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 TOTAL OF 219 METAGENOME-ASSEMBLED GENOMES OF MICROORGANISMS FROM ICELANDIC MARINE WATERS
Review round: 1
Reviewer: 2

Output:
Basic reporting: All looks good.
Experimental design: The research question - describing a set of MAGs from Icelandic waters - is not relevant or meaningful. This is a nice dataset but there is no real research question in this manuscript, just a description of MAGs. It is too descriptive without posed or addressing an interesting research question. (See comments below.)
Validity of the findings: No comment
Additional comments: Jégousse and colleagues describe a unique metagenomic dataset, including 31 shotgun metagenomes from coastal Icelandic waters and a set of MAGs reconstructed from these samples. They included a mock marine microbial community in these analyses as well. The dataset described here is excellent and fills a needed hole in the databases of marine metagenomic data, but there is not much of a story in the manuscript other than describing the MAGs – it describes the dataset but does not emphasize question/conclusions other than “can we get MAGs from these samples.” This is perhaps best underscored in the first line of the Conclusions section: the goal of just “reconstruct[ing] MAGs from 31 samples from Icelandic sea waters” is not very exciting. I therefore believe there is little scientific merit in the manuscript as currently written. Yes, this is a great dataset (and a very nice MAG collection), but what does it mean? What can it teach us about marine microbiology? As currently written, I believe the manuscript is appropriate for a more descriptive journal (e.g., Microbiology Resource Announcements, Scientific Data) than a journal focused on research findings, but it has a TON of potential, as the metagenomes and MAGs are very nicely done and undoubtedly rich with information.

My suggestion is to use the manuscript as currently written as a starting point to write a longer, more detailed manuscript actually analyzing the MAGs. What are their read mapping patterns across samples? What interesting metabolic genes/pathways are present? Are there any connections between the distribution of MAGs and the unique physical setting of these samples? Etc. There could even be more of an emphasis on comparing the binning algorithms and recovery of the mock community, to make this more of a MAG methodology paper instead of a microbial ecology paper.

However, I will re-emphasize that this is a really nice set of metagenomes and MAGs, and I recognize the amount of hard work that the authors have undergone to get the dataset to this point. In my opinion this work would be put to much better use if the manuscript told an actual story or two instead of just describing the MAG set.

SPECIFIC COMMENTS
Lines 15-24: Give more detail of any results in the Abstract. It mostly just sets up why the samples are interesting, but I am more interested in what was found. Cut out some of the background on the study site, etc. to make more space if needed.

Lines 95-104: Add information here about quality-control steps (trimming low-quality sequences, etc.) as well as assembly and binning software and parameters. In particular, please make note of any software parameters that deviate from defaults. I realize some of this information is in Fig. 1B but it should also be in this section.

Lines 125-126: A comment – instead of just picking the MetaBat2 MAGs only, the authors could consider using DAS Tool (https://doi.org/10.1038/s41564-018-0171-1, https://github.com/cmks/DAS_Tool) to select a set of non-redundant MAGs from the results of all three binning algorithms. (Which may increase the diversity of MAGs in the final set.) It is nice to see more benchmarking of binning algorithms and mock community work.

Lines 116-182: No analysis of read mapping to MAGs across the metagenomes? Or genes/pathways present in the MAGs? I would really love to see this, in addition to knowing the phylogenetic identity of the MAGs. Without any of these types of analyses I don’t think this article has enough to justify publication as a research article (though as I note above, it could be published as a descriptive article just laying out the dataset).

Lines 174-176: This is confusing. MGIIa-L2 and -L1 are both within the family Ca. Poseidoniaceae. How many Ca. Poseidoniaceae MAGs were there?

Lines 190-192: CONCOCT and MaxBin2 also use both nucleotide composition and differential coverage to bin contigs, so this alone won’t explain why MetaBAT2 performs best on these samples…


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: SINOMACROPS BONDEI, A NEW ANUROGNATHID PTEROSAUR FROM THE JURASSIC OF CHINA AND COMMENTS ON THE GROUP
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is well structured, has natural flow and progression with well-defined easy-to-navigate sections. The discussion is extremely detailed and accurately literature supported throughout. The figures are clear and support statements presented well (with one noted exception). There are some minor revisions however I will note down.
The abstract flows well and covers the aims and results of the paper nicely. Albeit I have some minor comments that might increase readability.

1.	On line 29 the specimen is described  “first anurognathid skull exposed in lateral view”, while it is the best-preserved skull in lateral view on record; arguably BSPG1922.1.42 or Anurognathus holotype crania is also preserved in lateral view. The preservation of that specimen is suboptimal due to heavy calcite replacement and missing elements. Better rephrase to “best-preserved anurognathid skull exposed in lateral view”, although arguably crania of your JPM-2012-001 looks to be more in ventrolateral view rather than lateral. Line 279 – again, the cranium looks to be exposed in ventrolateral view, albeit due to the heavy deformation this does not necessitate urgent correction.

2.	Lines 31-33, “As a result, we obtain a new hypothesis for the placement of the group, somewhat intermediate between other two recent proposals” is a little confusing, no proposals were noted prior in the abstract. Define the proposals: anurognathids being at the base of Pterosauria or sister to pterodactylia (or any other major phylogenetic take you explore in this study)

3.	On line 24, you use scansorial and arboreal interchangeably. While these are connected these are not interchangeable, scansoriality is locomotion type while arboreality is habitat occupation. A creature can be scansorial but not arboreal and vice versa. Adaptability to scansoriality is not mentioned later in the paper, but it is on arboreality (line 44) (Bennett 2007, Witton 2013, Lü et al. 2018). I would suggest just retaining arboreal and removing scansorial.

Other minor corrections can increase readability and be more approachable. The references used are comprehensive, recent, and well placed within the text, albeit I do have some minor suggestions noted below.

1.	On point 331 “(This alveolar) pattern is unprecedented for anurognathids”, it would be beneficial to describe alveolar spacing in other specimens rather than just reference papers citing these.

2.	Placing pterosaurs within any order of Archosauria is extremely arguable, note which paper you used to place it within the archosauromorph clade (there’s also Avemetatarsalia & Ornithodira and such). I would recommend citing Hone & Benton, 2007, or more recent study.

3.	For fossil record range, rather than using popular science book (Witton, 2013)(line 1133) maybe reference study mentioning Azdarchid bottleneck or other more recent papers (recommending Csiki-Sava, 2015 for extinction period, or the start of record by Andres, 2014).
Witton book while being a great resource, is a simplified, now somewhat outdated account that should be replaced with more direct studies.
Use of Witton, 2013 also happens on line 42, summarising synapomorphies, I would recommend Hone 2020 (already cited in your paper) as it does a better job for this purpose.

4.	You reference in your methodology using TNT dataset by Dalla Vecchia (2019), albeit that paper copies methodology of Britt 2018 (also referenced in your paper), with the only major change being the addition of Seazzadactylus. It would be beneficial for clarity and reproducibility to cite both, as one creates matrix and goes in-depth on methodology rather than just addition of a clade.
5.	643 small formatting issue

The figures are excellent, clearly annotated and help with visualisation and exploration of characters. With absolutely wonderful artwork and clear line arts.

1.	I would suggest the addition of a table of measurements of bone elements (with comparative taxa), and, if possible, stratigraphic section (I very strongly advise this for increase in study reproducibility and future research!)
2.	.A large aspect of the phylogeny relies on the elongation of the caudal series, in this specimen the caudals are not well preserved, nor well documented on the photograph. Can high resolution close under right light be provided to make this essential phylogenetic aspect more visible?
Experimental design: The study provides a throughout and valid look into anurognathid phylogeny with the addition of characters to a reputable established taxonomic dataset. The autapomorphies mentioned are valid and the specimen will definitively be welcomed as one of best Anurognathids on record. I am looking forward to the complimentary study on soft-tissue preservation. There is no comprehensive analysis of anurognathid phylogeny, and this study does not repeat too many elements of the recently published study by Hone (2020) also covering diversity in the clade. The TNT file is working, replicates results noted in the text and is sufficiently annotated in Mesquite to allow replication. However, I do have some considerations and corrections (and suggestions) to figures, methodology and facts in the text.

1.	One must bear in mind the Dalla Vecchia/Britt matrix relies on phylogenies established by Uwin and Kellner in 2003, at the eve of digital phylogenetic studies. Few characters included might be ontogenetic or act as poorly defined character bins (notably character 16 (Lacrimal, shape in lateral view); character 68 (DPC humerus shape) on which this study heavily relies. While Britt/Vecchia is one of better phylogenies in pterosaur literature it comes with its limitations and requires serious reworking, as attempted by Andres or Vidovic (well explored in your study with appropriate mention of the utilisation of continuous characters on the cranium and similar). It will be worth acknowledging these shortcomings in discussion and taken into consideration when assigning new clade names. Pterosaur phylogeny is a fluid, ever-expanding field and pterosaur phylogeny is overdue large reworking.
2.	Study relies on features and relative lengths of the caudal series. One of synapomorphies of newly defined clade of Anurognathini is “the loss of filiform processes of the caudal zygapophyses and haemapophyse” (lines 227-233). While this is true to most anurognathids, there are exceptions within the Novialoidea. Notably Bellubrunnus rothgaengeri (Hone, 2012) which “lacks elongate chevrons and zygapophyses”. Bellubrunnus was omitted from your phylogenetic study, its addition could push entire Anurognathid clade lower into the Novialoidea from current Wukongopteridea sister-condition if filiform processes are treated as discrete character. Much like anurognathids the pterosaur also has concave terminal wing phalange (albeit WP4 is not as reduced). Bellubrunnus also retains large orbit relative to cranial length (although this might be ontogenetic feature). I strongly recommend coding this taxa in. One cannot also forget posterior four bones in caudal section of most non-pterodactyloids lack zygapophyses too. It is not an exclusively pterodactyloid and anurognathid trait and that should get mentioned in some capacity. Even, one specimen of Changchengopterus pani (Lu, 2009) is known for having reduced caudal prezygapophyses and postzygapophysis.  Lu also suggested the specimen was a “a basal member of rhamphorhynchoids, and more closely related to Dorygnathus than to other rhamphorhychoids”. These were early phylogenetic studies however without notion of mosaic evolution within the clade.

