Authors Guidelines

Main Text

Due to the double-blind peer review system, you have to submit your manuscript (apart from the letter to the editor and supplementary material) as two separate files (for further details, see under Submission Guidelines):

(i) Cover part (with personal information)

Authors and Affiliations: Provide the complete names of all authors, and their addresses for correspondence, including e.g., institutional affiliation (e.g. university, institute), location (street, boulevard), city, state/province (if applicable), and country. One of the authors should be designated as the corresponding author. It is the corresponding author's responsibility to ensure that the author list, and the individual contributions to the study are accurate and complete. If the article has been submitted on behalf of a consortium, all consortium members and their affiliations should be listed after the Acknowledgements section.

(ii) Main part (anonymised)

Title: The title should be written in sentence case (only scientific names, geographic locations, or other proper nouns should be capitalized, i.e. Elater ferrugineus L., Germany, etc.), and should include an accurate, clear and concise description of the reported work, avoiding abbreviations.

Abstract and Key Words: Please have your abstract and key words ready for input into the submission module. Key words should be in alphabetical order and ideally differ from the words used in the title. The abstract should include the following sections: introduction (stating the problem and the purpose of the study), very concise methods, results, and conclusion. The abstract should be informative (without general words), original, factful (provide a summary of the content of the article and key results of the study), written in good English, concise (between 200 and 250 words). It should be followed by up to 6–8 key words that convey the main meaning of the article.

Body Text: All papers should be in grammatically correct English. Non-native English speaking authors are required to have their manuscripts checked by a native English speaker or professional English-language editor prior to submission. Use either British/Commonwealth or American English provided that the language is consistent within the paper. A manuscript must be written with precision, clarity, and economy. The voice - active or passive - and the tense used should be consistent throughout the manuscript. Avoid the use of parenthetical comments and italics or bold for emphasis. This journal discourages the use of quotation marks except for direct quotations, words defined by the author, and words used in unusual contexts. Short quotations should be embedded in the text and enclosed in double quotation marks ("). Long quotations should be on a separate line, italicized, but without quotation marks. Single quotation marks are to be used only for a quotation that occurs within another quotation.

Spacing, Fonts, and Page Numbering: Single-space all material (text, quotations, figure legends, tables, references, etc.). Separate paragraphs with a blank line. Use a 12-point font (preferably Times New Roman or Arial).

Capitals: First capital letters should be used only in the beginning of a sentence, in proper names and in headings and subheadings, as well as to indicate tables, graphs and figure/s within the text. Software programmes should be written with capital letters (e.g., ANOVA, MANOVA, PAUP).

Italicization/Underlining: Scientific names of species and genera, long direct quotations and symbols for variables and constants (except for Greek letters), such as p, F, U, T, N, r, but not for SD (standard deviation), SE (standard error), DF (degrees of freedom) and NS (non significant) should be italicized. These symbols in illustrations and equations should be in italics to match the text. Italics should not be used for emphasis, and not in abbreviations such as e.g., i.e., et al., etc., cf. Underlining of any text is not acceptable.

Abbreviations: Abbreviations should be followed by ‘.' (full stop or period; for instance: i.e., e.g., cf., etc.). Note that you shouldn't add a full stop at the end of abbreviated words if the last letter of the abbreviation is the same as the last letter of the full word. For example, you should abbreviate "Eds", "Dr", "Mr" without full stop at the end. All measures, for instance mm, cm, m, s, L, should be written without full stop.

On the use of dashes: (1) Hyphens are used to link words such as personal names, some prefixes and compound adjectives (the last of which vary depending on the style manual in use) (2) En-dash or en-rule (the length of an 'n') is used to link spans. In the context of our journal en-dash should be used to link numerals, sizes, dates and page numbers (e.g., 1977–1981; figs 5–7; pp. 237–258); geographic or name associations (Murray–Darling River; a Federal–State agreement); and character states combinations such as long–pubescent or red–purple. (3) Em-dash or em-rule (the length of an 'm') should be used rarely, only for introducing a subordinate clause in the text that is often used much as we use parentheses. In contrast to parentheses an em-dash can be used alone. En-dashes and em-dashes should not be spaced.

Footnotes: Avoid footnotes in the body text of the manuscript. It is always possible to incorporate the footnote into the main text by rewording the sentences, which greatly facilitates reading. Additionally, footnotes are not always handled well by software, and their usage may cause failures in the text processing.

Geographical coordinates: It is strongly recommended to list geographical coordinates as taken from GPS or online gazetteer, or georeferencer. Geographical coordinates must be listed in one of the following formats:

Definition: The locality consists of a point represented by coordinate information in the form of latitude and longitude. Information may be in the form of

  • Degrees, Minutes and Seconds (DMS),
  • Degrees and Decimal Minutes (DDM), or
  • Decimal Degrees (DD).

Records should also contain a hemisphere (E or W and N or S) or, with Decimal Degrees, minus (–) signs to indicate western and/or southern hemispheres.

Examples:

  • Example 1: 36°31'21"N; 114°09'50"W (DMS)
  • Example 2: 36°31.46'N; 114°09.84'W (DDM)
  • Example 3: 36.5243°S; 114.1641°W (DD)
  • Example 4: −36.5243; −114.1641 (DD using minus signs to indicate southern and western hemispheres)

Note on accuracy: Because GPS units are very commonly used today to record latitude/longitude, many authors simply give the GPS readings for their localities. However, these readings are much too accurate. For example, a GPS unit might give the latitude in decimal seconds as 28°16'55.87"N. Since one second of latitude is about 30 m on the ground, the second figure after the decimal in 55.87 represents 30 cm, yet a typical handheld GPS unit is only accurate at best to a few metres.

We therefore recommend two ways to report GPS-based locations. If you give the GPS reading without rounding off, make sure you include an uncertainty figure as a context for the over-accurate GPS reading. We recommend the Darwin Core definition of uncertainty (http://rs.tdwg.org/dwc/terms/index.htm#coordinateUncertaintyInMeters):

"The horizontal distance (in meters) from the given decimalLatitude and decimalLongitude describing the smallest circle containing the whole of the Location."

If you only give the GPS reading, please round it off to an implied precision appropriate to the error in the measurement, or to the extent of the area sampled. We suggest rounding off

  • to the nearest second in degree-minute-second format (28°16'56"N), which implies roughly ± 25-30 m at middle latitudes;
  • to four decimal places in decimal degree format (28.2822°N), which implies roughly ± 10-15 m at middle latitudes;
  • to two decimal places in decimal minute format (28°16.93'N), which implies roughly 15-20 m at middle latitudes.

Altitude: Many GPS users simply record the elevation given by their GPS unit. However, GPS elevation is NOT the same as elevation above sea level. GPS units record the elevation above a mathematical model of the earth's surface. The difference between this elevation and elevation above sea level can be tens of metres. In any case, the accuracy of a GPS elevation is often the same as the usual accuracy in horizontal position, so a GPS elevation such as '753 m' is much too accurate and should be rounded off to 'ca 750 m'.

We strongly recommend the use of Example 2 (the DDM format). The other three are also possible but will be recalculated to DDM during the process of online mapping from the HTML version of the paper.

The only restriction on format is in creating a KML (Keyhole Markup Language) file. KML latitudes and longitudes must be in the DD format shown above in Example 4.

Please also consider submitting a table of localities with your manuscript, either as a spreadsheet or in CSV text format. By doing so you will make your specimen localities much more easily available for use in biodiversity databases and geospatial investigations. The geospatial table will be put online as supplementary material for your paper. A minimum table will have three fields: species (or subspecies) name, latitude and longitude. A full table will have the same data for each specimen lot as appears in the text of your paper. Please check latitude/longitude carefully for each entry.

Units: Use the International System of Units (SI) for measurements. Consult Standard Practice for Use of the International System of Units (ASTM Standard E−380−93) for guidance on unit conversions, style, and usage.

Statistics: Use leading zeroes with all numbers, including probability values (e.g., P < 0.001). For every significant F−statistic reported, provide two df values (numerator and denominator). Whenever possible, indicate the year and version of the statistical software used.

Web (HTML) links: Authors are encouraged to include links to other Internet resources in their article. This is especially encouraged in the reference section. When inserting a reference to a web-page, please include the http:// portion of the web address.

Supplementary files: Larger datasets can be uploaded separately as Supplementary Files. Tabular data provided as supplementary files can be uploaded as an Excel spreadsheet (.xls), as an OpenOffice spreadsheets (.ods) or comma separated values file (.csv). As with all uploaded files, please use the standard file extensions.

Headings and subheadings: Main headings: The body text should be subdivided into different sections with appropriate headings. Where possible, the following standard headings should be used: IntroductionMethodsResultsDiscussionConclusionsAcknowledgementsReferences. These headings need to be in bold font on a separate line and start with a first capital letter. Please do not number headings or subheadings.

  • Introduction − The motivation or purpose of your research should appear in the Introduction, where you state the questions you sought to answer, and then provide some of the historical basis for those questions.
  • Methods − Provide sufficient information to allow someone to repeat your work. A clear description of your experimental design, sampling procedures, and statistical procedures is especially important in papers describing field studies, simulations, or experiments. If you list a product (e.g., animal food, analytical device), supply the name and location of the manufacturer. Give the model number for equipment used. Supply complete citations, including author (or editor), title, year, publisher, and version number, for computer software mentioned in your article.
  • Results − Results should be stated concisely and without interpretation.
  • Discussion − Focus on the rigorously supported aspects of your study. Carefully differentiate the results of your study from data obtained from other sources. Interpret your results, relate them to the results of previous research, and discuss the implications of your results or interpretations. Point out results that do not support speculations or the findings of previous research, or that are counter-intuitive. You may choose to include a Speculation subsection in which you pursue new ideas suggested by your research, compare and contrast your research with findings from other systems or other disciplines, pose new questions that are suggested by the results of your study, and suggest ways of answering these new questions.
  • Conclusion −This should state clearly the main conclusions of the research and give a clear explanation of their importance and relevance. Summary illustrations may be included.
  • References − The list of References should be included after the final section of the main article body. A blank line should be inserted between single-spaced entries in the list. Authors are requested to include DOIs and/or links to online sources of articles, whenever possible! 

Where possible, the standard headings should be used in the order given above. Additional headings and modifications are permissible.

Subordinate headings: Subordinate headings (e.g. Field study and Simulation model or Counts, Measurements and Molecular analysis), should be left-justified, italicized, and in a regular sentence case. All subordinate headings should be on a separate line.

 

English Language Editing

This journal has well-defined policies for English language editing. 

Authors are required to have their manuscripts written in fluent English or edited by a professional English language editor BEFORE submission. Authors have to confirm by checking a tick box in the submission process that they have followed the above requirement:

"The text is edited by a professional English language editor, duly acknowledged in the manuscript. I am aware that non-edited manuscripts could be rejected prior to peer-review".

The submission process includes an option to request a professional linguistic editing at a price of EURO 15 per 1800 characters:

The authors are NOT obliged to use Journal's linguistic services, but they must ensure that their manuscripts have passed a proper linguistic editing before submission.

 

Citations and References

Citations within the text: Before submitting the manuscript, please check each citation in the text against the References and vice-versa to ensure that they match exactly.

Citations in the text should be formatted as follows:

One author: Smith (1990) or (Smith 1990)

Note: The citations format depends on the way it is incorporated within the article’s text:

Example:

  1. According to Smith (1990), these findings…
  2. These findings have been first reported in the beginning of the nineties (Smith 1990).

Two authors: Brock and Gunderson (2001) or (Brock and Gunderson 2001)

Note: When choosing between formats refer back to examples above.

Three or more authors: Smith et al. (1998) or (Smith et al. 1998)

Note: When choosing between formats refer back to examples above.

When citing more than one source, in-text citations should be ordered by the year of publication, starting with the earliest one:

(Smith et al. 1998, 2000, 2016; Brock and Gunderson 2001; Felt 2006).

Note: When you have a few citations from the same author but from different years (such as the case with Smith et al. above), the first year is taken into consideration when ordering the sources (in this case 1998, which is why Smith et al. come first in the list).

When having two or more fully identical citations (this can happen when you have more than one reference with exactly the same authors and years for one or two authors, or the same first author and year for author teams of three or more), the references are distinguished by adding the letters 'a', 'b', 'c', etc. after the years and this marking is followed in the in-text citations, respectively:

(Reyes-Velasco et al. 2018a, 2018b)

Authorship references for species should include a "," between author and year:

Brianmyia stuckenbergi Woodley, 2012.

References: It is important to format the references properly, because all references will be linked electronically as completely as possible to the papers cited. It is desirable to add a DOI (digital object identifier) number for either the full-text or title and abstract of the article as an addition to traditional volume and page numbers. If a DOI is lacking, it is recommended to add a link to any online source of an article.

List all authors cited in the References. For multiauthored papers, give all author names in full; the abbreviation "et al." is only allowed in the text. All journal titles should be spelled out completely and should not be italicized. Ensure that the References are complete and arranged according to name and year of publication. Personal communications and submitted manuscripts should be listed as unpublished results in the text and not listed in the References section.

Please use the following style for the reference list (or download the Pensoft EndNote style): here. It is also available in Zotero, when searched by journal name or by "Pensoft Journals".

Published Papers:
Polaszek A, Alonso-Zarazaga M, Bouchet P, Brothers DJ, Evenhuis NL, Krell FT, Lyal CHC, Minelli A, Pyle RL, Robinson N, Thompson FC, van Tol J (2005) ZooBank: The open-access register for zoological taxonomy: Technical Discussion Paper. Bulletin of Zoological Nomenclature 62: 210–220.

Accepted Papers:
Same as above, but ''in press'' appears instead of the year in parentheses.

Electronic Journal Articles:
Mallet J, Willmott K (2002) Taxonomy: Renaissance or Tower of Babel? Trends in Ecology and Evolution 18(2): 57–59. https://doi.org/10.1016/S0169-5347(02)00061-7

Paper within conference proceedings:
Orr AG (2006) Odonata in Bornean tropical rain forest formations: Diversity, endemicity and applications for conservation management. In: Cordero Rivera A (Ed.) Forest and Dragonflies. Fourth WDA International Symposium of Odonatology, Pontevedra (Spain), July 2005. Pensoft Publishers, Sofia-Moscow, 51–78.

Book chapters:
Mayr E (2000) The biological species concept. In: Wheeler QD, Meier R (Eds) Species Concepts and Phylogenetic Theory: A Debate. Columbia University Press, New York, 17–29.

Books:
Goix N, Klimaszewski J (2007) Catalogue of Aleocharine Rove Beetles of Canada and Alaska. Pensoft Publishers, Sofia-Moscow, 166 pp.

Book with institutional author:
International Commission on Zoological Nomenclature (1999) International code of zoological nomenclature. Fourth Edition. The International Trust for Zoological Nomenclature, London.

PhD thesis:
Dalebout ML (2002) Species identity, genetic diversity and molecular systematic relationships among the Ziphiidae (beaked whales). PhD Thesis, University of Auckland, Auckland, New Zealand.

Link/URL:
BBC News: Island leopard deemed new species http://news.bbc.co.uk/

Citations of Public Resource Databases: It is highly recommended all appropriate datasets, images, and information to be deposited in public resources. Please provide the relevant accession numbers (and version numbers, if appropriate). Accession numbers should be provided in parentheses after the entity on first use. Examples of such databases include, but are not limited to:

Providing accession numbers to data records stored in global data aggregators allows us to link your article to established databases, thus integrating it with a broader collection of scientific information. Please hyperlink all accession numbers through the text or list them directly after the References in the online submission manuscript.

All journal titles should be spelled out completely and should NOT be italicized.

Provide the publisher's name and location when you cite symposia or conference proceedings; distinguish between the conference date and the publication date if both are given. Do not list abstracts or unpublished material in the References. They should be quoted in the text as personal observations, personal communications, or unpublished data, specifying the exact source, with date if possible. When possible, include URLs for articles available online through library subscription or individual journal subscription, or through large international archives, indexes and aggregators, e.g., PubMedCentral, Scopus, CAB Abstracts, etc. URLs for pdf articles that are posted on personal websites only should be avoided.

Authors are encouraged to cite in the References list the publications of the original descriptions of the taxa treated in their manuscript.

Ordering references: All references should be ordered alphabetically by author name (but see below).

If the references have the same first author and a varying number of co-authors, the ordering should be based on the number of co-authors starting with the lowest; all articles with the same first author and two or more co-authors (thus cited as et al. in the text) should be listed chronologically, as follows:

Smith J (2018) Article Title. Journal Name 1: 1–10. https://doi.org/10.3897

Smith J, Gunderson A (2017) Article Title. Journal Name 1: 10–20. https://doi.org/10.3897 

Smith J, Gunderson A, Brock B (2011) Article Title. Journal Name 1: 20–30. https://doi.org/10.3897

Smith J, Brock B, Gutierrez R, Gunderson A (2013) Article Title. Journal Name 1: 15–30. https://doi.org/10.3897

Smith J, Brock B, Gunderson A (2015) Article Title. Journal Name 1: 10–30. https://doi.org/10.3897

If both the first author and year of publication match within the categories above, the references are distinguished by adding the letters 'a', 'b', 'c', etc. after the year of publication and this marking is followed in the in-text citations, respectively.

 

Illustrations, Figures and Tables

Figures and illustrations are accepted in the following image file formats:

  • EPS (preferred format for diagrams)
  • TIFF (at least 300dpi resolution, with LZW compression)
  • PNG (preferred format for photos or images)
  • JPEG (preferred format for photos or images)
  • GIF
  • BMP
  • SVG

Vector files in any of the following formats EPS, SVG or PDF are requested for phylogenetic trees and cladograms.

The journal is printed in B5 paper size with the maximum printing area of 128 mm × 199 mm. Whenever possible, individual figures should be prepared as composite figures.

Should you have any problems in providing the figures in one of the above formats, or in reducing the file below 20 MB, please contact the Editorial Office at journals@pensoft.net

Figure legends: All figures should be referenced consecutively in the manuscript; legends should be listed consecutively immediately after the References. For each figure, the following information should be provided: Figure number (in sequence, using Arabic numerals − i.e. Figure 1, 2, 3 etc.); short title of figure (maximum 15 words); detailed legend, up to 300 words.

Illustrations of measurable morphological traits should bear mute scale bars, whose real size is to be given in the figure captions.

Please note that it is the responsibility of the author(s) to obtain permission from the copyright holder to reproduce figures or tables that have previously been published elsewhere.

Figure citations in the text should always be with Capital "F" and En-dash for ranges. One figure with a full stop, figures without.

Example: Fig. 1, Figs 1–3, Fig. 2A–E.

Citations of figures from other publications should always be Lower Case (fig. / figs). When two subsequent figures or parts are cited (for instance figures 1 and 2 or A and B), a comma should be used.

Example:  Figs 1, 2 and Fig. 1A, B.

Parts belong to one figure.

Example: Fig. 1A, B and Fig. 2A-E.

On the use of Google Maps
All uses of Google Maps and Google Earth Content must provide attribution to Google, according to Google Maps/Earth Additional Terms of Service (see also Permission Guidelines for Google Maps and Google Earth). The attribution should be visible on each map in the form, for example: "Map data 2019 (C) Google".

Tables: Each table should be numbered in sequence using Arabic numerals (i.e. Table 1, 2, 3 etc.). Tables should also have a title that summarizes the whole table, maximum 15 words. Detailed legends may then follow, but should be concise.

Small tables can be embedded within the text, in portrait format (note that tables on a landscape page must be reformatted onto a portrait page or submitted as additional files). These will be typeset and displayed in the final published form of the article. Such tables should be formatted using the 'Table object' in a word processing program to ensure that columns of data are kept aligned when the file is sent electronically for review. Do not use tabs to format tables or separate text. All columns and rows should be visible, please make sure that borders of each cell display as black lines. Colour and shading should not be used; neither should commas be used to indicate decimal values. Please use a full stop to denote decimal values (i.e., 0.007 cm, 0.7 mm).

Larger datasets can be uploaded separately as Supplementary Files. Tabular data provided as supplementary files can be uploaded as an Excel spreadsheet (.xls), as an OpenOffice spreadsheets (.ods) or comma-separated values file (.csv). As with all uploaded files, please use the standard file extensions.

 

Taxonomic Treatments

Criteria for publication of new species descriptions

Stand-alone single species descriptions will be considered in well-studied taxa, fossils or if they represent monotypic (monophyletic) groups. Additional criteria for considering stand-alone single species descriptions will be that the species exhibits unusual characters that can change the concept of the higher taxon to which it belongs; the material is rich, providing information on the  biogeography, phylogeny, biology or ecology of the species, and there is little chance that other material from this region can be brought together within the foreseeable future; the higher taxon to which it belongs has not been reported from the (larger) geographic area where it occurs; species collected in areas of high conservation importance (Galapagos, for example); the new species is economically or medically important, being proven to be a pest, invasive species, transmitter of diseases, or otherwise. 

Stand-alone single species descriptions in poorly studied or hyperdiverse groups should be avoided, unless they are placed into the context of a review or revision, or the study provides rich data on their biology, ecology, hosts/parasite species, life cycle and immature stages descriptions and others.

The following guidelines are provided to ensure that other elements of the work follow modern standards and enable the full advantage of the ARPHA platform.

  • Types and taxonomically important specimens
    • Mandatory: Verbatim data (or photos) of the specimen label(s) put in quotes, including, if known, the collection date, name of the collector(s), (old) locality name(s), field number(s), and date of deposition in the relevant museum should be included in the specimen records as well. Include latitude, longitude, elevation, habitat, microhabitat information of primary type material. For format of geographical coordinates see section "Main text" above.
    • Mandatory: The holotype should be deposited in a publicly accessible collection. For the other types or taxonomically important specimens the deposition in public collections is strongly recommended.
    • Strongly recommended: Permanent identifiers for all type specimens and related materials. Unique identifiers are for example museum collections specimen IDs. Unique identifiers can be provided also by international taxon-based databases that do not indicate ownership, such as AntWeb.org for ants, for example.
    • Strongly recommended:  Specimen occurrence records should follow the DarwinCore standard. Data on all types and related materials should be described in accordance to the following instructions, and, additionally, in a Linked table for primary biodiversity data.
    • Strongly recommended: Details on collection permits should be included.
  • Differential diagnosis
    • Mandatory: Differential diagnoses should be short, concise and meaningful. A diagnosis should be a means of confirming the identification after using the key, or allow a reader to recognize the distinctive features of the taxon at hand. Diagnoses should describe the species and not the sample, or in other words, they should be sample-independent. A list of diagnostic character states, or a diagnostic combination of character states, along with a statement about how each character state differs from closely related, or closely similar, species.
    • Mandatory: Include all relevant congeners and cite the reference taxonomy being followed, so that others can see which species have been considered.
    • Strongly recommended: Consider presenting the differential diagnosis in a table, if long lists of differences and/or species are included. 
    • Strongly recommended: The sample size for each species should be given whenever possible, so the reader can evaluate the strength of the evidence for diagnosability. 
  • Morphological description. To the extent accepted as a minimum standard in the respective taxon group, so that to provide the diagnostic evidence that the species is new. Rich illustrative material including images, drawings, and where possible microCT should be included.
  • KeyMandatory in all cases of stand alone species description which are not put into the context of a revision; keys should help to identify the new species in relation to the closest congeners; in case of availability of a key to the species group, the new species should be placed within the key.
  • DNA-based descriptions.  Given some controversies and criticism related to  "DNA-only" or "DNA-based" descriptions, such descriptions could be considered only in special cases, e.g. in a necessity of streamlined descriptions of multiple new species in megadiverse, poorly studied taxa with strong record on the informativeness of DNA barcodes (deep divergences) and correlated external features shown on rich illustrative material.
    • Mandatory: Rich illustrative material (photos, drawings) of the voucher (type) specimens and morphological details important for the identification of the taxon under study (microCT or others). 
    • Mandatory: The reason to use mostly DNA characters for diagnosing and descriptions of new species should be justified in the Materials and Methods section of the paper. 
    • Mandatory: Explain how the new species differentiates from the previous or related species decsribed in the same paper.
    • Mandatory: Etymology and differential diagnoses are mandatory in "DNA-based" species descriptions as well.
    • Strongly recommended: Morphological descriptions are to be included in "DNA-based" descriptions as well, whenever possible. Exceptions from this rule should be justified in the Material and Methods section of the paper.
    • Strongly recommended: DNA sequences of relevant existing name-bearing types, so that it is clear to which clade(s) the existing name(s) belong. If such sequences are not available, it is mandatory to explain how previous names are applied in the manuscript. 
  • DNA sequences. 
    • Mandatory: When new sequences are reported, their GenBank/EMBL/DDBJ accession number(s) should be included in the manuscript.
    • Mandatory: In all taxa where using DNA sequences is accepted as a norm; strongly recommended in all other taxa. 
    • Strongly recommended: Use the GenSeq terms if DNA sequences of type material are reported in the manuscript (see section Sequence data below and also Chakrabarty P, Warren M, Page L (2013) GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources. ZooKeys 346: 29-41). https://doi.org/10.3897/zookeys.346.5753). See 
    • Strongly recommended: Whenever possible, DNA sequences should be made available to the editors and reviewers. 
  • EtymologyMandatory: Including Latin form for species-group epithets (adjective, noun in apposition, noun in genitive case, or "random sequence of letters" not needing accord with generic gender) and gender for genus-group names.
  • Data on biology, ecology, and biotic interactions. 
    • Mandatory: Where such data are available. 
    • Strongly recommended:  Illustrative materials (habitat photos, videos of species’ behavior, etc.).  
  • Introduction, discussion and conclusions texts or sectionsMandatory.

Sequence data

Manuscripts containing novel amino acid sequences (e.g. primer sequences) will only be accepted if they carry an International Nucleotide Sequence Databases (INSD) accession number from the European Biology Laboratory (EMBL), GenBank Data Libraries (GenBank) or DNA Data Bank of Japan (DDBJ). We strongly recommend that authors include institutional catalog numbers for specimens preserved in collections, and information identifying sequences that are derived from type specimens (see below) when they deposit data in genetic databanks. A summary table with the INSD accession [catalog] numbers should be included in either Materials and Methods or Data Resources section of the paper. If specimens were not vouchered (tissued specimens should be vouchered whenever possible!), collection locality data and possibly photographs of tissued specimens must be provided. A nomenclature for genetic sequences for types and confidently identified nontype specimens has been proposed by Chakrabarty et al. (2013); a sequence from a holotype is identified as genseq-1, one from a paratype is identified as genseq-2, one from a topotype is genseq-3, etc. The genetic marker(s) used should also be incorporated into the nomenclature (e.g. genseq-2 COI).

Examples

Table 1. Ranking Sequence Reliability. Ranking of source materials of genetic sequences based on reliability of taxonomic identification. Examples of the source material are listed in the third column with the last column providing the corresponding GenSeq nomenclature (after Chakrabarty et al. (2013)).

Reliability Ranking

Source Materials

Examples

Corresponding GenSeq Nomenclature

Highest
1st

Primary Types

Holotype, Lectotype, Syntype, Isosyntype, Neotype, Isotype

genseq-1

2nd

Secondary Types

Paratype, Paralectotypes, etc.

genseq-2

3rd

Topotypes (vouchered), or non-type specimens listed in original description or redescription

Topotype, Non-type specimen listed in original description or redescription

genseq-3

4th

Collections-vouchered non-types (not from original description or redescription)

Vouchered specimen

genseq-4

5th

Photo voucher only

No specimen voucher but photo voucher available

genseq-5

Lowest

No voucher

Non-vouchered

No classification

 

Table 2. Example Reporting Table. Examples of how links between genetic sequences and vouchers in institutional collections could be displayed as a table in publications reporting new sequences.

Species

Specimen Catalog #

GenBank #

GenSeq Nomenclature

COI

ND1

Typhleotris mararybe

LSUMZ 13636 (holotype)

HM590594

HM590606

genseq-1 COI, ND1

Paretroplus tsimoly

AMNH 229558 (paratype)

JZ590596

NA

genseq-2 COI

Nandopsis haitiensis

UMMZ 236321 (topotype)

BK590595

BK590607

genseq-3 COI, ND1

Halieutichthys intermedius

FMNH 96353 (non-type specimen voucher)

AY722169

AY722306

genseq-4 COI, ND1

Equulites absconditus

NMNH 12345PV2 (photo voucher)

NA

BG34621

genseq-5 ND1

 

International Code of Zoological Nomenclature

This journal will publish papers that strictly adhere to the rules of the last edition of the International Code of Zoological Nomenclature and its amendment. Authors are also advised to follow all recommendations of the Code and to consult the guidelines below prior to submitting the manuscript.

General: Each first mentioning of an animal species name within the text must be provided with author(s)' name(s). Year of publication of an animal species should be given in taxonomic revisions with quotation of the work providing the original species’ description in the list of references.

New names: When new taxonomic acts are proposed, they should be explicitly indicated as being new by adding the respective abbreviation after the taxon name i.e., sp. nov., comb. nov., nomen nov. Authors of newly described taxa should be given any time the taxon is mentioned, if different from the publication authors.

Examples:

  • Genus X-us Smith, new genus (author(s) of the publication and authority (-ies) of the taxon is/are identical);
  • X-us albus Jones & Peters, new species (the publication is authored by persons different in composition or combination from the authority (-ies) of the taxon itself, e.g. Smith, Jones & Peters or Peters & Jones).

We highly recommend that authors of new species are also included as co-authors of the work where the taxa are described. If the authors of the work do not want to include the authors of the taxonomic name then to be absolutely certain that the authority for the name is unequivocal there should be a statement in the work saying that these authors (of the name) are responsible for making the name available under the code (Article 50.1.2, etc.) i.e. they are responsible for coining the name and for satisfying all other criteria for availability.

New family-group names: Although all family group names are derived/based on their type genus, the type genus is to be compulsorily designated in any description of a family-group name published after 31st December 1999 (Article 16.2). It is not sufficient that the type genus is mentioned as belonging to the new family-group name; it must be stated that this is the type genus. We recommend a single type line as: Type-genus: Musca Linnaeus, 1758.

New genus-group names: The origin ("etymology", or "derivatio nominum") of name and its gender should be indicated. The type-species and the character of the proposed taxonomic act should be specified for new genus-group names. The type species name should be given in its original combination with an author and year. If the type species is now considered a junior synonym there need to be a clear mention of that. The fixation type should derive from the International Code of Zoological Nomenclature (see Articles 68 & 69; original designation, monotypy, absolute tautonymy, Linnaean tautonymy, subsequent monotypy, subsequent designation).

Example:

  • Sympycnus Loew

Type-species: Porphyrops annulipes Meigen, 1824 by subsequent designation of Coquillett (1910: 610) =pulicarius Fallen, 1823.

New species-group names: According to the ICZN Art. 11.9, but also Art. 11.3 the origin "etymology", or "derivatio nominum") new species-group names should be supplemented by information on whether the epithet is an 1) adjective or participle in the nominative singular; 2) noun in the nominative singular; 3) a noun in the genitive case; 4) an adjective used a substative in the genitive case; or 5) an arbitrary combination of letters (ICZN Art. 11.3). For species-group names, there are two separate statements of type information that are needed:

  • the statement of species’ type locality – that is the exact place whence the primary type origins, including exact collecting dataplace with geographical coordinates, geographical or political unit (Area/ District/ State) and country;also, if possible, supplementary locality information should be included – habitat type, method of collecting, date, collector’s names, host name (for parasites), etc.
  • there should be a separate statement about the type specimen, exact quotation of its original label, condition of specimen (dry pinned, in alcohol, slide, fossil, etc.) and repository (organization’s name and city).

Examples:

For a new species:

  • Type locality: USA, Virginia: Fairfax County, Kingstowne, 38°46'N, 77°07'W, broad-leaf forest, under bark, 10 July 2000, J. Smith leg.
  • Type specimen: Holotype male, pinned, with genitalia in a separate microvial. Original label: "USA, VA, Fairfax, Kingstowne, 38°46'N, 77°07'W, 12 Oct 2003, BJ & FC Thompson" "USNM ENT 00033805" [Code 49 barcode], "HOLOTYPE / Xylota / x-us / Thompson [red handwritten label].

For a previously described species:

Lectotype male, pinned … [details] here designated to fix the concept of X-us albus Jones and to ensure the universal and consistent interpretation of the same. Or … [details then] by designation of Smith (1976: 999).

Previously published names: For a previously published name, please provide the year of description. Also use the parentheses convention for subsequent new combinations.

[Etymology]

Authors of new species name should state exactly what the epithet is in terms of the ICZN, as outlined in Article 11.9.1.1 to 11.9.1.4 as well as 11.3. A name may be a word in or derived from Latin, Greek or any other language (even one with no alphabet), or be formed from such a word. In short, a name can be declared as arbitrary combination (the best solution) or must be or be treated as:

  1. I) a word of two or more letters, or a compound word, and, if a Latin or latinized word must be, or be treated as:
  1. an adjective or participle in the nominative singular (as in Echinus esculentusFelis marmorataSeioptera vibrans), or
  2. a noun in the nominative singular standing in apposition to the generic name (as in Struthio camelus, Cercopithecus diana), or
  3. a noun in the genitive case (e.g. rosaesturionisthermopylarumgalliaesanctipaulisanctaehelenaecuvierimerianaesmithorum), or
  4. an adjective used as a substantive in the genitive case and derived from the specific name of an organism with which the animal in question is associated (as in Lernaeocera lusci, a copepod parasitic on Trisopterus luscus).
  1. II) An adjectival species-group name proposed in Latin text but written otherwise than in the nominative singular because of the requirements of Latin grammar is available provided that it meets the other requirements of availability, but it is to be corrected to the nominative singular if necessary.

