Research

My research interests are focused on the intersection of computer science, ecology, and evolutionary biology. This involves doing in silico experiments to understand general properties of ecology and evolution, and using principles from biology to solve computational problems. Often these goals intersect. Many of my in silico experiments are carried out on the Avida Digital Evolution Platform, an open source research platform developed and maintained by the Devolab. The primary theme uniting my research is that I am fascinated by how ecosystems evolve. This often leads me to ask questions about how evolutionary processes generate and maintain diversity, particularly in the presence of spatial structure.

Code for all of my projects is available on github.

Some specific projects that I’m currently working on include:

Impact of evolution on reserve placement effect

Phenotypes evolved in an environment with 25 6x6 reserves
Phenotypes evolved in an environment with 25 6×6 reserves

Most research on placing biological reserves (e.g. natural parks) in physical space has been based on the impact of different reserve configurations on short-term diversity fluctuations. However, one of the reasons that diversity is so important to conserve in the first place is to improve the chances that species will adapt to the changing environment. As such, the interaction between evolutionary processes and the diversity fluctuations under different reserve configurations is important to understand. Given the vast spatiotemporal scale on which these processes occur, relatively little research has been done on this topic thus far. We are using Avida to address these questions.

Configuration files, analysis scripts, and source code for the first paper on this project are available here.

Impact of patch shape on local adaptation

5_12figure_1

When a population is adapting to make use of a new feature of a landscape, that feature is usually distributed in a specific shape. How does this shape affect local adaptation to that feature? Do long and thin shapes facilitate adaptation more or less than more compact shapes? Landscape ecologists have developed a wide variety of ways of quantifying patch shapes, and we are using Avida to systematically test the effect of each on evolution.

Resource Spatial Heterogeneity

Phenotypes evolved in a spatially heterogenous environment in the Avida Digital Evolution Platform
Phenotypes evolved in a spatially heterogenous environment in the Avida Digital Evolution Platform

A central question in ecology has long been how such a wide diversity of life can evolve within a seemingly limited set of niches. Many suspect that spatial heterogeneity is an important factor in making this possible, but this is a very challenging principle to test in biological populations. To try and understand whether spatial heterogeneity is a general driver of diversity, we are experimentally testing it in Avida.