Dr. Camilla Speller is an Assistant Professor in the Department of Anthropology at UBC. Dr. Speller is a biomolecular archaeologist, and a specialist of ancient DNA and protein analysis. Her previous work includes the use of these techniques to reconstruct marine ecosystems, investigate the genetic history of domestic turkeys, and search for clues of past dietary practice in ancient dental tartar. In Spring of 2021, I interviewed her about her newly constructed lab facility, ADαPT, a centre for ancient DNA and ancient protein analysis at UBC.
—-Lindsey Paskulin, PhD student in the UBC Department of Anthropology and Graduate Academic Assistant, Communications (spring 2021)
LP: Congratulations on completing construction on facilities for ADαPT!
CS: Thank you! It’s taken 2 and a half years to get here, and I’m really excited about working in these new state-of-the-art facilities.
LP: I know I work there, but let’s pretend for this interview that I am unfamiliar with your new lab facility.
Can you tell me a little about ADαPT and your hopes for it going forward?
CS: The ADαPT facility is actually made up of multiple labs. It includes the biomolecular clean room located in the Museum of Anthropology, and a ZooMS facility in the Anthropology Department building. It also has a DNA sequencing preparation space as part of a shared facility in the Michael Smith Laboratories. Now that the lab is up and running, my hopes are that we will be able to make a real contribution to archaeology in BC. ADαPT could particularly benefit Indigenous communities by addressing some of their pressing research concerns over marine ecology and biodiversity, and rights and titles around Indigenous fisheries.
The lab, however, is not only focused in BC; we will also be doing work on ancient marine ecosystems in the North Atlantic and South Pacific, as well as research on ancient proteins more generally, including the analysis of proteins trapped in dental calculus and in pottery.
LP: What’s the difference between ancient protein analysis and DNA?
CS: A lot of us are familiar with DNA as our genetic blueprint, essentially the instruction manual for our body.
…In regard to the relationship between DNA and proteins, I like to think of DNA as the recipe for the body, and proteins are the meals— the cookies! — produced from this recipe…
DNA has two main functions. The first is to replicate itself and the second is to produce proteins. Proteins carry out most of the biological functions in our body; they hold our skeleton together, act as our hormones, build muscle, and make up our immune system. Our whole body is essentially protein. So— if by studying ancient genomics we can study the genetic blueprints of humans, plants, and animals in the past— by studying ancient proteins we can actually investigate the products of those blueprints; we can look at different tissues and how different biological systems worked in the past.
LP: That’s a great analogy. Can you walk us through some of the projects currently being undertaken in ADαPT?
CS: One of our major projects revolves around identifying marine organisms in archaeological contexts.
…We accomplish this through the analysis of bone collagen using Zooarchaeology by Mass Spectrometry (known as ZooMS), a rapid, cost-effective species identification method…
We’re using the ZooMS technique to look at the different species of marine organisms used in the past, including fish, whales, and other marine mammals. Something we’re working on now is the development of ZooMS for all kinds of British Columbia fauna. Applying this technique to a wider range of materials and species is a main goal of the lab.
Other projects include looking at ways in which genetic diversity of marine organisms have been impacted through time, especially by commercial harvesting in the last few centuries. We are also working actively on genome-based projects of species like herring, salmon, and whales. Finally, as part of the ancient proteins work, with my PhD student Lindsey Paskulin [pointed look], we’re examining how proteins preserve on archaeological ceramic pottery to understand ancient diet and subsistence in different contexts worldwide.
LP: Hey, that’s me! [laughing] Right now, there are only a few of us working in the labs. What could students do if they want to join us in ADαPT?
CS: First you have to undertake a lot of training [laughing] Ancient biomolecules like DNA and proteins are highly susceptible to contamination from modern sources. When we work in the lab, we have to wear intensive personal protective equipment, such as Tyvek suits, masks, gloves, and hairnets. The lab is equipped with a lot of anti-contamination protocols like UV lights to kill any modern contaminants on our work sources, and positive pressure to make sure modern DNA is kept out of the lab. The first thing we need to make sure is that everyone who works in that lab is trained in contamination controls.
…More broadly though, I look for students who are foremost excited and interested in doing biomolecular research…
The students who work in my lab are drawn from anthropology, biology, archaeology, and the Institute of Fisheries and Oceans; students are welcome from a wide array of disciplines. We always have the opportunity for training in techniques of ancient proteomics and genomics.
