Phylogenetic analysis under reticulate evolution

The usual assumption that species have evolved from a common ancestor by a simple branching process - where each branch is genetically isolated - has been challenged by the observation of frequent hybridization between specie s in natural populations. In fact, most plant species are thought to have h ybrid origins. This reticulate pattern of species evolution has posed probl ems in the definition of speciation and in phylogenetic reconstruction, esp ecially when molecular data are used. As a result, hybridization has been l argely treated as an evolutionary accident or statistical error in phylogen etic analysis. In this paper, I explicitly incorporate hybridization as an evolutionary occurrence and then conduct phylogenetic reconstruction. I fir st examine the reticulate evolution under a pure drift model, and then exte nd the theory to fit a mutation model. A least-squares method is developed for reconstructing a reticulate phylogeny using gene frequency data. The ef ficacy of the method under the pure drift model is verified via Monte Carlo simulations.