	Hone, D.W., Tischlinger, H., Frey, E. and Röper, M., 2012. A new non-pterodactyloid pterosaur from the Late Jurassic of Southern Germany. PloS one, 7(7), p.e39312.
	Lu, J., 2009. A new non‐pterodactyloid pterosaur from Qinglong County, Hebei Province of China. Acta Geologica Sinica‐English Edition, 83(2), pp.189-199.

3.	The study claims using Dalla Vecchia (2019) matrix used in this study mentions not treating any characters as ordered. The original methodology (as in Britt, 2018) “Three multistate characters were treated as ordered (character numbers 63, 75 and 92)”, this might affect final reading. Include ordered and unordered options should be run as a precaution test
4.	You note fusing of cranial elements (and state of scapula coracoid), noting relative ontogenetic stage is subjective but might help in future and assignment of growth stages for this clade. After all, it is known ontogeny has a strong effect on cranial, dental, humeral, and public morphology on Novialoidea (Bennett, 1995). It would also be helpful to have relative element lengths provided in a table, with other related taxa as a comparison.
5.	Presentation of Wukongopteridea being an exclusively Oxfordian taxon in Figure 7 & line 144 is untrue. The earliest evidence of Wukongopteridea comes from Bathonian Great Oolite group in the UK – this comprises of a segment of rostrum with antorbital fenestra and sagittal crest (NHMUK PV R 464), a cervical vertebra (NHMUK PV R 40126a), along with two metacarpals (MUM STR1244b, NHMUK PV R 28160b)(O’Sullivan, 2015; O’Sullivan, 2018) these elements are too partial to be included in the phylogeny. Nevertheless, this pushes the range of wukongopteridea to Bathonian (instead of Oxfordian). This suggests fully developed bauplan by Middle Jurassic. More basal members should therefore be expected in later periods extending wukongopteriod ghost lineage by few million years.

O'Sullivan, M., 2015. The taxonomic diversity of British Jurassic pterosaurs (Doctoral dissertation, University of Portsmouth).
O'Sullivan, M. and Martill, D., 2018. Pterosauria of the Great Oolite Group (Middle Jurassic, Bathonian) of Oxfordshire and Gloucestershire, England. Acta Palaeontologica Polonica, 63(4), pp.617-644.
Validity of the findings: The conclusions are well stated and reasonable, albeit more comments have to be made on the limits of the fossil record and used taxonomic parameters.

1.	The autapomorphies noted on 253 are reasonable. But, to quote Hone (2020): “one could make a credible case for either synonymising many of these putative genera and species, or if such limited traits are considered sufficient to diagnose taxa, elevating current species to genera and naming most of the unnamed specimens as new genera”. With poor preservation of specimens, usually at contorted angles, without knowledge of ontogeny, it is hard to accurately propose discrete species with a degree of accuracy. This might only be improved or refined with time and more specimens of good quality.

The specimen and proposed clade names fall within ICZN requirements, although I do hope more experienced reviewer can double-check this.

Comments on data, and suggestions for some rewording and acknowledgements of result validity – both in text and TNT matrix.

1.	Newly introduced character (ch37 on line 173) is possibly ontogenetic and might provide false signals and make subadult specimens sort in a same arbitrary category. Effects can be accentuated by small numbers of other valid characters to counteract the ontogenetic (or taphonomic) effect.
2.	Synapomorphy on line 238. Could poor preservation and taphonomic deformation affect shaft morphology? With specimens being so brittle taphonomic alteration to mandible morphology or any long bone dimensions or elements should be considered. Deformation or taphonomic influence have not been mentioned in the study and should when defining a small number of characters on variably preserved specimens.

There is no major unreasonable speculation outside of the record.
Additional comments: The entire paper is well worded, easy to follow and is first of such nature: exploring phylogeny of this interesting pterosaur clade. Along with a very robust, good description of the novel holotype, supported by useful figures. The conclusions are reasonable and sufficiently explored in the text, albeit more discourse about result validity would be beneficial.


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: SINOMACROPS BONDEI, A NEW ANUROGNATHID PTEROSAUR FROM THE JURASSIC OF CHINA AND COMMENTS ON THE GROUP
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper has some major issues that need to be attended to. All of these are covered in the attached marked-up document so I will not go into detail here but stick to the main points.

The diagnosis of the new genus is very weak. There are only 2 traits, one of which is clearly incorrect (the tibia is not unusually long as your own data show) and the other is not easy to code or see in most other taxa. As a result the support is very poor. This is then compounded by a complete lack of comparisons to any of the other names anuroganthids and any examination of their diagnoses (which were recently revised in Hone, 2020 which you cite but then ignore with areas like this). As such, despite the quality of the specimen, this is really not supported as a new taxon as described here.

The description is OK but the figures are not as clear as they could be. Various traits that are described are no visible on either the photos of line drawings which makes them hard to determine. If the authors are not even confident to draw them on their figures this is difficult to credit when reading the text.

Secondly, the phylogenetic analysis is not well explained. There needs to be much more information on the support for various nodes in terms of numbers of characters and what those character states are.

As a related point, the revised diagnosis is unnecessary. Naming a new clade supported by only a few traits in a highly unstable clade that changes in almost every analysis is just creating a name that will never survive even a year until another analysis overturns it. The other re-diagnoses of clades (including of the Anuroganthidae itself) are equally problematic for the same reason. This is actively making the taxonomy worse, not better.

The results are over reliant on the foundational analysis. That is not to criticise the choice here, but pterosaur systematics are notorious for varying greatly between different matrices and failing to recognise this is a major issue. These taxonomic revisions are all based on the assumption that this analysis is 'the' answer and really it is only one and will be contradicted by the next published analysis (indeed I know of two in the works by different groups that produce results different to those produced here). In short, these results need to be held in the context of the previous analyses and some awareness of how tenuous these are likely to be. (Take for example the coding of a confluent NAOF which is controversial in anuroganthids, and I am personally very confident is wrong, but this is glossed over her).

The long section discussing previous results of anuroganthid relationships is over long and large chunks can be taken out without losing anything important. As per the point about, some context would be welcome. Some of the criticism of papers from 2003 for example, that have different numbers and types of characters, and differently formulated OTUs fail to account for what this would have meant for coding at the time and the results produced. Pointing to errors in coding is one thing, but this is repeatedly framed as somehow proving that the results of analyses based on there were incorrect when of course that need not necessarily be the case. One would need to recheck and revise all codings and run the analysis again with the same taxa and methods, simply assuming alternate trees would be produced or the published ones not supported is incorrect. In short this section is over long, and is overly critical. This would be far better replaced with a discussion of the traits that do support your analysis and consideration of alternate codings for things like the NAOF than pointing out coding errors in 15 year old papers.
Experimental design: As per the point about, the methods are basically fine, but the reporting of the results is insufficient. The naming and revised diagnoses of the clades are poorly done.
Validity of the findings: Basically OK but the new genus is not well defined, and the 'assumption' that this result is totally correct and used as a platform for some overly harsh criticism of other analyses is misplaced.
Additional comments: The timing of this paper was clearly unfortunate coming out so soon after the Hone 2020 review. However, since you clearly saw this paper since you cited it and used the next taxonomy that included Luopterus, it is bizarre that you otherwise ignore it. A major review of the entire clade including a new diagnosis of the clade, revised characters of every genus and descriptions of every known specimen, descriptions of the anatomy, and more and yet you do not refer to any of this and often ignore or change things without any reference to it. I suggest you read it and cite it appropriately, currently you have clearly not done so.


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: SINOMACROPS BONDEI, A NEW ANUROGNATHID PTEROSAUR FROM THE JURASSIC OF CHINA AND COMMENTS ON THE GROUP
Review round: 1
Reviewer: 3

Output:
Basic reporting: Writing
Generally, this is a well written manuscript with few errors in the language.

There are typographical errors on lines: 31, 471, 539, 769, 788, 828
There are missing words or a poor use of language on lines: 103, 470, 497, 635, 764, 944
On lines 167 and 168 the authors confuse the species names belonging to their respective genera. “Dendrorhynchoides mutoudengensis and Luopterus curvidentatus” should be Dendrorhynchoides curvidentatus and Luopterus mutoudengensis.

In the results section, the way the clade Anurognathinae is reported reads like it is a stepwise succession from Dendrorhynchoides up to Anurognathus + Vesperopterylus. The authors should rewrite this section so that it is clear that Luopterus and Dendrorhychoides are in a monophyletic clade which is the sister group to Jeholopterus + (Anurognathus + Vesperopterylus) - if they find the same results once the corrections below are made.

Other problems with the manuscript include:
The list of institutional abbreviations does not list all of the abbreviations used throughout the paper.
There are missing elements from the list of abbreviations in figure 2 i.e. fe and mt
Figure 7 claims to be the strict consensus with a relationship recovered in a compromise tree indicated by a dashed line. This is an inappropriate representation of the tree, which is in fact a 50% majority rule compromise tree, but the relationships recovered in less than 100% of the most parsimonious trees are indicated by a dashed line.
References given in the text are not included in the reference list (e.g. Vidovic and Martill, 2017 - given the volume date 2018 in the submission) or recorded incorrectly (e.g. Jiang et al. 2014).

Literature review
The literature review is sufficient to give a reader new to the field a reasonable understanding of what work has been done on the group before, but it is incomplete in terms of understanding relevant work on pterosaur phylogeny and there are concerning oversights.

The authors claim their submission is the second to study all known anurognathid species in a cladistic analysis, seemingly unaware of Unwin’s early study of basal pterosaurs which included Anurognathus, Batrachognathus, Dendrorhynchoides and Jeholopterus (Unwin, 2003a) prior to Vesperopterylus and Luopterus being described. Other authors followed Unwin, meaning I have been able to identify at least 14 studies that came before this one which included all known anurognathid species at the time (Kellner, 2004; Wang et al., 2005, 2008, 2009; Lü and Ji, 2006; Lü et al., 2006; Dalla Vecchia, 2009; Lü, 2009; Andres, 2010; Andres, Clark and Xing, 2010; Andres and Myers, 2012; Andres, Clark and Xu, 2014). If the authors consider the possible anurognathid Mesadactylus important with respect to studying all anurognathids in a cladistic analysis, Bennett did not suggest the synsacrum may make it an anurognathid until 2007 (Bennett, 2007), meaning there were six studies considering all known anurognathids at the time of publication before this one.

In the discussion, the authors refer to Kellner’s (2003) cladogram as the first cladistic hypothesis of anurognathid interrelationships. However, Kellner’s work was contemporaneous with Unwin’s (2003b), being published in the same pterosaur themed volume. Furthermore, there were earlier studies which used computed cladistic analysis to place the Anurognathidae (Unwin, 1995; Kellner, 1996; Viscardi et al., 1999) and their phylogeny had been considered for decades earlier (Young, 1964; Kuhn, 1967; Wellnhofer, 1975, 1978; Unwin, 1992).

It is notable that the holotype specimen of Anurognathus ammoni Döderlein, 1923 has a cranium preserved in lateral view, while the authors claim that the specimen reported in this submission is the first anurognathid to have a cranium preserved in lateral view. This gives me cause for concern about the rigour of the work done and the authors knowledge of the literature they cite.

The authors should consider making a reference to a study on pterosaur feeding habits which specifically addressed anurognathids insectivory (Ősi, 2011).

Accuracy of reporting
There are several unfortunate issues with the rigour and accuracy of the reporting which let this manuscript down.

In the methodology section, it is reported that the characters are “unweighted” which is inaccurate because one cannot run a maximum parsimony analysis with unweighted characters. I think that the authors mean to say that equal weights were used?

In the results section, 321 is given as the tree length for the 9 most parsimonious trees (MPTs), but when I ran the matrix I recovered trees of 319 steps. If the reporting is accurate to what the authors found, I suspect the limited search function got stuck searching an island of tree morphospace. However, using a more robust search strategy, or testing the results sufficiently would have exposed this problem. I reran the analysis with a more robust new technology search with ratcheting to avoid becoming stuck in local optima and the shortest tree length was still recovered as 319. The tree differs from the one reported; most significantly, the clade containing Dendrorhynchoides and Luopterus is not recovered. In the same section, the ensemble consistency index and ensemble retention index (i.e. reported as CI and RI, not ci and ri) are given as ranges, which is confusing because they should be the same for all 9 MPTs. The minimum possible number of steps for this matrix will always be 168 and as long as the shortest recovered tree length is 319, the CI will always be 0.526.

These inaccuracies in the reporting are related to concerning problems with the experimental design and findings.
Experimental design: This submission studies a specimen of anurognathid pterosaur which is new to science. The specimen exhibits few but significant enough anatomical differences to be considered an entirely new taxon. However, it should be noted that proportions can be affected by allometric growth and the spacing between the mesial teeth is unknown in some other anurognathids. The study also purports to present a critical review of anurognathid phylogenetic relationships already in the literature. In places, this review descends into ‘why we’re right and they’re wrong’ ad hominem argumentation. It is my opinion that the general experimental design (not the execution) is sufficient to phylogenetically place the specimen and to lend a little consensus based support to the derived non-pterodactyloid theory (Andres, Clark and Xing, 2010), but it is by no means a gold standard to benchmark other cladistic analyses against.

The authors have supplemented the Dalla Vecchia (2009) basal pterosaur analysis with characters known to be synapomorphies and apomorphies for anurognathids. Similarities represented as synapomorphies are not the only information that leads to a groups placement in an analysis using maximum parsimony, it's also important ‘what the group is not'. I would feel more convinced of the authors strong argumentation for preferring their ‘new’ phylogenetic hypothesis if they were using the most comprehensive dataset studying the taxa to date, rather than simply incorporating some characters with transformations known to be associated with the group into a preferred analysis. Furthermore, there are numerous categorical characters describing continuous data in this analysis for which the states appear to have been chosen arbitrarily or based on the researchers’ opinions and therefore, unintentionally, their biases.  Ideally, these characters should be modified into continuous characters, or at the very least one of the many objective methods for assigning categorical states to continuous data should be employed (e.g. Thiele, 1993; Strait, Moniz and Strait, 1996; Rae, 1998).

With regard to one ‘continuous’ character, the authors say “in our analysis, we modified the character from Kellner (2003), now considering a humeral/femoral length over 1.70”. There was little merit in the original character for the reason given above, but the modification of the character in this case is a questionable practice because it seems to be designed to fit the author’s preconceived notion.

The methods are documented in enough detail to be able to rerun the analysis. However, the result cannot be replicated because the optimal MPTs were not reported. Furthermore, the method which is documented is not particularly rigorous considering the availability of functions in TNT (Goloboff and Catalano, 2016).

It is not easy and in some cases impossible to validate the coding in the data matrix supplied. This is mostly due to missing states in the list (e.g. characters 77, 89, 91), but there are also some states which do not make sense - possibly because states have been mixed between characters (e.g. character 25)?

The characters and states which it was possible to read and validate are not well coded in some cases. There is inconsistency, where the authors are willing to speculate and code features which are not preserved but can be inferred from other taxa, requiring a priori decisions about relationships (e.g. characters 1, 2, 5), whereas what can be reasonably inferred or assessed from the specimens is not necessarily coded (e.g. characters 4, 6, 17, 26, 43, 44, 46, 47).
Some other specific concerns about the coding include:
Ch. 3 - The downward curvature of the jaws should not be coded with any certainty because the observed curvature of the maxilla is likely due to taphonomic processes acting on the specimen. Note, the maxilla curves ‘down’ and the dentary curves ‘up’ while the exact opposite occurs in Anurognathus due to the same crushing effect. This character should be coded as unknown for Sinomacrops.
Ch. 7 - I am struggling to understand how the jaw shape in dorsoventral view in Sinomacrops is similar to Batrachognathus and those two are more similar to Scaphognathus than Scaphognathus is to Sordes. I also struggle to understand how this character is coded for some other specimens given their preservation.
Ch. 8 - “Premaxilla,_caudoventral=posteroventral_' present_ absent” - I am not sure what this refers to because the coding is not consistent with my only reasonable interpretation of this character. Please define it better.
Ch.9 - Some anurognathid specimens preserved in ventral view or in a poor state of preservation are coded as having no premaxillary crest, while the authors code it as unknown for this specimen which clearly demonstrates the state is absent.
Ch. 25 - The palatal elements of Sordes are reduced to very thin bars of bone - these elements are not unknown.
Ch. 30 - The authors went to great lengths to convince the reader that the nares were confluent with the antorbital fenestra but then do not code this for Sinomacrops. Although, I note there are characters that duplicate this one and they are coded.
Ch. 36 - It doesn’t make sense that the relative size of the orbit compared to the antorbital fenestra would be coded the same as Dimorphodon in anurognathids. Indeed, if the authors are following their own assessment this character should be coded with a dash.
Ch. 59 - The lack of serrations on distal teeth can be coded for a couple of anurognathids and monofenestratans. The presence/absence of the ascending process of the maxilla as a reference does not seem particularly important.
Validity of the findings: The authors have kindly supplied the CT data for the specimen described in this submission. However, there is a technical barrier to access because the hosting website is reported as a security risk by web browsers. I would appreciate it if this issue could be resolved or if the data could be deposited in another secure open repository.

I am struggling to confirm the distal expansion of wing phalanx 3 which the authors claim to indicate a fourth wing phalanx. I agree there probably is a fourth wing phalanx, but it remains inconclusive.

