Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: A LITTLE FROG LEAPS A LONG WAY: COMPOUNDED COLONIZATIONS OF THE INDIAN SUBCONTINENT DISCOVERED IN THE TINY ORIENTAL FROG GENUS MICROHYLA (AMPHIBIA: MICROHYLIDAE)
Review round: 1
Reviewer: 1

Output:
Basic reporting: Abstract – The MS has three parts: time-calibrated phylogenetic analysis, reconstructed biogeographic histories, and morphological evolution. I think the readers would appreciate it if you add a sentence stating the aim of the study (mentioning the different parts) before presenting a summary of the results of each part.
My comments on the introduction are mainly on framing the study.
Introduction, Paragraphs 1 and 2, Lines 66–98:
Paragraph 1 framed post-collision biotic interchange between the Indian Subcontinent and Eurasian landmass; whereas, Paragraph 2 framed (mainly) pre-collision biotic interchange.

In your 2nd paragraph, you opened the paragraph with a passing statement on the diversity of the indo-malayan realm, then discussed pre-collision biotic interchange. I think these two topics, along with the 1st paragraph on post-collision biotic interchange, could be better framed with the following suggestions:
1st Paragraph – a short paragraph on the extreme diversity in the Indomalayan Realm (for amphibians, Bain et al. 2008 is a good starting resource -- found in Stuart et al. 2008 [opensource]), then perhaps enumerating key geological and climatic histories as factors that caused such diversity. Also, I suggest not using "global biodiversity hotspots" as, although it infers high biological diversity, it is more of a biodiversity conservation-linked term, rather than a biogeographic (theoretical) term.
Bain, R., Biju, S. D., Brown, R. M., Das, I., Diesmos, A. C., Dutta, S., ... & Lau, M. W. N. (2008). Amphibians of the Indomalayan realm. Threatened Amphibians of the World. Lynx Ediciones,
Stuart, S. N. (Ed.). (2008). Threatened amphibians of the world. Lynx Edicions.

2nd and 3rd (or into one paragraph) Paragraphs – Frame the competing biogeographic hypotheses: you identified four potentially competing hypotheses – (1) post-collision “out-of-India”, (2) post-collision “out-of-Eurasia”, (3) pre-collision “out-of-India, (4) pre-collision “out-of-Eurasia”.
Few notes,
Introduction, Line 79: the use of “however” as conjunction infers the "out-of-India" and "out-of-Eurasia" hypotheses as competing (mutually exclusive) hypothesis. However, the fact that multiple evidence supports both hypotheses suggests non-unidirectional biotic interchange -- both may have co-occurred. "However" may not be the most appropriate conjunction.

Paragraphs 4 and 5, Lines 115–144 framed the genus Microhyla in terms of its known diversity, distribution, and phylogeny.
Lines 121–123: “Microhyla was questioned by …” omit sentence from the paragraph; I think it is better placed into the next paragraph.
Line 127: “muddying” – use another term.
Line 120: Cite the source of the geographic range maps used in creating the figure (e.g., adopted from a previous publication, IUCN, expert delimited, etc.).
Paragraph 5, Lines 132–144: frames the rationale of the study. This paragraph discusses the current knowledge of Microhyla phylogenetics and biogeography.
I recommend more synthesis of thought – (i) start with an overarching opening sentence (that covers phylogenetics and biogeographic inferences (rather than having both topics discussed separately within the paragraph). Else, break this paragraph to two: one for phylogeny and another for biogeography. (ii) synthesize (and give more justice) to literature -- rather than simply describing them in passing. (iii) lastly, enumerate the shortfalls or aspects where we can further advance our understanding of the froup’s phylogeny and biogeography.
There will definitely be some redundancy with parts of your discussion, but I think this is inevitable; I think it is important for you to show your readers that you have thoroughly dissected the current literature (especially that latest studies on Microhyla phylogenetics was very recent), identified shortfalls and areas of advancement. I agree that one of the major gaps in past research is the biased taxonomic/geographic representation of species (mostly assessed from the Indian Subcontinent), and that wider taxonomic sampling will result in phylogenetic trees and biogeographic inferences at finer resolutions – as what you have done in your study; leverage on this.

Lines 134–137: “However, they were … “ – break and rephrase this sentence.

Paragraph 6, Lines 145–155: the aims of the study.
Lines 147–148: “… ; phylogenetic information for 12 species and a number of undescribed species … “ make sure to explicitly express that these are presumably undescribed species.

Materials and methods
Taxon sampling

Lines 159–168 – make sure to cite at the end of this paragraph Table S1.
Lines 175–176 – Add a supplementary figure of distribution of samples; analogous to Fig S1 but delimited to species (instead of sampled and genbank) and with each point labeled accordingly (i.e., numbering of samples used in the MS). This gives a better picture of your taxonomic sampling, particularly for species with wide and disjunct ranges (putatively comprising of multiple sub/species – as shown in your study).

Lines 177 – “… removed …” – sampled?

Results
phylogenetic relationships, and species groups in Microhyla.
-	For brevity, and a matter of taste: in describing the distribution of species (or clades), maybe use a consistent geographical terminology; septically, I suggest consistently describing geographic distribution in the context of biogeographic areas (as enumerated in Figure 2 and described in Supp Info 1), rather than geopolitical regions (e.g., Myanmar, India, China, etc.).

Discussion, same comment with results.

Figure 1 – as mentioned above, cite the source of data on species geographic ranges. also cite the software used to create the maps.

Figure 4–7 – If you can follow one single theme for both figures; also, although I highly appreciate images of representative species (it definitely enables readers to better appreciate the size variations in the group), I think it somewhat clutters the figures (overwhelming) in some instances. I suggest selecting a good representative species for each clade (one that exemplifies the morphology of the clade), if possible. If it is not yet scaled in its current form, scale the figures of species by their size and include a scale bar.

Legends of the supplementary tables and figures were not supplied.

Add a supplementary figures/table detailing the results of the phylogenetic analysis on proximal nodes of the trees (intra-specific) – although may not be informative as the markers used may not be able to capture inter-population genetic variations. Detailed reconstruction of the phylogeny of numerous amphibian groups in the Indomalayan realm (e.g., Polypedates leucomystax – Brown et al. 2010; Duttaphrynus melanostictus – Reilly et al. 2017) revealed fairly recent inter-population admixtures, as a result of human-mediated dispersal and introduction, and biogeographers and invasion biologists speculate genetic admixtures to be common as well in other widely distributed amphibian groups (and other taxa) in the region. Microhyla is likely one of these amphibian groups; three Microhyla spp. (M. fissipes, M. pulchra, M. ornata, and potentially more) have been introduced (recently) and/or established outside their native ranges, and as mentioned in Lines 713–715, human-mediated dispersal and introduction have been previously hypothesized in M. kodial (but disproved by this study). Providing information on the findings of Phylogenetic analysis on the proximal nodes of the trees would be useful for future researchers interested in recent-human-mediated colonization events.
Experimental design: As mentioned in the previous section, give more context on current lit in the introduction.
In Supplementary Table S7, identify samples (you) measured in the study (for morphological evolution) and their corresponding accession numbers, if any. You did mention that you gathered data from the literature, and measured museum specimens.

For research ethics purposes, cite (in acknowledgment), where applicable, permits acquired to conduct the field sampling.
Validity of the findings: Overall, the primary contribution of their MS is the phylogenetic analysis, which has an almost complete representation of currently recognized (in addition to potentially undescribed) species and thereby, with a finer resolution. Secondly, with their time-calibrated phylogenetic analysis, the provided biogeographic inference that is arguably more robust than recent past studies; their overall findings on the biogeography of Microhyla conforms with previous studies – out-of-Asia colonization to Indian sub-continent. Microhyla thereby in all technicality supports the post-collision out of Asia hypothesis, but, as also a case of Microhylinae recolonization, does it really? Or is it strong evidence in support of the hypothesis?
Additional comments: It is a pleasure to be given the opportunity to read and comment on the manuscript (hereafter “MS”) of Gorin et al., which updated the current knowledge on the phylogeny of the genus Microhyla (family Microhylidae; with dating estimates, and a near-complete representation of currently recognized distinct species), reconstructed the group's biogeographic history and diversification, and analyzed their morphological evolution in the context of miniaturization

I am convinced that the MS is a significant contribution to the growing body of knowledge on faunal biogeography in the indo-malayan realm, and particularly to a cryptic and widely distributed group of amphibian(s) – Microhyla spp. – exhibiting a diverse, peculiar, and novel eco-morphological evolution.
The MS was well-written (great technical quality), its theoretical framework sufficiently contextualized (but can be further improved), and findings were well-described and discussed; however, the MS can further improve in few minor aspects on basic reporting and experimental design.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: A LITTLE FROG LEAPS A LONG WAY: COMPOUNDED COLONIZATIONS OF THE INDIAN SUBCONTINENT DISCOVERED IN THE TINY ORIENTAL FROG GENUS MICROHYLA (AMPHIBIA: MICROHYLIDAE)
Review round: 1
Reviewer: 2

Output:
Basic reporting: I found the MS titled “A little frog leaps a long way: Multiple invasions to the Indian
Subcontinent discovered in the Oriental tiny frog genus Microhyla (Amphibia: Microhylidae)” to be an interesting read. It provides an insight into the origins and biogeography of frogs in the genus Microhyla using molecular evidence.

The MS is clearly written, referenced with up to date citations and placed in the broad context of what is known about Microhyla biogeography. The work is relevant and an important contribution to advancing the field and the narrative throughout the MS is cogent and self-contained.

