A very nice and interesting manuscript that will be read widely among clock and general biologists. This is a well-written and easy to read synopsis of a great deal of work. A number of technical questions arose as I went through the ms, but as I read further, they were all answered. The scientific findings (as opposed to the technical ones) are described succinctly, and, unusually for this type of genomics paper, it does not degenerate into just a list of 'interesting' genes, but instead is nicely focused around what are the most germane features of Monarch biology. It also sends the stage for subsequent studies of population biology. It is informative and concise, and as such deserves to be published essentially as is. A couple of comments

I think that while significant, the turtle differential expression result is 'reaching'. Maybe the word 'marginal' might be used here as it is clearly a very small effect compared to some of the other genes.

Could the authors not weave any brief story out of the 8 visual genes (which may also relate to clock function)....or the olfactory genes?

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N.B. These are the general comments made by the reviewer when reviewing this paper in light of which the manuscript was revised. Specific points addressed during revision of the paper are not shown.