DOI: 10.5061/dryad.6gf28
title: Data from: Positive selection inhibits gene mobilization and transfer in soil bacterial communities

description: Horizontal gene transfer (HGT) between bacterial lineages is a fundamental
 evolutionary process that accelerates adaptation. Sequence analyses show
 that conjugative plasmids are principal agents of HGT in natural
 communities. However, we lack understanding of how the ecology of
 bacterial communities and their environments affect the dynamics of
 plasmid-mediated gene mobilization and transfer. Here we show, in simple
 experimental soil bacterial communities containing a conjugative mercury
 resistance plasmid, the repeated, independent mobilization of
 transposon-borne genes from chromosome to plasmid, plasmid to chromosome
 and, in the absence of mercury selection, interspecific gene transfers
 from the chromosome of one species to the other via the plasmid. By
 reducing conjugation, positive selection for plasmid-encoded traits, like
 mercury resistance, can consequently inhibit HGT. Our results suggest that
 interspecific plasmid-mediated gene mobilization is most likely to occur
 in environments where plasmids are infectious, parasitic elements rather
 than those where plasmids are positively selected, beneficial elements.
description: S1_VarDataCompiled table of evolved variants used to produce Figure 1. Columns refer to sample number (sample_number), whether the clone had evolved in a population with or without the plasmid (plasmid_trt, pQBR57 = plasmid-containing, plasmid- = plasmid free), with or without the other species (cul, ss = single-species, co=co-culture), the level of mercury treatment (mer, in µg/g), replicate (rep), species (spc, Pf = P. fluorescens, Pp = P. putida), whether the clone was carrying a plasmid (plasmid, P = plasmid+, T = contained Tn5042 but not the plasmid, 0 = contained neither plasmid nor Tn5042), the chromosome in which the variant was detected (chr, numbers are as the EMBL database with AM181176 referring to the P. fluorescens SBW25 chromosome, AE015451 to the P. putida KT2440 chromosome and LN713926 referring to pQBR57), the position of the variant (position and position.1, where the variant is a SNV/indel these numbers are identical and refer to the first base in question, where the variant is a TE insertion these numbers refer to the boundaries of the direct repeat caused on insertion, where the variant is a duplication or deletion these numbers refer to the start and end of the event respectively), the target gene (target, where the target it intergenic the upstream and downstream genes are given, separated by a dash), the type of mutation (type, either SNV/indel, or, if a TE insertion, the name of the TE), and the predicted effect of the mutation (effect, as determined by snpEff).S2_Hg_transfer_dataComma-separated values formatted file containing data presented in Figure 2. Columns refer to replicate (rep), transfer number (transfer), antibiotic marker of the donor strain (donor_marker), mercury treatment in µg/g soil (mercury), and the estimated densities of donors and recipients with and without plasmid in cfu/g soil.S3_Tn5042_PP_DataComma-separated values formatted file containing data presented in Figure 3. Columns refer to whether the population was evolved alone or in co-culture (cul, ss= single-species, co = co-culture), population (pop), transfer number (transfer), total clones tested (total_tested), total clones plasmid-free (free), total plasmid-containing clones with the focal Tn5042 insertion (p_focal_tn), total plasmid-free clones with the focal Tn5042 insertion (free_focal_tn), total plasmid-free clones with a different Tn5042 insertion (other_tn), and calculated frequencies of plasmid-free cells (free.f), plasmid-containing clones with the focal Tn5042 insertion (p_focal_tn.f), plasmid-free cells with the focal Tn5042 insertion (free_focal_tn.f), plasmid-free cells with a different Tn5042 insertion (other_tn.f), plasmid-free cells with no Tn5042 insertion (free_none.f) and plasmid-containing cells without the focal Tn5042 insertion (p_none.f)S4_Tn5042_PF_DataComma-separated values formatted file containing data presented in Figure 3. Columns refer to transfer number (transfer), total clones tested (total_tested), total clones plasmid-free (free), total plasmid-containing clones with the focal Tn5042 insertion (p_focal_tn), total plasmid-free clones with the focal Tn5042 insertion (free_focal_tn), total plasmid-free clones with a different Tn5042 insertion (other_tn), and calculated frequencies of plasmid-free cells (free.f), plasmid-containing clones with the focal Tn5042 insertion (p_focal_tn.f), plasmid-free cells with the focal Tn5042 insertion (free_focal_tn.f), plasmid-free cells with a different Tn5042 insertion (other_tn.f), plasmid-free cells with no Tn5042 insertion (free_none.f) and plasmid-containing cells without the focal Tn5042 insertion (p_none.f)ExtensiveGeneExchange_ScriptsZip file (17 files) containing scripts representative of those used to generate data presented in the manuscript.