A minor issue I had was with how the results were written. I have marked out sections of the results which need to be re-written because the authors simply point the reader to a table or a figure in the results by saying- results of this analysis are shown in fig xx. As a reader, I expect to read your results/interpretations and not see a figure and understand things from it. Figures and tables should be stand-alone but they should also complement your text.
Experimental design: The authors have sampled to include most of the species in the genus they are studying and use relevant resources already available as well. The raw data is provided and accession numbers to resources used from literature are provided. The methods provided are in sufficient detail to understand and even repeat the study.
Validity of the findings: The results from this paper are insightful and such a study was long overdue. In recent years, many species of Microhyla were described and it was only a matter of time till someone tested the hypothesis of their evolutionary origins. This MS bridges a large knowledge gap by providing an updated phylogeny, delimitation of potential undescribed lineages, and providing evidence to a SE Asian origin hypothesis.
Additional comments: I enjoyed reading your MS but struggled to easily grasp the details largely because of how results were presented and having had to go back and forth from one figure to another. I think your figures are good but contain too much information and need to be explained for e.g. see sections of the discussion highlighted in the PDF. With a little tweaking of how results are conveyed- I think the paper will be widely read and comprehended easily.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: A LITTLE FROG LEAPS A LONG WAY: COMPOUNDED COLONIZATIONS OF THE INDIAN SUBCONTINENT DISCOVERED IN THE TINY ORIENTAL FROG GENUS MICROHYLA (AMPHIBIA: MICROHYLIDAE)
Review round: 2
Reviewer: 1

Output:
Basic reporting: firstly, let me respond to their response to my comments/suggestions on the earlier version of the manuscript:
Regarding comment REV1C9, I meant proper citation of spatial data: see the “Citing Spatial Data” section in https://www.iucnredlist.org/about/citationinfo
Examples of full citations for spatial data:
IUCN (International Union for Conservation of Nature) 2019. Ochotona iliensis. The IUCN Red List of Threatened Species. Version 2020-1. http://www.iucnredlist.org. Downloaded on 19 March 2020.

I suggest further proofreading.

Abstract, Line 33:
Omit “The small-sized genus Microhyla” as this (its small size) has already been mentioned in the previous sentence. Replace this with “The genus”.

Abstract, Line 37–39:
“Our updated phylogeny of the genus with nearly complete taxon sampling includes 48 nominal Microhyla species and several undescribed candidate species.” This doesn’t sound right. Maybe try:
“Our updated phylogeny of the genus includes 48 nominal species and several undescribed candidate species, constituting a nearly complete taxon sampling.”

Abstract, Line 39:
“… both …” Both or combined?

Abstract, Lines 39–42:
“Phylogenetic analyses of 3207 bp of both mtDNA and nuDNA data recovered three well-supported groups: the Glyphoglossus clade, Southeast Asian Microhyla II clade (includes M. annectens species group), and a diverse Microhyla I clade including all other species.”
I have mixed opinions on the inclusion of “Glyphoglossus clade” here; wouldn’t it be more sound (with regards having a clear focus) to say instead “… supports monophyly in the genus Microhyla, with genus Gluphoglossus as its sister taxa. Moreover, our analysis recovered two well-supported groups within the genus: Microhylia I clade … ” Or something like that.

Introduction, Lines 73–76:
Suggested edit: “Notably, recent studies combining data on the region's tectonic history and paleoclimate with phylogenetics of different faunal and floral groups (e.g., De Bruyn et al., 2014; site ~2 more landmark papers) has enabled thorough examination of the biogeographic and evolutionary processes that ultimately lead to the region's high biodiversity.” Or something like that.

Introduction, Line 86:
“…) the so-called, ..”
Suggested edit: “; this biogeographic hypothesis has been referred to as …”

Introduction, Line 89:
“…animal…” ; be consistent in using: plant and animal vs. floral and faunal.

Introduction, Line 91:
“… during its collision”; during or post-collision?

Introduction, Line 94–95:
 “There is an ongoing debate on timing and topography of the ISC–Eurasian collision … ” The body of the paragraph does not relate to its opening. I suggest omitting the first sentence or transferring it to the previous paragraph.

Introduction, Line 100:
omit “demonstrating that they likely went in both directions: “out of India” and “out of Eurasia”; I suggest replacing this with “and suggested that the faunal exchange between regions went in both directions.”

Introduction, Line 102 – 104:
Suggested edit: “Despite recent advancements in our understanding of the biogeographic history of the region, the implications of pre- and post-collision “out-of-India” or “out-of-Eurasia” biogeographic scenarios on biotic exchanges between the ISC and the Asian mainland remains unresolved.”

Introduction, Line 121:
I suggest the following edit: “The genus Microhyla is the only Asian microhylid genus with a wide distribution over South, Southeast, and East Asia (see Fig. 1). It is also the most species-rich genus in the Microhylinae, currently comprising 50 recognized species (Poyarkov et al., 2014, 2019; Biju et al., 2019). Because of its wide distribution and high species diversity, It is an ideal model system for studies on Asian biogeography.”

Introduction, Lines 130–133:
“Molecular phylogenetic …”
I have mixed opinions on this sentence: You identified here a problem and a possible solution, but this isn’t exactly something addressed by your study (although iteratively repeated in the discussion); you only fulfilled one part of this herculean task –molecular phylogenetic analysis with a near-complete taxon sampling. You also elaborated gaps in knowledge of the species’ molecular phylogeny in the next paragraph.
Maybe omit this?

Introduction, Line 134–137:
I suggest omitting the first two sentences (the latter, I suggest transferring to the previous paragraph). Begin with “Phylogenetic relationships …”

Introduction, Line 150–151:
 “… molecularly previously unstudied …” doesn’t sound right.

Introduction, Lines 161:
maybe omit “the first”

Introduction, Lines 161 – 163:
This is not clear, can you revise this (especially the “links the Indian Subcontinent with Sundaland, Indo-Burma, and East Asia….”).

Materials and Methods, Lines 178–187:
Although I applaud that the field surveys (not yours) from which the specimens were collected were conducted ethically, I suggest transferring the listed permit numbers (and granting institutions) in the acknowledgement. You can simply write here: “Permits to conduct fieldwork and collect specimens, where applicable, were obtained from respective institutions.” Or something like that.

Materials and Methods, Line 327:
“… the tremendous geological complexity of the region through time,”
Not sure if this is correct: what about "Given the region's highly complex geological history"?

Discussion, Lines 550–566:
I suggest, prior to discussing your findings (updated phylogeny), give context first on earlier studies on Microhyla phylogeny. Thus, I suggest transferring Lines 551–556 (starting from “we present …” and as a paragraph) after paragraph Lines 579–591. Confer to how you discussed biogeography.

Discussion, Line 592:
Prior to discussing the individual species groups, is it possible to discuss very briefly the two major clades (Microhyla I and II), particularly their morphological differences.
Experimental design: Background on relevant theories and concepts are well contextualized. Relevant literature well and succinctly reviewed (in the introduction). Knowledge gaps and their implications were identified. Methods were sufficiently detailed, allowing replicability of the study. Their extensive supplementary materials detailing the materials used is a plus. The analysis (and data collection) were performed to a high ethical standard.
Validity of the findings: The conclusions addressed their original research question and were consistent with/limited to their findings. Recommendations for future research is a plus. The plausibility of their speculations was sufficiently argued, evidence-based, and logical. Underlying data shared as supplementary materials is a plus.
Additional comments: It was an absolute pleasure to be given the opportunity to comment to and provide suggestions for the improvement of Gorin et al.’s manuscript. It is good to know that they considered both reviewers comments; for my comments and suggestions, I am very satisfied with their point-by-responses. Overall, the manuscript significantly improved.
I commend how they thoroughly edited/revised the results and discussion section (not to mention extending their analysis). It is much clear now how their paper stacked-up to related literature (especially to very recent papers on the topic), and how it advanced our understanding on Microhylidae/Microhyla phylogenetics and biogeography, and Asian biogeography in general.
Although I have no more comments on the experimental design and the validity of the findings, I think the manuscript can still benefit with a few improvements on basic reporting.
1.	Introduction section. The background on theories and concepts have significantly improved, and current state of knowledge on Microhylidae and Microhyla phylogenetics sufficiently contextualized; however, I think the manuscript can benefit with some further improvement on the construction and flow of thought. I also suggest further proofreading. I enumerated my suggestions in the basic reporting section.
2.	Results section. I suggest limiting (if not omitting any) comparisons here (i.e., comparing your findings with previous studies, whether they conform or vary). I suggest strictly describing your findings here and keep your comparisons in the Discussion section. You did mention in your response that you wanted to keep the results concise; I think making comparisons here does the contrary.
3.	Discussion section. Overall, the discussion section is superb! I just have a minor suggestion (see the basic reporting section).
4.	Figures. I am satisfied with your response to my comment/suggestion on Figure 1. For the other figures (except figure 3), It’s important to note that both reviewers had similar comments on them (i.e., that some figures are a bit overwhelming). There were hardly any changes/improvements in the figures.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: A LITTLE FROG LEAPS A LONG WAY: COMPOUNDED COLONIZATIONS OF THE INDIAN SUBCONTINENT DISCOVERED IN THE TINY ORIENTAL FROG GENUS MICROHYLA (AMPHIBIA: MICROHYLIDAE)
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript has been revised sufficiently. The MS now has increased clarity and flow throughout.
Experimental design: It is nice of the authors to include the information on taxon sampling and permits.
Validity of the findings: The authors have improved the analysis and this provides more basis for the conclusions they are drawing. The discussion section is substantially improved as well.
Additional comments: None.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE IMPACT OF SHORT-TERM EXPOSURE TO NEAR SHORE STRESSORS ON THE EARLY LIFE STAGES OF THE REEF BUILDING CORAL MONTIPORA CAPITATA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Relatively clearly written, the only ambiguity was regarding descriptions in the methodology (detailed later).

Coverage of the literature was OK but needs updating, particularly with respect to the effects of sediments on the early life stages of coral (detailed later)

Structure good, Figures and Table need more description, Raw data needs some extra details

Self-contained with relevant results and hypotheses – but some clarification needed to describe the effects on survival and settlement as being latent (not directly due to the treatments).
Experimental design: Original primary research within Aims and Scope of the journal -  yes

Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap - more detail needed to show how this research fits with that of more recent studies.

Rigorous investigation performed to a high technical & ethical standard - yes

Methods described with sufficient detail & information to replicate - needs some clarification see general comments to the Author.
Validity of the findings: Results are valid but I would like to know if the methodology may have resulted in an experimental artefact that could affect the results. It is not clear to me exactly how this was done experimentally, but if the embryos were left with the original sperm for the first 24 h this could exacerbate the effect of all the treatments. Ideally the surviving successful embryos would be cleaned of sperm and placed in new seawater (or treatment seawater) and the experiment continued. Dying sperm will stick to sediments and increase bacterial loads, especially in high temperature treatments (maybe also low salinity treatments). The authors should clarify all of this in methods and discuss later if it is seen as an issue.
Additional comments: Abstract: needs considerable editing to make clear the sequence of exposures and the timing – the Abstract is far too ambiguous at present.

L32: “Effects of of sedimentation (100 mg l-1 and 200 mg l-1 ), osmotic stress through lowered salinity (28 ‰), and elevated temperature (31°C) on the successful fertilization, larval survival, and settlement” – were these separate, simultaneous or sequential? Please detail.

L32: The term “sedimentation” was used to describe two suspended (SS) concentrations. Sedimentaion means something different (the deposition of sediment), please change to “suspended sediment concentrations”

L35: I don’t think gametes can be exposed, for 24 h. After a few hours – 6? Gametes are either fertilised or dead? – rephrase please.

L36: How long were larvae exposed? How old were the larvae? Gametes do not develop into larvae until + 24 h. Please be more precise with descriptions of what exactly was exposed and for how long.

Introduction: Concise and clear but overlooks the most relevant prior literature

Line 45: “rapidly experiencing global decline” but you cite references 15 and 19 years old – please update

Line 55: more info on where “Kāne‘ohe Bay, O‘ahu” is in the world.

Line 69: how much warmer than the average summer maxima?

Line 75: update reference with more recent reviews (i.e. Jones et al., 2016 Mar. Pollut. Bull. 102:9-29)

Line 76: “However, very little is known about how these near shore stressors affect the early life stages of coral, especially in Hawaiian coral”. Maybe for Hawaiian coral but since 2015 there has been a very large body of work done on the effects of suspended sediments, sediment deposition and thermal stress on coral fertilisation, larval survival and larval settlement (see multiple relevant papers by Ricardo et al. and Humanes et al.,) and before that more than 10 studies on the effects of temperature alone on coral reproduction alone. Please refer to at least some of this very relevant literature.

Line 83: exposing gametes for 24 h. “gametes” are the eggs and sperm only. Please rephrase to let us know how old each of your life stages were.

Materials and methods: The treatment sequence is unclear and needs to be rewritten. It seems to me that the only treatment phase was during the first 24 h and then the embryos were moved back into control conditions?  The larval survival and settlement should then be referred to as a latent effect from the original exposure during fertilisation and early embryo development.

L102: what was the temperature of the bay and the water in the aquaria? (bring some of the information from L136 forward to here”)

112: how big was the beaker, how long was it washed for? Why was is washed, “to remove….?”

L112: are 100 and 200 mg/L ecologically relevant? See Jones et al., 2016.
L136: what was the temperature range, how was it measured?

L136: was it the current in the tank that simulated “mile wave motion” – please explain so others can repeat
L152: what is the approximate sperm concentration. The work of Ricardo et al shows that sperm concentration has a very strong influence on the sensitivity of fertilisation to suspended sediments and is likely to also affect the sensitivity to thermal and osmotic stress.

Table 1. This table needs improving. It is hard to see how it represents five treatments.
I suggest making things unambiguous.
Each row should tell us what the conditions were in each of the five treatments
Control treatment: 0 mg/L SS   34 PSU    27oC
Medium SS: 100 mg/L SS, 34 PSU, 27oC
High SS: 200 mg/L SS, 34 PSU, 27oC
High temp: 0 mg/L SS, 34 PSU, 27oC
Low salinity:  0 mg/L SS, 28 PSU, 27oC

Line 156: if two sperm-egg bundle were in a single vial and this represents one cross. How is this single cross exposed to all five treatments? Was each cross divided into five separate vials? If so, what about the excess sperm?

L158: How many eggs (range or mean and SD?) were in each vial?

L158: here you need to tell us that the exposure for fertilisation was actually 8 hours

L163: Need to more clearly describe the exposure sequence (could do a diagram). Please let me know if I get this right:
1. Expose gametes to each of 5 treatments for for 8 h and fertilisation counted.
2. Total exposure of gametes and developing embryos was 24 h (there was sperm in these vials the whole time).
3. After 24 h the embryos were transferred to clean vials (how many embryos per vial?, was this also a cleaning step). Embryos now in clean seawater only = control conditions?  Were they all kept at 27oC now or were the 31oC embryos kept at the elevated temperature?
4. Survival of early larvae were counted at T = 48 h (=24 h in the treatment conditions + 24 h in clean water at 27oC and normal salinity- this is not at all clear).
5. larvae transferred to 10 ml petri dishes, CCA added, water replaced every 2 d and settlement counted at 14 d (all in control conditions?).

L175: “metamorphosed” into what? Briefly define what this is with a reference.

Where is the statistics section in the M+M?

Results:

L191: were they statistically higher?

L199 – this is “latent” survival, after the initial 24 h exposure and 24 h at control conditions right?

L199: Please stat that the survival is a % of the successfully fertilised gametes. (not a % of the total eggs used?).

Figure 2. what is the number of replicate vials? Needs to be in the caption.  Say that each step is % of the previous. For example, survival is a % of the successfully fertilised.  Settled is a % of those that survived.

It would be useful to also include the total success to settlement relative to the number of eggs in each treatment.

Discussion: Missing comparisons with the most recent and relevant work on suspended sediments, needs more discussion on why these life stages are/are not affected.

Line 220: Stat that this is a one-off 24 h exposure and that survival and settlement were due to “latent” effects of the original treatment.

Lines 228-235: This section should instead focus on the work of Ricardo et al and Humanes et al.  Ricardo outlined shortcomings of the early Gilmour work and used measured sediment concentrations and tested the influence of sperm concentration on the fertilisation success. Humanes et al performed similar tests to those here (but included sediment x temperature treatments also).
It is critical that you contrast your work with that of others more specifically. You did not directly test the effects of sediments on larval settlement. The exposure was for the first 24 h so the effects on survival and settlement at latent effects (this is legitimate but you need to emphasise it). Recent work has shown that coral larvae are can be very resistant to suspended solids (mechanism were described) but settlement is very sensitive to fine layers of sediments. There should be discussion about the likely sensitivity of the test given the sperm concentrations used and the sediment type used (Ricardo extensively tested the effects of sediment type on fertilisation inhibition – type has a major effect.

Line 239 – Ricardo et al also demonstrated effects of films of sediment on larval settlement.

Line 246: what are the likely mechanisms for effect of low salinity on embryo and larval health?

Discuss future work with combinations of the stressors with Hawaiian corals (Similar to Humanes work).

Raw Data
Columns A and C do not have labels – what are they?


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE IMPACT OF SHORT-TERM EXPOSURE TO NEAR SHORE STRESSORS ON THE EARLY LIFE STAGES OF THE REEF BUILDING CORAL MONTIPORA CAPITATA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper studied the effects of temperature, salinity and sediment on fertilization, larval survival and settlement of the reef building coral M. capitata.
The authors performed a very simple experiment where they exposed eggs and embryos to different stressors independently.
It was very interesting to see the drastic effects of low salinity in larval survival and how fertilization and settlement were less affected by different stressors. I think this type of experiments are really important to better predict the resilience of coral reef ecosystems and the stressor effects on future generations.

I wish the authors had done simultaneous exposure of stressors, it would have been a more realistic and novel experiment, but I also understand the difficulty of performing this type of experiments.

The manuscript overall is not well written, the methods lack detail and both the introduction and discussion lack depth.
What are the hypotheses?
How could the stressors interact in the field?
Is there any evidence of synergistic or antagonistic effects?
Why do you think larvae was the more vulnerable stage?
What cellular/molecular mechanisms could be responsible for the patterns observed?
What is the ecological relevance of your results?
These questions need to be addressed in introduction and/or discussion.

ABSTRACT
Line 29: “It is critical…” This sentence is not well connected with the previous one.
Line 33: remove “osmotic stress through”
Line 33: add space “31 C”
Line 35: confusing sentence, you need to clarify that that eggs were not exposed to stressors simultaneously.
Line 38-41: I found this last sentence very hard to understand, I suggest authors to rewrite the end of their abstract. Why would you say that sediment stress is ongoing whereas “rain stress” is episodic.  What do you mean by sedimentation? In many cases, sedimentation is associated with rain events. You talk about currents and transport, but you have no evidence on this. What do you mean by “improved” conditions.
Keep in mind that larvae can also move and change their location vertically as well.

INTRODUCTION
Line 56: Paragraph lacks order. I suggest you delete “ …and recently consecutive bleaching….(Bahr et al. 2015b).” Focus first on the freshwater, then talk about temperature stress/bleaching.
Lines 63-67 repetitive, please condense.
Line 71: (Bahr…): You can not start the sentence with parenthesis.
Line 72: Weird/incomplete sentence, you first talk about recovery and then mortality. What did Bahr et al. 2017 found in the context of recovery.
Line 75: Be specific “… on adult coral PERFORMANCE”
Lines 80-82: repetitive
Line 83: clarify that is independent exposure to stressors
Line 86: Please include ranges of environmental conditions in Hawaii (relevant to the stressors in your experiments).
Line 89: What do you mean by “maintenance”? Change word choice.
Experimental design: METHODS
WHAT IS YOUR SAMPLE SIZE AND REPLICATION?
Line 95: Location, coordinates?
Lines 101, 102: corals (plural)
Lines 108-115: The methods for the sediment treatment are very obscure.
Why was the supernatant decanted?
Why <63um?
You need to include more detail in how you performed your weight to dry weight ratio.
Line 122-123: Sentence not well written and hard to understand.
Line 132: Add space “27 C” and “31 C”.
Lines 135-136: Not clear how you achieved “wave motion/agitation“ inside the vial. Floating rack?
Line 144-145: What do you mean by “pooled”? Be specific here (between individuals, high egg concentration?).
Line 145: Why “pooling” can affect the egg membrane?
Line 147: Replace Hagedorn et al. 2015 with Mate et al. 1997.
Line 153-56: Unclear if exposure was simultaneous or independent, please clarify.
Also, table 1 and its legend were confusing.
Line 212: confusing
Validity of the findings: DISCUSSION
Line 239: Replace “production” with “development”
Line 240: Not sure what you mean with “covered in varying levels”, be clear and specific here.
Line 246: Effects of LOW salinity….(include “low”)
Line 260-261: what do you mean by “well-mixed oceanic systems?”
Line 275: “…control and the treatments.” Do you mean temp, treatments? Be specific.
Line 276: Low replication? Include sample size
Line 283: what do you mean by “large scale” storms?
Line 285: what “magnitude”?
Line 285: … that MAY result in…
Line 284-287: Several ideas and not well connected.
Line 287: Replace “treatments” with “stressors”…
Line 293-295: What type of management strategies? In what context can your results inform conservation strategies? What type of mitigation efforts? What is the association with your data and predictive modeling?
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE IMPACT OF SHORT-TERM EXPOSURE TO NEAR SHORE STRESSORS ON THE EARLY LIFE STAGES OF THE REEF BUILDING CORAL MONTIPORA CAPITATA
Review round: 1
Reviewer: 3

Output:
Basic reporting: I have structured my feedback per the journal's instructions to reviewers  and not in order of importance.

1. English language
There are frequent typos, grammatical errors, and vague phrases in the text that should be addressed. I have made note of some here:
L26 - the use of "maintenance" is unusual. Is there a more appropriate word choice?
L27 - "due to greenhouse gases" implies a more direct relationship than in reality, implying that there are greenhouse gases in reef waters that are causing them to warm
L29 - missing word
L44 - insert comma after world
L52 - "all of these" is vague
L74 - insert comma after local. Also, elevated temperature is not a local, near-shore stressor. It is a global stressor.
L100 - typo
L151 - "this method" is vague
L172 - "and covered" - what does that refer to - the dish? Here and in the next sentence, make sure the subject of the sentence makes sense with both clauses.
L201 - ditto

2. Background and context
The justification of the treatment levels and the exposure length needs more support. How do you know that the levels are ecologically relevant? Why is this exposure length relevant? Include evidence that demonstrates that Kaneohe Bay experiences these treatment levels. The fact that the Bay has experienced warmer summers in 2014 and 2015 is not justification that the bay is warming due to climate change.

3. Article structure, figures, tables, data
The article is structured well with appropriate sections. Figure 1 and Table 1 do not add substantial value to the manuscript, and I recommend that they are removed because the information is sufficiently explained in the text. The authors should include a table with all of the statistical results, which could be included as supplementary information. I recommend breaking Figure 2 into three figures that better reflect the statistical analyses and comparisons discussed (i.e. sedimentation, salinity, temperature).

4. Results are relevant to hypotheses
Experimental design: I have structured my feedback per the journal's instructions to reviewers  and not in order of importance.

1. Research question and knowledge gap
I found the introduction to be misleading about the knowledge gap. For example, L74-78 states that the effects of sedimentation, low salinity, and warming have been characterized for adult corals but not for early life stages. However, in the discussion section, many studies looking at effects of these stressors on coral fertilization, larval survival, etc are referenced. The authors need to more clearly define the knowledge gap that this study fills.

Why were the stressors not examined in combination? I imagine that sedimentation, low salinity, and elevated temperature often co-occur on these reefs. Their combined effects may then be quite relevant to examine.

The research question is not clearly defined

2. Rigor of investigation
The level of replication needs to be clearly described. Were there replicate vials per parental cross per treatment condition? How many crosses or parental representation were present on each day?
Further, the experiment was conducted for 34 crosses by using egg-sperm bundles released on different days. The crosses need to be included in the statistical framework. Also, previous work with coral larvae has shown that offspring released on different days from the same parents have different physiological characteristics and sensitivities. The potential role of this phenomenon in the outcome of the present study should be acknowledged and discussed.

3. Methods were not described in sufficient detail for replication (See number 2 above)
Validity of the findings: I am unsure of the validity of the findings without knowing about the replication as described above.

The discussion should be revised to make sure that all of the results are interpreted (fertilization is over-represented) and to include a broad sense of how these results will improve our understanding of coral reef ecology under climate change.
Additional comments: The authors conducted a study to look at effects of sedimentation, low salinity, and warming on early life stages of a coral. These results of the study provide relevant information regarding the challenges that near-shore reefs face. The article requires significant revisions, most importantly a clear framing of the knowledge gap and more information about experimental design, and I hope the feedback is helpful in efforts to improve the manuscript.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE IMPACT OF SHORT-TERM EXPOSURE TO NEAR SHORE STRESSORS ON THE EARLY LIFE STAGES OF THE REEF BUILDING CORAL MONTIPORA CAPITATA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Much improved following revision. Clearly written, appropriately referenced, good tables and figures and self-contained from hypothesis to conclusions
Experimental design: Clarified in this second version. Original, a meaningful research question, scientifically rigorous, and methods now well described.
Validity of the findings: Scientifically valid and well described
Additional comments: The authors have comprehensively addressed all my previous comments. This is a nice paper and ready for publication. Well done.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE IMPACT OF SHORT-TERM EXPOSURE TO NEAR SHORE STRESSORS ON THE EARLY LIFE STAGES OF THE REEF BUILDING CORAL MONTIPORA CAPITATA
Review round: 2
Reviewer: 2

Output:
Basic reporting: I sincerely apologize for my delay with this review.
I have now reviewed the updated manuscript and have seen the author’s responses to the reviewers’s comments.  The authors have a done a good job addressing most comments and the manuscript in in much better shape.
However, there are still several grammatical errors that make some sentences confusing and/or do not accurate describe the methodology.

I have included revisions on the word document (highlighted in yellow and green).

I am also including additional comments.

Lines 160-164: The “compensation” part does not make a lot of sense. I suggest you delete these sentences and just add in the discussion the fact that it is important to take in consideration that sensitivity may vary depending on the timing of the release (Hedouin & Gates 2013).

Lines 229-232: Very confusing sentence, check grammar

Line 241: Unclear how did you obtain the value of 5 x 105 cells/mL
The sperm concentration of a bundle should not be “standardized” by volume. Because volume depends on the dilution you are working with, so is irrelevant. Please check grammar and correct word choice to have accurate meaning.

Line 244-245: “Each cross had 6 scintillation vials…”
This does not make sense, please change word choice to accurately reflect what you did.
Ex: each cross was exposed

Line 353-354: Very confusing sentence, since you did not find effects of treatments on fertilization.

After these revisions (and in word document), the manuscript should be ready to be accepted.

Kind regards,
Experimental design: ok
Validity of the findings: ok
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: A COMPARATIVE ANALYSIS OF THE COMPLETE CHLOROPLAST GENOMES OF THREE CHRYSANTHEMUM BOREALE STRAINS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The reviewed paper reports the results of chloroplast genome sequencing of three Chrysanthemum boreale strains. Complete chloroplast genome sequences were characterized and used for comparative and evolutionary studies. The article is well structured: manuscript include relative background information to the reported results; results are clearly and unambiguously presented and illustrated by appropriate figures and tables; all necessary raw data are provided; in the Discussion section Authors smoothly referred to adequate literature, sufficient in the respect to the number and content; conclusions are generally well supported. The manuscript is characterized by clear and professional English used throughout, with very few imperfections (detailed information on that issue is included in the "General comments" section).
Experimental design: The reviewed paper is an example of an interesting and valuable study with the correct and complementary methodological side. The applied methodology, high-throughput sequencing, provides high-quality data with many applications. Here, authors not only report complete chloroplast genomes of three Chrysanthemum boreale strains, but also based on the molecular data verified the systematic relationships of the studied material.
Validity of the findings: The described results perfectly correspond and are complementary to previous studies on history, evolution, and diversity of genus Chrysanthemum. The observations included in the reviewed manuscript may become a valuable element of the discussion not only in case of studies on evolution and diversity of Chrusanthemum boreale, but also for other closely related taxa.
Additional comments: Here I would like to list my detailed, minor comments concerning the manuscript:

L.22
"regions in Korea" replace with "regions of Korea"

L.64
- what is the difference between "conserved" and "stable", it sounds like redundancy, please rephrase this sentence

L.64-65
"maternally inherited" - it is only partially true, there are a number of examples where chloroplast genome is inherited with pollen grains (paternal inheritance; e.g. in Pinus, Picea), please rephrase it by pointing at rather uniparental mode of cp genome inheritance not maternal.

L.71-74
"Although whole cp sequences, gene content, and gene order are conserved..."
I would recommend to rephrase it a little bit to avoid redundancy:
"Although the structure of cp genome is generally conserved..."

L.95
There is no "Kim et al. 2006" among the references.

