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Please, don’t forget to add a sentence such as “The CT scan data in DICOM file format are freely and publicly accessible at: [Dryad DOI]”.
Thank you very much for submitting your manuscript for review to PeerJ. The reviewers are very positive about it. However, they made some suggestions that need to be addressed prior to formal acceptance. I would ask you, in particular, to check the size of the specimen, your list of characters and character states, and your character/taxon matrix. I would also recommend that the CT data be deposited in an appropriate public repository.
The article is well written and the text is unambiguous.
However, please check the size of the specimen that they use. It does not conform to sizes given in earlier papers for a specimen of the same Museum number
The research appears to be within the scope of the journal, and the methods are clearly described, although the equipment is beyond the reach of most researchers in the field.
Looks fine to me. Hard to apply statistics to a descriptive article based on one specimen, but the results are presented clearly, and well illustrated.
This is a professional and comprehensive analysis of the cranial endocast of a basal lungfish, Dipnorhynchus sussmilchi, using novel techniques, and a thorough comparison with related fishes. Thomson and Campbell (1971) and Campbell and Barwick (1982) have analysed the same species, but the results based on the current technique seem to me to be more reliable.
I realise that there are technical constraints in applying this technique to more than one specimen, but it seems that Campbell and Barwick (1982) had more than one and were able to describe the occipital region as well as more anterior structures.
Two comments. I have one slight quibble – according to the previous authors the specimen used, ANU 18815, is quite large, at least 18 cm across (eg Campbell and Barwick 1982, Fig. 17) but according to this paper, the specimen is 20mm across. The other is a bit less slight. The authors discuss in considerable detail the “nasal capsule”, by which I think they mean the skeletal structures surrounding the olfactory organ. They show the entry of the olfactory nerve and of a branch of nerve V, profundus, with no explanation of the role of nerve V in the “nasal capsule”, and no indication that it might come out again, and could only be passing through. I find this a little confusing?
The present study describes the first virtual cranial endocast of an already known Early Devonian lungfish, Dipnorhynchus sussmilchi. This is an interesting and potentially valuable manuscript, casting new light on the early evolution of lungfishes based on HRCT data. Clement et al present new endocast data of Dipnorhynchus sussmilchi, revising the previous incorrect interpretations and reconstructions on the neurocranium and the endocranial cavity of Dipnorhynchus sussmilchi. The experimental endocast-based-only phylogenetic analysis supports the basal placement of Dipnorhynchus in the stem dipnoans as other recent phylogenetic analyses do, and illustrates the value of neurocranial features for creating instructive phylogenetic hypotheses. This manuscript is well written, using appropriate methodologies and providing a clear line of argument. A few typos and questionable statements need to be revised or further explained.
Lines 23-24: “primitive character states”. What “primitive character states”, sarcopterygian? Osteichthyan? Lungfish? Should be clarified.
Lines 25-26: “a utricular recess differentiated from the sacculolagenar pouch like that seen in stratigraphically younger lungfish”
The utricular recess differentiated from the sacculolagenar pouch is also seen in early actinopterygians, coelacanths, onychodonts, and even in some sharks.
Line 49: “and early Devonian lungfishes are known from deposits across China, Russia, Europe, North America and Australia”. Reference needed.
Line 54: “the name ‘Ganorhynchus’ was originally used”. Reference needed.
Line 75: “Until relatively recently, … (Stensiö 1963)” I’m not sure if 1963 is “relatively recently”. Could be more precise here, like “Until 1960s,…”.
Lines 81-82: If there is no reference limitation, more work on virtual endocast of early vertebrates could be added here, such as Gai et al. 2011, Challands 2015, and Lu et al. 2016
Line 110: Since ANU 18815 is “a well-preserved, acid-prepared complete cranium”. I’m curious why the posterior part (including the rest part of horizontal semicircular canal, posterior semicircular canal, saccular, and relative brain cavity and nerves) of the cranial endocast is not presented in this paper.
Line 140: “Proportionally the nasal capsules are the longest structures of the endocast being approximately”. According to the ratio the authors provided, the longest structure of the endocast is mylencephalic cavity, not nasal capsule.
Line 155: Does the olfactory nerves belong to the telencephalic region?
Line 182: “Dorsal to the hypophysis lies a short, rounded hypothalamus”. Why the structure has been identified as “hypothalamus” here? According to its generally shape and position, is it possible that this structure corresponds to the saccus vasculosus?
