Drosophila serrata DsGRP and 5-panel MA wing size

Below are details of all files published and their relationships to one another. Each data file has its own README detailing all variables.

DATA FILES: There are three raw data files, analysed to generate all display items in the manuscript:

1. DsGRP_Size.csv contains the data used to choose the lines used as ancestors of the MA. Analysed in SAS to generate results in Supplementary Materials (see also #4).

2. Inbreeding.csv contains data for each MA line in each generation on whether they remained extant, and on whether brother-sister inbreeding was applied. For each line, in each generation, the cumulative number of inbred generations is recorded. Missing information indicates no emergence (hence no additional inbreeding) in that generation. Some lines were resurrected in the following generation using flies from back-up vials (maintained at a larger population size). These data were analysed to obtain basic information about the experiment (Table S1 & S2), restructured to analyse survival times (Figure 4), and to add a realised number of inbreeding generations to the wing size data file (#3).

3. MA_size_data.csv contains the wing size data of 49769 flies sampled from the 5 independent Mutation Accumulation panels (321 Lines in total) across 28 experimental time points. Analysed using SAS code to generate #5 & #6.

There are also three processed data files, analysed further in R code to generate display items:

4. DsGRP_BLUPS_SAS.csv contains the SAS output best linear unbiased predictors for each sex, plotted for Figure S2 and associated results.

5. MA_SAS_varcomp.csv contains the SAS output variance component (random effect) estimates, analysed further in R code to estimate mutational variance, and scale those estimates for reporting (Table 1 and Figure 1)

6. MA_SAS_asycov.csv contains the SAS output estimates of the error associated with each variance component estimate and is handled in R code with #5

CODE FILES: There is one code file containing the SAS codes, and one containing all R codes.

1. Code_SAS.sas contains annotated code for models fit as described in Methods and Supplementary Methods. File can be read (but not executed) using text editor. Code executed via either desktop SAS app or online SAS (free account for academics) https://welcome.oda.sas.com/

2. Code_R.Rmd contains all code for initial data processing of the raw data files, and of SAS output (processed files) to generate final results and display items. File can be read (but not executed) using text editor. Code executed via either desktop or online R & RStudio app.