Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita

1) The manuscript is not easy to read, in particular the Results and discussion part. Here, the text tends to be redundant and should be shortened.

We have done our best to clarify and shorten the Results and discussion section by reducing redundancy wherever possible. Implemented changes include:

Removing redundant descriptions of methodology.

Removing redundant descriptions of regulatory mechanisms.

Consolidating summary paragraphs at the end of each subsection.

We believe that these efforts improve the readability of our manuscript considerably, while preserving the hierarchical overall structure of the Results and discussion section. This structure is designed to provide the reader with a large amount of detailed information, while still retaining a focus on the big picture.

Box 1 is meant to help the reader, but is not easy to understand mainly because the sentences are difficult to read.

We have edited Box 1 to make it more readable and concise, as requested.

The authors may consider whether presenting a numbering scheme for boundaries in Supplementary file 2 would be a better formalism to describe the spatial patterning features in the text.

We are reluctant to use a boundary-numbering scheme as in Supplementary File 3 to identify expression features. While this would indeed make the text more concise, our use of explicit descriptions (e.g. “posterior boundary of the anterior hb domain”) has the advantage of being unambiguous and directly interpretable without use of a look-up table to remember which numbered boundary is which. In addition, it is consistent with boundary descriptions in previously published studies.

2) The caudal data should be discussed and clarified. In particular, it would be good to check whether hetero- or homozygosity of zygotic caudal alone affects gt and kni expression (this might be in the literature). If this is not the case, then it is likely that the observed shifts are due to the absence of maternal caudal.

We have clarified our description of the design and interpretation of the cad germ line clone experiment. Without quantitative measurements of absolute mRNA levels, we cannot distinguish between the effects of lacking maternal expression, or altered levels of zygotic cad in M. abdita compared to D. melanogaster.

This is now stated explicitly in the Results and Discussion, and Materials and Methods sections. What our germ line experiments in Drosophila establish is that altered expression of cad can explain delayed shifts of posterior gap domains. Whether this is governed by maternal or zygotic contributions to cad is not directly relevant at this level of argumentation. A proper quantitative investigation of these contributions goes beyond the scope of the current manuscript, which focuses on the downstream interactions that cause subsequent changes in shift dynamics.

In addition to the changes in response to editorial and reviewers’ feedback described above, we have also revised our supplementary information according to the discussion we had with the eLife editorial office. Detailed descriptions of gap gene expression patterns and cuticle phenotypes in Megaselia are now provided as two appendix sections (with additional Figures 10–12) in the main paper, as requested.