LP: Are there many labs like this in Canada?
CS: Actually no! Our lab is in fact unique in North America. Though there are other ancient DNA labs, there are currently no other labs dedicated to both ancient DNA and protein research, including ZooMS. We really have a full complement of biomolecular techniques represented at ADαPT.
LP: We really do! It seems as though ADαPT is the result of many years of your research and time. I’m curious: How’d you first become interested in ancient DNA and protein analysis?
CS: It happened by accident, really. After I finished my undergraduate degree in archaeology and biological anthropology, I worked a few years in a consulting environmental services firm. I did not find that very congenial. [laughing]
…I decided to go back to university to pursue a graduate degree in archaeology. At the time, I wasn’t sure what I wanted to focus on…
I knew I wanted to go into biomolecular anthropology and archaeology, but I didn’t really know what I wanted to specialise in. So, I went to see my head of department at the University of Calgary, Dr. Annie Katzenberg, who suggested I specialise in ancient DNA. I had never thought about pursuing this line of research before. She mentioned there was a new ancient DNA facility opening up at Simon Fraser University led by Dr. Dongya Yang. Even though I had no background in genetics, I thought this sounded like a lot of fun and so I applied!
I ended up doing my master’s and PhD research at Simon Fraser and that’s where I developed my expertise in ancient DNA analysis. Then, I was lucky enough to receive a Marie Skłodowska-Curie fellowship to the BioArCh Centre at the University of York in the UK. There, I started my first forays into ancient protein research, first with ZooMS and then later with proteomics under the mentorship of Matthew Collins, a world expert in ancient protein research. BioArCh is really where I developed the full complementary set of techniques that are reflected in the ADαPT facilities here at UBC.
LP: It sounds like being in the UK provided you with unique opportunities. Is research much different in the UK compared to here?
CS: There are a lot of really fantastic aspects of working in the UK and in Europe more generally. The BioArCh lab at the University of York is a world leader in ancient biomolecular research. So, the level of training and breadth of resources they were able to provide were excellent. But, I also love working in Canada — being able to work on coastal ecosystems, which are close to my heart, and being able to contribute to some of the pressing concerns of Indigenous people here in my home country, which I say with respect to my position as a white settler Canadian. Addressing some of these concerns on a national level has been an important and valuable goal for my own research.
LP: What’s it like working at UBC as a biomolecular specialist?
CS: What I like about UBC is being in the Laboratory of Archaeology (LOA) surrounded by great colleagues who work on a wide range of archaeological issues. Also, having the opportunity to work with First Nations communities in Vancouver.
…Having my home, my work, and my lab on the traditional, ancestral, and unceded territory of the Musqueam people, it is a privilege for me to be able to work with and for Musqueam, Tsleil-Waututh, and other Nations...
For me, that is one of the most exciting things about working here at UBC.
LP: You mentioned before that you often work with bone, and that you work closely with First Nations communities. What are some ethical challenges you’ve faced in your research?
CS: There are huge ethical considerations. The first are the ethics associated with any kind of destructive analysis. We have to be thoughtful about the samples we choose because once they have been extracted in the lab, we have destroyed that subsample of bone. In addition to the genetic material we can gain for samples, we need to make sure we can maximize the amount of information that we recover. As part of this, I’ve been trialling some non-invasive or minimally destructive methods, particularly for ZooMS, to reduce the amount of material we use and the impact of our analysis on cultural heritage material.
The second ethical question I often run up against, particularly in North American contexts, is the potential to be analysing ancestor or human remains. In our work, particularly when we are doing a species identification experiment, we sometimes encounter what we don’t know are ancestor or human remains until they are analysed. Sometimes we haven’t even considered the possibility that we might encounter ancestor remains when we start the project, due to the context or state of the samples. We’ve had a few projects now where we unknowingly uncovered ancestor remains as part of a project that we thought was focused only on faunal material. Now, this issue is much more at the forefront of my mind when I begin projects, and I think about that possibility as it may arise and try to talk to communities about this possibility before we begin projects.
The final ethical question is centred around community involvement. In the past, biomolecular archaeologists would often rifle through museum collections and take what they wanted to analyse, without thinking about permissions needs from descendent communities and their involvement in those projects.
