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MBE Advance Access published online on November 28, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn275
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Problems and solutions for estimating indel rates and length distributions

Reed A. Cartwright

Department of Genetics, Bioinformatics Research Center, North Carolina State University, Campus Box 7566, Raleigh, NC 27695-7566, USA, Email: racartwr{at}ncsu.edu, Cell: 1-706-248-4259, Fax: 1-919-515-7315

Received for publication August 21, 2008. Revision received October 27, 2008. Accepted for publication November 18, 2008.

Insertions and deletions (indels) are fundamental but understudied components of molecular evolution. Here we present an expectation-maximization algorithm built on a pair hidden Markov model that is able to properly handle indels in neutrally evolving DNA sequences. From a dataset of orthologous introns, we estimate relative rates and length distributions of indels among primates and rodents. This technique has the advantage of potentially handling large genomic datasets. We find that a zeta power-law model of indel lengths provides a much better fit than the traditional geometric model and that indel processes are conserved between our taxa. The estimated relative rates are about 12–16 indels per 100 substitutions, and the estimated power-law magnitudes are about 1.6–1.7. More significantly, we find that using the traditional geometric/affine model of indel lengths introduces artifacts into evolutionary analysis, casting doubt on studies of the evolution and diversity of indel formation using traditional models and invalidating measures of species divergence that include indel lengths.

Key Words: indel • power law • conservation • estimation • comparative genomics


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[Abstract] [Full Text] [PDF]


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