Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Wellcome Open Research
John A LeesSimon R Harris

Abstract

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree to...Continue Reading

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Citations

Jan 27, 2019·Genome Research·John A LeesNicholas J Croucher
Mar 19, 2019·Current Opinion in HIV and AIDS·Dennis M JunqueiraTulio de Oliveira
Jul 10, 2019·Annual Review of Microbiology·Kirsten I BosJohannes Krause
Jan 3, 2021·Molecular Phylogenetics and Evolution·William R ConnerMichael Turelli
Nov 14, 2019·NAR Genomics and Bioinformatics·Leonardo de Oliveira MartinsIan G Charles
Oct 28, 2021·Microbiology Spectrum·Mostafa Y Abdel-GlilChristian Seyboldt

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Software Mentioned

MAFFT
SeaView
mash
Progressive Cactus
pIRS
RevTrans
BIONJ
ML
Parsnp
R package ape

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