Dear Dr. Howard,

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, requiring a minor revision. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Provide more information about if/where the associated data can be obtained in the data availability statement. With this be available through the corresponding author, a database, other?

A bit more clarification is needed in the “Historical and Current Fish Distribution” methods to provide a full understanding of how fish species were targeted- of the 129 taxa, were they separated by different fish runs, as well (fall-run, spring-run, etc.), for relevant species?

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Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

Reviewer #1: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: No

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4. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: The stated goal of this study is to further the understanding of freshwater fish species persistence in a diverse array of watersheds, through the example of California and California-adjacent drainage basins, in the face of anthropogenic fragmentation and land management. To achieve this, a thorough study of the relationship between past (pre-1975) and current (post-1975) fish presence/absence data and local anthropogenic/environmental conditions was conducted through the use of Temporal Beta Index calculation and Random Forest variable importance assessment. My own expertise with respect to this study is mostly related to freshwater fish and their relationships to anthropogenic perturbations, and basic SDM-adjacent analyses, and I am less competent when it comes to the minutiae of spatial autocorrelation analyses on one hand, and interpretation of Spearman’s ranking coefficient on the other - but a bit of quick enlightenment on my part leads me to trust the analyses presented. This study’s major result is the likely importance of fragmentation and other human-lead disturbances in fish species loss in California, and it discusses the implications of such results - and the expected nuances. This study is notable : the extensive available data used in the study for environmental variables and fish presence guarantee its relevance at the local and international level, and its results are important : they rely on novel ideas and provide relevant and necessary information on anthropogenic impacts on freshwaters ecosystems and points to specific practices as likely causes for species loss on a wide geographical scale.

I consider the article’s form adequate, following the PLOS One author guidelines - although the heading level indication may require slight clarification - and only see minor modifications as necessary for publication in PLOS One. It seems scientifically sound as far as my knowledge allows, and rigorous in its testing and interpretations. Below are a few comments pertaining mainly to clarification in methodology and matters of discussion.

METHODS

Lines 152-154 : There is a slightly awkward use of the word “connectivity” in this study : you mention connectivity in a broader sense in your title and introduction as well as your discussion, which includes many concepts that would be classified under longitudinal connectivity and includes matters of fragmentation - an essential point of your work - but the “connectivity” layer of your variables includes a much narrower sense of distance to larger bodies of water. I would suggest either renaming this layer or provide a bit more explanation for what I would consider a strangely broad term for a very specific metric.

Lines 182-189 : With respect to the formation of FCNs - this question may stem from my own inexperience with the relevant datasets, please disregard if irrelevant - which were the criteria (if any) used to conclude functional disconnection by dams and waterfalls (height? Fish passage data? An aggregated metric?). Similarly, were all barriers kept for analysis in other processes (excluding the exceptions cited in the article, culverts, removed barriers etc.), or was height accounted for in some way? I am not suggesting any type of change in the building of the dataset, simply a bit more detail on something which was not immediately clear to me.

Lines 208-210 : My curiosity may stem from low knowledge of California watersheds, but were all recorded species in Californian rivers included? If not, how were they selected ? Did the inclusion of nonnative species pose a challenge? A bit of ichthyological context would be appreciated, even if it must be only a few phrases.

Lines 272-284 : A few words on your methods for obtaining variable importance data and partial dependence plots would be welcome - otherwise they are first mentioned in your results. You would benefit from it since I personally don’t seem to find that you overstep in terms of random forest interpretation, and providing clearer guidelines for work reproduction would prevent unfounded criticism.

RESULTS

Lines 309-311 : A very minor gripe, but the way you write about TBI results is a bit strange, almost suggesting that TBI calculation includes an appreciation of species gain and loss, also in Table2. A reader familiar with beta diversity calculation will be able to parse what you mean, but a philistine may misunderstand you (of course, since species loss is the only phenomenon recorded - more on that later - I may even suggest drastically simplifying this section and Table to clarify what was obtained and increase legibility).

LINES 433-487 : Only significant change advised. While I fully understand the purpose of this section of the results, they seem to bleed into the discussion below a bit too much - you mention historical and geographical explanations to environmental responses of fish communities - and would benefit from a drastic reduction, while these elements of discussion are transported below to strengthen your discussion even more.

Relatedly, DISCUSSION

Your discussion is much appreciated and nicely concludes your study. As mentioned above, a few elements of anthropogenic management and geographical context may be added. If it is possible and judged relevant by the authors, I would find interesting a short reflection or opening on the link between species range type and resilience, since anadromous species are clearly pointed as singularly affected in your results, and since you argue anadromous may be especially suited to this kind of approach. Again, this is to the discretion of the authors.

Reviewer #2: An interesting study that uses historic and present day fish distributions to investigate how patterns in species loss are related to changes in connectivity and land use or a large spatial area. Overall this is a nice study and paper so I have minor comments.

I could not evaluate whether the data are publicly available or not. The data availability statement does not state how the data will be made available once the manuscript is accepted. The authors could make the data available to reviewers via a private repository. A statement could also me made about where a reader can find the publicly available datasets the study makes use of.

Using the largest Functionally Connected River segment to represent habitat available/connectivity within each HUC-12 is a weakness that is acknowledged in the discussion.

The language in the discussion shifts from species loss and TBI to the use of fish species persistence. I think it is more appropriate to use species loss or decline in TBI to remain consistent with previous use and to better reflect how the introduction sets up the work.

Road culverts and water diversions were not included due to a lack of consistent data. There are likely a lot of road crossings in the study area with a side range in permeabilities for individual fish species. A good addition to the discussion would be a few sentences that acknowledge the limitation and state that road crossing can make up a large number of barriers, particularly on smaller streams where culverts, not bridges, are installed.

Line 51: I suggest using habitat heterogeneity instead of habitat options here.

Line 109: By options do the authors mean increased habitat heterogeneity? More specific language will better explain the emphasis.

Line 217: Does wide ranging mean >24,000 km2 and not anadromous? Please clarify in text.

Line 234: delete “best”

Line 254: Check consistent us of abbreviation “HUC-12” here and throughout

Line 286: Please include the threshold used to identify highly correlated variables

Table 2: Is the “mean TBI over all sites” column correct? There are no values, just an “*” in each cell which indicates significance. Based on the column title I expect to see values here.

Table 3 is very large. It may be more appropriate to put the table in an appendix and refer to main highlights in text as was done in the results.

Line 493-496: I think these sentences can be removed. They are redundant and not necessary to understand the findings of the study.

Lien 510: Are you referring to fish species data here? Please clarify.

Line 522: I don’t think there should be a reference to climate change here unless the intent is to state the variables identified as important are likely to change in response to climate change. If that is the case an explicit statement should be made.

Lines 585-610: These are two important, but long paragraphs, that state the contribution of the study to conservation in general. However, I think the should be edited and combined into one paragraph to concisely state the big picture conservation implications of the work. The majority of the paper is about linking changes in TBI to changes in connectivity and land use and the discussion should focus on these topics.

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Reviewer #1: No

Reviewer #2: No

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From Fragmentation to Resilience: Connectivity and Habitat Diversity as Drivers of Fish Persistence in California Watersheds

PONE-D-25-34116R1

Dear Dr. Howard,

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,

Jason Magnuson, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: