Biodiversity, Systematics, and Taxonomy of Ostariophysi (Osteichthyes, Actinopterygii): What We Know Today After Three Decades of Integration of Morphological and Molecular Data

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Review report on: Biodiversity, systematics, and taxonomy of Ostariophysi (Osteichthyes, Actinopterygii): what we know today after three decades of integration of morphological and molecular data

 

Manuscript number: taxonomy-3637153

 

This paper presents a comprehensive and valuable overview of the current knowledge on Ostariophysi, one of hyper-diverse superorders of fishes, comprising nearly 12.000 species, the majority of which inhabit freshwater environments. The author concisely summarize a wide range of different publications – including molecular genetic studies, taxonomic research, and morphological analyses – and presents our current knowledge on the various orders of Ostariophysi (e.g. Characiformes, Cypriniformes, Gonorynchiformes, Gymnotiformes and Siluriformes). The manuscript is well-written, and the study -based on thorough literature research- has been conducted with great care and appears appropriate to me. The final conclusions are well-founded, and I believe this review on the biodiversity, systematics and taxonomy of Ostariophysi will be widely acknowledged.  

However, I have some comments and suggestions regarding both minor and larger issues, that I believe the author could address:

 

In general:

I would recommend that you write out the full genus/species name when mentioned for the first time in the manuscript, including the authorities of respective species (the same of course apply for fossil taxa.):

 

e.g. Kryptoglanis shajii Vincent & Thomas 2011 instead of Kryptoglanis shajii (L340)

Further, the authorr might consider to give credit to the corresponding taxonomist and cite the corresponding reference. In example for Kryptoglanis shajii this would be Vincent, M. and J. Thomas  2011: Kryptoglanis shajii, an enigmatic subterranean-spring catfish (Siluriformes, Incertae sedis) from Kerala, India. Ichthyological Research v. 58 (no. 2): 161-165.

You can look up genus/species names (of extant taxa) and the corresponding references easily here: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp

 

Furthermore, I was wondering whether it would be possible to provide the authorities of the various orders, superorders, families discussed in the manuscript (since this paper is an review on the diversity, systematics and taxonomy of Ostariophysi). I understand that including them in the main text might affect the overall readability, so perhaps a table in the supplementary material could be a suitable solution. Just a suggestion.

 

Comments and issues by section:

Section: Main text:

 

L27-28: I suggest to rephrase this sentence: “Within this group we fin the group called Osteichthyes, composed…” e.g. “This clade includes a group called Osteichthyses, composed..” [This would avoid the expression “we find”]

 

L36-42: You provide a brief overview on the species number of the Ostariophysi, maybe you could provide size ranges for the Ostariophysi, and maybe as well for the other groups discussed throughout the manuscript.

L75-76: Many studies rely on mitochondrial data for divergence time estimates, and for understandable reasons. However, it may be worth mentioning the potential limitations of mitochondrial data, such as substitutional saturation, which can negatively impact the accuracy of divergence estimates, particularly for deep evolutionary nodes.

 

L103-111: This paragraph (especially L103-107) is partly repetitive to the paragraph in L36-42, although with slightly different numbers for the genera, species and families, which seems a little bit odd! Please carefully revisit both paragraphs and rephrase.

 

L138: ”…†Dastilbe, †Nanaichthys, †Tharrhias..” genus names should be in italic

 

L211-214: “As an example, we can observe that in Stout et al. 211 (2016), ….” maybe rephrase so that you avoid “we can observe” (just a suggestion). Further, please add information about what kind of data was used in Stout et al. 2011 and Hirt et al. 2017.

L233: †Megacheirodon unicus should be completely in italic.

L263: Maybe better “..the Cretaceous resulted 17 of the 23..” instead of “..the Cretaceous produced 17 of the 23..”

 

L293: Is there a phylogeny which shows the relationships of Cithariniformes?

L380-382: “…all mitochondrial protein coding genes of 239 catfish species representing…” instead of “…all protein coding genes of 239 catfish species representing…”; the study of Schedel et al. 2022 is based on mitochondrial genome data.

Section: Conclusion

You might consider explicitly mentioning the families for which no, or only limited, molecular data are available, and/or those whose phylogenetic relationships remain particularly difficult to resolve.

 

Figure & Figure captions:

Figure 2: Provides the phylogenetic relationships according to Fink and Fink (1981, 1986). Please provide information on which kind of data the presented relationships are based on (molecular or morphological?) in the figure caption. Further, another question are their more recent studies as well, showing the same relationships?

Figure 3: In the figure caption you state that b) is based on ”total evidence data”, what do you mean in this context (molecular + morphological data)? Please be more precise.

