Resco de Dios et al present an experimental study of circadian oscillations in plant canopies in field-like environments. The study of agriculturally relevant species (pea and cotton) at an agriculturally relevant scale provides useful context for the study of the molecular mechanisms of circadian regulation in model species (predominantly Arabidopsis). By measuring the diurnal and circadian dynamics of carbon and water fluxes at leaf and canopy scales, the authors are able to quantify the importance of circadian rhythms. The work is interesting, but some aspects of the methodology should be clarified further.

Major comments:

The model needs to be explicitly described (at least in supplementary material). Which datapoints are simulated with which equations? In order to make this clearer, a couple of examples of model simulations vs data could be shown in figures (e.g. for a few well-fitting examples of the many model fittings documented in Table 2).

I don't understand how the model is able to produce good predictions when parameterised using only data from continuous conditions (according to the Rsquared, which is as high as 0.82 (last rows, Table 2)). Is this because the model captures the right correlation, but makes quantitative errors? This would be clarified by a figure for this case (as mentioned above).

The description of how AIC is applied is unclear (e.g. line 289: "the weights (w i ) from the ratio between the relative likelihood of a model (e (-0.5AIC) ) to the sum of all relative likelihoods." - the meaning of the weights should be stated here).

The authors suggest that the diluted amplitude of circadian rhythms at the canopy scale as the result of a diminished amplitude of rhythms in shaded leaves (line 348). Another possible explanation is that shaded leaves have different periods of circadian rhythm. Having a range of circadian rhythms superimposed on one another would also give the appearance of a diminished amplitude at the bulk level. The lengthening of circadian rhythm at lower light intensities is well documented (known as Aschoff's rule), and may be occuring in these shaded leaves.

Minor comments:

Line 107 "In mammals, a hierarchical network of circadian clocks exists, with a unique central oscillator on the suprachiasmatic nucleus in the brain [22]. However, circadian clocks in plants are more autonomous and there is little evidence that the clock in different leaves is synchronized [23]."

I think these ideas aren't very relevant here. Mammals have a central clock, but peripheral oscillators display significant variability depending on environment (e.g. in the liver). Also, the idea that clocks in different leaves are autonomous has been challenged recently (Takahashi et al, Cell, 2015). The central point of the authors that "we could observe uncoupled circadian rhythms in different leaves within and across plants, potentially diluting any circadian effects at canopy scales" is still clear without referring to the mammalian clock.

Line 143: "Diurnal variation in canopy and ecosystem fluxes is largely attributed to direct environmental effects of PAR, T air and VPD" These terms should be defined on first use.

Line 142: "For instance, the magnitude of the clock- driven variation was 41-54% for A l (beancotton), but 20-38%" - These should be defined here (I think they're percentages of the maximal range?).

Line 319: "Instead, we observed that diurnal variation during a constant environment showed a period of ~24 h. The only mechanism currently known to create a self-sustained 24h cycle is the circadian clock [37, 38]." - A ~24h period defines a circadian rhythm, so I don't think it's necessary to point out this subtlety.

Line 333: "To fully understand the up-scaling of circadian rhythms, we need to explore further how canopy structure determines the canopy-level expression of circadian regulation. Circadian regulation in understory species has been shown to be less important than in overstory species [19]." - This paragraph begins by referring to differences between species, but most of the subsequent discussion is of differences within and between individuals of one species (which is what was really investigated here).

Are the methods appropriate to the aims of the study, are they well described, and are
necessary controls included?
If not, please specify what is required in your comments to the authors.

No

Are the conclusions adequately supported by the data shown?
If not, please explain in your comments to the authors.

Yes

Does the manuscript adhere to the journal’s guidelines on minimum standards of
reporting?
If not, please specify what is required in your comments to the authors.

Yes

Are you able to assess all statistics in the manuscript, including the appropriateness of
statistical tests used?
(If an additional statistical review is recommended, please specify what aspects require further
assessment in your comments to the editors.)

No, I do not feel adequately qualified to assess the statistics.

Quality of written English
Please indicate the quality of language in the manuscript:

Acceptable

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Authors' response to reviews: (https://static-content.springer.com/openpeerreview/art%3A10.1186%2Fs13742-016-0149-y/13742_2016_149_AuthorComment_V1.pdf)

I am happy with the changes made, addressing all of the points that I raised. The main point I raised about clarifying how the modelling works has been addressed both in the text and with a new additional figure.

Are the methods appropriate to the aims of the study, are they well described, and are
necessary controls included?
If not, please specify what is required in your comments to the authors.

Yes

Are the conclusions adequately supported by the data shown?
If not, please explain in your comments to the authors.

Yes

Does the manuscript adhere to the journal’s guidelines on minimum standards of
reporting?
If not, please specify what is required in your comments to the authors.

Yes

Are you able to assess all statistics in the manuscript, including the appropriateness of
statistical tests used?
(If an additional statistical review is recommended, please specify what aspects require further
assessment in your comments to the editors.)

Yes, and I have assessed the statistics in my report.

Quality of written English
Please indicate the quality of language in the manuscript:

Acceptable

Declaration of competing interests

Please complete a declaration of competing interests, considering the following questions:
1. Have you in the past five years received reimbursements, fees, funding, or salary from
an organisation that may in any way gain or lose financially from the publication of this
manuscript, either now or in the future?
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose
financially from the publication of this manuscript, either now or in the future?
3. Do you hold or are you currently applying for any patents relating to the content of the
manuscript?
4. Have you received reimbursements, fees, funding, or salary from an organization that
holds or has applied for patents relating to the content of the manuscript?
5. Do you have any other financial competing interests?
6. Do you have any non-financial competing interests in relation to this paper?
If you can answer no to all of the above, write 'I declare that I have no competing interests'
below. If your reply is yes to any, please give details below.

I declare that I have no competing interests

I agree to the open peer review policy of the journal. I understand that my name will be included
on my report to the authors and, if the manuscript is accepted for publication, my named report
including any attachments I upload will be posted on the website along with the authors'
responses. I agree for my report to be made available under an Open Access Creative Commons
CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments
which I do not wish to be included in my named report can be included as confidential comments
to the editors, which will not be published.

I agree to the open peer review policy of the journal.

Authors' response to reviewer: (https://static-content.springer.com/openpeerreview/art%3A10.1186%2Fs13742-016-0149-y/13742_2016_149_AuthorComment_V2.pdf)