Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius island, Indian Ocean

Understanding the organization and dynamics of social groups of marine mammals through the study of kin relationships is particularly challenging. Here, we studied a stable social group of sperm whales off Mauritius, using underwater observations, individual-specific identification, non-invasive sampling and genetic analyses based on mitochondrial sequencing and microsatellite profiling. Twenty-four sperm whales were sampled between 2017 and 2019. All individuals except one adult female shared the same mitochondrial DNA (mtDNA) haplotype—one that is rare in the western Indian Ocean—thus confirming with near certainty the matrilineality of the group. All probable first- and second-degree kin relationships were depicted in the sperm whale social group: 13 first-degree and 27 second-degree relationships were identified. Notably, we highlight the likely case of an unrelated female having been integrated into a social unit, in that she presented a distinct mtDNA haplotype and no close relationships with any members of the group. Investigating the possible matrilineality of sperm whale cultural units (i.e. vocal clans) is the next step in our research programme to elucidate and better apprehend the complex organization of sperm whale social groups.

b. Lines 302-304: Once "genetic individuals" were identified, which genotype was used as representative of that individual, and how was that decided? This could have big implications for the relatedness analyses.
c. What are the units for this error rate. Is this per amplification, per allele, per locus, or per genotype? These all mean very different things, but it is not clear what is being referred to here, or how this number was obtained.
5. Interpretation of relatedness analyses. All relatedness estimates are based on comparison to a "reference group", which is usually all of the genotypes of the study (unless otherwise specified). All relatedness estimators are standardized so that the average relatedness within a sample set is 0 (or approximately so). Because this group consisted of genotypes from one social unit, it is not appropriate for estimating the average relatedness within that unit (it will be about zero). To do this, many more genotypes, from other social groups, would be needed. Then it would be possible to say something about the relatedness of individuals within this group relative to the population as a whole. However, since all but two genotypes are from individuals within this group, it is not appropriate to use these data to estimate the average relatedness within the group. Therefore, the estimate obtained (average r = 0.048) does not mean anything, because the appropriate reference group has not been sampled. Therefore, all aspects of this should be removed from the Results and Discussion. It is still appropriate to use these data to identify specific relationships among pairs of individuals, but even here their estimated r-values will be lower than what they truly are, again because there is not an appropriate reference group for comparison.
Smaller-Scale Edits 1. Line 49: The statement that "Genotypes matched field identifications" is not accurate. There were some cases where this was not true, at least initially, and also such a statement is not possible (a genotype can't match a field identification). I would just remove this sentence.
The data collection and analysis methods are sound, but the authors over-interpret their results in a few places without sufficient support for their conclusions. I have made several comments in the attached document (Appendix A), highlighting places throughout the manuscript where the authors can rephrase or shift their interpretation of the results to more accurately reflect the data presented. I also make recommendations for additional background information that should be added to the introduction.
Decision letter (RSOS-200086.R0) 04-Mar-2020 Dear Dr Jung: Manuscript ID RSOS-200086 entitled "Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius Island, Indian Ocean" which you submitted to Royal Society Open Science, has been reviewed. The comments from reviewers are included at the bottom of this letter.
In view of the criticisms of the reviewers, the manuscript has been rejected in its current form. However, a new manuscript may be submitted which takes into consideration these comments.
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Royal Society Open Science openscience@royalsociety.org on behalf of Professor Michael Bruford (Associate Editor) and Pete Smith (Subject Editor) openscience@royalsociety.org Reviewers' Comments to Author: Reviewer: 1 Comments to the Author(s) This manuscript describes work to assess the patterns of relatedness within a sperm whale social unit in waters off Mauritius Island. For the most part the work seems good and the results interesting. However, I have a fair number of concerns regarding both the theoretical context of the paper, as well as with the application and interpretation of some of the analyses. I have outlined these below. I have divided my comments into larger-scale comments, and smaller-scale edits to the manuscript.
Larger-Scale Comments 1. As a whole, the entire section describing different aspects of social structure, and the relative strengths and weaknesses of group living could use stronger theoretical foundations. Some of these are listed below, but this whole section could be strengthened.
a. Lines 86-88: This idea needs explanation. The authors should clarify what they mean by, and explain the underlying theory, behind the statement "Low average relatedness...could be correlated in particular to high individual social relationships disparities.." I don't follow this at all.
b. Lines 91-92: The statement "Group size and relatedness are also correlated, in a species-specific manner" needs much more explanation/justification.
2. The context of what is known about sperm whale social groups does not seem to be properly represented, and therefore this whole section could use revision. For example Lines 140-153 give the impression that this is not well known, and that, for some unknown reason, different studies produce different results. However, this is not necessarily true, and is certainly inaccurate. Instead, we know that the social structure of sperm whale female units differs fairly substantially in different regions of the world (e.g., Whitehead & Kahn (1992) Can. J. Zool. 70: 2145-2149, Whitehead (2003 Sperm Whales: Social Evolution in the Ocean). Therefore, we would expect to obtain different results due to the differences in underlying biology in different areas, rather than due to some sort of analytical discrepancy.
3. The importance of underwater observations. The authors suggest that this aspect of their work is quite important, but I don't ever see this justified satisfactorily. Why, or under what conditions, are underwater observations better? The logistics seem difficult to me. If a group of 28 sperm whales swims by, on how many occasions can a snorkeler get identification photographs of all 28? Collecting data from the water seems fine, but is not adequately justified here. The authors should thoroughly explain why they are taking this approach rather than vessels. 4. Not enough information is provided on the genetic mismatches/genotyping errors.
a. Lines 300-302: How many alleles could differ between two genotypes and have them still be considered "similar". This should be explicit, and well-justified.
b. Lines 302-304: Once "genetic individuals" were identified, which genotype was used as representative of that individual, and how was that decided? This could have big implications for the relatedness analyses.
c. What are the units for this error rate. Is this per amplification, per allele, per locus, or per genotype? These all mean very different things, but it is not clear what is being referred to here, or how this number was obtained.
5. Interpretation of relatedness analyses. All relatedness estimates are based on comparison to a "reference group", which is usually all of the genotypes of the study (unless otherwise specified).
All relatedness estimators are standardized so that the average relatedness within a sample set is 0 (or approximately so). Because this group consisted of genotypes from one social unit, it is not appropriate for estimating the average relatedness within that unit (it will be about zero). To do this, many more genotypes, from other social groups, would be needed. Then it would be possible to say something about the relatedness of individuals within this group relative to the population as a whole. However, since all but two genotypes are from individuals within this group, it is not appropriate to use these data to estimate the average relatedness within the group. Therefore, the estimate obtained (average r = 0.048) does not mean anything, because the appropriate reference group has not been sampled. Therefore, all aspects of this should be removed from the Results and Discussion. It is still appropriate to use these data to identify specific relationships among pairs of individuals, but even here their estimated r-values will be lower than what they truly are, again because there is not an appropriate reference group for comparison.
Smaller-Scale Edits 1. Line 49: The statement that "Genotypes matched field identifications" is not accurate. There were some cases where this was not true, at least initially, and also such a statement is not possible (a genotype can't match a field identification). I would just remove this sentence.

Line 75: Should be Physeter macrocephalus (!)
3. Lines 96-97: The statement "...most individuals are undistinguishable" requires more justification. I know of many cetacean species for which every individual can be identified, and therefore this statement does not seem accurate.
4. Lines 174-175: "..attributed with enough confidence..." what does this mean? This statement requires much more explanation. 5. Line 99-100: I don't see how the previous sentences, regarding photo-ID and genetic sampling, lead to interest in social groups. This tie should be more clear.
6. Line 103: What is meant by "of first importance"? 7. Line 105: "nowadays" seems too informal for a scientific publication. 8. Line 120: What is meant by "outsize body"? Perhaps different wording. 9. Line 133-135: This sentence should be removed. The fact that no migrations were known, until recently, does not add to the paper.
10. Line 248: CITES requires both an import and an export permit, yet this is just one number. What is the other one? 11. Line 251: I thought that biopsy samples were not collected (that all were sloughed skin).
12. Line 258: What concentration was the DNA samples standardized to?
13. Lines 265-272: More details regarding microsatellite amplification are required: annealing temperatures, were they amplified singly or in multiplex reactions, primer concentrations, fluorescent labels, etc. This could be a Comments to the Author(s) Sarano et al. present a high-resolution study of kin relationships within a social group of sperm whales off the coast of Mauritius. While limited in scope by the small sample size and geographic range, the paper represents an important contribution toward understanding links between social structure and genetic structure in a social cetacean, the sperm whale.
The data collection and analysis methods are sound, but the authors over-interpret their results in a few places without sufficient support for their conclusions. I have made several comments in the attached document (Sarano et al. comments.pdf), highlighting places throughout the manuscript where the authors can rephrase or shift their interpretation of the results to more accurately reflect the data presented. I also make recommendations for additional background information that should be added to the introduction.

Do you have any ethical concerns with this paper? No
Have you any concerns about statistical analyses in this paper? No

Recommendation?
Major revision is needed (please make suggestions in comments)

Comments to the Author(s)
The manuscript is improved from the first draft; however, there is still quite a bit of room for improvement, although perhaps it is more cosmetic this time. I found in some parts, particularly the Abstract, but also elsewhere, the work was over-sold and the wording should be toned down. Additionally, I think the context of our knowledge of sperm whale social structure is not represented accurately in the Introduction, which provides a false context for this paper. Other than those, I have several more specific suggestions to improve the paper, as described below.
1. Line 48-49: I link it is overselling it to call the sampling technique "innovative" (it is just collecting skin that is seen floating in the water after the animals pass, after all). I suggest changing this to "using underwater observations, individual-specific identification, and genetic analyses based on mitochondrial sequencing and microsatellite profiling." 2. Lines 53-55: This statement is incorrect. Konrad et al. (2018) did the same thing for multiple groups in their paper (some of which were completely sampled).
3. Line 57: I think the word "adoption" here could be misleading. Technically, this would mean that a mother nurses and raises a calf that is not her own (which has been reported in whales). But it is not clear that that happened here, and it would be easy for readers to get confused. I would use clearer wording, perhaps "We highlight a likely case of an unrelated female being integrated into a social unit, presenting a mtDNA..." 4. Lines 81-83: I think "strongly dependent on kin relationships" is an over-statement. For some of these species it is definitely true, but I think the jury is still out on the importance of relatedness for some of them (e.g., long-finned pilot whales). 5. Line 91: It would be helpful if the authors define what is meant by a "fission-fusion model" so that all of the readers are on the same page.
6. Line 104: This isn't quite right. These aren't "genetically distinct" populations. It is true that maternally-direct site-fidelity in baleen whales leads to distinct structure of mitochondrial haplotypes between whales in different feeding grounds. But often whales from different feeding grounds all breed together in the winter. Thus, the feeding groups represent seasonal population structure, but certainly not "genetically distinct populations". 7. Lines 171-172: The statement that "all samples used in these studies were biopsies..." is not true. Many are based on sloughed skin.
8. Lines 173-177: This doesn't provide an accurate picture of the studies underlying our current knowledge of sperm whale social structure. It is very hand-wavy and inaccurate. This may be true for some populations, but not for others. Painting these studies in this way sets them up as a straw-man, presumably to make this current study look better. This does not seem appropriate. 9. Lines 222-224: I think is is over-selling it. Although perhaps true for this particular geographical region, social structure in sperm whales has been well-studied other places. This sentence also does not add anything to the paper.
10. Lines 292-306: It is a bit weird that some description of the mitochondrial sequencing and microsatellite genotyping are provided here, but then other aspects of these procedures are described separately, under their own subheadings. It would be clearer if the text from here was moved to its appropriate subheading, so that all of the information describing each procedure was kept together. Also on line 292 it states that 774 bp of the control region was amplified, but on line 310 it says 638. Why the difference? 11. Line 356: More information should be provided about how this error rate of 2.2% was calculated. Is it per allele, per locus, per genotype? Exactly how many discrepancies were identified? The authors should be very explicit in this explanation. I had this comment last time, and the authors address it in their response, but it should be added to the manuscript.
12. Lines 512-523: For adult females that were already adult when the study started, and that showed parent-offspring relatedness with each other, how did they authors decide who was the mother and who was the offspring (since all were adult upon the initiation of the study). This should be clearly explained.
13. Figure 2: I think the diagram is an intuitive and informative way to visualize the putative relationships. However, my concern is that they could be interpreted as "fact", whereas there is a lot of variation and uncertainty around relatedness estimates. I think this could be alleviated by just including a sentence in the caption saying something like "This diagram was constructed to be consistent with the analyses conducted; however, there is uncertainty around relatedness estimates and thus around some of these relationships".
14. Line 645-646: The authors say that Caroline "rarely took care of" Alexander, even though she was his mom. This seems to strong. Do the authors mean that she was "rarely associated" with him? Those could be two very different things, and my guess is that the authors cannot say anything about how good of a mother she is. Similarly in line 650: I would suggest removing "taking care of" and replace it with what the actually observed (e.g., "associated with").
15. I think the map ( Figure S1) should be in the paper rather than in the supplementary material.