L.140
Have you tested also other substitution models? Please add the appropriate information here.

L. 147-148
"We used the previously reported cp genome of strain 121002, which was 151,012 bp (Won et al. 2018)."
Something is missing here, isn't it? Please add adequate information here by giving the reason/purpose why you use that sequence.

L.162
"duplicates" replace with "duplicated"

Figure 1
The picture could be of better quality (higher resolution) - the gene names are not sharp enough.

Figure 2
Low-quality picture - the gene names are hard to read.

Figure 3
I suggest adding the LSC, IR and SSC symbols above the arrows indicating the elements of the cp genome.

Figure 4
I suggest to change the color scheme used in Figure 4A - it is hard to distinguish some of the used colors.

Figure 5
Low-quality picture - the bootstrap values supporting the tree nodes are not clear.

Table 1.
I suggest replacing "Number of genes" with "Number of unique genes"

Table 2.
In the main text you have mentioned that there are 15 genes containing introns, but in the table the asterisk (*) is placed next to only 14 genes (rpl2, rps16, rpoC1, trnA-UGC, trnI-GAU, trnK-UUU, trnL-UAA, trnS-CGA, trnV-UAC, ndhA, ndhB, atpF, clpP, ycf3).


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: A COMPARATIVE ANALYSIS OF THE COMPLETE CHLOROPLAST GENOMES OF THREE CHRYSANTHEMUM BOREALE STRAINS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript may have the potential to contribute to our understanding of relationships of geographical species, such as Chrysanthemum boreale strains, using plastome phylogenomics. While the current version is clear enough in some section for revision, other parts of the manuscript have some issues that make very difficult to understand it.

There is no information of where the tree, alignments and other appropriate data was deposited.
Experimental design: This paper focuses in three C. boreale strains varied in morphology and geographic, but you do not provide enough background about these species. What is the current classification for these strains based on morphology? Are they believed to be one species in taxonomic? What is the distribution for these strains separately? Also, you ended up focusing more in describing the three chloroplast and not much attention is put on the phylogenetics results and the systematics of the C. boreale strains, which is I understand is the main point of the paper.
Validity of the findings: It is clear that you generated new valuable data of C. boreale strains. In Hwang et al. (2013) (Karyomorphological Analysis of Wild Chrysanthemum boreale Collected from Four Natural Habitats in Korea), this species was identified four genotypes, I think generate new data of the other strains could improve the systematics of C. boreale.

On first mention of species name in the paper need to in correct scientific name with author from IPNI (https://www.ipni.org/), such as Line 20, 41, 54, 55, 76 etc.
Additional comments: Abstract:

Line 20: “Chrysanthemum boreale” should be “Chrysanthemum boreale Makino”
Line 29: Check for “80 unique protein-coding genes” or “80 protein-coding genes”

Materials & Methods

Line 135: Here, authors mentioned 73 shared protein-coding sequences, but unclear why not used complete cp genomes, which could improve node support.

Results

Line 199-201: The length of ycf1 protein in 121002 strain almost 640 amino acids shorter than IT232531 and IT 301358. I suggest authors should examine by Sanger sequence or agarose gel electrophoresis.
Line 246-247: “The total length of the cp genomes was within the expected size range of 120–160 kb (Thode & Lohmann 2019)” repeat with above.

References

Scientific name should be in italics.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: A COMPARATIVE ANALYSIS OF THE COMPLETE CHLOROPLAST GENOMES OF THREE CHRYSANTHEMUM BOREALE STRAINS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The overall structure and format of the article is appropriate for the journal. The manuscript by Tyagi and colleagues sequenced the chloroplast genomes of three Chrysanthemum boreale strains. They systematically analyzed three chloroplast genomes by assembled de novo, annotated, compared with one another, and Phylogenetic analysis. The three complete chloroplast genomes will be valuable genetic resources for studying the population genetics and evolutionary relationships of Asteraceae species. However, I have several suggestions as listed below for helping the authors to improve their manuscript:

1. Line 48-50: Chrysanthemum is considered to include around 40 different species native to Eurasia, especially in Korea, China, and Japan (Liu et al. 2012). However, some species and varieties are narrowly distributed in specific habitats (Kondo et al. 2003; Liu et al. 2012).
Line 284-286: Considering that ITS sequences can be short as 447 bp (Zhao et al. 2010), we would expect fewer informative polymorphisms from ITS than the cp as a whole.

They provide information for Chrysanthemum species, however, only very limited evolutionary information is available in the introduction and discussion about their evolutionary. It is suggested to increase the evolutionary relationship based on nuclear genome of Chrysanthemum species.

2. Line 50-53: Of particular importance to the present study is a wild relative, Chrysanthemum boreale, which bears small yellow flowers, and occurs in natural stands in eastern Asia (Hwang et al. 2013; Kim et al. 2014). Comparative transcriptomic analysis revealed that C. boreale diverged from the commercial cultivar Chrysanthemum morifolium about 1.7 million years ago.

I believe that the Chrysanthemum boreale of the article has important application value. However, the materials introduction to the research materials of Chrysanthemum boreale, which bears small yellow flowers, and occurs in natural stands in eastern Asia, is very limited. If the three Chrysanthemum boreale strains have no representative significance and value, this paper has very limited theoretical and practical significance.
Experimental design: The research methods are reasonable and feasible.
Validity of the findings: Statistical analysis needs to be added to make conclusions. The resolution Figure 2 and   Figure 5 need to be further improved.
Additional comments: The article should be accepted if the authors make some revisions, minor enough that I would NOT necessarily need to re-review it.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: A COMPARATIVE ANALYSIS OF THE COMPLETE CHLOROPLAST GENOMES OF THREE CHRYSANTHEMUM BOREALE STRAINS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The reviewed manuscript is the resubmission of a paper which reported the results of chloroplast genome sequencing of three Chrysanthemum boreale strains.
Complete chloroplast genome sequences were characterized and used for comparative and evolutionary studies. The article is well structured: manuscript include relative background information to the reported results; results are clearly and unambiguously presented and illustrated by appropriate figures and tables; all necessary raw data are provided; in the Discussion section Authors smoothly referred to adequate literature, sufficient in the respect to the number and content; conclusions are generally well supported. The manuscript is characterized by clear English used throughout, with very few imperfections (detailed information on that issue is included in the "General comments" section.
Experimental design: The reviewed paper is an example of an interesting and valuable study with the correct and complementary methodological side. The applied methodology, high-throughput sequencing, provides high-quality data with many applications. Here, authors not only report complete chloroplast genomes of three Chrysanthemum boreale strains, but also based on the molecular data verified the systematic relationships of the studied material.
Validity of the findings: The described results correspond and are complementary to previous studies on history, evolution, and diversity of genus Chrysanthemum. The observations included in the reviewed manuscript may become a valuable element of the discussion not only in case of studies on evolution and diversity of Chrusanthemum boreale, but also for other closely related taxa.
Additional comments: Thank you very much for your effort made to improve the manuscript. I am satisfied with the answers received for my previous comments and current version of the text.

However I have noticed some minor drawbacks which needs improvements:

L.55
"Almost 8 species" - I believe that this is a unfortunate expression here, authors should make this statement more accurate i.e. whether it is 8 or more/less species.

L.235
"ndfF" should be replaced with "ndhF"

L.235-236
"At the IRb/LSC junction, rpl2 and trnH-GUG were located with the distance of 122 bp to 124 bp." should be rephrased "At the IRb/LSC junction, rpl2 and trnH-GUG were located within the distance of 122 bp to 124 bp from each other"

L.260
"The phylogenetic trees were constructed with complete cp genome..." replace with "The phylogenetic trees were constructed based on complete cp genome sequences..."

L.350-351
"Phylogenetic trees using the cp and nuclear data..." should be replaced with "Phylogenetic trees based on cp and nuclear data..."

Table 1
I do not understand why there is information that the number of genes with introns is 13-15 depending on the C. boreale strain, whereas in line 185 you wrote that there is 16 such genes. Additionally, Table 3 contains details on intron content in 16 chloroplast genes in C. boreale strains.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: A COMPARATIVE ANALYSIS OF THE COMPLETE CHLOROPLAST GENOMES OF THREE CHRYSANTHEMUM BOREALE STRAINS
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: A COMPARATIVE ANALYSIS OF THE COMPLETE CHLOROPLAST GENOMES OF THREE CHRYSANTHEMUM BOREALE STRAINS
Review round: 2
Reviewer: 3

Output:
Basic reporting: The overall structure and format of the article is appropriate for the journal.
Experimental design: This original primary research is within the scope of the journal.
Validity of the findings: Conclusions are well stated.
Additional comments: The article meets the PeerJ criteria and should be accepted as is.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TREATING CORAL BLEACHING AS WEATHER: A FRAMEWORK TO VALIDATE AND OPTIMIZE PREDICTION SKILL
Review round: 1
Reviewer: 1

Output:
Basic reporting: An excellent and highly significant manuscript, well written, appropriately structured with good scholarship and self-contained.
Experimental design: Well described, well presented and rigorous.
Validity of the findings: The conclusions are well stated and reflect the results. My one concern is that weaknesses in the underlying data need to be stated more clearly in the methods and given more prominence in the discussion.
Additional comments: A great piece of research that should inspire much work to improve predictions of bleaching and better understand the factors that drive mass bleaching in addition to temperature.

The Hughes et al 2018 database is the best available but from my understanding of how it was put together it will almost certainly have missed many bleaching events in many of these 100 regions. As you point out, the data base almost certainly miss-classified the first mass bleaching of the modern era which occurred under the noses of an active marine science network on the GBR. You need to mention this and discuss how this might affect your results. You do mention this in brackets at line 206 but it needs more prominence.

