Ecological processes in food webs depend on species interactions. By identifying broad-scaled interaction patterns, important information on species' ecological roles may be revealed. Here, we use the group model to examine how spatial resolution and proximity influence group structure. We examine a data set from the Barents Sea, with food webs described for both the whole region and 25 subregions. We test how the group structure in the networks differ comparing (1) the regional metaweb to subregions and (2) subregion to subregion. We find that more than half the species in the metaweb change groups when compared to subregions. Between subregions, networks with similar group structure are spatially related. Interestingly, although species overlap is important for similarity in group structure, there are notable exceptions. Our results highlight that species ecological roles vary depending on fine-scaled differences in the patterns of interactions, and that local network characteristics are important to consider.
Spatial resolution and location impact group structure in a marine food web
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2020/05/20Oxford, 20-May-2020
Manuscript number: ELE-01328-2019.R2
Title: Spatial resolution and location impact group structure in a marine food web
Author(s): Ohlsson, Mikael; Eklöf, Anna
Type: Letters
Editor: Dr. Timothée Poisot
Manuscript received: 26-Nov-2019
Manuscript accepted:Dear Dr. Ohlsson,
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Author Response
2020/05/082020-05-08
Dr. Tim Coulson
Editor-in-chief
Ecology LettersDear Dr. Coulson
We are pleased to submit a revised version of our manuscript “Spatial resolution and location impact group structure in a marine food web", ELE-01328-2019.R1. We were happy to see that all three reviewers appreciated our revision. There was one lingering issue regarding the ambiguity of the notation of an equation. The issue has now been addressed, which we believe further clarifies our methods.
We thank all the reviewers and the editor for their dedicated time and effort with our manuscript.
Regards,
Mikael Ohlsson and Anna Eklöf
Linköping University
Theoretical Biology, IFM
SE-581 83 LinköpingAuthor response by
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- pre-publication peer review (ROUND 2)
Decision Letter
2020/04/27Mr. Mikael Ohlsson Linköping University Linköping University
Linkoping
Linkoping
Sweden
581 83Oxford, 27-Apr-2020
Dear Dr. Ohlsson,
UPDATE:
The coronavirus epidemic is impacting ecologists around the globe, with fieldwork, office work, and lab work all affected as people work from home and self-isolate. In addition, in some countries, schools are shut, which means many of us will be looking after children at home. We appreciate that this disruption can impact all aspects of work and home life. For that reason, we are pleased to provide extensions to manuscript revisions. If you miss a deadline to resubmit a manuscript, please do not worry – we will reopen the submission pipeline when you are ready to resubmit. Stay well. Best wishes, from all of us at Ecology LettersManuscript number: ELE-01328-2019.R1 Title: Spatial resolution and location impact group structure in a marine food web Author(s): Ohlsson, Mikael; Eklöf, Anna
We have now received the referees' reports on your manuscript. You will find them below. As you will see, the referees make a number of comments with the aim of improving the manuscript.
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Ecology LettersReferees' comments to the author(s):
Referee: 1
Comments for the Authors
I thank the authors for their clear and comprehensive responses to my comments, and especially for providing the code for their analysis. I have one lingering request for clarification. In my original review, I mentioned that I thought the asymmetry in group mapping seemed to pose a problem in the averaging of Jaccard indices (Eq. 5), but I was not clear why this might be the case. Having now seen exactly what is being done in the provided code, I better understand the underlying calculations, but would suggest altering the notation to better reflect the underlying analysis.In equation 5, the authors claim to be averaging the distance from group A (in network 1) to group B (in network 2) with the distance from group B to group A. My concern is that the identity of the groups is set by the order of the network comparison. As I read the text, B is defined to be the most similar group in network 2 to group A, however it is not necessarily the case that A is the most similar group in network 1 to group B. For example, consider a case where group A (network 1) is most similar to group B (network 2), but group B is most similar to group C (network 1). In this case, as I read the code, the RHS of eq 5 would effectively read:
(d(A, B) + d(B, C)) / 2,
which makes the notation confusing on two counts:
1) the identities of C^A and C^B differ across the two terms in the numerator
2) the LHS doesn't really map onto what is being calculatedReferee: 2
Comments for the Authors
The authors of the ms "ELE-01328-2019.R1" did a great job in revising their manuscript carefully according to the recommendations from the reviewers. I have no further suggestions, and wish the authors good luck.Referee: 3
Comments for the Authors
The authors did a very thorough job in addressing all my previous comments. Thank you for the efforts. This is a great paper, and I have no further suggestions. Looking forward to seeing the publicised version!Editor's comments to the author(s):
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2020/04/17The authors did a very thorough job in addressing all my previous comments. Thank you for the efforts. This is a great paper, and I have no further suggestions. Looking forward to seeing the publicised version!
