Peer Review History
| Original SubmissionOctober 27, 2020 |
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PONE-D-20-33797 Environmentally triggered shifts in steelhead migration behavior in the middle Columbia River PLOS ONE Dear Dr. Siegel, 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. ============================== Two reviews offer minor albeit important points to consider and edit - these are mandatory. In general, the manuscript is well written and worthy of publication. These minor changes should not be too difficult for the authors to complete. ============================== Please submit your revised manuscript by Jan 24 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
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Please ensure that you refer to Table 2 in your text; if accepted, production will need this reference to link the reader to the Table. Additional Editor Comments (if provided): Two reviews offer minor albeit important points to consider and edit. In general, the manuscript is well written and worthy of publication. These minor changes should not be too difficult for the authors to complete. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ********** 2. 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PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: This manuscript examines the variation in migration behavior of summer-run steelhead (anadromous rainbow trout, Oncorhynchus mykiss) through the Bonneville-McNary reach using PIT tag data from fish tagged as juveniles from different populations in the middle upper Columbia River basin, associated estimates of mortality, and the association of various environmental factors. Steelhead that migrate through this reach, which exhibits higher water temperatures due to retention time of the water in this lower reach, often seek thermal refugia and delay their migration to upper reaches for spawning. The authors find that populations show both similarities, such as a delay in migration that proceeded the highest annual temperatures and deceased daily mortality risk with delay despite increased cumulative within-reach mortality, and differences, including the temperature threshold at which delay is made, rates of delay, and associated mortality rates. As steelhead in the middle and upper Columbia are with few exceptions ESA-listed, and understanding the natural and anthropogenic factors that influence mortality in this therefore of great interest, I find that this paper is timely, adequately executed, and an insightful contribution to the relevant literature. I would recommend, at the authors’ discretion, that they consider clarifying their manuscript in one respect, which the authors allude to, but is not in my opinion sufficiently identified. The ultimate question for migrating Columbia River steelhead is one of total fitness (survivorship to spawn, fecundity, and survivorship of their offspring to reproduction). While migration through the lower Columbia reaches and the decision to delay and seek thermal refugia may create some differential in survivorship out of that reach, the survivorship of fish that do not delay but make it through the reach is not secured, as the authors mention, and more importantly even if they do survive to spawning tributary, this does not necessarily guarantee greater total fitness, since the additional components of fitness may also be affected by the choice to continue migrating through adverse conditions. Again, as the authors allude, a better measure of the cost/benefit (“bet hedging” advantage) provided by migration delay would be to measure the actual reproductive success of fish that delayed or continued through, which would be a cumulative result of those choices. While this is clearly beyond the scope of this study, I think it’s important to clarify that the patterns identified herein only represent one aspect of that overall measure. One other minor concern that I would have wished the authors to have addressed was that it was odd to me that the authors identified three distinct patterns in the data, both conceptually and in the fit of tri-modal models to the migration timing data. I have always inferred the “decisions” to 1) delay migration and seek thermal refugia and 2) overwinter outside of spawning tributary to be distinct, since the first (presumably) implies an active choice to seek a thermal refuge (usually a non-natal tributary), while the latter is likely more often simply pausing active migration because of lower kinetic limits. Moreover, the authors hardly discuss overwintering as a strategy distinct from the “slow” form of delay in the results, and indeed include them as a joint probability in additional models, which I think would rather make sense (in my mind, they are not distinct vis-à-vis initial choices to delay or not). Moreover, just because a fish does not overwinter in this lower Columbia stretch does not mean that it did not overwinter farther up but still outside the spawning tributary, a facet of fitness that is not assessable here. Given this, I wondered why it was necessary to consider these distinct modes at all. Relatedly, I wondered, given that despite obvious modes in the raw and log-transformed run-timing data there is considerable overlap in the two distributions associated with the ‘fast’ and ‘slow’ strategies, what the effect of arbitrarily assigning fish to either category based on highest probability (line 201). I wondered if there was a model variation that would allow using assignment probabilities directly rather than a priori assignment, or why the authors did not explore/utilize that. Reviewer #2: General comments. This was an interesting, well executed study and a well-written manuscript. Overall, I found the results convincing and most of the conclusions appeared to be reasonably well