Does global change increase the risk of maladaptation of Atlantic salmon migration through joint modifications of river temperature and discharge?

In freshwater ecosystems, water temperature and discharge are two intrinsically associated triggers of key events in the life cycle of aquatic organisms such as the migration of diadromous fishes. However, global changes have already profoundly altered the thermal and hydrological regimes of rivers, affecting the timing of fish migration as well as the environmental conditions under which it occurs. In this study, we focused on Atlantic salmon (Salmo salar), an iconic diadromous species whose individuals migrate between marine nursery areas and continental spawning grounds. An innovative multivariate method was developed to analyse long-term datasets of daily water temperature, discharge and both salmon juvenile downstream and adult upstream migrations in three French rivers (the Bresle, Oir and Nivelle rivers). While all three rivers have gradually warmed over the last 35 years, changes in discharge have been very heterogeneous. Juveniles more frequently used warmer temperatures to migrate. Adults migrating a few weeks before spawning more frequently used warm temperatures associated with high discharges. This has already led to modifications in preferential niches of both life stages and suggests a potential mismatch between these populations' ecological preference and changes in their local environment due to global change.

Global change does not include anything that is not global. These other are regional or local! Lines 64-73: migration timing is a heritable trait, mediated by biotic (internal state) and abiotic (env) factors. Local adaption in migration timing should be clearly stated here (since it is these local adaptations that are subject to mismatch due to climate change). Again, the historic conditions in the case study watersheds will dictate to some extent the relevance of the analyses.
Lines 84-why not use the widely accepted terms functional and realized niche? Lines 312-317; "In both cases, the smaller length and poorer physical condition of smolts reaching the sea could impair their ability to swim and escape predators, therefore impacting their survival rate [73] and the resilience of smolts to inhospitable marine conditions [74]. Moreover, global changes could lead to a growing mismatch between downstream migration triggers and suitable marine environmental conditions, with potential implications for adult return rates [75] and individual fitness [76,77]." Is there any evidence compare the historic conditions of smolt size and status, and migration timing mismatch, to the present, highly-modified and small populations? That is, smolt size and timing of these new, small populations might differ substantially from historic populations, that have evolved over thousands of years.
Lines 318-"Diversity of spawning migration strategies and evolutionary potential" : Again, a discussion of the diversity of the historic, endemic populations is warranted here. How much "shifting baselines" have you experienced. Are populations of 100 spawners even viable? How can the study help recommend restoration of truly resilient populations of 1000 or more spawners in there watersheds?
Lines 349-Conclusions: Do you consider the 100 spawners (down from 300) returning to the Nivelle River as NOT ALARMING? You should be less timid in drawing inferences from your study in terms of management. I would consider all of these populations to be exhibiting rather alarming trends.

Do you have any concerns about statistical analyses in this paper? If so, please specify them explicitly in your report. No
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Comments to the Author This clear and well written article uses a previously developed and deployed methodology (Choc) to examine the effects of systematic environmental variation (river temperature and discharge) due to primarily anthropogenic impacts upon the migration patterns of smolt and adult Atlantic salmon. The Choc method, in analyzing patterns based on how changes in the environment are affecting individual animal's environmental niches and the consequent impact of the changes upon population parameters, provides a predictor of population trends that is rooted in ecological (niche) theory. This offers a more satisfying and mechanistic approach to understanding the species' population dynamics compared to the more frequently used correlative approaches. Most of my comments are editorial in nature.
Regarding the title, It seems to me it is not the migration that is in jeopardy, but individual survival during the course of migration and it is survival probabilities that the authors have investigated. I suggest slightly changing the title to capture this, perhaps "Can global change jeopardize Atlantic salmon survival during migrations through joint modifications of river temperature and discharge?" l. 25 add "fish" before "migration" l. 33 add "a" before "few" l. 35 strike the first "then" then add "both life stages" before "preferential". Does that capture what the authors are trying to state? Also, add "these" before "population's". l. 36 change to "… changes in their local environments due to global change." l. 54 change "associations" to "combinations" and "subsequently" to "consequently"? Associations works for the rest of the MS l. 56 add "The" before "Atlantic salmon" l. 60 add "typically" before "1-4 years" l. 62 change "is" to "are" l. 65 add "minimum" before "temperatures" l. 70 change "The" to "This" l. 82 change "population's" to "population" l. 83 change "their" to "the species' " l. 88 change "this affinity of the species to the available" to "selected" l. 101 change to "niches among several rivers. Here it is applied……" l. 106 change "use" to "used" l. 145 Were the counting facilities enumerating all fish coming up the river? Or did they only cover part of the river and hence generating a partial count which may not scale among years predictably to the total population size? l. 153 How did you factor this variable stocking effort into your analysis and among-river comparisons? The numbers are small and perhaps were not expected to appreciably affect either smolt output or adult returns? Please explain. l. 161 change "salmons" to "salmon" l. 193 to read " there is a mix of fish that have spent one versus several winters at sea…." l. 213 change "salmons" to "salmon" l. 229 add "relatively" before "stable". l. 230 So the Oir River that had no stocking showed a significant increase in smolt production? What is your interpretation of this? l. 236 change "expect" to "except for" l. 284 change "original" to "unique" l. 290 Can you make this general statement of "profound effects" in the context of the work that you present? You have shown a slow increasing temperature trend and no general patterns for discharge. Are these profound changes? l. 299 change "between" to "among" l. 300 change "trophic availability" to "feeding conditions" l. 303 change to read "drive the motivation to migrate; for example Teichert et al…" l. 305 to read "migration and a prolongation of the migration period due to climate change…." l. 308 to read "A longer spring migration season such as that of the Bresle River….." l. 314 add "potentially" before "inhospitable" l. 322 change "salmons" to "salmon" l. 323 strike "at the moment" l. 327 add "the" before "spawning" l. 328 -348 I do not follow the logic of the statement that the evolutionary potential depends large on the duration of the migration season. Surely it depends on the genetics of the population? This needs to be better explained and defended. The argument surrounding the better capability of a population to adapt if the population has a longer migration period works depending on the definition that is being used for a salmon "population". If particular tributaries of the system have animals that migrate at different genetically determined times, and conditions deteriorate in the river such that particular runs that occurred at times that are now unfavorable disappear and those occurring in more favorable times surge, is this actually a "population" adaptation as opposed to a replacement of populations? Perhaps the salmon populations in your river are not structured into distinct population segments? l. 336 change "river" to "rivers" Conclusion and l. 358 in particular. According to Table 1, the Nivelle River is by far the least disturbed system in which you worked, having 58.6% of its watershed in "natural areas" compared to 3.5% and 19.1% for the Oir and Bresle Rivers, respectively, yet the Nivelle has the highest annual temperatures which seems curious to me. Have these percentages changed over the duration of the study period, or has there been a loss of natural habitat during this time? Since stocking of hatchery fish and habitat restoration are probably the two major activities currently employed for Atlantic salmon restoration, can your methodology and results inform either of these practices? Table 1, last entry on "Spawners migrating upstream", did the years included in the total number for each river system vary among systems?  Your manuscript has now been peer reviewed and the reviews have been assessed by an Associate Editor. The reviewers' comments (not including confidential comments to the Editor) and the comments from the Associate Editor are included at the end of this email for your reference. As you will see, the reviewers and the Editors have raised some concerns with your manuscript and we would like to invite you to revise your manuscript to address them.
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Best wishes, Dr Daniel Costa mailto: proceedingsb@royalsociety.org Associate Editor Comments to Author: Both reviewers consider this manuscript favourably. Both have provided useful comments for improving the manuscript that should be considered by the authors and incorporated into a revised manuscript.
Reviewer(s)' Comments to Author: Referee: 1 Comments to the Author(s) General comments: This is a good study describing a method to assess the effects of anthropogenic change on aquatic organisms (Atlantic salmon). It should be of broad general interest to conservation-minded biologists.
In order to fully convey the relevance of the analyses undertaken, the authors need to be more explicit about the case studies in both the Methods and the Discussion: A brief history and summary of population trends must be provided for each study river. Of particular relevance is 1) what were the historic population sizes and distributions within each watershed, and 2) a discussion of how the newly introduced populations (whether from other rivers or from hatcheries) likey differ from the original endemic populations in locally-adapted traits, particularly run timing and age at maturity.
