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Published online on April 12, 2005, 10.1073/pnas.0500383102

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Evolution
Rates of intron loss and gain: Implications for early eukaryotic evolution

( genome evolution )

Scott William Roy * and Walter Gilbert

Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138

Contributed by Walter Gilbert, February 16, 2005

We study the intron-exon structures of 684 groups of orthologs from seven diverse eukaryotic genomes and provide maximum likelihood estimates for rates and numbers of intron losses and gains in these same genes for a variety of lineages. Rates of intron loss vary from {approx}2 x 10-9 to 2 x 10-10 per year. Rates of gain vary from 6 x 10-13 to 4 x 10-12 per possible intron insertion site per year. There is an inverse correspondence between rates of intron loss and gain, leading to a 20-fold variation among lineages in the ratio of the rates of the two processes. The observed rates of intron gain are insufficient to explain the large number of introns estimated to have been present in the plant-animal ancestor, suggesting that introns present in early eukaryotes may have been created by a fundamentally different process than more recently gained introns.

*To whom correspondence should be addressed.

Scott William Roy, E-mail: scottroy{at}fas.harvard.edu

www.pnas.org/cgi/doi/10.1073/pnas.0500383102
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