Dissertation/ Thesis
Προβολή σε EDS

Improved models of biological sequence evolution

Λεπτομέρειες βιβλιογραφικής εγγραφής
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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  – Url: https://hdl.handle.net/10019.1/71870#
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  Data: Scheffler, Konrad<br />Stellenbosch University. Faculty of Science. Dept. of Mathematical Sciences.
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  Data: 2012
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  Data: <searchLink fieldCode="DE" term="%22Molecular+evolution%22">Molecular evolution</searchLink><br /><searchLink fieldCode="DE" term="%22Phylogenetic+models+--+Mathematical+models%22">Phylogenetic models -- Mathematical models</searchLink><br /><searchLink fieldCode="DE" term="%22Natural+selection%22">Natural selection</searchLink><br /><searchLink fieldCode="DE" term="%22Markov+processes%22">Markov processes</searchLink><br /><searchLink fieldCode="DE" term="%22Molecular+evolution+--+Data+processing%22">Molecular evolution -- Data processing</searchLink><br /><searchLink fieldCode="DE" term="%22Dissertations+--+Mathematical+sciences%22">Dissertations -- Mathematical sciences</searchLink><br /><searchLink fieldCode="DE" term="%22Theses+--+Mathematical+sciences%22">Theses -- Mathematical sciences</searchLink><br /><searchLink fieldCode="DE" term="%22Dissertations+--+Computer+science%22">Dissertations -- Computer science</searchLink><br /><searchLink fieldCode="DE" term="%22Theses+--+Computer+science%22">Theses -- Computer science</searchLink>
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  Data: 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 ...
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    Languages:
      – Text: English
    Subjects:
      – SubjectFull: Molecular evolution
        Type: general
      – SubjectFull: Phylogenetic models -- Mathematical models
        Type: general
      – SubjectFull: Natural selection
        Type: general
      – SubjectFull: Markov processes
        Type: general
      – SubjectFull: Molecular evolution -- Data processing
        Type: general
      – SubjectFull: Dissertations -- Mathematical sciences
        Type: general
      – SubjectFull: Theses -- Mathematical sciences
        Type: general
      – SubjectFull: Dissertations -- Computer science
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      – SubjectFull: Theses -- Computer science
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      – TitleFull: Improved models of biological sequence evolution
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            NameFull: Murrel, Benjamin
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            NameFull: Scheffler, Konrad
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              Y: 2012
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