Improved models of biological sequence evolution

[摘要] ENGLISH ABSTRACT: Computational molecular evolution is a field that attempts to characterizehow genetic sequences evolve over phylogenetic trees – the branching processesthat describe the patterns of genetic inheritance in living organisms. It has along history of developing progressively more sophisticated stochastic modelsof evolution. Through a probabilist's lens, this can be seen as a search formore appropriate ways to parameterize discrete state continuous time Markovchains to better encode biological reality, matching the historical processesthat created empirical data sets, and creating useful tools that allow biologiststo test specific hypotheses about the evolution of the organisms or the genesthat interest them. This dissertation is an attempt to fill some of the gaps thatpersist in the literature, solving what we see as existing open problems. Theoverarching theme of this work is how to better model variation in the actionof natural selection at multiple levels: across genes, between sites, and overtime. Through four published journal articles and a fifth in preparation, wepresent amino acid and codon models that improve upon existing approaches,providing better descriptions of the process of natural selection and bettertools to detect adaptive evolution.

[发布机构] Stellenbosch University