PONE-D-19-35579

A cost efficient spatially balanced hierarchical sampling design for monitoring boreal birds incorporating access costs and habitat stratification

PLOS ONE

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Reviewers' comments:

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Comments to the Author

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Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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5. Review Comments to the Author

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Reviewer #1: Your well-written paper provides a superb blueprint for addressing a very important need, how best to monitor terrestrial breeding bird populations across the boreal region of Canada. You proposed four scientifically rigorous sampling designs and used simulation modeling to test their efficiencies relative to cost, habitat-representativeness, and spatial balance, all of which are important for implementing a successful and robust monitoring program. You also tested the sampling design empirically in three large study areas, comparing actual vs. projected costs for implementation, a pragmatic consideration for successful adoption and funding of such a large-scale program. Overall, your paper is based on sound analytical procedures, knowledge of how birds are distributed across the landscape, thoughtful reasoning about how populations are likely to change over time, and an understanding of the logistical features needed to implement such an ambitious program in remote areas. Including your R code further illustrates the complexity of the task you have undertaken and will be extremely helpful to those who want to understand the details about how best to design such a program.

There are a few aspects that you could address more fully. First, you use maximization of the variance of diversity of species (with habitat as proxy) rather than minimization of the variance in estimates of population trends or population size as one of the key criteria for allocating effort in terms of primary sampling units (PSUs). I realize that optimization relative to estimating population size or trend would be difficult to achieve, particularly for an omnibus survey that encompasses a multitude of species with varying levels of population change and abundance. I surmise, however, that the proposed allocation would tend to weight southern areas of the boreal more heavily (where species richness is higher) and that there may be low power to estimate trends for populations that are declining rapidly (and have lower population sizes) or those that may be changing rapidly in northern ecotones (perhaps even increasing). It would be interesting if you could address some of these limitations or tradeoffs in the discussion.

Secondly, you mention that the monitoring program will use point count surveys with trained observers and/or autonomous recording units (ARUs). I assume that the decision on which of these methods to use would be related to cost of access for any given PSU. If so, I would conclude that more remote, northern areas could conceivably be monitored exclusively through the use of ARUs alone, because they can be deployed and retrieved least expensively via snow machine or ice roads in winter. It would be useful if the authors could expound at least minimally upon some of the implications of this aspect of the design. Use of ARUs alone without validation from comparable surveys by human observers can result in biased estimates of species’ occurrence and density, particularly for those species that are detected more often by visual than aural cues. ARUs can provide more detailed information on temporal and spatial occurrence of species in a given area if they are set to record samples throughout the season. Analysis of recordings, however, incurs a significant cost, particularly for monitoring of all species, which at this point cannot be automated efficiently. Also, I don’t believe that the cost of the ARUs was factored into the cost of access, but perhaps it should be. In the end, it might be worth a point of discussion to address some of the tradeoffs of using a combination of human observers and ARUs and to suggest that this is one other aspect of efficiency that remains to be designed. I would advocate for a spatially balanced use of human observers and ARUs so that any habitat- or temporal-related biases can be estimated and corrected for. A couple of other recent papers on ARUs in sparse northern habitats you might examine include Thompson et al. (2017, J. Wildl. Manage. 81:1228-1241) and Vold et al. (2017, Wildl. Soc. Bull. 10.1002/wsb.785).

Thirdly, I was a bit confused about how secondary sampling units (SSUs) were selected relative to the presence of water. It seems that any PSUs that encompassed only water were excluded from the sampling frame, which is reasonable. However, it was unclear how the mini-grids of 3 x 3 points were selected with respect to water features within a given PSU. From a cursory look at the R code, it appears that all points that fell within water were also removed from the sampling frame. I’m not certain what this did in terms of influencing which grids might be selected, but you might want to ensure that you are not biasing (low) your sample of points adjacent to water bodies, which are extremely important in terms of species richness and density in the boreal region.

Fourthly, given your proposed, very complicated sampling design, I anticipate that statistical analyses will be extremely complex, which you acknowledge in the discussion. The complexity will depend, of course, on what parameter you are estimating (e.g., habitat relationships, density, changes in distribution, or population trends). Once you add in the temporal dimension, with replication across years, the complexity will be even more challenging, particularly if your sampling intensity or inclusion probabilities change through time. I caution against changing the boundaries of your strata through time for long-term monitoring of population trends, particularly relative to habitat. Not only will vegetation be changing through time, but community composition will likely shift as well, with individual species responding differentially to changes in vegetation, temperature, precipitation, predator abundance, and other ecological factors. Thus, if you retain habitat diversity as a major determinant of inclusion probability, you should consider the ramifications of altering that through time. There are many powerful techniques for modeling trends through time, so this might not be a problem. There could be consequences, however, for the resulting precision of your estimates.

