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From the egg pads, newly hatched nymphs were collected weekly and used to establish a new generation according to their diet quality treatment and replicate population identity (i.e., there was no overlapping of generations).
This test was applied for each AR and TW replicate population.
The arrays were scanned in two batches of 16, balanced for replicate population of origin and replicate population of origin of the males to which they were mated [GEO GSE48385].
There was no nesting of competition assay plate within replicate population or replicate population within generation, and we thus assume that the variance among competition plates is the same for all populations and is maintained constant during experimental evolution.
However, the analysis of the standardized Ln RH values for each TW replicate population showed some significant results, though they were not consistent among replicates.
For hermaphrodite outcross-fitness and self-fitness data did not follow LMM assumptions and consequently we modelled the effects of generation and replicate population with generalized linear mixed models (GLMM) incorporating Gamma error distributions (see Methods).
To obtain fitted values in the original scale, particularly for w o and w s, we used the function predict within the stats package in R. For significance of replicate population effects (intercept of the models) and generation (slope) from zero, we employed z-tests as implemented in the multcomp R package cftest function [ 67].
Each replicate population comprised 1000 to 2000 mating individuals.
Interpopulation crosses were carried out between randomly picked males from one replicate population and randomly picked females from another replicate population of the same size.
After a total of 150 generations of growth, individual clones were isolated from each replicate population.
When mature, the parental flies for each replicate population were randomly picked among the respective offspring.
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