Genome Biology and Evolution Advance Access originally published online on April 30, 2009
Genome Biology and Evolution (2009) Vol. 2009:13; doi:10.1093/gbe/evp001 published on May 22, 2009
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Evidence That Replication-Associated Mutation Alone Does Not Explain Between-Chromosome Differences In Substitution Rates
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* Department of Biology and Biochemistry, University of Bath, Bath, Somerset, United Kingdom
The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
E-mail: l.d.hurst{at}bath.ac.uk.
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Abstract |
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Since Haldane first noticed an excess of paternally derived mutations, it has been considered that most mutations derive from errors during germ line replication. Miyata et al. (1987) proposed that differences in the rate of neutral evolution on X, Y, and autosome can be employed to measure the extent of this male bias. This commonly applied method assumes replication to be the sole source of between-chromosome variation in substitution rates. We propose a simple test of this assumption: If true, estimates of the male bias should be independent of which two chromosomal classes are compared. Prior evidence from rodents suggested that this might not be true, but conclusions were limited by a lack of rat Y-linked sequence. We therefore sequenced two rat Y-linked bacterial artificial chromosomes and determined evolutionary rate by comparison with mouse. For estimation of rates we consider both introns and synonymous rates. Surprisingly, for both data sets the prediction of congruent estimates of 
is strongly rejected. Indeed, some comparisons suggest a female bias with autosomes evolving faster than Y-linked sequence. We conclude that the method of Miyata et al. (1987) has the potential to provide incorrect estimates. Correcting the method requires understanding of the other causes of substitution that might differ between chromosomal classes. One possible cause is recombination-associated substitution bias for which we find some evidence. We note that if, as some suggest, this association is dominantly owing to male recombination, the high estimates of seen in birds is to be expected as Z chromosomes recombine in males.
Keywords: male-mutation bias, male-driven evolution, mutation, recombination, introns, rodents
Accepted March 5, 2009
1 Present address: Biotechnology and Toxicology Division, Environment Protection Training and Research Institute, Hyderabad, Andhra Pradesh, India.
2 Present address: European Molecular Biology Laboratory (EMBL)-European Bioinformatics Institute, Cambridge, United Kingdom.
3 Present address: John Innes Centre, Norwich Research Park, Colney, Norwich, United Kingdom.
4 These authors contributed equally.