PONE-D-23-31936Performance of different automatic photographic identification software for larvae and adults of the European fire salamanderPLOS ONE

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Reviewers' comments:

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Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: Yes

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Reviewer #1: No

Reviewer #2: No

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: This is a nice and well-written manuscript where authors compare the accuracy of four softwares for individual recognition of species with well defined pattern, in the specific case for the fire salamander. I find it interesting but with a too narrow scope for this journal. I would recommend to target a more sectorial journal, especially because the whole study is focused on a single species. Furthermore, the used dataset is missing as supplementary material

Reviewer #2: Schulte et al. describe a study in which they compare a series of programs used in automatic photographic identification for photo-mark-recapture techniques. I find this topic to be a valuable contribution to the field, and I think the authors describe their results succinctly and relatively clearly. My only major reservation is that the authors never define “Recognition Rate”, which makes some of the results uninterpretable. I think that this is something that the authors could easily fix, though. Below are some more minor line-by-line comments.

Line 26: There is a mismatch in singular vs. plural here. I would recommend changing it to “An alternative can be found among non-invasive techniques…” or something like that.

Line 32: I think that “computer-based” is redundant and unnecessary here.

Lines 34–35: As I understand it, this is a current limitation of this software. But it may not be permanent. So I would say, “…larvae can currently only be identified…”. Perhaps new modules will become available in the future, so to make sure this study remains accurate through time, I would encourage the authors to rephrase this.

Line 36: Change “larvae” to “larval”. In general, this manuscript is well-written and the English is clear. There are several places where it could use some minor improvement, but I do not view this as a barrier to publication. If the authors are interested, the Society for the Study of Amphibians and Reptiles does offer a Manuscript Review Service for this purpose (see details here: https://ssarherps.org/publications/manuscript-review-service/).

Line 51: There is an updated analysis that was recently published on this topic. “Ongoing declines for the world’s amphibians in the face of emerging threats” by Luedtke et al. (2023). The authors may wish to cite this for the latest information.

Line 61: Unless I am misunderstanding, I think these are more often referred to as “bands” than “rings”.

Lines 119–120: It is not technically wrong to say “…the following five software”, but it would be more common in English to say “…the following five software programs”, even if it is unnecessarily redundant in meaning. Just an idiosyncrasy of the language. I don’t think a change here (and in other places throughout the manuscript where this comment is relevant) is necessary, but the authors may want to consider it.

Lines 182–184: I think the authors should consider citing “Computer-assisted photo identification outperforms visible implant elastomers in an endangered salamander, Eurycea tonkawae” by Bendik et al. (2013) as another example of Wild-ID being applied to salamanders. Perhaps the information in the discussion of this paper would also prove valuable.

Line 186: As the authors describe earlier, image processing is recommended for Wild-ID, but it is not required. This should be clearer in the table.

Line 231: Recognition Rate should also be defined clearly here. The results are hard to interpret otherwise.

Line 233: Does “we used the existing FRR from Faul et al. (2022)” mean that the authors simply adopted the definitions from this paper, but recalculate these values? Or that they simply report the exact same values originally calculated in that study?

Line 256: Should this say “FRR” instead of “FFR”? Likewise on Lines 257, 267, and several other places.

Line 296: As noted earlier, I think it is critical that “Recognition Rate” (RR) is defined. I would have assumed that it means something like “the probability of identifying a true match somewhere in the list of potential matches”. However, this doesn’t appear to be possible. For example, an FRR1 of 15.12 in Wild-ID would suggest that the correct match *was* identified in the first position for ~85% of photographs. However, the RR is only 37.88. This seems to mean that my intuition is wrong about the definition of RR. I think that a better explanation of this should be a priority.

Line 337: I think the authors may consider expanding their discussion in two ways: 1) Would there be value in combining several of these methods? The authors acknowledge that manual visual inspection + software is very effective. But what about, for example, ARW + Wild-ID? Would that improve the ability to do this reliably?; and 2) This seems like a field that is likely to change quickly and dramatically with the advent of modern artificial intelligence tools. Is there reason to believe that all of these existing tools (i.e., the ones compared in this study) might be replaced in the near future? I am not asking the authors to speculate wildly, but a brief discussion of the future directions for these methods might prove useful.

Line 374: This does not appear to satisfy the PLOS Data policy. I recommend making these underlying data available in a public repository.

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Reviewer #1: No

Reviewer #2: No

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Performance of different automatic photographic identification software for larvae and adults of the European fire salamander

PONE-D-23-31936R1

Dear Dr. Schulte,

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.

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Kind regards,

Christopher Nice, Ph.D.

Academic Editor

PLOS ONE

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