PONE-D-23-19233

Pellioditis pelhami n. sp. (Nematoda: Rhabditidae) and Pellioditis pellio (Schneider, 1866), earthworm associates from different subclades within Pellioditis (syn. Phasmarhabditis Andrássy, 1976)

PLOS ONE

Dear Dr. Fitch,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Aug 24 2023 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Aashaq Hussain Bhat

Academic Editor

PLOS ONE

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at 

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide.

3. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data.

4.  Please take this opportunity to be sure you have met all of our guidelines for new species. For proper registration of a new zoological taxon, we require two specific statements to be included in your manuscript.

a. In the Results section, the globally unique identifier (GUID), currently in the form of a Life Science Identifier (LSID), should be listed under the new species name, for example:  

  Anochetus boltoni Fisher sp. nov. urn:lsid:zoobank.org:act:B6C072CF-1CA6-40C7-8396-534E91EF7FBB

 Another LSID for the manuscript itself should also appear within the Nomenclature statement. You will need to contact Zoobank (zoobank.org/About) to obtain a GUID (LSID). You should receive one LSID for your manuscript and a separate, unique LSID for the new species.  b. Please also insert the following text into the Methods section, in a sub-section to be called "Nomenclatural Acts":   The electronic edition of this article conforms to the requirements of the amended International Code of Zoological Nomenclature, and hence the new names contained herein are available under that Code from the electronic edition of this article. This published work and the nomenclatural acts it contains have been registered in ZooBank, the online registration system for the ICZN. The ZooBank LSIDs (Life Science Identifiers) can be resolved and the associated information viewed through any standard web browser by appending the LSID to the prefix "" ext-link-type="uri" xlink:type="simple">http://zoobank.org/". The LSID for this publication is: urn:lsid:zoobank.org:pub: XXXXXXX. The electronic edition of this work was published in a journal with an ISSN, and has been archived and is available from the following digital repositories: PubMed Central, LOCKSS [author to insert any additional repositories]. All PLOS ONE articles are deposited in PubMed Central and LOCKSS. If your institute, or those of your co-authors, has its own repository, we recommend that you also deposit the published online article there and include the name in your article. Following a recent ruling by the International Commission on Zoological Nomenclature, electronic journals are now a valid format for publication of new zoological taxa. In order to ensure the valid publication of your new species, please be sure to include the updated version of Nomenclatural Acts (above). A complete explanation of our guidelines for publishing new species can be found on our website: http://www.plosone.org/static/guidelines#zoological.

5. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments:

The work is presented nicely and will surely solve the ambiguities in the taxonomy of Phasmarhabditis. The authors have done the cross-hybridization studies, but the procedure used for carrying out crosses is missing. Authors should briefly describe this in methodology. Also, I noticed grammatical errors in some parts of the manuscript which authors need to carefully check. I also encourage authors to write genus name in full while describing it for the first time. The description or redescription of any species should follow usual pattern as is followed in all descriptions of a new species.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

********** 

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: N/A

********** 

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

********** 

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

********** 

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Submitted paper is outstanding contribution to the knowledge of rhabditids. It is known that many free-living rhabditids have biotic relationships with invertebrate and in few cases with vertebrate animals. The problem of relationships between rhabditid nematodes and terrestrial mollusks is a separate phenomenon. Unfortunately, studies in this field faced in recent years some problems: not resolved relationships with other rhabditids, contradictions in the nomenclature. The study of this group started in mid-nineteen century, when the standards of the species description were completely different. The main peculiarity of the submitted paper is in combination of several modern methods of nematological examination (nucleotide sequence analysis, SEM, staining with monoclonal antibodies) with profound and extremely accurate morphological analysis. Such a combination of approaches was only possible through the joint efforts of literally all leading specialists in this field of nematology. The paper is completely ready for publication – the text is very accurately edited. The plates of line-art drawings and SEM images are very informative. I am sure that this paper upon the publication will be actively cited in other studies of invertebrate-associated nematodes. One of the reasons for such predicable interest toward this publication is in the important taxonomic decision. After years of controversy, the authors of submitted paper finally solved problem of the interrelationships between Pellioditis and Phasmarhabditis. I am sure that after the publication of this paper the use of the generic name Pellioditis will be the only possible and reasonable.

To fix this long-lasting problem the authors are proposing in-depth redescription of Pellioditis pellio, isolated from type locality. The re-description is richly illustrated with all possible methods of morphological description including SEM an DIC images. DIC-microphotographs deserve special praise. E.g. it is quite a rare occasion when inner structure of spicules and the shape of gubernaculum are so clearly seen as on Fig. 2, G. Another valuable demonstration of the power of basic morphological information is on the Fig.2 D where the formation of anterior and posterior dorsal rays of bursa is demonstrated on the image of fourth-stage juvenile.

