CSE Guidelines for Marine Biology
A complete application of Council of Science Editors (CSE) citation conventions to marine biology, oceanography, fisheries science, and aquatic ecology — covering Name-Year and Citation-Sequence systems, every source type from journal articles to datasets and field reports, binomial nomenclature in citations, and the formatting details that distinguish correct scientific referencing from approximate compliance.
CSE formatting errors are one of the most consistent sources of lost marks in marine biology assignments — not because the science is wrong, but because citation conventions in the natural sciences are specific, the details matter, and most students apply them from memory rather than from the actual guidelines. A comma in the wrong position, a journal name in the wrong case, a volume number formatted as “Vol. 45” instead of “45” — none of these are large errors in isolation, but they accumulate into a reference list that signals either carelessness or unfamiliarity with scientific writing standards, both of which your professor will notice. This guide applies Council of Science Editors (CSE) guidelines specifically to marine biology, with worked examples drawn from the actual literature of the discipline.
What CSE Is and Why Marine Biology Uses It
The Council of Science Editors (CSE) publishes Scientific Style and Format: The CSE Manual for Authors, Editors, and Publishers, currently in its 8th edition. It is the authoritative style guide for biological sciences writing and citation — covering everything from number formatting and unit abbreviations to the construction of reference lists for every source type a scientific paper might cite. Within marine biology specifically, CSE is the default citation system for course papers and is the basis for the citation conventions of many of the discipline’s most important journals, including Marine Ecology Progress Series, Coral Reefs, Journal of Experimental Marine Biology and Ecology, and Estuarine, Coastal and Shelf Science.
Understanding why CSE is used in marine biology — rather than simply memorising its rules — makes applying it more reliable. Scientific citation systems serve two functions: they give credit to the researchers whose work is being built upon, and they provide a reproducible trail that allows readers to locate every source cited. CSE’s Name-Year system fulfils the second function particularly well for biological sciences because it places the source date immediately in the text — allowing readers to assess, at a glance, whether a claim is based on recent findings or older foundational work, which matters substantially in a field where understanding of, for example, coral bleaching thresholds or species distribution has shifted considerably over the past two decades.
The Three CSE Documentation Systems — Which One to Use
CSE offers three distinct documentation systems. Each produces a different in-text citation format and a different reference list organisation. The choice between them is determined by your professor’s instructions, the journal you are submitting to, or — where neither specifies — by disciplinary convention. For marine biology course papers, Name-Year is the default. Understanding all three prevents confusion when encountering different formats in the published literature you are reading and citing.
A third system exists — Citation-Name (C-N) — which assigns numbers to sources in alphabetical order. In-text, sources are cited by their number (like C-S) but the reference list is alphabetical (like N-Y). It is rarely used in marine biology or ecology contexts and is not covered in depth here. If your assignment specifies C-N, the reference list construction rules are identical to N-Y (alphabetical), but in-text citations are numbers, not author-year parentheticals.
CSE Name-Year In-Text Citations — Complete Rules with Marine Science Examples
In-text citations in CSE Name-Year format place the author’s surname and the publication year directly in the text, either within parentheses at the end of a sentence or clause, or integrated into the sentence when the author’s name is part of the grammatical structure. The format is specific and differs from APA in several details that frequently cause errors when students switch between the two styles.
One Author — Basic Format
Cite by surname and year, no comma between them. Place in parentheses at the end of the relevant clause or sentence, or integrate into the sentence text. Both positions are correct: “Coral bleaching events have increased in frequency over the past three decades (Hughes 2003)” — or — “Hughes (2003) documented a significant increase in bleaching frequency across the Great Barrier Reef.” In the second form, only the year goes in parentheses; the name is part of the sentence. Note the absence of a comma between “Hughes” and “2003” — this is a defining difference from APA (which requires a comma) and a consistent source of deduction in CSE papers.
Two Authors
List both surnames joined by “and” (not “&” — the ampersand is APA convention, not CSE). In parentheses: (Hughes and Connell 1999). Integrated: “Hughes and Connell (1999) showed that…” The word “and” rather than “&” applies both in parenthetical and in-text integrated citations. This is another common error when writers apply APA muscle memory to CSE papers.
