Among vertebrates, many of the largest genomes are found within the Plethodontidae, the most speciose family of salamanders. Extreme variation in genome size exists among plethodontid species, from ~14.5 Gb to ~74.5 Gb. These values are larger than all bird, mammal, reptile, and frog genomes, as well as the vast majority of fish genomes. This size variation reflects differing levels of transposable elements and repetitive DNA, as in most eukaryotes; however, such elements remain almost completely uncharacterized. We have used 454 sequencing to generate large-scale sequence datasets for diverse plethodontids and are analyzing these data, in conjunction with phylogenetic hypotheses and modeling efforts, to understand how mutational processes translate into variable genomic expansion through time.

In addition to unusually large, repetitive nuclear genomes, plethodontid salamanders also have some of the largest mitochondrial genomes among vertebrates; some contain novel gene orders, pseudogenes, and both tandem and non-tandem repeat elements, all of which are rare among vertebrates. We are studying the evolutionary history of mitochondrial genomes in four plethodontid clades, each of which experienced independent genomic expansion and reorganization. Our analyses integrate mutation, selection, and drift to generate a comprehensive picture of mitochondrial genome expansion in a spatially and phylogenetically explicit context.

Mitochondrial genome evolution in plethodontid salamanders

Research in the lab is motivated by three main questions: (1) How do genomes evolve, particularly those at the extremes of vertebrate genome size? (2) How should genetic data be used to estimate phylogenetic trees? (3) What does the Tree of Life tell us about the evolution and diversification of lineages? We focus on the nuclear and mitochondrial genomes of plethodontid salamanders, combining genomic sequence data, simulations, natural history collections, and fieldwork to answer diverse questions in genome evolution and phylogenetics. Here are some examples of ongoing projects in the lab, as well as their funding sources:

Nuclear genome evolution in plethodontid salamanders

Epigenetics and speciation in plethodontid salamanders

Genomes have heritable epigenetic controls (DNA methylation, histone modification, and populations of small RNA molecules) that play critical roles in maintaining genome integrity and translating genotype into phenotype via transcriptional networks. Diverging lineages can accumulate both genetic and epigenetic differences that cause hybrid inviability and, thus, underlie reproductive isolation. We are studying the role of epigenetic divergence during species formation in plethodontids to test whether the impact of DNA methylation/small RNA divergence on hybrids is mitigated by large genome size.