Such small populations as found in the present study (100 adult spawners, probably below minimum viable population size) are likely far below historic levels when locally-adapted subpopulations were probably found throughout each watershed. Each of these subpopulations would have had unique migration adaptations (some of which would have led to a "portfolio effect" a la Schindler et al. 2010, against climate change).
So, while the Choc method may be suitable for understanding trends for the current populations, the authors should be explicit that historic populations would likely have been far more diverse and resilient to climate change (or other anthropogenic factors).
A few specific comments: Line 33 "a" few weeks Lines 41-43: add "in addition to photoperiod" and appropriate citations Lines 48-49: not "emergence" -"evolution" is the correct word Lines 50-52: "Global change (including climate change and other anthropogenic pressures such as water withdrawal for human consumption, irrigation, industry and hydropower production)" Global change does not include anything that is not global. These other are regional or local! Lines 64-73: migration timing is a heritable trait, mediated by biotic (internal state) and abiotic (env) factors. Local adaption in migration timing should be clearly stated here (since it is these local adaptations that are subject to mismatch due to climate change). Again, the historic conditions in the case study watersheds will dictate to some extent the relevance of the analyses.
Lines 84-why not use the widely accepted terms functional and realized niche? Lines 312-317; "In both cases, the smaller length and poorer physical condition of smolts reaching the sea could impair their ability to swim and escape predators, therefore impacting their survival rate [73] and the resilience of smolts to inhospitable marine conditions [74]. Moreover, global changes could lead to a growing mismatch between downstream migration triggers and suitable marine environmental conditions, with potential implications for adult return rates [75] and individual fitness [76,77]." Is there any evidence compare the historic conditions of smolt size and status, and migration timing mismatch, to the present, highly-modified and small populations? That is, smolt size and timing of these new, small populations might differ substantially from historic populations, that have evolved over thousands of years.
Lines 318-"Diversity of spawning migration strategies and evolutionary potential" : Again, a discussion of the diversity of the historic, endemic populations is warranted here. How much "shifting baselines" have you experienced. Are populations of 100 spawners even viable? How can the study help recommend restoration of truly resilient populations of 1000 or more spawners in there watersheds?
Lines 349-Conclusions: Do you consider the 100 spawners (down from 300) returning to the Nivelle River as NOT ALARMING? You should be less timid in drawing inferences from your study in terms of management. I would consider all of these populations to be exhibiting rather alarming trends.
Referee: 2 Comments to the Author(s) This clear and well written article uses a previously developed and deployed methodology (Choc) to examine the effects of systematic environmental variation (river temperature and discharge) due to primarily anthropogenic impacts upon the migration patterns of smolt and adult Atlantic salmon. The Choc method, in analyzing patterns based on how changes in the environment are affecting individual animal's environmental niches and the consequent impact of the changes upon population parameters, provides a predictor of population trends that is rooted in ecological (niche) theory. This offers a more satisfying and mechanistic approach to understanding the species' population dynamics compared to the more frequently used correlative approaches. Most of my comments are editorial in nature.
Regarding the title, It seems to me it is not the migration that is in jeopardy, but individual survival during the course of migration and it is survival probabilities that the authors have investigated. I suggest slightly changing the title to capture this, perhaps "Can global change jeopardize Atlantic salmon survival during migrations through joint modifications of river temperature and discharge?" l. 25 add "fish" before "migration" l. 33 add "a" before "few" l. 35 strike the first "then" then add "both life stages" before "preferential". Does that capture what the authors are trying to state? Also, add "these" before "population's". l. 36 change to "… changes in their local environments due to global change." l. 54 change "associations" to "combinations" and "subsequently" to "consequently"? Associations works for the rest of the MS l. 56 add "The" before "Atlantic salmon" l. 60 add "typically" before "1-4 years" l. 62 change "is" to "are" l. 65 add "minimum" before "temperatures" l. 70 change "The" to "This" l. 82 change "population's" to "population" l. 83 change "their" to "the species' " l. 88 change "this affinity of the species to the available" to "selected" l. 101 change to "niches among several rivers. Here it is applied……" l. 106 change "use" to "used" l. 145 Were the counting facilities enumerating all fish coming up the river? Or did they only cover part of the river and hence generating a partial count which may not scale among years predictably to the total population size? l. 153 How did you factor this variable stocking effort into your analysis and among-river comparisons? The numbers are small and perhaps were not expected to appreciably affect either smolt output or adult returns? Please explain. l. 161 change "salmons" to "salmon" l. 193 to read " there is a mix of fish that have spent one versus several winters at sea…." l. 213 change "salmons" to "salmon" l. 229 add "relatively" before "stable". l. 230 So the Oir River that had no stocking showed a significant increase in smolt production? What is your interpretation of this? l. 236 change "expect" to "except for" l. 284 change "original" to "unique" l. 290 Can you make this general statement of "profound effects" in the context of the work that you present? You have shown a slow increasing temperature trend and no general patterns for discharge. Are these profound changes? l. 299 change "between" to "among" l. 300 change "trophic availability" to "feeding conditions" l. 303 change to read "drive the motivation to migrate; for example Teichert et al…" l. 305 to read "migration and a prolongation of the migration period due to climate change…." l. 308 to read "A longer spring migration season such as that of the Bresle River….." l. 314 add "potentially" before "inhospitable" l. 322 change "salmons" to "salmon" l. 323 strike "at the moment" l. 327 add "the" before "spawning" l. 328 -348 I do not follow the logic of the statement that the evolutionary potential depends large on the duration of the migration season. Surely it depends on the genetics of the population? This needs to be better explained and defended. The argument surrounding the better capability of a population to adapt if the population has a longer migration period works depending on the definition that is being used for a salmon "population". If particular tributaries of the system have animals that migrate at different genetically determined times, and conditions deteriorate in the river such that particular runs that occurred at times that are now unfavorable disappear and those occurring in more favorable times surge, is this actually a "population" adaptation as opposed to a replacement of populations? Perhaps the salmon populations in your river are not structured into distinct population segments? l. 336 change "river" to "rivers" Conclusion and l. 358 in particular. According to Table 1, the Nivelle River is by far the least disturbed system in which you worked, having 58.6% of its watershed in "natural areas" compared to 3.5% and 19.1% for the Oir and Bresle Rivers, respectively, yet the Nivelle has the highest annual temperatures which seems curious to me. Have these percentages changed over the duration of the study period, or has there been a loss of natural habitat during this time? Since stocking of hatchery fish and habitat restoration are probably the two major activities currently employed for Atlantic salmon restoration, can your methodology and results inform either of these practices? Table 1, last entry on "Spawners migrating upstream", did the years included in the total number for each river system vary among systems? Decision letter (RSPB-2021-1882.R1)

12-Nov-2021
Dear Dr Arevalo I am pleased to inform you that your Review manuscript RSPB-2021-1882.R1 entitled "Does global change increase the risk of maladaptation of Atlantic salmon migration through joint modifications of river temperature and discharge?" has been accepted for publication in Proceedings B.
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Sincerely, Dr Daniel Costa Editor, Proceedings B mailto:proceedingsb@royalsociety.org Associate Editor Comments to Author: The authors appear to have addressed the two reviewers comments in their revision. I have suggested a small number of editorial clarification which will assist non-experts reading this manuscript in understanding the study and its results easily. If the authors could please make the suggested amendments it would be appreciated.

17-Nov-2021
Dear Dr Arevalo I am pleased to inform you that your manuscript entitled "Does global change increase the risk of maladaptation of Atlantic salmon migration through joint modifications of river temperature and discharge?" has been accepted for publication in Proceedings B.
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Dear Associate Editor,
We would like to thank the reviewers for their in-depth reading of our manuscript and their useful comments. Please find below the point-by-point answers (in red) to questions of the reviewers and the changes made to our article entitled "Does global change increase the risk of maladaptation of Atlantic salmon migration through joint modifications of river temperature and discharge?". We attached the revised manuscript with the changes highlighted. As the length of the manuscript is limited, we modified the bibliographic list to be able to respond to the reviewers' suggestions as well as possible, with a balanced number of references. Therefore, we addressed the major issue of the manuscript (the lack of a population history) by adding a section in Supplementary Material as this information, although useful, does not change the perspective of our results.
Referee: 1 Comments to the Author(s) General comments: This is a good study describing a method to assess the effects of anthropogenic change on aquatic organisms (Atlantic salmon). It should be of broad general interest to conservation-minded biologists.
