Endangered predators and endangered prey: Seasonal diet of Southern Resident killer whales

M. Bradley Hanson; Candice K. Emmons; Michael J. Ford; Meredith Everett; Kim Parsons; Linda K. Park; Jennifer Hempelmann; Donald M. Van Doornik; Gregory S. Schorr; Jeffrey K. Jacobsen; Mark F. Sears; Maya S. Sears; John G. Sneva; Robin W. Baird; Lynne Barre

doi:10.1371/journal.pone.0247031

Peer Review History

Original SubmissionMay 14, 2020
26 Jun 2020 Decision Letter - David Hyrenbach, Editor PONE-D-20-14399 Endangered predators and endangered prey: Seasonal diet of Southern Resident killer whales PLOS ONE Dear Dr. Hanson, 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. In addition to the comments and suggestions from the two reviewers, I would like you to focus on the following improvements: - Clarify Terminology: Select and use one designation for ‘prey remains’ is needed for clarity. Define seasons Do they refer to calendar seasons or are they tied to the ecology of the whales or of their prey? - Provide more background Information: The Northern Resident stock should be introduced somewhere in the Introduction or in the Methods (first mention is in the caption of Fig 8). Finally, the authors refer to ‘whales’ instead of ‘killer whales’. I would suggest introducing the common name at the beginning of the paper, and using it consistently. Readers unfamiliar with the SRKW and the NRKW could benefit from a brief introduction of their population trends, and the body condition and demography of these two ecotypes. - More effective use of tables: The tables included in the ms are rather large and have many empty cells. I would urge the authors to consider moving tables 1, 2, 3 and 4 to the supplementary materials section, and including more distilled tables (or figures) in the ms. For instance, table 2 could be aggregated by season, rather than by month. Additionally, in Table 2, the “+” sign in some of the cells is confusing, it would be better to provide a range of the individuals contributing to the fecal sample. - More effective use of figures: The introductory map and the insert set the stage. However, the other two maps (Figure 3 and 4) are not very effective because the points are small and overlay each other, and large scale maps are used to capture distributions with outliers. I would suggest using a larger study are map (figure 1), where you define the various geographic zones, and use inserts to identify the geographic locations mentioned in the text. Then, given the detailed depiction os these geographic areas (and their inclusion in the summary tables), I would remove the two other maps. Figure - If you removed figure 3 and 4, you could addition a map showing the range of the two populations and the locations of some of the primary rivers. Alternatively, if you wanted to highlight specific samples that were distinct / unique in the map, I would suggest you limit the mapping of the samples to few numbered and color-coded symbols. Figure 8b – The y axis label should read “Proportion”. Please fix this typo. Please submit your revised manuscript by Aug 10 2020 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: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. 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Competing interests can arise in relationship to an organization or another person. Please follow this link to our website for more details on competing interests: http://journals.plos.org/plosone/s/competing-interests Additional Editor Comments (if provided): [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. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? 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: Comments to the Authors #General comments The authors present the results of dietary analyses conducted for the (endangered) Southern Resident killer whale (SRKW) population in the eastern North Pacific Ocean. Using visual and molecular methods, they identify consumed prey species (salmonids and other fish) from prey remains and fecal samples collected from 2004 through 2007 in various areas and times of the year. The authors also aged and identified stocks of origin of the Chinook salmon prey consumed in order to assess the stocks of particular importance for the recovery of this killer whale population. The manuscript is well structured with the information clear and presented in a straightforward manner. The analyses seem appropriate and the discussion is adequate, and not overly speculative. Overall, this study constitutes a good contribution to the killer whale literature and is of particular relevance and importance for the management and recovery of the SRKWs. I recommend publication of the manuscript after some corrections. There is a need for a thorough check of all numbers throughout the ms (see detailed comments below). I also think that chosing one designation for ‘prey remains’ and sticking to it is needed for clarity. Seasons i.e. fall, winter, spring should be defined (whether they refer to typical calendar seasons or are tied to the whales’ or prey’s ecology). The Northern Residents should be introduced somewhere in the Introduction or in the Methods (first mention is in the caption of Fig 8). I am wondering if reference to Tables and Figures should be added in the Discussion. There is inconsistency with capital letters e.g., Chinook salmon, coho, chum