Arranging sections within species treatments (sections in square brackets are requested for new descriptions only!):

[Name]
[Material]
    - [Type material]
    - Other material
[Diagnosis]
[Description]
[Etymology]
Distribution
Ecology (including phenology)
Conservation status (optional, we encourage authors to follow the IUCN categories and criteria, please see http://www.iucnredlist.org/static/categories_criteria_3_1#critical))
Discussion (optional, but very desirable)

 

Materials Examined Formatting Guidelines

Authors are strongly encouraged to adhere to the new fine-grained formatting of the material examined (species occurrence records) as shown below. Please note that this new fine-grained formatting is NOT COMPULSORY and is introduced for testing for an undefined period, during which we hope to receive your feedback. Nonetheless, it is recommended to follow the guidelines to ensure accurate conversion of your records to XML and consequent indexing in GBIF, Plazi, and other important resources. Indexing of each individual occurrence record in GBIF and linking back to your article will provide much higher visibility, data usability, dissemination, and citation probability of your work! Adapted from: CETAF best practices in electronic publishing in taxonomy (https://doi.org/10.5852/ejt.2018.475). 

Order

Each material citation is composed of diverse data fields (material, locality, date, etc.) that are tagged, using Darwin Core (DWC) terms. To efficiently perform this, it is important to ensure that the different fields of a material citation are consistently presented in the same order throughout the article or, at the very least, within a taxon treatment.

The preferred order is as follows:

COUNTRY • specimens [e.g. 1 ♂ (or M, or male), size]; geographic/locality data [from largest to smallest]; coordinates; altitude/elevation/depth [using alt./m a.s.l. etc.]; date [format: 16 Jan. 1998]; collector [followed by "leg."]; other collecting data [e.g. micro habitat/host/method of collecting]; barcodes/identifiers [e.g. GenBank: MG779236]; institution code and specimen code [e.g. CBF 06023].

For botanical and mycological data, please use "Collection number" instead of "collector [followed by "leg."]". The collection number encompasses all gatherings from a single specimen (e.g., leaves, flowers, piece of wood) which may be preserved on different herbarium sheets and in different herbaria.

The preferred format for botanical/mycological data should be as follows:

GABON - Estuaire • J.J. Wieringa et al. 6543 (IEC, K, LBV, MO, P (P01234567), US, WAG (WAG0012345, WAG0012346, wood: WAG0012347, fl in spirit: WAG0012348)); 35 km NE of Libreville; 0°38.8'N, 9°58.9'E; alt. 30 m; 12 Feb. 2017; fl • E.L.A.N. Simons 1212 (P, LBV, WAG (WAG0987654), Z); Libreville, Sibang arboretum; 0°27.8'N 9°29.4'E; alt. 16 m; 15 Jul 2017; fr. - Ogooué-Maritime • J.J. Bos 10123 (P, WAG); around Port Gentil; 0.82°S, 8.80°E; alt. 5 m; 4 Apr 1986; fl, fr.

Punctuation

A bullet point (• [unicode: 2022]) is used to signify the beginning of a material citation. Within each citation, the different fields are delimited by a semicolon. A single field can be composed of several elements, which are separated by commas (e.g. the details region, area, town and street for the ‘locality’ field).

Semicolons should not be used elsewhere in a material citation.

Repetitive data

Authors can indicate repetitive data with indications such as "same data as for holotype", "same data as for preceding", "same locality", "ibid", etc. as long as the same method and wording are used consistently throughout the paper.

If a material citation is identical to another with only one or two differences, the exceptions should be listed after the mention of repeated data e.g.:

‘Missing’ elements

It is not necessary to include information such as "no date" or "no locality data"; just list the elements that are available.

Label citations

We recommend including photos of labels as figures if they contain data that cannot be standardised. Double quote marks (" ") must be used to represent label citations that do not correspond to (or cannot be reliably interpreted as) specific DWC terms. This data will simply be parsed as a verbatim citation.

Only quote marks should be used to present verbatim label data and they should not appear elsewhere in a material citation.

Author interpretation

Use square brackets [ ] to distinguish data that has been interpreted by the author e.g., coordinates interpreted from a locality, or translations of label data:

Data fields

The different data fields that are tagged in a material citation are explained below, along with the formatting needed to achieve maximum output and precision.

Any specimen data presented in a separate table cannot be linked back to the citation and tagged for conversion.

Country (country / waterBody)

The citations must be listed by either country or water body, using a separate paragraph for each new zone. Countries should be listed in alphabetical order. If another method is used (e.g. geographic groups) please state this in the Material and Methods section.

If the material is organised by region, please use the following format:

Material (organismQuantity / organismQuantityType / sex / typeStatus)

This field comprises several indications about the specimens cited: numbertype (e.g. specimen, juv., shell, excuviae), sex and type status. All subsequent elements of a citation will be applied to the specimens presented in this field.

Locality (higherGeography)

The locality data is listed from least to most specific, using commas to divide each detail. It is recommended to employ the English name in current usage where possible.

If there is a particular reason to use a different system, e.g. spelling/transcription variations or archaic names, such details should preferably be identified using quotes, with their current names given in square brackets, but this is not mandatory.

Geo-coordinates (decimalLatitude / decimalLongitude)

Diverse formats are accepted but it is important to include the degrees symbol (° [unicode: 00B0]), which distinguishes the data as a geo-coordinate. It is also preferable to include the direction (N/E/S/W):

  •  degrees minutes seconds: 40°26'46"N, 79°58'56"W
    ●    degrees decimal minutes: 40°26.767'N, 79°58.933'W
    ●    decimal degrees: 40.446°N, 79.982°W

Geo-coordinates should be presented to a maximum of 5 decimal places.

Altitude/elevation/depth (verbatimAltitude / verbatimDepth)

This type of measurement should be explicit in the material citations, e.g.:

  •  Altitude: alt. 489 m or 547 m a.s.l.
    ●    Depth: depth 20 m

Collection date (eventDate)

Format: d(d) Mmm. YYYY

Date ranges should be shown with an n-dash, e.g.:

Jan.–Mar. 2018 / 5 Feb.–6 Apr. 2016 / 14 Dec. 2008–3 Feb. 2009 / 1950–1953

Collector (recordedBy)

The name(s) of the collector(s) should always be followed by "leg."; for institutions or collecting programmes, "exped." can be used, e.g. MNHN exped.

For botanical and mycological data, "Collection number" instead of "collector [followed by "leg."]". The collection number encompasses all gatherings from a single specimen (e.g., leaves, flowers, piece of wood) which may be preserved on different herbarium sheets and in different herbaria.

Additional data

Ideally, the data fields identified above should be listed before other collection data. If you choose to use a different order, it is important to be as consistent as possible throughout the paper, or at least within a single treatment. You may use a semicolon to separate the additional data into appropriate fields, e.g.:

Additional data can also be given in the appropriate field between brackets, e.g.:

Associated sequences

Accession numbers and barcodes should be identified as such, e.g.:

GenBank: U34853.1

Repository data (institutionCode / catalogNumber)

The repository data field should be composed of an institution acronym and a catalogue number (where available), using a colon to separate the two elements.

Institution acronym

All acronyms for repositories must feature in a distinct list in the Materials and Methods section, under the title Repositories, Institutional acronyms or Institutional abbreviations.

Specimen code

The specimen/catalogue code(s) should be listed after the institution code.

Where a specimen code is available, it should be explicit which specimen it refers to. This guarantees unambiguous interpretation, both by readers and upon XML conversion.

E.g., in the citation below, we cannot distinguish which specimens are catalogued under which code:

NAMIBIA • 2 ♂♂, 4 imm.; Grootfontein, Nosib Cave; 8 Feb. 1995; SEGL leg.; SAMC B7732, B8870.

This citation should be presented as follows:

NAMIBIA • 2 ♂♂; Grootfontein, Nosib Cave; 8 Feb. 1995; SEGL leg.; SAMC B7732 • 4 imm.; same data as for preceding; SAMC B8870.

Exceptions:

  1. If several specimens share the same code, e.g.:

SOUTH AFRICA • 2 ♀♀, 4 imm.; same data as for preceding; SAMC B8890.

  1. If the specimens possess identical data, including the sex, their specimen codes can be given together, e.g.:

SOUTH AFRICA • 5 ♂♂; Windhoek, Daan Viljoen Game Reserve; 22°32′16.14″ S, 16°54′44.16″ E; 12 Aug. 2005; G. Binford leg.; NMNW 45845, 4590 to 4593 • 4 ♂♂; Northern Cape Province, Eselsfontein, south of Grootdrink; 28.62° S, 21.68° E; 13 Nov. 2005; M. Burger, P. Braad and A. Hill leg.; PPRI 2009/3830 to 3833.

Ranges & multiple specimens

Use the word "to" in order to show a range of specimen numbers. E.g.:

NHMUK 213584 to 213595

 

Materials and Methods

In line with responsible and reproducible research, as well as FAIR (Findability, Accessibility, Interoperability and Reusability) data principles, we highly recommend that authors describe in detail and deposit their science methods and laboratory protocols in the open access repository protocols.io.

Once deposited on protocols.io, protocols and methods will be issued a unique digital object identifier (DOI), which could be then used to link a manuscript to the relevant deposited protocol. By doing this, authors could allow for editors and peers to access the protocol when reviewing the submission to significantly expedite the process.

Furthermore, an author could open up his/her protocol to the public at the click of a button as soon as their article is published.

Stepwise instructions:

  1. Prepare a detailed protocol via protocols.io.
  2. Click Get DOI to assign a persistent identifier to your protocol.
  3. Add the DOI link to the Methods section of your manuscript prior to submitting it for peer review.
  4. Click Publish to make your protocol openly accessible as soon as your article is published (optional).
  5. Update your protocols anytime.

 

Supplementary Files

Online publishing allows an author to provide datasets, tables, video files, or other information as supplementary information, greatly increasing the impact of the submission. Uploading of such files is possible in Step 6 of the submission process.

The maximum file size for each Supplementary File is 20 MB.

The Supplementary Files will not be displayed in the printed version of the article but will exist as linkable supplementary downloadable files in the online version.

While submitting a supplementary file the following information should be completed:

  • File format (including name and a URL of an appropriate viewer if format is unusual)
  • Title of data
  • Description of data

All supplementary files should be referenced explicitly by file name within the body of the article, e.g. 'See supplementary file 1: Movie 1" for the original data used to perform this analysis.

Ideally, the supplementary files should not be platform-specific, and should be viewable using free or widely available tools. Suitable file formats are:

For supplementary documentation:

  • PDF (Adobe Acrobat)

For animations:

  • SWF (Shockwave Flash)

For movies:

  • MOV (QuickTime)
  • MPG (MPEG)

For datasets:

  • XLS (Excel spreadsheet)
  • CSV (Comma separated values)
  • ODS (OpenOffice spreadsheets)

As for images, file names should be given in the standard file extensions. This is especially important for Macintosh users, since the Mac OS does not enforce the use of standard file extensions. Please also make sure that each additional file is a single table, figure or movie (please do not upload linked worksheets or PDF files larger than one sheet).