Three or More Authors — “et al.”
For three or more authors, use the first author’s surname followed by “et al.” (not italicised in CSE). Note that “et al.” includes a period after “al” — this is an abbreviation of “et alii” (and others). Example: (Hoegh-Guldberg et al. 2007) or Hoegh-Guldberg et al. (2007). The period after “al.” is required. If using “et al.” at the end of a sentence before a full stop: “…were documented by Hoegh-Guldberg et al. (2007).” — only one period is needed because the abbreviation period serves double duty.
Multiple Citations in One Parenthesis
When citing multiple sources supporting the same claim, list them in chronological order (oldest first), separated by semicolons within a single pair of parentheses: (Orr et al. 2005; Doney et al. 2009; Feely et al. 2009). If two sources share the same year, list alphabetically: (Hoegh-Guldberg et al. 2007; Hughes et al. 2007). Do not use separate parenthesis for each source in a run — (Orr et al. 2005)(Doney et al. 2009) is incorrect. A single set of parentheses with semicolons is the CSE convention.
Same Author, Multiple Works, Same Year
When the same author published multiple works in the same year that you are citing, distinguish them with lowercase letters immediately after the year, with no space: (Hughes 2003a) and (Hughes 2003b). The letters are assigned in the order the works are listed in the reference list (alphabetical by title). Ensure the reference list entries match exactly: “Hughes TP. 2003a. Title…” and “Hughes TP. 2003b. Title…” — the letter must appear in both the in-text citation and the reference list entry.
No Author — Institutional or Corporate Author
When the source has a corporate, institutional, or government author rather than a named individual, use the institution’s name (abbreviated if a standard abbreviation exists) as the author in-text: ([NOAA] 2022) or ([IPCC] 2021). The square brackets around the abbreviation in the reference list signal that it is an abbreviation of the full institution name; in-text citations may use the abbreviation alone after first use. When the issuing institution is the only authoring entity and has no individual name associated, this is the correct format.
Citing a Specific Page or Figure
When citing a specific page, figure, table, or equation within a source — as when quoting directly or referring to a specific data point from a large study — include the locator after the year: (Hughes 2003, p 1240) or (Hoegh-Guldberg et al. 2007, Figure 2). Note: CSE uses “p” not “p.” for page (no period after p), and “pp” for a page range: (Smith 2015, pp 45–47). Direct quotation in marine biology papers is rare — the convention is to paraphrase and cite — but when a specific methodological description or exact value needs attribution to a precise location, the page locator format applies.
Personal Communications, Unpublished Data, and In Preparation
Personal communications (emails, conversations) and unpublished data are cited in-text but not included in the reference list (because they are not independently retrievable). Format: (J. Smith, Department of Marine Biology, personal communication, 2023 Mar 15). The full date is given because personal communications cannot be otherwise located. “In preparation” manuscripts are cited similarly in-text: (Hughes et al., in preparation) — italicise “in preparation.” Both should be used sparingly; peer-reviewed published sources are strongly preferred for any significant claim.
CSE Citation-Sequence Format — When and How to Apply It
Although Name-Year is the default for most marine biology course papers, Citation-Sequence (C-S) appears in some marine pharmacology, marine biotechnology, and biomedical marine science journals. If your assignment brief or target journal specifies C-S, the in-text mechanics are different but the reference list content (what information is included for each source type) is identical — only the reference list ordering changes from alphabetical to order-of-appearance.
In-Text Format — C-S
Sources are cited by number — either superscript (1) or in brackets ([1]) — immediately following the relevant clause or sentence. The number is assigned the first time a source appears in the text and used for every subsequent citation of that same source. “Coral bleaching has increased in frequency over the past two decades.1 Temperature anomalies above 1°C above the seasonal maximum trigger bleaching responses.2,3“
Multiple sources at the same location are listed as a comma-separated range where consecutive: 1–3 (for references 1, 2, and 3) or 1,4,7 (for non-consecutive references 1, 4, and 7).
