Lancaster EPrints

Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey.

Axelsson, Erik and Smith, Nick G. C. and Sundström, Hannah and Berlin, Sofia and Ellegren, Hans (2004) Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey. Molecular Biology and Evolution, 21 (8). pp. 1538-1547. ISSN 1537-1719

Full text not available from this repository.

Abstract

To investigate mutation-rate variation between autosomes and sex chromosomes in the avian genome, we have analyzed 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 approximately 43,000 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 (m) from Z/A, Z/W, and A/W comparisons at 1.71, 2.37, and 2.52, respectively. Because 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%. Because divergence may vary within chromosomal classes as a result of 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 to 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 to 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.

Item Type: Article
Journal or Publication Title: Molecular Biology and Evolution
Uncontrolled Keywords: male-biased mutation • Z chromosome • W chromosome • adaptive mutation rates • nonparametric bootstrapping
Subjects: Q Science > QA Mathematics
Departments: UNSPECIFIED
ID Code: 9368
Deposited By: Mrs Yaling Zhang
Deposited On: 05 Jun 2008 15:25
Refereed?: Yes
Published?: Published
Last Modified: 26 Jul 2012 18:35
Identification Number:
URI: http://eprints.lancs.ac.uk/id/eprint/9368

Actions (login required)

View Item