MBE Advance Access published online on May 12, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh157
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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1 Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden
* To whom correspondence should be addressed. E-mail: Hans.Ellegren{at}ebc.uu.se.
In order to investigate mutation rate variation between autosomes and sex chromosomes in the avian genome we have analysed divergence between chicken (Gallus gallus) and turkey (Meleagris galopavo) sequences from 33 autosomal, 28 Z-linked and 14 W-linked introns with a total ungapped alignment length of 43000 bp. There are pronounced differences in the mean divergence among autosomes and sex chromosomes (autosomes [A] = 10.08%, Z chromosome = 10.99% and W chromosome = 5.74%) and we use these data to estimate the male-to-female mutation rate ratio ( Key Words:
male-biased mutation, Z chromosome, W chromosome, adaptive mutation rates, nonparametric bootstrapping
Original Articles
Male-Biased Mutation Rate and Divergence in Autosomal, Z-Linked and W-Linked Introns of Chicken and Turkey
Abstract 
m) from Z/A, Z/W and A/W comparisons at 1.71, 2.37 and 2.52, respectively. As the m estimates of the three comparisons do not differ significantly we find no statistical support for a specific reduction in the Z chromosome mutation rate (Z reduction estimated at 4.89%, p=0.286). The idea of mutation rate reduction in the sex chromosome hemizygous in one sex (i.e. X in mammals, Z in birds) has been suggested on the basis of theory on adaptive mutation rate evolution. If it exists in birds the effect would thus seem to be weak; a preliminary power analysis suggests that it is significantly less than 18%. As divergence may vary within chromosomal classes due to variation in mutation and/or selection, we developed a novel double bootstrapping method, bootstrapping both by introns and sites from concatenated alignments, to estimate confidence intervals for chromosomal class rates and for m. The narrowest interval for the m estimate is 1.88-2.97 from the Z/W comparison. We also estimated m using maximum likelihood on data from all three chromosome classes: this method yielded m = 2.47 and approximate 95% confidence intervals of 2.27-2.68. Our data are broadly consistent with the idea that mutation rate differences between chromosomal classes can be explained by the male mutation bias alone.
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