Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Probabilistic Reconciliation Analysis for Genes and Pseudogenes
KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.ORCID iD: 0000-0002-8034-7834
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.
Series
TRITA-CSC-A, ISSN 1653-5723 ; 2015:03
Keyword [en]
Phylogenetics, Evolution, Reconciliation Analysis, Bayesian Inference
National Category
Bioinformatics (Computational Biology)
Research subject
Computer Science
Identifiers
URN: urn:nbn:se:kth:diva-162150ISBN: 978-91-7595-488-2 (print)OAI: oai:DiVA.org:kth-162150DiVA: diva2:797181
Public defence
2015-04-15, Air, SciLifeLab, Tomtebodavägen 23A, Stockholm, 09:00 (English)
Opponent
Supervisors
Note

Q 20150326

Available from: 2015-03-26 Created: 2015-03-23 Last updated: 2015-03-26Bibliographically approved
List of papers
1. Genome-wide probabilistic reconciliation analysis across vertebrates
Open this publication in new window or tab >>Genome-wide probabilistic reconciliation analysis across vertebrates
2013 (English)In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 14, S10- p.Article in journal (Refereed) Published
Abstract [en]

Gene duplication is considered to be a major driving force in evolution that enables the genome of a species to acquire new functions. A reconciliation - a mapping of gene tree vertices to the edges or vertices of a species tree explains where gene duplications have occurred on the species tree. In this study, we sample reconciliations from a posterior over reconciliations, gene trees, edge lengths and other parameters, given a species tree and gene sequences. We employ a Bayesian analysis tool, based on the probabilistic model DLRS that integrates gene duplication, gene loss and sequence evolution under a relaxed molecular clock for substitution rates, to obtain this posterior. By applying these methods, we perform a genome-wide analysis of a nine species dataset, OPTIC, and conclude that for many gene families, the most parsimonious reconciliation (MPR) - a reconciliation that minimizes the number of duplications - is far from the correct explanation of the evolutionary history. For the given dataset, we observe that approximately 19% of the sampled reconciliations are different from MPR. This is in clear contrast with previous estimates, based on simpler models and less realistic assumptions, according to which 98% of the reconciliations can be expected to be identical to MPR. We also generate heatmaps showing where in the species trees duplications have been most frequent during the evolution of these species.

Keyword
Gene Tree Reconstruction, Sequences, Evolution
National Category
Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:kth:diva-139525 (URN)10.1186/1471-2105-14-S15-S10 (DOI)000328316700010 ()
Conference
11th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics, OCT 17-19, 2013, Lyon, France
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish e‐Science Research Center
Note

QC 20140115

Available from: 2014-01-15 Created: 2014-01-14 Last updated: 2017-12-06Bibliographically approved
2. Gene-Pseudogene Evolution: a Probalitistic Approach
Open this publication in new window or tab >>Gene-Pseudogene Evolution: a Probalitistic Approach
Show others...
(English)Manuscript (preprint) (Other academic)
National Category
Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:kth:diva-162934 (URN)
Funder
Swedish e‐Science Research Center
Note

QS 2015

Available from: 2015-03-26 Created: 2015-03-26 Last updated: 2015-03-26Bibliographically approved
3. Probabilistic inference of lataral gene transfer events
Open this publication in new window or tab >>Probabilistic inference of lataral gene transfer events
Show others...
(English)Manuscript (preprint) (Other academic)
National Category
Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:kth:diva-162935 (URN)
Funder
Swedish e‐Science Research Center
Note

QS 2015

Available from: 2015-03-26 Created: 2015-03-26 Last updated: 2016-10-12Bibliographically approved

Open Access in DiVA

Thesis(1534 kB)187 downloads
File information
File name FULLTEXT02.pdfFile size 1534 kBChecksum SHA-512
8b202cf24b3f8788b932dee9a6ef675e51126fe7927c0c7aca6d00692c8d97db661675e7aba4557313ce37825d172a607bf496afe571911fcad2fb3bed72a030
Type fulltextMimetype application/pdf

Authority records BETA

Mahmudi, Owais

Search in DiVA

By author/editor
Mahmudi, Owais
By organisation
Computational Biology, CB
Bioinformatics (Computational Biology)

Search outside of DiVA

GoogleGoogle Scholar
Total: 187 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 539 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf