Alignment Modulates Ancestral Sequence Reconstruction Accuracy.
Alignment Modulates Ancestral Sequence Reconstruction Accuracy.
复制标题
对准调节祖先序列重建精度。
DOI：
10.1093/molbev/msy055
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发表时间：
2018-07-01
影响因子：
10.7
通讯作者：
Goldman N
中科院分区：
文献类型：
--
作者：
Vialle RA;Tamuri AU;Goldman N
Accurate reconstruction of ancestral states is a critical evolutionary analysis when studying ancient proteins and comparing biochemical properties between parental or extinct species and their extant relatives. It relies on multiple sequence alignment (MSA) which may introduce biases, and it remains unknown how MSA methodological approaches impact ancestral sequence reconstruction (ASR). Here, we investigate how MSA methodology modulates ASR using a simulation study of various evolutionary scenarios. We evaluate the accuracy of ancestral protein sequence reconstruction for simulated data and compare reconstruction outcomes using different alignment methods. Our results reveal biases introduced not only by aligner algorithms and assumptions, but also tree topology and the rate of insertions and deletions. Under many conditions we find no substantial differences between the MSAs. However, increasing the difficulty for the aligners can significantly impact ASR. The MAFFT consistency aligners and PRANK variants exhibit the best performance, whereas FSA displays limited performance. We also discover a bias towards reconstructed sequences longer than the true ancestors, deriving from a preference for inferring insertions, in almost all MSA methodological approaches. In addition, we find measures of MSA quality generally correlate highly with reconstruction accuracy. Thus, we show MSA methodological differences can affect the quality of reconstructions and propose MSA methods should be selected with care to accurately determine ancestral states with confidence.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
3.3
作者：
Md Mukarram Hossain AS;Blackburne BP;Shah A;Whelan S
通讯作者：
Whelan S
影响因子：
10.7
作者：
Groussin, Mathieu;Hobbs, Joanne K.;Gouy, Manolo
通讯作者：
Gouy, Manolo
影响因子：
10.7
作者：
Hanson-Smith V;Kolaczkowski B;Thornton JW
通讯作者：
Thornton JW
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T