Erik van Nimwegen
Erik van Nimwegen
Center for Molecular Life Sciences
University of Basel
Bacterial phylogenies reflect complex patterns of recombination rates
It is well-known that, through homologous recombination, cells can incorporate DNA from other cells into their genome. However, so far it has been difficult to quantify to what extent genome evolution is impacted by this process. I will discuss new methods that use statistics of single-nucleotide polymorphisms (SNPs) in the core genome alignment of a set of bacterial strains, to quantify the effects of recombination, and show that bacterial genome evolution is almost entirely driven by recombination. Because each locus in the alignment has been overwritten by recombination hundreds of times in its history, it is impossible to reconstruct the clonal phylogeny of the strains, and instead of a consensus phylogeny, tens of thousands of different phylogenies occur along the genome alignment.
These findings may appear at odds with the well-known fact that phylogenies reconstructed from whole genome alignments exhibit robust structure with apparently well-defined phylogroups. Using statistics of SNP patterns again, I will show that, although bacterial populations do not evolve clonally, they also do not recombine freely. Instead, they show complex patterns of population structure such that recombination rates between different lineages vary along a continuum spanning several orders of magnitude, with a unique pattern of rates for each lineage. The robust phylogenetic structures that are observed in the data do not reflect ancestry, but reflect these complex pattern of recombination rates across lineages.
Erik van Nimwegen studied theoretical physics at the University of Amsterdam. He performed his PhD studies at the Santa Fe Institute (SFI) in Santa Fe New Mexico, receiving his PhD from the Faculty of Biology at Utrecht University in 1999. This was followed by a year of post-doc studies at the SFI, and three years as a fellow at the Center of Studies in Physics and Biology at the Rockefeller University, New York. Since 2003 he is Professor of Computational Biology at the Biozentrum of the University of Basel, and group leader at the Swiss Institute of Bioinformatics since 2004.
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