Line 101-103. Fisk and Done (1985) is a better reference than Harriott 1985. Her data don’t support her claim of an increase in mortality at Lizard Island and she didn’t see any bleaching. I am sure you are correct in that this was a major bleaching event but only Oliver 1995 addresses the potential scale of the event so this specific criticism of the Hughes et al 2018 database is a little harsh. Perhaps just say that your assessment of these largely anecdotal reports suggest it was a major event. Also, please clarify in the text if this was in 1982 or 1983. My reading suggests that the bleaching occurred in early 1982.

Line 217 – see also Guest et al. (2012)

Line 248+ - when put this way it doesn’t sound like much. Are your values correct ie 7-6 days?

Fisk DA, Done TJ (1985) Taxonomic and bathymetric patterns of bleaching in corals, Myrimidon Reef (Queensland). Proc Fifth Inter Coral Reef Congress 6:149-154
Guest JR, Baird AH, Maynard JA, Muttaqin E, Edwards AJ, Campbell SJ, Yewdall K, Affendi YA, Chou LM (2012) Contrasting patterns of coral bleaching susceptibility in 2010 suggest an adaptive response to thermal stress. Plos One 7:e33353


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TREATING CORAL BLEACHING AS WEATHER: A FRAMEWORK TO VALIDATE AND OPTIMIZE PREDICTION SKILL
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript by DeCarlo outlines an elegant improvement of predictions of coral bleaching. This is the type of work NOAA should be doing, but full credit goes to DeCarlo for taking the lead and fixing the problem. This manuscript should be definitely published with some minor changes. The manuscript was very well written. The literature was contemporary and appropriate. The code for the figures and the calculations were shared and accessible. Hypotheses were relevant, although I would have liked a few more sentences on methods tried that didn't improve the model skill.

Line 22. Change the main results in the Abstract to be more assertive and specific.

Change: “Adjustments to the degree heating weeks (DHW) metric, regional DHW
thresholds, and adding an El Niño threshold, together resulted in a 45% increase in prediction skill relative to standard methods.”

to

“Removing the 1 °C above the maximum monthly mean cutoff in the degree heating weeks (DHW) definition, adjusting the DHW window from 12 to 9 weeks, using regional-specific DHW thresholds, and including an El Niño threshold already improves the model skill by 45%.

Line 110 to 114. I’d like to see equations regarding the different tests that were run to assess skill (I guess Table 2 works, but some equations in the text would clarify the methods).
Line 116. Could use a table here with some details.
Line 161, should read “is”, not “in”
Lines 168 to 177. This text should be in the methods. These are not results.
Line 182. This sentence should be in the Abstract.
Line 206. Include a comment that bleaching temperatures may change over time here.
Figure 1 was overloaded. It was difficult to follow. Best to place all of the pairwise figures in the supplementary document.

Figure 3. It was not immediately clear what to focus on in Figure 3. It took me far too long to get the point of this figure. Best to try a different approach. The DHW colors seemed to work but things get messy with the gray, black and dashed lines. Pretend you are giving a seminar and that you have to get your point across within less than 20 seconds. What do you want the viewer (i.e., reader in this context) to focus on? Highlight that point in the figure.
Experimental design: The manuscript outlines an important piece of original research. The rationale was clear and the work fills knowledge gaps. The calculations were appropriate for the research. The analysis was a sophisticated approach to an important problem. The details of the methods was appropriate.
Validity of the findings: The results are extremely useful and should be applied globally. Figures 1 and 3 need some refinement.
Additional comments: The DeCarlo manuscript was well written and is an excellent contribution to the literature.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: PRESERVATION OF LATEST CRETACEOUS (MAASTRICHTIAN)—PALEOCENE FROGS (EORUBETA NEVADENSIS) OF THE SHEEP PASS FORMATION OF EAST-CENTRAL NEVADA AND IMPLICATIONS FOR PALEOGEOGRAPHY OF THE NEVADAPLANO
Review round: 1
Reviewer: 1

Output:
Basic reporting: Clear and unambiguous, professional English used throughout.
The article is well written and it is really easy to follow the reasoning all along. To the best of my knowledge, the English used is correct and should not be improved (the authors’ English is much better than mine)

Literature references, sufficient field background/context provided.
This is clearly one of the major weaknesses of the paper. The geological context is clear and well documented, but the relevant part of the paper, the study and description of frog preservation, is mainly based in 2 or 3 old references, which disregards the value of modern actuotaphonomic and observational papers. For instance, it is a surprise to read a paper on exceptional frog preservation that ignores great contributions to the field of taphonomy of frogs such as McNamara et al. PALAIOS, 27(2):63-77 or Báez Cret. Res. 41:90–106. Even if the geological periods or the chemistry of the lake are not the same, the paper would benefit of a comparative taphonomy with previous exceptional fossils. In addition, the authors support their findings on actualistic studies from 1973 and 1985 and they do not cite an actuotaphonomic study performed with frogs studying their preservation on microbial mats, which seems quite interesting in this context (Iniesto et al 2017 Scientific Reports 7:45160). Consequently, I think that literature has to be revised before publication.

Professional article structure, figures, tables. Raw data shared.
The structure of the paper and figures are appropriate and informative. I suggest the introduction of a more general map in Fig.1 in order to better locate the formation in USA. I commend the authors for Fig.2 which is a clear but very complete stratigraphic section.

Self-contained with relevant results to hypotheses.
The authors present a huge amount of information from a coherent body of work.
Experimental design: Original primary research within Aims and Scope of the journal.
This article fits into PeerJ’s aims and scope.

Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.
The present paper present a high altitude Konservat-Lagerstätten which is quite rare, making the manuscript interesting. Through a combination of observational and geological observations they tried to reconstruct the ancient ecology of the system and the preservation context. Although not explicitly presented, their objectives and questions can be inferred from the text (lines 69-72).

Rigorous investigation performed to a high technical & ethical standard.
The ethical and rigorousness of the study cannot be questioned. However, to reach a high technical standard, the paper would benefit from the incorporation of several common techniques used in taphonomic studies such as electronic microscopy, or infrared or Raman spectroscopy. For instance, the identification of mats is based only crenulated laminations (line 249) and anoxic conditions are presented as a possible explanation for preservation (lines 254-257). However, the geochemical and mineralogical analysis of the sediment surrounding the fossils would incorporate strong support (or not) to these hypothesis. Although classical taphonomy is highly welcome and appreciated, in my opinion it does not stand without analytical information.
Moreover, several references that shows several discrepancies with the text should not be avoided and taken into account. For instance, line 350 states that frogs can remain articulated for 45 days according to Dodson (1973) but more recent studies showed that frogs can decay quite fast and show disarticulation in a few days (Iniesto et al 2017 Scientific Reports 7:45160). You are welcome to interpret that one result is more likely than other but an explanation is needed (for more examples, see below -section “speculation”-)

Methods described with sufficient detail & information to replicate.
The information is sufficient.
Validity of the findings: Impact and novelty not assessed. Negative/inconclusive results accepted. Meaningful replication encouraged where rationale & benefit to literature is clearly stated.
As stated previously and explained in the text of the manuscript, the authors studied a high altitude Konservat-Lagerstätten which is rare, making their ecological and taphonomic study relevant to the field. However, the most interesting observation (the preservation of articulated frogs within microbial mats) has to be revisited, better explained and supported with more data.

All underlying data have been provided; they are robust, statistically sound, & controlled.
It is difficult to address the robustness of the data presented. Although the authors state a number of times that these results are supported by “numerous frog specimens” (e.g. line 239), they should explicit the number of specimens studied for each member of the formation and present a statistical description of these specimens (N total, N articulated, N complete, fragmentation, etc). This information will help to understand the magnitude of their work.

Conclusions are well stated, linked to original research question & limited to supporting results.
Conclusions are aseptic and contained, based on the observation exposed in the previous sections.

Speculation is welcome, but should be identified as such.
Although most of the paper is merely a description of their observations, there is a speculative section aimed to explain the first of the modes of preservation (lines 243-262). Despite speculation is frequently necessary for the understanding of this kind of complex processes, it has to be consistent and well supported by previous information.
It is reasonable to infer the presence of microbial mats based on these crenulated laminations but more supporting data are more than welcome. However, anoxic conditions and carbonate precipitation on mats generates a few concerns:
- First, in Iniesto et al. we have investigated the preservation of frogs in mats and preservation in mats using microelectrodes and such anoxic conditions were not observed. If the authors have data supporting these anoxic conditions they should present it or, in absence of these data, stick to the literature. I am fully aware of the use of “anoxic conditions” is frequent in taphonomy to explain delayed decay, but it has to be well supported.
- Subsequently, they discard the effect of anoxia based on the record observation (if you don’t have data supporting anoxia and the presence of a number of invertebrates can tell the opposite, why are you using this argument?) and they linked the absence of scavenging to carbonate precipitation. However, this carbonate precipitation can occur in two different modes. First, microbial mats are known to generate carbonates (Ludwig et al 2005 Limnology and Oceanography 50(6):1836-1843 or Kaźmierczak 2015 Life 5(1): 744–769) but they are not lithified structures. Consequently, scavengers would have complete access to frog corpses. In fact, the precipitation rate presented by the authors does not relate to any observation on mats and is merely experimental. Actual observations on freshwater microbialites (Brady 2009 Geobiology 7(5):544-55) estimated a microbialite growth rate of 0.05 mm per year (73 times less than what authors said). And this applies to microbialites and not to microbial mats (second mode of precipitation). If carbonate precipitation is dominant and really active (as stated by the authors), microbial communities can form lithified microbial mats known as microbialites. In that context frogs would be laying over an actual rock at the bottom of the lake and their burial will be then very difficult. The authors should not use microbial mats as a Deus ex machina being soft and smooth and able to cover frogs quickly and then mineralized and hard to avoid scavenging just after burial.
Additional comments: This study has the potential to be a useful addition to palaeoecological literature. The documentation of exceptional preservation is this high altitude formation is abundant and can be useful for further studies in taphonomy, ecology and evolution in this kind of formations. However, major aspects have to be amended prior to consider it publication as it stands.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: PRESERVATION OF LATEST CRETACEOUS (MAASTRICHTIAN)—PALEOCENE FROGS (EORUBETA NEVADENSIS) OF THE SHEEP PASS FORMATION OF EAST-CENTRAL NEVADA AND IMPLICATIONS FOR PALEOGEOGRAPHY OF THE NEVADAPLANO
Review round: 1
Reviewer: 2

Output:
Basic reporting: EXCEPTIONAL PRESERVATION OF ?LATEST CRETACEOUS (MAASTRICHTIAN)-PALEOCENE FROGS (EORUBETA NEVADENSIS) OF THE SHEEP PASS FORMATION OF EAST-CENTRAL NEVADA AND IMPLICATIONS FOR PALEOGEOGRAPHY OF THE NEVADAPLANO

This paper is focused on the different states of preservation of specimens of a fossil frog discovered In the type section of the Sheep Pass Formation and on this basis makes some paleoecological inferences.

Title: It puts too much emphasis on the “exceptional” preservation, a characterization that usually has a different meaning in the literature (e.g., Poyato Ariza & Buscalioni, 2016). In fact, the specimens shown in the pictures are not exceptionally well preserved. It should better say  something like “Preservation aspects of the latest Cretaceous………”, better reflecting the topics dealt with in the paper.
42 plant remains
48 ..and invertebrates such as mollusks…
61-62 Excellent preservation involves integrity, anatomic connection, and osteological detail. You are not showing a fully articulated specimen in the figure.
64 that represents …
103 a diverse mammalian assemblage, including also lizards, snakes, and anurans.

147 a diverse assemblage of plants, etc.

149. the term edentulous is ambiguous (teeth are not preserved?)

 248. Microbial mat development may also have been responsible for maintaining articulation of the frog skeletons for prolonged periods. Articulation of skeletons of frogs remained unbroken after 24 months in experiments (see.g.,  Iniesto et al., 2016, Lopez-Garcia et al., 2016)). This aspect was not thoroughly explored.

Figure 7: This is an incomplete skeleton partially disarticulated (e.g., clavicles are separated from scapulae and coracoids, skull disarticulated from axial column, etc)

Figure 8: Most skeletal elements are disarticulated, although they remain near their natural positions.

Iniesto, M., Buscalioni, AD., Guerrero M.C., Benzerara, K., Moreira, D., Lopez-Archilla, A.I., 2016. Involvement of microbial mats in early fossilization by decay delay and formation of impressions and replicas of vertebrates and invertebrates. Scientific Reports 6:25716 | DOI: 10.1038/srep25716

Lopez-Garcia, A., Martin-Abad, H., Cambra-Moo, O., 2016. Anuran biostratinomy. In: Poyato-Ariza, F.J.,  Buscalioni, A.D., (editors), Las Hoyas: A Cretaceous wetland, pp. 211-215.
Poyato-Ariza, F.J.,  Buscalioni, A.D., 2016. Exceptional preservation. In: Poyato-Ariza, F.J.,  Buscalioni, A.D., (editors), Las Hoyas: A Cretaceous wetland, pp. 229- 230.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: PRESERVATION OF LATEST CRETACEOUS (MAASTRICHTIAN)—PALEOCENE FROGS (EORUBETA NEVADENSIS) OF THE SHEEP PASS FORMATION OF EAST-CENTRAL NEVADA AND IMPLICATIONS FOR PALEOGEOGRAPHY OF THE NEVADAPLANO
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This is an interesting manuscript describing a rather unique locality that is set apart by both its paleogeography (high altitude lake) and taphonomy (various frog horizons/preservational modes).  I found the manuscript well organized and clearly written, the science sound and the conclusions very reasonable.  I do have a few minor recommendations and I would hope that the corresponding changes would improve the effectiveness of the paper. These are outlined below followed by simple editing corrections. Given that I have no criticism of the underlying science, I would recommend publication with minor changes.

Taphonomic modes:  There should be consistent treatment of these.  They are numbered incompletely in the abstract, but not in the main body of the text. I would recommend that the five modes be numbered 1 thru 5 in the text and abstract. Also, the authors should include a table that lists the 5 modes, tapho description, their associated lithologies, member (B or C), and interpretation. This would be a helpful guide for the reader, and then useful for people potentially applying these modes elsewhere.

Better photographs: Could better pictures be provided for Figures 3, 5 and 8?  Figure 8 seems to be somewhat unfocused, and the objects in 3 and 5 could be more visible. For figure 10, rather than showing two sides of the same cut surface, could one side be replaced by a close-up showing the ostracod lining? In Figure 12, could the contrast be enhanced so that the bones stood out a bit more?

Timing: The Sheep Pass Formation spans a very long time and the K/Pg.  Please add a paragraph under Geologic Setting that discusses the age or potential age of Members B and C.  I realize that there is likely uncertainty here, but it would be helpful for the reader to know what is known or unknown in terms of age.  Specifically, do B and C and their frogs post date the K/Pg or span the K/Pg? Could any horizons reflect the K/Pg or can this all be confidently eliminated?

[Note: numbers are line numbers.]

64 - Reword “ an exception is“ to ‘except for’.

87- Omit “estimated to be”.

97 - Should be ‘Winfrey, 1958, 1960;’

99 - Replace “While” with ‘Whereas’.

101 - Omit “Sheep Pass”.

108-109 - Can you say something about Eorubeta? To what family or clade does it belong?  Does this say anything about its ecology?  Might this be relevant to the interpretation of the taphonomy?

120-121. Please explain these abbreviations here, when first used.

137-138. Here degree of association and degree of disassociation is recorded?  Isnt’ this redundant?  If so, simplify text.  If not, explain what the difference is.

139. Light micriscope…Might there be something to be seen using a different light source to examine these specimens, e.g. UV?  I’m not suggesting this is needed here, but perhaps moving forward with specimens.

178. Can you say anything about the plants relative to past palynology work (e.g., Fouch 1979)?

214-220.  Doesn’t this section on decopods belong earlier with lines 189-196?

244.  The wording here is confusing in terms of the dolomitic mudstones.  So rather than, “within the crenulated-fabric, dolomitic mudstones”, revise to ‘only within those dolomitic mudstones with a crenulated fabric.’  Otherwise it sounds that all dm have crenularted fabric.

247-248.  I didn’t understand the meaning nor context of this sentence.  “This interpretation is supported by the stratigraphic distribution of specimens that had settled onto microbial mats in life position and were subsequently buried and preserved.”  Can you help me out?

259. Make new sentence beginning with “Modern rates…..”

268.  Can you describe a little more of what you mean by “more out of “life position”’?

296. Pers. communication - There are published references on crayfish that might be better here, although I don’t know if they discuss ostracods in the wall.

Hasiotis, S.T., Mitchell, C.E., Dubiel, R.F., 1993b. Application of morphologic burrow interpretations to discern continental bur- row architects: lungfish or crayfish. Ichnos 2, 315–333.
Hasiotis, S.T., Kirkland, J.I., 1997. Crayfish fossils and burrows from the Upper Jurassic Morrison Formation, Colorado Plateau, USA: implications for crayfish evolution. Freshwater Crayfish 11, 106–120.
Hasiotis, S.T., Mitchell, C.E., 1993. A comparison of crayfish bur- row morphologies: Triassic and Holocene fossil, paleo- and neo- ichnological evidence, and the identification of their burrowing signatures. Ichnos 2, 291–314.
333. Could there be other causes: anoxic events, water turnover, etc?
Genera; Q: Is there any size variation in the frogs between the various taphonomic modes?
References: Fiorillo 1989 and Eberth et al. 2006 are listed, but I did not find them in the text.  These should be removed.

Figures.  See also comments above.

Figure 5.  Some labelling is needed here to know what is being referred to.  Also, the word ‘left’ (?) is missing in the caption.

Figure 8. This image is just too blurry.

Figure 9. Could this be the trace Cochlichnus?

Figure 10. A close-up of the wall could one side of the burrow slice.

Figure 12 caption refers to a Figure 13.  Either omit or add figure 13.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: PRESERVATION OF LATEST CRETACEOUS (MAASTRICHTIAN)—PALEOCENE FROGS (EORUBETA NEVADENSIS) OF THE SHEEP PASS FORMATION OF EAST-CENTRAL NEVADA AND IMPLICATIONS FOR PALEOGEOGRAPHY OF THE NEVADAPLANO
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Revisions look good and have addressed all my concerns.

A few minor typos/edits:
75 - which
185 - Could simply say 'toothless mammal jaw' or 'edentulous mammal jaw'.
202 - Fourth not Forth.
301 - as not ais.
418 - Space needed between 'in' and 'Ontario'.
448-449 - 'those in Member C....events.' is redundant with next sentence.  Should omit and combine two sentences.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: DIMINISHING RETURNS AS A FUNCTION OF DISTURBANCE
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript is on the question whether skewed residuals can cause SLODR to arise in intelligence datasets. Generally, the manuscript is well written and understandable. I liked reading this manuscript.
Experimental design: The methods used in this study are outdated. That is, the authors used principal component analysis (PCA) following (Deary et al, 1996). There are many more recent paper that present well-established and well-accepted methods to study differentiation. E.g.:

The mixture approach by Reynolds et al
Reynolds, M. R., Keith, T. Z., & Beretvas, N. (2010). Use of factor mixture modeling to capture Spearman's law of diminishing returns. Intelligence, 38, 231−241.

