Reduced efficacy of natural selection on codon usage bias in selfing Arabidopsis and Capsella species.
Reduced efficacy of natural selection on codon usage bias in selfing Arabidopsis and Capsella species.
复制标题
自然选择对自交拟南芥和荠菜物种密码子使用偏差的功效降低
DOI：
10.1093/gbe/evr085
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发表时间：
2011
影响因子：
3.3
通讯作者：
Charlesworth D
中科院分区：
文献类型：
--
作者：
Qiu S;Zeng K;Slotte T;Wright S;Charlesworth D
种群遗传学理论预测，自交物种的自然选择效率应低于异交物种，因为近亲繁殖使自交物种的有效种群规模（Ne）减小。然而，先前对拟南芥（自交）和拟南芥（异交）的比较分析并没有发现这一预测的确凿支持。在这项研究中，我们通过检查沉默位点多态性（同义位点和内含子位点）来解决这个问题，这有望提供有关Ne变化的信息。进行了两种比较：拟南芥与柳叶芥、风疹芥（自交）与大花芥（异交）。通过整理已发表的文献资料，并对风疹菌的354个外显子位点和桔梗菌的89个外显子位点进行测序，获得了广泛的多态性数据集。为了有效地从数据中提取信息来研究这些问题，我们扩展了最近开发的两个模型，以研究同义密码子、突变偏差和偏倚基因转换（BGC）之间的详细选择差异，同时考虑到近期种群规模变化的影响。我们发现有证据表明，自交者对同义密码子的选择明显弱于异交者，这种差异不能完全由突变偏差或BGC来解释。
Population genetic theory predicts that the efficacy of natural selection in a self-fertilizing species should be lower than its outcrossing relatives because of the reduction in the effective population size (Ne) in the former brought about by inbreeding. However, previous analyses comparing Arabidopsis thaliana (selfer) with A. lyrata (outcrosser) have not found conclusive support for this prediction. In this study, we addressed this issue by examining silent site polymorphisms (synonymous and intronic), which are expected to be informative about changes in Ne. Two comparisons were made: A. thaliana versus A. lyrata and Capsella rubella (selfer) versus C. grandiflora (outcrosser). Extensive polymorphism data sets were obtained by compiling published data from the literature and by sequencing 354 exon loci in C. rubella and 89 additional loci in C. grandiflora. To extract information from the data effectively for studying these questions, we extended two recently developed models in order to investigate detailed selective differences between synonymous codons, mutational biases, and biased gene conversion (BGC), taking into account the effects of recent changes in population size. We found evidence that selection on synonymous codons is significantly weaker in the selfers compared with the outcrossers and that this difference cannot be fully accounted for by mutational biases or BGC.
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DOI：
10.1073/pnas.96.8.4482
发表时间：
1999-04-13
影响因子：
11.1
作者：
Duret, L;Mouchiroud, D
通讯作者：
Mouchiroud, D
影响因子：
9.8
作者：
Berglund, Jonas;Pollard, Katherine S.;Webster, Matthew T.
通讯作者：
Webster, Matthew T.
影响因子：
10.7
作者：
Foxe, John Paul;Dar, Vaqaar-un-Nisa;Wright, Stephen I.
通讯作者：
Wright, Stephen I.
影响因子：
3.3
作者：
Kawabe, Akira;Forrest, Alan;Charlesworth, Deborah
通讯作者：
Charlesworth, Deborah
影响因子：
10.7
作者：
Eyre-Walker, Adam;Keightley, Peter D.
通讯作者：
Keightley, Peter D.