Research themes

Much of our work involves trying to better understand some aspect of species, such as traits or geographical distributions, by incorporating their evolutionary history (phylogeny). Below are some of the ways we commonly do this, along with some examples of the kinds of projects you could pursue in the lab if you were to join!

Evolutionary ecology and community phylogenetics

A picture take from one of our field sites in near Logan, Utah

Community phylogenetics (sometimes called eco-phylogenetics) attempts to link the evolution of species communities to their ecology in the present day. We maintain the R package pez (Pearse et al. 2015), which implements a large number of community phylogenetic metrics and models (see Pearse et al. 2014 for a review). We use these approaches (and more that we develop!) to study how plant communities, such as those in our field sites in Utah, have evolved, and then to use these insights to predict how our communities (and others throughout the world) might look in the future.

Potential student projects: Making use of existing global databases of species’ distributions, do closely-related species tend to co-occur and, if so, why? Re-analyse our field site data to find something new out about the species there – now go collect even more data to test your ideas out!


An example of our approach applied to estimate flowering times from historic data

It’s increasing clear that climate change isn’t just affecting where species are found, it’s also affecting when we find them doing things. Plants are blooming earlier, birds are migrating earlier, and it’s our job to figure out how and why. Recently, we have developed new statistical approaches that let us measure rates of phenological change from data that weren’t collected for that purpose (Pearse et al. in press). We’re just starting using machine learning tools to apply this technique to global datasets (e.g., iNaturalist) and our own field sites.

Potential student projects: Are flowering times in [your favourite species] keeping track with changing climate? Where are they (not), and why?

Conservation planning

Map of Britain highlighting areas with potentially dangerous species. Part of my EDAM conservation prioritisation scheme
Conservation prioritisation map of the United Kingdom’s plants

It is time that makes historical sites like castles so intuitively priceless to humans, and phylogeny can reveal the millions of years of time that make species intuitively valuable. Many of the empirical and methodological advances I have described above have implications for predictions of future change, but I strongly believe phylogeny itself can directly inform conservation decision-making. We have already prioritised the conservation of British flora using our novel ‘EDAM’ approach, which incorporates phylogeny, threat, and uncertainty in both (Pearse et al. 2015).  We are currently collaborating with the Zoological Society of London to make practical use of our prioritisation research, and the lab has played a major part in the updating of the EDGE program.

Potential student projects: Pick a country and/or group of species. Using our prioritisation approach, find out which species and/or parts of the world are most at threat, and help us make useful products that will affect conservation interventions in the real world, not just the lab!

Trait evolution

Analysing leaf shape using stalkless: detecting shape in a noisy background
Analysing leaf shape using stalkless: detecting shape in a noisy background

Species’ traits define everything from what they look like to how they interact with their environment. Understanding how traits evolve can help us understand how we might expect species’ to evolve in response to climate change and other stressors. We’re particularly interested in how multiple trait co-evolve, constraining and trading-off against each other, and understanding how multiple shapes can evolve with the same functional consequences for species. Much of our work to-date has focused on plant leaves for this, making use of our stalkless image analysis pipeline.

Potential student projects: Compare the rates of evolution of plant function traits (e.g., photosynthetic rates) with morphological traits (e.g., leaf symmetry) – which are fastest, and why? Are there groups of traits that have evolved in concert, and if so why?

Software development

Overview of the workflow in phyloGenerator version 1. Version 2 is somewhat different.
Overview of the workflow in phyloGenerator version 1- help us update version 2!

Asking new kinds of questions means writing the software to answer those questions, and so we spend a lot of time writing code. Much of the code we have written has been focused on phylogenetic methods (phyloGenerator; Pearse et al. 2013). We also spend a lot of time working with existing data, and working on new ways to share the data we have collected ourselves.

Potential student projects: We are writing an automatically-updated database of species’ traits – help us! Help write the update to phyloGenerator (currently at version 2) that allows it to build even larger phylogenies more rapidly.