Multiple evolutionary rate classes in animal genome evolution

Oldmeadow, Christopher, Mengersen, Kerrie, Mattick, John, & Keith, Jonathan (2010) Multiple evolutionary rate classes in animal genome evolution. Molecular Biology and Evolution, 27(4), pp. 942-953.

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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.

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11 citations in Scopus
8 citations in Web of Science®
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ID Code: 42645
Item Type: Journal Article
Refereed: Yes
Additional Information: Articles free to read on journal website after 12 months
Keywords: noncoding,conservation, neutral evolution, constraints
DOI: 10.1093/molbev/msp299
ISSN: 0737-4038
Subjects: Australian and New Zealand Standard Research Classification > MATHEMATICAL SCIENCES (010000)
Australian and New Zealand Standard Research Classification > ENVIRONMENTAL SCIENCES (050000)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > GENETICS (060400)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Past > Schools > Mathematical Sciences
Deposited On: 13 Jul 2011 13:05
Last Modified: 05 Feb 2015 05:05

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