Figure 4: In general, I believe it would be advantageous to specify in the figure captions what type of molecular data was used (e.g., mitochondrial, nuclear markers, RAD/ddRAD, whole-genome data, etc.), as you did e.g. for Figure 5.

Figure 5: I believe this Figure could be reworked a little bit. Figure 5A: includes a group called loaches, which is a trivial name. Which taxon are you referring here? Cobitoidei? Further, 5A is mainly showing the different relationships between the families of Cyprinoidea, however by fare not all families are included in the tree (e.g. Tincidae, Leptobarbidae, Sundadanionidae etc., see for example e.g. Tan & Armbruster et al. 2018 -> Phylogenetic classification of extant genera of fishes of the order Cypriniformes (Teleostei: Ostariophysi;, Schedel et al. 2022 -> Towards the phylogenetic placement of the enigmatic African genus Prolabeops Schultz, 1941), maybe it would be worth mentioning this.

For Figure 5B is mainly depicting the relationships between the different suborders, therefore I suggest to indicate the Cobitoidei (represented in this tree by Botidae, Vaillantelliidae, Balitoridae, Nemacheilidae)

Furthermore, you might also consider including a figure depicting the relationships among the subfamilies of Cyprinidae—one of the most species-rich families of teleosts (as you did for the Characidae). This element is currently missing from the manuscript, but its inclusion could make the overview more complete…

 

Figure 6: Is depicting the relationships for the of the different subfamilies of the Characidae, please add on which data it is based (UCE loci).

 

Figure 7: You might consider to briefly mention which siluriform families are not included in the phylogeny (e.g. the Lacantuniidae were only described afterwards), or give a statement X out of X siluriform families were included in the analysis (something similar would be helpful for the other Figures depicting family level relationships as well).

 

Figure 10: “…including all mitochondrial protein coding genes of representatives of 33 families.” instead of “…including all protein coding genes of representatives of 33 families.”

 

Figure 11: a ) is missing at the end of the figure caption.

 

Thank you again for this fascinating overview of our knowledge on the Ostariophysi. I really enjoyed reading your manuscript! I hope my comments and suggestions will help to improve your manuscript even further!

 

 

 

Author Response

Review report on: Biodiversity, systematics, and taxonomy of Ostariophysi (Osteichthyes, Actinopterygii): what we know today after three decades of integration of morphological and molecular data

 

Manuscript number: taxonomy-3637153

 

This paper presents a comprehensive and valuable overview of the current knowledge on Ostariophysi, one of hyper-diverse superorders of fishes, comprising nearly 12.000 species, the majority of which inhabit freshwater environments. The author concisely summarize a wide range of different publications – including molecular genetic studies, taxonomic research, and morphological analyses – and presents our current knowledge on the various orders of Ostariophysi (e.g. Characiformes, Cypriniformes, Gonorynchiformes, Gymnotiformes and Siluriformes). The manuscript is well-written, and the study -based on thorough literature research- has been conducted with great care and appears appropriate to me. The final conclusions are well-founded, and I believe this review on the biodiversity, systematics and taxonomy of Ostariophysi will be widely acknowledged.  

Thank your for these comments.

However, I have some comments and suggestions regarding both minor and larger issues, that I believe the author could address:

 

In general:

I would recommend that you write out the full genus/species name when mentioned for the first time in the manuscript, including the authorities of respective species (the same of course apply for fossil taxa.):

 

e.g. Kryptoglanis shajii Vincent & Thomas 2011 instead of Kryptoglanis shajii (L340)

 

Further, the authorr might consider to give credit to the corresponding taxonomist and cite the corresponding reference. In example for Kryptoglanis shajii this would be Vincent, M. and J. Thomas  2011: Kryptoglanis shajii, an enigmatic subterranean-spring catfish (Siluriformes, Incertae sedis) from Kerala, India. Ichthyological Research v. 58 (no. 2): 161-165.

You can look up genus/species names (of extant taxa) and the corresponding references easily here: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp

 All genera and species were authored when first cited. References were provided when discussed in the text.

 

Furthermore, I was wondering whether it would be possible to provide the authorities of the various orders, superorders, families discussed in the manuscript (since this paper is an review on the diversity, systematics and taxonomy of Ostariophysi). I understand that including them in the main text might affect the overall readability, so perhaps a table in the supplementary material could be a suitable solution. Just a suggestion.

This suggestion is interesting but it seems to me that it goes a little beyond the scope of the work and it really seems to me that it would make the text more difficult to read. 

Comments and issues by section:

Section: Main text:

 

L27-28: I suggest to rephrase this sentence: “Within this group we fin the group called Osteichthyes, composed…” e.g. “This clade includes a group called Osteichthyses, composed..” [This would avoid the expression “we find”]

Corrected.