In order to fully convey the relevance of the analyses undertaken, the authors need to be more explicit about the case studies in both the Methods and the Discussion: A brief history and summary of population trends must be provided for each study river. Of particular relevance is 1) what were the historic population sizes and distributions within each watershed, and 2) a discussion of how the newly introduced populations (whether from other rivers or from hatcheries) likey differ from the original endemic populations in locally-adapted traits, particularly run timing and age at maturity. Authors: The monitoring of these populations began in the 1980s with the construction of fish passes and counting stations. Prior to this, it is quite difficult to obtain data on the size of the populations, and consequently very few precise estimations of historic population sizes or distributions are available. Furthermore, stocking operations were implemented before the start of these monitoring programmes, so we cannot currently measure the impact of these operations on the population dynamics. However, stocking operations were carried out using eggs from Scottish and Polish spawners and it is now known that the mortality rates for stocking at this stage with foreign strains are very high. We can therefore assume that the impact of stocking on these populations was limited. Insofar as this information is necessary for the understanding of these three populations but does not influence the results, we added a new part containing all relevant historical information existing in the literature on the history of these populations and the management measures that have been applied in Supplementary Material, Appendix A.
Such small populations as found in the present study (100 adult spawners, probably below minimum viable population size) are likely far below historic levels when locally-adapted sub-populations were probably found throughout each watershed. Each of these subpopulations would have had unique migration adaptations (some of which would have led to a "portfolio effect" a la Schindler et al. 2010, against climate change). So, while the Choc method may be suitable for understanding trends for the current populations, the authors should be explicit that historic populations would likely have been far more diverse and resilient to climate change (or other anthropogenic factors). Authors: The earliest articles mentioning these populations refer to smaller population sizes than those observed today (for example, 10-30 spawners / year on the Nivelle in the 1970s; Dumas & Prouzet 2003;Baglinière 1990). These extremely low population sizes were due to a deterioration of the habitat and especially to the construction of impassable dams in the early 20 th century. Despite the small size of these populations, they were maintained and the number of spawners increased significantly when measures to improve habitat quality (reduction of pollution) were taken or when fish ladders were built to allow access to the most productive areas. We added these ideas to better describe the situation of each of these populations in the part dealing with the historic of the populations in Appendix A. In addition, climate change and anthropogenic pressures most likely induced a selection of certain strategies and life history traits but unfortunately our data do not allow us to infer this kind of mechanism.
A few specific comments: Line 33 "a" few weeks Authors: As proposed, we modified the sentence (line 33).
Lines 41-43: add "in addition to photoperiod" and appropriate citations Authors: We revised the sentence to include photoperiod as a key environmental trigger for migration, with appropriate reference in the context of Atlantic salmon (Teichert et al. 2020;lines 42-43). We also underlined the significance of the photoperiod in the introduction (line 66) as well as in the discussion (lines 302).
Lines 50-52: "Global change (including climate change and other anthropogenic pressures such as water withdrawal for human consumption, irrigation, industry and hydropower production)". Global change does not include anything that is not global. These other are regional or local! Authors: We restructured the sentence to emphasise the interaction between global climate change and local anthropogenic pressures and the effects of this interaction on aquatic organisms (lines 51-53).
Lines 64-73: migration timing is a heritable trait, mediated by biotic (internal state) and abiotic (env) factors. Local adaption in migration timing should be clearly stated here (since it is these local adaptations that are subject to mismatch due to climate change). Again, the historic conditions in the case study watersheds will dictate to some extent the relevance of the analyses. Authors: Global changes alter environmental conditions and the occurrence of favourable water temperature and discharge simultaneously. When confronted with these new conditions, species could change the timing of their migration to track the same "favourable" conditions (phenological shift), or try to adapt to the new conditions (local adaptation). We specified this explanation in lines 54-57. Regarding the background of these three populations, this is a point that was raised as a major comment and we provided the information to better understand the challenges faced by these populations (Supplementary Material, Appendix A).
