Diyendo Massilani

Geneticist Diyendo Massilani explores humanity’s history through DNA

Speaking with Diyendo Massilani is an absolute delight, not only because he is one of the friendliest people I have ever met, but also because his research has captivated me for a long time.

Diyendo is an Assistant Professor at Yale University and an expert in ancient DNA (aDNA).

He honed his craft in the laboratory of Svante Pääbo, who received the Nobel Prize in 2022 for his groundbreaking work in aDNA and evolutionary genetics. Old human remains are crucial for this fascinating kind of research. Interestingly, Diyendo and his team take the field a step further by retrieving this precious kind of aDNA not only from bones, but also from sediment, allowing them to investigate the evolution of both modern and extinct human populations.

This fascinating line of research allows Diyendo to travel to some of the most remarkable places on Earth, where he applies the methods he has developed to safely retrieve the precious samples that enable him to act as a true time detective.

I caught up with Diyendo between trips at his office at Yale University for an exciting interview, or rather, a journey through time.

Could you please share with us where you grew up and when you realized you wanted to make science your profession?

I grew up in Gabon, which is a small country right on the equator in central Africa by the Atlantic Ocean. The cities can be quite busy and crowded, and it can be difficult even to get proper electricity or running water. You can imagine growing up at the end of the 80s and the beginning of the 90s we did not have lot to do as kids. When you are not at school you are just sitting at home, and I used to keep myself busy. As a young kid, I think I did a lot of science on my own without even knowing it. I would go outside and play with herbs or soil and I would mix things together. If I wanted to create some greenish water, I could mix water with specific leaves that would make that color. I think this is how I came to a career in science but not because I wanted to become a scientist. I wanted to be a teacher since elementary school.

I remember when I would get out of school, I would go behind the garden in the backyard, and the herbs were my students. I would teach them what I learned that day at school for 30 minutes and even give them names.

I just wanted to teach but I was also getting very good grades in science, especially in biology and chemistry. When I had my first class in genetics, I was totally mesmerized by it. I had always asked myself the question of why people look different, especially because my grandfather is French, my mom is quite mixed with very light skin, and my sister is much more like light skinned than me and my hair is a little bit different than hers as well. My family circle was showcasing different phenotypes and dominant and recessive genes, topics I learned a lot about in these courses. When I started at university, I decided to focus on the subjects I had the best grades in, biology and chemistry, and then I just kept going, had a lot of fun and became a researcher, not a teacher.

How did your university experience shape you as a scientist? Did you learn a lot more about your curiosity?

I saw many people doing amazing science and I was not critical enough to recognize bad or good science, it was all so interesting. I focused on figuring out what kind of scientist I wanted to be by looking at my professors as role models and finding inspiration from them. That is also why I wanted to teach when I was younger.

Could you please tell us a little bit about the research focus of your laboratory: evolutionary history of modern and extinct human populations? How does your work with ancient DNA (aDNA) help reveal human population history and adaptation?

Evolution is amazing. It is remarkable how subtly environments can shape organisms, allowing them to change and grow. It is beautiful to think about life evolving over millions of years. When we talk about humans, it becomes even more fascinating, because we are talking about ourselves—how we came to be what we are today. It is truly mind-blowing to compare humans with other animals and ask how we reached this level of complexity. We all started as a single cell, yet we became thinking organisms capable of shaping our environment. How is that possible? What mechanisms led us here?

There are many characteristics involved—social, psychological, and biological—but what fascinates me most is genetics. Genetics is the blueprint of any organism. I am interested in how our DNA evolved to create the incredible diversity we see today. Even among present-day humans across the globe, we are remarkably diverse, despite sharing a common ancestor around 300,000 years ago. This diversity exists because of the different environments humans have lived in. The question is how does the environment modulates organisms’ genetics to shape traits that improve survival?

Often, this happens through small, specific changes in DNA, like substitutions that affect gene expression or create new protein variants. These changes can lead to features that make an organism better adapted to its environment.

Traditionally, we infer the past by studying the DNA of people living today. However, ancient DNA allows us to do something extraordinary. We can directly study the genetic makeup of people who lived thousands of years ago. We can compare genomes from individuals who lived 2,000, 10,000, or even 40,000 years ago with modern genomes to see what has changed and what has remained the same. This is incredibly powerful—almost like traveling back in time. Ancient DNA allows us to reconstruct how people looked, what environments they adapted to, and how populations changed over time.

My work focuses on retrieving ancient DNA, reconstructing genomes from past individuals, and using this information to understand how past populations led to present-day humans. One of the most exciting questions in the field involves extinct forms of humans. Today, only modern humans exist, but archaeological evidence shows that many different human forms lived tens or hundreds of thousands of years ago. By extracting DNA from these extinct humans and comparing it to ours, we can begin to understand why they went extinct and why modern humans persist, and ultimately thrive.

You are a pioneer in isolating aDNA from unusual sources and materials. What has been the most surprising or curious source from which you have been able to isolate aDNA?

One of the most surprising sources of ancient DNA I have worked with is sediment. Advances in methods have shown that almost any material derived from a living organism can preserve traces of DNA. Beyond bones and teeth, DNA can be recovered from feathers, plant remains, and even soil. Humans constantly shed DNA into their environment through touch, breathing, blood, and waste, and probably more so for ancient humans. This DNA can become preserved in sediment.

By extracting DNA from sediment layers that are tens of thousands of years old, we can identify the humans who once stood there. Sediments are particularly valuable because they are abundant at archaeological sites. However, working with sediment for ancient DNA analyses poses distinct challenges because sediments are complex mixtures of organic and inorganic material that can vary over fine spatial scales, undergo post-depositional mixing, and preserve ancient DNA inconsistently, with both DNA sources within sediments and preservation conditions still poorly understood. We are consistently developing new techniques, like suspending sediment in resin, that allow us to extract ancient DNA at the microscale and improve control over its spatial provenance.