Review form: Reviewer 2
Is the manuscript scientifically sound in its present form? Yes

Are the interpretations and conclusions justified by the results? Yes
Is the language acceptable? Yes Do you have any ethical concerns with this paper? No

Recommendation?
Accept with minor revision (please list in comments) Comments to the Author(s) Sarano et al. have done an excellent job responding to comments from both reviewers. I have a few additional minor comments below, but otherwise look forward to seeing this manuscript in press. Line 81: add scientific names for long and short-finned pilot whales Line 200: Please add here how many individuals have been photo identified in the population, whether there is an abundance estimate for the local population, and if so what it is. Line 421: should this be "<=" ?
Decision letter (RSOS-201794.R0) We hope you are keeping well at this difficult and unusual time. We continue to value your support of the journal in these challenging circumstances. If Royal Society Open Science can assist you at all, please don't hesitate to let us know at the email address below.

Dear Dr Jung
The Editors assigned to your paper RSOS-201794 "Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius Island, Indian Ocean" have now received comments from reviewers and would like you to revise the paper in accordance with the reviewer comments and any comments from the Editors. Please note this decision does not guarantee eventual acceptance.
We invite you to respond to the comments supplied below and revise your manuscript. Below the referees' and Editors' comments (where applicable) we provide additional requirements. Final acceptance of your manuscript is dependent on these requirements being met. We provide guidance below to help you prepare your revision.
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Kind regards, Andrew Dunn Royal Society Open Science Editorial Office Royal Society Open Science openscience@royalsociety.org on behalf of Prof Pete Smith (Subject Editor) openscience@royalsociety.org Associate Editor Comments to Author: The reviewers are largely happy with the scientific/analytical changes you have implemented, but there are a number of linguistic/typographic changes recommended that would improve the work. We'd like you to take advantage of this opportunity to tweak the language and punctuation to improve the readability -you might benefit from the use of a language editing service such as those at https://royalsociety.org/journals/authors/benefits/language-editing/. We'll look forward to reading your final version soon.
Reviewer comments to Author: Reviewer: 1 Comments to the Author(s) The manuscript is improved from the first draft; however, there is still quite a bit of room for improvement, although perhaps it is more cosmetic this time. I found in some parts, particularly the Abstract, but also elsewhere, the work was over-sold and the wording should be toned down. Additionally, I think the context of our knowledge of sperm whale social structure is not represented accurately in the Introduction, which provides a false context for this paper. Other than those, I have several more specific suggestions to improve the paper, as described below. 5. Line 91: It would be helpful if the authors define what is meant by a "fission-fusion model" so that all of the readers are on the same page.
6. Line 104: This isn't quite right. These aren't "genetically distinct" populations. It is true that maternally-direct site-fidelity in baleen whales leads to distinct structure of mitochondrial haplotypes between whales in different feeding grounds. But often whales from different feeding grounds all breed together in the winter. Thus, the feeding groups represent seasonal population structure, but certainly not "genetically distinct populations". 7. Lines 171-172: The statement that "all samples used in these studies were biopsies..." is not true. Many are based on sloughed skin. 8. Lines 173-177: This doesn't provide an accurate picture of the studies underlying our current knowledge of sperm whale social structure. It is very hand-wavy and inaccurate. This may be true for some populations, but not for others. Painting these studies in this way sets them up as a straw-man, presumably to make this current study look better. This does not seem appropriate.
9. Lines 222-224: I think is is over-selling it. Although perhaps true for this particular geographical region, social structure in sperm whales has been well-studied other places. This sentence also does not add anything to the paper.
10. Lines 292-306: It is a bit weird that some description of the mitochondrial sequencing and microsatellite genotyping are provided here, but then other aspects of these procedures are described separately, under their own subheadings. It would be clearer if the text from here was moved to its appropriate subheading, so that all of the information describing each procedure was kept together. Also on line 292 it states that 774 bp of the control region was amplified, but on line 310 it says 638. Why the difference? 11. Line 356: More information should be provided about how this error rate of 2.2% was calculated. Is it per allele, per locus, per genotype? Exactly how many discrepancies were identified? The authors should be very explicit in this explanation. I had this comment last time, and the authors address it in their response, but it should be added to the manuscript.
12. Lines 512-523: For adult females that were already adult when the study started, and that showed parent-offspring relatedness with each other, how did they authors decide who was the mother and who was the offspring (since all were adult upon the initiation of the study). This should be clearly explained.
13. Figure 2: I think the diagram is an intuitive and informative way to visualize the putative relationships. However, my concern is that they could be interpreted as "fact", whereas there is a lot of variation and uncertainty around relatedness estimates. I think this could be alleviated by just including a sentence in the caption saying something like "This diagram was constructed to be consistent with the analyses conducted; however, there is uncertainty around relatedness estimates and thus around some of these relationships".
14. Line 645-646: The authors say that Caroline "rarely took care of" Alexander, even though she was his mom. This seems to strong. Do the authors mean that she was "rarely associated" with him? Those could be two very different things, and my guess is that the authors cannot say anything about how good of a mother she is. Similarly in line 650: I would suggest removing "taking care of" and replace it with what the actually observed (e.g., "associated with").
15. I think the map ( Figure S1) should be in the paper rather than in the supplementary material.
Comments to the Author(s) Sarano et al. have done an excellent job responding to comments from both reviewers. I have a few additional minor comments below, but otherwise look forward to seeing this manuscript in press. Line 81: add scientific names for long and short-finned pilot whales Line 200: Please add here how many individuals have been photo identified in the population, whether there is an abundance estimate for the local population, and if so what it is. Line 421: should this be "<=" ? ===PREPARING YOUR MANUSCRIPT=== Your revised paper should include the changes requested by the referees and Editors of your manuscript. You should provide two versions of this manuscript and both versions must be provided in an editable format: one version identifying all the changes that have been made (for instance, in coloured highlight, in bold text, or tracked changes); a 'clean' version of the new manuscript that incorporates the changes made, but does not highlight them. This version will be used for typesetting if your manuscript is accepted. Please ensure that any equations included in the paper are editable text and not embedded images.
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RSOS-201794.R1 (Revision)
Review form: Reviewer 1 Is the manuscript scientifically sound in its present form? Yes

