Current research in the lab is motivated by three main questions: (1) How do genomes evolve, particularly those at the extremes of genome size? (2) How do transposable elements shape genome biology and evolution? (3) How does genome size impact cell biology, organismal biology, and the evolutionary trajectories of lineages? We focus on the nuclear and mitochondrial genomes of salamanders, both of which are greatly expanded relative to other vertebrate species. With collaborators, we also work on copepods and giant viruses. Our research combines genomic sequence data, simulations, phylogenetics, natural history collections, and fieldwork. Here are some examples of ongoing projects in the lab:

Genomic gigantism in salamanders

Salamanders have the largest genomes among tetrapod vertebrates; genome sizes range from ~15 Gb to ~120 Gb, depending on the species. We have shown that these genome sizes reflect unusually high levels of diverse transposable element families, most of which are found in other vertebrate genomes at much lower levels. We have shown that deletions — both large and small — are less common in salamanders, contributing to the accumulation and persistence of transposable elements. We have also shown that salamander genomic gigantism does not reflect unusually strong genetic drift, hypothesized to be a main driver of eukaryotic genomic expansion. Our current interests lie in understanding why the balance between transposable element proliferation and host cell suppression of transposable element activity has evolved to a new dynamic equilibrium point in salamanders. Our focus is the piRNA pathway and its activity in the germline.

Metabolic rate and mitochondrial biology in salamanders

Salamanders have the lowest metabolic rates among tetrapod vertebrates. The mitochondrial genomes of salamanders encode proteins associated with aerobic metabolism, as in other eukaryotes; however, salamander mitochondrial genomes are unusually large, containing pseudogenes, repeat elements, and novel gene orders. We have shown that the OXPHOS proteins encoded by salamander mitochondrial genomes are under weak purifying selection, consistent with relaxed functional constraint mediated by low metabolic requirements. Our current interests lie in understanding how low metabolic rate impacts coevolution between the nuclear- and mitochondrial-encoded subunits of multi-protein complexes and how this, in turn, affects the evolution of species boundaries. In addition, we are focusing on how OXPHOS capacity and efficiency co-evolve with low metabolic rate.

Functional solutions to cell-size evolution’s geometry problem

We have recently begun a project exploring how the changing surface-to-volume ratios that accompany evolutionary increases in cell size affect cell ultrastructure and function. This work will integrate CT data, transcriptomics, high-resolution light microscopy, and mathematical modeling.

Chromatin diminution in copepods (with G. Wyngaard and D. B. Walton, James Madison University

Across the Tree of Life, independent taxa have evolved the capacity to eliminate some portion of their genome from pre-somatic cell lineages during development through a process called chromatin diminution. The freshwater copepod Mesocyclops edax is one such species; chromatin diminution in M. edax produces an organism with a large germline genome (~15 Gb) and a much smaller somatic genome (~3 Gb). We have shown that the majority of sequences excised from the pre-somatic cell lineages are relatively recently active repeat elements. We have also shown that several hundred genes are excised, precluding their expression from all somatic tissue. Our current interests lie in identifying preferentially excised repetitive sequences, their mechanism of excision, and the evolutionary significance of chromatin diminution.