Species Divergence: Computational Methods to Explore and Resolve Biological Questions Related to the Evolution of Species

Species divergence is the formation of a new species by the accumulation of changes in the DNA between different populations of the same species. The formation of these new species can be caused by various factors, but many times the deep effect of these changes remains unknown until the newly diverged or currently diverging species can be genetically examined. Focusing on two primary divergences, that of Rhagoletis pomonella, a fly that is in the process of switching host plants, and the Anopheline mosquitoes, the only vectors of human malaria, we present software and methods to examine these divergences. From RAD sequencing to explore Rhagoletis divergence, to ancestral reconstruction to examine the history of Anophelines, to using ancestral gene blocks to improve Anopheles genomes for better analysis, this work provides biological researchers with tools they need to answer questions about species divergence in many stages. Computationally, the masses of data and the complex problems lead to the oft-encountered difficulty of run time versus solution approximations, which plays a large role in this research. By finding a balance between these two integral parts of computation we provide as correct of data as possible in a reasonable amount of time, and we enable biologists to study organisms by providing them with useful tools.