Sediment is the most abundant ancient material excavated at an archaeological site, so while human DNA in sediment is diluted among DNA from many organisms, the sheer volume of material allows us to recover meaningful data. What makes sediment DNA especially exciting is that it provides a holistic picture. Only looking at human DNA does not tell you the whole story of that human’s life. From just one gram of sediment, we can recover human DNA alongside DNA from plants, animals, microbes, and pathogens. This allows us to study not only human genetics but also diet, environment, and disease all at once. It opens the door to integrative approaches that link genetic change with environmental change.

If you could sample ancient DNA from any archaeological site or material on earth, where would it be and why?

East Asia is my dream area to sample, and I am already working in Mongolia. East Asia has a lot of archaeological evidence for many different forms of humans. Researchers think Homo erectus was in Southeast Asia going back to 50,000 years ago when, in other parts of the world, like in Europe, we think they disappeared around 700,000 years ago. Asia seems to have preserved a diversity of human life which overlaps for quite a long period of time, certainly more than Europe.

Africa would also be a dream location because Africa is still a black box. Very little archaeology has been conducted on the continent, so we know more about Eurasia and East Asia. A cave site where I am working has evidence of human occupation over 500,000 years ago, so it would be phenomenal to get human DNA that has been there for 500,000, 400,000 and 300,000 years ago too.

East Asia is where we discovered the Denisovans, a different form of archaic human that was not known in the archeological records. We know the whole morphology of Neanderthals in Europe but there was a counterpart of Neanderthal in Asia which we only discovered on the basis of DNA that was extracted from skeletal remains. We are going to learn so much about human evolution from East Asia.

In central Africa we have evidence of “ghost populations” that existed in the past and contributed ancestry to present day humans, inferred from traces of highly divergent DNA found within the genome of present-day humans, even though these populations themselves remain unknown. We need to figure out who they are, how they are related to us, how they contributed to our gene pool and why they went extinct, to gain deeper insight into human evolutionary history and biology.

What is your favorite career milestone so far?

I was working on a sample from Mongolia which we first thought was an archaic human, but it turned out to be a modern human. What was interesting was that this modern human lived 34,000 years ago in Mongolia but one third of their genome was from western Eurasia and the rest was for eastern Eurasia. This shows that ancient humans, even in prehistoric times, were more cosmopolitan than previously thought, despite more obvious constraints on movement and transportation. People used to think about evolution as a linear trajectory – one species evolves into another species into another species. Now we are discovering that one of the forces driving evolution is the mixing of individuals from different groups, which create new combinations of genetic variants that enable novel adaptive capabilities. This mixture is a web of connections between people, and I love to think about the power of admixture in human evolution. People need to realize that movement, exploration, and interaction with different groups are intrinsic to our nature, and these encounters have driven biological innovation. We are curious animals, through exploration, we evolve.

That paper was my chance to introduce the world to this individual who died 34,000 years ago. I also got noticed by people at Yale with that paper. They were having an open application and invited me to apply and I ended up there.

Could you share one of your laboratory’s future research goals?

I want to look at sediments and focus not only on human DNA but also try to reconstruct the whole environment associated with those humans. However, this is very difficult. You cannot just command sequence everything in the sediment. We are developing tools that target specifically pathogens, and we had good results recently with parasites like nematodes.

Parasites have been infecting humans for so long, but we do not see pandemic level infection for nematodes or gut parasite, for example. I have started thinking about the notion of symbiosis between human and some of those parasites because it is difficult to imagine that human did not take advantage of being infected by these parasites for almost all of human history. I want to study the DNA of those past parasites and then study their diversity and look at their co-occurrence with humans to try to understand if there is a symbiotic link.

Who is/are your biggest supporter/supporters?

My past supervisors were very supportive but maybe even sometimes too supportive. There have been times when they think I am still in their labs and want me to drop everything and join a project. Overall though, I am very lucky. My PhD supervisors treat me like their own family, and they still call me from time to time just to ask how I am doing and how they can help.

This is also true for my postdoc supervisor. We have a friendship-type relationship now where we call and talk about both work and personal life issues. My father is also very supportive, but he cannot support me the same way my supervisors can because they are in the field and they can really give advice and help push things for me. It is also important to recognize when I was given bad advice, although from their perspective it was good advice with good intentions.

Who, what, when, where & why?

Who?

- would you like to conduct research with if you had the chance?

Marie Curie.

What?

- do you like to do in your free time?

Mostly hang out with my friends.

When?

- do you find inspiration for your research?

When I am analyzing my data.

Where?

- is your favorite travel destination?

I would say Mongolia – the Gobi Desert is amazing.

Why?

- did you choose your specific research topic(s)?

Simply put, because I love evolution.

How?

- do you deal with setbacks?

I do not let myself down. I just keep on going because I do not like to feel defeated.

…or?

Attend a party or be the host?

Be the host.

Museum or movie theatre?

Movie theatre.

Sneakers or dress shoes?

I would actually say boots.

Optimist or pessimist?

I have to say I am a weird pessimistic person. I will try not to think about outcomes but try hard nevertheless, probably trying to protect myself from disappointment. I just don’t dare being too optimistic somehow.

See the future or change the past?

Change the past – but this question is not really about changing the past or seeing the future. It is really a question about being active or being passive. I choose changing the past because it is more of an active role.

The interview was conducted by Nicole Kilian and has been edited and condensed for clarity.

Image sources: Diyendo Massilani.

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Diyendo Massilani and his team in 2025.