PONE-D-20-37830

A process-based assessment of landscape change and salmon habitat losses in the Chehalis River basin, USA

PLOS ONE

Dear Dr. Beechie,

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The authors merely need to address the few questions posed in the detailed review and make necessary changes. These comments are minor and should not take a great deal of time.  Overall this manuscript is well written and executed.

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Madison Powell, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (if provided):

The authors of this manuscript provide worthwhile data and provide a detailed summation of a variety of data regarding habitat types etc. The manuscript is well written and generally easy to follow. The manuscript's information is of interest to a variety of fish biologists and habitat biologists outside of salmonid biology. The authors need to address the comments provided in the detailed review and answer the questions posed by the reviewer.

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Reviewers' comments:

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Comments to the Author

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Reviewer #1: Yes

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

Reviewer #1: Yes

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Reviewer #1: Yes

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Reviewer #1: Yes

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5. Review Comments to the Author

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Reviewer #1: General

This manuscript is part of a multi-paper contribution outlining a framework to estimate 1. historical habitat conditions compared to present day and 2. which changes are most likely to limit fish recovery. This manuscript addresses goal #1 of this framework by quantifying changes in the amount of different habitat types. The authors analyze an impressive range of data to characterize historical conditions, and they find that marsh habitats have seen the largest reductions compared to baseline conditions. While identifying limiting factors via life-cycle modeling is a potentially contentious exercise that can be difficult to parameterize with existing data, characterizing changes in habitat quantity is generally less complex and contentious (though it is important and certainly not easy to pull off). I found this paper was easy enough to read and it clearly supported its claims with robust analyses.

Specific

77: authors do a nice job placing the objectives of this paper in the context of the 3-step approach

85: If the restoration is process-based, why is the measure of impact pattern based?

88: How about natural conditions varying temporally, given giant variation in salmon production prior to contemporary land use (e.g., Rogers et al. PNAS 2013 Centennial-scale fluctuations)? Could help to briefly address temporal variation when introducing spatial variation, so it doesn’t come off as assuming that the past was static.

90: could end with ‘,respectively’ I had to read this twice to understand this sentence.

99: Does ‘dial’ imply that they can be manipulated by management?

134: Is there typically enough data to quantify population bottlenecks in terms of the habitat features being restored? For example, if marshes provided flood refuge or spring foraging, when is there the data to understand how area of marsh and fish density translate into survival? Isn’t the resolution of data more coarse than that needed to address the processes and functions being restored? [OK I see that the life-cycle paper is separate from this one, so this comment doesn’t need to be addressed in this manuscript]

221: Many readers may wonder how climate change fits in with this and how we assess baseline conditions if they unlikely to occur in future climates.

Fig. 1 Why is floodplain connectivity a driver? Isn’t this a habitat condition? The Driver/Habitat conditions differentiation isn’t that clear for me, so it could be explained a little more when introduced…. Or the terms could be reworded to sound like drivers. For example floodplain connectivity (a habitat condition in my mind) could be rephrased so that it was parallel with terms such as road density and channel straightening. But in general the mix up between mechanisms and patterns here is confusing.

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Reviewer #1: No

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A process-based assessment of landscape change and salmon habitat losses in the Chehalis River basin, USA

PONE-D-20-37830R1

Dear Dr. Beechie,

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,

Madison Powell, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Minor revisions are complete. Authors have addressed all editorial comments.

Reviewers' comments: