The US-variation manuscript finally is coming together

(Yes, I know I've said this before...)

Abstract

Uptake signal sequences are DNA motifs that promote DNA uptake by competent bacteria in the family Pasteurellaceae and the genus Neisseria. The genomes of these bacteria contain many copies of their canonical uptake sequence (often >100-fold overrepresentation), causing the uptake machinery to prefer DNA derived from close relatives over DNAs from other sources. However the molecular and evolutionary forces responsible for both the uptake bias and the abundance of uptake sequences in these genomes are not well understood. Here we thoroughly evaluate the simplest explanation, that uptake sequences accumulate in genomes by a form of molecular drive, generated by biased DNA uptake and genetically neutral recombination. A computer simulation model shows that these simple assumptions are sufficient to drive uptake sequences to high densities, with the spacings, stabilities and strong consensuses typical of real uptake sequences. In the absence of strong evidence of selection for a recombination function, it may thus be more parsimonious to treat uptake sequences as an epiphenomenon of biased DNA uptake rather than as evidence for a sexual function of natural competence.