Gene Tree Affects Inference of Sites Under Selection by the Branch-Site Test of Positive Selection

Evolutionary Bioinformatics Online
Yoan Diekmann, José B Pereira-Leal

Abstract

The branch-site test of positive selection is a standard approach to detect past episodic positive selection in a priori-specified branches of a gene phylogeny. Here, we ask if differences in the topology of the gene tree have any influence on the ability to infer positively selected sites. Using simulated sequences, we compare the results obtained for true and rearranged topologies. We find a strong relationship between "conflicting branch length," which occurs when the set of sequences that experiences selection for a given topology and foreground is changed, and the ability to predict positively selected sites. Moreover, by reanalyzing a previously published data set, we show that the choice of a gene tree also affects the results obtained for real-world sequences. This is the first study to demonstrate that tree topology has a clear effect on the inference of positive selection. We conclude that the choice of a gene tree is an important factor for the branch-site analysis of positive selection.

References

May 29, 2002·Molecular Biology and Evolution·Ziheng Yang, Rasmus Nielsen
May 29, 2002·Molecular Biology and Evolution·Maria AnisimovaZiheng Yang
Oct 8, 2003·Systematic Biology·Stéphane Guindon, Olivier Gascuel
Feb 4, 2005·Molecular Biology and Evolution·Ziheng YangRasmus Nielsen
Feb 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ziheng Yang
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
May 9, 2009·Molecular Biology and Evolution·William Fletcher, Ziheng Yang
Jan 15, 2010·BMC Bioinformatics·Jaime Huerta-CepasToni Gabaldón
May 8, 2010·Molecular Biology and Evolution·William Fletcher, Ziheng Yang
Nov 23, 2010·Molecular Biology and Evolution·Ziheng Yang, Mario dos Reis
Jun 15, 2011·Molecular Biology and Evolution·Sergei L Kosakovsky PondKonrad Scheffler
Jul 21, 2011·Molecular Biology and Evolution·Eyal PrivmanTal Pupko
Nov 4, 2011·Molecular Biology and Evolution·Gregory Jordan, Nick Goldman
Feb 24, 2012·Systematic Biology·Fredrik RonquistJohn P Huelsenbeck
Nov 13, 2012·Molecular Biology and Evolution·Benjamin P Blackburne, Simon Whelan
Mar 19, 2013·PLoS Computational Biology·Pouria DasmehEugene I Shakhnovich

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Citations

Feb 11, 2021·Communications Biology·Yash SondhiAkito Y Kawahara

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Software Mentioned

Pal2Nal
Ensembl Compara
ETE
BEB
MrBayes
Phylogenetic Analysis by Maximum Likelihood ( PAML )
PAML
Biopython
INDELible

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