PONE-D-24-09528Do local and landscape context affect the attractiveness of flower gardens to bees?PLOS ONE

Dear Dr. Russo,

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Reviewer #1: Partly

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: This paper presents a study on the interplay between landscape and local-scale factors in shaping the attractiveness (in terms of plant-pollinator interactions and alpha diversity metrics) of floral bee gardens. This study considers two relevant spatial scales and investigates how important factors, such as resource availability and habitat amount, shape bee communities across human-dominated landscapes. The paper seems to be based on the master work of one of the authors, and thus, the limitations regarding sampling size (e.g., replicates per treatment) can be understood regarding the (probaly) limited humanpower and existing time constraints. The paper is well-written, structured, and organized. The authors have made the data available as declared.

Having said that, we have a number of major concerns regarding the (1) statistical analyses (families used and model assumptions, colinearity in the variables, definition of variables, model assembly, assumptions), (2) some of the methods, (3) some rationals regarding the conceptualisation of the study, and (4) the available datasets, which seem to have not been properly cleaned and are not sufficiently documented to reproduce and re-use the data (we have tried ourself and wasn’t able to reproduce the work). Thus, together, these points question the study as a whole and prevent to recommend the paper for publication in its current form. We think that there might be potential for publication, but this will require work.

I have added my comments below, which we hope will be useful for the authors

### Major comments: ###

- Statistical analyses:

o Correlations among predictors: The authors do not mention any collinearity check on their predictors, but this is a basic standard check. We’ve check the correlations of some of the predictors and they are quite high: floral display at the local scale vs. development; floral display at the local vs. plant richness at the local, plant richness at the local vs. development. The authors checked collinearity before building the models and checked the variance inflation factor (VIF) of the model. We guess the authors are familiar with it, but there is a large number of problems related to colinearity. This issue raises questions regarding the validity of the models.

o Statistical families of the models: The authors seem to have used Gaussian families for all their variables, despite working with count data (i.e., the assumptions of Gaussian do not necessarily work when you have count data, which is limited to countable values). While gaussian families are adequate when count data is faily large, it shouldn’t be used when the counts are “small” and there are zeros. This violates the assumption of constance variance. In your case, I think you should use “Poisson” family if there is no overdispersion, or using a negative binomial if overdispersion. This puts all models and results into question, as they are now.

o Model specifications and Table 1: The random effect structure specified in the method section and the one presented in table 1 do not match. In the methods, it is said that the random effects were site and sampling date nested in the site. However, in Table 1, it appears that garden type (or plot) was used in the random effect. It makes sense to use plot and sampling data as random effect to account for the lack of independence of these two factors, so perhaps there was an error in the method section.

Another problem is that there are five sampling rounds, but in Table 1, it appears that there are only four rounds. Please clarify this discrepancy.

- Other methods

o Ranking floral diversity and floral abundance: The authors used a scale of to 1-10 to quantify floral diversity and floral abundance. As presented in the Methods section, it is unclear what criteria were used to attribute the different scale values to the existing features. It feels that this is a purely subjective guess from the observer. It is also strange that no method based on coverage (E.g., Braun-blanquet scale or similar) was used. The authors should better explain how the assessment of their scale was done, how they dealt with the potential subjectivity of the observer, etc. As it is now, it leaves too many doubts on a variable that is key for the analyses.

o Estimation of floral abundance: the authors state that they counted inflorescens to assess floral abundance at both plot and local scales. They did not mention how they assessed single flowers (and they should mention it), but one can assume that they were counted individually. However, the major problem I see here is the lack of detail on the definition of inflorescences. Surprisingly, the authors did not use standard methods based on floral units (references). For example, how did you consider compound umbellas, compound capitulums, etc? A classification criteria for the different types of inflorescences and they way they were counted is necessary (e.g., see https://doi.org/10.1016/j.dib.2021.107243, https://doi.org/10.1038/s41559-018-0769-y for examples).

- Conceptual aspects:

o Definition of pollinator-friendly plants: The authors mention that they used pollinator-friendly plant species native to the study area. However, it is unclear what is used to define plant species as pollinator-friendly. Was this based on what nurseries and plant providers say? Is this based on actual research? This is crucial, as it has been found that what is reported by nurseries does not always reflect the reality.

o Functional ecology aspects: While the study stands as it is, I think it is difficult to justify why the authors did not use any functional metrics and quantify resources (and resource quality) solely using taxonomic metrics. In conclusion, the authors suggest increasing plant diversity and floral display, but we know that this is a poor recommendation without actually considering the value of plants for pollinators (one could add many grasses, plant varieties that do not provide rewards, or plants that have mismatches in their flowering season with the phenology of the pollinators). This can be achieved by integrating the functional traits of plants, which are quite widely available (TRY database, datapapers), such as blossom class, symmetry, flowering start and duration, growth form, and even nutritional metrics (e.g., sugar in pollen or nectar). Computing functional metrics could really better underpin your results and provide strong support for your conclusions, which at the moment feel vague and unspecific.

e.g.,: https://www.sciencedirect.com/science/article/pii/S2352340921005278,

https://doi.org/10.1002/2688-8319.12248, https://esajournals.onlinelibrary.wiley.com/doi/10.1002/ecy.3705,

- Problems with the provided data: The authors made the data available. However, we found a number of problems that prevented reuse and reproduced the results:

o In general, you should provide a read-me file (separated as a text document or as a new sheet in the excel), where you clearly explain the columns of both sheets. It is unclear what site and block are (one has four levels, the other has five). You should define all variables, their column names, units, etc. So an external user can understand everything

o Sheet “specimens’: There is something wrong with this sheet. For example, between rows 39-72, the plant species and plant long columns are wong: it says local and UT Arboretum. There is no information on the block, plot type, local-garden scale, and so on. No columns with full site names.

o Sheet for data analyses: You should add the development metric here, so it simplifies reproducing the analyses. The differences between the site and the block are unclear.

### Other comments: ###

INTRODUCTION

- The introduction does not provide sufficient information on key concepts. The authors should devote some text and references to them.

o Central place foragers: This is critical because we know that most bees forage within the proximity of their nest, with some exceptions. Thus, the local-scale factors may be significant. There is plenty of literature in that regard: 10.1002/ecy.3809, https://doi.org/10.1002/eap.2727, https://www.sciencedirect.com/science/article/abs/pii/S0065250415000367

o Filtering: The third hypothesis of this study refers to filtering. However, the term is not adequately introduced, even though there is literature on the topic for bees: https://onlinelibrary.wiley.com/doi/abs/10.1111/jbi.13772, 10.1098/rspb.2014.2849 , 10.1038/s41467-020-14496-6

o Attractiveness: The authors disclose the drivers of attractiveness without properly defining the term and provide an overview of what has been found to influence it. E.g.: https://doi.org/10.1111/1365-2435.12178, 10.7717/peerj.3066

o Honeybees and their effects on wildbees: It would be beneficial to explain the potential effects of managed pollinators, such as honeybees, on wild bees, especially where they are not native. It will also help understanding why some analyses were done excluding honeybees. https://peerj.com/articles/14699/ , https://esajournals.onlinelibrary.wiley.com/doi/10.1002/ecy.3939

- L94: The phrasing of the sentences is a bit unusual, and it is difficult to understand what was done.

METHODS

- Experimental design: How far were the sites? What criteria were used to select them? (permisions and special features??). Please clarify.

- L106: here it is said there are 5 sites, in the data, the column “site” has only 4 levels…

- L166: provide the version of ArcGIUS

- L167: provide the resolution of the NLCD

- L186: Provide the version of R. If you used Rstudio, provide citation and version as well

- You should provide a list of packages and versions used in the supplementary

- L188: Predictors were scaled only or centered.

- L193-204: This paragraph could be better written and explained; that is, the information could be presented in a more efficient way. For us, it is not clear that local- and garden-scale models were done separately. This can be said earlier, and is better specified. The random effects did not match those presented in Table 1. There was no mention of how assumptions for the model were checked (e.g., spatial autocorrelation).

DISCUSSION

- L326-330: The authors discuss evenness here, but this is a metric that has not been presented before in the introduction or methods. Please integrate this into the manuscript.

- The authors could add some information regarding the following aspects, which are not unfamiliar to them:

o Nutritional aspects of floral resources: In addition to discussing the effects of resources based on alpha-diversity metrics, the authors could make use of the existing literature (including the work of the senior author) to add depth to the discussion of how floral resources shape bee communities (niche partitioning, health, etc.), the role of nutritional landscapes in floral restoration, etc.

- It feels more references could be integrated, e.g.,: https://advaudo.weebly.com/uploads/1/2/6/8/126897510/current_opinion_in_insect_science_2015_vaudo.pdf, http://www.woodardlab.com/uploads/6/4/9/6/64969235/1-s2.0-s2214574517300615-main.pdf,

CONCLUSIONS

- L347: What does “healthy” mean here? This concept has not been previously addressed. The authors could use previous work to develop it more: https://www.cell.com/trends/ecology-evolution/fulltext/S0169-5347(21)00333-5?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0169534721003335?showall=true,

- L349: What are the specific traits of plants? It is always the more the better?

- L359: What do you mean by “high quality”? I think you can develop this much more in the Introduction and Discussion, and as mentioned before, even include it by using plant traits.

TABLE 1

- Effect size: The authors report effect size, but do not explain what metric was used in the methods. If this is the estimate of the predictor, why is it not called an estimate? Otherwise, please define the effect size. The estimate with the standard error is provided in Table 1.

FIGURES:

- Figure 1: You can add a map and a better representation of the nested design.

- Figure 2: (b) explain what was used for the smooth line (lm?); (C) state again what the shaded bands indicate

- Figure 3: The points represent the raw data? Are the smooth lines based on the model predictions? If not, they should be based on your models, so that we can see how they fit the data. Again, explain how the lines are calculated (linear models?) and shaded bands, respectively.

- Figre 4: what was the stress of the NDMS? Maybe add it to the supplementary.

Reviewer #2: This is an interesting study and the methods are solid. The taxonomic resolution of bee species is especially impressive. Also, the discussion was well-organized and effective. I left many comments in the attached document. None are "make or break" for the paper, but some of them may (1) suggest easy modifications to the analysis (considering more radii than just 2000m, considering quasipoisson or negative binomial models) or (2) improve how the statistical methods are described.

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Reviewer #1: No

Reviewer #2: No

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PONE-D-24-09528R1Do local and landscape context affect the attractiveness of flower gardens to bees?PLOS ONE

Dear Dr. Russo, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Aug 25 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

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• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Dr. Janice L. Bossart

Academic Editor

PLOS ONE

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Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments:

The revised version has corrected most of the problems identified by reviewers.  Thank you for your efforts to address their concerns.  Below I list remaining issues that need attention.

Line 124.  Missing 'the'.  Three of the...

Line 439.  Missing word.  There 'was' ?

Line 728.  Please spell out linear model(s) so it's not confused with 1m, and either make model plural or add an 'a' before linear.

Table 1.  Delete the extraneous 's' at the end.

Figure S1.  The legend struck me as a bit odd given 'Bees' aren't an Order.  Maybe Hymenoptera-Bees and Hymenoptera-Non Bees?  Or maybe you can think of some other way that all terms fit.

Figure 3C.  Given the overlap of confidence intervals of 'Mixed' and at least 'Organic', I'm not sure I buy the interpretation that both 'Forage' and 'Mixed' had higher Shannon Diversity than all others.

--Mismatch between Figure 3 and Figure 3 caption.  Letter designations in the Figure caption don't match letter designations associated with plots in the actual figure.  Also, there is no plot of local bee abundance and land development (I'm guessing it's the caption that's incorrect given what is stated in the Results section).  

--Mismatch between Table 1 and text in the Methods.  Is sampling round nested within Site or nested within Plot?  The Table says Plot, the text says Site (Line 273).  Regardless of which is correct, the text would read better if you delete 'identity'.

--Loose use of 'diversity' throughout.  Given diversity can be used in multiple ways, please don't use it when you are referring specifically to species richness of either bees or flowers.  Otherwise, readers can't be sure whether you mean diversity, in terms of both richness and evenness, or simply richness.  Please carefully go through the manuscript, including figures and tables, and replace your use of 'diversity' with 'richness' anywhere you are explicitly referring to richness.

--Be consistent across Text, Figures, Tables, etc. including supplemental.  For example, Figure S2 uses Shannon Diversity and Figure 2C uses Shannon Index.  I didn't check every use, but Shannon diversity is often used in the text so perhaps that would be the way to go throughout.  Also, Figure S2C is unnecessary given it is identical to Figure 2C.  

--Rarefaction & Coverage methods. There is insufficient information in this section of the manuscript, e.g. approx. 256-267, to understand data shown in the resultant Figures.  iNEXT calculates Hill numbers, which at least needs to be pointed out as these are different calculations than other methods use.  Also, your figures don't correspond with figures generated by iNEXT for sample coverage or completeness, e.g. I'm expecting coverage or completeness to be an axis label.  No doubt I'm missing something, but if I am then others will likely also be confused.  Please add a bit of text to clarify how coverage was estimated and depicted.

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Do local and landscape context affect the attractiveness of flower gardens to bees?

PONE-D-24-09528R2

Dear Dr. Russo,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.  Congratulations!

There are two minor issues that first need to be corrected.  I have alerted the journal editor that these should be corrected before publication:

• Line 754.  Figure 3 Caption.  Move (E) forward to follow 'richness' versus where you currently have it.
• Figure S2 Caption, line 5. Should be '...abundant species affects...', i.e. affect should be plural.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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PLOS ONE

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