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. If divergence with gene flow is common, then hybridization may often be an important transient phase in animal speciation. Furthermore, in such cases, phylogeny estimation in such cases will be rendered particularly difficult because introgression is expected to be heterogeneous across the genome.

The radiation of western American chipmunks (Tamias, subgenus Neotamias) represents an excellent study system for diversification with gene flow. One of the historically intriguing features of the group is its penchant for stark niche partitioning between and among congeners and the extremely narrow zones of contiguous allopatry that commonly result. In addition, they are characterized by strong interspecific differentiation in genital bones (esp. the bacula, or os penis), with little intraspecific variation. However, we have identified numerous instances where mtDNA has introgressed across parapatric taxonomic boundaries at several taxonomic levels (e.g., Good et al. 2003; 2008). However, poor phylogenetic resolution of the genus has obfuscated an historical understanding of the role of divergence with gene flow in the genus.

To address this, we are estimating the phylogeny of the genus using a diverse array of data sets, including mtDNA, ncDNA. This will provide the historical framework required for testing particular hypotheses about the extent and nature of hybridization. Furthermore, we are assessing interspecific gene flow across several transects using microsatellite data at which either preliminary data or incongruence among data sets suggests introgression.