Phylogeography of Mesophotic Coral Ecosystems: Squirrelfish and Soldierfish (Holocentriformes: Holocentridae)

Round 1

Reviewer 1 Report

This study examines the population structure of two mesophotic reef fish species in an effort to compare their population genetic patterns to three shallow water species in the same family. In general, I find their effort and approach commendable, although it is not perfect. However, on the geographic scales of the species they are studying, and across the depths these species occur at, perfect does not exist. 

I do have some major concerns with the study. These primarily deal with the fact that they are relying on a single mitochondrial locus (that is different than the one used in prior studies for the shallow water species), and that they are comparing species that occur in different ocean basins, among a few other minor concerns. Yet the authors acknowledge these caveats very transparently at the beginning of the section 4.1, which I appreciate. There are still areas that I believe could be improved, though. 

One suggestion I have deals with Figure 5. This is the main comparative figure, so it should be strong and very informative, but the colors are arbitrarily assigned and impossible to interpret (at least for the shallow water species). One must refer to the original publications to understand the geographic context of the haplotype networks, which is not ideal. Ideally there would be two maps (Atlantic and Indo-Pacific) so the reader could understand this, yet this would also result in a difficult and busy figure. One possibility would be to include more specific figures in supplemental figures. At the very least readers would not have to get access to prior publications just to interpret the comparisons in this study. 

I also would recommend that the authors include a table that compare the phiST values, haplotype and nucleotide diversity values, and coalescent estimates for all five species compared in this study. This data is presented textually in the Discussion, but a table would make it very easy for a reader to compare these values. It may be somewhat redundant with the other tables and Figure 3, but Figure 3 doesn't contain the nucleotide and haplotype diversity values for the shallow water species and that data isn't reported in the other tables. It would also be very easy to make this table, but I'll leave it up to the authors if they think it would be helpful or not.

These species all have considerable depth ranges. While some are more common in shallow waters or deep waters, many depth ranges overlap. The authors comment on this, but I was wondering if they could discuss specific transect data that shows what depths species are most abundant. I know that transect data is not likely available across entire ranges, and may be spotty, but it would make a stronger statement than the authors just saying what depth they think a species is most abundant at. Lastly, there is a lot of discussion on PLD and how it might influence these results. Perhaps the authors could discuss if there are any differences in depth where the larvae of all species occur in the water column. While adults may be found at different depths, larvae may all be behaving similarly, which could be another factor that could result in similar connectivity patterns in deep and shallow species.

Overall, while not perfect, I did enjoy reading this manuscript and think that it presents very valuable information and data for a region of the worlds oceans that are extremely difficult to sample. I commend the authors for their effort in obtaining these samples, and hope to eventually see this manuscript in print soon. 

Author Response

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Author Response File: Author Response.docx

Reviewer 2 Report

The manuscript presented by Copus, et al. describes the patterns of population divergence for two coral reef fishes of the Holocentridae family with mesophotic habit in the Western Pacific (mostly the Hawaiian Islands). The main aim of the study is to determine if populations of mesophotic fishes are older than shallow water ones, as described by the "Habitat persistence hypothesis" For this the authors analyzed mitochondrial sequences (COI), and compared the results to shallow water species of the same family, characterized in previous manuscripts. The results suggest frequent connectivity for one of the species across the sampled range, while another species has a small number of significant population breaks. The study concludes that there is no real difference in the patterns of mitochondrial divergence and time to most recent common ancestor, which does not support the habitat persistance hypothesis. 

 

Overall the manuscript is well written, it is a relevant topic for marine science, and the data mostly supports the conclusions. Yet there are some minor items that should be addressed before publication. 

 

Major considerations: 

One of the biggest issues with the manuscript is the suggestion that the mutation rate for COI and CytB is the same. Across many studies of phylogeography, it is evident that CytB has a slightly faster mutation rate than COI, which usually leads to many more haplotypes, and different estimates of time to most recent common ancestor. I agree with the authors that there is no reason to think there will be large differences between shallow and mesophotic species, yet using the same rate is not appropriate. I would encourage the authors to re-estimate the results of time to recent ancestor of COI with Beast, using the mutation rates of COI discussed by Lessios 2018 (The great american schism), and present both results in the MS. This might be more convincing that using the same rates as CytB. 

 

Another issue is that the hypothesis of having different Ne's in mesophotic species is largely speculative, specially for fishes with high abundance like the Holocentrids. I think it is much more plausible to have a mitochondrial sweep that erases signatures of stability, or that mesophotic environments are not as stable as previously described (Following Rocha's observations). Another important consideration is that many of these Holocentrids move to shallower waters at night, and thus the distinction might not be as clear as for species that are exclusively found in mesophotic ecosystems. Hence I would encourage the authors to re-consider the last section of the conclusion. 

 

Minor comments: 

Unfortunately the line numbers stopped after a certain page, so it will be a bit challenging to identify the different sections. 

 

Line 33: Eliminate the last section of the line (relative to MCE fishes). 

Line 64-65: This needs a citation, perhaps Ludt, W. B., & Rocha, L. A. (2015). Shifting seas: The impacts of Pleistocene sea‐level fluctuations on the evolution of tropical marine taxa. Journal of Biogeography, 42(1), 25-38.

Lines 101-103. Somewhere around this section there should be reference made to Tables 1 & 2, so that readers can see the collection sites and number of samples per site. 

Line 139-140: How was this analyzed? Was there a specific program? More details would be helpful. 

Page 10- Second paragraph of the discussion: the authors should consider including Ludt et al. 2012. Living in the past: phylogeography and population histories of Indo-Pacific wrasses (genus Halichoeres) in shallow lagoons versus outer reef slopes. PLoS One, 7(6), e38042. THis manuscript deals with a similar concept using the genus Halichoeres. 

Page 11 - several sections: For whatever reason the whole genus name for the species is presented here, and not just the first initial. Please adjust this for clarity. 

 

Conclusion: I am not convinced this is the first phylogeography treatment for mesophotic species. Just mention that it is one of the few ones.  

 

Figure 5: I think this figure is somewhat misleading, given the fact that the data was collected with different markers and that the samples come from different sites. I would suggest to include the sample sites so the readers can actually see which locations have been included, and that the authors mark which networks use CytB and which ones COI. If that is too big, it can always be moved to the supplement. 

Author Response

Please see the attachment

Author Response File: Author Response.docx