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I liked this paper on the first read, and I like it more now that the language has been improved around the description of the markers used and the causal locus for back color. Thanks for addressing the comments.

Two things I noticed on re read:

L251 should this be "r package" genetics?

L489L “..there might be several candidate genes within the major effect color locus and
these genes could be simultaneously involved in shaping the observed color variation”

I am unclear what simultaneously means it - multiple genes simultaneously, or the causal locus and other genes? If I am reading it right I think the authors meant something like “..there are several candidate genes within the major effect color locus and one or more of these gene may be involved in shaping the observed color variation.”

The authors have done a nice job addressing previous comments. On re-reading, I continue to enjoy this story, and feel it is an important contribution to this system and also linking genotype and phenotype in the wild.

Fig S3: I could not find a textual reference to the upper panel (allele age) and couldn't quite make sense of it as the data is reproduced from another publication. If it is not used in the text, I suggest removing it as extraneous.

L438: "that appeared to enjoy a fitness advantage (Krüger et al., 2001)." I suggest avoiding the word "enjoy", perhaps "that appeared to experience a fitness advantage"