Constructive comments have been received by two reviewers and a short online comment. I thank the authors for responding to each of these and considering how to incorporate the suggested changes and clarifications. On the whole the reviewer concerns have been addressed, but there are several where clarification is still required and/or edits to the manuscript should be considered.

1) Reviewer 1’s first comment indicated that there could be greater value in introducing more of the context and rationale for the study in the Introduction. The authors have replied that they prefer to keep a short introduction and leave the detail in the Discussion section. I agree with Reviewer 1 that some further details on the palaeo-context and application of these morphological changes would be valuable, and so ask the authors to consider increasing the detail (either in the Introduction or Discussion, as they see fit): for example, can the authors explain how these previous papers have used morphological changes for palaeoclimate reconstruction, rather than just citing the papers? Or where have debates emerged in the literature about the interpretations of morphological changes? I agree with the Reviewers that at present the manuscript needs some more depth, so that readers can see the link to the important issues in palaeoclimate interpretation. For example, in response to Review 1 comment 6 the authors note that “frequently made assumptions” in the literature are being tested (and see reply to Reviewer 2 lines 47-48), but I did not find these assumptions to be clearly explained nor cited in the manuscript. Reviewer 2 (line 41-43) also suggests citing a source to justify the assumption being tested: if this can’t be done (as the author reply seems to suggest: the response does not clarify this), then I agree that a few lines of additional explanation would help the reader to understand this assumption. The authors do a good job where they address Reviewer 2 concerns about the malformations under higher CO2 (response to lines 235-242); this approach could be applied elsewhere. In summary, by addressing these concerns by the reviewers and explaining more about the literature context, I think a stronger foundation for the study will in turn lead to increased clarity about how these results can be applied.

2) Reviewer 1 queried the different control conditions exhibited in Figure 2. It would be useful for the authors to include in their main text or figure caption, the information about the different timing of the experiments to account for the differences. I’m not clear from the reply whether the same control sample was used for all experiments, but stored in between, or if different control samples were generated each time an experiment was started. Could the authors please clarify?

3) Reviewer 1 queried why the wider range of morphological measurement parameters was not outlined in the manuscript. Although the authors indicate that in some way this data might detract from their focus of comparing species (and the main assumption they outline for testing), could this information not be valuable for considering the within-species responses, and providing some interesting discussion on what kinds of morphological changes can be observed? I ask the authors to consider whether this information could be included, even though the measurements are not uniform across all species. It could make the manuscript a more comprehensive discussion of morphological change, and add to the finding that different species have different responses.

Minor concerns:
Reviewer 2 noted confusion about the timing of the divergences. I ask the authors to separately state the timing of the divergence of E.huxleyi and G.oceanica compared to the much older divergence of G.oceanica with the other two species. The timing of E.huxleyi / G.oceanica divergence is never stated, but should be somewhere, especially as it is not visible on Figure 1. Mixing the ‘hundred thousand years’ with millions of years in the suggested edit doesn’t provide clarity.

Reviewer 2 also indicated that on Fig 1 the numbers on the nodes were not clearly explained. The authors have added “Node, representing following divergence, used for calibrating...”. I’m not still not clear what this numbers mean: is some text missing here?

Reviewer 2 queried (for line 138) why non-linear regression was used. The author reply does not provide clarification: is it because no linear relationship was determined? or because the structure of the changing light intensity experiments does not lend itself to linear regression? or something else?

The change to Figure 3 is valuable for showing the detailed structure of the data more clearly. Comments have raised concern about how easy the text on the figures is to read. For Figure 3 I would recommend considering plotting this graphic as 2 x 2 panels rather than 1 x 4, which would allow larger versions of each panel to be displayed. The authors should also consider increasing the font size wherever they are able, across Figures 3 and 4.

In a revised version of the manuscript the authors should check that the number of coccoliths observed is clearly stated. This was raised several times and although the authors indicate that “this information was highlighted in the text and in the caption” (reply to reviewer 1) I did not find it in the original manuscript either.

Dear authors,

Thank you for submitting your responses to the reviewers, as well as your planned corrections. I asked one of the reviewers to examine your responses, and you will find a small set of suggested changes from the reviewer. I have looked at these carefully and agree that if you can make these minor revisions the impact of (and interest in) your manuscript would be enhanced. If you feel that any of the suggestions are not appropriate then please respond to outline your rationale.

Best wishes,
Erin McClymont

Dear authors,

Thank you for submitting the minor revisions and for incorporating the feedback from reviewers. Your comprehensive new Table 1 will hopefully act as a resource for other researchers - thank you for including this here.