Open-source evolution

EEB’s Will Pearse, who was recently named a Robert May Young Investigator by the British Ecological Society, has developed a modular tool accessible to all that speeds the creation of evolutionary trees.

Developing phylogenies can be time-consuming work. The process of constructing a phylogeny, or evolutionary tree, involves a series of painstaking steps from collecting and analyzing DNA, making comparisons to other species, and identifying the appropriate relationships. Now, thanks to Will Pearse, a post-doctoral researcher in the lab of Jeannine Cavender-Bares (Ecology, Evolution and Behavior), creating these very necessary roadmaps to the relationship between species is significantly less onerous. Pearse recently received a Robert May Young Investigator Award from the  British Ecological Society for a paper about phyloGenerator, a program he developed that does the heavy lifting for researchers. “phyloGenerator is particularly useful for calculating meaningful measures of evolutionary diversity among organisms that occur in a community or region,” says Cavender-Bares, who invited Pearse to join her team to investigate plant diversity patterns in household yards across six major metropolitan areas in the United States. “Using this approach, Will has been able to rigorously examine the ‘homogenization hypothesis,’ (i.e., whether humans are causing the evolutionary diversity of plants that occur in urban areas to be more similar than expected given the regional flora in natural areas.” Pearse took a break from his research to talk about what drew him to ecology and phylogeny, the role of technology in ecology and the research questions that he’d like to explore.

Q: How did you become interested in ecology and, specifically, phylogeny?

I used to go for lots of walks in the forest with my family as a child. I remember thinking that one day I wanted to walk through that forest and know what everything was. So that’s where it starts. Then at University I read a paper looking for general rules in ecology asking questions like “why is there more diversity in the tropics” and “why is it that there are so many species of beetle.” I wanted to find ways to answer these basic questions. I got interested in using phylogeny to understand ecology because of that. It allows you to compare information about birds and butterflies and plants. That’s what I really liked about it, that ability to ask interesting questions that link ecology and evolutionary biology.

Q: What inspired you to develop a program to automate the creation of phylogenies?

When I was a kid I started programming because I kept losing at this old DOS game called Nibbles. I realized you could look at the source code and fiddle around with it to make yourself invincible, so that’s how I learned to program. I stopped at around 13, but when I started doing my master’s project with my Ph.D. advisor Andy Purvis (Imperial College London) that I realized that if I picked up some of those computer skills again I’d be able to use them constructively. I used to spend a lot of time making phylogenies, but then I developed this nerve condition in my neck that meant it was very painful to type and I couldn’t use a mouse at all. So I was looking for a way to automate the steps I used to do myself by hand and quickly realized it was something that could be useful to other researchers.

Q: What kinds of questions are you interested in exploring further?

I feel at the moment like there’s a bit of a disconnect between ecology, which is what species are doing right now, and the evolution of species, which is how those species came to be through processes of speciation and extinction. We talk in ecology about local extinction. We talk in evolution about the mechanisms by which species speciate. What I’d really like to do is understand how the mode of the evolution of species affects the way they interact in the present day and the impact on present-day ecology.



phyloGenerator radically simplifies the process of creating a phylogeny, automating the download of DNA data and the use of modern phylogenetic software to produce a dated, defensible phylogeny. phyloGenerator provides a common framework through which ecologists and evolutionary biologists can describe their analyses quickly and make the results repeatable.