The non-linear factor analysis approach:
Tucker-Drob, E. M. (2009). Differentiation of cognitive abilities across the life span. Developmental Psychology, 45, 1097−1118.
Molenaar, D., Kő, N., Rózsa, S., & Mészáros, A. (2017). Differentiation of cognitive abilities in the WAIS-IV at the item level. Intelligence, 65, 48-59

The moderated factor model approach:
Molenaar, D., Dolan, C.V., Wicherts, J.M., & van der Maas, H.L.J. (2010). Modeling Differentiation of Cognitive Abilities within the Higher-Order Factor Model using Moderated Factor Analysis. Intelligence, 38, 611-624.

Most importantly, it is well established, that PCA is a suboptimal method to study intelligence in general (see e.g., Dolan, 2000) and SLODR in particular (see e.g., Molenaar et al 2010 above). Key of the problem is that PCA does not explicitly separate the residuals from the g-variance and does not explicitly model the intelligence structure

Dolan, C. V. (2000). Investigating Spearman's hypothesis by means of multi-group confirmatory factor analysis. Multivariate Behavioral Research, 35(1), 21-50.
Validity of the findings: Given the above, the results cannot be considered valid. As for instance demonstrated by Molenaar et al (2010), PCA can give very misleading results concerning SLODR. Ideally, the present research question should be studied in one of the contemporary formal modeling approaches above for the results to be interpretable. (i.e., if data is simulated according to one of the models above and the residuals are skewed, how does this skewness show up in the model?) or ofcourse in a new and appropriate formal model.
Additional comments: The literature review is not very thorough. Many studied have been done into SLODR and spurious results (e.g., Murray, Dixon, & Johnson, 2013; Tucker-Dob, 2009, Molenaar et al., 2017), and many advanced modeling techniques have been developed to counter these spurious effects.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: DIMINISHING RETURNS AS A FUNCTION OF DISTURBANCE
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is an interesting paper testing a fascinating idea: that ability differentiation is the result of a disturbing factor which is possibly negatively skewed. (SLODR and differentiation are synonymously used in the literature, I prefer differentiation because SLODR with its “diminishing returns” analogy from economics implies that one “invests in” one’s g which is already interpretative.)

It is an embarrassing moment for me because as an author I am not greatly fond of reviewers who use the opportunity to shamelessly promote their own work. However, in this particular instance, I cannot help but point to papers which I authored and which are, I believe, greatly relevant both empirically and theoretically.

The authors point out that a kind of disturbance could be a deficiency in some central system. This is most pronounced at the end of the paper (162-170):

“Still, even if findings that support SLODR would be due to the influence of disturbance, this does not necessarily mean that SLODR is just an artefact. For example, according to Detterman's (1993) explanation of SLODR, the “disturbing factor” could be a deficit in some important general cognitive process which restrains the functioning of the whole system. Without this deficit, test scores are mainly due to more specific processes and, consequently, less correlated and g saturated. If Detterman’s hypothesis is correct, and if studies using more contemporary criteria start supporting SLODR (it does not look very promising so far), one of the contributions of the present simulation would be to predict that most people experience only
low degrees of this deficit while a few experiences a very high level.”

Detterman’s explanation is actually similar to process overlap theory, a more recent account of the positive manifold and differentiation. See:

Kovacs, K., & Conway, A. R. A. (2016). Process overlap theory: A unified account of the general factor of intelligence. Psychological Inquiry, 27, 151–177.

Kovacs, K. & Conway, A. R. A. (2019). What is IQ? Life beyond general intelligence. Current Directions in Psychological Science, 28, 189-194.

Please allow me to quote from the latter paper:

 “This explanation, called process-overlap theory
 (POT), does not propose a general cognitive ability and
therefore does not endorse psychological g. Instead, it
proposes that intelligence is determined by multiple
components, both domain-general and domain-specific.
Certain domain-general processes (often called executive
functions  in the literature, e.g., Diamond, 2012)
overlap with domain-specific processes during mental
test performance. These executive processes are central
to human intelligence in the sense that they are tapped
by a large number of tests. Specific processes, on the
other hand, are mostly tapped by tests with corresponding
specific (verbal, spatial, etc.) content only.
Executive processes thus function as a bottleneck:
They constrain performance in a wide variety of tests
that tap different domains. Hence, performance in these
different, specific domains (verbal, spatial, etc.) correlate,
and the positive manifold emerges. Moreover,
the lower the level of executive functions, the stronger
the bottleneck effect and the higher the correlations
between diverse tests: This, according to POT, is the
explanation of ability differentiation.”

and:

“This executive bottleneck, represented in a formal
mathematical model, is the primary proposal of POT
(Kovacs & Conway, 2016). Besides the positive manifold
itself, it also explains ability differentiation and the
worst-performance rule. People who generally perform
below average on cognitive tasks (low ability) are likely
to exhibit deficits in executive processes that impact
performance across a range of domains. In contrast,
people who generally perform above average on cognitive
tasks (high ability) are unlikely to exhibit deficits
in executive processes, so their performance primarily
reflects domain-specific processes. That is, the lower
the level of executive functions, the stronger the bottleneck
effect and the higher the correlations between
diverse tests: This, according to POT, is the explanation
of ability differentiation.”

As the latter quote says, this bottleneck effect is formalised a mathematical model in the Psych Inquiry paper. It is in fact a multi-dimensional item response theory model which specifies the probability of correctly answering a test item as the function of passing two independent dimensions. Under this account, it is the domain-general dimension, limiting performance in different domains, that is equivalent of a “disturbance” in the MS.

The Current Directions paper just came out very recently, but the Psych Inquiry paper appeared in more than 3 years ago and, according to Google Scholar, has already been cited 126 times, so I like to believe that it is not due to my horrible narcissism that I think it should be mentioned.

Moreover, it was a strong prediction of the theory that differentiation must manifest itself in working memory capacity, too, and we recently published a paper demonstrating just that on two data sets:

Kovacs, K., Molenaar, D., & Conway, A. R. A. (2019). The domain specificity of working memory is a matter of ability. Journal of Memory and Language, 109, 104048.

Also, differentiation might occur in higher-order models, too, as a decrease of the 2nd order factor loadings as the function of g. This should be discussed.

Kristof Kovacs
Experimental design: Given how accurately it is described in the papers by Molenaar and Tucker-Drob (which are cited in the paper) that the methods described in the MS as the “Traditional paradigm” are suboptimal I see no reason to include them. The sections under “More contemporary operationalisation” already drive the point home, there is nothing the reader gains from additional evidence obtained with methods that are suboptimal, as is acknowledged in the paper.
Validity of the findings: The findings are important for the explanation of differentiation but their theoretical interpretation is not elaborate enough (see more under "Basic reporting").

Also, the authors repeatedly mention three possible sources of disturbance: low motivation, illness, linguistic confusion. Each of these is problematic. For motivation, see

Gignac, G. E. (2018). A moderate financial incentive can increase effort, but not intelligence test performance in adult volunteers. British Journal of Psychology, 109(3), 500-516.

Linguistic confusion as a source of differentiation does not sound likely, as such results were often obtained on test standardisation samples where great care is taken to avoid such confusion. Differentiation in working memory capacity is also hard to explain this way. Illness is a plausible account but without further specification it is somewhat vague. Probably the explanation by Detterman’s system theory (and, if added, process overlap theory) should be discussed other than an endnote.

Overall, these come across as speculative examples that the authors wanted to include for "disturbance" not to look vague.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: DIMINISHING RETURNS AS A FUNCTION OF DISTURBANCE
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript needs more context and elaboration. For example, the introduction should include more information about (a) what “g saturation” means (line 47); (b) how they original hypothesis was operationalized (lines 45-48); (c) why it is still important even though empirical support is lacking (lines 50-51); (d) how the hypothesis has been operationalized more recently, and why it was updated (move lines 84 to 86 to the introduction); and (d) why it is important to compare both the traditional and contemporary operationalizations. Figure 1 is not referenced in the text. Would the figure be different for traditional vs. contemporary hypotheses?
Experimental design: In the methods section there should be more information about (a) why the number of repetitions and/or N varies between different analyses (simulations: line 77 – 20, line 93 – 1000; N: 10,000 for most, N = 500 in Figure 3); and (b) why transformations of the data were needed. Specifically, (1) what was factor analyzed? (line 95); (2) why use the un-rotated and not the rotated principle component? (lines 75-76); (3) why use the logarithm of residual variance and not simply residual variance? (line 97); and (4) why use both g and g-squared in the regression analysis? (line 99). Also, the difference between traditional and contemporary operationalizations appears to involve how the subgroups are formed (lines 72-74 and 84-86) but this is not clear. Finally, I see the contemporary operationalization of the contemporary hypothesis (lines 88-89) but I did not see the equivalent for the traditional hypothesis.
Validity of the findings: I have no doubt about the validity of the findings, as the simulations seem rigorous and reproducible. However, the results should be reported so that the reader knows what pattern(s) to expect (look for) in the tables and figures. What pattern of data tells us whether (a) adding disturbance produced the same results as expected by SLODR (i.e., what patterns are we looking for?); and (b) whether the disturbance model fits the traditional vs. contemporary hypotheses equally well. There is some explanation regarding the contemporary operationalization (lines 116-128). Still, what is “subtest skewness”? What does a pattern of diminishing returns look like? How do we know whether there is “larger residual variance among those with high compared to low g?” And, what is non-linear g loading onto? Regarding the figures, the diagram in Figure 1 should be enlarged. The other figures are beautiful.
Additional comments: My questions and suggestions are meant to help the research reach a broader audience. I appreciate that in the last paragraph the author(s) reflected on the possibility that the disturbance factor “could be a deficit in some important general cognitive process which restrains the functioning of the whole system” (lines 164-165). And, I agree with the statement that regarding the contribution of the current simulations (lines 169-170).