Another trend-setting moment of the paper is in phylogenetic analysis. As leading specialists in nematode molecular phylogeny are between the authors, some novel (at least for me) approach is proposed (supertrees from several datasets, weighted parsimony etc.). Several approaches of authors are provoking special interest and invite to use the same approach, including idea to create concatenating sequences even if primary sequences were obtained from different strains. Such an action can be justified with the fact of very uneven knowledge of separate species and strains of rhabditid nematodes.

I am sure that the paper is completely ready for publication but would like only to attract authors’ attention to few minor moments.

E.g. both in description of Pellioditis pelhami n. sp. and in re-description of Pellioditis pellio (Schneider, 1866) the number of paratype and neotype, correspondingly. in the Nematode Collection at the University of California, Davis is given: “as slide ____.” Probably number will be provided from UC Davis only on later stages, but in modern shape it looks strange. To be honest the idea to mount several specimens on the same slide with only one specimen between those serving as type looks quite new for me, but authors ensure completely precise identification of paratype/neotype with indication like ‘the rightmost male is the holotype’ and in fact the slides are soon sent to the collections.

Fig. 3G – probably an explanation is needed here – to help for the reader to find lateral field. Near the vulvar opening one can find longitudinal ridges which are probably artefact of critical-point drying. The fine features of the lateral field (true lateral field) might be traced out near the margin of the image – in the overexposed portion of the body. It is obvious if compare this image 3G with e.g. Fig.7 J – the position of lateral field in the latter is quite obvious and explained by the inset image.

And finally – authors use the binomial Angiostoma norvegicus – page 32, but primary in the first description by Ross et al (Angiostoma norvegicum n. sp. (Nematoda: Angiostomatidae) a parasite of arionid slugs in Norway) the spelling was different. Probably it would be better to add citation of the publication where this changed speclling was proposed (as we can understand to comply with neutral gender?).

Reviewer #2: The manuscript contains a description of a new species. Morphological and morphometrical description is acceptable. However, probably, the specific name proposed for the species could be not correct, which should be ending in "-ensis" because it correspond with a place/locality. Other comments and suggestions are included in the MS file.

********** 

6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Attachments

Attachment

Submitted filename: PONE-D-23-19233_reviewer (revised).pdf

PONE-D-23-19233R1Pellioditis pelhamensis n. sp. (Nematoda: Rhabditidae) and Pellioditis pellio (Schneider, 1866), earthworm associates from different subclades within Pellioditis (syn. Phasmarhabditis Andrássy, 1976)PLOS ONE

Dear Dr. Fitch,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

ACADEMIC EDITOR: ulliThe authors have made most of the changes as suggested, but the typical format for nematode species descriptions is not fully met yet. I kindly request the authors to make the following changes in the description to adhere to the standard format for publication in PLOS ONE. With these changes, the nematode species description will align with the typical format required for publication in PLOS ONE.

Stoma wider and shorter in adults than in juveniles (delete is)

Pharynx corpus cylindrical, about two times as long as isthmus with slightly enlarged metacorpus narrowing into isthmus, and a bulbous postcorpus (basal bulb) longer than wide, with striated valvular apparatus; isthmus slightly longer than basal bulb (Fig 1A, 2C) (insert comma after isthmus, and delete that is)

Sperm also found in the uteri (delete is)

Uteri of mature females often filled with developing embryos (delete are).

In older females, hatched juveniles of various stages also present inside of the female uterus (delete are).

The anterior dorsal GP in position 5 (counting from the anterior) (delete is)

The posterior dorsal GP terminal, or originates at the same level as the most posterior GP (v7) (delete is and it). 

The phasmids form small ventral papillae not fully embedded in the bursal velum (delete that are).

In strain EM434, variations in the spacing of GP1, GP2 and GP3 observed.

Aberrations also found: males with abnormal numbers of rays (one having 13 GPs on one side!) and one adult male with a long (leptoderan) tail tip (delete are).

Thus, the formula (following [11, 29]), follows: (delete is)

Please submit your revised manuscript by Sep 07 2023 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-emailutm_source=authorlettersutm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Aashaq Hussain Bhat, Ph.D.; Postdoctoral Fellow

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

[Note: HTML markup is below. Please do not edit.]

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Pellioditis pelhamensis n. sp. (Nematoda: Rhabditidae) and Pellioditis pellio (Schneider, 1866), earthworm associates from different subclades within Pellioditis (syn. Phasmarhabditis Andrássy, 1976)

PONE-D-23-19233R2

Dear Dr. David,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter, and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Aashaq Hussain Bhat, 

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: