Genome-scale phylogeny and the detection of systematic biases

被引:348
作者
Phillips, MJ [1 ]
Delsuc, F [1 ]
Penny, D [1 ]
机构
[1] Massey Univ, Allan Wilson Ctr Mol Ecol & Evolut, Palmerston North, New Zealand
关键词
D O I
10.1093/molbev/msh137
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Phylogenetic inference from sequences can be misled by both sampling (stochastic) error and systematic error (nonhistorical signals where reality differs from our simplified models). A recent study of eight yeast species using 106 concatenated genes from complete genomes showed that even small internal edges of a tree received 100% bootstrap support. This effective negation of stochastic error from large data sets is important, but longer sequences exacerbate the potential for biases (systematic error) to be positively misleading. Indeed, when we analyzed the same data set using minimum evolution optimality criteria, an alternative tree received 100% bootstrap support. We identified a compositional bias as responsible for this inconsistency and showed that it is reduced effectively by coding the nucleotides as purines and pyrimidines (RY-coding), reinforcing the original tree. Thus, a comprehensive exploration of potential systematic biases is still required, even though genome-scale data sets greatly reduce sampling error.
引用
收藏
页码:1455 / 1458
页数:4
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