Data from: Positive selection inhibits gene mobilization and transfer in soil bacterial communities

Hall JPJ, Williams D, Paterson S, Harrison E, Brockhurst MA

Date Published: July 31, 2017

DOI: http://dx.doi.org/10.5061/dryad.6gf28

 

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Title S1_VarData
Downloaded 2 times
Description Compiled 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).
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Title S2_Hg_transfer_data
Downloaded 3 times
Description Comma-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.
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Title S3_Tn5042_PP_Data
Downloaded 2 times
Description Comma-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)
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Title S4_Tn5042_PF_Data
Downloaded 3 times
Description Comma-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)
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Title ExtensiveGeneExchange_Scripts
Downloaded 6 times
Description Zip file (17 files) containing scripts representative of those used to generate data presented in the manuscript.
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When using this data, please cite the original publication:

Hall JPJ, Williams D, Paterson S, Harrison E, Brockhurst MA (2017) Positive selection inhibits gene mobilization and transfer in soil bacterial communities. Nature Ecology & Evolution, online in advance of print. http://dx.doi.org/10.1038/s41559-017-0250-3

Additionally, please cite the Dryad data package:

Hall JPJ, Williams D, Paterson S, Harrison E, Brockhurst MA (2017) Data from: Positive selection inhibits gene mobilization and transfer in soil bacterial communities. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.6gf28
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