Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey
Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey
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DOI：
10.1093/molbev/msh157
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发表时间：
2004-08-01
影响因子：
10.7
通讯作者：
Ellegren, H
中科院分区：
文献类型：
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作者：
Axelsson, E;Smith, NGC;Ellegren, H
为了研究鸟类基因组中常染色体和性染色体之间的突变率变化，我们分析了33个常染色体，28个Z连锁和14个W连锁内含子的鸡（原鸡）和火鸡（Meleagris galopavo）序列之间的分歧，总无帽对齐长度约为43，000 bp。常染色体和性染色体之间的平均分歧有明显的差异（常染色体[A] = 10.08%，Z染色体= 10.99%，W染色体= 5.74%），我们使用这些数据来估计Z/A，Z/W和A/W比较的男女突变率比（α（m））分别为1.71，2.37和2.52。由于三次比较的α（m）估计值没有显著差异，因此我们没有发现Z染色体突变率具体降低的统计学支持（Z降低估计为4.89%，P = 0.286）。在一种性别中半合子的性染色体中突变率降低的想法（即，哺乳动物中的X，鸟类中的Z）是根据适应性突变率进化理论提出的。如果它存在于鸟类中，那么这种影响似乎很弱;初步的功效分析表明，它明显低于18%。由于分歧可能会有所不同的染色体类的突变和/或选择的变化的结果，我们开发了一种新的双自举方法，自举的内含子和网站从串联比对，估计置信区间的染色体类率和α（m）。根据Z/W比较，alpha（m）估计值的最小区间为1.88至2.97。我们还使用来自所有三个染色体类别的数据的最大似然估计alpha（m）;该方法产生alpha（m）= 2.47和约95%的置信区间2.27至2.68。我们的数据与染色体类别之间的突变率差异可以单独由男性突变偏好解释的想法大致一致。
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 (alpha(m)) from Z/A, Z/W, and A/W comparisons at 1.71, 2.37, and 2.52, respectively. Because the alpha(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 mutationrate 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 alpha(m). The narrowest interval for the alpha(m) estimate is 1.88 to 2.97 from the Z/W comparison. We also estimated alpha(m) using maximum likelihood on data from all three chromosome classes; this method yielded alpha(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.