R notebooks for data formatting, data normalisation and statistical analyses

These R notebooks were done using R studio. They allow 1) to format the data sets after running empiricIST; 2) to do data normalisation for all the analyses performed in the manuscript; 3) to perform all statistical analyses and create the plots for the manuscript. Please note that these notebooks assume that you have run the empiricIST in the data set (the empiricIST is available at https://github.com/Matu2083/ empiricIST). The data analysed here, as indicated in the manuscript, is available from the publication: Bank C, Hietpas RT, Wong A, Bolon DN, Jensen JD (2014). A Bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: Uncovering the potential for adaptive walks in challenging environments. Genetics 196: 841–852

Mathematica Notebook Fitness landscapes statistics and adaptive walk

This notebook allows to replicate the data analyses corresponding to the section of the manuscript called "The shape of the codon fitness landscape with and without synonymous effects". Please note that the data set necessary to run the analyses is obtained through the R notebooks also available within this repository

Raw Data and Average statistics

In this excel book you can find the raw data for the three populations analyzed in each continent (Europe and South America) and the two generations of the European populations analyzed (6 and 25). Additionally, there are also tables with the basic statistics (average and standard deviation) of centroid size and wing shape for each inversion analyzed, separated by replicate population and generation

MCC.xlsx

Data for the study of mate-choice copying, and its impact on hybridisation, in Drosophila subobscur

Genotypes for the 6 Foundations_Dryad

Individual genotypes for 9 microsatellites of the six foundations at generations zero (G0), three (G3) and 14/15 (G14/G15)three fold replicated for generations 3 and 14/15 - data used for estimating genetic variability and differentiation. The first three digits correspond to one allele and the next three to the other allele at each locus

Phenotypic data for the 6 Foundations_Dryad

Mean values of life-history traits per generation and foundation that were used to trace evolutionary trajectories. Mean values were obtained as the difference between each replicate value and the control replicate with the same randomly defined number

Raw data for juvenile life history traits

Raw data for juvenile traits for each population, generation and temperature assayed. MV refers to missing value

Individual Karyotypes

This data corresponds to the individual karyotypes analyzed at generations 2, 6, 15, 25 and 40, during laboratory adaptation of the foundations Ad (Adraga), Mo (Montpellier) and Gro (Groningen)

Raw data for adult life history traits

Raw data for adult life history traits for each population, generation and temperature assayed. MV indicates missing values

Fecundity, starvation resistance and size data

Data from Fecundity, starvation resistance and body size assays performed on the three experimental populations and the controls (Ad - Adraga, Mo - Montpellier, Gro - Groningen, TA - Controls). Assays were performed at generations 6, 11, 14, 18 and 22 of laboratory adaptation