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As part of the submission process, authors are required to check off their submission's compliance with all of the following items, and submissions may be returned to authors that do not adhere to these guidelines.

  • 1. On behalf of my co-authors, I submit the following manuscript for publication consideration in JoTT. I add all my co-authors' details and my details in the metadata section. I have checked that names of the authors and the order of authorship are the same in both the author metadata and in the manuscript. I understand the submission will be declined if I don't provide all the above detail in the metadata section.
  • 2. In preparing the manuscript and/or as a corresponding author, I have also ensured the following:
    i) The submission file is in Microsoft Word document file format.
    (a) One complete manuscript file WITHOUT author details and Acknowledgements (WORD, not more than 10MB)
    (b) One complete manuscript file WITH author details and Acknowledgements (PDF, not more than 10MB)
    ii) Where available, URLs for the references have been provided.
    iii) The text is 1.5 line-spaced; uses a 12-point font; employs italics, rather than underlining (except with URL addresses); and all images, figures, and tables are placed at the end, rather than within the text at the appropriate points.
  • 3. Valid, current, and working email IDs of all authors along with their affiliations and complete postal address (including zip / pin codes where available) have been included.
  • 4. I submit a Cover letter with a Checklist. [Make a checklist of documents submitted (e.g.: Manuscript, 3 Images)].
  • 5. I submit a general Ethics statement signed by me, the corresponding author.
  • 6. I have indicated three subject experts, with their Title, complete name, Institutional Affiliation, and working e-mail address, as referees in the "Comments for the Editor" text editor of this submission process at the bottom of the 'Start' page. I have not included any names from my organization or names of my co-published authors in the last one year.
  • 7. Names of non-preferred reviewers, if any (maximum 2). Indicate this in the "Comments for the Editor" on the Start page of the submission process.
  • 8. I understand the objectives of the Journal and have formatted the manuscript to fit the style and needs of the Journal.
  • 9. I understand the procedure followed in the review process.
  • 10. I affirm that the manuscript has been prepared for and sent only to JoTT for publication consideration and is not submitted to any other journal or any other type of publication (including web hosting) either by me or any of my co-authors.
  • 11. I understand that there is an article processing charge (APC) for publication in the Journal of Threatened Taxa, which will be paid at the time of the galley proof stage in order to be published. I have understood the basis of the APC and will make one complete payment on behalf of the entire team of authors.
  • 12. I understand there are no other kinds of charges including subscription charge, membership charge, page charge or any other hidden charge. However, I also understand that in case any of my co-authors or I decide to withdraw the manuscript from publication after one week from the date of submission, a penalty of USD 10/- per page (authors residing outside of India), or INR 500/- per page (for authors residing within India) as indicated in the Checklist (of total pages submitted in A4 size page as per standard JoTT format, including text and illustrations) will be deposited before the submission is considered withdrawn.
  • 13. If submitting to a peer-reviewed section of the journal, the instructions in 'Ensuring a Blind Review' have been followed.
  • 14. The text adheres to the stylistic and bibliographic requirements outlined in the 'Author Guidelines', which is found in About the Journal.
  • 15. All co-authors of the manuscript have been consulted and the submission is made on the behalf of all authors after approval.
  • 16. I understand that by not complying with the above, the manuscript process will get delayed and I do not hold the Journal responsible for the delay.
  • 17. If, after peer-review, the manuscript is finally accepted for publication:
    i) I/We understand the copyright belongs to me and my co-authors.
    ii) I/We grant WILD permission to publish the article in JoTT.
    iii) I/We recognise WILD as the original publisher, grant WILD commercial rights to promote the article and JoTT, and distribute/sell hard copies of the Journal and article to any buyer.
    iv) I/We understand JoTT is registered under the Creative Commons Attribution 4.0 International License (CC-BY), which allows authors to retain copyright ownership.
    v) Under the CC-BY license, I/We allow anyone to download, cite, use the data, copy and distribute provided the authors and source of publication are credited through appropriate citations.
    vi) I/We understand that users of the data do not require specific permission from the authors or the publisher.