Line 215: There is no label for “abducens (n. VI) nerve” in figure 4.
Line 230: How to define “large”? Maybe the location of the sacculus is a more precise reference of size?
Line 288: There is no label for “sacculolagenar pouch”. Although the posterior part has not be segmented for the moment, do the authors think it is possible to use the dot-line to illustrate the unsegmented part to give readers a general impression about the whole shape of the Dipnorhynchus endocast in Fig. 6?
Line 306: Missed Qingmenodus here.
Line 312: “Two slight bulges”. It is a little difficult to see the bulges from Figure 4.
Line 338: The “ventrally-extensive hypophyseal recess” is also present in coelacanth Diplocercides.
Lines 341-342: “These features lend support to the primitive placement of Dipnorhynchus within the Dipnoi more basally than other lungfish” “These features” need to be listed to avoid confusion.
Lines 349-352: It is hard to say “sinus superior that extends above the roof of the rhombencephalon” is a derived feature since we do not know the condition in stem osteichthyans/sarcopterygians. The “clear segregation of the utricular recess from the sacculus” is also present in Diplocercides and Qingmenodus.
Line 359: Youngolepis is also lack of intracranial joint.
Figures: The figures 2-5 might be clearer in white background.
Figure 2: The scale bar in panel A is too small and unclear.
Figure 3: The label of “ampulla for anterior semicircular canal” should be “ampulla for horizontal semicircular canal”
Figure 4: The “anterior semicircular canal” and “horizontal semicircular canal” look like the same canal.
Figure 6: With or without the notochordal canal should be consistent.
References: There are some typos and small mistake in the references which need to be carefully examined.
All “-” connects the pages should be “–”
Line 449: “Diabolepis”, Italics.
Line 463: “Yu X”. Should be “Yu XB”
Line 30: In the table, “(Lu et al. 2016) (Lu et al. 2016)”. Duplicated.
Line 72: Character 7. Do authors think “Pineal eminence” is an endocast character? Besides, I don’t think the pineal eminence is present in Qingmenodus.
This paper presents an endocast of the Devonian lungfish Dipnorhynchus sussmilchi, along with a phylogenetic analysis of lungfish based only on endocranial characters. The paper is well written and organized, with a thorough description and comparisons between Dipnorhynchus and other lungfish in which endocranial data are known. This paper adds to the increasing dataset of endocranial morphology for lungfishes and will be very useful to researchers in the future. I have just a few comments that should be addressed.
- On line 40, you mention that early dipnoan phylogeny is contentious and unresolved. Perhaps include a sentence or two about the different hypotheses of relationships and who proposed them.
- It would be great to include the details of how Campbell and Barwick reconstructed the endocranial cavity previously, to highlight how these methods are superior. This is brought up in the discussion, but would be helpful to have in the introduction as well. (~line 68)
- In line 81-82 you list references for fish in which endocast morphology is known. It would be useful to include the names and classification of those taxa along with the references.
- This is well done, but could use more figure references. There were several places in which it was hard to find the best figure for the anatomy that was described. A few examples: line 148 should reference figure 3, line 164 could possibly reference figure 5, line 179 should reference figure 2, line 187 should reference figure 4, and line 213 should reference figure 3.
Figure 6 is nicely illustrated, but if possible, please add taxon names below/to the right of each endocranial reconstruction. Interpreting the figure would be much easier if the reader did not have to refer to the figure caption to determine which endocast belonged to which fish.
Both the CT scan parameters and phylogenetic analysis methods are well described and meet the standard for paleontological data collection.
There is an error in the character list in the supplemental text file for the phylogenetic analysis. Characters 15 and 16 have no zero state, while they do in the data matrix. Instead, the character states start with 1, which I'm sure is a typo.
You include descriptions or notes with some of the new characters, but this is lacking in characters 16, 17, 19, and 20. It would be great to have a bit of discussion about these character states in the supplemental text, as not all of these are thoroughly discussed in the text.
It would be great to see some slice images showing the CT scan in section, to assure readers that the contrast is high enough to isolate fine details like individual nerve tracts. Perhaps include this as a figure in the supplemental data.
Figure 2A is dark and hard to see, compared to the other CT reconstructions in figures 3-5. It looks a bit too transparent. If possible, please adjust this reconstruction so that it matches the other figures.
The CT data should eventually be submitted to an online repository and made publicly available.
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