Wild dogs at stake: deforestation threatens the only Amazon endemic canid, the short-eared dog (Atelocynus microtis)

The persistent high deforestation rate and fragmentation of the Amazon forests are the main threats to their biodiversity. To anticipate and mitigate these threats, it is important to understand and predict how species respond to the rapidly changing landscape. The short-eared dog Atelocynus microtis is the only Amazon-endemic canid and one of the most understudied wild dogs worldwide. We investigated short-eared dog habitat associations on two spatial scales. First, we used the largest record database ever compiled for short-eared dogs in combination with species distribution models to map species habitat suitability, estimate its distribution range and predict shifts in species distribution in response to predicted deforestation across the entire Amazon (regional scale). Second, we used systematic camera trap surveys and occupancy models to investigate how forest cover and forest fragmentation affect the space use of this species in the Southern Brazilian Amazon (local scale). Species distribution models suggested that the short-eared dog potentially occurs over an extensive and continuous area, through most of the Amazon region south of the Amazon River. However, approximately 30% of the short-eared dog's current distribution is expected to be lost or suffer sharp declines in habitat suitability by 2027 (within three generations) due to forest loss. This proportion might reach 40% of the species distribution in unprotected areas and exceed 60% in some interfluves (i.e. portions of land separated by large rivers) of the Amazon basin. Our local-scale analysis indicated that the presence of forest positively affected short-eared dog space use, while the density of forest edges had a negative effect. Beyond shedding light on the ecology of the short-eared dog and refining its distribution range, our results stress that forest loss poses a serious threat to the conservation of the species in a short time frame. Hence, we propose a re-assessment of the short-eared dog's current IUCN Red List status (Near Threatened) based on findings presented here. Our study exemplifies how data can be integrated across sources and modelling procedures to improve our knowledge of relatively understudied species.


Recommendation?
Major revision is needed (please make suggestions in comments)