Are the interpretations and conclusions justified by the results? Yes
Is the language acceptable? Yes

Recommendation?
Accept with minor revision (please list in comments)

Comments to the Author(s)
The authors have done a good job revising their manuscript and responding to reviewer comments. One main comment I have remaining is data accessibility. The authors only make their mitochondrial sequences available, but the microsatellite data are not. The majority of the paper hinges on the microsatellite data, and therefore those need to be available if the work is to be replicable. I also have two minor comments below.
1. First, I still don't agree with the statement that maternally directed site-fidelity in humpback whales results in "genetically-distinct populations at very small geographical scales." (lines 109-111). It certainly leads to populations structuring at small scales (indicated by the papers cited, among others), but these are not genetically distinct populations. There is wide gene flow among humpback whales that utilize difference feeding/breeding areas, and they cannot be classified as distinct populations, and no one does (see listings in all relevant countries). The authors should change to "This maternally-directed fidelity leads, for instance, to population structure at very small geographical scales..." 2. Lines 118-119: The statement that "Boat observations only allow occasional identification of individuals..." is misleading. Indeed, the vast majority of marine mammal research is based on this. Many species can be very predictably and reliably studied with this approach, and it is hardly that individuals are 'only occasionally identified'. The authors even cite "pioneering work" on cultural transmission that is based on photo-identification. The authors should re-frame this, perhaps saying that although photo-identification is useful, it does not provide relatedness information (except for mother-calf pairs). Therefore, genetic analyses must be paired with photoidentification efforts to truly understand the relationship between kinship and social structure in marine mammals.

Decision letter (RSOS-201794.R1)
The editorial office reopened on 4 January 2021. We are working hard to catch up after the festive break. If you need advice or an extension to a deadline, please do not hesitate to let us know --we will continue to be as flexible as possible to accommodate the changing COVID situation. We wish you a happy New Year, and hope 2021 proves to be a better year for everyone.

Dear Dr Jung
The Editors assigned to your paper RSOS-201794.R1 "Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius Island, Indian Ocean" have now received comments from reviewers and would like you to revise the paper in accordance with the reviewer comments and any comments from the Editors. Please note this decision does not guarantee eventual acceptance.
We invite you to respond to the comments supplied below and revise your manuscript. Below the referees' and Editors' comments (where applicable) we provide additional requirements. Final acceptance of your manuscript is dependent on these requirements being met. We provide guidance below to help you prepare your revision.
We do not generally allow multiple rounds of revision so we urge you to make every effort to fully address all of the comments at this stage. If deemed necessary by the Editors, your manuscript will be sent back to one or more of the original reviewers for assessment. If the original reviewers are not available, we may invite new reviewers.
Please submit your revised manuscript and required files (see below) no later than 21 days from today's (ie 06-Jan-2021) date. Note: the ScholarOne system will 'lock' if submission of the revision is attempted 21 or more days after the deadline. If you do not think you will be able to meet this deadline please contact the editorial office immediately.
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Thank you for submitting your manuscript to Royal Society Open Science and we look forward to receiving your revision. If you have any questions at all, please do not hesitate to get in touch.
Kind regards, Royal Society Open Science Editorial Office Royal Society Open Science openscience@royalsociety.org on behalf of Prof Pete Smith (Subject Editor) openscience@royalsociety.org Associate Editor Comments to Author: Thank you for your patience over the festive period. The reviewer who has commented observes that there are a couple of points outstanding that you need to address before we can accept the paper.
Particularly problematic is the absence of part of the dataset -this needs to be made accessible before we can accept the paper (if it is already accessible, please make sure this is clarified in the data access statement of the paper). There remains a slight concern regarding the clarity of the writing in the paper -there may be an element of personal taste in the styling of parts of the language in the paper, but we would encourage you to take a final look at this in case any additional clarity can be introduced through careful editing.
Reviewer comments to Author: Reviewer: 1 Comments to the Author(s) The authors have done a good job revising their manuscript and responding to reviewer comments. One main comment I have remaining is data accessibility. The authors only make their mitochondrial sequences available, but the microsatellite data are not. The majority of the paper hinges on the microsatellite data, and therefore those need to be available if the work is to be replicable. I also have two minor comments below.
1. First, I still don't agree with the statement that maternally directed site-fidelity in humpback whales results in "genetically-distinct populations at very small geographical scales." (lines 109-111). It certainly leads to populations structuring at small scales (indicated by the papers cited, among others), but these are not genetically distinct populations. There is wide gene flow among humpback whales that utilize difference feeding/breeding areas, and they cannot be classified as distinct populations, and no one does (see listings in all relevant countries). The authors should change to "This maternally-directed fidelity leads, for instance, to population structure at very small geographical scales..." 2. Lines 118-119: The statement that "Boat observations only allow occasional identification of individuals..." is misleading. Indeed, the vast majority of marine mammal research is based on this. Many species can be very predictably and reliably studied with this approach, and it is hardly that individuals are 'only occasionally identified'. The authors even cite "pioneering work" on cultural transmission that is based on photo-identification. The authors should re-frame this, perhaps saying that although photo-identification is useful, it does not provide relatedness information (except for mother-calf pairs). Therefore, genetic analyses must be paired with photoidentification efforts to truly understand the relationship between kinship and social structure in marine mammals.

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Decision letter (RSOS-201794.R2)
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Dear Dr Jung,
It is a pleasure to accept your manuscript entitled "Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius Island, Indian Ocean" in its current form for publication in Royal Society Open Science.
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Please see the Royal Society Publishing guidance on how you may share your accepted author manuscript at https://royalsociety.org/journals/ethics-policies/media-embargo/.  105: "mammal" should be "mammalian" 116: "valuable" -do you mean "plausible"? 120: Please explain the connection between sperm whale body size/anatomy and cultural traditions, or remove the seemingly superfluous mention that they are large animals.
148: Here, instead of samples "taken from the sea surface", it would be good to state directly that you are referring to tissue biopsies, most often collected using a crossbow dart. In most genetic studies, the biopsied animal is easily identified through photographs -if that isn't the case here, it will be helpful for you to explain why. 458: What about Vanessa? Figure 2 shows no first or second degree relationships between Vanessa and other members of the group, yet she is one of the oldest females in the group. Does Vanessa have the same haplotype as the rest of the group members (SW_M), despite an apparent lack of kinship with the group? Further discussion of Vanessa, both in the results and the discussion sections, seems warranted.
469: "observed only 28 times" -please specify what years those sightings occurred in.
491-496: Supporting information needs to accompany this section, if you are going to include it, e.g. table of dyad relatedness calculations for these two individuals with the others in the study. It would also be good to include these individuals in Figure 2, specifying that they are from a different social group.

Discussion
533-536: This is too strong a statement based on the results of the current study. This study examines a single social group found off the coast of Mauritius -its scope is limited. The authors should base this statement on a larger sample size covering a greater portion of the local population. If there are published data on mtDNA CR haplotype frequencies in the larger population, those can be used to provide context to the results for this specific social group. However, it cannot be assumed a priori that the prevalent mtDNA CR haplotype in this study isn't common in the local population just because it isn't common in other parts of the Indian Ocean. 574-579: Please define both social relational complexity and organisational complexity, and discuss any implications of this framework on our understanding of sperm whale socio-genetic structure.
580-599: These are very interesting observations -some attempt to quantify this behavior should be undertaken, either as part of this study or a future study. It would be useful to compare dyad relatedness and probable kinship relationships with an overall index of pairwise association among individuals or with an index of the rate of nursing or other care-type behaviors, in order to determine the importance of alloparental care within the group. 595-599: This statement is unclear, in part because organisational complexity hasn't yet been defined. Please describe why alloparental care is more consistent with organizational complexity. Please also clarify the link you are trying to make, between the positive phylogenetic signal of alloparental care in mammals, and sperm whales having a relational complexity.
663-664: Again, this statement is strong given the sample size, and lack of sample coverage from other social groups in the population. Microsatellite markers indicated low within-group relatedness compared to other studies. Several of the adult females (e.g. Vanessa, Claire) have no relationship to other animals in the group. These findings do not support "strict matrilineality" as stated here. 697: Replace "most" with "more" -many marine species exhibit socially transmitted cultural behaviors and socially driven genetic structure. Answers to reviewer comments.
Our answers are in blue.

Reviewers' Comments to Author:
Reviewer: 1 Larger-Scale Comments : 1. As a whole, the entire section describing different aspects of social structure, and the relative strengths and weaknesses of group living could use stronger theoretical foundations. Some of these are listed below, but this whole section could be strengthened.
The whole paragraph has been removed (L83-L92), as we also removed our results and discussion about the average relatedness in the Irène's group (following Rq. 5 of reviewer 1).
More examples of what is known about cetacean kinship and social structure has been added (second paragraph of the introduction) a. Lines 86-88: This idea needs explanation. The authors should clarify what they mean by, and explain the underlying theory, behind the statement "Low average relatedness...could be correlated in particular to high individual social relationships disparities.." I don't follow this at all.

