DOI: 10.5061/dryad.w9ghx3fqp
title: Causation without correlation: Parasite-mediated frequency-dependent selection and infection prevalence

description: Parasite-mediated selection is thought to maintain host genetic diversity
 for resistance. We might thus expect to find a strong positive correlation
 between host genetic diversity and infection prevalence across natural
 populations. Here, we used computer simulations to examine host–parasite
 coevolution in 20 simi-isolated clonal populations across a broad range of
 values for both parasite virulence and parasite fecundity. We found that
 the correlation between host genetic diversity and infection prevalence
 can be significantly positive for intermediate values of parasite
 virulence and fecundity. But the correlation can also be weak and
 statistically non-significant, even when parasite-mediated
 frequency-dependent selection is the sole force maintaining host
 diversity. Hence correlational analyses of field populations, while
 useful, might underestimate the role of parasites in maintaining host
 diversity.
description: This is a computer simulation written in Excel.  It includes a
 data set from a representative run, assuming virulence was equal to 0.7
 with a mean parasite fecunity equal to 15.  Virulence and parasite
 fecundity can be reset by the user (see usage notes).   
description: Directions for simulation 1) Download and open
 the .xlsm file. 2) A dialog box will pop up.  Click
 "enable macro" 3) The file will open, and a
 "bootstrap" dialog box will pop up.  Close the box.
 4) To change parameter values, click on the "data1"
 tab. 5) You will see a list of parameter values on the
 left-hand side of the sheet. 6) We left the birth rate
 of uninfected hosts (bu) at 10, but it could be changed. 
 7) To change the birth rate of infected hosts (bi), simply change
 the bold blue entry next to "bi".<br>      Virulence is
 calculated as 1 - (bi/bu).  8) To change the mean
 realized fecundity of parasites, change "MeanBeta".
 9) To change the Standard Deviation for the birth rate of
 uninfected hosts, change "STD_bu". 10) Other
 variables can be changed in the sim, such as the probability of infected
 (or uninfected) migrants, but we left them as in
 "data1"  11) The simulation can be run at any
 time for a single generation by pressing "control +"
 12) To iterate the simulation for multiple generations, click on
 Excel's developer tab at the top of the page. 13)
 Then click on the "Visual Basic" icon on the top left-hand
 side. 14) The macro will open up.  Press the run icon
 (which is a triangle shaped icon pointed to the right)
 15) The "Bootstrap" dialog box pops up.  Select either
 100, 1000, or 10000 iterations.  The macro will begin running
 automatically.  1000 iterations takes about 30 mins.  
 16) When to run has completed, close the bootstrap box.
 17) The macro will have created a new sheet (to the left of
 "data1") with the data.  The new tab is named after the date and
 time.  We suggest renaming the tab as the virulence, e.g., Vir = 0.4.
   18) The data are in columns.  The definitions of the
 column headers are "Div-Prev" = the
 correlation between host clonal diversity and prevalence of
 infection.  "Prev-Beta" = the correlation
 between prevalence of infection and mean parasite fecundity (which varies
 among populations).  "Div-Beta" = the
 correlation between host clonal diversity and mean parasite
 fecundity. "Mean_Inf" = the average
 prevalence of infection across the 20 populations.
 "STD_Inf" = the Standard Deviation of prevalence across
 the 20 populations. "Mean_Diversity" = the
 average clonal diversity across the 20 populations.
 "STD_Diversity" = the observed Standard Deviation of
 clonal diversity across the 20 populations.
 "Pvalue_Div-Prev" = the P-value for the correlation
 between diversity and prevalence.
 "Pvalue_Prev-Beta" = the P-value for the correlation
 between prevalence and parasite fecundity.
 "Pvalue_Div-Beta" = the P-value for the correlation
 between host diversity and parasite fecundity.
 "Pvalue_Div-STDbu" = the P-value for the correlation
 between host diversity and the Standard Deviation in the birth rate of
 uninfected hosts. "starting_Freq_A_pop1" =
 the randomly assigned frequency of allele A in population 1.  (This is
 test of the random number generator.)
 "starting_bu_AX_pop1" = the randomly assigned fecundity
 for uninfected hosts having genotype AX in population 1.  (This is test of
 the random number generator.) 19) To rerun the
 simulation, return to tab "data1" to change parameter values.  
 Then follow the directions above for running the macro. 
 Notes. The "Calcs" sheets are the
 calculations for each of the 20 populations.  e.g., "Calcs (2)"
 gives the calculations for Population 2. The simulation
 allows for sexual reproduction, but we set the recombination rate to 0,
 making the hosts effectively clonal.