This manuscript used genomics, transcriptomics, spectroscopy and chromatography to investigate the genetic basis for complex coloration in the plumage of Chrysolophus pheasants. Given their striking differences in coloration but close sister relationship, they seem to be an excellent model for understanding pathways leading to divergence of coloration in birds.

I do not have any major concerns about this manuscript, but I do have a few suggestions for how to improve it:

General comment 1: Probably the most important issue is that this needs to undergo more thorough editing of its English. It is largely understandable as is, albeit with some confusing passages, but it would benefit from being checked by a fluent English-speaker.

General comment 2: I think this manuscript would benefit greatly from some expansion in the discussion regarding the evolution of coloration in birds. The manuscript currently reads as if it is simply reporting results without diving into how these results relate to the broader issue of the evolution of complex coloration in birds. Here we have an excellent example of closely related species with starkly contrasting coloration patterns, with some possible evidence of differences in gene expression and mutations, but not much is made of this, nor or is it related to the broader literature. Has anyone else looked at gene expression differences related to coloration in birds in a genome-wide scale? What about candidate gene approaches such as that of CYP2J19? Are there any overlaps with gene-specific studies? And more broadly, what might this mean about how the evolution of the same coloration can proceed via similar or divergent pathways? This might help draw more readers to your system and make an effort to dive into these questions in more detail. Of course, do not try to stretch your conclusions more than the data allow, and there is no need to review the entire literature, but I think there should certainly be more extensive exploration of what your data mean in the bigger picture.

Page 7, lines 6-8: while I appreciate the effort to reconstruct the phylogeny of Chrysolophus relative to Meleagris and Gallus, this seems to be uncontroversial with other studies having supported the Chrysolophus+Meleagris relationship with far better taxon sampling (e.g., Wang et al. 2013 PLoS One). Even though the authors here use many more loci to resolve this relationship, it seems to simply recapitulate a result that was already pretty clear, and it is ultimately not relevant to the focus of this study.

Page 8, lines 15-17: note that the two studies on CYP2J19 only looked at passerines, whereas Emerling 2018 (Molecular Phylogenetics and Evolution) provided evidence that this gene is responsible for the production of red carotenoids more broadly across Aves. I think this is interesting and significant for the broader question of coloration in birds (see General Comment 2 above). For example, why did the Chrysolophus species not co-opt CYP2J19 to create their striking red coloration? This of course is not testable in the current study, and perhaps merely speculative, but I think this is relevant to the broader question of how and why birds convergently evolved similar coloration but often via different mechanisms.

Page 9, line 12: you discuss lineage specific "varied" genes in Chrysolophus. First of all, it is not clear what is meant by varied genes and the significance of this, but I assume this is getting at genetic synapomorphies (substitutions) or something of that nature. First of all, I'm unsure if such a metric is relevant because it is not clear if you're referring to all substitutions/variations, or simply those that are nonsynynomous, which are usually what researchers discuss. Regardless, you refer to them as being lineage specific and discuss it in the context of Chrysolophus. It is important, however, to note that any substitutions present in Chrysolophus may also be shared by at least another six genera (Wang et al. 2013). So any significance gleaned from these analyses should be tempered by the understanding that they might not be specific to Chrysolophus only.

I believe the authors satisfactorily addressed my comments and the manuscript should now be acceptable for publication.