Sentence removed
b. Lines 91-92: The statement "Group size and relatedness are also correlated, in a species-specific manner" needs much more explanation/justification.

Sentence removed
2. The context of what is known about sperm whale social groups does not seem to be properly represented, and therefore this whole section could use revision. For example Lines 140-153 give the impression that this is not well known, and that, for some unknown reason, different studies produce different results. However, this is not necessarily true, and is certainly inaccurate. Instead, we know that the social structure of sperm whale female units differs fairly substantially in different regions of the world (e.g., Whitehead & Kahn (1992) Can. J. Zool. 70: 2145-2149, Whitehead (2003 Sperm Whales: Social Evolution in the Ocean). Therefore, we would expect to obtain different results due to the differences in underlying biology in different areas, rather than due to some sort of analytical discrepancy.
We acknowledge this point and a new paragraph has been added there that describes some main geographical differences between Atlantic and Pacific sperm whale social groups. The last sentences of the paragraph have also been rephrased to lower their significance 3. The importance of underwater observations. The authors suggest that this aspect of their work is quite important, but I don't ever see this justified satisfactorily. Why, or under what conditions, are underwater observations better? The logistics seem difficult to me. If a group of 28 sperm whales swims by, on how many occasions can a snorkeler get identification photographs of all 28? Collecting data from the water seems fine, but is not adequately justified here. The authors should thoroughly explain why they are taking this approach rather than vessels.
We have described the results of our underwater observation works in another manuscript, which is presently submitted, and that we included in this submission as "response to referees", and which is cited in the present manuscript (ref 54). "Underwater observation allows for instance to distinguish juveniles, who rarely fluke and whose caudal fin often present no distinctive mark. More generally, underwater observation strongly increases the number of distinctive marks per individual." 4. Not enough information is provided on the genetic mismatches/genotyping errors.
a. Lines 300-302: How many alleles could differ between two genotypes and have them still be considered "similar". This should be explicit, and well-justified.
Samples from a same individual were identified using the Identity Analysis in CERVUS, which determines the probability (pID) of a same genotype to occur in two unrelated individuals, given allele frequencies. The analysis was conducted allowing up to 2 divergent loci to consider possible genotyping errors (i.e. null, missing or discordant alleles), though probabilities are only generated for pairs which match at all compared loci. Samples with more than 2 divergent loci (n=2) were not considered. Sample pairs presenting one or two divergent loci were further analyzed: In all the cases, a null allele was involved (one locus was apparently homozygous for a sample, and heterozygous for the other sample). In any case divergent alleles were observed.
b. Lines 302-304: Once "genetic individuals" were identified, which genotype was used as representative of that individual, and how was that decided? This could have big implications for the relatedness analyses.
Fuzzy matching genotypes were only due to the presence of a null allele at a locus, no discordant alleles were notified. Exact matching genotypes and fuzzy matching ones were assumed to correspond to skin samples taken at different occasions from a same individual and define a genetic individual (see Table S1). When one genotype of an individual had an allele clearly detected in some PCRs and not in another PCR (a null allele), that allele was retained in the final genetic profile of the individual. No other corrections were done to determine the genotypes of the "genetic individuals".
c. What are the units for this error rate. Is this per amplification, per allele, per locus, or per genotype? These all mean very different things, but it is not clear what is being referred to here, or how this number was obtained.
Seventeen individuals were genotyped on at least 3 independent DNA extracts (Table S1). These different samples of a same individual allowed us to perform replicate PCRs for all the nuclear loci and to estimate the genotyping errors linked to possible poor-quality DNA extracts. All loci (n=14) have 61 PCR replicas for which 38 out of 1708 alleles were incorrect (or 25 out of 854 loci were incorrect). We calculated an overall per-allele error rate of 2.2% which was subsequently used in kinship analysis.
5. Interpretation of relatedness analyses. All relatedness estimates are based on comparison to a "reference group", which is usually all of the genotypes of the study (unless otherwise specified). All relatedness estimators are standardized so that the average relatedness within a sample set is 0 (or approximately so). Because this group consisted of genotypes from one social unit, it is not appropriate for estimating the average relatedness within that unit (it will be about zero). To do this, many more genotypes, from other social groups, would be needed. Then it would be possible to say something about the relatedness of individuals within this group relative to the population as a whole. However, since all but two genotypes are from individuals within this group, it is not appropriate to use these data to estimate the average relatedness within the group. Therefore, the estimate obtained (average r = 0.048) does not mean anything, because the appropriate reference group has not been sampled. Therefore, all aspects of this should be removed from the Results and Discussion. It is still appropriate to use these data to identify specific relationships among pairs of individuals, but even here their estimated r-values will be lower than what they truly are, again because there is not an appropriate reference group for comparison.
We agree with the reviewer, and we thank him for this analysis. We removed all discussions about the average relatedness, excepted to compare its value between the Irene's group and the two subgroups.