Comments to the Author(s)
Wild dogs at stake: Deforestation threatens the only Amazon endemic canid, the short-eared dog (Atelocynus microtis); Rocha et al.; RSOS Rocha et al. present a fascinating study of the severely under-studied short-eared dogs, combining historic presence records, camera trapping and species distribution models to predict current and future distribution of the species. The authors also present a multi-scale perspective (regional and local), which sheds some light on the scale-specific factors affecting the species' association with habitat. Overall, the paper is very well written and the authors have done a commendable job-considering the effort it would have taken to coordinate, initiate collaborations and compile information about a rare species from multiple sources and institutions. I do have some concerns related to the local scale analysis (explained below).
Introduction: Specific comments: L127: Please revise the sentence: "Besides the alarming deforestation rates, there is growing concern…" Methods: General comments: If I understood correctly, the authors use all presence records (post-rarifying) from 2000 onwards. Does this include data from 2009 to 2018/19? If so, there would be some mismatch in the forest cover (i.e. potential habitat) and current distribution right? The forest cover layer is from 2009, but presence records are from subsequent years as well. I get that this may be a limitation because of access to updated forest cover data. But this issue needs to be acknowledged in the Methods section.
Local scale analysis: Given that that authors list habitat loss, prey decline, disease from domestic dogs and other anthropogenic factors (road related mortality) as factors that negatively impact short-eared dogs, I wonder why none of these covariates, or variables that could serve as surrogates of these factors, were not considered for modeling habitat use. The authors also list lowland forests, areas close to water etc. as purported "good habitats" for the focal species. The large-scale predicted distribution also clearly indicates importance of protected areas for the species to persist in the long term. Elevation, distance to protected area boundary, distance to water bodies, proximity to human settlement, human footprint index, encounters of hunters/logging machinery, encounters of domestic dogs etc. are all really good potential covariates that would make the local scale analysis very interesting while also better informing management/conservation. The three covariates used to model occupancy PSI may be too broad to have show any influence at the local scale; this is evident in the estimates of the slope coefficients. Both forest cover and edge density have high SE values (95% CI overlaps 0, so no statistical significance), suggesting weak effects of the predictors. I strongly suggest that the authors re-analyse the local-scale data incorporating some/all the covariates listed above.
Specific comments: L335: revise the sentence to state that the sample units are "likely" smaller than the "presumed" home-range size of the species.
Results: General comments: Move Table S4 to main manuscript. This is the primary result of your study. Similarly, combine three panels of Figures S5, S6, S7 and present it as one figure in main manuscript. The results related to local-scale analysis would change when the data are reanalysed. Please present revised results accordingly.
Discussion: General comments: The section is well written for the most part, and makes a compelling case for revising the IUCN status of short eared dog. I think the paper would benefit from expanding the narrative, both, in the Introduction and in the Discussion sections. As it stands, the focus is a bit narrow. If at all the species does qualify to be considered a "flagship" for conservation of forest systems in the Amazon, then the entire Discussion should make a more convincing case by establishing links between the short-eared dogs, their prey, competing predators and humans. The authors go some length in doing so in the last paragraph. But the argument is lacking in that it only makes a passing mention of the benefit to other species.
Decision letter (RSOS-190717.R0) 17-Jul-2019 Dear Mr Rocha, The editors assigned to your paper ("Wild dogs at stake: Deforestation threatens the only Amazon endemic canid, the short-eared dog (Atelocynus microtis)") have now received comments from reviewers. We would like you to revise your paper in accordance with the referee and Associate Editor suggestions which can be found below (not including confidential reports to the Editor). Please note this decision does not guarantee eventual acceptance.
Please submit a copy of your revised paper before 09-Aug-2019. Please note that the revision deadline will expire at 00.00am on this date. If we do not hear from you within this time then it will be assumed that the paper has been withdrawn. In exceptional circumstances, extensions may be possible if agreed with the Editorial Office in advance. We do not allow multiple rounds of revision so we urge you to make every effort to fully address all of the comments at this stage. If deemed necessary by the Editors, your manuscript will be sent back to one or more of the original reviewers for assessment. If the original reviewers are not available, we may invite new reviewers.
To revise your manuscript, log into http://mc.manuscriptcentral.com/rsos and enter your Author Centre, where you will find your manuscript title listed under "Manuscripts with Decisions." Under "Actions," click on "Create a Revision." Your manuscript number has been appended to denote a revision. Revise your manuscript and upload a new version through your Author Centre.
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If you wish to submit your supporting data or code to Dryad (http://datadryad.org/), or modify your current submission to dryad, please use the following link: http://datadryad.org/submit?journalID=RSOS&manu=RSOS-190717 • Competing interests Please declare any financial or non-financial competing interests, or state that you have no competing interests.
• Authors' contributions All submissions, other than those with a single author, must include an Authors' Contributions section which individually lists the specific contribution of each author. The list of Authors should meet all of the following criteria; 1) substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; 2) drafting the article or revising it critically for important intellectual content; and 3) final approval of the version to be published.
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We suggest the following format: AB carried out the molecular lab work, participated in data analysis, carried out sequence alignments, participated in the design of the study and drafted the manuscript; CD carried out the statistical analyses; EF collected field data; GH conceived of the study, designed the study, coordinated the study and helped draft the manuscript. All authors gave final approval for publication.
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Once again, thank you for submitting your manuscript to Royal Society Open Science and I look forward to receiving your revision. If you have any questions at all, please do not hesitate to get in touch.
Kind regards, Andrew Dunn Royal Society Open Science Editorial Office Royal Society Open Science openscience@royalsociety.org on behalf of Professor Michael Bruford (Associate Editor) and Kevin Padian (Subject Editor) openscience@royalsociety.org Editor comments: Thank you for your submission. As you will see the reviewers are generally happy with it but have a series of fairly minor concerns that you should be able to address handily. Best wishes in your revisions.

