Abstract
An open question in evolutionary biology is how does the selection–drift balance determine the fates of biological interactions. We searched for signatures of selection and drift in genomes of five endosymbiotic bacterial groups known to evolve under strong genetic drift. Although most genes in endosymbiotic bacteria showed evidence of relaxed purifying selection, many genes in these bacteria exhibited stronger selective constraints than their orthologs in free-living bacterial relatives. Remarkably, most of these highly constrained genes had no role in the host–symbiont interactions but were involved in either buffering the deleterious consequences of drift or other host-unrelated functions, suggesting that they have either acquired new roles or their role became more central in endosymbiotic bacteria. Experimental evolution of Escherichia coli under strong genetic drift revealed remarkable similarities in the mutational spectrum, genome reduction patterns and gene losses to endosymbiotic bacteria of insects. Interestingly, the transcriptome of the experimentally evolved lines showed a generalized deregulation of the genome that affected genes encoding proteins involved in mutational buffering, regulation and amino acid biosynthesis, patterns identical to those found in endosymbiotic bacteria. Our results indicate that drift has shaped endosymbiotic associations through a change in the functional landscape of bacterial genes and that the host had only a small role in such a shift.
Highlights
The interactions between biological entities and their role in evolution has enthralled scientists for decades, but the causes and consequences of such interactions remain poorly characterized
To compare the bacterium Escherichia coli K12 evolving experimen- selective pressures acting in endosymbiotic bacteria tally under population dynamics that emulate those vs those acting in free-living bacteria, we used two of maternally inherited endosymbiotic bacteria
Indexed RNAseq libraries were constructed using strand-specific cDNA synthesis (TruSeq RNA Library Preparation Kit, Illumina), pooled in equimolar concentration and subjected to Signatures of drift and selection in endosymbiotic bacteria of insects Endosymbiotic bacterial genomes evolve under more relaxed selective constraints when compared with their closest free-living relatives (Moran, 1996; Wernegreen, 2002; Moran et al, 2008; Wernegreen, 2011)
Summary
The interactions between biological entities and their role in evolution has enthralled scientists for decades, but the causes and consequences of such interactions remain poorly characterized Starring these biological interactions is the symbiosis of bacteria with plants and animals, considered an important engine of eukaryote ecological diversification (McFall-Ngai et al, 2013; Archibald, 2014). We estimated ing selection imposed by the host and that emerging the strength of selection by calculating the nonin a symbiotic context but being independent from synonymous-to-synonymous divergence ratio the host. Teasing apart these levels of selection (ω = dN/dS) using yn00 implemented in PAML version remains a major challenge. To compare the bacterium Escherichia coli K12 evolving experimen- selective pressures acting in endosymbiotic bacteria tally under population dynamics that emulate those vs those acting in free-living bacteria, we used two of maternally inherited endosymbiotic bacteria
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