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Reviewer report
2020/04/06The authors of the ms "ELE-01328-2019.R1" did a great job in revising their manuscript carefully according to the recommendations from the reviewers. I have no further suggestions, and wish the authors good luck.
Reviewed by
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Reviewer report
2020/04/03I thank the authors for their clear and comprehensive responses to my comments, and especially for providing the code for their analysis. I have one lingering request for clarification. In my original review, I mentioned that I thought the asymmetry in group mapping seemed to pose a problem in the averaging of Jaccard indices (Eq. 5), but I was not clear why this might be the case. Having now seen exactly what is being done in the provided code, I better understand the underlying calculations, but would suggest altering the notation to better reflect the underlying analysis.
In equation 5, the authors claim to be averaging the distance from group A (in network 1) to group B (in network 2) with the distance from group B to group A. My concern is that the identity of the groups is set by the order of the network comparison. As I read the text, B is defined to be the most similar group in network 2 to group A, however it is not necessarily the case that A is the most similar group in network 1 to group B. For example, consider a case where group A (network 1) is most similar to group B (network 2), but group B is most similar to group C (network 1). In this case, as I read the code, the RHS of eq 5 would effectively read:
(d(A, B) + d(B, C)) / 2,
which makes the notation confusing on two counts:
1) the identities of C^A and C^B differ across the two terms in the numerator
2) the LHS doesn't really map onto what is being calculatedReviewed by
Cite this review
Author Response
2020/03/202020-03-20
Dr. Tim Coulson
Editor-in-chief
Ecology LettersDear Dr. Coulson
We are pleased to submit a revised version of our manuscript “Spatial resolution and location impact group structure in a marine food web", ELE-01328-2019. We were very happy to see that all three reviewers and the subject editor found our research interesting and relevant, and we greatly appreciate the many helpful suggestions for clarification and improvements they provided. We have addressed and responded to all the comments, listed in the attached file. In line with the feedback, we have especially put effort into presenting a better structured and rewarding discussion, clarifying parts of our methods, and performed an additional sensitivity analysis. We also share the code used for our analyses.
We are grateful for all the comments, and we are confident that addressing them have improved the quality of our manuscript.
Regards,
Mikael Ohlsson and Anna Eklöf
Linköping University
Theoretical Biology, IFM
SE-581 83 LinköpingAuthor response by
Cite this author response
- pre-publication peer review (ROUND 1)
Decision Letter
2019/12/27Mr. Mikael Ohlsson Linköping University Linköping University
Linkoping
Linkoping
Sweden
581 83Oxford, 27-Dec-2019
Dear Dr. Ohlsson,
Manuscript number: ELE-01328-2019 Title: Spatial resolution and location impact group structure in a marine food web Author(s): Ohlsson, Mikael; Eklöf, Anna
We have now received the referees' reports on your manuscript. You will find them below. As you will see, the referees make a number of comments with the aim of improving the manuscript.
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Thank you for considering Ecology Letters for the publication of your finest and most exciting work.
Yours sincerely,
Tim Coulson
Editor in Chief
Ecology LettersReferees' comments to the author(s):
Referee: 1
Comments for the Authors
See attachementComments to authors
General
This is an interesting and timely paper with some new and relevant findings for spatial food web ecology. It advances our understanding of spatial food web ecology by demonstrating how species roles change depending on food web resolution and location.
The methodology is well explained and rigorously performed. However, the environmental data used in this study is not described nor referenced. The paper reads well, but the language can still be improved. Some places commas and words are missing. The structure is also problematic at times. Ex. Figs. S1 and S3 from the supplementary material are not referenced in the result section, but described and referenced in the discussion. In addition, some findings are not discussed and referenced until the conclusion. Perhaps this is a matter of style and taste, but it feels disturbing that analyses, which have not been previously described, are suddenly discussed, and that some aspects (e.g. traits) are discussed in the conclusion. The mixing of results into the discussion makes the discussion somewhat descriptive, and some passages would perhaps do better in the result section. Besides, it is more interesting with a discussion that addresses the ecological relevance, interpretation and implications of the findings than a discussion that describes the findings, which is also my main concern with the manuscript. Although the authors discuss some implications of the findings and give a few examples of species changing their functional role with habitat and environment, it would improve this manuscript greatly if the discussion would be elaborated to include more reflections on the ecological relevance and implications of the findings. Any biological, functional and evolutionary considerations? The group model has previously identified ecologically relevant groups of species reflecting trophic guilds and habitat patterns. The link between groups and functional role is not entirely clear to me in this manuscript. For example, why does the sea spider in the Barents Sea change group affiliation, or role, with habitat and environment? Is it due to changes in its prey and/or predators or habitat, or all of these? Any ideas, is this finding meaningful at all, or an artefact of the data? It would be great with more explicit ecological considerations concerning the change (or lack of change) of species’ functional roles in a biogeographic context. For example, some groups of species seem to have higher species-wise turnover rates than others, how can this be explained in terms of ecology, can it be linked to species traits?
