以子囊菌部分类群的rRNA数据为例,评估不同分区策略对贝叶斯分析效果的影响(英文)  

Performance of partitioning rRNA data — an example of Bayesian inference in Ascomycota

作　　者：刘超洋[1,2] 庄文颖[2] 

机构地区：[1]西南科技大学生命科学与工程学院,四川绵阳621010 [2]中国科学院微生物研究所真菌学国家重点实验室,北京100101

出　　处：《菌物学报》2013年第3期563-573,共11页Mycosystema

基　　金：Supported by the National Natural Science Foundation of China (No. 31070015)

摘　　要：在使用rRNA基因进行系统发育分析过程中,不同位点间进化速度的差异性可能是导致系统误差的一个重要原因。以52个真菌为研究对象,利用rRNA二级结构特征构建分区策略,探讨不同分区策略对贝叶斯分析的影响。结果显示各结构分区的最优核酸替代模型及其参数与分区类型密切相关。与传统的贝叶斯方法相比,使用结构环的分区策略对结果没有显著影响,而引入臂元素的方法却导致更高的边际似然值和支持率。此外,不考虑结构特征,简单的增加子分区数量的分区策略尽管也能导致贝叶斯因素值的增加,却没有提高解决亲缘关系的能力,说明一个合理的分区策略应该基于生物学功能(或二级结构特征)而非纯数学因素。Rate variation of evolution among-site in rRNA genes is a potential problem leading to a systematic error in phylogenetic inference. In this study, we applied different partitioning strategies based on the characters of rRNA secondary structure to examine this problem. Based on a phylogenetic analysis of 52 fungal taxa, we assessed the performance of different partitioning schemes on Bayesian inference. The comparison of evolutionary models demonstrated the relative sensitivities of the best-fit models and parameter estimates to different structural partitions. In contrast to traditional unpartitioned method, partitioning schemes based on loop elements of secondary structure have little effects on phylogenetic analyses, while the use of stem elements improve the marginal likelihoods and the ability to estimate phylogenies. Additionally, despite strong support by Bayes factors, simply including more partition subsets do not to improve ability to estimate phylogenies, which means that biological factors （or secondary structure characters） instead of mathematics ones should be considered to yield a reasonable partitioning strategy for rRNA genes.

关 键 词：核糖体RNA 二级结构 分区分析 结构特征 贝叶斯因素 进化模型 

分 类 号：Q949.32[生物学—植物学]