| The process of species diversification transcends scales: interactions that occur at the level of organisms and populations manifest themselves in patterns at the species level, in phylogenies. A better understanding of speciation and extinction therefore requires a harmonious union of population biology and phylogenetics.; One potential complication to this union is hybridization. Phylogenetic methods assume that gene genealogies reflect the history of divergence between species, which will be false when species continue to exchange genes through introgression. Thus, the utility of phylogenies for studying microevolutionary processes depends upon the rarity of introgression.; In Section 1, I develop a series of simple deterministic models to demonstrate that introgression occurs much more easily when species are separated by several common forms of prezygotic isolation (e.g., assortative mating) than by postzygotic isolation (e.g., hybrid inviability or sterility). The expected rapidity of introgression is especially striking for maternally inherited genes, such as mitochondrial DNA in animals and chloroplast DNA in plants, molecules frequently used for phylogenetic reconstruction. Surprisingly, introgression through prezygotic barriers may occur considerably more rapidly when species exchange infrequent migrants than when they meet in hybrid zones of near-equal abundance.; In Section 2, I build upon earlier models with more complex deterministic and stochastic models. Counter to intuition, the major findings from Section 1 apply even when both females and males are choosy for conspecific mates. The expectations of rapid and mt/cpDNA-biased introgression hold in a variety of ecological scenarios, but depend critically on the magnitude of migration: when too many organisms migrate each generation, introgression slows or species lose their integrity. By explicitly calculating the probability of phylogenetic conflict, I also demonstrate that introgression between a set of species easily results in misleading gene genealogies.; In Section 3, I consider the use of phylogenetic tree shape for investigating diversification. Given the paucity of appropriate methods for this purpose, I develop novel statistics to test for the presence and location of shifts in diversification rate. I both assess the ability of these statistics to detect diversification rate variation, and demonstrate their application to several supertrees using my freely available software SymmeTREE. |