The number appears as superscript directly after the punctuation mark in some journal styles, or before it in others — check the specific journal’s author guidelines. For course papers, follow your professor’s specification; superscript after the full stop is the most common marine science convention.
Reference List — C-S Order
In Citation-Sequence, the reference list is numbered and ordered by first appearance of the source in the text — Reference 1 is the first source cited anywhere in the paper (usually in the Introduction), Reference 2 is the next new source cited, and so on. The reference list is not alphabetical.
The content of each reference entry — what information is included and how it is formatted — is identical to Name-Year. The only differences are the number at the start and the non-alphabetical ordering.
Once a source is assigned a number (e.g., Hughes 2003 = reference 7), every subsequent citation of that source in the text uses the same number (7 or 7). It does not get a new number if cited again in a different section.
Reference List Construction — The General Rules Governing All Entry Types
Before covering individual source types, understanding the general architectural rules that govern every CSE reference list entry prevents systematic formatting errors. These rules apply regardless of whether you are citing a journal article, a book, a dataset, or a government report — and several of them differ specifically from APA conventions in ways that catch students who have recently switched styles.
Author Name Format
Last name followed by initials (no periods between initials, no spaces): “Hughes TP” not “Hughes, T.P.” Multiple authors are separated by commas with no “and” before the final author in the reference list (unlike in-text). Up to 10 authors listed; 11+ listed as first 10 followed by “, et al.”
Title Case Rules
Article, chapter, and report titles: sentence case — only the first word, proper nouns, and the first word after a colon are capitalised. Journal, book, and database names: title case (all major words capitalised) and italicised. This is the opposite of APA, where article titles are also sentence case but journal names are title case AND italicised in the same way.
Italics Rules
Journal names, book titles, database names: italicised. Article titles, chapter titles, report titles: not italicised. Species names within titles: italicised (biological convention overrides title formatting rules). Volume numbers: not italicised. “et al.” in reference lists: not italicised (it is italicised in some other styles).
Volume and Issue Numbers
Volume number appears immediately after the journal name with no label (“Vol.” is not used): Marine Ecology Progress Series. 400:45–62. Issue number in parentheses directly after volume with no space: 400(3):45–62. Pages follow a colon directly. No space before or after the colon. No “pp” before page numbers in journal citations.
DOIs and URLs
DOIs should be included for all sources that have them, formatted as full URLs: https://doi.org/10.1038/nature09444. If no DOI exists, include the URL of the online source. Include an access date for any online source whose content could change: “Accessed 2024 Jan 15.” For stable published articles with a DOI, no access date is needed.
Section Heading
The reference list section is headed “References Cited” in CSE — not “References,” “Bibliography,” or “Works Cited.” These last two are humanities style conventions. “References Cited” signals that every entry in the list corresponds to an in-text citation, and that sources consulted but not cited are excluded (unlike a bibliography, which includes all sources consulted).
Citing Journal Articles — Marine Science Worked Examples
Journal articles are the primary source type in marine biology research papers, and their CSE formatting is the most important to apply correctly. The structure is consistent across all journal article types: Author(s). Year. Article title. Journal Name. Volume(Issue):Pages. DOI.
CSE permits but does not require journal name abbreviation. Major academic journals have standard abbreviations (registered in the ISSN portal and the NLM catalog): Marine Ecology Progress Series → Mar Ecol Prog Ser; Journal of Experimental Marine Biology and Ecology → J Exp Mar Biol Ecol; Coral Reefs → Coral Reefs (no standard abbreviation shorter than the full name). The critical rule is consistency: use either full names or standard abbreviations throughout the reference list — never mix the two formats within the same document.
For undergraduate course papers, using the full journal name is the safest approach — abbreviations require knowing the correct NLM abbreviation for each journal, and an incorrect abbreviation is worse than the full name. The full name is always verifiable against the source you are citing.
Books, Book Chapters, and Edited Volumes — Marine Biology Applications
While journal articles dominate marine biology reference lists, books and edited volumes appear for foundational ecological theory, statistical methods, species identification guides, and multi-author synthetic volumes. CSE formats these differently depending on whether you are citing the entire book or a specific chapter within an edited volume.