that needs to be fixed throughout the manuscript. Also, too often the authors refer to ‘whales’ instead of ‘killer whales’. This may be confusing for people who may not be familiar with the killer whale literature. Specific comments Abstract L29: What is ‘the Pacific coast’ – I suggest being more specific here; same with ‘coastal waters’ L31 – This would emphasize better the relatively large area investigated in this study L30: Shouldn’t it be ‘fecals’ or ‘feces’ here? L31: Add ‘of 2004-2017’ after May L37: Add ‘salmon’ after ‘Chinook’ L38: Add ‘selectively’ before ‘consume’ L39: What is ‘coastal samples’? L41: Could ‘effective’ be a better word than ‘useful’? Introduction L54-58: There may be missing info on the SRKW – Suggest adding a sentence or two telling about the status of the SRKW population (to highlight how critical – since L77 mentions ‘recovery’) and also emphasize the differences between the three different pods – could set the why it is important/relevant to look into dietary variations at the pod level in this study. L65: Add ‘killer’ before ‘whale’ L67: ‘For characterizing these killer whales’ diet’ L69: Missing ref after ‘Salish Sea’, same for L71. L70: Missing scientific name for coho salmon here L77-80: I would also add to get insights into plasticity in feeding behavior (prey switch) and thus resiliency to declining preferred prey (further useful to model long-term population trends) L81: Replace ‘the whales’ diet’ by ‘the SRKWs’ diet’ L83-84: Suggest rewording to ‘We further extended the analyses to genetically identify the stocks of origin for Chinook salmon prey’. Methods Line 73 (Caption Figure 1): add ‘between October and May from 2004 to 2017’. Line 89: Replace ‘prey capture remains’ by ‘remains from prey capture events’. L90: Add ‘between October and May’ before ‘from 2004 to 2017’ L93: An explanation of what a pod is and why it is relevant to investigate at the pod level would be useful, either here or in the introduction. L93: ‘…, allowing for results to be presented for each pod, separately. L102: replace ‘estimate stock composition of Chinook salmon prey samples’ by ‘determine stock identity of Chinook salmon prey samples’. L103. End the sentence after ‘samples’, and start the new sentence with ‘Specifically, sample genotypes at 13 nuclear microsatellite DNA loci were compared to a coast-wide…’ L112: why pooled? L143: coastal waters of? Results L154: ‘(JdF/SJI): 3 days and northern Georgia Strait (NGS): 3 days)’ L156: move ‘(36 days)’ after ‘California’ L157: More details would be useful here: samples from how many distinct prey capture events? 158? Were the 154 samples collected over the 156 days of killer whale encounters? Same for the 81 fecal samples: from how many encounter days? L160 (Table 1): What is the number after the year in column 1? Not clear. It would be helpful to mention in the table caption what a single prey sample refers to: does it represent a unique predation event? or are different types of remains e.g. when both scales and tissues were collected from a single prey capture event refered to as multiple samples? The total of prey samples comes to 155 whilst L157 indicates 154 samples collected. Needs correction. L169: Adjust the percentage of scale/tissue samples after correction on total number of samples collected. As it stands here, it suggests 155 samples collected (and not 154). L170: Revise accordingly here too. L174 and 178: Add the number of samples collected before ‘scale/tissue samples’. L181: Explain what are the pods somewhere in the Introduction or in the Methods. L182: Again, there is contradiction between total count of prey samples collected in PS here (93) compared to Table 1 (94). L188-190: Check correct numbers here also L203: be consistent with having either ‘Table S3’ or ‘S3 Table’ (see L190) L217-220: This is redundant with content from Figure 5 – There are a lot of Figures in the article. Maybe this one is not necessary, even though the visual representation may be better than having it in text. L258-278: I suggest placing this section before the one on Species composition diet from fecal samples for consistency with the Method section. L259: New contradiction with the number of prey samples collected L262-264: Check correct numbers here, and also what months the authors refer to for the different seasons. Numbers seem to be incorrect. L269: Replace ‘Table 1, Table 2’ by ‘Tables 1, 2’ L281: Table caption does not read well – suggest rewording L292: Add ‘ were’ after 18.1% - Note that the total comes to 18.2% though L335-337: there is no reference to NRKW before that Discussion L346: Replace ‘highlight that this species is a’ with ‘confirm this species as a’ L350: Remove one of the two ‘winter’ L351: Suggest replacing ‘this time of the year’ by ‘winter’ for clarity. L356: add ref for summer L360: be consistent with locations names – use either full names or abbreviations throughout the text L370: wrong as written since ref #8 (Ford and Ellis 2006) is also about SRKWs – Suggest rewording L371: Replace ‘whales’ by ‘killer whales’ L393: Add ‘that’ between ‘feces’ and ‘appeared’ L394: I suggest highlighting better that Halibut was reported as prey, not for any killer whale population in BC but specifically for resident type killer whales (Ford et al. 1998, Ford and Ellis 2006) L398: Remove ‘been’ before ‘previously’ L422: add ‘itself’ after ‘samples’ L434: Remove ‘and’ L435: I suggest rewording to ‘…could be due to biases associated with sampling methods, and behavior of both killer whales and prey species.’ L437-41: heavy sentence. Needs rewording. It may be enough just to say that sampling of prey remains is likely to only give access to (and therefore enable identification of) prey species that are consumed at/near the surface, and are large enough to require tearing into pieces and/or sharing. L450: ‘was primarily’ and ‘comprised of’ L471: I would replace ‘differences’ with ‘variations’ L471-474: Very long heavy sentence – Needs rewording. L481: If Tables (or Figures) are going to be cited in Discussion, then they should be added many other places throughout the Discussion. L499: Even though there appears to be strong selectivity for Chinook salmon, they do eat other salmonids and fish so I suggest down-grading this statement for more accuracy here. Also add ‘two’ after ‘These’ L501-504: Suggest rewording to: ‘Limited diet data are available for northern resident killer whales apart for summer data that indicated this population to be consuming a similar number…’ L504: ref (this study, Tables) after ‘consumed in winter’ L504-506: I don’t understand this. How is that? L516: Add ‘is’ after ‘and’ L517: Reword to ‘for determining its caloric value?’ L520: add ‘from’ before ‘fish that were younger than..’ L521: Reword to: ‘Besides SRKWs generally consuming younger fish of both chinook and chum salmon, the youngest age class…’ L526: Reword to: ‘Geographically, due to most west coast originating Chinook salmon maturing in the waters of..’ L541: Add ‘also’ before ‘increase’ since it has been identified as a goal for the summer already (maybe add a ref fr that) L542-545: this could be shortened since it largely repeats the previous sentence – I suggest ‘However, the increased dietary diversity in the winter months also underscores the importance of other species at particular times and in specific locations.’ L548: Reword to ‘Both K and L pods were documented…’ L562: Is reproduction relevant here? L577: add ‘suggested’ before ‘the best fit’ L578: REPLACE ‘was’ by ‘to be’ L579: ‘…and their chinook salmon prey’ L604: Replace ‘in the whales’ prey’ with ‘in the SRKWs’ prey’ and ‘about the whales’ fall…’ with ‘about these killer whales’ fall…’, and ‘diet’ with ‘diets’ L606: Replace ‘the prey available to the whales’ with ‘the prey available to this critically endangered killer whale population’ L607-608: suggest remove since it is redundant with the following, more complete sentence L609: Suggest replacing ‘fill gaps in the whales’ prey base’ with ‘fill gaps in the SRKWs’ prey base’ L611: Replace ‘whales’ with ‘killer whales’ L612: Replace ‘whales’ with ‘SRKWs’ L613: What are these biological features? L616-618: Suggest rewording to: ‘Although substantial new information has been gained on the diet of the SRKWs in fall, winter and spring, data is still lacking for parts of the year and geographical ranges for some or all pods. L619: Add ‘relatively’ before ‘documented’, Replace ‘the whales’ by ‘the SRKWs’ L628: Replace ‘for whales’’ with ‘for the SRKWs’’ L630: replace with ‘an adverse impact’? L631: Replace ‘the whales’ by ‘the SRKWs’ L632: Replace ‘not necessarily’ by ‘that may not or less be’ L633: ‘these environmental conditions; another..’ L636: ‘detections of the SRKWs’ presence/occurrence near the’ L643: Replace ‘for this whale population’ with ‘for this killer whale population’ Reviewer #2: REVIEWER COMMENTS Data presented in this paper represent a significant contribution to our understanding of SRKW diet and expand the available information for conservation and management decisions. The authors have collected a spatially diverse library of fecal samples and prey remains throughout the SRKW’s range and over a series of years to amass a detailed overview of SRKW diet and provide narrative on the composition of diet and potential implications for conservation. The methodologies are well described with attention to validation and control samples. The findings are informative with respect to the increased diversity in winter diet, differences between coastal and inland prey base, and the authors provide an interesting discussion on conservation implications of the data. The manuscript is well written, well referenced and a pleasure to read. The comments on potential SRKW impacts from NRKW competition is intriguing and worthy of further discussion. Readers unfamiliar with the two populations of this fish-eating ecotype would benefit from knowing that the NRKW have maintained an increasing population trajectory of 2% annually and have a four-fold higher population (Towers 2018). In addition, information on body condition from both populations is available; these data are not discussed in this MS, but are relevant in relation to the interesting finding on inter-population differences in stock diversity, differences in age/size of prey and the implications to the energetic cost vs yield of foraging. Improvement in the quality of the map and addition of the range of the two populations and the locations of some of the primary rivers (Columbia, Fraser, Thompson, Taku, Skeena, Snake, etc) would be beneficial. The authors present interesting information on the relative proportion of wild vs hatchery stocks and the population’s dependence