Comments to Author:
Reviewers' Comments to Author: Reviewer: 1 Comments to the Author(s) This is a very good piece of work, contributing additional knowledge on the current distribution of short-eared dogs and assessing future impact of current and projected deforestation rates. The data and methodology are well presented, the results are clear, and the discussion advances the state of knowledge of the distribution of this little known Amazonian canid. I found your choice of future horizons as 2027 and 2045 poorly justified by a 6 year generation time which is not supported by any demographic data and clearly too high for a mid-size canid. Also, unclear why to go for a landcover database that is 10 years old, when more recent data is available? Below I list a few comments that I hope will help improve the final version of this work. L106. 'Interfluve' technical term that is not widely used outside technical literature. You should define on first mention L110. You can make a recommendation for a Red List reassessment, but should not make the recommendation to what category, since that will only determined by challenging the RL criteria with your new data. And this paper does not formally do that. You may want to want to say 'upgrading… its Red List status…' L130. It's odd to use work that is 20 and 10 years old to support expectations of climate change impact on Amazonian biodiversity. Some of those authors predictions may be already supported by data, of refuted. There must be more recent work you could consider. L126. and References henceforth. Your reference manager seems to have mangled many authors names, sometimes including given names, or initials, or listing way too many authors. (eg L146 DEL Maria Renata Pereira. Surname is Leite Pitman; L151. DEL M.R.P.). Please be careful to review your citations carefully before resubmission. L140. You are using a fild guide as a reference for patchy distribution. There are more detailed references (eg IUCN Action Plan; Macdonald & Sillero canid book, Wallace work) to support this statement. L170 scale-dependent, use hyphen L194. Fine to use crab-eating foxes as proxy for HR, but you should look more broadly and cite other studies, not just Courtenay's work. How about hoary foxes? L214 & 216. There should be at least an overlap between datasets. You are using 1970-2000 for climate, but 2009 for land cover. Why not use more recent climate data, since it is readily available? And why 2006 land corver and not a more recent dataset? L232. Soares-Filho 2006 predictions. How good were they 13 years later? That will give you an inkling whether his predictions will be any good going forward. L237. Red List criteria. You need to use v3.1 2nd edition (IUCN 2012, NOT IUCN 2001 L238. Generation time cannot be 6 years, when most canids of similar or larger since have generation times of 2-3 years (The RL assessment used 4 years). The later will take you to the 10 year window to assess decline (or 12 years, if you use 4 years, but not sure that can be sustained, since ther is not actual demographic data to support it). This will work for your 2027 scenario, if you start from the end of your database assemblage. Less clear why you also provide a 2045 scenario. I'd use 30 or 50 years for the long-term scenario, as a matter of personal preference. Justify why use 2045. For a RL reassessment you can look at past changes, or use inferences of future changes. L485. I have an issue with the choice of time window. When the RL reassessment takes place, it will be based on a 10 year window (with a realistic generation time of 2-3 years). Therefore, for this paper to be informative you should provide prediction for the right time interval. L510. You need to properly reference your mention of disease as a potential risk. L513. No need to repeat scientific name. L516-517. This is a worthwhile recommendation but it should be a recommendation to reassess the species status, in light of the new data and analysis. You can't pre-adjudicate this assessment will necessarily be to 'Vulnerable'. That will be the outcome of testing against the criteria. It is, after all, a quantitative process, not a qualitative one. Reword accordingly. L574. Address lots of typos and formatting.

Reviewer: 2
Comments to the Author(s) Wild dogs at stake: Deforestation threatens the only Amazon endemic canid, the short-eared dog (Atelocynus microtis); Rocha et al.; RSOS Rocha et al. present a fascinating study of the severely under-studied short-eared dogs, combining historic presence records, camera trapping and species distribution models to predict current and future distribution of the species. The authors also present a multi-scale perspective (regional and local), which sheds some light on the scale-specific factors affecting the species' association with habitat. Overall, the paper is very well written and the authors have done a commendable job-considering the effort it would have taken to coordinate, initiate collaborations and compile information about a rare species from multiple sources and institutions. I do have some concerns related to the local scale analysis (explained below).
Introduction: Specific comments: L127: Please revise the sentence: "Besides the alarming deforestation rates, there is growing concern…" Methods: General comments: If I understood correctly, the authors use all presence records (post-rarifying) from 2000 onwards. Does this include data from 2009 to 2018/19? If so, there would be some mismatch in the forest cover (i.e. potential habitat) and current distribution right? The forest cover layer is from 2009, but presence records are from subsequent years as well. I get that this may be a limitation because of access to updated forest cover data. But this issue needs to be acknowledged in the Methods section.
Local scale analysis: Given that that authors list habitat loss, prey decline, disease from domestic dogs and other anthropogenic factors (road related mortality) as factors that negatively impact short-eared dogs, I wonder why none of these covariates, or variables that could serve as surrogates of these factors, were not considered for modeling habitat use. The authors also list lowland forests, areas close to water etc. as purported "good habitats" for the focal species. The large-scale predicted distribution also clearly indicates importance of protected areas for the species to persist in the long term. Elevation, distance to protected area boundary, distance to water bodies, proximity to human settlement, human footprint index, encounters of hunters/logging machinery, encounters of domestic dogs etc. are all really good potential covariates that would make the local scale analysis very interesting while also better informing management/conservation. The three covariates used to model occupancy PSI may be too broad to have show any influence at the local scale; this is evident in the estimates of the slope coefficients. Both forest cover and edge density have high SE values (95% CI overlaps 0, so no statistical significance), suggesting weak effects of the predictors. I strongly suggest that the authors re-analyse the local-scale data incorporating some/all the covariates listed above.
Specific comments: L335: revise the sentence to state that the sample units are "likely" smaller than the "presumed" home-range size of the species.
Results: General comments: Move Table S4 to main manuscript. This is the primary result of your study. Similarly, combine three panels of Figures S5, S6, S7 and present it as one figure in main manuscript. The results related to local-scale analysis would change when the data are reanalysed. Please present revised results accordingly.
Discussion: General comments: The section is well written for the most part, and makes a compelling case for revising the IUCN status of short eared dog. I think the paper would benefit from expanding the narrative, both, in the Introduction and in the Discussion sections. As it stands, the focus is a bit narrow. If at all the species does qualify to be considered a "flagship" for conservation of forest systems in the Amazon, then the entire Discussion should make a more convincing case by establishing links between the short-eared dogs, their prey, competing predators and humans. The authors go some length in doing so in the last paragraph. But the argument is lacking in that it only makes a passing mention of the benefit to other species.
Author's Response to Decision Letter for (RSOS-190717

Are the interpretations and conclusions justified by the results? No
Is the language acceptable? Yes

Do you have any ethical concerns with this paper? No
Have you any concerns about statistical analyses in this paper? No

Recommendation?
Accept with minor revision (please list in comments)

Comments to the Author(s)
As stated in my original review this is a very good piece of work, contributing additional knowledge on the current distribution of short-eared dogs and assessing future impact of current and projected deforestation rates. The data and methodology are well presented, the results are clear, and the discussion advances the state of knowledge of the distribution of this little known Amazonian canid.
That assessment still stands. However, I was disapointed by the authors' reluctance to review the value of their guessed generation time for the species (not supported by any demographic data).
A 6 year generation time does not reflect what we know about the reproductive biology of similar sized canids. Therefore a proxy generation time should be used, revised down to 3 years (max 3.5 years) to reflect that observed across similar size canids. Future horizons should change accordingly. The choice of such a conservative generational time weakens the authors' argument for uplisting the species Red List status.

Review form: Reviewer 2
Is the manuscript scientifically sound in its present form? No

Do you have any ethical concerns with this paper? No
Have you any concerns about statistical analyses in this paper? Yes

Recommendation?
Major revision is needed (please make suggestions in comments)

Comments to the Author(s)
Provided as a separate document (Appendix B).

14-Feb-2020
Dear Mr Rocha, Manuscript ID RSOS-190717.R1 entitled "Wild dogs at stake: Deforestation threatens the only Amazon endemic canid, the short-eared dog (Atelocynus microtis)" which you submitted to Royal Society Open Science, has been reviewed. The comments of the reviewers are included at the bottom of this letter.
Please submit a copy of your revised paper before 08-Mar-2020. Please note that the revision deadline will expire at 00.00am on this date. If we do not hear from you within this time then it will be assumed that the paper has been withdrawn. In exceptional circumstances, extensions may be possible if agreed with the Editorial Office in advance. We do not allow multiple rounds of revision so we urge you to make every effort to fully address all of the comments at this stage. If deemed necessary by the Editors, your manuscript will be sent back to one or more of the original reviewers for assessment. If the original reviewers are not available we may invite new reviewers.
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In addition to addressing all of the reviewers' and editor's comments please also ensure that your revised manuscript contains the following sections before the reference list: • Ethics statement If your study uses humans or animals please include details of the ethical approval received, including the name of the committee that granted approval. For human studies please also detail whether informed consent was obtained. For field studies on animals please include details of all permissions, licences and/or approvals granted to carry out the fieldwork.
• Data accessibility It is a condition of publication that all supporting data are made available either as supplementary information or preferably in a suitable permanent repository. The data accessibility section should state where the article's supporting data can be accessed. This section should also include details, where possible of where to access other relevant research materials such as statistical tools, protocols, software etc can be accessed. If the data have been deposited in an external repository this section should list the database, accession number and link to the DOI for all data from the article that have been made publicly available. Data sets that have been deposited in an external repository and have a DOI should also be appropriately cited in the manuscript and included in the reference list.
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All contributors who do not meet all of these criteria should be included in the acknowledgements.
We suggest the following format: AB carried out the molecular lab work, participated in data analysis, carried out sequence alignments, participated in the design of the study and drafted the manuscript; CD carried out the statistical analyses; EF collected field data; GH conceived of the study, designed the study, coordinated the study and helped draft the manuscript. All authors gave final approval for publication.
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Finally, we note that the following two email addresses are invalid, so please ensure that these are updated in the ScholarOne system when submitting your revised manuscript: The two referees who reviewed your manuscript have come back with additional comments, one of which potentially requires additional analysis. Please consider these requests and carry out the additional analysis if necessary Subject Editor Comments to Author: One reviewer feels strongly that you did not address what appears to be an unrealistic estimate of generation time, given what is known of canids. These and other concerns will need to be addressed fully in your final version of submission; please be explicit and best wishes for your revisions.
Reviewer comments to Author: Reviewer: 1 Comments to the Author(s) As stated in my original review this is a very good piece of work, contributing additional knowledge on the current distribution of short-eared dogs and assessing future impact of current and projected deforestation rates. The data and methodology are well presented, the results are clear, and the discussion advances the state of knowledge of the distribution of this little known Amazonian canid.
That assessment still stands. However, I was disapointed by the authors' reluctance to review the value of their guessed generation time for the species (not supported by any demographic data). On behalf of the Editors, I am pleased to inform you that your Manuscript RSOS-190717.R2 entitled "Wild dogs at stake: Deforestation threatens the only Amazon endemic canid, the shorteared dog (Atelocynus microtis)" has been accepted for publication in Royal Society Open Science subject to minor revision in accordance with the referee suggestions. Please find the referees' comments at the end of this email.
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All contributors who do not meet all of these criteria should be included in the acknowledgements.
We suggest the following format: AB carried out the molecular lab work, participated in data analysis, carried out sequence alignments, participated in the design of the study and drafted the manuscript; CD carried out the statistical analyses; EF collected field data; GH conceived of the study, designed the study, coordinated the study and helped draft the manuscript. All authors gave final approval for publication.
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23-Mar-2020
Dear Mr Rocha, It is a pleasure to accept your manuscript entitled "Wild dogs at stake: Deforestation threatens the only Amazon endemic canid, the short-eared dog (Atelocynus microtis)" in its current form for publication in Royal Society Open Science.
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Please see the Royal Society Publishing guidance on how you may share your accepted author manuscript at https://royalsociety.org/journals/ethics-policies/media-embargo/. Thank you for your submission. As you will see the reviewers are generally happy with it but have a series of fairly minor concerns that you should be able to address handily. Best wishes in your revisions. ANSWER: We are grateful for the Editor and Reviewers' positive feedback and valuable comments.

Reviewers' Comments to Author:
Reviewer: 1 Comments to the Author(s) This is a very good piece of work, contributing additional knowledge on the current distribution of short-eared dogs and assessing future impact of current and projected deforestation rates. The data and methodology are well presented, the results are clear, and the discussion advances the state of knowledge of the distribution of this little known Amazonian canid. ANSWER: Thank you for the positive feedback and helpful comments.
I found your choice of future horizons as 2027 and 2045 poorly justified by a 6 year generation time which is not supported by any demographic data and clearly too high for a mid-size canid. Also, unclear why to go for a landcover database that is 10 years old, when more recent data is available? Below I list a few comments that I hope will help improve the final version of this work. The main issue raised by Reviewer1 is our choice of generation time length (6 years). Reviewer1, argues that we should have used a 4-year generation time as proposed by the IUCN Red List assessment for the species (Leite Pitman and Williams, 2011). We based our estimate on the Brazilian Red List assessment for the short-eared dog, which was published two years later by the same first author (Leite Pitman and Beisiegel, 2013). We agree with the Reviewer1 that 6 year might be a long generation time for a canid of this size, however, we do not have any biological information from the species based on field studies to decide between the two generation time length proposed. In view of this lack of reliable data, we decided to stick with the 6-year generation length. We will address this issue, including our reason to keep the longer generation length, in greater depth later in this review. The issue about the land cover database was also raised by Reviewer2, who raised some additional questions. Please, check our response to Reviewer2 further down on this document (Reviewer2 methods comments).
L106. 'Interfluve' technical term that is not widely used outside technical literature. You should define on first mention ANSWER: We have added "(i.e portions of land separated by large rivers)" the first time we mention "interfluves" in the manuscript. [L.21] L110. You can make a recommendation for a Red List reassessment, but should not make the recommendation to what category, since that will only determined by challenging the RL criteria with your new data. And this paper does not formally do that. You may want to want to say 'upgrading… its Red List status…' ANSWER: We changed the wording; it now reads "Hence, we propose re-assessing the current shorteared dog's IUCN Red List status of Near Threatened, as upgrading its status may be warranted." [L. [26][27] L130. It's odd to use work that is 20 and 10 years old to support expectations of climate change impact on Amazonian biodiversity. Some of those authors predictions may be already supported by data, of refuted. There must be more recent work you could consider. L126. and References henceforth. Your reference manager seems to have mangled many authors names, sometimes including given names, or initials, or listing way too many authors. (eg L146 DEL Maria Renata Pereira. Surname is Leite Pitman; L151. DEL M.R.P.). Please be careful to review your citations carefully before resubmission. ANSWER: There was a problem with reference manager. We have fixed all citations.
L140. You are using a fild guide as a reference for patchy distribution. There are more detailed references (eg IUCN Action Plan; Macdonald & Sillero canid book, Wallace work) to support this statement. ANSWER: We have made changes as suggested by the reviewer. We have replaced the citation by "Sillero-Zubiri, Claudio, Michael Hoffmann, and David Whyte Macdonald, eds. Canids: foxes, wolves, jackals, and dogs: status survey and conservation action plan. Gland, Switzerland: IUCN, 2004 L194. Fine to use crab-eating foxes as proxy for HR, but you should look more broadly and cite other studies, not just Courtenay's work. How about hoary foxes? ANSWER: We have not made changes. The idea was to reduce spatial bias in the locations of the shorteared dog presence records due to unbalanced survey effort across our study region. To do so, we used a study on crab-eating fox home range in the Amazon as a reference to set a minimal distance between our records. Small differences in that distance will have little effect on the final model outputs, as long as we select a reasonable distance. To our knowledge, the Macdonald and Courtenay (1996) study has the most relevant data (closest taxonomic and geographic) we could use to support this decision.
L214 & 216. There should be at least an overlap between datasets. You are using 1970-2000 for climate, but 2009 for land cover. Why not use more recent climate data, since it is readily available? And why 2006 land corver and not a more recent dataset? ANSWER: For the climate variables, we used the WorldClim Version2, which has average monthly climate data for minimum, mean, and maximum temperature and precipitation for 1970-2000. This is the most used climate dataset (more than 20000 citations in Google Scholar considering all versions) in species distribution models, particularly for those with continental distribution range. We are not aware of any other climate dataset that is available for our entire study area, at such a fine resolution (~1 km). We added the sentence "To our knowledge, more recent climate variables with comparable resolution were not available". [L.139-140] There is more flexibility for the land cover variable. The species location dataset we used in the species distribution modeling has records spanning from 2000 to 2018. We chose GlobCover because it is from 2009, the middle point within in the temporal range of the species record dataset, and has a very good resolution (~300 m).
L232. Soares-Filho 2006 predictions. How good were they 13 years later? That will give you an inkling whether his predictions will be any good going forward. ANSWER: It is beyond the scope of this study to conduct a formal assessment of how good these future deforestation projections are. However, in the figure below, we visually contrast the future deforestation projected by Soares-Filho et al. (2006) for the year 2018 and the accumulated deforestation mapped by PRODES (2019)* for the same year, which is readily available for the Brazilian Amazon (http://terrabrasilis.dpi.inpe.br/downloads/). Based on these figures, Soares-Filho et al. projections have performed well in predicting deforestation, at least for Brazil, the country that encompasses most of the short-eared dog's distribution. We added the following sentence to the manuscript: "When contrasting Amazon basin forest cover modeled by Soares-Filho et al. (2006) against current maps of deforestation in Brazil (PRODES, 2019), these models have performed well in predicting deforestation, at least for Brazil, the country that encompasses most of the short-eared dog's distribution (see Figure S1)." [L.159-160] * The PRODES project performs satellite monitoring and produces annual deforestation rates for the Brazilian Amazon, information that has being used by the Brazilian government since 1988. L238. Generation time cannot be 6 years, when most canids of similar or larger since have generation times of 2-3 years (The RL assessment used 4 years). The later will take you to the 10 year window to assess decline (or 12 years, if you use 4 years, but not sure that