Smaller-scale edits
1. Line 49: The statement that "Genotypes matched field identifications" is not accurate.
There were some cases where this was not true, at least initially, and also such a statement is not possible (a genotype can't match a field identification). I would just remove this sentence. The sentence has been removed 2. Line 75: Should be Physeter macrocephalus (!) Corrected. Sorry for this mistake 3. Lines 96-97: The statement "...most individuals are undistinguishable" requires more justification. I know of many cetacean species for which every individual can be identified, and therefore this statement does not seem accurate. The sentence has been modified 4. Lines 174-175: "..attributed with enough confidence..." what does this mean? This statement requires much more explanation. This part of the sentence has been removed 5. Line 99-100: I don't see how the previous sentences, regarding photo-ID and genetic sampling, lead to interest in social groups. This tie should be more clear.
This paragraph is an attempt to explain that, although there are specific difficulties to study marine mammals at sea, their social organisation draws a lot of attention from the scientific community. The previous sentence has been modified to reinforce this idea.
6. Line 103: What is meant by "of first importance"?
The sentence has been rephrased to clarify its meaning 7. Line 105: "nowadays" seems too informal for a scientific publication.
The sentence has been rephrased 8. Line 120: What is meant by "outsize body"? Perhaps different wording.
The sentence has been rephrased 9. Line 133-135: This sentence should be removed. The fact that no migrations were known, until recently, does not add to the paper.

Sentence removed
10. Line 248: CITES requires both an import and an export permit, yet this is just one number. What is the other one?
The export permit number has been added in the text 11. Line 251: I thought that biopsy samples were not collected (that all were sloughed skin).
"Biopsies" has been removed 12. Line 258: What concentration was the DNA samples standardized to? 10ng/µL (added in the text) 13. Lines 265-272: More details regarding microsatellite amplification are required: annealing temperatures, were they amplified singly or in multiplex reactions, primer concentrations, fluorescent labels, etc. This could be a table in the Supplementary Material. Moreover, how were they size-separated and visualized? What sort of equipment?
The paragraph has been completed, and a supplementary table S2 presenting the amplification conditions has been added 14. Lines 546-549: This statement is not true. Konrad et al. (ref. 60) used genetic data to show that some individuals in social groups did not have close genetic ties therein, much like "Claire" here.
We modified the sentence.
In our understanding, Konrad et al. (2018) showed in fact that some individuals presented no genetically detectable level of kin relationships with other members of a same social group, but they did share the same mitochondrial haplotype. We discuss about the possibility that some individuals of a same matrilineal group do no present high (detectable) genetic relationships (third paragraph of "The Irène's sperm whale group is matrilineal and shows extensive allomaternal care" in the discussion). Therefore, in our understanding, there is no clear evidence that the individuals described in Konrad et al. (2018) are mergers from other social groups.
Here, Claire has no close kin in the group, but moreover, she is the only one in the Irene's group to possess a different mitochondrial haplotype. This point is strongly supporting the transfer from another group. This last paragraph explicit main points of high interest we, and certainly others, would like to address in our future works. We would like to keep it as it is. More examples of what is known about cetacean kinship and social structure has been added (second paragraph of the introduction). We thank the reviewer for this relevant list of publications.

99-100: incomplete sentence
The sentence has been completed to clarify its meaning 101-103: This sentence is vague -please explain what "first importance" means, and describe the pioneering works referred to in the sentence and how they demonstrate that cultural behavior is important.
The sentence has been modified (also following a remark from reviewer 1) 105: "mammal" should be "mammalian" This has been corrected 116: "valuable" -do you mean "plausible"? Yes, word modified 120: Please explain the connection between sperm whale body size/anatomy and cultural traditions, or remove the seemingly superfluous mention that they are large animals.
The sentence has been modified (following also a remark from reviewer 1) 148: Here, instead of samples "taken from the sea surface", it would be good to state directly that you are referring to tissue biopsies, most often collected using a crossbow dart. In most genetic studies, the biopsied animal is easily identified through photographs -if that isn't the case here, it will be helpful for you to explain why.
The sentence has been modified and the word "biopsies" is now used. The reason why sperm whales can be difficult to identify from a boat are developed in the manuscript submitted (Sarano et al.) which is joined to this submission.
154-163: Much of this section is superfluous and can be shortened. Most of it belongs in the methods, rather than the introduction.
We agree in part to this remark. But in this paragraph, we wanted to highlight the work done in the field by Mauritian and French NGOs. We would like to keep it for this reason 154: It would be good to have more information about the local sperm whale populationhow big is it? What geographic area does it cover? What portion of their range does your study area comprise? Is Irene's group the only resident social group? If so, what portion of the year are other individuals or social groups present? Any background information you have will provide helpful context about the social group and this study. Done. A new paragraph has been added.

Methods:
All the field work protocols are now described in the other manuscript joined to this submission (Sarano et al. submitted). Some more information are given below 199-201: What platform was used for the field work? Small boat? Tour ships? Research Vessel?
The boat was a 15m cabin cruiser designed for divers and that has a regular mooring at Trou aux Biches (Mauritius) The paragraph is now at the beginning of the result section 226: Please explain why sloughed skin was used rather than more traditional tissue biopsies.
Sloughed skin sampling was used first because it allowed frequent individual-specific sampling (strongly more frequent than by taking biopsies with a crossbow for sperm whales). Moreover, sloughed skins are non-invasive samples.
240: How close did snorkelers get to the whales? This is described in Sarano et al. submitted. Snorkelers were "passive" waiting for the sperm whales to approach. They can be some meter close to the whales when taking the skin samples 268: "amplified and analyzed as described" -this seems out of place?
The sentence has been rephrased 302: Please define Pid and describe how it is calculated.
Done 316-317: Please describe the method used to calculate error rate.
Described in detail in the answer to questions 4 of reviewer 1 326: What was done after the first investigation? Were mis-matched samples removed from the study?
Or was an attempt made to match those samples to the "correct" individual? If so, what was the protocol for re-matching DNA sample to a different individual?
The correlation between genetic individuals and field-identified individuals was done for each skin sample. In case of disagreement between the two identifications (a skin sample attributed to one individual in the field but presenting a genotype corresponding to another genetic individual, this occurred for 4 samples), the first investigation was to analyze more in detail the video recording of the taking of the skin sample, and to determine if the genetic individual could have been close to the sampling site, leading to a misidentification of the sloughed skin in the field. This was the case for the 4 misidentified samples, which were then reattributed to the correct individual and kept in the analyses. 332: Do you specifically mean avuncular here, We do not clearly catch the point of this remark. We mean avuncular as "any of the four relationship categories involving uncles or aunts with nephews or nieces" (definition from Blouin, Trends in Ecology, 2003).

