Dissertation/ Thesis
Improved models of biological sequence evolution
| Τίτλος: | Improved models of biological sequence evolution |
|---|---|
| Συγγραφείς: | Murrel, Benjamin |
| Συνεισφορές: | Scheffler, Konrad, Stellenbosch University. Faculty of Science. Dept. of Mathematical Sciences. |
| Στοιχεία εκδότη: | Stellenbosch University |
| Έτος έκδοσης: | 2012 |
| Συλλογή: | Stellenbosch University: SUNScholar Research Repository |
| Θεματικοί όροι: | Molecular evolution, Phylogenetic models -- Mathematical models, Natural selection, Markov processes, Molecular evolution -- Data processing, Dissertations -- Mathematical sciences, Theses -- Mathematical sciences, Dissertations -- Computer science, Theses -- Computer science |
| Περιγραφή: | Thesis (PhD)--Stellenbosch University, 2012. ; ENGLISH ABSTRACT: Computational molecular evolution is a field that attempts to characterize how genetic sequences evolve over phylogenetic trees – the branching processes that describe the patterns of genetic inheritance in living organisms. It has a long history of developing progressively more sophisticated stochastic models of evolution. Through a probabilist’s lens, this can be seen as a search for more appropriate ways to parameterize discrete state continuous time Markov chains to better encode biological reality, matching the historical processes that created empirical data sets, and creating useful tools that allow biologists to test specific hypotheses about the evolution of the organisms or the genes that interest them. This dissertation is an attempt to fill some of the gaps that persist in the literature, solving what we see as existing open problems. The overarching theme of this work is how to better model variation in the action of natural selection at multiple levels: across genes, between sites, and over time. Through four published journal articles and a fifth in preparation, we present amino acid and codon models that improve upon existing approaches, providing better descriptions of the process of natural selection and better tools to detect adaptive evolution. ; AFRIKAANSE OPSOMMING: Komputasionele molekulêre evolusie is ’n navorsingsarea wat poog om die evolusie van genetiese sekwensies oor filogenetiese bome – die vertakkende prosesse wat die patrone van genetiese oorerwing in lewende organismes beskryf – te karakteriseer. Dit het ’n lang geskiedenis waartydens al hoe meer gesofistikeerde waarskynlikheidsmodelle van evolusie ontwikkel is. Deur die lens van waarskynlikheidsleer kan hierdie proses gesien word as ’n soektog na meer gepasde metodes om diskrete-toestand kontinuë-tyd Markov kettings te parametriseer ten einde biologiese realiteit beter te enkodeer – op so ’n manier dat die historiese prosesse wat tot die vorming van biologiese ... |
| Τύπος εγγράφου: | thesis |
| Περιγραφή αρχείου: | 1 v. (various pagings); application/pdf |
| Γλώσσα: | English |
| Relation: | https://hdl.handle.net/10019.1/71870 |
| Διαθεσιμότητα: | https://hdl.handle.net/10019.1/71870 |
| Rights: | Stellenbosch University |
| Αριθμός Καταχώρησης: | edsbas.95A6CA16 |
| Βάση Δεδομένων: | BASE |
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