on these stocks in the spring and fall. In the summer months, prey are dominated by Fraser River stocks, a system comprised of stocks with minimal or no hatchery production. The condition of SRKW reputedly improves from their return to the waters of the Salish Sea in the early summer to their relative dispersal in the fall; these data indicate that this foraging period is primarily supported by wild salmon populations. SPECIFIC LINE EDITS/COMMENTS 519 – data on NRKW age of prey from Ford and Ellis 2006 is from prey remains collected in 2003-2005. To better support the observation that NRKW consume older/larger Chinook, authors may consider application of a correction factor for the 15 year lag between the NRKW and SRKW data sets presented Fig 8a and B. 555 – suggest rewording for clarity – confusing statement. 624 – bioaccumulation of PBDEs provide insight into past foraging behaviours (Krahn et al, 2007) and these data represent foraging events that have occurred prior to 2007 (and with bioaccumulation and selective mobilization of lipids and thus contaminants, they may represent foraging events from decades in the past). Suggest modifying to indicate these data support the historic foraging conditions. Figure 8b – y axis label should read “Proportion” ****** 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: No [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. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: PONE-D-20-14399_review.pdf.docx https://doi.org/10.1371/journal.pone.0247031.r001
Revision 1
27 Jan 2021 Author Response Below you will find my responses, in bold, to your comments and those of the reviewers for PONE-D-20-14399. In general I made nearly all of the requested changes. If you have any further questions please let me know. Editor and reviewer comments In addition to the comments and suggestions from the two reviewers, I would like you to focus on the following improvements: - Clarify Terminology: Select and use one designation for ‘prey remains’ is needed for clarity. – I have changed all these designations to “prey remains”. Define seasons Do they refer to calendar seasons or are they tied to the ecology of the whales or of their prey? - I have defined the seasons as “fall-early winter” (Oct-early January), “mid winter-early spring” (Late January – April) and “spring” (May) and further explained that these are tied to the ecology of the whales in that they reflect at least some part of their seasonal occurrence in some areas. - Provide more background Information: The Northern Resident stock should be introduced somewhere in the Introduction or in the Methods (first mention is in the caption of Fig 8). – A few sentences have been added to the introduction providing pertinent information about the northern resident killer whale population. Finally, the authors refer to ‘whales’ instead of ‘killer whales’. I would suggest introducing the common name at the beginning of the paper, and using it consistently. – All “whales” have been changed to “killer whales”. Readers unfamiliar with the SRKW and the NRKW could benefit from a brief introduction of their population trends, and the body condition and demography of these two ecotypes. - A section has been added to the introduction providing pertinent information about the northern resident killer whale population. - More effective use of tables: The tables included in the ms are rather large and have many empty cells. I would urge the authors to consider moving tables 1, 2, 3 and 4 to the supplementary materials section, and including more distilled tables (or figures) in the ms. For instance, table 2 could be aggregated by season, rather than by month. – Per this request I reduced the number of tables in the manuscript to 3, moving table 1 to the supplemental materials and reducing tables 2 and 3 in size by consolidating data in the columns by season. Additionally, in Table 2, the “+” sign in some of the cells is confusing, it would be better to provide a range of the individuals contributing to the fecal sample. – I have changed all the “+” signs to “>” in order to more accurately convey that for some of the pooled samples, the prey species identified occurred in at least one of the pooled of samples but could have been present in more of them. - More effective use of figures: The introductory map and the insert set the stage. However, the other two maps (Figure 3 and 4) are not very effective because the points are small and overlay each other, and large scale maps are used to capture distributions with outliers. I would suggest using a larger study are map (figure 1), where you define the various geographic zones, and use inserts to identify the geographic locations mentioned in the text. Then, given the detailed depiction os these geographic areas (and their inclusion in the summary tables), I would remove the two other maps. - Figure 1 was revised to incorporate the range of both southern and northern resident killer whales as well as better delineate areas referred to in the study area. Figure - If you removed figure 3 and 4, you could addition a map showing the range of the two populations and the locations of some of the primary rivers. Alternatively, if you wanted to highlight specific samples that were distinct / unique in the map, I would suggest you limit the mapping of the samples to few numbered and color-coded symbols. - Figures 3 and 4 were deleted and primary rivers added to the Figure 1 Figure 8b – The y axis label should read “Proportion”. Please fix this typo. - Corrected ________________________________________ 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: Comments to the Authors #General comments The authors present the results of dietary analyses conducted for the (endangered) Southern Resident killer whale (SRKW) population in the eastern North Pacific Ocean. Using visual and molecular methods, they identify consumed prey species (salmonids and other fish) from prey remains and fecal samples collected from 2004 through 2007 in various areas and times of the year. The authors also aged and identified stocks of origin of the Chinook salmon prey consumed in order to assess the stocks of particular importance for the recovery of this killer whale population. The manuscript is well structured with the information clear and presented in a straightforward manner. The analyses seem appropriate and the discussion is adequate, and not overly speculative. Overall, this study constitutes a good contribution to the killer whale literature and is of particular relevance and importance for the management and recovery of the SRKWs. I recommend publication of the manuscript after some corrections. There is a need for a thorough check of all numbers throughout the ms (see detailed comments below). - All numbers have been checked and corrected I also think that chosing one designation for ‘prey remains’ and sticking to it is needed for clarity. – all variations of references to prey remains have been changed to “prey remains”. Seasons i.e. fall, winter, spring should be defined (whether they refer to typical calendar seasons or are tied to the whales’ or prey’s ecology). I have defined the seasons as “fall-early winter” (Oct-early January), “mid winter-early spring” (Late January – April) and “spring” (May) and further explained that these are tied to the ecology of the whales in that they reflect at least some part of their seasonal occurrence in some areas. The Northern Residents should be introduced somewhere in the Introduction or in the Methods (first mention is in the caption of Fig 8). - A few sentences have been added to the introduction providing pertinent information about the northern resident killer whale population. I am wondering if reference to Tables and Figures should be added in the Discussion. – I only referenced Fig 4 in the discussion as it pertains to a comparison of previously published data on ages of northern resident killer whale prey There is inconsistency with capital letters e.g., Chinook salmon, coho, chum that needs to be fixed throughout the manuscript. – these have been corrected Also, too often the authors refer to ‘whales’ instead of ‘killer whales’. This may be confusing for people who may not be familiar with the killer whale literature. - All “whales” have been changed to “killer whales”. Specific comments Abstract L29: What is ‘the Pacific coast’ – I suggest being more specific here; same with ‘coastal waters’ - I have changed this L31 – This would emphasize better the relatively large area investigated in this study L30: Shouldn’t it be ‘fecals’ or ‘feces’ here? – changed to feces L31: Add ‘of 2004-2017’ after May - added L37: Add ‘salmon’ after ‘Chinook’ added L38: Add ‘selectively’ before ‘consume’ added L39: What is ‘coastal samples’? – changed to “outer coast Chinook samples” L41: Could ‘effective’ be a better word than ‘useful’? – changed as suggested Introduction L54-58: There may be missing info on the SRKW – Suggest adding a sentence or two telling about the status of the SRKW population (to highlight how critical – since L77 mentions ‘recovery’) and also emphasize the differences between the three different pods – could set the why it is important/relevant to look into dietary variations at the pod level in this study. - A few sentences have been added to the introduction providing pertinent background information about the southern resident killer whale population. L65: Add ‘killer’ before ‘whale’ - added L67: ‘For characterizing these killer whales’ diet’ – changed as suggested L69: Missing ref after ‘Salish Sea’, same for L71. – added appropriate references to each sentence L70: Missing scientific name for coho salmon here - added L77-80: I would also add to get insights into plasticity in feeding behavior (prey switch) and thus resiliency to declining preferred prey (further useful to model long-term population trends) - added L81: Replace ‘the whales’ diet’ by ‘the SRKWs’ diet’ – changed as suggested L83-84: Suggest rewording to ‘We further extended the analyses to genetically identify the stocks of origin for Chinook salmon prey’. – changed as suggested Methods Line 73 (Caption Figure 1): add ‘between October and May from 2004 to 2017’. – changed as suggested Line 89: Replace ‘prey capture remains’ by ‘remains from prey capture events’. – changed as suggested L90: Add ‘between October and May’ before ‘from 2004 to 2017’ - added L93: An explanation of what a pod is and why it is relevant to investigate at the pod level would be useful, either here or in the introduction. – The introduction was revised address this comment L93: ‘…, allowing for results to be presented for each pod, separately. – changed as suggested L102: replace ‘estimate stock composition of Chinook salmon prey samples’ by ‘determine stock identity of Chinook salmon prey samples’. – changed as suggested L103. End the sentence after ‘samples’, and start the new sentence with ‘Specifically, sample genotypes at 13 nuclear microsatellite DNA loci were compared to a coast-wide…’ – changed as suggested L112: why pooled? – added an explanation that was due to available resources at the time of analyses L143: coastal waters of? – changed to outer coast waters of the U.S. west coast Results L154: ‘(JdF/SJI): 3 days and northern Georgia Strait (NGS): 3 days)’- changed L156: move ‘(36 days)’ after ‘California’ - changed L157: More details would be useful here: samples from how many distinct prey capture events? – each sample collected was from what appeared to be a single prey capture but as noted in the manuscript and detailed in S3 Table a second fish was sometimes identified L158? Were the 154 samples collected over the 156 days of killer whale encounters? Same for the 81 fecal samples: from how many encounter days? – we attempted to collect both prey remains and feces on all encounter days listed in S3 Table. Most days yielded one or both types of samples but breaking down by day would not be insightful due to the variability in conditions experienced on any given day. A variety of factors that potentially impacted the our ability to collect samples included, but was not limited to the length of the encounter or follow, weather conditions, behavior and speed of the animals, as well as the presence of vessels engaged in whale watching L160 (Table 1): What is the number after the year in column 1? Not clear. – as shown in the column heading it is the year of the fall sampling with the winter/spring of the subsequent year after the hyphen It would be helpful to mention in the table caption what a single prey sample refers to: does it represent a unique predation event? or are different types of remains e.g. when both scales and tissues were collected from a single prey capture event referred to as multiple samples? - Sample type has been detailed in the table caption and column title was changed to reflect The total of prey samples comes to 155 whilst L157 indicates 154 samples collected. Needs correction. - Sample numbers have been revised L169: Adjust the percentage of scale/tissue samples after correction on total number of samples collected. As it stands here, it suggests 155 samples collected (and not 154). - Sample numbers and percentages have been revised accordingly L170: Revise accordingly here too. - Sample numbers and percentages have been revised accordingly L174 and 178: Add the number of samples collected before ‘scale/tissue samples’. – these figures were deleted. L181: Explain what are the pods somewhere in the Introduction or in the Methods. – this has been addressed in the introduction. L182: Again, there is contradiction between total count of prey samples collected in PS here (93) compared to Table 1 (94). - Sample numbers have been revised L188-190: Check correct numbers here also - Sample numbers have been revised L203: be consistent with having either ‘Table S3’ or ‘S3 Table’ (see L190) – references to all supplemental tables have been revised to the correct format L217-220: This is redundant with content from Figure 5 – There are a lot of Figures in the article. Maybe this one is not necessary, even though the visual representation may be better than having it in text. – Figure 5 has been deleted from the article L258-278: I suggest placing this section before the one on Species composition diet from fecal samples for consistency with the Method section. – Earlier versions of the manuscript were configured as suggested but discussion by co-authors concluded that because the fecal samples played an important role in establishing the diversity of the winter diet that it should be featured up front in the discussion. L259: New contradiction with the number of prey samples collected- Sample numbers have been revised L262-264: Check correct numbers here, and also what months the authors refer to for the different seasons. Numbers seem to be incorrect.- Sample numbers have been revised L269: Replace ‘Table 1, Table 2’ by ‘Tables 1, 2’ - not changed due to revisions of tables that were included L281: Table caption does not read well – suggest rewording – caption reworded to clarify what table includes L292: Add ‘ were’ after 18.1% - added - Note that the total comes to 18.2% though – 100 - 67.2 -14.7 = 18.1 L335-337: there is no reference to NRKW before that – northern residents are now described in the introduction Discussion L346: Replace ‘highlight that this species is a’ with ‘confirm this species as a’ – replaced as suggested L350: Remove one of the two ‘winter’ – deleted as suggested L351: Suggest replacing ‘this time of the year’ by ‘winter’ for clarity. - Replaced as suggested L356: add ref for summer – was referenced in earlier part of the sentence L360: be consistent with locations names – use either full names or abbreviations throughout the text – JdF/SJI was defined initially on line 179 pf the Results sections and have replaced other places this was spelled out L370: wrong as written since ref #8 (Ford and Ellis 2006) is also about SRKWs – Suggest rewording – corrected this by adding #8 to portion referencing SRKW L371: Replace ‘whales’ by ‘killer whales’ - replaced L393: Add ‘that’ between ‘feces’ and ‘appeared’ – added ‘that’ L394: I suggest highlighting better that Halibut was reported as prey, not for any killer whale population in BC but specifically for resident type killer whales (Ford et al. 1998, Ford and Ellis 2006) – added reference to Ford and Ellis (2006) and revised Alaska reference as an unknown ecotype L398: Remove ‘been’ before ‘previously’ – ‘been’ removed L422: add ‘itself’ after ‘samples’ – added ‘itself’ L434: Remove ‘and’ – ‘and’ removed L435: I suggest rewording to ‘…could be due to biases associated with sampling methods, and behavior of both killer whales and prey species.’ – reworded as suggested L437-41: heavy sentence. Needs rewording. It may be enough just to say that sampling of prey remains is likely to only give access to (and therefore enable identification of) prey species that are consumed at/near the surface, and are large enough to require tearing into pieces and/or sharing. - reworded as suggested L450: ‘was primarily’ and ‘comprised of’ – suggested changes made L471: I would replace ‘differences’ with ‘variations’ – ‘differences’ replaced with ‘variations’ L471-474: Very long heavy sentence – Needs rewording. – was missing a couple of words which impacted clarity, have reworded to improve clarity L481: If Tables (or Figures) are going to be cited in Discussion, then they should be added many other places throughout the Discussion. – reference to Table 3 was deleted L499: Even though there appears to be strong selectivity for Chinook salmon, they do eat other salmonids and fish so I suggest down-grading this statement for more accuracy here. – revised to reflect this sentiment Also add ‘two’ after ‘These’ – ‘two’ added L501-504: Suggest rewording to: ‘Limited diet data are available for northern resident killer whales apart for summer data that indicated this population to be consuming a similar number…’ – reworded as suggested L504: ref (this study, Tables) after ‘consumed in winter’ – cited as suggested L504-506: I don’t understand this. How is that? – revised as follows: This A further comparison suggests that SRKWs have relatively fewer potential stocks available to them when they are in the inland water portion of their summer range compared to northern resident killer whalesNRKW. This is likely the case in that most of the Chinook stocks consumed by SRKWs during summer come mostly primarily from one basin, the Fraser River, which is only comprise of five stock groups [64] ,each with different temporal run timing [64] , which was reflected in the observed peaks in consumption [11] that are likely related to peak run timing for these few stocks [64]. L516: Add ‘is’ after ‘and’ – ‘is’ added L517: Reword to ‘for determining its caloric value?’ – reworded as suggested L520: add ‘from’ before ‘fish that were younger than..’- ‘from’ added as suggested L521: Reword to: ‘Besides SRKWs generally consuming younger fish of both chinook and chum salmon, the youngest age class…’ - reworded as suggested L526: Reword to: ‘Geographically, due to most west coast originating Chinook salmon maturing in the waters of..’- reworded as suggested L541: Add ‘also’ before ‘increase’ since it has been identified as a goal for the summer already (maybe add a ref fr that) – ‘also’ added before ’increase’ L542-545: this could be shortened since it largely repeats the previous sentence – I suggest ‘However, the increased dietary diversity in the winter months also underscores the importance of other species at particular times and in specific locations.’ - reworded as suggested L548: Reword to ‘Both K and L pods were documented…’ - reworded as suggested L562: Is reproduction relevant here? – changed to fecundity L577: add ‘suggested’ before ‘the best fit’ – added ‘suggested’ before ‘best fit’ L578: REPLACE ‘was’ by ‘to be’ – reworded as suggested L579: ‘…and their chinook salmon prey’ - added words as suggested L604: Replace ‘in the whales’ prey’ with ‘in the SRKWs’ prey’ - reworded as suggested, and ‘about the whales’ fall…’ with ‘about these killer whales’ fall…’, - reworded as suggested, and ‘diet’ with ‘diets’- reworded as suggested L606: Replace ‘the prey available to the whales’ with ‘the prey available to this critically endangered killer whale population’- reworded as suggested L607-608: suggest remove since it is redundant with the following, more complete sentence – removed sentence as suggested L609: Suggest replacing ‘fill gaps in the whales’ prey base’ with ‘fill gaps in the SRKWs’ prey base’ - reworded as suggested L611: Replace ‘whales’ with ‘killer whales’ - reworded as suggested L612: Replace ‘whales’ with ‘SRKWs’- reworded as suggested L613: What are these biological features? – added (i.e., water quality, prey availability, and passage conditions) to this sentence as these are the biological features identified for SRKW as part of the Critical Habitat designation under the ESA. L616-618: Suggest rewording to: ‘Although substantial new information has been gained on the diet of the SRKWs in fall, winter and spring, data is still lacking for parts of the year and geographical ranges for some or all pods. – reworded as suggested L619: Add ‘relatively’ before ‘documented’, - added ‘relatively’ before ‘documented’, Replace ‘the whales’ by ‘the SRKWs’ – replaced as suggested L628: Replace ‘for whales’’ with ‘for the SRKWs’’ - replaced as suggested L630: replace with ‘an adverse impact’?