Research

Our research focuses on macroevolution and paleobiology. The overarching goal of our lab is to understand how the genotype and phenotype interact across major evolutionary transitions during the history of life on earth. This is a central challenge in macroevolutionary theory that we tackle using evolutionary models to integrate a wide range of data, from fossils and paleogeography to genome sequencing.

Macroevolutionary Ecomorphology

How do species functionally adapt to new environmental challenges, ecological interactions, and balance internal constraints over geologic time? We have several ongoing projects in this area. We are working with collaborators (Kim Cooper), (Talia Moore), and (Ceri Weber) on the evolution, development, and biomechanics of mammalian tails. We are also currently investigating the evolution of limb retraction by allowing the parameters of functional equations (lever arms) to evolve at differential rates across the Mesozoic dinosaur tree. Our results suggest that locomotor evolution is associated with speciation through dispersal or niche partitioning. This project builds on previous research showing that gigantic theropod dinosaurs had unique biomechanical spinal adaptations (Wilson et al., PLoS ONE, 2016) and evolved bony display structures (Gates, Organ, and Zanno, Nature Com., 2016).

The figure to the right shows an analysis of lever arm (gear ratio) evolution for the primary forelimb retractor muscles in dinosaurs. Warmer colors indicate increased evolutionary rates, and cooler colors decreased rates. Numbers indicate the median estimated rate shifts (posterior probability). Silhouette colors correspond to points in the lower-right plot. Note that despite their size, the arms of small, feathered dinosaurs provided more torque and evolved at faster rates. Despite orders-of-magnitude increases in body size, the lever arms of gigantic sauropods evolved gradually.

Heterochrony & Development

We are reconstructing the phylogenetic-developmental relationships of human tissues to evaluate how developmental history influences genetic and biophysical traits. In other words, we expect tissues with shared developmental history to covary in their characteristics, such as which genes are expressed. However, standard approaches to study tissues and organs ignore this potentially important source of information. Our results reveal a strong and previously unrecognized developmental structure in gene expression and cancer-relevant pathways, including DNA repair and tumor-suppressor function. Our findings indicate that much of biomedical research on cells, tissues, and organs should account for developmental history. We are also keenly interested in modeling heterochrony (evolution by shifts in growth rate and timing), which we plan to use to study human and hominoid evolution, as well as precocial running ability in vertebrate predators and prey.

Paleo- and Evolutionary Genomics

We are interested in the patterns and processes of genome biology over geologic time. We pursue this by integrating molecular, genomic, and fossil data. For example, Chris’ work on the coelacanth genome revealed genetic adaptations in the urea cycle that allowed the water-to-land transition in vertebrates roughly 375 mya, consistent with fossil evidence (Amemiya et al., Nature 2013). We are currently interested in why some lineages (e.g., coelacanths, tuatara, ginkgo) evolve slowly despite persistent environmental change of geological timescales. This project will use Bayesian models to identify ecological and genomic factors that modulate evolutionary rates across the tree of life. This research will help connect biology with paleontology and inform conservation by clarifying how slowly evolving lineages respond to ongoing climate and habitat shifts. This follows work Chris did on the slowly evolving genome of the tuatara, a ‘living fossil’ reptile endemic to New Zealand (Gemmell et al., Nature 2020).

The figure to the left shows a graphical abstract for our Living Fossils project. Why do some lineages evolve very slowly (1st panel on the left)? We can answer this by integrating data from paleontology, genomics, and ecology (2nd panel). Bayesian models combine these data using computational platforms in Python (3rd panel). We expect to develop novel models and discover traits associated with evolutionary stasis, as well as evolutionary processes relevant to biodiversity and climate change (4th panel).

Paleobiology

We are interested in the macroevolutionary processes that give rise to biological traits in extinct species. For example, sensory and sympathetic nerves penetrate bone tissue as a vast network, including the periosteum, bone marrow, and cortical bone. These nerves regulate bone growth, remodeling, and repair, and they also mediate pain, linking the skeletal system to overall physiology and disease. Yet, virtually nothing is known about bonne innervation outside of humans and rodents. This research is at the earliest stages of development: with collaborators (Dana Rashid) and (Erica Scheller), we are studying signatures of bone innervation diversity and constraint in several model organisms. We aim to quantify nerve–vessel relationships, characterize nerve-type variability across bone layers, and identify microarchitectural proxies for nerve presence using micro-CT, immunohistochemistry, and AI-based image analysis. Comparative sampling (e.g., domestic sheep, chickens, African clawed frogs) will generate broadly relevant insights into bone health and disease.

Student Participation

Students are welcome in our lab – no experience needed. You can learn the fundamentals of research on exciting topics like evolution, paleobiology, dinosaurs, physiology, and genomics. You will have opportunities to become proficient in data science tools like Python, R, and computer modeling, which are in high demand across academia and industry. You can expect to be supported along a gradual progression of responsibility, starting with small, semester-length projects that focus on fundamental technical skills, knowledge, and research culture. And if you are dedicated and have grit, you could contribute to scientific publications. If this sounds interesting, drop an email to Chris.

Funding

We are grateful for support from the National Institutes of Health and the National Science Foundation.