individuals in the necropolises you study tell us about the culture of past human populations?
A: Some time ago, I worked at the Almoloya site (Murcia), which belongs to the Argaric society of the Bronze Age, where we sequenced all individuals to study their biological kinship. What we found was that adult women had no adult sisters or daughters at the site, while men did. This pattern of maintaining the settlement through the paternal line, or virilocality, and of women marrying out to nearby sites can only be verified genetically. At the same time, it helps interpret the cultural context—how knowledge, material culture, and even language were transferred between populations. In this case, it’s more likely that women were the ones who moved to other settlements.

Q: Archaeogenomics requires close collaboration with archaeology and history. How do you engage with those disciplines?
A: I defended my thesis in a History faculty, and I believe the major studies being published today are thanks to how well archaeology or historical context is integrated with genomics. That’s why I try to maintain ties with the archaeology groups I’ve worked with, especially from the Iberian Peninsula, both from recent prehistory and from Antiquity and the Middle Ages. For example, right now we have a student working on Islamic chronology in the Tauste necropolis (Zaragoza), and another focused on Neolithic communities in the central Pyrenees and northeastern Iberia. We collaborate with archaeologists from the Autonomous University of Barcelona, the Complutense University of Madrid, and other places like Burgos and Albacete.

Q: However, until now you had mostly worked with Paleolithic-era material, and your CV includes high-impact publications on that period.
A: Yes, in my doctoral thesis and postdoctoral stage, I studied the impact of the last Ice Age, between about 25,000 and 20,000 years ago, on hunter-gatherer communities in the Iberian Peninsula compared to the rest of Europe. We know it was a dramatic event for populations living in Central Europe, who had to move south to the Iberian, Italian, and Balkan peninsulas to survive in more favorable conditions.

Q: What were the consequences of that event?
A: It caused a significant reduction in genetic diversity within populations, which became fragmented and underwent structural changes. When the glacial period ended and the climate improved around 14,000 years ago, everything began to reconnect—but the Iberian Peninsula was one of the least connected regions. That’s why we still see lineages that existed before the Ice Age and survived into the postglacial period, even nearly interacting with the first farmers who arrived later. Through genomics, we’ve been able to connect the Upper Paleolithic with almost Neolithic chronologies.

Q: Is working with such ancient material from the Paleolithic the same as working with more recent material, like from the Islamic period?
A: In Paleolithic contexts, we have very few individuals—we’re placing a data point every thousand years on the timeline. Paleolithic remains are highly degraded, and a human bone fragment might appear among thousands of animal remains, whereas in an Islamic necropolis, we find whole individuals whose genetic material may be more or less degraded. That’s why, when dealing with the oldest chronologies, you have to try many times, and the results aren’t always satisfactory, or you don’t achieve the resolution you’d like.

Q: What questions remain unanswered due to this lack of older material?
A: Ideally, we’d be able to compare interactions between hunter-gatherer groups from different areas. I continue collaborating on other projects to better interpret these population dynamics and make more sense of the genetic data in relation to their archaeological context. In the Iberian Peninsula, we see cultural changes in the form of different tools, techniques, and knowledge—just like in other parts of Europe—but here, our genetic signature changes very little. So, trying to understand how these technocomplexes emerged means figuring out whether it was due to environmental adaptation, cultural exchanges with other populations that didn’t leave a genetic trace, or other reasons.

Q: One of the central problems archaeogenomics tries to solve is precisely the scarcity of very poorly preserved material that, until recently, was unrecoverable. When this becomes possible through the development of paleogenomics, a whole universe of possibilities opens up. What was it like working in the lab founded by the father of this discipline, Svante Pääbo?
A: I was a postdoctoral researcher at the Max Planck Institute for Evolutionary Anthropology (Germany) when Svante was leading the center. There, I worked with Johannes Krause, one of Svante’s top protégés, who, for example, was part of the Neanderthal genome project published in 2010. He’s also the first author of the first sequencing of the Denisovan mitochondrial genome—closely related to Neanderthals—based on a phalanx fragment. That’s how this group, of which very few remains exist, was first described.

Because of my interest in very ancient chronologies, Johannes gave me the opportunity to participate in a project—published in December 2024—in which we sequenced, at high coverage, the oldest genomes in Europe, around 46,000 years old. Their bone remains are so fragmented that, until now, only their material culture had been studied, which led to the assumption that they might be Neanderthals, since it wasn’t known that modern humans had existed that far back. Thanks to sequencing, we now know that Neanderthal and modern human populations coexisted in the same area of Europe at that time.

Q: You’ve now returned to IBE and share the center with another major expert in paleogenomics, Carlos Lalueza-Fox, who co-authored the 2010 publication with Pääbo and others announcing that humans and Neanderthals interbred while coexisting. How do you approach working with your lab students?
A: I want the students in my group to have a very diverse background. I’d love for archaeologists eager to learn genomics to join us, as well as bioinformaticians and geneticists who respect archaeological and historical heritage. I’m a molecular biologist, but I want to act as a bridge between both worlds and help them learn what I believe is necessary to practice this discipline in a truly collaborative way.

ANA LOZANO DEL CAMPO / Content produced within the framework of the CSIC – BBVA Foundation Scientific Communication Grants Programme, 2023 Call