Graduate student Diana Aguilar Gómez tells the story of Joana Rocha, a visiting scholar in the Rasmus Nielsen lab who ventured into the Sahara Desert to study the genetic adaptations that help desert foxes thrive in extreme environments. From the desert to the command line, Aguilar Gómez explores how Rocha’s genomic project was developed, and how organisms evolve to cope with low water availability and unbearable heat.
By Diana Aguilar Gómez
“All grownups were once children—although few of them remember it.” — The Little Prince (1943) by Antoine de Saint-Exupéry
All scientists were full of curiosity once—although few of them remember it. This story is about a scientist with the curiosity of a child, the kind of curiosity that makes someone brave enough to enter a conflict zone in the Sahara Desert. The story begins with a graduate student and a quest that would lead her across the globe.
A project led by Ph.D. student Joana L. Rocha, who is co-advised by Professor Rasmus Nielsen at UC Berkeley and Raquel Godinho from CIBIO-InBio at the University of Porto, aims to discover how different fox species have adapted to the desert. Rocha is interested in understanding how life can cope with low water availability, sandstorms, intense UV radiation, and extreme temperatures. “Unlike what many people think, deserts are hotspots of biodiversity, they are centers for endemism, which means they have a lot of species that can only be found in a particular area and nowhere else in the world. Deserts have species that are uniquely adapted to cope with life in such hard conditions,” Rocha says.
The project seeks to understand the physiological and genetic adaptations these foxes have from life in the desert. An example of physiological adaptation would be the ability of concentrating urine, which would reduce the loss of water in a dry habitat like the desert. To answer these questions, the researchers selected four North African fox species: the red fox, the Rüppell’s fox, the fennec fox and the pale fox. Getting samples for this project required Rocha to master her explorer fieldwork skills, since looking for foxes in the Sahara is not an easy task.
A collaboration was established with Professor Abdeljebbar Qninba, a conservationist and biodiversity advocate from the University of Rabat. He contributed to the project by providing guidance on obtaining research permits and suggesting locations where the team could look for foxes.
Into the Sahara
Rocha embarked on her journey to the Sahara Desert with Nuno Santos, a wildlife veterinary, and Monia Nakamura, a field technician with experience in capturing Iberian wolves. For this team everything was unknown, because they were not used to this environment. On their first expedition there was a lot of frustration. They drove all the way from Porto in Portugal, crossing by ferry into Morocco, until they reached the Draa Valley. The whole trip takes approximately three days. On the first expedition, after a month in the desert the team only managed to capture one fox. The second expedition was a success, but it was a lot riskier because they ventured into the Western Sahara, a territory disputed by the Kingdom of Morocco and the Sahrawi Arab Democratic Republic. This time they also had local guides, Mohamed Lamine Samlali, and Bhaya Habib, who are part of the NGO Association Nature Initiative. Having local guides made all the difference; since Samlali and Habib are familiar with the desert and know it very well, they made sure to keep the team safe and lead them to the foxes. It is a dangerous area, which still has landmines forgotten from conflicts in the 70s.
Among other challenges, J.L. Rocha had to use different languages through her project to establish collaborations and work around the desert. Her native language is Portuguese, and her research is conducted in English, but for her fieldwork, she had to use some Spanish, French and even tried to learn a bit of Arabic. Moreover, the group camped in the desert, without the commodities of electricity or bathrooms for several weeks.
Setting up the traps was an art: they had to bait them and make sure they didn’t taint them with human odor. Captured in video, the team saw clever foxes who were able to get the bait without activating the trap. Other unwanted, yet beautiful visitors to the traps included a golden wolf and a sand cat. Once they were successful in capturing a fox, they had to act fast: go to the trap, sedate the fox, take tissue and blood samples, and release it back to the desert. Fieldwork in the Sahara required endurance from the team. After getting the samples, a sky full of millions of stars, and the beautiful golden dunes, made all the effort worth it.
