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 sekwensies gelei het nageboots
word, en dat nuttige metodes geskep word wat bioloë toelaat om spesifieke hipotesisse
met betrekking tot die evolusie van belanghebbende organismes of
gene te toets. Hierdie proefskrif is ’n poging om sommige van die gapings
wat in die literatuur bestaan in te vul en bestaande oop probleme op te los.
Die oorkoepelende tema is verbeterde modellering van variasie in die werking
van natuurlike seleksie op verskeie vlakke: variasie van geen tot geen, variasie
tussen posisies in gene en variasie oor tyd. Deur middel van vier gepubliseerde
joernaalartikels en ’n vyfde artikel in voorbereiding, bied ons aminosuur- en
kodon-modelle aan wat verbeter op bestaande benaderings – hierdie modelle
verskaf beter beskrywings van die proses van natuurlike seleksie sowel as beter
metodes om gevalle van aanpassing in evolusie te vind.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/71870 |
| Date | 12 1900 |
| Creators | Murrel, Benjamin |
| Contributors | Scheffler, Konrad, Stellenbosch University. Faculty of Science. Dept. of Mathematical Sciences. |
| Publisher | Stellenbosch : Stellenbosch University |
| Source Sets | South African National ETD Portal |
| Language | en_ZA |
| Detected Language | Unknown |
| Type | Thesis |
| Format | 1 v. (various pagings) |
| Rights | Stellenbosch University |
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