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

Sakoparnig, Thomas and Field, Chris and van Nimwegen, Erik. (2021) Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species. eLife, 10. e65366.

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Official URL: https://edoc.unibas.ch/81160/

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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.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (van Nimwegen)
UniBasel Contributors:van Nimwegen, Erik and Sakoparnig, Thomas and Field, Christopher
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:eLife Sciences Publications
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:31 Aug 2021 11:55
Deposited On:31 Aug 2021 11:55

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