defended. I have three broadly general concerns and a number of mostly minor questions and suggestions (see specific comments below). My first concern regards why the authors chose to ignore the extensive additional PIT-tag detection data that were collected for the studied steelhead upstream from McNary Dam? Most readers familiar with the Columbia River basin will recognize that these additional data were available and could have provided considerably more information about the survival questions addressed in the study. My second concern is that the authors have identified a daily-scale survival benefit from cool and cold water refuges, but they have provided little to no commentary about the need to protect or restore these habitats in light of projected regional climate warming. Ensuring the persistence of such habitats is central to ongoing management efforts in the basin. Third, I think the manuscript would be more effective and potentially reach a broader audience if some effort was made to broaden the geographical scope of the messaging. Steelhead are widely distributed and many populations are vulnerable to warming river conditions, especially in the southern portion of the species’ range. I appreciate the opportunity to review this work and to see how the authors have built upon some of the early studies on this subject by our research lab. Sincerely, Matthew Keefer, University of Idaho Specific comments. 1. Title. The current title captures the behavior element of the study but neither the reach survival nor instantaneous mortality aspects. 2. Animal Research. Although the study authors did not handle any fish in this study, approval was presumably required for the dozens of PIT-tagging studies that made this analysis possible. Please also see next comment. 3. Data Availability. The PIT-tag data used in this study were available only due to years of effort by many state, federal, and tribal agencies. The PTAGIS data-use-policy states:“Data users should contact data contributors to gain context and to ensure that their intended use of the data is appropriate.” It is not clear to me in the disclosures that the authors took this step, though perhaps there is a special arrangement between NOAA-Fisheries and the juvenile steelhead tagging groups? Regardless, I think the author should – at a minimum - include a nod to the participating agencies in the Acknowledgments section and give some lip service to the appropriateness of included data. Line 25. ‘tag data = ‘tag detection data’ Line 27. ‘migrate’ ‘delay’ ‘take’ - should these verbs be past tense since they reflect post-analysis data? Line 33. I think it would be appropriate to clarify here that there were five aggregated or multi-stock index populations, rather than just “different populations”. Line 39. “This suggests that this” is a very ambiguous phrase. Line 40. My research group and others have advocated for using the term “thermal refuges” rather than “thermal refugia”. The latter term is generally used in reference to much larger geographic scales than the small tributary confluences described in the manuscript. Line 49. Another case where an ambiguous “This” begins a sentence. Line 51. As noted in general comments, this idea about protecting habitats does not really reemerge in the Discussion section. Line 69. Consider rephrasing. “Basins” do not have migrations. Line 73. Consider adding “U.S.” before Endangered Species Act, since the Columbia River basin includes rivers in Canada. Line 100. Should “frequency” be replaced with a term like “individual probability” or “likelihood”? Line 114. Perhaps ‘mid-Columbia River (hereafter mid-Columbia)’ Line 126. Insert “many” before “inland”? There are several summer-run steelhead populations East of the Cascade Crest that do not pass through this reach. Line 129. Although a zip file with environmental data was provided, the manuscript itself does not very clearly show this interannual variability. Line 132. It was not clear to me how the presented data could be used by dam managers to mitigate mortality? Line 133. The authors might want to include some hypotheses in this paragraph. Doing so would help structure and organize the rest of the manuscript. Line 137. The term “known-origin” applies to both hatchery and wild fish. Line 141. The term “kelts” should probably be changed to “repeat spawners” because kelts really just refers to downstream-migrating adults. Line 152. Insert “adult” before “migration timing”. Line 155. It is not clear to me why the John Day and Umatilla populations are singled out here? Several other summer-run steelhead populations originate downstream from McNary Dam but east of the Cascade Crest, including Deschutes, Wind and Klickitat River, Fifteenmile Creek, and Rock Creek populations. Figure 2 caption. I recommend defining the reach endpoints here, and clarifying that times were for pit-tagged adult steelhead. In addition, I think the authors refer to the study reach as mid-Columbia, not lower Columbia, elsewhere. Line 191. Some readers may question why there are~32,000 fish here but ~43,000 in line 143. Presumably, the ~11,000-fish difference mostly reflects mortality given the high detection efficiency at McNary Dam? Lines 207,212 .’is’ = ‘was’? Past tense for completed work. Line 233. “Season” is vague in this context. Spring – fall? Line 235. Perhaps this expectation about variable effects could be restated as a hypothesis in the introduction. Alternately, please provide some rationale for why this was expected. Line 244. Keefer et al. (2008, Ecol App) and Tattam & Ruzycki (2020, TAFS) also highlighted juvenile barging effects on adult steelhead. See full citations below. Lines 266, 267. ‘are’ = ‘were’? Also consider changing “as adults” to “in adults”. Line 279. Rephrase. No fish were released from Bonneville Dam, only detected