PONE-D-24-52763What's in a database? Insights from a retrospective review of penguin necropsy records in Aotearoa New ZealandPLOS ONE

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Each reviewer identified merit in the manuscript, it is well organized and the data is detailed. The comments provided by the reviewers will enhance the quality of the manuscript.

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Reviewer #1: No

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

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The authors aimed at performing a mix literature review and base description of the Wildbase Pathology Register database in New Zealand, focusing on Sphenisciformes. The paper is very well written and available to wider audiences. However, while I admire the efforts that were put into curating the dataset, I’m left skeptical about the goal of the paper. From my perspective, the manuscript in its current form describes what any researcher does when doing big data analysis (e.g. start with extensive data curation, explore the dataset), but significantly lacks multiple key components, such as a ‘why’ statement and quantitative statistical analysis. At the moment, the paper is mostly descriptive and does not inform on the inferences that can be made from large scale publicly available datasets such as this one. That being said, I think there is value to the work of the authors, and that a few improvements would make the manuscript much stronger and suitable for publication.

First and foremost, I would recommend the authors to strengthen the last part of the introduction. I really enjoyed reading this section, it’s clear and concise, but it lacks purpose toward the end. While the aim and intentions are clearly defined, I do not feel that they align with the rest of the work. For instance, the first sentence of the discussion reads: we describe spatial and temporal trends in submission data for penguins in the Wildbase Pathology Register, noting the influence of variables such as year, month, age, species, and location of submission on the dataset. However, in the introduction, the authors claim that they intend to ‘ predict limitations of demographic representation across species’, but I fail to see any spatial analysis in the rest of the paper, aside from figure 3, which simply describes samples locations. In my opinion, statistically linking human population density from available online raster with the necropsy data from the Wildbase Pathology Register would have been much more interesting and useful than simply describing samples abundance across New Zealand. The same is true for temporal trends, which could be more robustly analyzed than the current descriptive format.

Related to that, I believe that statistical approach in this manuscript to be flawed. When working with such wealth of data, much more informative statistical approaches than p-value difference-based tests should be used. When analysing big datasets like this one, the question should not be: is there a difference? But what is the magnitude of the difference?, at least in my opinion. As such, I would recommend the authors to at least use a generalized mixed effect models (package: lme4) in R to infer on the wide array of factors that they explore.

Lastly, if the goal of the current manuscript is to only explore the dataset and not infer from it, I would recommend the authors to include a figure showing the trend of publications on morbidity/diseases of Sphenisciformes vs what’s being made available by the public. This could help informing on current biases in the datasets (e.g. is the big jump in 2005 related to more reporting?).

Reviewer #2: This manuscript provides a very detailed documentation of the use of retrospective mining of a wildlife disease database using Sphenisciformes, and in particular the hoiho (yellow eyed penguin, Megadyptes antipodes) and kororā (blue penguin, Eudyptula minor). The manuscript is well written and follows a logical approach. Below I have included a couple of minor questions, clarifications, and suggested comments for consideration by the authors that I think will further add to the quality of the manuscript:

1. Abstract: I appreciate that the authors have also listed some important identified limitations right in the abstract as this further highlights the factors that need consideration in such retrospective studies and could help highlight some factors to consider in the generation of these databases going forward.

2. Material and methods; line 140-143; there is some repetition here with the introduction section; however, I think this still fits into the word count recommendations; however, if not it would make most sense to have this more detailed description still under the materials and methods section.

3. Material and methods; line 146-148; I think this would imply that necropsies of deceased wildlife are performed at the Auckland Zoo in addition, but it might be somewhat unclear to some readers, and could it be possible that this could be read that necropsies from captive or Zoo managed breeding programs could be included?

4. Material and methods; line 156-158; was this interpretation conducted by a single person or multiple authors? And how was this standardized?

5. Material and methods; table 1: The depiction of what information needed to be reviewed and interpreted in table form is a very nice descriptive visual. Why the decision to divide by 1.8 specifically? How was this decided?

6. Material and methods; line 172-173; was this ambiguous enough that it could not be included in the data that was interpreted? Would the availability of this information have any additional penguin conservation impact albeit then still even more biased?

7. Material and methods; line 180-190; do the authors touch on potential causes for lack of representation of the other six species of penguins in the database?

8. Material and methods; line 184-186; this makes sense. More a question of curiosity but why so few submissions in the earlies years? Was this impacted by conservation decisions and allocation of government funding? If yes to the latter, it might further allow for illustration of the important impact these reviews or database generation can have on governmental decisions.

9. Material and methods; line 187-192; does spatial location data allow for identification of differences between specific populations if significant site fidelity exists?

10. Material and methods; line 199-201; I assume that part of the redundancy consolidation also included consistency in assigning specific diagnoses to DAMNITV categories and that this was again standardized as referred to in comment 4 above?

11. Results; line 209-215; This is a very clear presentation of the demographics of species submissions and the data in general with both percentage and numbers being reported. Thank you for this clarity.

12. Results; line 221-225; please see comment 5 above with regards to the 1.8 factor.

13. Results; line 236-238; please refer to comment 8 why these two temporal spikes (2005 and 2008) in submissions? And how does that affect data interpretations? This is partially explained for the 2011 submissions of korora with the Rena oil spill.

14. Results; line 305-308; Could this conversely also be affected by spatial association to the nearest veterinary diagnostic laboratory and ease of transport/accessibility to these sites? E.g. majority of inland veterinary submissions originated from Palmerston North. Is this something that could also be further interpreted from data sets such as this to increase accessibility of diagnostic testing/evaluation for these wildlife species - e.g. penguins could be relatively easily couriered?

15. Results; line 322; is trauma related to marine traffic or land traffic? Is it worth further separating these out?

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Reviewer #1: No

Reviewer #2: Yes:  Heindrich N Snyman

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What's in a database? Insights from a retrospective review of penguin necropsy records in Aotearoa New Zealand

PONE-D-24-52763R1

Dear Dr. Saverimuttu,

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.

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Stephen Raverty

Academic Editor

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Additional Editor Comments (optional):

Thank you for your detailed responses to the reviewers suggestions and comments. The content and flow of the paper is improved. The paper is a valuable contribution to the health of penguins in Aotearoa New Zealand.

Reviewers' comments: