Review Reports - Shorebird Monitoring Using Spatially Explicit Occupancy and Abundance

Round 1

Reviewer 1 Report

I have reviewed this manuscript which I deem worthy of acceptance. There are some typos but they are trivial compared to work that is well structured, with appropriate methods and sustainable results.

For future works; I advise the authors to also take into consideration the analysis of isotopes, both to observe the change in trophic availability (with Carbon and Nitrogen isotopes), and to evaluate the difference in migration movements and spatial distribution with the Hydrogen isotope.

Author Response

Thank you for your comments. This is a very interesting approach. Previous research has revealed the differences in migration patterns and distribution of hydrogen isotopes for shorebirds, whose migration patterns vary in duration and intensity from year to year. We will consider it for future research.

Reviewer 2 Report

Dear authors,

This interesting manuscript focuses on the ability of a thin plate spline occupancy model to analyse the habitat use of the pipping plover as well as of other shorebird species. Developing better models to describe more accurately distributions of species is essential, for instance to improve conservations efforts. This study uses different model approaches (null, spline with detection, and spline assuming perfect detection=1) to highlight the advantages of the thin plate spline occupancy approach.

However, in this study I was missing a detailed comparison between the different approaches in the discussion, highlighting the different advantages and disadvantages of the three approaches and a clear take home message for the readers of this manuscript. Also the potential of the results for usage in conservation decisions, as mentioned in the abstract, should be discussed in more detail in the manuscript. More information is needed on the collection of the data, and lastly, the figures are currently in a very bad shape and need a makeover.

For more details see my comments below as well as some other considerations I have.

Best regards.

Abstract:

1. You asses the ability of your model to identify locations for the different bird species. Please elaborate what you mean by identify locations. Do you mean hotspots, resting sites, home ranges, distributions…

2. You mention that hotspot priority regions for the conservation of piping plovers have been identified. This should then also be elaborated on in the discussion. How will your data in particular be used for conservation?

Introduction:

1. (page 1: such as climate change and land use or land cover change) Is land use and land cover change not more or less the same? And the „and“ should be replaced by a comma.

2. (page 2: Statistical analysis can be confounded autocorrelation issues) Do you mean confounded BY autocorrelation issues?

3. (page 3: We conducted an experiment to determine…) Conducted an experiment sounds like you manipulated some variables so prove or falsify a hypothesis. I would reformulate this sentence to prevent possible confusion.

4. (page 3: In an effort to pinpoint the spatial distribution of a overlapping groups of species, the benefits and drawbacks of employing spatial spline terms in models to determine species richness.) Do you mean with „a overlapping groups“ „an overlapping group“ or „overlapping groups“? And the second part of this sentence is not complete. Do you maybe mean „the benefits and drawbacks of employing spatial spline terms in models to determine species richness are shown“?

Materials and Methods:

1. (page 3) You mention that sand was pumped to the island during data collection. Is this information relevant for the study or the interpretation of the results? If yes, please discuss its potential effects. If not, this part is not necessary.

2. (page 3) In the legend for figure 1, the dot colour is almost not visible as the dots are so small. Please make them bigger (not necessarily in the figure itself) , so make a differentiation between the dot colours possible.

3. (page 4: The common overwintering grounds of these birds can become highly disturbed) Can you please explain how the common overwintering grounds can become highly disturbed and why the less frequented areas are not part of environmental disturbances?

4. (page 4: Data collection) Please elaborate on the collection method you used. Did you use transects? How far were animals allowed to be to still count them? How much space was between „trails“ to ensure all birds were observed in between? How many surveyors were sampling at the same time? Were the GPS coordinates taken of the observed animal or the surveyor observing the animal? Was the distance to the animal recorded (to be used for examppe in distance sampling)? Give enough information to allow reproducibility.

5. (page 5, Table 1) with total detections, do you mean the sum of all observation in one year over all at least 14 surveys? If yes, is it not a problem, that you do not have the same number of surveys for each year (at least 14) as more surveys will lead to higher numbers and thus also higher numbers of occupied grid cells?

6. (page 5-7) Please site all the packages and software that you used (e.g. DHARMa).

7. (page 6: Although very efficient, the parametric approach can be limiting for modeling new data and is easily parameterized incorrectly) Can you please elaborate, why the parametric approach can be limiting when working with new data in particular?

Results:

1. (Figures 2-4) The quality of figure 2, 3 and 4 is very bad. The different maps of the island have different sizes, are sometimes distorted (the relation between hight and length differs between maps), borders around maps are sometimes there, sometimes only visible a little and sometimes not at all, the headings are not uniform, the map is sometimes cut of (figure 4 last row) and the description of the x and y coordinates of the original data are far to small to read and should be enlarged or removed. I recommend to redo the figures from scratch and make them look uniform and professional. They are the heart of your paper and you do not want the first impression readers get when looking at your current figures.

Discussion:

1. (page 11: In order to aid in research and conservation efforts for multiple species, the results of this study provide critical quantitative baseline information on shorebird spatial patterns during migratory peak piping plover activity and nonbreeding site within the Louisiana barrier islands) What do you mean with „During migratory peak piping plover activity and nonbreeding site“?

2. (page 11: Three or four additional migratory shorebirds were found to share a similar distributional pattern) Are there three or four additional species? Please specify what you mean.

3. (page 11: This type of research can validate the concept of an umbrella species as applicable to downstream species protections and conservation benefits for a community of species sharing a habitat.) I would like to see the discussion if your research validates the concept of an umbrella specie.

4. (page 11, second paragraph) The whole paragraph should be part of the introduction or methods and not the discussion, as you are not discussing you results nor putting them into relation to previous work.

5. (page 11: tide stage, Julian date, Julian date2) Please specify what you mean with Julian date2?

6. (page 11: Estimates of occupancy, number of occupied grid cells, mean abundance across grid cells, and total abundance for the island all were significantly altered after the inclusion of detection covariates) You mention those differences, but what do they really mean? Which models are probably best representing reality, what are the conclusions that should be drawn from your study for other studies? What do you mean with „Researcher should carefully consider a selection of detection covariates“?

7. (page 12: Furthermore, N-mixture models' spline terms largely overestimated population abundance, with mean N and total N for the island being much higher than expected) You mentioned that the results vary considerably between the null, spline with detection, and spline assuming perfect detection=1. I am missing a detailed discussion what those differences mean for future studies. What is the main message you want your readers to take home?

Conclusions:

1. (Models that did not include the spatial thin-plate spline or occupancy covariates were unable to identify fine-scale distributions or distinct spatial patterns) How do you know that the fine-scale distributions and distinct spatial patterns you have observed with the spatial thin-plate spline are representing more the reality than models that did not include the spatial thin-plate spline?

2. (We hope that our paper will provide new insights into the benefits and limitations of using spatially explicit occupancy models (as well as N-mixture) for shorebird monitoring or other fine-scale monitoring data, and possibly contribute to the improvement of future shorebird monitoring program designs.) But what are the insights of the benefits and limitations between the different approaches?

Author Response

Thank you for your willingness to review our manuscript, and I genuinely appreciate the time you spent recommending revisions. Please see the attached file for a response to the revisions.

Author Response File: Author Response.docx

Reviewer 3 Report

This study applied single-species occupancy models with thin plate spline approach in predicting the hotspots that should be prioritized for conservation of five shorebird species on the Whiskey Island of Louisiana including the Piping Plover of high conservation status. The paper is well-written and has a clear problem statement highlighting problems dealing with spatial autocorrelation and imperfect detection in modeling species distributions. The pros and cons of using different models have also been highlighted.

I only have minor comments on descriptions of the study site. I feel that more descriptions should be given about the island, such as habitat features, any form of disturbance, and size of the land area.

Author Response

Thank you for reviewing our manuscript, and I truly appreciate the time you spent suggesting modifications. Please refer to the attached file for the response to the proposed changes.

Author Response File: Author Response.docx

Round 2

Reviewer 2 Report

Dear authors,

after your revisions you now go into more detail concerning the differences between the different strategies and how this research might be beneficial for conservation decisions. I really like the development of this paper and have only three final minor comments:

1. Figure 1 now has bigger dots which does look already much better, as it is possible to see the colour. However, it would look even better if the dots would not be so blurry.

2. You now give an explanation of why the common overwintering grounds are getting disturbed (like hurricanes). However, it still does not explain why the less frequented overwintering grounds are less affected by such environmental disturbances and can therefore act as a place of refuge.

3. Figure 2-4 already look now much better than before! I still have one remark: Some of those island maps are squeezed, where the relation of height to length differs between maps, making them look not uniform. For example, when you compare in figure 4 the maps from years 1 with the maps from year 2, you see that the maps from year 1 are higher, although having the same length as the maps from year 2.

Author Response

Thank you so much for pointing out these final changes and suggestions to improve our manuscript.

Dear authors,

Figure 1 now has bigger dots which does look already much better, as it is possible to see the colour. However, it would look even better if the dots would not be so blurry.

Thank you, I have corrected the figure.

You now give an explanation of why the common overwintering grounds are getting disturbed (like hurricanes). However, it still does not explain why the less frequented overwintering grounds are less affected by such environmental disturbances and can therefore act as a place of refuge.

Thank you for highlighting that. I proceeded to rewrite the sentence. I am unable to locate the source from which I obtained this information.

Figure 2-4 already look now much better than before! I still have one remark: Some of those island maps are squeezed, where the relation of height to length differs between maps, making them look not uniform. For example, when you compare in figure 4 the maps from years 1 with the maps from year 2, you see that the maps from year 1 are higher, although having the same length as the maps from year 2.

Thank you, I have corrected the figure so that the figures are all uniform.