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Weather conditions on Quadra and Clavert Island

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Behind Hakai: Rute Carvalho - Hakai Institute

Behind Hakai: Rute Carvalho

A blog series highlighting the people who play an integral role behind the scenes to ensure the data keeps flowing and the Hakai Institute keeps running.

DNA plays an increasingly pivotal role in the Hakai Institute’s research into coastal biodiversity. Our researchers collect a lot of genetic material: samples from marine worms and terrestrial beetles collected during bioblitzes, microscopic plankton captured through weekly surveys, microbiomes of mussel tissues and sea star surfaces, environmental DNA (eDNA) shed into water by a myriad of sea creatures, and much more. But collecting samples is just the start. To identify species, strands of DNA need to be carefully extracted from each sample and sequenced, all without contaminating them with other genetic material (like your own). And that’s where Rute Carvalho comes in. All DNA collected by the Hakai Institute and various university, community, and government collaborators, passes through lab processes Rute sets up and oversees.

Started at Hakai

April 2020


Genomics lab manager

Home Base

Campbell River, BC

Photo by Carolyn Prentice

How long have you worked at the Hakai Institute?

I got the job in March 2020, and we were planning the first day would be April 15. I traveled to Brazil for vacation, then the pandemic started and I had to rush back to Canada. Everything was organized for my move to BC [from Ontario], then no flight tickets, no travelling, no anything. We rented a car, put all the kids in, and moved across Canada when the pandemic started. It’s been really, really nice, but it started in a crazy way!

What do you do at the Hakai Institute?

I am the genomics lab manager—I am in charge of the Marna Genome Lab, specifically keeping that lab working. I take care of safe working procedures, I help the technicians troubleshoot experiments, I look after equipment. I also am responsible for designing some experiments, for example implementing new protocols with the researchers.

Our technicians collect water samples, bring them to the lab, filter them, then we extract DNA from the filters, and from that DNA we prepare the genetic libraries, and then from the libraries we get the DNA sequences. So we have all the steps happening here—it’s awesome.

What got you into this kind of work?

When I was an undergrad student, I was very interested in morphology and morphometrics—analyzing shape and size and the differences between individuals, populations, and species. I was really interested in that because I love math. Then I did my masters in zoology, and I was working with all the stuff I like—math and modeling, and I was really loving that—but at the same time I faced a problem that I could not answer a question with only morphometrics. I needed to learn how to step forward and use genetics as a tool to answer my questions. So I started my PhD, and I could actually mix all of that knowledge with genetics. It’s awesome because it answers many questions. I see genetics not as a closed box, but something that you can apply together with other tools to answer scientific questions.

Genetics is a very powerful tool to solve many problems that we cannot solve just by having some physical samples. For example, we can figure out what species we have in the water using genetics. You have the visual surveys, but the human eye cannot visualize everything. Here it’s very common that after analyzing we find some whale DNA in the water. They didn’t see it; it could have passed by a few hours or minutes before they sampled the water, but you can identify it by DNA. It’s awesome that we can go further than visual surveys.

Is there a particular taxonomic group that interests you?

My roots are herpetology—reptiles and amphibians. Then I just opened the branch for different species: I have publications with birds and with fish, because genetics is a sort of tool can be applied to anything—so it’s not a closed box. You have infinite possibilities.

And polar bears as well! While I was working at Queen’s University [in Ontario] we were developing tools for identifying individual bears by their scat. From the scat that the Inuit were collecting in the field and sending to us, I could tell you which individual it was. This means that in the near future we don’t actually need to see a specific bear to know that it was walking in that area, or how far that individual walked through that habitat.

“I’m a hands-on person, so as with the other technicians I also prepare libraries for sequencing, and I oversee MiSeq, which is the sequencer. We run all the libraries on it that we prepare in-house, and also libraries that some collaborators send to us. So lots of data!” First photo: Hakai’s MiSeq genome sequencer, acquired in late 2019. Photo by the Hakai Institute. Second photo: exploring a Quadra Island beach. Photo by Rute Carvalho

What’s your favorite project you’ve worked on for Hakai?

Right now I’m really involved in the Integrated Coastal Observatory [ICO] project. This is a coordinated network of partners along the coast of British Columbia who are using environmental DNA to monitor marine biodiversity. These partners are members of communities that volunteer by sampling water and sending the samples to Hakai. At Hakai, we process the samples by extracting the DNA and preparing them for DNA sequencing. The end result is a list of fish species that are present in the area where each sample was collected. The resulting information will be shared with partners.

ICO is very exciting because it involves First Nations—it’s very important to have them involved in something that will be returned for their and our benefit. Their sample results contribute to a website we are creating to share information about which species of fish were found in different locations, and if there are differences between months or years. This information will help with monitoring biodiversity and sustainable fisheries.

What’s a unique challenge you’ve had to overcome that people outside your role might not think of?

When we need to implement a new technique, it looks easy because you just read the paper and you say, “Okay we can get the chemicals, we have the equipment.” Then we try to repeat the conditions we saw in the paper, but it doesn’t work. And sometimes it takes a long time to troubleshoot that. The timing of this is sometimes pretty long, and this is a challenge because we need to produce results; some projects depend on that laboratory analysis.

The current one we are developing is to identify fish specifically. We are using one sort of marker called 12S that is very established to identify fish in the water. But it’s tricky, because the universal primer that we use for that DNA fragment also amplifies bacterial DNA, and you have bacteria in everything, including the water. So when you extract DNA from the water, you have fish for sure, but you also have lots of bacterial DNA, and that primer is going to target both groups. To figure out how to troubleshoot that to get exclusively the fish DNA took about two to three months. But it’s awesome when we get the sequencing done and we find many species of fish in our samples.

*This interview has been edited for brevity and clarity.

How does DNA sequencing help biodiversity research?