Multiple evolutionary rate classes in animal genome evolution

Oldmeadow, Christopher, Mengersen, Kerrie, Mattick, John S. and Keith, Jonathan M. (2010) Multiple evolutionary rate classes in animal genome evolution. Molecular Biology and Evolution, 27 4: 942-953. doi:10.1093/molbev/msp299


Author Oldmeadow, Christopher
Mengersen, Kerrie
Mattick, John S.
Keith, Jonathan M.
Title Multiple evolutionary rate classes in animal genome evolution
Journal name Molecular Biology and Evolution   Check publisher's open access policy
ISSN 0737-4038
1537-1719
Publication date 2010-04-01
Year available 2009
Sub-type Article (original research)
DOI 10.1093/molbev/msp299
Volume 27
Issue 4
Start page 942
End page 953
Total pages 12
Editor Marcy Uyenoyama
Place of publication Lawrence, Kansas, U.S.A.
Publisher Society for Molecular Biology and Evolution
Language eng
Formatted abstract
The proportion of functional sequence in the human genome is currently a subject of debate. The most widely accepted figure is that approximately 5% is under purifying selection. In Drosophila, estimates are an order of magnitude higher, though this corresponds to a similar quantity of sequence. These estimates depend on the difference between the distribution of genomewide evolutionary rates and that observed in a subset of sequences presumed to be neutrally evolving. Motivated by the widening gap between these estimates and experimental evidence of genome function, especially in mammals, we developed a sensitive technique for evaluating such distributions and found that they are much more complex than previously apparent. We found strong evidence for at least nine well-resolved evolutionary rate classes in an alignment of four Drosophila species and at least seven classes in an alignment of four mammals, including human. We also identified at least three rate classes in human ancestral repeats. By positing that the largest of these ancestral repeat classes is neutrally evolving, we estimate that the proportion of nonneutrally evolving sequence is 30% of human ancestral repeats and 45% of the aligned portion of the genome. However, we also question whether any of the classes represent neutrally evolving sequences and argue that a plausible alternative is that they reflect variable structure-function constraints operating throughout the genomes of complex organisms.
© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Keyword Noncoding
Conservation
Neutral evolution
Constraints
GC content
Nucleotide substitution
Eukaryotic genomes
Drosophila genome
Mutation rates
Elements
Rodents
DNA
Identification
Covariation
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Advance Access publication December 2, 2009

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2011 Collection
Institute for Molecular Bioscience - Publications
 
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Citation counts: TR Web of Science Citation Count  Cited 9 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 12 times in Scopus Article | Citations
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Created: Sun, 02 May 2010, 10:03:04 EST