Datasets, Databases, and Repositories — Critical for Marine Science
Marine biology research increasingly relies on publicly archived datasets — coral bleaching records in NOAA CoRIS, sea surface temperature data from AVHRR and MODIS satellite products, species occurrence data from GBIF, genomic sequences from NCBI GenBank, and oceanographic datasets from the World Ocean Database. Citing these correctly is both a CSE requirement and a scientific transparency obligation — data citations allow other researchers to access and verify the exact dataset version underlying published findings.
Government Reports, Agency Publications, and Grey Literature
Marine biology research draws on government and intergovernmental sources that sit outside the peer-reviewed journal literature: IPCC reports on sea-level rise and ocean warming, NOAA fisheries stock assessments, FAO global fisheries statistics, IUCN Red List assessments, Convention on Biological Diversity national reports, and regional marine protected area assessments from bodies such as IUCN or the Reef Check Foundation. These sources are collectively termed grey literature — formally produced, authoritative publications that are not peer-reviewed in the conventional journal sense.
Online Sources, Websites, and Digital Marine Science Resources
Marine science research increasingly draws on high-quality digital resources that exist only online — monitoring programme portals, real-time oceanographic data dashboards, coral reef mapping databases, and satellite data products. CSE provides citation formats for these sources, though the general principle that peer-reviewed primary literature should be preferred wherever it exists remains applicable. Online sources are appropriate for: real-time or frequently updated data with no equivalent journal publication; institutional monitoring reports not published in traditional formats; and definitional or taxonomic resources that serve as authoritative databases.
Organisation or Programme Website
Format: [Organisation Abbreviation]. Year [updated]. Page or resource title [Internet]. Location: Publisher. Available from: URL. Accessed: Date.
[AIMS]. 2023 [updated 2023 Oct]. Australian Institute of Marine Science long-term monitoring program [Internet]. Townsville (Australia): Australian Institute of Marine Science. Available from: https://www.aims.gov.au/monitoring. Accessed 2024 Jan 12.
Citizen Science and Monitoring Platform Data
Reef Check, CoralNet, MERMAID, and similar platforms produce citable data outputs. Treat as datasets with the platform as the publisher.
Reef Check Foundation. 2022. Reef Check survey data for Great Barrier Reef zone, 2020–2022 [dataset]. Pacific Palisades (CA): Reef Check Foundation. https://www.reefcheck.org/tropical-program/tropical-data/. Accessed 2024 Jan 18.
FishBase, WoRMS, Ocean Biodiversity Information System
Taxonomic and biodiversity databases are cited with the database as publisher and the specific record’s stable URL or DOI. Include the access date because taxonomic treatments are periodically revised.
Froese R, Pauly D, editors. 2023. FishBase [Internet]. Available from: https://www.fishbase.org. Accessed 2024 Feb 8.
Unreviewed Preprint Articles
Preprints are citable in CSE but must be identified as such. Include the repository name, preprint server identifier, and a note that it is a preprint not yet peer-reviewed. Use only for very recent work not yet available in peer-reviewed form.
Smith J, Jones A. 2024. Thermal tolerance thresholds in Indo-Pacific Acropora [preprint]. ESSOAr. https://doi.org/10.22541/essoar.xxxxx. Accessed 2024 Mar 1.
Theses, Dissertations, and Conference Papers
Marine biology research papers at advanced undergraduate and postgraduate level frequently engage with the primary research published in theses and dissertations — particularly for regional or site-specific fieldwork that has not been published in journals. Conference papers, symposium proceedings, and published conference abstracts are also cited in marine science, especially for cutting-edge work presented before journal publication.
Species Names and Binomial Nomenclature in CSE Marine Biology Citations
Binomial nomenclature — the Linnaean system of genus and species names — operates under formatting conventions that exist independently of citation style and apply throughout a marine biology paper. The interaction between these biological naming conventions and CSE citation formatting creates specific questions that arise frequently in marine science papers: how species names appear in reference titles, how taxonomic revisions are cited, and how newly described species are referenced when the original description is the primary source.