405-408:
Please include details about any discrepancies among individuals that may have been due to genotyping error or other sample processing error. I.e., did genotypes of all genetic individuals match A new paragraph has been added, describing the differences observed between different samples of a same individual (null alleles in all the cases) 100%? What was the rate of mismatch among samples within an individual? If any mismatch was identified, was it found in the mtDNA haplotype or in the microsatellites?
No mismatch was found in the mitochondrial DNAs (all samples from a same individual were identical). For NuDNA, mismatches were only due to missing null alleles in the genotypes of some samples.
422-425: This should be in the methods section.
The paragraph has been moved to the methods section 452: This number seems very low, given the high levels of relatedness among most individuals within the group. Average pairwise relatedness is higher in other studies of highly-social mammals, e.g. among female elephants within a core group relatedness was 0.15 (Archie et al. 2006); average pairwise relatedness within pilot whale social units was ~0.18 (Van Cise et al. 2017). The review by Briga et al. (2012) cited in this study reports average relatedness among female sperm whales within a group to be 0.19 (reported from Quellar and Goodnight (1989)). How was average relatedness within groups calculated? It would be good to report relatedness for all dyads in the study in a supplemental table. The discussion should include some explanation for the low within-group relatedness values reported here, compared to previously reported values for sperm whales and other social cetaceans.
Following the remark 5 of reviewer 1, and because of the absence of a reference group in our study, we removed from our manuscript all the analysis of the average r value of the Irene's group.
We also added a supplementary table (supplementary table S4) listing relatedness values for  all dyads. 458: What about Vanessa? Figure 2 shows no first or second degree relationships between Vanessa and other members of the group, yet she is one of the oldest females in the group. Does Vanessa have the same haplotype as the rest of the group members (SW_M), despite an apparent lack of kinship with the group? Further discussion of Vanessa, both in the results and the discussion sections, seems warranted.
Among all adult females, two, Claire and Vanessa, shared no first-or second-degree relationships with other members of the group, and another, Yukimi, shared only one seconddegree relationship with an adult female. However, Vanessa and Yukimi have the same mitochondrial haplotype than the rest of the group. But Claire presented a different mitochondrial haplotype, thus reinforcing her marked genetic difference with the rest of the group.
A sentence about Yukimi and Vanessa has been added in the discussion 469: "observed only 28 times" -please specify what years those sightings occurred in.
In 2019 (added in the text) 491-496: Supporting information needs to accompany this section, if you are going to include it, e.g. table of dyad relatedness calculations for these two individuals with the others in the study. It would also be good to include these individuals in Figure 2, specifying that they are from a different social group.
A new table (supplementary table S7) listing all the relatedness values between ClanReshna 1 and ClanReshna 2 and all members of the Irene's clan has been added Discussion 533-536: This is too strong a statement based on the results of the current study. This study examines a single social group found off the coast of Mauritius -its scope is limited. The authors should base this statement on a larger sample size covering a greater portion of the local population. If there are published data on mtDNA CR haplotype frequencies in the larger population, those can be used to provide context to the results for this specific social group. However, it cannot be assumed a priori that the prevalent mtDNA CR haplotype in this study isn't common in the local population just because it isn't common in other parts of the Indian Ocean.
Sharing a common haplotype, minor in the Indian Ocean, is in line with the idea of a matrilineal social group. We have added a sentence about the requirement to obtain more data form the local population of sperm whales. 574-579: Please define both social relational complexity and organisational complexity, and discuss any implications of this framework on our understanding of sperm whale socio-genetic structure.
Following the remark 5 of reviewer 1, and because of the absence of a reference group in our study, we removed from our manuscript all the analysis of the average r value of the Irene's group, including paragraph 568-579. 580-599: These are very interesting observations -some attempt to quantify this behavior should be undertaken, either as part of this study or a future study. It would be useful to compare dyad relatedness and probable kinship relationships with an overall index of pairwise association among individuals or with an index of the rate of nursing or other care-type behaviors, in order to determine the importance of alloparental care within the group.
We agree with the reviewer. This will be part of next steps of our study. 595-599: This statement is unclear, in part because organisational complexity hasn't yet been defined. Please describe why alloparental care is more consistent with organizational complexity. Please also clarify the link you are trying to make, between the positive phylogenetic signal of alloparental care in mammals, and sperm whales having a relational complexity.
Here again, following the remark 5 of reviewer 1, we removed from our manuscript all the analysis of the average r value of the Irene's group, including this paragraph (593-599). 663-664: Again, this statement is strong given the sample size, and lack of sample coverage from other social groups in the population. Microsatellite markers indicated low within-group relatedness compared to other studies. Several of the adult females (e.g. Vanessa, Claire) have no relationship to other animals in the group. These findings do not support "strict matrilineality" as stated here.
In the literature, social groups can be considered matrilineal when most females (or all offspring) remain, for life, with their mothers and other close female relatives. Taken together, the observation of the same individuals over a long time period, the mtDNA haplotype homogeneity and the number of first-and second-degree relationships are in agreement with this definition and have highlighted the matrilineality of this social group. 697: Replace "most" with "more" -many marine species exhibit socially transmitted cultural behaviors and socially driven genetic structure.