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Genome-wide probabilistic reconciliation analysis across vertebrates
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
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.
2013 (English)In: BMC Bioinformatics, 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.

Place, publisher, year, edition, pages
2013. Vol. 14, S10- p.
Keyword [en]
Gene Tree Reconstruction, Sequences, Evolution
National Category
Bioinformatics (Computational Biology)
URN: urn:nbn:se:kth:diva-139525DOI: 10.1186/1471-2105-14-S15-S10ISI: 000328316700010OAI: diva2:687666
11th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics, OCT 17-19, 2013, Lyon, France
Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish e‐Science Research Center

QC 20140115

Available from: 2014-01-15 Created: 2014-01-14 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
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