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

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Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey. / Axelsson, Erik; Smith, Nick G. C.; Sundström, Hannah et al.
In: Molecular Biology and Evolution, Vol. 21, No. 8, 08.2004, p. 1538-1547.

Research output: Contribution to Journal/MagazineJournal articlepeer-review

Harvard

Axelsson, E, Smith, NGC, Sundström, H, Berlin, S & Ellegren, H 2004, 'Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey.', Molecular Biology and Evolution, vol. 21, no. 8, pp. 1538-1547. https://doi.org/10.1093/molbev/msh157

APA

Axelsson, E., Smith, N. G. C., Sundström, H., Berlin, S., & Ellegren, H. (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), 1538-1547. https://doi.org/10.1093/molbev/msh157

Vancouver

Axelsson E, Smith NGC, Sundström H, Berlin S, Ellegren H. Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey. Molecular Biology and Evolution. 2004 Aug;21(8):1538-1547. doi: 10.1093/molbev/msh157

Author

Axelsson, Erik ; Smith, Nick G. C. ; Sundström, Hannah et al. / Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey. In: Molecular Biology and Evolution. 2004 ; Vol. 21, No. 8. pp. 1538-1547.

Bibtex

@article{e7ac8109334b463981a85e0e4e0d3ccf,
title = "Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey.",
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.",
keywords = "male-biased mutation • Z chromosome • W chromosome • adaptive mutation rates • nonparametric bootstrapping",
author = "Erik Axelsson and Smith, {Nick G. C.} and Hannah Sundstr{\"o}m and Sofia Berlin and Hans Ellegren",
year = "2004",
month = aug,
doi = "10.1093/molbev/msh157",
language = "English",
volume = "21",
pages = "1538--1547",
journal = "Molecular Biology and Evolution",
issn = "1537-1719",
publisher = "Oxford University Press",
number = "8",

}

RIS

TY - JOUR

T1 - Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey.

AU - Axelsson, Erik

AU - Smith, Nick G. C.

AU - Sundström, Hannah

AU - Berlin, Sofia

AU - Ellegren, Hans

PY - 2004/8

Y1 - 2004/8

N2 - 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.

AB - 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.

KW - male-biased mutation • Z chromosome • W chromosome • adaptive mutation rates • nonparametric bootstrapping

U2 - 10.1093/molbev/msh157

DO - 10.1093/molbev/msh157

M3 - Journal article

VL - 21

SP - 1538

EP - 1547

JO - Molecular Biology and Evolution

JF - Molecular Biology and Evolution

SN - 1537-1719

IS - 8

ER -