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

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.

Gene regulation is commonly selected for high plasticity and low noise

“…We also included the corresponding downstream annotated ORFs (Blattner et al, 1997). We then identified and aligned homologous regions from the 135 environmental isolates of E. coli (Breckell & Silander, 2020; Sakoparnig et al, 2021). To increase the likelihood of capturing homologous IGRs, we included 100 base pairs (bp) of the upstream and downstream ORFs (see Methods ).…”

“…Throughout, we refer to IGRs together with the flanking sequences as “promoters”. The genomes of 135 environmental E. coli strains (Breckell & Silander, 2020; Ishii et al, 2006; Sakoparnig et al, 2021) were then blasted against the promoter sequences extracted from MG1655 with e-value cut-off set to 10 -10 ; Blast version 2.7.1 (Altschul et al, 1990). Blast hits not more than 100 bp shorter than the MG1655 reference sequence were extracted as segregating promoter variants from each of the 135 environmental E. coli strains.…”

“…To characterise the relationship between genetic variation, phenotypic variation, and selection on gene regulation, we first quantified genetic variation in intergenic regions (IGRs) and open reading frames (ORFs) from 135 environmental isolates of E. coli (Ishii et al, 2006) that span the genetic diversity of E. coli (Sakoparnig et al, 2021) . We assumed that a substantial portion of gene regulatory phenotypes depend on the sequence of these IGRs.…”

Adaptive evolution of hybrid bacteria by horizontal gene transfer

“…horizontal gene transfer | experimental evolution | fitness landscape H orizontal gene transfer (HGT) plays an important role in bacterial evolution (1,2), which includes speeding up the adaptation to new ecological niches (3,4) and mitigating the genetic load of clonal reproduction (5,6). On macroevolutionary time scales, HGT occurs between bacteria of different species and also between bacteria and eukaryotes (1, 2, 7); these dynamics have very heterogeneous rates (8), and the permanent integration of transferred genes into regulatory networks is slow (9). An important mechanism of HGT is transformation, the active import and inheritable integration of DNA from the environment (10,11).…”

Comparative Population Genetics in the Human Gut Microbiome

“…To quantify recombination in bacteria, researchers have begun to characterize the statistical association of alleles at different loci (i.e., linkage disequilibria), where the degree of association can be viewed a function of the recombination rate. For several species found in the gut, as well as environmental samples and pathogens, linkage disequilibria tends to decay as the genetic distance between a pair of loci increases, which suggests that recombination may be common (Crits-Christoph et al 2020;Sakoparnig et al 2021;Lin & Kussell 2019). Such rampant recombination suggests that while microbes reproduce clonally, the label "asexual" is a misnomer.…”