From the Desert to the Command Line
When the desert fox from Antoine de Saint-Exupéry’s The Little Prince says, “what is essential is invisible to the eye,” he probably wasn’t referring to DNA, but genomic data was definitely essential for this research project in the Sahara Desert. After the fieldwork ended, the next step was to go to the laboratory at UC Berkeley to proceed with the experiments. Besides the DNA, J.L. Rocha collected physiological samples such as blood or plasma from which she was going to measure different metabolites and hormones. The challenge with these samples is to preserve the original concentrations after extracting them in the scorching desert. The project used almost 100 samples, some of them from the desert captured foxes, some from roadkill and some from zoos. The roadkill is particularly difficult samples since they usually have been rotting for a few days and can be contaminated with genomic material from bacteria.
Different qualities of samples required our fox finder to adjust the concentration of DNA with precision, she needed to make sure she would obtain the same coverage for her samples. Coverage, in genomic terms, refers to the amount of reads per position. Researchers can check which letter (A, T, C, or G) is a particular position in the genome of an individual. A researcher, for example, may read a sequence 10 times, and nine out of ten times, the position is detected as an A. This position would most likely be an A, with the other result being a sequencing error. This position would have coverage of 10. Having all samples with the same coverage would make it easier for giving everything the same treatment and running through the same computational workflow, which will hopefully avoid biases and bioinformatic artifacts. Why are bioinformatics and computers required in this project? The fox genome consists of gigabytes of information, ~2,5000,000,000 ATCG letters in a particular combination, with more than 100 samples, it is impossible to analyze DNA sequences without a computer.
Rocha, by now, had mastered the fieldwork and the benchwork, but perhaps the most challenging part of the project was the computational one. Rocha had zero coding experience and her training had been purely as a biologist in the most traditional sense, where programming is not part of the curriculum. She overcame this lack of previous computational training skillfully and did everything herself: from genome assembly and annotation, to writing her own scripts to run methods that have not been implemented before. Out of her many exciting results, surprisingly she found that the genetic differentiation between the Rüppell’s fox and the red was larger than expected, making it impossible to use some software that she was expecting to use. But, what is a Ph.D. without unexpected results and more challenges than what was originally foreseen?
There are many mechanisms by which species can adapt to certain environments. Some variation in the genome might be useful under certain selective pressures and therefore a certain gene with a mutation/variant will increase in frequency. This means that more individuals in the population would have the gene with the variant responsible for the advantageous characteristic. However, there are also other sources of variation for selection, like adaptation through introgression. Adaptive introgression is when an older resident species, which has been in that environment for longer, hybridizes (couples) with the newcomer species, passing a gene (or a region with several genes) that is functionally relevant for surviving in those conditions. For example, some populations of humans that have adapted to extreme environments, like the Arctic and High-Altitudes, got some of their adaptive genes from older resident hominids. Another example is the dog breed Tibetan mastiff, which got its adaptive gene for hypoxia (low levels of oxygen) from the Tibetan wolf that had been living in the high mountains of Tibet for longer.
“One of the things that I expected was that the desert adaptation would mostly be from pre-existing variation in the genome,” Rocha says, explaining some of the team’s most surprising results. “In our case, we found introgression from the fennec fox, which is the cute little desert fox with big ears, to the Rüppell’s fox, which is another desert species. “
To learn the details of Rocha and collaborators’ work, you will have to hold on to the edge of your seats until the scientific article gets published—the team is currently writing a review paper that will soon be submitted to scientific journals for publication. Could the results of this study on fox adaptation can tell us anything about human adaptation? Rocha notes that scientists have looked at adaptive traits in humans, including aboriginal Australians who are known to have significantly lower thyroid hormone levels compared to Australians of European descent. Population genomic work has found thyroid hormone-related genes under selection, resulting in slower metabolism.
Rocha also notes that a slower metabolism helps desert species optimize the use of limited resources in the desert. Another known pattern that many desert mammals evolved is the urine concentrating ability, which is a response to the low availability of water in the desert. “Having lower metabolism induced by the thyroid-hormone is common in desert environments, this has also been found in rodents in the desert,” Rocha says. “This is an interesting evolutionary pattern.”
To learn more about desert adaptation, stay tuned for Rocha’s coming review on the subject.