Pertinent to this point is the temporal replication of sampling. It would be helpful to mention what you have in mind for this aspect of your sampling design, particularly for estimating changes in distribution or population size (will there be annual estimates of population trend?). You should also address the possible ramifications of missing data from repeated samples, which will inevitably occur and will prove no small headache, particularly in remote areas where access is so challenging and unpredictable. Typically, repeated samples at the same sites will be more efficient statistically in estimating population trends, but an alternative would be to set up different sampling frames at various intervals through time, with changes in inclusion probabilities. In the boreal zone, sampling individual sites on a biennial basis may be more efficient than sampling them every year because of high interannual correlation (Handel and Sauer 2017). I was glad to see you consider the important issue of how best to incorporate legacy sites. Such data sets can provide key information on long-term changes in distribution and abundance but provide their own challenges when trying to account for potential bias in terms of selection of samples.

Finally, I note a few other minor points that would be helpful to clarify or correct:

P. 11, line 8. What landcover map did you use and how many cover classes were there?

P. 15, line 16. Ralph et al. (1993) is missing from Lit Cited and Matsuoka et al. (2014) should be cited as numbered reference. I also noted that references 71-80 don’t seem to be cited in the text.

P. 19, line 14. Final sentence of the paragraph seems to be missing text after ‘where.’

P. 21, line 17. I would change this to ‘red-filled squares’ so that it is clear what you are referencing. It took me a bit to figure this out (I had to go back to methods to understand what you were saying, especially since red is also used for the triangles representing cost).

P. 22, lines 6-10. I think you meant to reference Fig. 10 instead of Fig. 8. I was confused, however, by the number of PSUs listed. I counted only 2 PSUs in Newfoundland and Labrador (not 16), 2 in the Yukon (not 26), and 12 in Saskatchewan (not 43).

P. 23, lines 9-12. I did not understand the sentence beginning “In addition, the distribution of spatial balance metrics…”

P. 28, line 6. Two l’s in Boreal Avian ‘Modelling.’

Figure 1. You might consider outlining jurisdictions that you sampled in bold lines.

Figure 2. Consider adding a distance scale to each of these submaps or else noting in the figure heading that hexagons are 5 km in diameter and points are spaced 300 m apart.

Figure 4. ‘Proportional’ is misspelled on x-axis label.

I commend you all for this impressive and well-executed effort.

Colleen M. Handel

USGS Alaska Science Center

Reviewer #2: This is a nicely written paper. I would suggest that the authors provide a stronger background on spatial sampling, and sampling optimization:

Delmelle, E. M., & Goovaerts, P. (2009). Second-phase sampling designs for non-stationary spatial variables. Geoderma, 153(1-2), 205-216.

Van Groenigen, J. W., Stein, A., & Zuurbier, R. (1997). Optimization of environmental sampling using interactive GIS. Soil Technology, 10(2), 83-97.

Delmelle, E. (2009). Spatial sampling. The SAGE handbook of spatial analysis, 183, 206.

Reviewer #3: This paper by Van Wilgenburg et al. is well-written, technically sound, and of broad interest to the research community. There are too few papers on the topic of sampling design when it comes to broad scale monitoring programs supported by public funds; and it is critical that we develop strategic methods in areas like the Boreal where many countries have an international responsibility to maintain biodiversity in the face of multiple stressors.

I selected minor revisions because most of my recommended changes can be made fairly easily and no re-analysis or major reworking of the MS are necessary. I made comments directly on the pdf if that helps. More substantive comments can be found from p12 on. My most major concern is that the authors need to carefully consider their use of the term optimal. The optimization literature uses this term in a very specific and mathematical way and it is not clear from this work that the authors performed an optimization. I think a better way of describing what they did was to perform a spatial benefits costs analysis of various broad scale monitoring strategies. They do balance trade offs, but it is not clear that their preferred design is 'optimal' per se. I also think that they might want to call their approach something other than Boreal Optimal Sampling Strategy (BOSS).

The discussion is on the long side. It talks a lot about the advantages of their approach. I think the authors can shorten it. But I also think they should work in a discussion of other literature that examines large scale monitoring programs and trade offs between spatial coverage, costs, and target species representation.

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Reviewer #1: Yes: Colleen M Handel

Reviewer #2: No

Reviewer #3: No

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PONE-D-19-35579R1

A cost efficient spatially balanced hierarchical sampling design for monitoring boreal birds incorporating access costs and habitat stratification

PLOS ONE

Dear Mr Van Wilgenburg,

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.

I appreciate the time and care you put into your responses to the reviewers. I believe you have addressed their concerns fully, and the manuscript is nearly suitable for publication. In reading through revision 1, I noticed some minor editorial errors (omitted words, punctuation, or the like). Rather than list them here, I've attached a tracked changes version of the manuscript for your reference. Once you address these and resubmit, I will move quickly to accept your manuscript. You do not need to submit point-by-point responses to any of my edits or comments.

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Frank H. Koch, PhD

Academic Editor

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A cost efficient spatially balanced hierarchical sampling design for monitoring boreal birds incorporating access costs and habitat stratification

PONE-D-19-35579R2

Dear Dr. Van Wilgenburg,

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Additional Editor Comments (optional):

Thank you for addressing the latest set of comments. The manuscript reads well and should interest many in the PLOS ONE audience.

Reviewers' comments: