Adapting genetic algorithms for artificial evolution of visual patterns under selection from wild predators

Emmanuelle S. Briolat; George R. A. Hancock; Jolyon Troscianko

doi:10.1371/journal.pone.0295106

Peer Review History

Original SubmissionNovember 14, 2023
6 Mar 2024 Decision Letter - Matthew Shawkey, Editor PONE-D-23-37346Adapting genetic algorithms for artificial evolution of visual patterns under selection from wild predatorsPLOS ONE Dear Dr. Briolat, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Apr 20 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Additional Editor Comments: I apologise for the length of time this review process has taken. It was difficult to find willing reviewers and then one reviewer ultimately let us down after a long period of waiting. We have obtained one review and I have read the paper myself. I agree with the reviewer that this is an interesting and well-done paper, but also that the effects of uv coloration need to be taken into account and discussed in the manuscript. I look forward to receiving your revision. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). 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You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: In this manuscript the authors present an extension to the well-established field, laboratory, and computational methods that are widely used in studies of colour evolution and function. By developing a novel experimental and computational protocol they link field predation studies, screen-based detection experiments, and genetic algorithms. This protocol is tested using physical targets and wild birds and then compared to a similar experiment using digital targets and human participants. The main focus of the manuscript is to describe and test the methodological approach, in this regard the two protocols (field and screen-based) do find similar results when the same starting parameters (i.e., target colour space) are used (although starting conditions are shown to affect the results in the screen-based experiments). I think the authors have done an excellent job at explaining their study in a clear, engaging, and concise manner in both the main text and supplementary material. I only really have one main question about the methodology/interpretation and a couple of minor comments on the text. Firstly, the colour space used throughout the field experiment is CIELAB Lab* which does not extend into the ultraviolet. Did the background or any visible part of the targets (e.g., the white tack if visible) reflect UV? If so, could the inability of the printer/colour space to replicate UV (or near UV for VS birds) reflectance have rendered all targets highly detectable? For example, is it possible that if UV contrast is high for all targets selection on Lab* colours may have been reduced? I think this could be discussed in the Methods and/or SI1. Similarly, how may a mismatch between the printed colour space and the full range of visible colours affect the success of these evolutionary field studies? And are there any mitigations/cautions that you recommend be considered when designing these treatments/experiments (i.e., only use where UV will have a negligible effect)? I think limitations of the approach should be examined in the Discussion. Minor comments: Lines 101-103: Does the replication with humans also allow for assessment/benchmarking of the novel approach relative to established protocols? If you agree, I think you could add this as an additional benefit of your approach. Line 213: I am not familiar with waterslide transfer paper, but I assume this is not just sticking waterproof paper to the white tack - can you explain that this is a transfer more explicitly please (here or in the SI)? Lines 440-442: Do these similar psychophysics experiments use the full or a restricted colour space? Lines 445-448: It is not clear to me how your data relate to predator learning. Here, are you referring to observer learning in your dataset or describing the results presented in citation 33 (Troscianko et al. 2013. PLoS ONE)? ******** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0295106.r001
Revision 1
17 Apr 2024 Author Response We have addressed all editorial and reviewer comments in our cover letter for the resubmitted manuscript, and the "response to reviewers3 document attached with the submission. The cover letter contains a revised funding statement, following guidance from the decision letter. I have also pasted our responses to the reviewer's comments below: Editor comments: We have obtained one review and I have read the paper myself. I agree with the reviewer that this is an interesting and well-done paper, but also that the effects of uv coloration need to be taken into account and discussed in the manuscript. I look forward to receiving your revision. Thank you for reading our manuscript, and for your overall positive response. We have addressed the issue of UV vision in our avian predators in response to the reviewer’s comments on this subject, with additional clarification in the methods and discussion sections (see response to reviewer comments below for details). Reviewer #1: In this manuscript the authors present an extension to the well-established field, laboratory, and computational methods that are widely used in studies of colour evolution and function. By developing a novel experimental and computational protocol they link field predation studies, screen-based detection experiments, and genetic algorithms. This protocol is tested using physical targets and wild birds and then compared to a similar experiment using digital targets and human participants. The main focus of the manuscript is to describe and test the methodological approach, in this regard the two protocols (field and screen-based) do find similar results when the same starting parameters (i.e., target colour space) are used (although starting conditions are shown to affect the results in the screen-based experiments). I think the authors have done an excellent job at explaining their study in a clear, engaging, and concise manner in both the main text and supplementary material. I only really have one main question about the methodology/interpretation and a couple of minor comments on the text. We thank you for the generally positive review of our manuscript, and for your comments suggesting further improvements. Firstly, the colour space used throughout the field experiment is CIELAB Lab* which does not extend into the ultraviolet. Did the background or any visible part of the targets (e.g., the white tack if visible) reflect UV? If so, could the inability of the printer/colour space to replicate UV (or near UV for VS birds) reflectance have rendered all targets highly detectable? For example, is it possible that if UV contrast is high for all targets selection on Lab* colours may have been reduced? I think this could be discussed in the Methods and/or SI1. The patterns of the printed targets used in the field experiment were generated in CIELAB space by the CamoEvo software, but we then photographed the target patterns and backgrounds with bandpass filters allowing us to measure reflectance in the visible and UV range, and analysed colour contrasts using tetrachromatic models of bird vision (see Supplementary Information). This means that the contrast values between targets and backgrounds we provide in the results section account for any UV reflectance of the targets and backgrounds, and the full range of avian vision. Results from the new average colour difference metric, based on segmenting the target patterns and backgrounds into different colour patches, show close matches between at least some printer colours and background patches (ΔS1), demonstrating that the printer can produce colours that closely match the background, even accounting for UV (see figure 4a,b(ii) and supporting data). In this case, both the gravel backgrounds and targets have low UV reflectance. We have amended the text to explain this in the methods section (l. 218-225). Similarly, how may a mismatch between the printed colour space and the full range of visible colours affect the success of these evolutionary field studies? And are there any mitigations/cautions that you recommend be considered when designing these treatments/experiments (i.e., only use where UV will have a negligible effect)? I think limitations of the approach should be examined in the Discussion. The explanation in the methods section should already address some of these concerns, highlighting why the absence of control over the UV component of target patterns was not a substantial limitation in our case study. However, this is a really valid point: in general artificial predation experiments are somewhat limited by the ability to produce only a restricted range of colours, in this case based on the printer’s colour gamut. We have added a short section in the discussion to address the potential limitations of printing patterns, as well as to highlight how some of these difficulties can be overcome, or at least accounted for – by using different materials that do allow higher UV reflectance if this is required, and at least by photographing the actual prey items to analyse their coloration using models that do account for the full range of predator vision (see l. 533-548). Minor comments: Lines 101-103: Does the replication with humans also allow for assessment/benchmarking of the novel approach relative to established protocols? If you agree, I think you could add this as an additional benefit of your approach. Thank you for the suggestion – we have added in a note to that effect (l.102-103). Line 213: I am not familiar with waterslide transfer paper, but I assume this is not just sticking waterproof paper to the white tack - can you explain that this is a transfer more explicitly please (here or in the SI)? Waterslide paper is effectively a clear transfer film, bonded to an opaque white backing sheet so that it can easily be used in a standard printer. When the paper is briefly soaked in water, the clear film separates from the backing sheet, and can be placed on the surface of the target item (this can be a layer of white tack, as in our case study, or directly onto a thermoplastic or 3D printed shell). When damp, the clear film adheres well to the new surface, and then becomes very difficult to remove, so it lasts well even in field conditions. We have added a sentence in the methods to explain the process more explicitly (l. 215-218). Lines 440-442: Do these similar psychophysics experiments use the full or a restricted colour space? The colour space used in the paper cited here (Hancock Troscianko, 2022) corresponds to CamoEvo’s default settings (CIELAB space with a luminance range of 0, 100, A range of −60, 60, and B range of −10, 70) and is very similar to the full colour space used in the field trials in this present manuscript (L: 0 – 100, A: -50 – 50, B: -10 – 70, see Methods). We have added a note to make that similarity explicit (l. 452-453) Lines 445-448: It is not clear to me how your data relate to predator learning. Here, are you referring to observer learning in your dataset or describing the results presented in citation 33 (Troscianko et al. 2013. PLoS ONE)? In this sentence, we are indeed describing the findings in reference 33 (Troscianko et al. 2013); we have now added more description of their results to make this clearer (l. 455-463). Since the same birds are returning day after day to the trays in our field experiments, we expect learning to be an important component of how these birds respond as the experiments progress. In Troscianko et al. (2013), a series of screen-based experiments with human “predators” clicking on targets employing various camouflage strategies (distractive markings, disruptive camouflage, background-matching), trends in detection times across trials revealed differences in how participants improved in detecting the different target types, based on the design of the experiments, i.e. whether targets were shown sequentially or simultaneously on the same screen, and if the latter, how many targets were shown at once. This difference in target presentation is therefore likely to be an important factor in determining the strategies employed by predators searching for the targets; this will affect which targets are found first, hence shaping the evolution of target patterns in our experiment, and likely explaining some of the difference in outcomes between our setup (where multiple prey are shown at once) and comparable experiments in Hancock Troscianko (2022), where targets are shown one at a time. We have now amended the text to more explicitly explain this (l. 455-466). Attachments Attachment Submitted filename: Response to reviewers.docx https://doi.org/10.1371/journal.pone.0295106.r002
30 Apr 2024 Decision Letter - Matthew Shawkey, Editor Adapting genetic algorithms for artificial evolution of visual patterns under selection from wild predators PONE-D-23-37346R1 Dear Dr. Briolat, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Matthew Shawkey Academic Editor PLOS ONE Additional Editor Comments (optional): Congratulations on your interesting work! Reviewers' comments: https://doi.org/10.1371/journal.pone.0295106.r003
Formally Accepted
3 May 2024 Acceptance Letter - Matthew Shawkey, Editor PONE-D-23-37346R1 PLOS ONE Dear Dr. Briolat, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Matthew Shawkey Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0295106.r004

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