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Volume 7, Issue 12

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments Open Access

Abstract

Homoplasic SNPs are considered important signatures of strong (positive) selective pressure, and hence of adaptive evolution for clinically relevant traits such as antibiotic resistance and virulence. Here we present a new tool, SNPPar, for efficient detection and analysis of homoplasic SNPs from large whole genome sequencing datasets (>1000 isolates and/or >100 000 SNPs). SNPPar takes as input an SNP alignment, tree and annotated reference genome, and uses a combination of simple monophyly tests and ancestral state reconstruction (ASR, via TreeTime) to assign mutation events to branches and identify homoplasies. Mutations are annotated at the level of codon and gene, to facilitate analysis of convergent evolution. Testing on simulated data (120 alignments representing local and global samples) showed SNPPar can detect homoplasic SNPs with very high specificity (zero false-positives in all tests) and high sensitivity (zero false-negatives in 89 % of tests). SNPPar analysis of three empirically sampled datasets (, and ) produced results that were in concordance with previous studies, in terms of both individual homoplasies and evidence of convergence at the codon and gene levels. SNPPar analysis of a simulated alignment of ~64 000 genome-wide SNPs from 2000 genomes took ~23 min and ~2.6 GB of RAM to generate complete annotated results on a laptop. This analysis required ASR be conducted for only 1.25 % of SNPs, and the ASR step took ~23 s and 0.4 GB of RAM. SNPPar automates the detection and annotation of homoplasic SNPs efficiently and accurately from large SNP alignments. As demonstrated by the examples included here, this information can be readily used to explore the role of homoplasy in parallel and/or convergent evolution at the level of nucleotide, codon and/or gene.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bacteria , evolution , homoplasy and phylogeny
Funding
This study was supported by the:
  • department of health and human services, state government of victoria
    • Principle Award Recipient: BernardPope
  • australian research council (Award DE190100805)
    • Principle Award Recipient: SebastianDuchene
  • sylvia and charles viertel charitable foundation
    • Principle Award Recipient: KathrynE Holt
  • bill and melinda gates foundation (Award OPP1175797)
    • Principle Award Recipient: KathrynE Holt
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2021-12-07
2024-04-26
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SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments
M Gen 7, 000694 (2021); https://doi.org/10.1099/mgen.0.000694
/content/journal/mgen/10.1099/mgen.0.000694
/content/journal/mgen/10.1099/mgen.0.000694
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