L36-42: You provide a brief overview on the species number of the Ostariophysi, maybe you could provide size ranges for the Ostariophysi, and maybe as well for the other groups discussed throughout the manuscript.

I added a frase showing the variation in the superorder that is more or less the same for all groups.

The size range among Ostariophysi is remarkably diverse, ranging from tiny species such as Paedocypris progenetica Kottelat, Britz, Tan & Witte, 2006, with an adult length of 7.9–10.3 mm, medium-sized species (the vast majority) such as Paracheirodon axelrodi (Schultz, 1956), with an adult length of 2–20 cm, to very large species such as Brachyplatystoma filamentosum (Valenciennes, 1840), with an adult length reaching 3.6 m.

L75-76: Many studies rely on mitochondrial data for divergence time estimates, and for understandable reasons. However, it may be worth mentioning the potential limitations of mitochondrial data, such as substitutional saturation, which can negatively impact the accuracy of divergence estimates, particularly for deep evolutionary nodes.

I agree and added a phrase in the text to remember this.

L103-111: This paragraph (especially L103-107) is partly repetitive to the paragraph in L36-42, although with slightly different numbers for the genera, species and families, which seems a little bit odd! Please carefully revisit both paragraphs and rephrase.

 

Corrected.

 

L138: ”…†Dastilbe, †Nanaichthys, †Tharrhias..” genus names should be in italic

 Corrected.

L211-214: “As an example, we can observe that in Stout et al. 211 (2016), ….” maybe rephrase so that you avoid “we can observe” (just a suggestion). Further, please add information about what kind of data was used in Stout et al. 2011 and Hirt et al. 2017.

The prhase was corrected. The data used for both authors were cited in the begining of the paragraph.

 

L233: †Megacheirodon unicus should be completely in italic.

Correted

 

L263: Maybe better “..the Cretaceous resulted 17 of the 23..” instead of “..the Cretaceous produced 17 of the 23..”

 Corrected

 

L293: Is there a phylogeny which shows the relationships of Cithariniformes?

Cithariniformes is composed by only two families (Citharinidae and Distichodontidae) but the relationshiip among species or genera were not extensively studied yet.

 

L380-382: “…all mitochondrial protein coding genes of 239 catfish species representing…” instead of “…all protein coding genes of 239 catfish species representing…”; the study of Schedel et al. 2022 is based on mitochondrial genome data.

Corrected.

 

Section: Conclusion

You might consider explicitly mentioning the families for which no, or only limited, molecular data are available, and/or those whose phylogenetic relationships remain particularly difficult to resolve.

I corrected the text trying to make clearer the main problems that may be related to our limited knowledge of the relationships between some groups.

 

Figure & Figure captions:

Figure 2: Provides the phylogenetic relationships according to Fink and Fink (1981, 1986). Please provide information on which kind of data the presented relationships are based on (molecular or morphological?) in the figure caption. Further, another question are their more recent studies as well, showing the same relationships?

I added the information (morphological). As discussed in the text these relationships haven’t been corroborated in more recente studies using molecular data. There are not new phylogenies using only morphological data.

Figure 3: In the figure caption you state that b) is based on ”total evidence data”, what do you mean in this context (molecular + morphological data)? Please be more precise.

Corrected.

Figure 4: In general, I believe it would be advantageous to specify in the figure captions what type of molecular data was used (e.g., mitochondrial, nuclear markers, RAD/ddRAD, whole-genome data, etc.), as you did e.g. for Figure 5.

Corrected.

 

Figure 5: I believe this Figure could be reworked a little bit. Figure 5A: includes a group called loaches, which is a trivial name. Which taxon are you referring here? Cobitoidei? Further, 5A is mainly showing the different relationships between the families of Cyprinoidea, however by fare not all families are included in the tree (e.g. Tincidae, Leptobarbidae, Sundadanionidae etc., see for example e.g. Tan & Armbruster et al. 2018 -> Phylogenetic classification of extant genera of fishes of the order Cypriniformes (Teleostei: Ostariophysi;, Schedel et al. 2022 -> Towards the phylogenetic placement of the enigmatic African genus Prolabeops Schultz, 1941), maybe it would be worth mentioning this.

For Figure 5B is mainly depicting the relationships between the different suborders, therefore I suggest to indicate the Cobitoidei (represented in this tree by Botidae, Vaillantelliidae, Balitoridae, Nemacheilidae)

Figures 5A and 5B were corrected to split the loaches in the families studied (5A) and Cyprinoidea in the families studied (5B).

