The authors present a very interesting study on the cryptochrome gene family evolution birds.

They explain that Cry genes are critical for night migratory orientation by magnetoreception. Cry is a gene family composed of three genes and Cry4 seems to be critically involved in magnetoreception.

Interestingly, Cry4 is missing in some tropical birds clade, including clade that contains currently migratory species such as hummingbirds and Tyrannids. Gene loss analyses are very convincing as the authors use both genome and transcriptome data. Indeed, gene loss have been subject to some debates as some claims of losses there subsequently proven wrong (Lovell et al. 2014; Hron et al. 2015). But most “missing” genes (very GC rich) are actually present in the transcriptome (Botero-Castro et al. 2017).

Then, the authors performed analyses to detect the positive selection. Again, surprisingly, the branch-site models was only significant were the whole passerines clade were considered as foreground branches and bot were only the migratory clade are selected. Finally, a analyses of rate shifts also identify protein sites that shift from less constraint in non-passerines to more constrained in passerines. This kind of analyses are rarely performed and are quite interesting as shift in constraints are also expected with functional changes due to phenotypical changes.

Overall the study is very interesting and well writing. I think that the analyses are well performed and sounds. This work raises many interesting questions and opens the way for future studies on the genetic basis of orientation in migratory birds.

I have no major comment regarding the manuscript and I recommend it for publication in Proceedings of the Royal Society B.

Minor comment:
- I found it strange to compare the robin Cyr4 to the pigeon as I though that pigeon were good at orienting themselves.
- I appreciated that the alignments were made available as Supplementary Data. For full reproducibility, the authors should also made the phylogenetic available.