can be sustained, since ther is not actual demographic data to support it). This will work for your 2027 scenario, if you start from the end of your database assemblage. Less clear why you also provide a 2045 scenario. I'd use 30 or 50 years for the long-term scenario, as a matter of personal preference. Justify why use 2045. For a RL reassessment you can look at past changes, or use inferences of future changes. ANSWER: As mentioned in the manuscript, the short-eared dog is one of the least studied canids in the world. Consequently, there is a lack of information on the short-eared dog's biology, particularly on its demography (e.g. lifespan, reproductive system, sexual maturity, number of broods per year, brood size). To our knowledge, the species does not exist in a captive population in any Zoo or other facilities for ex-situ studies that could be used as reference. The IUCN (2012) defines generation length as "…the average age of parents of the current cohort (i.e. newborn individuals in the population). …Generation length is greater than the age at first breeding and less than the age of the oldest breeding individual…" (p.11). Leite Pitman and Williams (2011) propose 4year generation in the IUCN Red List assessment. Two years later, Leite Pitman and Beisiegel (Leite Pitman and Beisiegel, 2013) updated the generation length to 6 years, neither publication provided supporting biological data, likely because such information is not available. As pointed out by the reviewer, other canid species of body size similar to the short-eared dog have assumed generation length of 3-4 years (see, IUCN Red List assessment for species of the South American Lycalopex genus). Leite Pitman conducted an unpublished study with a tamed male short-eared dog and observed that this individual did not display sexual features (e.g. testicles descended and complex call) until three years of age, which is late for a dog/fox (Hance, 2014). For instance, one-year old male hoary foxes (Lycalopex vetulus) are active reproductively (Lemos, F.G., personal communication). From the conservation perspective, adopting a longer generation length would be a conservative approach, because opting for a shorter generation length implicates that individuals are successful in reproducing earlier in life. In face of the lack of sound data on the short-eared dog reproductive biology and the conservation implication for the species, we decided to keep the 6-year generation length for predicting the species' future distribution. We have added a short version of these arguments to the Methods section to justify out choice [L.171-184]. We also added a possible caveat of our choice in the Discussion section: "These estimates are based on a 6-year generation length, and there is considerable uncertainty about that quantity due to lack of biological data. If the generation length used here is overestimated, our predictions of habitat loss and degradation within 3 generations may be somewhat pessimistic." [L.441-444] If deemed important by the editor, we can project species distributions for future horizons compatible with 4-year generation length; however this would cause delays the revision process, as we would need to go back to the first stages of the modeling procedure.
L254-257. Explanation a bit woolly. Tighten up. ANSWER: We made a small change removing unnecessary parts. It now reads "Even though our presence-only species data were not collected using systematic surveys, we believe we meet this assumption, given that covariate values at species record locations cover most of the distribution of covariates across our area of inference (see Figure S3 L287. Definition unclear. Are you saying that protected areas INCLUDE indigenous land? This will require different wording. ANSWER: To make it clear that we are including indigenous land as protected areas, we have changed the sentence. It now reads "We assessed the current and future total area predicted to be occupied by the short-eared dog per country (including all countries in which the species has been recorded), per interfluve (Amazon basin sub-regions limited by the main rivers, see Figure S4) and within/outside protected areas and indigenous land (hereafter collectively referred to as protected areas)." [L. [229][230][231][232] We are open to change the word if deemed necessary by the editor.
L304. This methodology needs greater detail. It does not tell me how many of those cameras were deployed at a given time. 180 cameras at the same time?, 60 moved to three different arrays at different times? Also how far apart were the cameras set up form each other?
Wild dogs at stake: Deforestation threatens the only Amazon endemic canid, the short-eared dog (Atelocynus microtis); Rocha et al.; RSOS; R1 I appreciate the authors' detailed responses and justifications to my previous comments. They have also done a good job with revising the narrative based on suggestions made by the reviewers.
One of my primary concerns in the previous version was with the local-scale analysis. I see that the authors have used some additional covariates based on my suggestions and analysed the data again (presented in Table S8). I must apologize for my oversight here, but I missed seeing this error in the previous version. The models where the authors have used p(EFF), psi(.) should have THREE parameters (p, beta-effort, psi), and associated AIC would be 186.2 (as is the case for all the model sets with the new covariates). But for forest cover, edge density and patch density, the same model seems to have only TWO parameters and the AIC is 230.9. There is an error either in the new set of covariate models (water, road, elevation HFI), or in the forest-based covariates from before. If the correct AIC for p(EFF), psi(.) is actually 186.2, then this model would consistently rank the highest (least AIC) across all model combinations, and none of the models even with forest-based covariates would be statistically significant.
If my observation above is correct, then I suggest the authors check for additive and/or interactive effects of the covariates. This may produce some covariate models that rank higher than p(EFF), psi(.), and the authors could revise their results and discussion based on that. If, by chance, even after these changes the model with least AIC happens to be p(EFF), psi(.), then the authors can present all the models/results, and deliberate on the "indicative" effects (magnitude and direction) of the covariates, while explicitly stating that none of the covariate models received adequate statistical support.
Minor comments: L26-29: I suggest rewording this to "We propose a re-assessment of the short-eared dog's current IUCN Red List status (Near Threatened) based on findings presented here. Our study also exemplifies how data can be integrated across sources and modeling procedures to improve our knowledge of relatively understudied species." L40-41: Reword: "…given the recent human-induced environmental changes in Amazonia." L49: Replace "predict species distribution" with "predict distribution patterns" L81-82: Suggested edit: "we used occupancy models to investigate how habitat use by the short-eared dog is affect by attributes related to forest cover at a fine spatial scale (local scale)." L83-86: Delete these lines, or include them in the Discussion (but I think a slightly different version is already in the Discussion).
Paragraph L87-L98: May be a better fit as the penultimate paragraph of the Discussion section.

