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Gene-Pseudogene Evolution: a Probalitistic Approach
KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-8034-7834
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(English)Manuscript (preprint) (Other academic)
National Category
Bioinformatics (Computational Biology)
URN: urn:nbn:se:kth:diva-162934OAI: diva2:798164
Swedish e‐Science Research Center

QS 2015

Available from: 2015-03-26 Created: 2015-03-26 Last updated: 2015-03-26Bibliographically approved
In thesis
1. Probabilistic Reconciliation Analysis for Genes and Pseudogenes
Open this publication in new window or tab >>Probabilistic Reconciliation Analysis for Genes and Pseudogenes
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Phylogeneticists have studied the evolution of life from single celled organisms to the astonishing biodiversity around us for a long time now. The relationship between species is often expressed as a binary tree - the tree of life. Availability of fully sequenced genomes across species provides us the opportunity to investigate and understand the evolutionary processes, and to reconstruct the gene and species phylogeny in greater detail and more accurately. However, the effect of interacting evolutionary processes, such as gene duplications, gene losses, pseudogenizations, and lateral gene transfers, makes the inference of gene phylogenies challenging.

In this thesis, probabilistic  Bayesian methods are introduced  to infer gene hylogenies in the guidance of species phylogeny. The distinguishing feature f this work from the earlier reconciliation-based methods is that evolutionary vents are mapped to detailed time intervals on the evolutionary time-scale. he proposed probabilistic approach reconciles the evolutionary events to the pecies phylogeny by integrating  gene duplications, gene losses, lateral gene ransfers and sequence evolution under a relaxed molecular clock. Genome- ide gene families for vertebrates and prokaryotes are  analyzed using this pproach that provides interesting insight into the evolutionary processes.

Finally, a probabilistic  model is introduced that  models evolution  of genes and pseudogenes  simultaneously. The model incorporates birth-death  pro- cess according to which genes are duplicated, pseudogenized and lost under a sequence evolution  model with  a relaxed molecular clock.  To model  the evolutionary scenarios realistically, the model employs two different sequence evolution  models for the  evolution  of genes  and pseudogenes. The recon- ciliation  of evolutionary events to the species phylogenies enable us to infer the evolutionary scenario with  a higher resolution.  Some subfamilies of two interesting gene superfamilies,  i.e.  olfactory receptors and zinc fingers, are analyzed using this approach, which provides interesting insights.


Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2015. vi, 58 p.
TRITA-CSC-A, ISSN 1653-5723 ; 2015:03
Phylogenetics, Evolution, Reconciliation Analysis, Bayesian Inference
National Category
Bioinformatics (Computational Biology)
Research subject
Computer Science
urn:nbn:se:kth:diva-162150 (URN)978-91-7595-488-2 (ISBN)
Public defence
2015-04-15, Air, SciLifeLab, Tomtebodavägen 23A, Stockholm, 09:00 (English)

Q 20150326

Available from: 2015-03-26 Created: 2015-03-23 Last updated: 2015-03-26Bibliographically approved

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Mahmudi, OwaisLagergren, Jens
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Computational Biology, CBSeRC - Swedish e-Science Research CentreScience for Life Laboratory, SciLifeLab
Bioinformatics (Computational Biology)

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