When discussing the anurognathids exclusion from Novialoidea and Breviquartossa, the authors neglect to report Unwin (2003b) had tested and discussed the hypothesis that anurognathids were the sister group to Pterodactyloidea and presented his cladogram ‘C’ demonstrating this possible relationship. In the assessment of anurognathids as non-breviquartossan novialoids, the final paragraph is written in such a way that it seems to question the validity of Dalla Vecchia’s (2019) findings and synapomorphies, simply because this study did not find the same result. I think this paragraph could be reworked to more plainly state that these relationships and therefore the synapomorphies were not corroborated by this analysis.

Similarly, there are several misrepresentations of the scaphognathid hypothesis. In this submission, the authors discuss numerous synapomorphies which are not coded in the original analysis. Vidovic and Martill (2017) do not code any anurognathids for the character “Angle of quadrate to the dental plain” because it is impossible to measure, even in Anurognathus. Nor do they code “Inferior temporal fenestra/orbit ratio (maximum length)” for any anurognathid.

Also, the authors make the statement “Tooth crowns, recurved”...”was coded as “?” in Rhamphorhynchus, Dorygnathus, Campylognathoides and Dimorphodon” which is incorrect. Vidovic and Martill (2017) studied numerous specimens of these species, detailed in their supplementary material, and coded Rhamphorhynchus, Dorygnathus, Campylognathoides zitteli and C. liasicus, and Dimorphodon ‘0&1’. The authors also argue with correct coding in this analysis. They claim the quadrate position under the orbit was miscoded by Vidovic and Martill (2017) in wukongopterids, saying “all wukongopterids” orbits are anterior to the quadrate. However, the articular end of the quadrate is typically located under the portion of the orbit approximating its centre and often approaching the lacrimal process of the jugal in wukongopterids and basal pterodactyloids. Finally, the authors say “tooth crown curvature displacement”...”is not present in anurognathids, as can be seen from the well-preserved teeth of Anurognathus, Batrachognathus, Dendrorhynchoides and Jeholopterus”. Vidovic and Martill (2017) also coded this state as absent in Anurognathus, but coded it as present in the other 3 species studied. Batrachognathus clearly exhibits strongly curved teeth and Dendrorhynchoides curvidentatus is even named for the curvature of its teeth.

Similar to Unwin (2003b) testing different hypotheses of anurognathid relationships and discussing them, Vidovic and Martill (2017) noted they were unconvinced of their findings which may be affected by a lack of transitional forms and paedomorphism. This warrants some discussion in these sections.

I am unconvinced by the sixth condition which includes anurognathids in Breviquartossa “metatarsal IV shorter than metatarsals I-III”. Because of the preservation, it is difficult to be sure of when the metatarsals III and IV terminate without looking down the microscope, but if metatarsal IV is shorter than the others, it is by much less than the width of its diaphysis. Looking at many other breviquartossans, the fourth metatarsal is significantly shorter than its diaphysis’ width compared to the other metatarsals.
Additional comments: This submission is interesting, describing a new specimen which provides valuable insights into anurognathid palaeobiology. I do not necessarily agree with your assessment of parts of the specimen, in some cases I concede this is down to personal judgement and you are entitled to your opinions. However, in parts the cladistic analysis is coded incorrectly or more confidently than it can be. Furthermore, the methodological approach is insufficient to critically appraise the work of others. The quality of the cladistic analysis, its execution and reporting are left wanting and some of the criticisms made of other studies are unwarranted or not clearly stated as your own opinions. My recommendation is to focus on the specimen and not to get bogged down in trying to fix the phylogeny of the anurognathids.

You must make some changes to your data matrix to ensure the OTUs are coded faithfully and removing subjective alterations to the characters. In the sections above, I have picked out some specific concerns, but I have not comprehensively reviewed the matrix. When you run your analysis, please ensure that you use a robust search strategy.
If you still wish to pursue comprehensively reviewing the phylogeny, please include information about all the hypotheses presented and discussed by Unwin (2017) and Vidovic and Martill (2017) - who were clearly not entirely convinced of their own results but reproduced them faithfully. Also, a much more comprehensive understanding of what has come before is required, but I probably would not have noticed the absence of some studies if the importance of this contribution had not been so overstated in parts.


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: SINOMACROPS BONDEI, A NEW ANUROGNATHID PTEROSAUR FROM THE JURASSIC OF CHINA AND COMMENTS ON THE GROUP
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is much improved compared to the first version and the major issues have been addressed in the text or response letter. There are still some odd phrases or things that are not clear and I have marked these up and suggested alternatives in the marked up document.
Experimental design: Fundamentally fine. However, I notice now (which I think I missed in the original submission) that all characters are run as unordered even when there are some traits that should be ordered. There is a comment on this and suggested reference in the marked-up document but in short a character that has three states that are e.g. square shape, round shape and triangular shape should indeed be unordered as any transformation from one to the other has no obvious polarity. However, something with states long, medium and short, cannot go from long to short without having 'passed through' medium, this should therefore be ordered. This error is commonly replicated across phylogenetic analyses and should not be perpetuated here.

Given the low support values and constant shifting clade placement in pterosaur phylogenies I would not be surprised if correcting this did change your phylogeny quite significantly and so this really needs to be looked at.
Validity of the findings: Aside from the point about about the stability of the phylogeny this is fine.
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: SINOMACROPS BONDEI, A NEW ANUROGNATHID PTEROSAUR FROM THE JURASSIC OF CHINA AND COMMENTS ON THE GROUP
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript is generally in good order with clear English and article structure. The literature cited is sufficient, and provides good context.

There is one example where the authors could unintentionally misrepresent Unwin 2003 to readers without sufficient knowledge of pterosaur discoveries (line 627).

With reference to "Dimorphodon" weintraubi on line 384, I believe the convention of putting a genus in quotation marks indicates that the author is questioning the validity of the genus, whereas, in this case the authors are questioning the specific combination of "Dimorphodon weintraubi".

There appears to be a problem with the reporting of the number of most parsimonious trees recovered from the cladistic analysis. The number currently reported might be historic and needs updating to reflect the trees recovered by analysis of the data presented in the supplementary material. The associated figure appears accurate to my findings.

I am also concerned that there is still a claim (line 787/8) that this new specimen is the first with a skull in lateral view, which is not accurate. I wonder if this is a remnant from a previous draft? I think it is remarkable that this is only the second specimen ever described in lateral view and it is valuable to science as a result.

The abbreviations in the figures need checking. There appear to be some missing.

I have made notes and comments on the PDF of the submission which could help.
Experimental design: The experimental design and associated comparisson with other similar analyses has been revised. The overall quality, readability and accuracy of the manuscript is significantly improved as a result of the well defined research question and relevant results.

I was able to replicate the analysis with ease, but the authors could consider including their search commands in the TNT file for better reproducibility.
Validity of the findings: I personally disagree with the authors' interpretation of the nasoantorbital fenestra, but this is only an opinion informed by the images. I think it is clear that the authors recognise better material is required before a final assessment can be made. I think with the exception of the mistake regarding the occurrence of anurognathids preserved in lateral view, the conclusions are reasonable and based on the findings.
Additional comments: Overall, I think this is a much more coherent paper. There is very little that is objectively wrong with the paper itself and the specimen is a vital contribution to our science.

I notice that one of the figures (13) is stylistically slightly different and I just want to sense check that this is original to this submission? If not, it will need an appropriate citation. If it is original, I don't think the stylisation is so different that it would be necessary to change anything.

I have made notes on the PDF. I have approached this review as succinctly as possible, so I do encourage you to ensure my few comments on the PDF are addressed.


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: USE OF CONDITIONED MEDIA (CM) AND XENO-FREE SERUM SUBSTITUTE ON HUMAN ADIPOSE-DERIVED STEM CELLS (ADSCS) DIFFERENTIATION INTO UROTHELIAL-LIKE CELLS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article subject is relevant but significant changes need to be made to improve its quality.

The English language needs to be improved. The authors sometimes use informal words or sentences. Some examples: lines 65 (“What facilitates...”) and 90 (“Until now...”). Even, an orthografic error was found at line 93: word trans-differentiation.

I could no open the Supplemental files bacause of its extension .sav.

The references need to be actualized to recent findings and either standardized. See lines 102/103 and 316 for example.
The color of the text needs to be reviewed. Eg., lines 280, 337 and 343 (references).

All the figures need to be reviewed. The size of the letters are not uniform, some figures are distorted. Fluorescent images need to be with a higher quality. The legends are doubled.

It’s necessary to put the asteristic symbol (*) in the grafics whether the comparison was statistic relevant. I suggest to add in all legends the number of experiments performed.

Some ponctual alterations in the figures:

Figure 1: I suggest do divide this figure in two. The B section could be another figure and the figures letters in the following way: A, B, C... Also, its important top ut arrows or another symbol to point the structures you referenced., as lipid droplets.
Figure 2: Graphic distorted. Compare CM versus UCM data set.
Figure 3: The letter A is hidden. I suggest to include at least images of UCM-FBS condition to verify if is FBS or CM the protagonist eliciting ADSCs urothelial differentiation. Improve fluorescent images quality.
Figure 4: Graphic distorted. Compare CM versus UCM data set.
Experimental design: The research question and aim of the study and, consequently, the work originality are not clear. Did the authors want to verify whether ADSCs urothelial differentiation depended on the use of UCM and CM or FBS and pHPL? Or both?

Explain why did the cells were used at passage 3-5. Also, explain why did the analyses were performed after 14 days of differentiation (ADSCs into adipocytes or urothelial cells) or 21 days (ADSCs into osteoblasts).

I suggest to include a Materials and Reagents topic in the beginning of Method section.
Validity of the findings: The authors have not proved that the CM is the protagonist eliciting ADSCs urothelial differentiation.

According to the results, FBS seems to be the major contributor to this process. I suggest to include a CM condition or CM-Free condition (without FBS or pHPL) in the experiments, aiming to evaluate whether the CM has a predominant role promoting urethelial differentiation or if is the FBS. Even, I suggest to compare the data set of CM with UCM to support this issue.

In conclusion, the entire article needs to be reviwed extensively. The aim and results need to be more clear and robust. The discussion and introduction need to be atualized and modief depending on changes in aim and results.
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: USE OF CONDITIONED MEDIA (CM) AND XENO-FREE SERUM SUBSTITUTE ON HUMAN ADIPOSE-DERIVED STEM CELLS (ADSCS) DIFFERENTIATION INTO UROTHELIAL-LIKE CELLS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper aimed to investigate the role of unconditioned urothelial cell media (UCM) and pooled human platelet lysate (pHPL) as alternatives to conditioned urothelial cell media (CM) and fetal bovine serum (FBS) to induce differentiation of adipose-derived stem cells (ADSCs) into urothelial cells.

The search for alternatives to undefined culture medium is of great relevance, especially when dealing with cells with therapeutic potential, since undefined factors present in cells-derived conditioned media or FBS can affect cellular biology and physiology in uncountable ways. Besides, use of xenogenic products are also hampered by ethical concerns.

The manuscript is well-written in most of its parts (see exception below), but a couple of references would help to contextualize the problem and improve the discussion. Kolle et al. 2013 (doi:10.1016/j.jcyt.2013.01.217) showed that adipose-derived stem cells cultivated in serum-free medium supplemented with pHPL present normal chromosomal stability and differentiation capacity toward adipogenic, osteogenic or chondrogenic lineages. Besides, treatment of cells with pHPL reduced the cell population doubling time. Karadjian et al. 2020 (doi:10.3390/cells9040918) showed that the proliferation rate of bone-marrow-derived mesenchymal stromal cell (BMSC) cultured in medium supplemented with pHPL exceeded the observed in medium containing FBS. Also, differentiation of those cells toward osteogenic lineage was not negatively affected by pHPL. Thus, it’s tempting to analyse how differentiation of ADSCs into urothelial cell lineage would be affected by pHPL.

Raw data has been included, although I was unable to open the files with the provided extensions.

Microscopy images are nicely presented overall, but improvements can be made in the scale bars. All graphs shown are in very poor quality (thin lines, narrowed letters, no statistical data in the graphs, low resolution). Figure subtitles should include the number of experiments and/or replicates performed.
Experimental design: The most important issue concerns to the methods used for obtaining the conditioned media and inducing cell differentiation, which are confusingly and/or incompletely described.

Authors state that “SV-HUC-1 cells were cultured in F-12K medium supplemented with 10% FBS and 1% streptomycin and penicillin. Conditioned medium derived from SV-HUC1 was collected and used to induce the ADSCs differentiation towards the urothelial-like cell lineage”. If that description is correct and complete, the CM used in the experiments contains FBS by itself, what would invalidate all data concerning the effect of pHPL alone in cell differentiation.

Authors present data showing that expression of some urothelial cell markers (cytokeratin-18, cytokeratin-19 and uroplakin-2) is increased only in the presence of FBS, either using CM or UCM, as seen either by immunofluorescence and qRT-PCR. Additionally, production of the main growth factors released by urothelial cells in culture (EGF, PDGF and VEGF) is increased following treatment with CM or, to a lesser extent, UCM, supplemented with either FBS or pHPL. Use of pHPL had little or no effect on differentiation of cells. To validate those findings, a serum-free CM must be used.
Validity of the findings: Included in the above comment.
Additional comments: As authors conclude themselves, since UCM doesn’t affect expression of urothelial markers, it will be necessary to add growth factors, cytokines or others molecules to increase differentiation potential of the culture medium. Further studies will help to clarify the question of what combination of molecules are necessary and sufficient to direct differentiation of a stem-cell toward a urothelial cell without the need of xenogeneic components? By now, we still need to use the undefined conditioned medium with FBS to produce those cells.


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: USE OF CONDITIONED MEDIA (CM) AND XENO-FREE SERUM SUBSTITUTE ON HUMAN ADIPOSE-DERIVED STEM CELLS (ADSCS) DIFFERENTIATION INTO UROTHELIAL-LIKE CELLS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The English language was improved. The prior cited orthographic error has not been adjusted yet (word trans-differentiation – line 95 (more recent revision). Even, I suggest to rewiew the word immunofluorescence along the manuscript.

The figures and grafics are with a better quality and presentation. The immunofluorescence images as well.
Minor changes:
Figure 2 (Legend):  I suggest to change the form that you write the figures letters when mentioning only two of them. Instead of writing B-D, for example, it would be better to write B&D or B and D. Because it seems to be B until D.
Figure 4: The description of each image on the left side need to be up adjusted a little up.
Standardize the graphics size.
Figure 3 (Text): I suggest adding to the sentences (lines 241 and 243) which conditions were been compared, as it was indicated at line 244.
Experimental design: The research question and aim of the study are more evidente along the paper. I just suggest to add in the conclusion section of the Abstract that “Efficient ADSCs urothelial differentiation is dependent on the use of CM AND FBS”.
Validity of the findings: I still believe that using a CM-Free condition (without FBS or pHPL) in the experiments, would be better to validate these findings. However, I understand the limitations.
However, by making the aim of the work clearer together with the comparison of the CM and UCM data set, it helped to strengthen its results.

In conclusion, the paper as a whole have improved. The changes suggested by the editor and reviewers provided insights to the authors organize the main question of the work and enrich the manuscript
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: USE OF CONDITIONED MEDIA (CM) AND XENO-FREE SERUM SUBSTITUTE ON HUMAN ADIPOSE-DERIVED STEM CELLS (ADSCS) DIFFERENTIATION INTO UROTHELIAL-LIKE CELLS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: As I explained in the first review, the main flaw of the work is in the methods used to obtain the conditioned medium and induce cell differentiation.

The authors use FBS in either unconditioned and conditioned media to treat cells, and than they compare the effects of these media and conclude that "induction of ADSCs towards the urothelial phenotype requires the presence of both conditioned media and FBS", which in fact has has not been proven, since FBS was present in all conditions. The authors argue that "any effect coming from FBS would be minimum", but a concentration of 2% FBS (concentration used by the authors in the 'non-serum' condition) can impact various biological processes, such as those shown by the authors (regulation of expression of cell markers and production of growth factors).
Validity of the findings: In my opinion, the data presented by the authors cannot be validated if additional experiments are not carried out using a conditioned medium prepared without FBS.
Additional comments: No comment.


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: NEW ALIGNMENT-BASED SEQUENCE EXTRACTION SOFTWARE (ALIBASEQ) AND ITS UTILITY FOR DEEP LEVEL PHYLOGENETICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: Overall, the experimental design meets PeerJ standards; however, I did find it a bit difficult to determine how exactly the software differs from existing software. That being said, I am sure the software is different and I suggest the authors emphasize the differences in the Methods section and their discussion where they evaluate software performance.
Validity of the findings: no comment
Additional comments: Introduction
•	Lines 35-37 ‘Because of the relative…type of sequence data’: I think this should be re-worded because it sounds like the reason orthologous genes are used is due to the ease of estimating homologs. We use orthologs because they are the result of speciation events, while paralogs are due to duplications. Using paralogs violates some assumptions of phylogenetic models and will most-likely disagree with the true species tree.
•	Lines 44-45 ‘As sequencing costs…genome skimming has become…’: Is it possible to define ‘genome skimming’ and even supply a citation or two? I know what you mean here but, I just reviewed another manuscript and the author was referring to genome skimming as a method that includes using restriction enzymes to cut the gDNA (i.e., RAD approach). I am worried that ‘genome skimming’ is becoming a term used interchangeably with different methods.
•	Line 51 ‘However, data obtained…’: Here, is ‘data’ referred to as the raw sequence data or the assemblies from genome skimming? I ask because on line 54 you refer to ‘annotations are unavailable’ and I think this will have to be modified if you are referring to the raw data because the annotations then fall on the scientist generating the data.
•	Lines 55-57 ‘As opposed to typical…and non-target loci’: This sentence needs a citation. Also, what if the targeted locus resides in a genomic region with relatively higher G+C content?
•	Lines 60-61 ‘This potential lack…currently available software.’: Why does the lack of a closely related reference make this challenging? On Line 35-36 you say, ‘…relative ease to determine homology…’.
•	Lines 64-75: I like this paragraph describing these software tools. One suggestion is rephrasing the second sentence to mention that raw/curated reads are usually assembled with the help of reference orthologs. I mention this because ‘identifies reads of interest’ is a little confusing here because you are specifically targeting loci that you pre-determined as homologous/orthologous.
•	Lines 76-95: I would also include OrthoFinder (Emms & Kelly 2019; https://doi.org/10.1186/s13059-019-1832-y) as an additional piece of software for this type of software
•	Lines 78-79 ‘However, especially for…time-demanding procedure’: I am not sure I agree with this statement. I have used HaMStR for taxa that share a most recent common ancestor (MRCA) >300 Ma and did not notice any memory issues or time-demanding processes because of the age of the MRCA. Instead, I would argue the numbers of loci and taxa are the rate-limiting items.
•	Lines 83-84 ‘However, genomic assemblies…of varying sizes.’: I am not sure I see your point here because genome assemblies include predicted proteins, which are the necessary data for many of the programs you listed here. Are you referring to generating genome skimming data and not annotating it?
•	Lines 92-93 ‘Phyluce was originally…longer multiexon genes.’ I disagree with this statement. Sure, the probes sites are highly conserved, but Phyluce does not need a reference to assemble a locus; therefore, sequence conservation is irrelevant here. Furthermore, the sequences are assembled de novo using Abyss, Trinity, or Velvet, which will have no impact on ‘longer multiexon genes’ because the locus content is not considered when assembling loci.
•	Line 111 ‘…no special software…’: I am not sure what you mean here. Can you clarify this?

Methods
•	Line 134 ‘like BLAST and HMMER’: Can you list all of the alignment programs that your software can parse the output?
•	Line 135 ‘For each query-hit pair…’: you may want to consider changing ‘hit’ to ‘subject’. I suggest this because you already use the terminology from the BLAST application (e.g., query and HSP), and using ‘Subject’ would continue the trend. BLAST is arguably the most used bioinformatics software and I think most would welcome the familiar term usage.
•	Line 150 ‘…on divergent taxa.’: If the taxa share an MRCA so long ago that homology may be an issue with DNA, why not use the amino acids? Using amino acids to infer homology and orthology is standard practice in the genomics realm.
•	Line 155 ‘ranked by alignment scores.’: What are the alignment scores and how are they used here? How do you distinguish between two alignments with the same score or nearly the same score? This second question is driven by using genome skimming data and the potential for multiple alleles. For example, let’s say your bait is a protein-coding exon with one site that is heterozygous. How does your software choose between the two assembled alleles?
•	Lines 168-169 ‘The procedure…on the alignment tables’: Since the outcomes of your software depends heavily on alignment software, I think it is best to include the specific command lines that you use in your example below. Furthermore, based on your experience, can you offer suggestions on settings for each of your alignment programs your software uses? I think this would go a long way with your users because I am very familiar with BLAST and there are a TON of options available.
•	Line 170 ‘BLAST, HMMER, LASTZ’: I think it is best to include version numbers for the software used in case the output format changes in the future. That being said, does the output from BLAST need to be in a specific format (e.g., csv, tsv, xml, etc.)? Also, does your software work with BLASTN, BLASTP, tBLASTX, etc?
•	Line 184 ‘…evaluate the software’s performance…’: I think you should be specific in regard to what performance means here. For example, does performance mean computation time to perform an operation, computational efficiency (e.g., least amount of RAM needed), etc? Also, I think you should be specific in regard to your goals with comparing software. For example, are you testing the ability to assemble homologs from the sequence data and/or testing how well you can predict orthologs from the assembled homologs using RBH? One thing to keep in mind is that your RBH criteria may differ from the OrthoDB criteria for orthology prediction; therefore, your final set of predicted orthologs may differ from OrthoDB and the other programs depending on their specific criteria. I think it is important to standardize the aspect as you did with other settings from software that you describe.
•	Line 190 ‘regions’: Do you mean ‘orthologs’ or ‘orthologs and adjacent non-coding regions’?
•	Line 237 ‘truncated alignments until…’: Do you mean trimmed the alignment till both sequences were equal length? “both sequences were present” is throwing me off because both are present because you just aligned them with MAFFT.
•	Lines 257-258 ‘The default settings…causing suboptimal performance’: Why are they inappropriate? Why not use the amino acids instead of nucleotides for the deep divergences you are trying to assemble?
•	Lines 288-289 ‘We additionally capped…performance comparison fair’: Can you describe the RAM requirements, if any? Also, can ALiBaSeq be optimized on a High Performance Computing Cluster with different schedulers?
•	Lines 304-305 ‘We also evaluated…assembly-based tools only).’: I agree that introns can be difficult to assemble since they typically are not part of the bait sequence(s). But the other difficulty with the introns is repetitive motifs within them. It may be a good idea to touch on this with your simulations and mention the abundance of repeats and whether or not that impacts your performance with some of these. My guess is that all of these software applications struggle with them.

Results
•	Line 326 ‘…around 1,500 loci,…’: In the results section you use terms and symbols referring to uncertainty or estimates (e.g., ‘around’, ‘~’, etc.). Since they are results, can you specify the exact numbers for each?

Discussion
•	General questions: What is different about your code relative to other assembly-based software that makes it slower or faster than them? Is there any particular reason(s) why researchers should use your software over the others? The latter question is just to help you pitch your software to the audience. It may be a good idea to clearly emphasize these reasons in the discussion.
•	Lines 457-460 ‘With regard to…additional false positives’: I find this interesting because I am not sure why you obtained this result. It may be useful to your audience if you expand on this. Also, the ultimate question may be whether a systematist wants to relax the RBH to get more loci, but also adding potentially poor signal in their datasets by adding false positives.
•	Line 475 ‘on a bioinformatics cluster’: I made a comment above regarding this, but you may want to also add something about it in the methods too.

Figures
•	Figure 1: Since the requirement for your program is assembled contigs, then you may want to consider adding something to the left of ‘NCBI BLAST, HMMER…’ representing that initial step needed that your program does not perform.
•	Figures 2 & 3 & 4 & 5: I can not read the left y-axis, but I am not sure if that is due to the review copy that I have.

Github Repo
The repo looks good and I looked over the code and it is well-written; however, please note that I did not test it (I can if the paper gets kicked back to me again). One thing I would suggest is to work-up a simple test dataset (e.g., 2 genes and 5 taxa) that is used with some form of a tutorial. I suggest this because, as a user, I typically choose software that has the best documentation, tutorials, and simple test data. For example, I primarily use Phyluce and Hybpiper because, in my opinion, the documentation is second to none. I would encourage you to have a look at their docs and think about possibly adding a thorough tutorial to your Github repo.


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: NEW ALIGNMENT-BASED SEQUENCE EXTRACTION SOFTWARE (ALIBASEQ) AND ITS UTILITY FOR DEEP LEVEL PHYLOGENETICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper presents a method to stitch the output from a sequence similarity program like BLAST and present homologs. The method is limited in novelty but also interesting because it can consider similarity sequence output from any program. Overall the study is fine, the simulation is okay although I think performance on more pair of genomes would be interesting to report (perhaps of varying divergence).

My main concern is the lack of recent methods that use exact alignment and high performance computing to identify similarity between divergent genomes. For example take NextGenMap, MaxSSmap, SSW, and CUDA-SW++. Each of these have shown to capture distant homologs more accurately than hash-table based searches of BLAST and HMMER. Does AliBaSeq identify more homologs if exact alignment methods were used to identify sequence similarity? The answer would be interesting either way.
Experimental design: The design is fine but I think showing performance on more pair of genomes would be interesting. A graph showing performance on increasing divergence.

What read lengths were simulated? I don't see that mentioned in the paper.
Validity of the findings: The authors conclude their method works but I'm not convinced. I think when it comes to a study claiming to find similarity at the deep phylogenetic level you have to include recent methods designed for high divergences and show more data (perhaps simulation).
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: NEW ALIGNMENT-BASED SEQUENCE EXTRACTION SOFTWARE (ALIBASEQ) AND ITS UTILITY FOR DEEP LEVEL PHYLOGENETICS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Generally, I think that “alibaseq” is a useful tool/software for large-scale analyses of multilocus datasets, which may not be limited to protein coding genes. It is certainly of interest to many biologists. The article is well written, features and utilities are explained well, and advantages of alibaseq is highlighted compared to other software designed for similar use. But a couple of concerns:

a)	The article seems better suited for a Bioinformatics Software or Methods paper than a research article.
b)	Even though the article is well written overall, the writing needs to be polished in the beginning – abstract and the first few sentences of introduction. Somewhat odd grammar/structure interrupted my concentration and slowed the reading.

Addressing the following might help clarity of description.

1)	False positives of what: Retrieval of orthologs?
2)	Is the problem of false positives more relevant to eukaryote genome assemblies? it will be useful to specify that.
3)	“Whole genome sequence’ (WGS) data” sounds simpler than ‘whole genomic sequencing’.
4)	May be It can be stated that the software/pipeline is geared toward phylogenetic analyses using nucleotide sequences/WGS data.

W.r.t (3), the statement “Available tools especially struggle at deep phylogenetic levels and necessitate amino-acid space searches, increasing rates of false positive results.” in the abstract seems to contradict one of the very first results (lines 323-325):

“Protein based approaches (tblastn, tblastx, and 324 phmmer) performed best, with relaxed nucleotide-based searches (blastn with wc9 and 325 discontinuous megablast) performing almost as well.”
Experimental design: -- not applicable --
Validity of the findings: -- not applicable --
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: NEW ALIGNMENT-BASED SEQUENCE EXTRACTION SOFTWARE (ALIBASEQ) AND ITS UTILITY FOR DEEP LEVEL PHYLOGENETICS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have satisfactorily addressed all of my comments. Furthermore, I did not identify any other issues that need to be addressed.