there. Line 297. The statement about harvest is somewhat unclear. Does post-release mortality mean fish that were released from recreational fisheries? How were the Jording harvest data estimated and/or vetted? Worth describing because there is considerable agency disagreement about steelhead harvest rates in the study reach. Line 312. Was migration resumption based solely on Fish detection at McNary Dam? Line 323. “simulate”= “simulated”. See previous verb tense comments. Line 341. I recommend that the authors use “daily mortality rate” rather than “mortality rate” in most cases. It is important to establish and maintain that this is a daily estimate to avoid potential confusion with reach survival language. Line 366. Consider adding “by index population” to the bold text portion of the caption. Line 381. Consider adding “d” or “days” after 236. Lines 402, 450. “are”= “were”. Line 403. “This combination” is somewhat ambiguous because no combination has been mentioned. Line 434. “delay” = “delayed”. I suggest carefully checking the manuscript for appropriate verb tense usage. Line 488. “Snake River models” = “models for Snake River index populations”? Line 495. It might be a good idea to capture this proportional changes idea in the Abstract. Line 510. “This aligns” - somewhat ambiguous this and questionable verb tense. Lines 517,521. Insert “daily” before “mortality rates”, as suggested previously. Line 531. “this period” is somewhat vague given long separation from line 525. Line 535. Are these r values for pairwise correlations? Line 548. Typo – delete 2nd ‘migrants’. Line 579. Consider rephrasing “stressful dam interactions” Line 589. This is one of the statements that makes me question why other PIT detections (i.e., at upstream dams and tributaries) were not considered in the analysis. See general comments. Line 603. “Stream”= “River” “is”= “was”? Line 606. Should the term “annual” be inserted before “reach survival”? Line 608. Should a term like “instantaneous” be inserted before “impacts”? Line 627. I think it is important that the authors clarify somewhere in the manuscript that the Zone 6 harvest estimates are for main stem Columbia River fisheries only, these estimates do not include harvest inside most thermal refuge areas, to the best of my knowledge. Line 643. “Chinook” = “Chinook salmon” and the scientific name should be added here. Line 657. Add “River” after “Salmon” and “Clearwater”. Line 697. This statement is not accurate. Lower reaches of both rivers, but especially the Salmon River, can be very warm in late summer and early fall. Clearwater River water temperatures are also manipulated by coldwater releases from Dworskak Dam. Line 711. Add “River” after “Columbia”. Line 724. It is worth mentioning that the state of Oregon has recently imposed steelhead fishery closures inside thermal refuge sites. Line 739. “Stock-specific” lines 744. Typo: ‘taging’. Reference #32 would be very appropriate here. Line 750. Keefer & Caudill (2016) documented steelhead use of thermal refuges in the reach between Ice Harbor and Lower Granite dams. Line 1005. Seems like the word steelhead should appear in this and other captions. I also suggest that the word “Dam” should follow Bonneville and McNary in almost every use. Lines 1014,1022. Some variables need to be defined in the captions. Figure 1. In the legend, migration-blocking should be hyphenated. Figure 5. I question why the temperature scale starts at 18°C, since some steelhead migrating in June, September, and October almost certainly encountered cooler temperatures? Note that figure 6 scale starts at 17° C. Figure 7. It is not clear to me why the harvest rates were only applied to two index populations? Figure 8. Panel C shows an interesting pattern. Is it possible that the upswing in mortality rates reflect the timing of fishery effort? Figure 9. There is a lot of information presented here. Perhaps too much to interpret in a single figure? Supplementary figures. I found these interesting and useful. Some potentially useful references to consider: Hess, M. A., and coauthors. 2016. Migrating adult steelhead utilize a thermal refuge during summer periods with high water temperatures. ICES Journal of Marine Science 73(10):2616-2624. Keefer, M. L., and C. C. Caudill. 2016. Estimating thermal exposure of adult summer steelhead and fall Chinook salmon migrating in a warm impounded river. Ecology of Freshwater Fish 25:599-611. Keefer, M. L., C. C. Caudill, C. A. Peery, and S. R. Lee. 2008. Transporting juvenile salmonids around dams impairs adult migration. Ecological Applications 18(8):1888-1900. Tattam, I. A., and J. R. Ruzycki. 2020. Smolt transportation influences straying of wild and hatchery Snake River steelhead into the John Day River. Transactions of the American Fisheries Society 149:284-297. ********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: Yes: Matthew Keefer [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. 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| Revision 1 |
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Environmentally triggered shifts in steelhead migration behavior and consequences for survival in the mid-Columbia River PONE-D-20-33797R1 Dear Dr. Siegel, 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. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Madison Powell, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): All edits have been addressed. Reviewers' comments: |
| Formally Accepted |
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PONE-D-20-33797R1 Environmentally triggered shifts in steelhead migration behavior and consequences for survival in the mid-Columbia River Dear Dr. Siegel: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Madison Powell Academic Editor PLOS ONE |
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