DOI: 10.5061/dryad.5qfttdzjs
title: Cumulative effects of mutation and selection on susceptibility to bacterial pathogens in <em>Caenorhabditis elegans</em>

description: Understanding the evolutionary and genetic underpinnings of susceptibility
 to pathogens is of fundamental importance across a wide swathe of
 biology.  Much theoretical and empirical effort has focused on
 genetic variants of large effect, but pathogen susceptibility often
 appears to be a polygenic complex trait.  Here we investigate the
 quantitative genetics of survival over 120 hours of exposure
 ("susceptibility") of C. elegans to three bacterial species of
 varying virulence, along with a fourth strain, the OP50 strain of E. coli,
 the standard laboratory food for C. elegans.  We compare the
 genetic (co)variance input by spontaneous mutations accumulated under
 minimal selection to the standing genetic (co)variance in a set of 47 wild
 isolates.  Three conclusions emerge.  First, mutations
 increase susceptibility to pathogens. Second, susceptibility to pathogens
 is uncorrelated with fitness in the absence of pathogens.  Third,
 with the possible exception of S. aureus, pathogen susceptibility is
 clearly under purifying directional selection of magnitude roughly similar
 to that of competitive fitness in the MA conditions.  The results
 provide no evidence for fitness tradeoffs between pathogen susceptibility
 and fitness in the absence of pathogens.
description: # Cumulative effects of mutation and selection on susceptibility to
 bacterial pathogens in *Caenorhabditis elegans* Dataset DOI:
 [10.5061/dryad.5qfttdzjs](10.5061/dryad.5qfttdzjs) ## Description of the
 data and file structure The purpose of the experiment was to estimate the
 cumulative effects of spontaneous mutations on the susceptibility of C.
 elegans to bacterial pathogens.  The experimental methods are described in
 detail in the accompanying manuscript.  The two data files
 (Supplemental_Table_S1.xlsx and  Supplemental Tables S2-S7.xlsx) consist
 of Excel worksheets.  Each data sheet has its own accompanying
 "Readme" document on the following worksheet. The missing data
 from an empty cell is changed to a "." ### Files and variables
 #### File: Supplemental_Tables_S2-S7.xlsx **Description:** An Excel file
 containing Supplemental Tables S2 through S7 from the accompanying
 article.  Each data worksheet, titled "TSx..." (where the x is
 the number of the table) has its accompanying explanatory
 "Readme" document following the data worksheet.  ##### Variables
 * See the relevant "Readme" worksheet for each table. #### File:
 Supplemental_Table_S1.xlsx **Description:** An Excel file containing
 Supplemental Table S1, contains the information about "going to
 backup" (defined in the Methods section of the text).  Worksheet
 "N2" contains data for the N2 lines, worksheet "PB306"
 contains data for the PB306 lines.  The worksheet titled
 "Readme" contains the explanatory information. **Description**:
 The two preceding worksheets show the the outcome of the transfer of a
 worm in each MA line at each generation. In both strains, transfers
 occurred at four-day intervals. Rows are MA lines, columns are transfers
 at a given generation of MA (1→Gmax). A cell with a "."
 indicates a successful transfer. A cell with a "b" (for
 "backup") indicates that the worm was either dead, missing, or
 obviously sterile, so a worm was taken from the backup plate from the
 preceding generation (see Methods for details). A cell with an
 "h" (for "holdover") indicates that either the parent
 worm had not reproduced but was gravid, or that it had reproduced but the
 offspring on the plate had not reached at least the L2 stage. If a worm
 that was held over in one generation had not reproduced by the next
 generation, it was scored as a failure, and the worm was replaced with a
 worm from the backup generation. In the "N2" and
 "PB306" worksheets, in the last ten columns (IQ-IZ) , the column
 headings are labeled, in order, "Nhold", "Nback",
 "Ntotal", "Nfail", "Ncorrtotal", "N
 gens in Notes", "Gmax-Ncorr", "Discrepancy_corr",
 "%back" and "Best Estimate". Nhold and Nback are as
 above. Ntotal is the sum of Nhold and Nback. Nfail is as above. Ncorrtotal
 is the difference between Ntotal and Nfail ("corr" indicates
 "corrected"). "N gens in Notes" is the number of
 bottlenecks recorded in what was the data notebook of record at the
 conclusion of the experiment. However (see Methods), there is some
 uncertainty about this number, because one data notebook was lost (prior
 to G60) and some backups and holdovers went unrecorded. The MA
 bottlenecking protocol was interrupted at Gmax=194 to cryopreserve and
 ship worms from Indiana to Florida. Gmax-Ncorr is the difference between
 Gmax (194+50 generations of MA following the move = 244 gens) - Ncorr.
 Discrepancy_corr is the difference between Gmax-Ncorr and N gens in Notes.
 %back is = 1-Nhold/Ncorrtotal. The Best Estimate (of the actual # of MA
 generations) is N gens in Notes - %back*Discrepancy_corr. ## Code/software
 Microsoft Excel (or other software to read a .xlsx file).