…One of the most important ethical considerations now is including descendent communities in our research, and making sure that they are not just consulted, but are actively involved in research design and in interpretation of the results…
LP: Your work seems very lab focused. Do you get to do any fieldwork as part of your job?
CS: Sadly, no [laughing] Every other archaeologist gets to go out and dig in these wonderful places, like Jamaica, China, Europe, and Africa. Everyone just sends me samples. So, I’ll be sitting in the lab while everyone else gets to be on the beach. Sometimes it can be disappointing.
When I can, I try to visit field sites. But one of the things I’ve been trying to push in my research is using archaeological material that has already been excavated. A lot of material ends up in repositories where it is, in a sense, abandoned there for ‘future research’. We have these extraordinary repositories filled with biological archives and one of the things I want to do is showcase the use of all this material we keep for posterity.
…My work mostly focuses on museum collections and archaeological material that has been previously excavated — making good use of the information that has already been recovered from the archaeological record…
Archaeological remains are non-renewable— we can never go back and dig a site again. It’s much better if we can return to material that has already been excavated and ask questions made possible by new techniques and technology.
LP: Is there a particular story you have from your lab experiences that has particularly stuck with you?
CS: Hmm…maybe the first time I worked on Neanderthal remains. Oddly enough, I actually worked on some remains from Denisova Cave in Russia really early on, maybe in 2006 or 2007. I worked on a project with Dr. Eddy Rubin’s lab at the U.S. Department of Energy’s Joint Genome Institute in California. We were attempting to extract DNA from faunal remains from Denisova Cave before we actually moved on to some of the more precious hominins remains.
After we successfully recovered DNA from musk ox and Canid remains from a few Upper Palaeolithic sites in Siberia and Russia, the postdoc from the Rubin Lab brought us some hominin samples from various sites— what were presumed to be Neanderthal samples. We had to use a Dremel tool to cut off a tiny bit of bone to preserve the majority of the remains for further study. Even though we were wearing masks and protective equipment, when we were sampling these Neanderthal remains, we could see the bone dust rising into the air. You could smell it and you just knew you were breathing in this Neanderthal bone dust.
At the end of the day, it occurred to me then that I had a very strange job, thinking about how I probably breathed in some Neanderthal bone dust and it was now a part of me [laughing]. Sadly though, we couldn’t recover DNA from those remains with our techniques of the time. At that time, we were still using old-school methods; it was before geneticists were able to sequence whole genomes using the high throughput sequencers that we have today. So, unfortunately, the project wasn’t successful. But I laugh thinking about the fact that I very likely held in my hand one of the earliest Denisovans from Denisova Cave and we just couldn’t get DNA. Had the project happened just a few years later, we could have been part of the great research that led to the discovery of Denisovans.
LP: That’s so unfortunate— you were so close! [laughing] So, then, what’s next for you and for ADαPT?
CS: I am really excited to share ZooMS with both consulting and academic archaeologists all over Canada. We’ve already begun collaboration with archaeologists in BC, in Ontario, and throughout many parts of the United States.
…ZooMS is a really great technique that can address a lot of questions around zooarchaeology, subsistence, diet, hunting practices, Indigenous management practices, and so on…
It’s a method that I hope will be adopted by more labs and continue to grow. I have similar hopes for proteomics more generally. North America hasn’t built labs for ancient protein research and the use of these methods has been fairly limited. By expanding the use of this technique, we want to highlight the role ancient protein analysis can play in archaeology.
LP: Do you have any advice for students interested in biomolecular archaeology?
CS: I sure do! [laughing]
…My first piece of advice is to think broadly in your education…
It is wonderful to have a good foundation in anthropological and archaeological method and theory. Equally important, though, is to have a good foundation in some scientific methods particularly biology and genetics, or biochemistry in the case of proteomics. It helps to have a solid knowledge base about those biomolecules, how they interact in the body, and what influences them.
My second piece of advice is to get comfortable with coding. A lot of biomolecular datasets now are too large and complex to be visualised by eye; it needs to be processed through computer programming software. So, it helps to become comfortable with programs like R, Python, and Linux. These are the important side skills that you need to have as you move into biomolecular archaeology.
In a post-Covid world, Camilla hopes to see more students pursuing research in the ADαPT facilities. Meanwhile, she divides her time between the department building, ADαPT, and her new Bengal kitten.