Species Name Formatting Rules — Biology Overrides Citation Style
Binomial names are always italicised: genus capitalised, species in lower case — Porites lobata, Acropora millepora, Halimeda opuntia. This convention applies everywhere in the paper — in the body text, in figure captions, in table headers, and in reference list titles. The fact that CSE formats article titles in sentence case (not italics for the article title text itself) does not override the biological requirement to italicise species names within those titles.
After first full mention in a section, the genus may be abbreviated to its initial: A. millepora, P. lobata. Never abbreviate on first mention. If two genera with the same initial letter appear in the same section, spell both out in full to avoid ambiguity — do not use the same abbreviation for both.
Author names appended to species binomials (taxonomic authority citations) — e.g., Acropora millepora (Ehrenberg, 1834) — are not italicised and are placed in parentheses if the species was originally described under a different genus. These authority citations are standard in taxonomic papers but are omitted in most ecological research papers unless the taxonomic identity of the organism is central to the paper’s argument or the species has recently been synonymised or reclassified.
When citing the primary taxonomic description as a reference — the paper in which a species was originally formally described — treat it as any other journal article citation in CSE format. The species name within the reference title retains its italics.
Citation Styles of Leading Marine Science Journals
While CSE Name-Year is the appropriate format for marine biology course papers, understanding how leading journals modify or adapt these conventions helps students read the published literature critically and prepares them for graduate-level writing where journal-specific formatting becomes important. Each journal publishes author guidelines specifying its citation requirements; the formats below reflect those guidelines as of the time of writing.
The Most Common CSE Errors in Marine Biology Papers
Reference list errors in marine biology papers follow predictable patterns — the same mistakes recur because they reflect specific misunderstandings or confusions between CSE and other citation styles students have previously used. The following are the errors most frequently noted in feedback on undergraduate and postgraduate marine biology papers, with the specific correction for each.
Comma Between Author and Year
Writing “(Hughes, 2003)” instead of “(Hughes 2003).” The comma between author and year is APA convention, not CSE. In CSE Name-Year there is no comma between the author surname and the year — in either the in-text citation or the reference list entry. This error is overwhelmingly the most frequent in papers written by students transitioning from social science APA courses to biology CSE courses. The reference list entry reads: “Hughes TP. 2003.” — no comma after “Hughes TP.”
Title Case in Article Titles
Formatting article titles in title case — capitalising every major word — when CSE requires sentence case for article, chapter, and report titles. “Coral Reefs Under Rapid Climate Change and Ocean Acidification” should be “Coral reefs under rapid climate change and ocean acidification.” Only the first word, the word after a colon, and proper nouns are capitalised. This includes ocean names (Pacific Ocean), species names (Acropora millepora), and place names (Great Barrier Reef) but not general biological terms (“bleaching,” “reef,” “coral”) regardless of their importance to the paper.
Italicising Article Titles Instead of Journal Names
Italics apply to journal names, book titles, and database names — not to article or chapter titles. Writing Coral reefs under rapid climate change and ocean acidification with the article title in italics is incorrect. The article title is in roman type, sentence case. Science — the journal name — is in italics. Many students confuse which element gets italics, particularly when formatting from memory.
“Vol.” Before Volume Numbers
Writing “Science. Vol. 301(5635):929–933” instead of “Science. 301(5635):929–933.” CSE does not use “Vol.” before the volume number in journal citations. The volume number follows the journal name directly, separated only by a period and a space. Issue number follows in parentheses with no space between the volume number and the opening parenthesis: “301(5635)” not “301 (5635)” and not “Vol. 301(5635).”
Using Full First Names Instead of Initials
Writing “Hughes, Terry P.” or “Hughes, T.P.” instead of “Hughes TP.” CSE reference list entries use surname followed by initials with no periods between initials and no space between them. No comma between surname and initials. The format “Hughes TP” is correct; “Hughes T. P.” (with periods), “Hughes, T.P.” (with comma and periods), and “Terry P. Hughes” (with first name) are all incorrect for CSE reference lists.