- replaced as suggested L631: Replace ‘the whales’ by ‘the SRKWs’ replaced as suggested L632: Replace ‘not necessarily’ by ‘that may not or less be’ replaced as suggested L633: ‘these environmental conditions; another..’ replaced as suggested L636: ‘detections of the SRKWs’ presence/occurrence near the’ - changed as suggested L643: Replace ‘for this whale population’ with ‘for this killer whale population’ replaced as suggested Reviewer #2: REVIEWER COMMENTS Data presented in this paper represent a significant contribution to our understanding of SRKW diet and expand the available information for conservation and management decisions. The authors have collected a spatially diverse library of fecal samples and prey remains throughout the SRKW’s range and over a series of years to amass a detailed overview of SRKW diet and provide narrative on the composition of diet and potential implications for conservation. The methodologies are well described with attention to validation and control samples. The findings are informative with respect to the increased diversity in winter diet, differences between coastal and inland prey base, and the authors provide an interesting discussion on conservation implications of the data. The manuscript is well written, well referenced and a pleasure to read. The comments on potential SRKW impacts from NRKW competition is intriguing and worthy of further discussion. Readers unfamiliar with the two populations of this fish-eating ecotype would benefit from knowing that the NRKW have maintained an increasing population trajectory of 2% annually and have a four-fold higher population (Towers 2018). – information relating to NRKWs was included in the introduction In addition, information on body condition from both populations is available; these data are not discussed in this MS, but are relevant in relation to the interesting finding on inter-population differences in stock diversity, differences in age/size of prey and the implications to the energetic cost vs yield of foraging. – while an interesting aspect of a comparison of these 2 populations, addressing it is beyond the scope of this paper Improvement in the quality of the map and addition of the range of the two populations and the locations of some of the primary rivers (Columbia, Fraser, Thompson, Taku, Skeena, Snake, etc) would be beneficial. – Fig1 has been revised to address this comment The authors present interesting information on the relative proportion of wild vs hatchery stocks and the population’s dependence on these stocks in the spring and fall. In the summer months, prey are dominated by Fraser River stocks, a system comprised of stocks with minimal or no hatchery production. The condition of SRKW reputedly improves from their return to the waters of the Salish Sea in the early summer to their relative dispersal in the fall; these data indicate that this foraging period is primarily supported by wild salmon populations. – there is no specific request to address these comments and as such no changes were made SPECIFIC LINE EDITS/COMMENTS 519 – data on NRKW age of prey from Ford and Ellis 2006 is from prey remains collected in 2003-2005. To better support the observation that NRKW consume older/larger Chinook, authors may consider application of a correction factor for the 15 year lag between the NRKW and SRKW data sets presented Fig 8a and B. – we are not aware of a “correction factor” that could be used to normalize the Chinook age data between these two data sets 555 – suggest rewording for clarity – confusing statement. – reworded for clarity 624 – bioaccumulation of PBDEs provide insight into past foraging behaviours (Krahn et al, 2007) and these data represent foraging events that have occurred prior to 2007 (and with bioaccumulation and selective mobilization of lipids and thus contaminants, they may represent foraging events from decades in the past). Suggest modifying to indicate these data support the historic foraging conditions. – added a sentence to indicate that these data support that the whales we likely doing this historically Figure 8b – y axis label should read “Proportion” – revised as suggested Attachments Attachment Submitted filename: Response to Reviewers.doc https://doi.org/10.1371/journal.pone.0247031.r002
1 Feb 2021 Decision Letter - David Hyrenbach, Editor Endangered predators and endangered prey: Seasonal diet of Southern Resident killer whales PONE-D-20-14399R1 Dear Dr. Hanson, We’re pleased to inform you that, after addressing the reviewer comments and suggestions, 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, David Hyrenbach, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Thank you for effectively addressing all the reviewer comments and suggestions. Your work augmenting the background and the supplementary materials, greatly improved the ms. Reviewers' comments: https://doi.org/10.1371/journal.pone.0247031.r003
Formally Accepted
8 Feb 2021 Acceptance Letter - David Hyrenbach, Editor PONE-D-20-14399R1 Endangered predators and endangered prey: seasonal diet of Southern Resident killer whales Dear Dr. Hanson: 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. David Hyrenbach Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0247031.r004

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