 

Furthermore, you might also consider including a figure depicting the relationships among the subfamilies of Cyprinidae—one of the most species-rich families of teleosts (as you did for the Characidae). This element is currently missing from the manuscript, but its inclusion could make the overview more complete…

A new figure with the relationships among subfamilies of Cyprinidae was added.

Figure 6: Is depicting the relationships for the of the different subfamilies of the Characidae, please add on which data it is based (UCE loci).

 Corrected.

 

Figure 7: You might consider to briefly mention which siluriform families are not included in the phylogeny (e.g. the Lacantuniidae were only described afterwards), or give a statement X out of X siluriform families were included in the analysis (something similar would be helpful for the other Figures depicting family level relationships as well).

 I’d like this idea but since in many studies several lineages were absent it’s difficult to list all this information. The important points were discussed in the text.

Figure 10: “…including all mitochondrial protein coding genes of representatives of 33 families.” instead of “…including all protein coding genes of representatives of 33 families.”

 Correted.

Figure 11: a ) is missing at the end of the figure caption.

 I guess the citation of figure a and figure b are corrected.

 

Thank you again for this fascinating overview of our knowledge on the Ostariophysi. I really enjoyed reading your manuscript! I hope my comments and suggestions will help to improve your manuscript even further!

Thank you very much for your good reading and suggestions!

 

Reviewer 2 Report

Comments and Suggestions for Authors

Recommendation on the manuscript “Biodiversity, systematics, and taxonomy of Ostariophysi (Osteichthyes, Actinopterygii): what we know today after three decades of integration of morphological and molecular data”

 

Recommendation: Minor revisions

 

Dear Editor,

 

The manuscript entitled “Biodiversity, systematics, and taxonomy of Ostariophysi (Osteichthyes, Actinopterygii): what we know today after three decades of integration of morphological and molecular data” is an important contribution to world ichthyological science, as well as to a better understanding of the classification and evolution of Ostariophysi, and deserves to be published. In my opinion the manuscript only needs minor adjustments and corrections, which are listed below.

1 - My main suggestion (which is not mandatory, it is just a suggestion) regarding the manuscript is the inclusion, similar as Nelson et al. (2016) did, illustrations (preferably) or photographs of the main groups addressed.This, in addition to enriching the work, is important to familiarize the reader with the fish group being discussed.

2 - Keywords should be presented in a logical order. I suggest alphabetical order. In addition, I suggest changing the keywords “Biodiversity” and “Systematic” to "phylogenomics" and "ichthyology" (see my comments made directly in the manuscript file.

3- Other minor suggestions were made directly in the manuscript file.

 

All the best,

 

 

 

Comments for author File: Comments.pdf

Author Response

1 - My main suggestion (which is not mandatory, it is just a suggestion) regarding the manuscript is the inclusion, similar as Nelson et al. (2016) did, illustrations (preferably) or photographs of the main groups addressed.This, in addition to enriching the work, is important to familiarize the reader with the fish group being discussed.

Figures of the fishes are provided.

2 - Keywords should be presented in a logical order. I suggest alphabetical order. In addition, I suggest changing the keywords “Biodiversity” and “Systematic” to "phylogenomics" and "ichthyology" (see my comments made directly in the manuscript file.

I corrected the Keywords and put them in alphabetical order.

3- Other minor suggestions were made directly in the manuscript file.

All suggestions were accepted.

Reviewer 3 Report

Comments and Suggestions for Authors

The manuscript is engaging, well-written, and accessible. However, in its current form, it does not constitute a primary research article. Rather, it serves as a comprehensive review of existing knowledge on the biodiversity, systematics, and taxonomy of the diverse group of bony fishes known as Ostariophysi.

The structure of the manuscript does not follow the conventional format expected of original research articles, namely: Introduction, Materials and Methods, Results, and Discussion. Nonetheless, if the editorial policy of the journal permits more flexible formats—particularly for review-type contributions—I would be inclined to support its acceptance.

The content largely synthesizes previously published information, without presenting novel data, interpretations, or hypotheses. If both the journal and the Editor-in-Chief find this format acceptable, I believe the manuscript could be suitable for publication in Taxonomy because it is really well written as a review article.

Additional specific comments have been annotated directly in the attached PDF.

Comments for author File: Comments.pdf

Author Response

The content largely synthesizes previously published information, without presenting novel data, interpretations, or hypotheses. If both the journal and the Editor-in-Chief find this format acceptable, I believe the manuscript could be suitable for publication in Taxonomy because it is really well written as a review article.

The proposal of the ms is just be a review of our actual knowledge about the group.

 

Additional specific comments have been annotated directly in the attached PDF.

All questions and suggestions were answered in the annexed pdf.

 

Author Response File: Author Response.pdf