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: NEW ALIGNMENT-BASED SEQUENCE EXTRACTION SOFTWARE (ALIBASEQ) AND ITS UTILITY FOR DEEP LEVEL PHYLOGENETICS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I appreciate the author rebuttal comments but I believe they are slightly flawed. All three tools NextGenMap, SSW, and MaxSSmap actually produce HSP regions which is why I suggested them in the first place. Yes, both BLAST and HMMER are far more widely used and from that perspective it makes sense to have ALiBaSeq work for them. But both are also weak on divergent data. I'm not sure if a claim on utility for deep-level phylogenetics makes sense if baseline methods designed for high divergences are ignored. This claim is a main motivator of ALiBaSeq as given in the second sentence of the abstract "Available tools especially struggle at deep phylogenetic levels and necessitate amino-acid space searches, which may increase rates of false positive results."

This can easily be addressed by evaluating on a pair of more divergence species. The result would likely show missed regions and a suggestion for using baseline tools for higher divergence may be made (perhaps as part of future work).


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: LEARNING TO PERFORM ROLE-FILLER BINDING WITH SCHEMATIC KNOWLEDGE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The abstract does not make it as clear as it could be what a network understands in this context, e.g., what is a structural relationship, what role-filler binding is, and what schemas are.

In the intro I would have expected some overview of the history into schema theory, and especially into the models proposed by other scientists. Schemas presumably have a long history in psychology and there are a multitude of theories and models out there to deal with predicting and understanding the mechanisms and functions involved. This seems pivotal to making a case for why this manuscript is valuable as well as orienting the reader.

The paragraph starting at line 37 is lacking. What is the difference between the work here and prior work? On lines 45-47, I can’t understand the caveat being raised. Is it that provided words are already known to the network then it can do role-filler binding? What kind of network and how was it used? These questions need to be answered at appropriate length, either directly or indirectly, for the whole of the citations given in this paragraph since architecture and training regimes could differ dramatically and since this seems to be the springboard for this research.

It might be good to include references to others who have performed decoding analyses on artificial neural networks, for example, see the work and references in this preprint: https://doi.org/10.1101/626374 — it has a variety of papers that will help situate this part of the work into the wider literature on neural networks’ internal states.

Lines 253-4 really are the results here and I would love to see more on what this means. You need to do a bit more justice to your results and discuss them more. I feel like a broken record to keep repeating this, but it’s important and I struggle to judge this work without the authors writing a more self-contained piece.

Lines 255-258 describe a difference between your work and those of Puebla et al. I would have liked more here, expounding on the meanings of these differences in findings. Do you have any hypothesis or even overarching theory as to why an external memory is important here?
Experimental design: The paper is clearly written in most places and provides information on the experiments carried out but not an appropriate amount to situate this fully into the literature. Citing relevant papers in the literature is the first step, which seems to be attempted to a point, but the authors could also explain how their work is situated and what it builds on more. What theoretical account or position on schemas does this modelling work espouse? And in the discussion: what do the results mean for the literature and schema theory as well as for connectionist modelling? To be very blunt, I am not convinced the authors have engaged enough with the literature they cite and/or appropriately cite it.

The experiments' rationale is explained since the authors wish to show that it is possible to train networks to perform dynamic role-filler binding. However, as I mentioned already there needs to be more information to explain why these questions are important to psychology, connectionism, etc.

The supplementals could be, and maybe should be, incorporated into the main text and the code repository also linked to from the main manuscript.
Validity of the findings: I would be better placed to comment on this if the manuscript had more context here and explained the important details relevant to situating these findings into the wider field.
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: LEARNING TO PERFORM ROLE-FILLER BINDING WITH SCHEMATIC KNOWLEDGE
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper reports artificial neural network simulation results exploring various network architectures in search of one that can learn to process encoded “word” sequences in such a way so as to allow the network to correctly identify the word that fills a particular event schema role that is queried after sequence presentation. Importantly, a network is sought which can learn this task (1) without roles being explicitly labeled in the word sequence and (2) in a way that generalizes to arbitrary role-filler combinations.

For the most part, the article is clear and easy to read. The simulations appear to have been performed with competence, and the simulation results reveal salient differences in the capabilities of various network architectures to master the targeted role-filler binding task from training data.

There are three primary ways in which the presentation of this work could be improved, clarifying its contribution to the relevant literatures.

First, further technical detail is needed concerning the simulations that were performed, allowing for replication of the work. Some of the important missing details are outlined below.

Second, the document needs to be extremely explicit about what the authors view as sufficient evidence that a network can “perform role-filler binding”. I suspect that some readers will firmly reject the provided interpretation of the simulation results because they are committed to a conception of “role-filler binding” that is defined by some formal computational properties rather than defined by behavioral capabilities. The manuscript needs an explicit statement approximately of the form, “We interpret any system exhibiting behavior with properties X, Y, & Z as capable of performing general role-filler binding.” Ideally, this statement would be supported by citations to publications that make use of similar operationalizations of the notion of role-filler binding. (If this capability is thought to be exercised by humans during language understanding, there must be some aspects of human linguistic behavior that justify ascribing this capability to people.) I expect that being explicit about this matter will make transparent the degree to which residual contention is merely the result of different theoretical commitments concerning the defining characteristics of “role-filler binding”.

Third, the article should more thoroughly highlight the most focal feature of this work — the ability to perform using completely novel fillers. The current draft seems to put emphasis on the lack of explicit role labels, discussing the capability to deal with arbitrary fillers in a somewhat secondary way. While both of these features are important to the reported work, the ability to deal with completely novel fillers in a learning network seems to provide the focal contribution to the literature. (This emphasis does appear in some portions of the paper, such as “This occurs with words that were never seen during training, and with inputs that do not explicitly encode role-filler pairs.” [lines 48-50]) Consider, for example, that the Sentence Gestalt (SG) network (St. John & McClelland, 1990) received input word sequences without role labels, but it was able to answer role queries very similar to the ones that were used in the simulations reported here. Other work with simple recurrent networks (Elman, 1990) did not involve explicitly answering role queries, but still discussed networks that learned role bindings in a manner that improved prediction tasks. Thus, the focal contribution of this work involves generalization to arbitrary filters. Of course, there has been previously published research involving systems that can handle arbitrary fillers but require role labels. (One important example of such research, which is not cited by this manuscript, involves the work on Holographic Reduced Representations (Plate, 1995), including their neural network implementation in the Semantic Pointer Architecture (Eliasmith et al., 2012).) Such past systems have not acquired the capability to use arbitrary filters in the context of learning, however. Thus, I would suggest, the focal contribution of the work reported in this article involves the ability to learn to process sequences in a manner that generalizes to completely novel fillers. This feature should be more clearly highlighted.
Experimental design: As previously mentioned, there are a variety of technical details that are important for understanding (and replicating) the reported work which have been elided in the current draft. Some of these details appear in the supplementary materials but would be appropriate for the body of the paper. For example, the information in the sections on “Epoch Sizes” and “Network Details” in the supplement should largely appear in the manuscript, proper. The use of “nonsense word” pads should also be mentioned in the primary manuscript, and further detail concerning the number and frequency of such padding words should be included. Making changes of this kind will, for example, make Figure 2 more clear, as the meaning of “epoch” will be made transparent. The number of filler vectors used (rather than describing them simply as a finite set [line 96]) would be welcome in the body of the paper. Other important missing technical details include:

* From what distribution were the 50-dimensional word vectors drawn [line 87]? Were they binary vectors? Were the elements selected independently and uniformly at random over some range? This distribution is important. For example, the Fast Weights architecture could benefit from binary representations.

* The modifications to the NTM should be further justified. For example, the paper states that, “We remove these links because role-filler binding should not require the network to maintain links between adjacent buffer slots” [lines 133-134]. Do such links get in the way of good performance? Do they slow training? While such links might seem clearly unnecessary, removing them raises the question of whether or not they are detrimental to the task at hand.

* The decoding analysis [lines 151-157] is unclear. For example, was the ridge regression performed including memory state vectors that appeared in the middle of processing an input sequence? Was there essentially one regression per potential filler or one regression per dimension in the 50-dimensional word vector space? This technique is an interesting contribution of the paper, but it needs to be more clearly explained.
Validity of the findings: As previously discussed, some readers might reject the offered interpretation of the results due to differing theoretical commitments concerning what “role-filler binding” is. This submission would benefit from an explicit statement concerning the kinds of behaviors that are posited to require a role-filler binding capability.

While the reported findings are valuable, by themselves, the provided efforts to explain these findings are somewhat unsatisfying. Some of the results are explained by the claim that, “Previous work found that neural networks perform quite poorly when the distribution of the training set differs from that of the test set …” [lines 200-203]. This doesn’t seem like a good characterization of the issue. The fact that the training and test distributions differed isn’t sufficient to explain the results. Consider, for example, training using “Unlimited Filler Training” but testing on a small subset of the fillers that appeared during training (or a small set of novel fillers). In this case, the training and testing distributions differ, but it is very likely that good test set performance will be found. It is more likely that generalization performance is being driven by specific properties of the training set distribution, as is suggested by the notion of “sufficient diversity” in “This suggests that networks require a sufficient diversity of training examples to learn relational structure, rather than learning non-generalizable statistical correlations” [lines 258-259; see also lines 276-279].

