Nuclear genome evolution in plethodontid salamanders

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, and reptile genomes, as well as the vast majority of frog and 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. In collaboration with David Pollock (U.C. Denver) and the Consortium for Comparative Genomics, we are using 454 sequencing to generate large-scale sequence datasets for diverse plethodontids. We will analyze 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 such genomes contain novel gene orders, pseudogenes, and both tandem and non-tandem repeat elements, all of which are extremely rare among vertebrates. We are studying the evolutionary history of mitochondrial genomes in five plethodontid clades, each of which experienced an independent duplication event resulting in genomic reorganization. More generally, we are using these pseudogene sequences as a model system to understand the dynamics of neutral mutation in the mitochondrial genome. Our analyses of deletions are a good proxy to model the process through which an ancestral bacterial genome was streamlined into the present-day mitochondrial genome.

Phylogenetic methodology

Phylogenies for the same taxa estimated using different genes are often incongruent, indicating that genes vary in their ability to yield accurate estimates of relationships. Therefore, choosing appropriate molecular markers is critical to the success of phylogenetic analyses and to any research that builds on these results, ranging from the evolution of phenotypic traits to the structure of ecological communities. The characteristics of genes likely contribute to the phylogenetic utility of genes; however, no formal method exists for selecting loci based on such characteristics. We are using a combination of empirical data, including whole mitochondrial genomic data and published phylogenies from numerous taxa, and large-scale simulations to test the effects of different gene characteristics on phylogenetic performance. Our results will allow us to develop a predictive model for genes that allow these relationships to be estimated correctly.

Mitochondrial genome evolution in plethodontid salamanders

The effects of missing data on phylogeny estimation have been well studied. However, no comparable analyses exist that address the effects of missing data on branch length estimates. Numerous analytical techniques in evolutionary biology, including divergence date estimation and Comparative Methods-based approaches to character evolution, rely on accurate branch lengths. Molecular systematists are generating ever-larger datasets to estimate phylogenies and divergence dates, motivated by cheaper sequencing and better appreciation of the importance of dense taxon sampling and multi-gene datasets. The probability of incomplete data increases with the size of the dataset. Thus, many studies that rely on accurate branch lengths contain missing data, and the consequences remain unexplored. We are quantifying the effects of missing data on branch length estimation by systematically removing data and examining the consequences. Our results will allow us to make general predictions about the extent to which missing sequence data compromises evolutionary analyses. 

Ongoing Projects:

Overview:

Research in the lab is motivated by three main questions: (1) How do genes and genomes evolve? (2) How can genetic data be used to estimate phylogenetic trees? (3) How can the Tree of Life be used to study evolution and diversification of lineages? Our current work is focused on vertebrates — primarily amphibians. We combine genomic sequence data, simulations, natural history collections, and fieldwork to answer diverse questions in phylogenetics and evolution.