PONE-D-24-54431Connecting Colombia's protected areas: Using a functional approach for tapir speciesPLOS ONE

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Reviewer #1: Partly

Reviewer #2: Partly

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

Reviewer #1: I Don't Know

Reviewer #2: I Don't Know

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Reviewer #1: No

Reviewer #2: No

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Reviewer #1: No

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: This is a very interesting paper on improving connectivity for Tapir species in Colombia, with potential to improve conservation planning for mammals such as the tapir at the national level. The authors have done a very detailed analysis using SDMs, Circuit Theory and LCC modeling to look at existing connectivity for 3 tapir species and how this can be improved.

There are some major issues which have to be addressed before this paper can be accepted for publication. The main issue is with lack of clarity with some steps in the analysis and the presentation of the work. The entire analysis is based on the species distribution models for these three species. However, in the methods the authors need to justify the selection of the predictor variables based on the ecology of the species (with reference to relevant studies). No reasons are stated for the selection of these variables as opposed to others. Also, while they have mentioned that collinearity was considered they have not provided a final list of variable selected to model distributions of each species. Instead this is left to the reader to infer from the tables in the Supplementary Material.

Similarly, with the connectivity analysis, while they have consulted experts to rank the permeability of different landcover types with respect to tapir movement, they have not provided the actual rankings. Also, I could not find Table 1 which contains information on home range size etc for the study species!

In general, the information on the ecology, behaviour and movement of the study species' is hard to find throughout the manuscript and also is not provided in the Supplementary material, making their results hard to assess critically from a species' ecology perspective.

The figure captions are too brief and hard to understand. the legend of the figure is not clearly explained (in the case of the species connectivity maps). The results do not present the SDM findings at all in the text, which is odd. Figures 2-4 A and B are nowhere referred to in the text of the Results section.

Finally, the writing requires extensive editorial assistance. There are several sentences that are very unclear due to perhaps incorrect usage of language. For instances lines 97-99, the use of the term 'model'? or the use of the term 'figure' in line 118. In general, I found parts of the paper, especially the introduction hard to follow due to the use of many regional or national level terms such as SINAP or 'department'. Therefore, I suggest the authors use more accessible language for international readers. Another suggestion I have is that they move lines 123- 130 to the Methods section and replace it with a paragraph on the biogeography and conservation status of tapirs and more information on the ecology of the 3 study tapirs, in order to bolster their argument that this taxa is a good model for understanding functional connectivity for large mammals at a national level.

While the authors have said that the data is available, I was not able to make out where they have made it available.

In summary, the paper would greatly benefit from more transparency on the methods, (especially with regard to the SDMs) - to enable evaluation and review of their results, providing access to the actual data and finally improving the language and writing. The authors have done a lot of complicated analysis and one suggestion may be to consider publishing the work as two papers instead.

Reviewer #2: Mosquera-Guerra and his co-authors use the wide-ranging tapirs of Colombia to make a case for connecting the country's protected areas through functional corridors. They combine species distribution models, movement resistance surface and least-cost corridors to identify critical areas for connectivity and spatial models to identify conservation priorities and restoration opportunities. Such assessments can guide conservation efforts while meet national commitments for biodiversity conservation, as the authors indicate.

However, the manuscript needs substantial methodological, reasoning and grammatical reworking and to a smaller extent, some corrections to punctuation and scientific notation. The authors could start by reconsidering the use of elevation as a predictor to build species distribution models (SDMs). It is well known that elevation influences a number of biophysical and climatic variables and its importance in an SDM typically masks underlying, and even multiple, driving variables. A careful consideration of each species' habitat requirements, expert input and existing literature (e.g. Ortega-Andrade et al. 2015; https://doi.org/10.1371/journal.pone.0121137) would help choose biologically relevant variables.

Secondly, the authors use advanced spatial analysis tools and measures to identify priority conservation sites and restoration sites within these tapirs. Although the findings of these analyses are reasonably well described in the results section of the paper, there is regrettably very little in the discussion describing the implications of these findings. For instance, the authors find that forests cover 36-46% of the proposed corridors across all three species (lines 280-290) and they prioritise ~29,700 sq. km. of non-native grasslands, shrublands and croplands for restoration (lines 339-241). Yet the discussion does not examine approaches stakeholders could consider for pursuing these targets, lessons from other regions or landscapes or other important considerations. Instead, much of the discussion is devoted to highlighting threats that the current PA network faces e.g. droughts and fires (lines 435-453), but it's unclear if these threats also apply to the proposed corridors. I would recommend the authors rework most, if not all of the discussion so it improves the flow of the paper and builds the author's arguments.

Finally, I close with a couple of recommendations:

1. I suggest the authors upload spatially explicit versions (e.g. shapefiles or GeoTIFFs) of their maps (i.e. Figures 2-4) to a public data repository and include links within the paper. This might be useful for land managers, conservation planners and governments.

2. Presence-only SDMs make a few assumptions. Some of these can be tested, e.g. if the authors include a sensitivity analysis that tests the influence of changing the threshold for delineating habitat (and non-habitat) from the Maxent outputs.

3. Include other SDM-relevant information (e.g. the response curves as supplementary information) and species occurrence data on their maps (e.g. Fig. 2A-4A).

4. A few errors in punctuation and formatting need to be fixed (e.g. commas need to be replaced with decimals in Tables S1-S3 and the formatting of "cloglog" on Line 222).

5. The paper needs grammatical reworking in parts. The use of "figures" (lines 117 and 480) and "tensors" (Line 425) seem out of place and might need to be substituted with more appropriate terms. The section on focal tapir species is particularly unreadable as it declares certain landscapes and other considerations as ecological characteristics (Lines 173-178).

I hope these comments help the authors improve the manuscript and present a compelling case for improving the functional connectivity of Colombia's PAs.

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Reviewer #1: No

Reviewer #2: No

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Connecting Colombia's protected areas: Using a functional approach for tapir species

PONE-D-24-54431R1

Dear Dr. Mosquera - Guerra,

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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Kind regards,

M. Arasumani

Academic Editor

PLOS ONE

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