| As sequence data has accumulated, emphasis in evolutionary molecular biology has been placed on identifying homologous gene families and, from gene families, reconstructing evolutionary histories for genes and species. However, evolutionary processes such as gene duplication, gene loss, and horizontal gene transfer can result in incongruence between gene and species trees. In this thesis, we present algorithms for tree reconciliation and species tree reconstruction within both a parsimony framework and a likelihood framework. Our focus is on the likelihood model that integrates sequence evolution, macrogenomic processes, and a relaxed molecular clock for substitution rates. We validate our algorithms by simulation studies, and we demonstrate their utility in case studies with real sequence data to estimate rates of evolutionary events, infer subsystem and species phylogenies, and detect horizontal gene transfer. |