Find my detailed (minor) comments and suggestions below.
Intro
“The group model” used and discussed in this study is not the only model that has been applied to detect groups with ecological relevant interpretations. Other group detection models ex. modularity, structural and regular equivalence, and/or the TG model by Gauzens et al. 2015 could be briefly discussed in this context.
Line 27: The concept trophic species or trophospecies was defined and used before 2006. For example, by Yodzis in a paper from 1988. https://www.jstor.org/stable/pdf/1940449.pdf?refreqid=excelsior%3Af680aa06d43f46a301c323784dfea9c3
Line 33: Reference(s) to the stochastic block model are missing.
Line 45: in the final sentence of the introduction, the authors write: «the group model reveals additional structural patterns, which likely have implications for the functioning of ecological communities”
What are these additional structures, can you be more specific, are these discussed? What are the ecological implications?
Method section
Line 104: in this sentence the authors write “species within a group tend to eat and be eaten by the same other groups”. The group model partitions the food web in a “relaxed” way without including any biological information. It would be interesting to know, how often it happens that species from the same group do not share trophic interactions. Did the authors investigate this?
Line 113-115: This sentence is a bit unclear.
Line 119: What are these parameters?
Line 300: Do you mean trophic rewiring by this “mechanism”?
Line 204: Where do these environmental data (i.e, temperature and water depth) come from? They are not referenced anywhere, how were they sampled? There is also no figure or results showing the analyses, yet the results are discussed.
Discussion
I would recommend some restructuring and elaboration of the discussion section, some result passages could be moved to the result section and other paragraphs could be expanded. Overall, be careful that the discussion does not become too descriptive. It is more interesting with a discussion that addresses the ecological implications of the findings. You could also consider collapsing the result and discussion section into “Results and Discussion” instead of having them as two separate sections.
Lines 255-268: the intro paragraph of the discussion sounds more like an introduction.
Line 257: can you be more specific here, which factors?
Line 260: The authors write: “The trophic roles defined by the group model can be thought of as functional groups” It is not clear to me from this study what these functional groups are. Could this be made clearer, either with some additional analyses or by defining and discussing the groups more explicitly?
Lines 275 and 315: these findings are not new and were already described in the Kortsch et al. paper 2018b, and should be referenced here.
Lines 324-326: You mention a positive correlation between group structure and ocean depth and temperature. What data and analyses do you refer to in this sentence? If this environmental data is derived from another study, it should be referenced here.
Lines: 327-336: Here the discussion becomes very descriptive, and sounds more like result section.
Lines 347-352: Finally, some documented empirical examples of how species change their diet and trophic position (role) with habitat. However, this paragraph is very short, and a more thorough discussion on the ecological relevance could follow here. Why do species change their role, is it due to changes in prey and predators, or habitat, or all of these?
Line 354: This result is a methodological artefact of the dataset. Primary producers have no spatial turnover because they are present in every polygon (local food web) in the Kortsch et al. dataset. This is a bias and artefact of the dataset, because no detailed spatially resolved information exists for phytoplankton in the Barents Sea. Therefore, this result should be removed from figure 3 and not be discussed further, as it has no ecological meaning, but is an artefact of the data.
Line 357: This result (Fig 3b and c) is interesting but hardly discussed. Figure 3 shows that benthic species (e.g. Polychaeta and Ophiuroidea), being more sessile, have a higher species-wise group turnover than motile species such as Mammalia. Motility is a measurable trait. Can this specific trait be linked to the species-wise group turnover rates? Which functional implications does this finding have? Note: The sea spider is also a benthic species with high species-wise group turnover.
Line 367: “species with more links had lower turnover rates”. This is also an interesting finding that could be discussed more. It has previously been documented that species with more links (e.g. cod, see Kortsch et al. 2015 Climate change alters the structure of arctic marine food webs due to poleward shifts of boreal generalists ) are trophic and habitat generalists. Therefore, it makes sense that they exhibit lower species-wise group turnover rates, or?
Conclusion
Lines 378-380: This discussion about traits and the reference (Coux et al. 2016) should have come earlier in the discussion, not in the conclusion. I would suggest moving it from the conclusion to the discussion, e.g. related to Figure 3.
Lines 380-383: Again these lines belong to a discussion more than a conclusion. This discussion should have come earlier, and just be summarized briefly in the conclusion. Again, this might be matter of taste and style, but I would suggest the authors to be more stringent about the structure of the manuscript.
