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Deletion rate evolution and its effect on genome size and coding density
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
2009 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 26, no 6, 1421-1430 p.Article in journal (Refereed) Published
Abstract [en]

Deletion rates are thought to be important factors in determining the genome size of organisms in nature. Although it is indisputable that deletions, and thus deletion rates, affect genome size, it is unclear how, or indeed if, genome size is regulated via the deletion rate. Here, we employ a mathematical model to determine the evolutionary fate of deletion rate mutants. Simulations are employed to explore the interactions between deletions, deletion rate mutants, and genome size. The results show that, in this model, the fate of deletion rate mutants   will depend on the fraction of essential genomic material, on the   frequency of sexual recombination, as well as on the population size of the organism. We find that there is no optimal deletion rate in any state. However, at one critical coding density, all changes in deletion rate are neutral and the rate may drift either up or down. As a consequence, the coding density of the genome is expected to fluctuate around this   critical density. Characteristic differences in the impact of deletion rate mutations on prokaryote and eukaryote genomes are described.

Place, publisher, year, edition, pages
2009. Vol. 26, no 6, 1421-1430 p.
Keyword [en]
genome size, junk DNA, insertion-deletion dynamics, deletion bias, modifier evolution
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-96072DOI: 10.1093/molbev/msp054ISI: 000266116500018PubMedID: 19295120OAI: oai:DiVA.org:uu-96072DiVA: diva2:170530
Available from: 2007-09-04 Created: 2007-09-04 Last updated: 2011-03-04Bibliographically approved
In thesis
1. Modeling Genome Evolution: Creation, Change and Destruction
Open this publication in new window or tab >>Modeling Genome Evolution: Creation, Change and Destruction
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Historically, evolution has been studied either by looking at morphological traits in living organisms and the fossil record, or by using bioinformatics and comparative genomics. While highly useful for deducing evolutionary history, these approaches are not particularly well suited for studying the mechanisms of evolution. In order to address such issues, other methods are needed. Mathematical modelling is one of the most powerful options available, and it is the approach used in this thesis. By constructing models of biological systems, the work aims to resolve some of the many unresolved questions regarding evolutionary processes, such as how new genes evolve and how selection acts in fragmented populations. Some answers have been reached, and thus the thesis makes a small contribution to our overall understanding of evolution.

The creation of novel genes was studied both directly and by extension of an analogous system, which revolved around reversion of a frameshift mutant. The results pointed to gene amplification as a likely mechanism for both reversion of the frameshift mutant and creation of new genes.

Selection in fragmented populations is shown to be effective even when sub-populations, rather than individuals, are competing against each other. Modeling of a system of bacterial symbionts living in aphids indicates that, although the bacterial population within a single host is small and subject to rampant genetic drift, the bacterial population as a whole is regulated by selection on the host level. Thus, deleterious mutations do no accumulate and the population maintains its fitness over time.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2007. 37 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 324
Molecular biology, Theotretical biology, Population genetics, Stochastic modeling, Genome evolution, Molekylärbiologi
urn:nbn:se:uu:diva-8163 (URN)978-91-554-6941-2 (ISBN)
Public defence
2007-09-25, Zootissalen, Evolutionsbiologistcentrum, Norbyvägen 18, Uppsala, 10:00
Available from: 2007-09-04 Created: 2007-09-04Bibliographically approved

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