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Origin and early evolution of eukaryotes

We study how the eukaryotic cell came to be, and how eukaryotic genomes have evolved since.

Our work sits at the intersection of comparative genomics, phylogenomics, and the biology of understudied microbial eukaryotes. We sequence and analyze the genomes of protists from deep-branching lineages, we develop and stress-test the phylogenetic methods needed to resolve relationships across billions of years of divergence, and we work on the prokaryotic lineages from which eukaryotes descend. A growing part of the lab is dedicated to the evolution of the epigenetic systems in lineages far outside the model organisms where these systems are usually studied.

Most of what we do is computational, but the lab also maintains protist cultures and generates its own sequencing data.

We are based in the Department of Cell and Molecular Biology at the University of Rhode Island.

Current focus

Protist genomes from the deep branches
High-quality genomes and transcriptomes from lineages with almost no genomic representation — ancyromonads, mantamonads, and other orphan taxa — to reconstruct the gene content of the last eukaryotic common ancestor and the overall structure of the eukaryotic Tree of Life.

Epigenetics beyond the model organisms
Characterizing DNA modifications in deep-branching protists, and tracing the evolutionary history of the enzyme families that write and read them across eukaryotic diversity.

Phylogenomics of ancient divergences
Developing and evaluating substitution models and analytical strategies for the hardest phylogenetic problems, including the position of eukaryotes within the tree of life and the root of the eukaryotic tree.

Protist diversity in the ocean
Recovering protist genomes directly from marine metagenomes.