The following documents and details are compulsory for the manuscript to be processed for review.  Failure in submission of these documents will result in the submission not processed. Incomplete submissions will be rejected and archived after a month of submission.

1. Checklist. Make a checklist of documents submitted (e.g.: Manuscript, 3 Images).
2. Names, affiliations, complete postal address and working email IDs of all authors. 
3. Names of 3 preferred reviewers (see guidelines).  Indicate this in the "Comments for the Editor" in the Start page of the submission process.
4. Names of non preferred reviewers, if any (maximum 2).  Indicate this in the "Comments for the Editor" in the Start page of the submission process.
5. Manuscript file in .doc or .docx format (consult preparation guidelines). Do not submit manuscripts as PDFs.
6. Figure and images (consult preparation guidelines).
7. A general Ethics statement signed by corresponding author.
8. Cover Letter -- use the following template:

Editor JoTT,

On behalf of my co-authors (List names of all co-authors), I (Insert your name) submit a new manuscript titled “(Insert the title of the manuscript)” for publication in the Journal of Threatened Taxa.  I understand the objectives of the JoTT and have formatted the manuscript to fit the style and needs of the Journal.  I also understand the procedure followed in the review process.

I affirm that the manuscript has been prepared for and sent only to the JoTT for publication consideration and is not submitted to any other journal or any other type of publication (including web hosting) either by me or any of my co-authors.

The submission is a (Indicate whether it is a Monograph, Full length article, Short length article, or Brief article — check out the APC section under ‘About’ online.).

I list at least three Referees (experts in the field of my manuscript subject) who may be considered for reviewing this manuscript.  These do not include any names from the same organization as that of the authors, or names of those who have co-published with any of the authors in the last one year.  Further, at least one of the suggested Referees/Reviewers is from outside the country of research.

Reviewer 1: 
i. Name:
ii. Topic/s of expertise:
iii. Affiliation:
iv. Full correspondence address:
v. Working email ID:

Reviewer 2: 
i. Name:
ii. Topic/s of expertise:
iii. Affiliation:
iv. Full correspondence address:
v. Working email ID:

Reviewer 3: 
i. Name:
ii. Topic/s of expertise:
iii. Affiliation:
iv. Full correspondence address:
v. Working email ID:

I request that the following experts not be contacted as Referee/Reviewer for my manuscript (not more than 2).

Non-preferred Reviewer 1: 
i. Name:
ii. Working email ID:

Non-preferred Reviewer 2: 
i. Name:
ii. Working email ID:

I understand that there is an article processing charge (APC) for publication in the JoTT.  I have read about the APC and understand it and agree to pay the APC at the time of the final acceptance of the manuscript for publication.

I also understand that in case any of my co-authors or I decide to withdraw the manuscript from publication after a week from the date of submission, a penalty of USD 10/- per page (authors residing outside of India), or INR 500/- per page (for authors residing within India) as indicated in the Checklist (of total pages submitted in A4 size page as per standard JoTT format, including text, figures, images, tables, and data) will be deposited before the submission is considered withdrawn. 

Thanking you,


Correspondence email id:



Submit as Original File:
Manuscript with Title, Abstract, Keywords, Running Title, Text, Tables, Figures, Images, References and Appendices as a WORD document only (no PDFs or any other format).  This document should not have names of authors, affiliations, acknowledgements and roles.

Submit as Supplementary Files:
1.  Complete manuscript along with author names, affiliations and acknowledgements as a PDF.
2.  High resolution images.
3.  Cover Letter (as per the template given above).
4.  Checklist of documents submitted as WORD of PDF.
5.  Signed Ethics statement as WORD or PDF.
6.  Other documents of import and as required.

Submit under Article Metadata:
1. All author names in the order of listing in the manuscript.
2  All author details including titles, affiliations, complete postal address as indicated in the manuscript, and working e-mail ids.
3.  ORCID id for every author.  This is compulsory and is an easy and free process to register (www.orcid.org).  This may be submitted at the time of final acceptance of the manuscript. Please click here to download the steps to connect ORCID to your article.
4.  Fill in all the boxes as required in the submission page.  This will ensure better handling of review and editing processes.

Make sure that you read and understand the various steps under the Start of the 5-step Submission process regarding the undertaking, listing of referees/subject experts, and copyright.

List of Potential reviewers
Put together a list of three potential referees that you will inform in the text box "Comments for the Editor" during the electronic submission process. These should not include any names from the same organization as that of the authors, or names of those who have co-published with any of the authors in the last one year.  Further, at least one of the suggested Referees/Reviewers is from outside the country of research. In the list you must provide the Title, complete name, Institutional Affiliation, and working e-mail address.

All submissions to JoTT are considered complete only if the checklist of attachments (e.g., text, number of tables, number of images, figures, audio or video files, formats, etc.) is provided along with a letter listing all authors, their affiliations and current email ids., of the manuscript. We presume that authors from institutions with formalities have submitted manuscripts through the 'right channels'. Provide names, addresses and working email ids of at least three experts on the subject who would be appropriate reviewers for your manuscript. Make sure that at least one of the suggested reviewers is from a country other than yours. The reviewers should not be from the same institution as that of the affiliation of any of the authors. Authors are encouraged not to mention the names of reviewers with whom they have published in the last two years. Authors may indicate a maximum of two non-preferred reviewers. However, the final decision on selection of reviewers for the manuscript is left to the chief editor.

General format for manuscript submission
Manuscript should be typed in MS word processing software on A4 page with 1-inch margin on all sides. The MS should be typed in Calibri or Arial font point 12 with 1.5 line spacing.

Title and author details:

1. Provide systematic position of the taxon mentioned in title to a maximum of three superior levels of hierarchy [e.g.: Genus species Author, Date (Class: Order: Family); Family Author, Date (Class: Order); subspecies or group (Order: Family: Genus species)].
2. Provide complete current/valid correspondence address of all authors.
3. Provide current/valid email ids of ALL authors. Author for correspondence must indicate "Corresponding Author" in parenthesis after the email ID.
4. Provide complete names of all authors by expanding all initials, wherever possible.
5. In countries/regions where the ordering practice of first, middle and last names are not always consistent with global usage [e.g. Bexel Ayyachamy Daniel], make sure to provide the citation name last [in the above example, Bexel is the middle name, Ayyachamy is the last/family name and Daniel is the first name]. In standard global usage, it would be arranged as Daniel Bexel Ayyachamy. However, if the author wishes to place the onus (citation name) on first name rather than family name, arrange the name as shown above in the first example (Bexel Ayyachamy Daniel). The citation would then be Daniel, B.A. (how the author desires) rather than Ayyachamy, B.D. (the global first-middle-last name citation standard).


1. All acronyms must be defined clearly on first usage in the text [e.g., head-body length (HBL)].
2. Numbers from one to nine must be spelt in running text, and from 10 onwards must be numerical.
3. Only scientific names should be in italics [e.g., Acinonyx jubatus].
4. Common names in any taxonomic group must begin with capitals [e.g., Aardvark, Atlantic Needlefish, Round-leaved Chaff Flower, Blind Cave Beetle].
5. Standard Latin and Greek notations such as in situ, nomen nudum, etc. should not be italicized.
6. Vernacular names/terms must not be italicized. The first use of a vernacular term must be in single quotes and accompanied by the language and meaning in parenthesis. [e.g., ‘tal’ (Hindi: Lake); ‘beel’ (Bengali: Lake)]
6. Ranges in text, tables, caption or anywhere in the manuscript must be separated by en dashes [e.g. 12–15, January–March] and not just by hyphens. [Note: to get en dash, type ˜ 'control' and '˜minus' in Windows Office, or 'option' and 'hyphen' in Office for Mac].
7. Consistency in style of English [e.g., British, American] should be followed throughout the manuscript.
8. Commas, colons and semicolons in running text should be followed by a single space.
9. Dates in the text must always follow the format 01 January 2011, while dates in tables must follow the format 01.i.2011.
10. Abbreviations in citations must follow the following format with the first and last name spelled out [e.g., Arun Karim pers. obs. 18.xii.2010; Nguyen Hien pers. comm. 17.iii.2001; Kate Jones in litt. 02.ii.2009; Noémie Goossens unpub.].
11. Articles formally accepted for publication must be cited as ‘in press’ [e.g., Smith in press.], while articles not yet formally finally accepted must be cited as ‘submitted’ [e.g., Wu submitted].
12. Multiple citations in the text must be arranged chronologically (alphabetically only in instances with multiple citations with same year) and must be separated by semicolons [e.g., Johansson 1996; Rehak 2008, 2009a,b; Qin & Nyhus 2010; Raghavan et al. 2010].


Only English language manuscripts are accepted. JoTT allows authors to choose either British or American English styles to be used consistently throughout the manuscript.

Local Language Abstract:

One of the features that JoTT includes in the article is a local language Abstract along with the English Abstract. The vernacular Abstract can be in any language of authors' choice (up to a maximum of three languages). Authors wishing to provide such an Abstract, will have to supply the text and take responsibility for its correctness and proof reading. Authors must provide the vernacular font along with the text. The local language Abstract may or may not reflect the same content as in the English Abstract but must summarize the content of the paper only without including any extraneous information or topics.

Layout and Contents:

Article/ Communication / Review /Monograph shall contain the following headings:
1. Abstract: Not more than 300 words highlighting key points including Rationale, Methods, Results and Conclusion. The authors have the option of providing the Abstract with separate headings as indicated above, or as a single paragraph.
2. In the case of New Descriptions, include key diagnostic characters of the taxon newly described.
3. In case of multiple taxa described in a paper, key points of analysis should be provided.
4. Key words: Maximum of ten words or phrases unless warranted.
5. Abbreviations: Expand all Abbreviations used in the text except the standard units of measurements. List them alphabetically.
6. Introduction: Must be crisp and include applicable history of the subject, state the problem, important literature review, the hypothesis, the need and the objectives.
7. Materials and Methods: Must include the dates of study, study area with map, design, programmes used and data analysis.
8. Results: Should be precise supported with tables,
9. Discussion
10. Comparative material
11. References
12. Tables
13. Figures -- illustrations, maps (Line drawing)
14. Images -- colour or black & white photographs, scans, radiographs, SEMs, raster maps, Google Earth images etc.
15. Audio files -- maximum length of one-minute duration, and a maximum of six files (unless absolutely warranted), in .wmv or .wav format.
16. Video files -- maximum of two-minute duration, and a maximum of six files (unless absolutely warranted), in .mp4 format 15. Appendices
16. Author details if in case of Papers, Communications, and Reviews of not more than 50 words each. This should include author contributions to the paper.
17. Logos of home institutes and sponsors for Papers, Communications and Reviews: Authors wishing to highlight the home institutes and funding agencies are encouraged to send good quality and clear scans (JPEG or TIFF files) of institution logos. This facility is not provided for Notes, Opinions, Book Reviews and Letters. All units of measurement should be in metric, or preferably SI units; All pages should be numbered; Tables and Figures should be numbered and captioned and included in separate pages at the end of the text; Original drawings and figures should be submitted; Photographs must be digitized and must be clear with no types, watermarks, emboss, or markings; Captions for all images and figures should be attached separately at the end of the manuscript; Photo credit must be provided along with image caption; Spellings should be consistent with the type of English chosen (British or American). Manuscripts using the IUCN Red List Categories must enter the categories starting with capital. For example, Paphiopedilum druryi is a Critically Endangered plant (IUCN 2008). Whereas, the description of status of a species should be in lower case. For example, Paphiopedilum druryi is a highly endangered orchid.

All references cited in the text should be quoted completely in this section. Journal names should be expanded. Please do not insert abbreviations. For example, expand PNAS to Proceedings of the National Academy of Sciences, or, J. Bom. Nat. Hist. Soc. to Journal of the Bombay Natural History Society. Provide Digital Object Identifier (doi) for articles wherever available.

References should be listed in the following format:
Ricketts, T.H. (2004). 
Tropical forest fragments enhance pollinator activity in nearby coffee crops. Conservation Biology 18(5): 1262–1271. https://dx.doi.org/10.1111/j.1523-1739.2004.00227.x
Singh, M., M. Singh, A.K. Sharma & B.A. Krishna (2003).
Methodological considerations in measurement of dominance in primates. Current Science 84: 709–713.

Open Access Journal:

Canestrelli, D., M. Zampiglia & G. Nascetti (2013).
Widespread occurrence of Batrachochytrium dendrobatidis in contemporary and historical samples of the Endangered Bombina pachypus along the Italian peninsula. PLoS ONE 8(5): e63349. https://dx.doi.org/10.1371/journal.pone.0063349

Preprint online Journal publications:

Pino-Del-Carpio, A., A.H. Ariño, A. Villarroya, J. Puig & R. Miranda (in press). 
The biodiversity data knowledge gap: assessing information loss in the management of biosphere reserves. Biological Conservation Available online 8 December 2013. https://dx.doi.org/10.1016/j.biocon.2013.11.020.

Srinivasulu, C. & B. Srinivasulu (2012).
South Asian Mammals: Their Diversity, Distribution, and Status. Springer, New York, 467pp.

Edited Book:
Mittermeier, R.A., A.B. Rylands & D.E. Wilson (Eds.) (2013).
Handbook of the Mammals of the World: Primates. Lynx Edicions, Spain, 952pp.

Edited Book (multiple volumes):
Wilson, D.E. & D.M. Reeder (eds.) (2005). Mammal Species of the World: A Taxonomic and Geographic Reference, 3rd edition, Vol. 1 & 2. The Johns Hopkins University Press, Baltimore, pp.i-xxxv+1–743 & pp.i-xvii+745–2142.

Book Chapter:
Chivers, D.J., M.V. Anandam, C.P. Groves, S. Molur, B.M. Rawson, M.C. Richardson, C. Roos & D. Whittaker (2013).
Family Hylobatidae (Gibbons), pp. 875–912. In: Mittermeier, R.A., A.B. Rylands & D.E. Wilson (eds.). Handbook of the Mammals of the World: Primates. Lynx Edicions, Spain, 952pp.

Peer-reviewed Monograph:

Nguyen, M.T., D.T. Pham & P.T. Nguyen (2003).
Conservation of rodents in tropical forests of Vietnam, pp. 246–250. In: Singleton, G.R., L.A. Hinds, C.J. Krebs & D.M. Spratt (eds.). Rats, Mice and People: Rodent Biology and Management. ACIAR Monograph No. 96, Canberra, 564pp.


Kumar, S., B.V. Shetty, D. Bennet & S. Molur (2000). 
Report of the Conservation Assessment and Management Plan Workshop on Endemic Orchids of the Western Ghats. Zoo Outreach Organisation & CBSG South Asia, Coimbatore, India, 150pp.

Rodriguez, J.P. (1999). Ecology of contraction of geographical distributions. PhD Thesis. Department of Ecology and Evolutionary Biology, Princeton University, viii+143pp.

Web resource:

China Plant Specialist Group (2004). 
Aristolochia westlandii. In: IUCN 2008. 2008 IUCN Red List of Threatened Species. Downloaded on 26 January 2009.
Eschmeyer, W.N. & J.D. Fong (2013). Species by Family/Subfamily. https://research.calacademy.org/research/ichthyology/catalog/SpeciesByFamily.asp Electronic version accessed 21 December 2013. In preparation/submitted manuscripts: (authors are encouraged not to cite unpublished work but under absolute necessity, they can cite it as follows; without mentioning the name of the journal) Surname, I.N. & I.N. Surname (submitted). Title of the paper.

Miscellaneous citations in the text:

In litt.: Any information used in the text that is derived from a formal communication must be cited only in the text with full names (first and surname) and the date of receipt of the communication as shown (Expanded Surname in litt. Date) Pers. comm.: Any information used in the text that is taken from informal communication must be cited only in the text with full names (first and surname) along with the date of communication, or at least the month and year of communication when exact details are unavailable, as shown (Expanded Surname pers. comm. Date).

New descriptions

1. All new descriptions must follow the guidelines provided by the International Codes (ICZN, IPNI, or MycoBank).
2. Latin abbreviations such as gen. nov., sp. nov., ssp. nov., nom. nov., syn. nov., and comb. nov. must follow new taxa, synonymies, or new combinations.
3. The complete data of the types, name-bearing (e.g., holotype, lectotype, syntype) or otherwise (e.g., paratypes, topotypes), and the name of the depository should be provided in the original description.
4. Type material should contain the following details: registration number, sex, date of collection, exact name of the site of collection, broader area name, District/Province/State, Country, latitude longitude information of the site of collection (decimal degrees only), elevation (in m), collector’s name.
For example: Holotype: Registration number, Female, 26.i.2009, Gopal Nagar, Peelamedu, Coimbatore, Tamil Nadu, India, 13.27'°N 75.25'°E, 280m, coll. B. Ravichandran. Paratypes: Registration number, 1 ex., male, 30.i.2009, same information as in holotype; Registration numbers, 2exs. Females, the same information as in holotype; Registration number, 1ex., male, 10.i.2009, Kara Valley, Rohitam, Andhra Pradesh, India, 25.48'°N, 77.33'°E, 608m, coll. I. Reddy.

New descriptions of Fungi:

Annually around 1,400 new scientific names for fungi are established in various journals throughout the world. Coordinating and documenting this diversity is of utmost concern and coordinating information on these names is essential. The International Mycological Association (IMA) has assumed responsibility for managing MycoBank initiated in 2004 by the Centraalbureau voor Schimmelcultures of the Royal Academy of Science of the Netherlands. All newly described fungi species and names are deposited in MycoBank along with key nomenclatural and descriptive material. All names are checked with IndexFungorum and provided with a unique reference number. JoTT encourages all new fungi descriptions submitted for publication to provide the unique reference number. Obtaining the number is mandatory for acceptance of the new description in JoTT. JoTT also recognizes that for countries with strict biodiversity laws that does not permit sending biological material out of the country for such deposition (e.g., India, Brasil), at least the new names should be registered with MycoBank and the registration number indicated in the manuscript. For further information on registering new descriptions and names, contact MycoBank at or for further queries contact the members of its Scientific Advisory Board.

Important: Manuscripts will not be accepted if the registration numbers and names of the depository are not mentioned. While it is important to have types deposited in renowned national or international museums/herbariums or collections, JoTT accepts manuscripts of types not deposited in such institutes due to national legislations and other difficulties such as poor collection maintenance records of such authorized institutes. However, a clear description as to why types are not deposited in national or international collections is required in the cover letter along with detailed information on the institute the types are deposited in and the registration numbers in the text. Please ensure that types deposited in alternate institutes and museums are accessible to future taxonomists and parataxonomists for examination. Also ensure that such institutes have a long term strategy for preserving and maintaining well such collections, or with a reasonable approach/time frame for transferring the materials to other responsible institutes. Personal collections with a history of good maintenance should have adequate and responsible transfer strategies in case of death or incapacitation of the collector. Single experts in universities or institutes with collections should have a strategy for the transfer of types and other materials to other responsible institutes if a responsible successor is not identified.

Guidelines for conservation evidence
If the manuscript is on conservation management, action, or restoration, indicate if there is any existing evidence published for the intervention you are proposing in the write-up.  This is best indicated in the Introduction with the citation.  If there is no formal publication summarizing the evidence for conservation action, please do a literature review on the subject and summarize evidence pertaining to the subject.  If there are absolutely no studies or actions or available evidence regarding similar actions, please express this explicitly.  A good source for summaries related to evidence is in the journal Conservation Evidence (www.conservationevidence.com).

Guidelines for reporting statistical analysis
1. It is essential that authors understand the applicability and relevance of the methods employed to analyze data and that the analysis is described in sufficient detail for others to check for potential errors and/or misapplication. Use the minimum and most appropriate statistical analysis required for data interpretation (i.e., do not use multiple tests to make the same point unless an explicit aim of the study is to compare statistical approaches).
2. Software used for statistical analysis should be mentioned, along with appropriate references for freeware or open-source packages.
3. Descriptive statistics must be presented in text, tables, and graphical elements with indicators of variation in the data sets they describe. Specifically: i) percentages should be accompanied by ranges and sample sizes; ii) statistical estimates (mean, slope, etc.) should be accompanied by error calculations in the form of standard deviation, standard error or confidence intervals, with the latter preferred; iii) graphs, charts, and histograms should indicate data variability with error bars.
4. There is no need to explain or give references for basic statistical analysis methods, however, it is necessary to provide sufficient information for modifications or specialized techniques to allow reviewers to assess how and why the methods were used. For example, if a method is used for hypothesis testing, then the null hypothesis should be mentioned. Details should also cover the input format for the method (e.g., describe dependent and independent variables, covariates, etc.).
5. The terms  'significant' and 'not significant' must be restricted to their formal statistical context, accompanied by appropriate P values. Rather than reporting the P-value as P < 0.05 or P < 0.01 or P > 0.50, report actual P values up to three decimal places except when P < 0.001, in which case  P < 0.001 is sufficient. Authors should state whether the significance was tested at a two-tailed or one-tailed level.
6. The statement often put in the methods section that 'significance of the test was checked at P < 0.05' should read: 'significance of the test was checked at ± = 0.05', where ± is the probability of committing a type I error. Since most studies use ± = 0.05 it is not mandatory to make this statement, however, if authors are performing several univariate tests on the same data they should check test significance with appropriate correction of alpha (e.g., Bonferroni or sequential Bonferroni correction). In such cases, only P values less than Bonferroni-corrected ± should be considered statistically significant.
7. If there are several dependents and/or independent variables in the study, it is advisable that rather than (or in addition to) performing univariate analysis between pairs of variables, authors should use appropriate multivariate analysis. This is important because i) if there are several univariate tests the Bonferroni correction produces a very conservative ±; ii) variables can act in combination; iii) multivariate analysis can detect some data patterns more effectively. Click on JoTT Toolbox for Authors for details and links for free statistical software and other resources.

Guidelines for reporting molecular work

1. Specimens used for DNA extraction should be submitted to a museum and permanent voucher registration numbers obtained. These numbers must be mentioned in the manuscript, along with the latitude and longitude of the collection site.
2. All primer sequences used must be listed with proper references (i.e., it is not sufficient to mention that primers have been adapted from a given reference). Tm values of primers should be provided, and if primers are designed for a study the text should state how they were designed (i.e., software used) and the reference gene sequence(s) used (accompanied by GenBank accession number, below).
3. PCR thermal profile should be mentioned.
4. All novel gene sequences mentioned in the paper should be submitted to NCBI, and the GenBank accession numbers should be provided in the manuscript latest by the proof stage.
5. Sequences submitted to NCBI should come in the public domain within 15 days after publication of the paper.
6. When the paper containing the molecular information is published authors should update the publication details in NCBI.
7. GenBank accession number, along with the voucher specimen registration number and collection site for the voucher specimen, if available, for all the sequences used for comparison should be mentioned (preferably in a table format).
8. Details of the molecular analysis along with the software used for the analysis should be mentioned.
9. When performing the maximum likelihood analysis, it is mandatory that the authors perform model tests and mention the nucleotide substitution model used for the analysis.
10. Reliability of phylogenetic trees (generated by any method) should be checked before reporting the results.
11. If real-time/quantitative PCR is used in the study, authors should give the details of the preparation of standards and results of positive and negative controls.

Toolbox for Authors

A variety of open-source software programmes, freeware programmes, and free resources are available on the World Wide Web, which can help authors in analyzing their data and creating graphics in a more presentable format. Some of these open-source software programmes, freeware programmes, and free resources, along with their links, are listed below. Note that it is neither mandatory nor necessary for the authors to use only these software programmes or resources. JoTT takes no responsibility for the integrity of the analysis done in these software programmes. Authors should read the license agreement for individual freeware carefully before using the freeware for their study. Freeware/free resources should be cited appropriately in the text and in the reference section. All trademarks and registered trademarks are the property of their respective owners.


PAST: Freeware for statistical analysis developed by Øyvind Hammer, David A.T. Harper, and P.D. Ryan. It performs univariate statistics, multivariate statistics, biodiversity analysis, etc. and has a good graphical output. URL: https://folk.uio.no/ohammer/past/.

BiPlot: A freeware for multivariate analysis and visualization of analysis using biplots created by Eric P. Smith. URL: https://www.stat.vt.edu/facstaff/epsmith.html.

POP Tools: An add-in for Microsoft Excel® which performs analysis of matrix population models and simulates stochastic processes. Created by Greg Hood, it also performs calculation of bootstraps and statistics of resampling. URL: https://www.poptools.org/.

TANAGRA: A free data mining software created by Ricco Rakotomalala for exploratory data analysis, statistical learning, machine learning, etc. Good for several multivariate and clustering techniques. URL: https://eric.univ-lyon2.fr/~ricco/tanagra/en/tanagra.html.

SIPINA: A freeware for making decision trees (also called as Classification Trees) based on algorithms such as ID3, CHAID, C4.5, etc. created by Ricco Rakotomalala. URL: https://eric.univ-lyon2.fr/~ricco/sipina.html.

ESTIMATES: Created by Robert Colwell, Estimate S can be used for performing rarefaction, creating species accumulation curves, estimating species richness and diversity indices and estimation of shared species and biotic similarity indices. URL: https://viceroy.eeb.uconn.edu/EstimateS. PSPP: Open source software for a variety of univariate and multivariate statistical analysis developed under the GNU Project. URL: https://www.gnu.org/software/pspp/get.html

ViSta (The Visual Statistics System): Open source software written by Forrest W. Young, has very unique ways of visualizations, which are highly dynamic and very interactive, showing you multiple views of your data simultaneously. URL: https://forrest.psych.unc.edu/research/index.html

VassarStats: Website for statistical computation designed by Richard Lowry. It is dedicated to the free dissemination of knowledge on the world-wide-web. It is a web-based package for statistical analysis. It most interesting module is “Statistical Tables Calculator” that calculates P values for the given statistics. URL: https://faculty.vassar.edu/lowry/VassarStats.html

Molecular biology:

MEGA5: Molecular Evolutionary Genetics Analysis (MEGA) in its fifth version created by Koichiro Tamura, Daniel Peterson, Nicholas Peterson, Glen Stecher, Masatoshi Nei, and Sudhir Kumar, is an integrated tool for DNA and protein sequence alignment, performing the model test, inferring phylogenetic trees, estimating rates of molecular evolution and testing evolutionary hypotheses. The software also provides a good graphical output. URL: https://www.megasoftware.net/

DAMBE: A software package for extensive data analysis in molecular biology and evolution created by Xuhua Xia. URL: https://dambe.bio.uottawa.ca/dambe.asp BioEdit: A sequence alignment editor designed by Thomas Hall. Good for checking and editing different formats of sequence files including ab1. URL: https://www.mbio.ncsu.edu/bioedit/bioedit.html

Figure/photo editing:

GIMP: An Image Manipulation Program developed under GNU project. It is a freely distributed piece of software for such tasks as photo retouching, image composition, and image authoring. URL: https://www.gimp.org/ Inkscape: An open-source vector graphics editor developed under GNU project. Excellent for editing vector graphics, line drawings, graphs, etc. URL: https://inkscape.org/ Draw: A vector graphics editor developed under open-office software suite. Good for line drawings and processing of graphs. URL: https://www.openoffice.org/product/draw.html GIS: DIVA-GIS: A free program for mapping and geographic data analysis. The website also provides free spatial data for the whole world that you can use in DIVA-GIS. URL: https://www.diva-gis.org/

MAXENT: Developed by Steven J. Phillips, Miroslav Dudík and Robert E. Schapire, Maxent is a free software for species habitat modeling. URL: https://www.cs.princeton.edu/~schapire/maxent/ DesktopGarp: A software package for biodiversity and ecological research that helps to predict and analyze species distributions. URL: https://www.nhm.ku.edu/desktopgarp/index.html.