Lines 84-why not use the widely accepted terms functional and realized niche? Authors: The concept of ecological niches is commonly used in ecology. Hutchinson recognizes a species' fundamental niche, a multidimensional 'cloud' of favourable conditions determined by all environmental (abiotic and biotic) variables where the species can reproduce and survive. The functional niche refers rather to the functional role of a species or its position in a food web. These definitions do not reflect what we were analysing (i.e., the trends within all the environmental conditions offered by the environment). We thought it wise to introduce new terms, "the available niche" and "the preferential niche", as we had not found a satisfactory equivalent. Lines 312-317; "In both cases, the smaller length and poorer physical condition of smolts reaching the sea could impair their ability to swim and escape predators, therefore impacting their survival rate [73] and the resilience of smolts to inhospitable marine conditions [74]. Moreover, global changes could lead to a growing mismatch between downstream migration triggers and suitable marine environmental conditions, with potential implications for adult return rates [75] and individual fitness [76,77]." Is there any evidence compare the historic conditions of smolt size and status, and migration timing mismatch, to the present, highly-modified and small populations? That is, smolt size and timing of these new, small populations might differ substantially from historic populations, that have evolved over thousands of years. Authors: In the present article, we focused on long-term temporal trends in environmental conditions, examining how conditions historically known as "favourable" for salmon migrations have changes over time and whether they were still available. In response to these environmental changes, we showed in Supplementary material ( Figure S2) that the passage date of 95% of smolts on the Bresle River occurs significantly later today than in 1985 and that the passage dates of 5% and 95% of smolts on the Oir River tend to occur earlier in the season. These elements allowed us to discuss a possible mismatch between the migration date of smolts and the favourable conditions at sea (lines 306-314).
To support our comments about smolts in "bad conditions" and to follow the recommendations of the reviewer, we added in Supplementary Material the trends in annual averages fork lengths of smolts caught on the Bresle and Oir rivers and we performed Mann-Kendall trend tests on these records. The Mann-Kendall statistics are available on Figure S3. The length of smolts has tended to decrease on the Bresle River (tau = -0.23; p-value = 0.07) and has decreased significantly on the Oir River (tau = -0.27; p-value = 0.03) since 1985. We improved the references to figures and to Mann-Kendall statistics in the text to make it clearer, from line 306 to line 313.
Lines 318-"Diversity of spawning migration strategies and evolutionary potential" : Again, a discussion of the diversity of the historic, endemic populations is warranted here. How much "shifting baselines" have you experienced. Are populations of 100 spawners even viable? How can the study help recommend restoration of truly resilient populations of 1000 or more spawners in there watersheds? Authors: Migration strategies were different between these three populations. The spawning migration period was defined between June and November on the Bresle River, between October and December on the Oir River and between April and November on the Nivelle River ( Figure 2D and Figure S2). Difference in spawning migration periods among rivers was related to the age structure of the population: on the Oir river, most spawners spent one winter (1SW) at sea (which preferentially migrated in fall), while there was a mix of one winter and several winters at sea (MSW; which migrated preferentially in spring) on the two other rivers (lines 186-192). Consequently, the diversity of migration strategies was higher on the Nivelle and Bresle rivers. However, salmon scale readings are ongoing and the age of salmon caught in traps is not currently available, which prevented us from performing the Choc analysis by year class (lines 319-324). There is no known critical threshold for Atlantic salmon population below which the number of individuals is too low and the population threatened. For example, the number of spawners on the Nivelle River has significantly reduced since the 2000s (visible in Figure 2 but also observed in Prévost & Lange 2019). However, the number of juveniles (number of parrs observed in fall) remained stable over time. This might reflect that egg deposition is saturating the currently available habitat. The objective is therefore not to have more than 1000 spawners colonising the watershed but to have a sustainable population. However, if the number of spawners continues to decline, egg deposition by females may no longer saturate the habitat, at which point a decline in parr numbers in fall may be observed. A decline in the number of spawners could reduce the diversity of life history traits, which could reduce the resilience of the population during catastrophic events. We added some elements in this sense in the discussion (lines 346-348).