Italicising “et al.” in the Reference List
In many other citation styles and general academic writing, “et al.” is italicised as a Latin abbreviation. In CSE, “et al.” in both in-text citations and reference list entries is in roman type — not italicised. The confusion arises because some style guides (including some versions of APA) do italicise it. In CSE: (Hoegh-Guldberg et al. 2007) and “Hoegh-Guldberg O, … et al.” — not “et al.” in italics in either position.
Heading the Reference List “References” or “Bibliography”
The correct CSE heading is “References Cited” — not “References,” “Bibliography,” “Works Cited,” or “Literature Cited” (the last being a common biology alternative but not the standard CSE heading). “Bibliography” implies a list of all sources consulted, whether cited or not — a humanities convention. “References Cited” signals that the list contains exactly and only the sources cited in the text, which is the CSE standard.
Missing or Incorrect DOI Format
Including a DOI in the old “doi:10.1038/…” format instead of the current recommended full URL format “https://doi.org/10.1038/…” — or omitting the DOI entirely for sources that have one. Since 2017, the standard DOI format in reference lists is the full resolvable URL: https://doi.org/ followed by the DOI string. The old “doi:” prefix without the https:// is technically functional but no longer the recommended format in CSE 8th Edition guidance. Always include DOIs for journal articles — they are now a standard component of the reference entry.
Building a Complete CSE Reference List — The End-to-End Process
A correctly formatted CSE reference list is not assembled by formatting each source individually and then combining them. It is built as an integrated document with consistent formatting decisions applied across all entries. The following workflow produces reference lists that are consistent, complete, and correctly ordered — the three criteria against which professors check them.
Step 1 — Export From Your Reference Manager in CSE Format
Zotero, Mendeley, and EndNote all support CSE output. In Zotero, select all cited sources, choose “Create Bibliography from Items,” and select “Scientific Style and Format (CSE Name-Year)” as the citation style. This produces a formatted reference list that is 80–90% correct. The remaining 10–20% requires manual review because reference managers cannot apply every nuance of CSE formatting automatically — particularly for unusual source types, non-standard author configurations, and sources with missing metadata fields. Never submit a reference manager output without reviewing it against the rules above.
Step 2 — Verify Alphabetical Order
Confirm the list is alphabetical by first author surname. Hyphenated surnames (Hoegh-Guldberg) are alphabetised by the full hyphenated surname, treating the hyphen as if it were absent — so “Hoegh-Guldberg” files under “H” as “Hoeghguldberg.” Institutional authors ([NOAA], [FAO], [IPCC]) are alphabetised by the abbreviation within the brackets. Check that multiple works by the same first author are ordered chronologically: Hughes 2003 before Hughes 2017. Same-author, same-year works are ordered alphabetically by title: Hughes 2003a, Hughes 2003b.
Step 3 — Cross-Check Every In-Text Citation Against the Reference List
Every source cited in the text must appear in the reference list, and every entry in the reference list must be cited in the text. Discrepancies in both directions are common: sources cited in a draft that were later removed from the text but not from the reference list (phantom references); sources added to the reference list during writing that were never actually cited in text (orphaned references). Read through the paper and tick off each in-text citation against the reference list. Any that do not match exactly — including spelling of author names and years — need correction in whichever location contains the error.
Step 4 — Verify DOIs and Check Source Access
Click or copy every DOI in your reference list to confirm it resolves to the correct article. DOI typos are common and produce broken links. For sources without DOIs, verify the URL is current and accessible. For a paper with 20–40 references, this takes ten minutes and prevents the embarrassment of citing sources with broken identifiers — which your professor may check during grading. If a DOI resolves to a different article than the one you cited, the entire citation is incorrect and must be identified and fixed.
Step 5 — Final Consistency Check Against the Eight Common Errors
Run through the eight common errors listed above as a final checklist: no commas between authors and years; sentence case in article titles; italics only on journal and book names; no “Vol.” prefix; initials-only for author first names; “et al.” not italicised; heading reads “References Cited”; all DOIs in https://doi.org/ format. A reference list that passes this checklist will receive full marks for citation formatting in any marine biology assignment requiring CSE.
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