Genetic slippage after sex maintains diversity for parasite resistance in a natural host population

Data associated to the manuscript:

Ameline, C., Vögtli, F., Andras, J.P., Dexter, E., Engelstädter, J., Ebert, D., 2022. Genetic slippage after sex maintains diversity for parasite resistance in a natural host population. Science Advances 8(46):eabn0051, DOI: 10.1126/sciadv.abn0051

List of files:

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Script #1: sampling and hatching plots

- dynamics_ScAdv_sampling-hatching.R: R script

The R script uses the following files:

1. Field monitoring of resistance, prevalence and ephippia laying

- chh.txt: resistotype, prevalence and ephippia laying data for 2010 to 2018

- chh4l.txt: same as chh, but with 4-latter resistotypes for the hatching plot

- chhcolorcode.txt: color code for resistotypes

- chhn.txt: sample sizes to annotate Fig. 1

- resstat.txt: resistotype values of each P. ramosa isolate for each year for mean and se calculation

- chh2021.txt: sampling data for 2020 and 2021 for Fig. S8

2. Slippage plot

- slippage.txt: data for slippage plot, Fig. 2

3. Hatching plots

- prophatch_all_genos.xlsx: for calculations of expected resistotypes proportions from hatching of resting eggs

- prophatch_bbDDfreqCE.xlsx: same as above

- legend_chhhatching_expected.png: legend of hatching figures

- scatterhatch.txt: for Fig. 4

- legend_scatterhatch.png: legend Fig. 4

4. Hathcing experiment Fig. S3

figure

- eggbanknum.csv

- eggbankrpe.txt

- eggbank14.txt

stats

- spring14_hatch.txt

- spring14eggbank.txt

- spring15eggbank.txt

- spring16eggbank.txt

- spring18eggbank.txt

5. Resting stages laying, counting and hatching success Fig. S2

- hatchdates.txt

- hatching14151718.txt

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Script #2: modelling the genetic model of resistance using peas and matrices

- dynamics_ScAdv_modelling.R: R script

The R script uses the following files:

- chh4l.txt: to get the resistotype proportions at each timepoint

user input of allele frequency within the different resistotypes:

- freq_all_genos.csv

- freq_all.csv

- freq_all_bbDDfreqCE.xlsx

- freq_all_onegeno.xlsx

output files from the script

- prophatch_all_genos.xlsx

- prophatch_all_onegeno.xlsx

- prophatch_bbDDfreqCE.xlsx

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Script #3: environmental variables - Fig. S1

- dynamics_ScAdv_env.R: R script

The R script uses the following files:

- chh.txt: resistotype, prevalence and ephippia laying data for 2010 to 2018

- chh_temp_201119.csv: data from temperature logger in the pond

- chhvar.txt: sampling variables: water level, daphnia species, sexes, density.

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