Therefore, we perform additional simulations varying the fluid input from depth by plus or minus one order of magnitude at t = 0 (Fig. 14).
However, we did perform additional simulations assuming smaller litter sizes (two females, two males), and unbalanced sex-ratio (eight total offspring with one to seven females), and compared all three sets of assumptions (4-4, 2-2, 8) to the greedy approach of setting up breeders as soon as any sibling mating pairs are available.
To test this hypothesis, we performed additional simulations to mimic metagenomic samples of 16S rRNA sequences from individuals belonging to three types of gut microbiome communities.
Since it is possible that the proximity of the Q1 locus to the end of the chromosome could account for its different behavior, we performed additional simulations to test whether or not similar proximity to the chromosome end could affect coverage probabilities for a simulated QTL placed between widely spaced markers.
We performed additional simulations to compare the performance of these two approaches for obtaining conditional predictions in terms of calibration, and their performance was very similar (full results in the Additional file 1: Table S2 and Table S3).
To test this, we first performed additional simulations where population size was increased 2-fold.
It was felt that this would require re-doing and/or performing additional simulations to determine whether results remained the same.
Regardless, we agree that it is worth investigating whether this lower hydrophobicity of TMD1 impacts the reported conclusions; having performed additional simulations to investigate this point, we find that it does not have a significant impact.
In recognition of the editorial view that addressing these concerns would require "re-doing and/or performing additional simulations to determine whether results remained the same", we have carried out substantial additional simulations and analysis that we believe addresses in full the issues raised by the reviewers and further strengthens the conclusions of our study.
To determine if results depend on initial population size we performed additional simulations from initial N = 10 000 to N = 300, 100, and 50 (97%, 99%, and 99.5% declines).
