Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species

Abstract
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Abstract

Although recombination is accepted to be common in bacteria, for many species robust phylogenies with well-resolved branches can be reconstructed from whole genome alignments of strains, and these are generally interpreted to reflect clonal relationships. Using new methods based on the statistics of single-nucleotide polymorphism (SNP) splits, we show that this interpretation is incorrect. For many species, each locus has recombined many times along its line of descent, and instead of many loci supporting a common phylogeny, the phylogeny changes many thousands of times along the genome alignment. Analysis of the patterns of allele sharing among strains shows that bacterial populations cannot be approximated as either clonal or freely recombining, but are structured such that recombination rates between lineages vary over several orders of magnitude, with a unique pattern of rates for each lineage. Thus, rather than reflecting clonal ancestry, whole genome phylogenies reflect distributions of recombination rates.

Data availability

All data generated or analyzed during this study are available from public databases and links to all the source data are provided in the article.

The following data sets were generated

(2018) Sequencing, assembly and annotation of naturalized E. coli isolates from Lake Superior Watersheds
NCBI Bioproject, PRJNA432505.

https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA432505

Article and author information

Author details

Thomas Sakoparnig

Biozentrum, University of Basel, Basel, Switzerland

Competing interests
The authors declare that no competing interests exist.
Chris Field

Biozentrum, University of Basel, Basel, Switzerland

Competing interests
The authors declare that no competing interests exist.
Erik van Nimwegen

Biozentrum, University of Basel, Basel, Switzerland

For correspondence
erik.vannimwegen@unibas.ch

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-6338-1312

Funding

Swiss National Science Foundation (31003A_135397)

Erik van Nimwegen

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.