Perhaps a better explanation of the reported results involves the ways in which some architectures are insensitive to spurious correlations in the training set. The literature on artificial neural networks is full of examples in which combinatoric generalization is thwarted by spurious correlations. Consider the reported “Robustness Tests”. In these analyses, the training set is designed to contain perfect anti-correlations between particular roles and particular fillers, and the networks are expected to ignore these anti-correlations in order to generalize. In the case of “Limited Filler Training”, the training set is designed so that only certain combinations of 50-dimensional word vector elements are allowed as outputs, with other vectors never appearing during training. A network that is able to learn the statistical distribution of output vectors would recognize that other combinations of output elements are never appropriate. This poses few problems when “previously seen” vectors are used during testing, but any network sensitive to these “spurious correlations” will clearly have problems if “previously unseen” filler vectors are used. From this perspective, the network architectures that succeed, in this paper, are those that contain a mechanism to retain filler vectors, as they were presented to the network, without distorting them based on the learned expected distribution of such vectors. Fast weights change in essentially the same way in response to a given input vector regardless of the past distribution of such input vectors. The reduced NTM contains explicit registers for maintaining arbitrary vectors. From this perspective, the inclusion of mechanisms that are insensitive to spurious correlations — they do not learn statistical regularities that are present in the training examples — are important for role-filler binding that generalizes in a combinatoric way.

The literature contains a variety of approaches to turn a blind eye to spurious (and other) correlations. Some mechanisms, like Holographic Reduced Representations (Plate, 1995; Eliasmith et al., 2012), don’t use any form of statistical learning, supporting generalization by design. Some mechanisms have involved fast weight learning in the context of highly sparse representations, such as some models of the hippocampus (Norman & O’Reilly, 2003). Some mechanisms have involved structured architectures with multiplicative gating (O’Reilly & Frank, 2006; Kriete & Noelle, 2011; Kriete et al., 2013). The approaches share the common goal of improving combinatoric generalization by limiting the effects of statistical learning on internal representations.

This submission takes a step beyond these previous efforts by (1) focusing very explicitly on binding, (2) focusing very explicitly on a lack of role labels, and, most importantly, (3) generalization to truly arbitrary filler vectors in a learning framework. Understanding the reported findings in terms of mechanisms for avoiding the learning of spurious correlations situates this work within the broader network learning literature.
Additional comments: The zero results for “Previously Unseen Filters” in Figure 3 makes the diagram somewhat confusing, with the blank spaces where graph bars are expected being disorienting. Perhaps the “Previously Unseen Filters” results should simply be removed from the graph, with the caption explaining that all values were zero.

In summary, this is work that is worthy of publication. My only recommendations are in terms of strengthening the presentation of the work.


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: LEARNING TO PERFORM ROLE-FILLER BINDING WITH SCHEMATIC KNOWLEDGE
Review round: 1
Reviewer: 3

Output:
Basic reporting: I was not a reviewer on the previous submission of this ms., and so am commenting on the paper as a reviewer seeing the paper for the first time.

In short, I don’t think the simulations reported in the paper justify the paper’s main claims. I try to elaborate on this point below. I think the paper could be published if the claims are refined, and the relevant literature is addressed.

First, while this paper cites a bunch of papers on previous work on representing role-bindings in neural networks (I believe suggested by a previous reviewer), these papers haven’t been very carefully read, and it shows. For one thing, the claim that previous models required labelled role-bindings in the input is patently wrong for at least one of the cited models (Doumas et al.). Also, the cited St.John model uses the exact same input and test procedure as the one used in the current paper, so it’s odd to say that version uses labeled role-filler bindings while the previous one doesn’t. I think reading the literature would be really helpful in framing the current paper.

Second, the kinds of role-bindings that the current model could learn in principle are not dynamic and should be contrasted to dynamic role-filler bindings. Again, there’s a long literature on this topic, some of which is mentioned by the previous reviewer (e.g., Doumas & Hummel, 2005, 2012; Hummel, 2012). Reading that work would be helpful.

Third, the result in the paper seems very likely the result of the model learning to ignore certain bits of information when asking certain questions, rather than literal role-binding. This result was also reported in the cited Puebla et al. paper. In that paper, the finding was that when all fillers appeared in all roles with roughly similar frequency—as actually occurs in the current model as the small distributed encoding space of possible fillers (50 nodes) and large numbers of generated fillers almost assures all of the 50 nodes appeared in each role (though not in all possible combinations); this process is called spanning the input space and the practice as it relates to role-filler binding is covered in the previous literature suggested by the previous reviewer (Doumas & Hummel, 2012)—the model effectively learned to ignore context when answering specific questions. For example, if trained that a set of 4 people go to four coffee shops and order 4 different things and all combinations are roughly equally present in training, the model learns to return a copy of the y item in the sentence “x ordered y” in response to the question, “what was ordered?”. The problem is that then the model loses the capacity to learn any systematic context effects. If the model is then trained that John always orders cake when he goes to the coffee shop (“John went to the coffee shop” “John ordered cake”), the model is no more likely to return cake as, say, carrots when given the sentence “John went to the coffee shop” and asked “what did John order”. In other words, training as the done in the current paper, makes the model insensitive to context, while training with specific systematic statistical regularities (as in the other Puebla et al. sims) makes the model fail at returning the correct items when the statistically regular role-bindings are violated.

Finally, there’s a brief mention of a test where the sentences were mixed up (violated the regular story structure), and the model failed to correctly answer role-binding questions. Am I reading that right? Does that mean that when the model was given a story like, “John left the coffee shop; John listened to an MC; John left the coffee shop; John ordered coffee”, and asked what did John order, the model did not return coffee? If so, that’s a clear indication of failing to perform role-binding.

As a minor point, the story schema used was very regular and followed a specific structure where a basic story could be augmented, but the basic structure was always consistent. Did that have any effect on the results, perhaps?
Experimental design: No comment.
Validity of the findings: See above.
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: LEARNING TO PERFORM ROLE-FILLER BINDING WITH SCHEMATIC KNOWLEDGE
Review round: 2
Reviewer: 1

Output:
Basic reporting: I applaud the authors on refining their points and improving their manuscript. I think it's clearly written and the figures are fine — although I would suggest figures 3, 4 and 5 really need to have a larger font size to be readable.

Given their edits, clarifications, and expositions, I am pleased to say it has helped me get to grips more with the area and I suggest they look into the following papers I linked to below. Literature review is really important, so I am glad the steps being taken towards carrying it out are happening.

This body of work by Martin and Doumas seems particularly important for the authors to get grips with and I believe will help them engage with the wider context of their subfield/work. I list these just as pointers, I do not expect them to cite them (all) necessarily. However, I want to make sure the authors are aware of this body of work because it is modern, reflecting the current state of the field (which is important to prove relevance and facilitate communication and I believe the more historical papers like ones from the 1990s are covered, as well as the 2000s). I will leave it to the authors, and trust them fully, to connect these papers to their own theories and experiments as they see fit.

Martin, A. E. (2020). A Compositional Neural Architecture for Language. Journal of Cognitive Neuroscience.

Martin, A. E. & Doumas, L. A. A. (2019). Tensors and compositionality in neural systems. Philosophical Transactions of the Royal Society B: Biological Sciences.

Martin, A. E. & Doumas, L. A. A.  (2019). Predicate learning in neural systems: Using oscillations to discover latent structure. Current Opinion in Behavioral Sciences.

Doumas, L. A. A., & Martin, A. E. (2018). Learning structured representations from experience. Psychology of Learning and Motivation, 69, 165-203.

Martin, A. E., & Doumas, L. A. A. (2017). A mechanism for the cortical computation of hierarchical linguistic structure. PLoS Biology, 15(3), e2000663
Experimental design: In line with the Aims & Scope of the journal (1 and 2) and with aiding understanding, each experimental manipulation should be clearly and carefully paralleled with something biological organisms do, in this case people. To really clarify and bring home the points the authors wish to make. I think the manuscript is really taking shape and this is perhaps the final important step outside addressing some further gaps in literature review I mention above.

On a less vital but still important note, I think it’s good for the author to engage with relevant papers on theory and use of neural networks. For example, when the authors state: "No networks consistently succeed in performing role-filler binding with shuffled story test sets.” Can the authors perhaps relate their results to these: https://arxiv.org/abs/1611.03530 — where networks are able to learn with shuffled labels? Again as with above, references to other articles should be taken as pointers to engage with the literature and not as requests for citation necessarily.
Validity of the findings: The discussion should include clear and numerous pointers to past work and how the current work adds to our understanding of the human organism and human behaviour: the explicit biological phenomena and capacities of interest here. Based on that the authors might benefit from looking at the papers I linked them to above and doing a bit more interlacing of their literature review with their own findings. Zooming out in other words and correctly contextualising their word within the social and biological sciences of linguistics and psychology — if their work is meant to be seen as a cognitive computational model of such phenomena the similarities and differences should pop out to the reader.

Bearing in mind the Aims & Scope of the journal (1 and 2 — as I mentioned previously), it's of importance to take these modelling results and tie them back in to the theories and hypothesis being tested and explored. This is important for readers to understand the contribution here and appreciate the work the authors have carried out. To really see why this is vital and why making their theory explicit will pay dividends, see, e.g., https://doi.org/10.31234/osf.io/rybh9 which explains in detail.
Additional comments: No additional comments