John "Jack" M. Sullivan

Our understanding of the processes of nucleotide substitution (DNA sequence evolution) has been expanding greatly over the last 10 years. Furthermore, it has become apparent that ignoring such processes as heterogeneity of base composition, substitution pattern, and rate variation among nucleotide sites can compromise attempts to estimate phylogeny from DNA sequence data. Therefore, model-based analyses of DNA sequence data have become increasingly wide spread because such approaches afford the investigator the opportunity to account for such processes explicitly.

• Phylogenetic Methods
  Phylogenetic analysis, the estimation of evolutionary trees, has become the cornerstone of evolutionary biology. In addition to their more traditional applications in evolutionary biology, molecular phylogenies (i.e., phylogenies that have been estimated from molecular data such as DNA sequences) are being applied to an ever-widening array of disciplines. These include biomedicine (e.g., tracing infection pathways for HIV and other pathogens), bioinformatics (e.g., genome evolution), and forensics (phylogenies estimated from HIV sequences have recently been allowed as evidence in murder trial). Because of this, the development and testing of phylogenetic methods assumes a position of critical importance and extremely broad relevance. Furthermore, the influx of molecular sequence data and the adoption of an explicitly statistical approach to data analysis have led to the requirement to refine methods of phylogenetic inference.
• Comparative Phylogeography
  This project surveys genetic diversity in multiple elements of mesic forests of the Pacific Northwest in the context of explicit biogeographic and landscape hypotheses that make testable genetic predictions. The general objectives of this research are to differentiate the influence of past geological and climatic events from current landscape level processes on the geographic structure of genetic variation in several codistributed highland forest species.
• Divergence  With Geneflow In Chipmunks
  Determining the frequency and genetic impact of hybridization during animal speciation remains a central and unresolved issue in evolutionary biology. If reproductive isolation is incomplete when nascent species come into contact, even moderate gene flow may result in population fusion. Thus, recurrent hybridization among animal species has traditionally been viewed as rare. Alternatively, genetic factors underlying speciation may continue to accumulate between divergent populations despite on-going gene flow, eventually leading to the evolution of complete reproductive isolation. Consistent with this second model (divergence with gene flow), several recent studies have shown that closely related taxa may retain differentiation despite high levels of cryptic hybridization and introgression. The radiation of western American chipmunks (Tamias, subgenus Neotamias) represents an excellent study system for diversification with gene flow. Thus, we are estimating the phylogeny of the genus using a diverse array of data sets, including mtDNA, ncDNA.