Associate Editor Comments to Author (Professor Michael Bruford):
The two referees who reviewed your manuscript have come back with additional comments, one of which potentially requires additional analysis. Please consider these requests and carry out the additional analysis if necessary ANSWER: Thank you; please see our response to the reviewer comments below.

Subject Editor Comments to Author:
One reviewer feels strongly that you did not address what appears to be an unrealistic estimate of generation time, given what is known of canids. These and other concerns will need to be addressed fully in your final version of submission; please be explicit and best wishes for your revisions. ANSWER: Thank you; please see our response to the reviewer comments below.

Reviewer comments to Author:
Reviewer: 1 Comments to the Author(s) As stated in my original review this is a very good piece of work, contributing additional knowledge on the current distribution of short-eared dogs and assessing future impact of current and projected deforestation rates. The data and methodology are well presented, the results are clear, and the discussion advances the state of knowledge of the distribution of this little known Amazonian canid. That assessment still stands. However, I was disapointed by the authors' reluctance to review the value of their guessed generation time for the species (not supported by any demographic data). A 6 year generation time does not reflect what we know about the reproductive biology of similar sized canids. Therefore a proxy generation time should be used, revised down to 3 years (max 3.5 years) to reflect that observed across similar size canids. Future horizons should change accordingly. The choice of such a conservative generational time weakens the authors' argument for uplisting the species Red List status. ANSWER: We feel that this question is not one of right or wrong (as there are essentially no data on reproductive ecology of this species, from the wild or captivity), but rather of opinion -whether to use the suggested generation length published in 2011 or that published in 2013. We opted for the latter, because, as we already laid out in the previous response to reviewer comments, it is the more recent value, and both were published by the same first author (who is also a coauthor of this study). In the last round of revisions, we added justification and caveats for this choice to the manuscript [L.171-184 and L.441-444 of the clean version of our manuscript].
To further evaluate potential consequences of choosing one generation length over the other for our analysis, we looked at the amount of deforestation projected to happen within the short-eared dog's distribution over three times each generation length (according to IUCN criterion of loss of distribution over 3 generations). Based on the most likely scenario (Business as Usual), the proportion of the current short-eared dog distribution deforested by 2027 (6-year generation length) is estimated to be 24.9%. If we adopt Reviewer 1's suggestion of a 4-year generation length (i.e., if we look at projected deforestation by year 2021), this proportion changes to 21%. As in our model the changes in predicted