Text box and “Sea spider”
It is great that the authors us a concrete example (the sea spider) to illustrate how species change group membership, or functional role. However, why does the sea spider change group, is it an artefact of the data (due to e.g. false positive interactions as discussed) or due to some relevant ecological information. Is it due to changes in its prey or predators between regions, or due to environmental changes (temp. and sea ice) or the habitat (depth)? Why do sea spiders suddenly group with fish, due to changes in shared prey or predator, or both? Is there any ecological information in this findings, which could be discussed and help us understand why some species such as the sea spider change group affiliation (or functional role) across space.
Why is “changing groups” put in quotation marks here? Not necessary.
Language, spelling, commas
Line 11: consider to exchange the word “differ” with “vary”
Lines 77-79: verb and commas missing in this sentence. “The Barensts Sea is a shelf sea with a heterogeneous environment, bordering the Atlantic Ocean with the dissipating Gulf Steam in the west, and the Arctic Ocean to the north-east. “ or “The Barents Sea, a shelf sea with a heterogeneous environment, borders the Atlantic Ocean with the dissipating Gulf Steam in the south-west and the Arctic Ocean in the north-east.”
Line 6: write subregional food web with “al”, instead of subregion food webs
Line 103: “Groupings with a high likelihood have groups of species which acts in a similar way, that is…” “groupings have groups” does not sound good.
Line 113: word missing after looking in this sentence. Ex. “looking at”?
Line 135: “insight into”?, instead of insight in. Generally, this sentence does not read well.
Line 219: prey, not preys. “Prey” plural is always without the s.
Line 267: “prone to changes in group”.
Line 386: “Nevertheless” is not appropriate here. This sentence is not in contrast to the sentence before it.
Figures
Figure caption Fig 3. Do you mean species-wise group turnover here? You write species-wise turnover.
Figure 4. What are the ecological or functional roles of the groups in this figure? Is there any way to describe these groups in a relevant ecological way?Referee: 2
Comments for the Authors
In this research paper the authors compare the group structure of a meta-foodweb encompassing a whole region to the group structures of sub-regional food webs, which contain a subset of the species and interactions of the meta-food web. They find that the association of species to the same groups varies between sub-regional food web and between each subregional food web and the metaweb.Overall I find that the manuscript provides a substantial contribution to our understanding of the spatial variation in the structure of ecological networks. I think the authors have done a thorough job. I do not have any major comments, but I do have some suggestions and comments regarding the analysis.
I was missing information on how the subregions were defined. Even though subregions may be “relatively homogeneous with respect to hydrography and bathymetry”, they must be similar in some ways because this is a continuous system. This is especially true because the subregions were defined in another study. I think that a sensitivity analysis of how the results vary with the definition of subregions is necessary.
Also, just to clarify: each species and interaction occurrence had a GPS data point associated with it? Otherwise how do you know which species/interaction was recorded in which place? This should be specified in the methods.
Was the modification for Sebastes spp. Done only for that species? Any other species?
What algorithm was used to search for groups? Allesina and Pascual 2009 used a genetic algorithm. Is the MC3 a greedy algorithm?
Please provide the FULL CODE AND DATA. I cannot see how this study is reproducible unless the authors provide both (including data on subregions).
The authors state: “We then divided the number of species in the most similar group by the total number of unique species in groups k and l from both webs”. I do not see this division in equation 4.
I am not sure how the simplification implied by eq. 5 affects the results? If one repeats the analysis twice, based on eq.4 (once for A-->B and once for B-->A), would it provide similar results?
What results show what was done in L166?
L. 170-171: “We arbitrarily set the minimum cluster size to three subregions”. How does the cluster size affect the results? Also, maybe expand a bit on the UMAP method? I feel I did not fully understand it.
Can the authors add a conceptual figure specifying the process of the data analysis? For example, it is difficult to follow what is species overlap vs group overlap. It will also help to understand how the metaweb data were divided into subregions etc.
Put Svalband on the map in 2A.
Did the authors only include significant interactions between abiotic conditions and group structure? How will this change if subregions are redefined?
For the species-specific turnover, an equation will be nice to have.
L.280. I am not familiar with the assumption that a pair of species that co-occur must interact. In fact, Poisot 2012 Ecol Lett does not assume that (the authors state so as well later on). I also did not follow the logic for how from this assumption one infers that using local food webs will give a more accurate description of group structure. I dont think there even exists an accurate description. The group structure will change with method (modularity vs SBM), scale (where to put the limit between regions) and sampling effort.
I think it would be worthwhile to quantify the interaction turnover between the 25 subregions using Poisot’s 2012 framework. It will be a good source of information to understand where does the variation in group structure come from. Currently, only species are accounted for (and interactions, indirectly in the SBM), but interaction turnover can also have an effect. Such analysis can be in the SI but it seems important.
In Fig 2 subregions 25 and 33 seem like outliers. Why??
Fig 4: I cannot understand how the same group is defined over more than one region. For example, is group 1 in subregion 25 the same as group 1 in subregion 22? If not, then how can you actually make this alluvial diagram? One could give some arbitrary names to groups and then the diagram would change, no?
Referee: 3
Comments for the Authors
Ohlsson et al. provide a succinct analysis of the effect of spatial sub-sampling on ecological models of food-web structure. They use the group model as a case-in-point, showing that species groupings can be remarkably different from one another even when there is high species overlap.I enjoyed this work, but have two conceptual concerns that I believe could be better addressed in the text.
First:
There are some nuances to the group mapping between subregions that I think need to be expanded on. Namely, this method does not provide a 1:1 mapping between groups (indeed, it cannot, as the number of groups might differ between subregions). As such, the mapping has the potential to differ depending on the direction of the comparison (e.g. for a grouping A = [X, Y, Z, ...] and a grouping B = [x,y, z, ...], it could be that group X corresponds to group x when considering the species in X, but group x corresponds to group Y when considering the species in x). The authors mention that the index differs with direction, but do not mention that the mapping can as well.This seems to be an issue in particular when averaging the Jaccard indices (equation 5).
Moreover, there is the potential for more than one group to have equal (dis)similarity to other groups. Consider for example a group that splits into n groups -- each of these n groups would have 0 dissimilarity to the composite group, thereby being equally viable mappings. The inverse is also true: n groups which merge into one would have dissimilarities proportional to their relative contribution to the composite group (equal in the case of equally sized contributions.
Finally, is the normalization mentioned in Figure S1 the same as that presented in equation 5?
Second:
Though the authors pay a substantial portion of the discussion toward discussing this issue, I think the inability to account for species interaction variation (in addition to species presence variation) is a key limitation to this study. I found the discussion on this issue to be too wordy and lacking focus. I would recommend tightening up this section (i.e. lines 269-308) and adding some mention of this issue to the introduction.On a related note, the authors write: "Inferred from this, our results can be considered as representing the maximum possible similarity between groups, with species’ roles likely being more variable in reality." -- I don't think this is necessarily true. Since the group model does not take species identity into account, but rather wider network structure, it could be that two nodes with completely distinct interactions could nevertheless be more consistently grouped together than do two overlapping subsets of interactions from a meta-web.
Finally, one minor curiosity:
The authors use trophic level in some of their analyses. This calculation suffers the same issues as the group model insofar as it is a measure that is dependent upon the overall network structure. In particular, a given species' trophic level would depend upon which other species (and interactions, of course) are present in the subregion web. Have the authors looked into how the distribution of trophic levels varies across the subregions?Minor comments:
Figure 1 B -- why is the horizontal axis labelled distance "classes"?
line 250 - not not convinced... but just due to other similarities? i.e. temp?
legend is cut off in Figure S2 D, though superfluous
I would recommend having the same horizontal axis direction on the two sides of Figure S3. Also, why is only one side colored?Several small grammatical issues throughout, e.g.:
line 77: "The Barents Sea is a shelf sea..."
line 103: "species which act in a similar way"
line 267: "changes in group membership."
line 291: "prey" (not "preys")Editor's comments to the author(s):
Editor
Editors Comments for the Author(s):
Dear Drs. Ohlsson & Eklöf,I have received three reviews on your recent submission, and they are all very positive. This matches with my own prior assessment of the manuscript, which I found enjoyable to read in addition to being a strong contribution to our understanding of food webs in space.
Reviewers 1 and 2 made a lot of suggestions about how the manuscript should be improved - ranging from minor wording details, to interrogations that will require a comprehensive answer, to suggestions about re-ordering some of the text. I think that there is indeed a lot of writing changes you will need to make, and in particular make sure that the content falls within its proper section, as well as making sure that the discussion is not simply a description of the results. I encourage you to conduct extensive re-writing in the revision, and to provide me with a very detailed summary of what you have changed if you decide to submit a revision.
Reviewer 2 suggested that you deposit the code and data - I think that this would be a good idea. I will in fact expect to see the code alongside the revision, not necessarily as supplementary material, but at least as additional information for the reviewers and myself to read through.
Montréal, Dec. 23. 2019
Timothée PoisotHow to submit your revised manuscript:
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Reviewer report
2019/12/17Ohlsson et al. provide a succinct analysis of the effect of spatial sub-sampling on ecological models of food-web structure. They use the group model as a case-in-point, showing that species groupings can be remarkably different from one another even when there is high species overlap.
I enjoyed this work, but have two conceptual concerns that I believe could be better addressed in the text.
First:
There are some nuances to the group mapping between subregions that I think need to be expanded on. Namely, this method does not provide a 1:1 mapping between groups (indeed, it cannot, as the number of groups might differ between subregions). As such, the mapping has the potential to differ depending on the direction of the comparison (e.g. for a grouping A = [X, Y, Z, ...] and a grouping B = [x,y, z, ...], it could be that group X corresponds to group x when considering the species in X, but group x corresponds to group Y when considering the species in x). The authors mention that the index differs with direction, but do not mention that the mapping can as well.This seems to be an issue in particular when averaging the Jaccard indices (equation 5).
Moreover, there is the potential for more than one group to have equal (dis)similarity to other groups. Consider for example a group that splits into n groups -- each of these n groups would have 0 dissimilarity to the composite group, thereby being equally viable mappings. The inverse is also true: n groups which merge into one would have dissimilarities proportional to their relative contribution to the composite group (equal in the case of equally sized contributions.
Finally, is the normalization mentioned in Figure S1 the same as that presented in equation 5?
Second:
Though the authors pay a substantial portion of the discussion toward discussing this issue, I think the inability to account for species interaction variation (in addition to species presence variation) is a key limitation to this study. I found the discussion on this issue to be too wordy and lacking focus. I would recommend tightening up this section (i.e. lines 269-308) and adding some mention of this issue to the introduction.On a related note, the authors write: "Inferred from this, our results can be considered as representing the maximum possible similarity between groups, with species’ roles likely being more variable in reality." -- I don't think this is necessarily true. Since the group model does not take species identity into account, but rather wider network structure, it could be that two nodes with completely distinct interactions could nevertheless be more consistently grouped together than do two overlapping subsets of interactions from a meta-web.
Finally, one minor curiosity:
The authors use trophic level in some of their analyses. This calculation suffers the same issues as the group model insofar as it is a measure that is dependent upon the overall network structure. In particular, a given species' trophic level would depend upon which other species (and interactions, of course) are present in the subregion web. Have the authors looked into how the distribution of trophic levels varies across the subregions?Minor comments:
Figure 1 B -- why is the horizontal axis labelled distance "classes"?
line 250 - not not convinced... but just due to other similarities? i.e. temp?
legend is cut off in Figure S2 D, though superfluous
I would recommend having the same horizontal axis direction on the two sides of Figure S3. Also, why is only one side colored?Several small grammatical issues throughout, e.g.:
line 77: "The Barents Sea is a shelf sea..."
line 103: "species which act in a similar way"
line 267: "changes in group membership."
line 291: "prey" (not "preys")Reviewed by
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Reviewer report
2019/12/15In this research paper the authors compare the group structure of a meta-foodweb encompassing a whole region to the group structures of sub-regional food webs, which contain a subset of the species and interactions of the meta-food web. They find that the association of species to the same groups varies between sub-regional food web and between each subregional food web and the metaweb.
Overall I find that the manuscript provides a substantial contribution to our understanding of the spatial variation in the structure of ecological networks. I think the authors have done a thorough job. I do not have any major comments, but I do have some suggestions and comments regarding the analysis.
I was missing information on how the subregions were defined. Even though subregions may be “relatively homogeneous with respect to hydrography and bathymetry”, they must be similar in some ways because this is a continuous system. This is especially true because the subregions were defined in another study. I think that a sensitivity analysis of how the results vary with the definition of subregions is necessary.
Also, just to clarify: each species and interaction occurrence had a GPS data point associated with it? Otherwise how do you know which species/interaction was recorded in which place? This should be specified in the methods.
Was the modification for Sebastes spp. Done only for that species? Any other species?
What algorithm was used to search for groups? Allesina and Pascual 2009 used a genetic algorithm. Is the MC3 a greedy algorithm?
Please provide the FULL CODE AND DATA. I cannot see how this study is reproducible unless the authors provide both (including data on subregions).
The authors state: “We then divided the number of species in the most similar group by the total number of unique species in groups k and l from both webs”. I do not see this division in equation 4.
I am not sure how the simplification implied by eq. 5 affects the results? If one repeats the analysis twice, based on eq.4 (once for A-->B and once for B-->A), would it provide similar results?
What results show what was done in L166?
L. 170-171: “We arbitrarily set the minimum cluster size to three subregions”. How does the cluster size affect the results? Also, maybe expand a bit on the UMAP method? I feel I did not fully understand it.
Can the authors add a conceptual figure specifying the process of the data analysis? For example, it is difficult to follow what is species overlap vs group overlap. It will also help to understand how the metaweb data were divided into subregions etc.
Put Svalband on the map in 2A.
Did the authors only include significant interactions between abiotic conditions and group structure? How will this change if subregions are redefined?
For the species-specific turnover, an equation will be nice to have.
L.280. I am not familiar with the assumption that a pair of species that co-occur must interact. In fact, Poisot 2012 Ecol Lett does not assume that (the authors state so as well later on). I also did not follow the logic for how from this assumption one infers that using local food webs will give a more accurate description of group structure. I dont think there even exists an accurate description. The group structure will change with method (modularity vs SBM), scale (where to put the limit between regions) and sampling effort.
I think it would be worthwhile to quantify the interaction turnover between the 25 subregions using Poisot’s 2012 framework. It will be a good source of information to understand where does the variation in group structure come from. Currently, only species are accounted for (and interactions, indirectly in the SBM), but interaction turnover can also have an effect. Such analysis can be in the SI but it seems important.
In Fig 2 subregions 25 and 33 seem like outliers. Why??
Fig 4: I cannot understand how the same group is defined over more than one region. For example, is group 1 in subregion 25 the same as group 1 in subregion 22? If not, then how can you actually make this alluvial diagram? One could give some arbitrary names to groups and then the diagram would change, no?
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Reviewer report
2019/12/13See attachement
Comments to authors
General
This is an interesting and timely paper with some new and relevant findings for spatial food web ecology. It advances our understanding of spatial food web ecology by demonstrating how species roles change depending on food web resolution and location.
The methodology is well explained and rigorously performed. However, the environmental data used in this study is not described nor referenced. The paper reads well, but the language can still be improved. Some places commas and words are missing. The structure is also problematic at times. Ex. Figs. S1 and S3 from the supplementary material are not referenced in the result section, but described and referenced in the discussion. In addition, some findings are not discussed and referenced until the conclusion. Perhaps this is a matter of style and taste, but it feels disturbing that analyses, which have not been previously described, are suddenly discussed, and that some aspects (e.g. traits) are discussed in the conclusion. The mixing of results into the discussion makes the discussion somewhat descriptive, and some passages would perhaps do better in the result section. Besides, it is more interesting with a discussion that addresses the ecological relevance, interpretation and implications of the findings than a discussion that describes the findings, which is also my main concern with the manuscript. Although the authors discuss some implications of the findings and give a few examples of species changing their functional role with habitat and environment, it would improve this manuscript greatly if the discussion would be elaborated to include more reflections on the ecological relevance and implications of the findings. Any biological, functional and evolutionary considerations? The group model has previously identified ecologically relevant groups of species reflecting trophic guilds and habitat patterns. The link between groups and functional role is not entirely clear to me in this manuscript. For example, why does the sea spider in the Barents Sea change group affiliation, or role, with habitat and environment? Is it due to changes in its prey and/or predators or habitat, or all of these? Any ideas, is this finding meaningful at all, or an artefact of the data? It would be great with more explicit ecological considerations concerning the change (or lack of change) of species’ functional roles in a biogeographic context. For example, some groups of species seem to have higher species-wise turnover rates than others, how can this be explained in terms of ecology, can it be linked to species traits?
Find my detailed (minor) comments and suggestions below.
Intro
“The group model” used and discussed in this study is not the only model that has been applied to detect groups with ecological relevant interpretations. Other group detection models ex. modularity, structural and regular equivalence, and/or the TG model by Gauzens et al. 2015 could be briefly discussed in this context.
Line 27: The concept trophic species or trophospecies was defined and used before 2006. For example, by Yodzis in a paper from 1988. https://www.jstor.org/stable/pdf/1940449.pdf?refreqid=excelsior%3Af680aa06d43f46a301c323784dfea9c3
Line 33: Reference(s) to the stochastic block model are missing.
Line 45: in the final sentence of the introduction, the authors write: «the group model reveals additional structural patterns, which likely have implications for the functioning of ecological communities”
What are these additional structures, can you be more specific, are these discussed? What are the ecological implications?
Method section
Line 104: in this sentence the authors write “species within a group tend to eat and be eaten by the same other groups”. The group model partitions the food web in a “relaxed” way without including any biological information. It would be interesting to know, how often it happens that species from the same group do not share trophic interactions. Did the authors investigate this?
Line 113-115: This sentence is a bit unclear.
Line 119: What are these parameters?
Line 300: Do you mean trophic rewiring by this “mechanism”?
Line 204: Where do these environmental data (i.e, temperature and water depth) come from? They are not referenced anywhere, how were they sampled? There is also no figure or results showing the analyses, yet the results are discussed.
Discussion
I would recommend some restructuring and elaboration of the discussion section, some result passages could be moved to the result section and other paragraphs could be expanded. Overall, be careful that the discussion does not become too descriptive. It is more interesting with a discussion that addresses the ecological implications of the findings. You could also consider collapsing the result and discussion section into “Results and Discussion” instead of having them as two separate sections.
Lines 255-268: the intro paragraph of the discussion sounds more like an introduction.
Line 257: can you be more specific here, which factors?
Line 260: The authors write: “The trophic roles defined by the group model can be thought of as functional groups” It is not clear to me from this study what these functional groups are. Could this be made clearer, either with some additional analyses or by defining and discussing the groups more explicitly?
Lines 275 and 315: these findings are not new and were already described in the Kortsch et al. paper 2018b, and should be referenced here.
Lines 324-326: You mention a positive correlation between group structure and ocean depth and temperature. What data and analyses do you refer to in this sentence? If this environmental data is derived from another study, it should be referenced here.
Lines: 327-336: Here the discussion becomes very descriptive, and sounds more like result section.
Lines 347-352: Finally, some documented empirical examples of how species change their diet and trophic position (role) with habitat. However, this paragraph is very short, and a more thorough discussion on the ecological relevance could follow here. Why do species change their role, is it due to changes in prey and predators, or habitat, or all of these?
Line 354: This result is a methodological artefact of the dataset. Primary producers have no spatial turnover because they are present in every polygon (local food web) in the Kortsch et al. dataset. This is a bias and artefact of the dataset, because no detailed spatially resolved information exists for phytoplankton in the Barents Sea. Therefore, this result should be removed from figure 3 and not be discussed further, as it has no ecological meaning, but is an artefact of the data.
Line 357: This result (Fig 3b and c) is interesting but hardly discussed. Figure 3 shows that benthic species (e.g. Polychaeta and Ophiuroidea), being more sessile, have a higher species-wise group turnover than motile species such as Mammalia. Motility is a measurable trait. Can this specific trait be linked to the species-wise group turnover rates? Which functional implications does this finding have? Note: The sea spider is also a benthic species with high species-wise group turnover.
Line 367: “species with more links had lower turnover rates”. This is also an interesting finding that could be discussed more. It has previously been documented that species with more links (e.g. cod, see Kortsch et al. 2015 Climate change alters the structure of arctic marine food webs due to poleward shifts of boreal generalists ) are trophic and habitat generalists. Therefore, it makes sense that they exhibit lower species-wise group turnover rates, or?
Conclusion
Lines 378-380: This discussion about traits and the reference (Coux et al. 2016) should have come earlier in the discussion, not in the conclusion. I would suggest moving it from the conclusion to the discussion, e.g. related to Figure 3.
Lines 380-383: Again these lines belong to a discussion more than a conclusion. This discussion should have come earlier, and just be summarized briefly in the conclusion. Again, this might be matter of taste and style, but I would suggest the authors to be more stringent about the structure of the manuscript.
Text box and “Sea spider”
It is great that the authors us a concrete example (the sea spider) to illustrate how species change group membership, or functional role. However, why does the sea spider change group, is it an artefact of the data (due to e.g. false positive interactions as discussed) or due to some relevant ecological information. Is it due to changes in its prey or predators between regions, or due to environmental changes (temp. and sea ice) or the habitat (depth)? Why do sea spiders suddenly group with fish, due to changes in shared prey or predator, or both? Is there any ecological information in this findings, which could be discussed and help us understand why some species such as the sea spider change group affiliation (or functional role) across space.
Why is “changing groups” put in quotation marks here? Not necessary.
Language, spelling, commas
Line 11: consider to exchange the word “differ” with “vary”
Lines 77-79: verb and commas missing in this sentence. “The Barensts Sea is a shelf sea with a heterogeneous environment, bordering the Atlantic Ocean with the dissipating Gulf Steam in the west, and the Arctic Ocean to the north-east. “ or “The Barents Sea, a shelf sea with a heterogeneous environment, borders the Atlantic Ocean with the dissipating Gulf Steam in the south-west and the Arctic Ocean in the north-east.”
Line 6: write subregional food web with “al”, instead of subregion food webs
Line 103: “Groupings with a high likelihood have groups of species which acts in a similar way, that is…” “groupings have groups” does not sound good.
Line 113: word missing after looking in this sentence. Ex. “looking at”?
Line 135: “insight into”?, instead of insight in. Generally, this sentence does not read well.
Line 219: prey, not preys. “Prey” plural is always without the s.
Line 267: “prone to changes in group”.
Line 386: “Nevertheless” is not appropriate here. This sentence is not in contrast to the sentence before it.
Figures
Figure caption Fig 3. Do you mean species-wise group turnover here? You write species-wise turnover.
Figure 4. What are the ecological or functional roles of the groups in this figure? Is there any way to describe these groups in a relevant ecological way?Reviewed by
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