Lines 349-Conclusions: Do you consider the 100 spawners (down from 300) returning to the Nivelle River as NOT ALARMING? You should be less timid in drawing inferences from your study in terms of management. I would consider all of these populations to be exhibiting rather alarming trends. Authors: The size of these populations has been constantly decreasing since the beginning of the monitoring, so it is important to identify the pressures on these populations. Our method revealed mismatches between the preferential conditions and those actually used by smolts on the Bresle River and by spawners on the Oir River. On other stages and/or rivers, environmental changes during migratory events do not seem to explain the decline in these populations. However, there were other pressures that significantly affected the size of these populations (overexploitation, conditions for growth in freshwater or at sea). Consequently, we reformulated the conclusion to emphasize more on the need for management actions to make these populations sustainable (lines 365-366).
Referee: 2 Comments to the Author(s) This clear and well written article uses a previously developed and deployed methodology (Choc) to examine the effects of systematic environmental variation (river temperature and discharge) due to primarily anthropogenic impacts upon the migration patterns of smolt and adult Atlantic salmon. The Choc method, in analyzing patterns based on how changes in the environment are affecting individual animal's environmental niches and the consequent impact of the changes upon population parameters, provides a predictor of population trends that is rooted in ecological (niche) theory. This offers a more satisfying and mechanistic approach to understanding the species' population dynamics compared to the more frequently used correlative approaches. Most of my comments are editorial in nature.
Regarding the title, It seems to me it is not the migration that is in jeopardy, but individual survival during the course of migration and it is survival probabilities that the authors have investigated. I suggest slightly changing the title to capture this, perhaps "Can global change jeopardize Atlantic salmon survival during migrations through joint modifications of river temperature and discharge?" Authors: We do not focus directly on fish survival in the Choc analyses but it is true that the potential mismatches revealed by our method can have direct or indirect consequences on the growth, survival and fitness of individuals and their offspring. In response to this comment, we retitled the manuscript as "Does global change increase the risk of maladaptation of Atlantic salmon migration through joint modifications of river temperature and discharge?", maladaptation including threats to the survival and growth of the fish and their offspring. l. 25 add "fish" before "migration" Authors: As proposed, we mentioned "fish migration" (line 25).
l. 33 add "a" before "few" temperatures throughout the year, in all seasons, observed on the Nivelle River. Moreover, in the predictive models of the IPCC (2014) or also in Dayon et al. (2018), the Nivelle River was included in the Mediterranean region. The percentages of natural areas might have slightly change over time (we don't have precise figures on this aspect), but nothing drastic and clearly not the cause of the temperature differences.
Since stocking of hatchery fish and habitat restoration are probably the two major activities currently employed for Atlantic salmon restoration, can your methodology and results inform either of these practices? Authors: Our method show whether favourable environmental conditions still match with a key life cycle event. If the environmental conditions change, this method reveals whether the species appears to have been able to adapt to the new conditions. Applied to anthropized rivers, this could reveal a water deficit at a critical period and the management measures that could be taken would be limited water abstraction or water releases (lines 363). In the dataset, the origin of fishes (natural or stocking) was not available; it would have been interested to make separate analysis by origin to explore the influence of restocking though the number of individuals would have probably been too limited. Table 1, last entry on "Spawners migrating upstream", did the years included in the total number for each river system vary among systems? Authors: The study period reported in the table (1985-2019, 1987-2019 and 1986-2019 for the Bresle, Oir and Nivelle rivers respectively) covered all data, i.e., water temperature, discharge, smolt and spawner counts. For each river, if a given year was excluded for a given variable (e.g. if data were missing more than 3 consecutive weeks for water temperature or discharge), this year was also excluded for the other variable (e.g. salmon passages). We clarified this at lines 154.  Are the values presented catches? Or are they the counts in the various counting systems used on the different rivers? I would rephrase the description of the axes on both Figures to read that the X and Y axes plot your standardized scores, and the italicized secondary axes plot true values of the variables. The term "natural" is confusing. Authors: For Figure 2, we added "caught in the traps" to the caption to make it clear that this referred to the gross number of salmon (388-389). For the Figure 3-4, the values on the Y and X axes represented the empirical cumulative distribution functions of water temperature and discharge. We added natural values in italics to give ecological significance to the quantiles. For example, in figure 4, in the available niche of the Bresle River, 50% of the time the water temperature was below 14.94°C. Similarly, 50% of the time, the discharge was less than 1.85 m 3 s -1 . We completed the caption accordingly (lines 396-398 and 411-413).