Locus-specific decoupling of base composition evolution at synonymous sites and introns along the Drosophila melanogaster and Drosophila sechellia lineages.
Locus-specific decoupling of base composition evolution at synonymous sites and introns along the Drosophila melanogaster and Drosophila sechellia lineages.
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DOI：
10.1093/gbe/evp008
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发表时间：
2009-05-25
影响因子：
3.3
通讯作者：
Aquadro CF
中科院分区：
文献类型：
--
作者：
DuMont VL;Singh ND;Wright MH;Aquadro CF
选择被认为对许多果蝇物种中同义位点的分子进化模式负有部分责任。最近，已经开发了“每个位点”和似然方法来检测正选择是同义位点进化的主要组成部分的基因座。然而，这些方法的基本假设是同质突变过程。为了解决这个潜在的缺点，我们进行了互补分析，对配对同义位点和内含子替换率朝向和远离核苷酸 G 和 C 进行逐个基因比较，因为首选密码子是以 G 或 C 结尾的果蝇。这种比较可以降低每个位点和似然方法的假阳性率（由于突变的广泛异质性）和假阴性率（由于缺乏比较少量位点的能力）。我们检测到具有暗示同义位点选择压力的进化模式的基因座，该压力分别主要有利于果蝇和果蝇谱系的不偏好和偏好密码子。内含子选择压力似乎不足以解释所有这些结果，因为同义和内含子进化差异的大小取决于重组环境和染色体位置，其方向支持选择性驱动同义固定的假设。这一比较确定了 101 个基因座，其密码子偏好在黑腹果蝇和黑腹果蝇之间存在明显的转变，这种模式以前仅在 Notch 基因座上观察到。
Selection is thought to be partially responsible for patterns of molecular evolution at synonymous sites within numerous Drosophila species. Recently, “per-site” and likelihood methods have been developed to detect loci for which positive selection is a major component of synonymous site evolution. An underlying assumption of these methods, however, is a homogeneous mutation process. To address this potential shortcoming, we perform a complementary analysis making gene-by-gene comparisons of paired synonymous site and intron substitution rates toward and away from the nucleotides G and C because preferred codons are G or C ending in Drosophila. This comparison may reduce both the false-positive rate (due to broadscale heterogeneity in mutation) and false-negative rate (due to lack of power comparing small numbers of sites) of the per-site and likelihood methods. We detect loci with patterns of evolution suggestive of synonymous site selection pressures predominately favoring unpreferred and preferred codons along the Drosophila melanogaster and Drosophila sechellia lineages, respectively. Intron selection pressures do not appear sufficient to explain all these results as the magnitude of the difference in synonymous and intron evolution is dependent on recombination environment and chromosomal location in a direction supporting the hypothesis of selectively driven synonymous fixations. This comparison identifies 101 loci with an apparent switch in codon preference between D. melanogaster and D. sechellia, a pattern previously only observed at the Notch locus.
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影响因子：
3.3
作者：
Haddrill, Penelope R.;Charlesworth, Brian
通讯作者：
Charlesworth, Brian
影响因子：
1.5
作者：
Akashi, H;Kliman, RM;Eyre-Walker, A
通讯作者：
Eyre-Walker, A
影响因子：
5.8
作者：
Beissbarth, T;Speed, TP
通讯作者：
Speed, TP
影响因子：
1.5
作者：
Charlesworth, B
通讯作者：
Charlesworth, B
影响因子：
3.9
作者：
Bachtrog, Doris
通讯作者：
Bachtrog, Doris