Version 2.0 · Updated October 2026

From first draft to reviewer response

A quantitative ecology manuscript often grows into a small project: equations and proofs, figures and tables, a supplement, separate references, and a response letter that must point to the right lines. This template keeps those parts connected while making the files easier to edit.

Download the complete template ↓ Read the full guide →

Upload the ZIP to Overleaf as a new project, or build it locally with pdfLaTeX, latexmk and Biber. All examples are illustrative; the download contains no manuscript text or actual reviewer correspondence.

What changed in this version

The original template solved several small but recurring problems in writing ecology papers. This version develops that workflow further, drawing on the practical structure of my current manuscripts and response letters.

  • A simpler file structure. Edit manuscript details in one place; keep the abstract, main text and supplement in separate files. A shared style file holds the formatting tools. Inline comments explain the editing points, compilation order, modes, labels and supplementary numbering. The title page stays uncluttered, without a submission-details box.
  • Review and reading modes. Produce two PDFs from the same content. The review copy has line numbers and wider spacing; the reading copy is compact and removes draft notes. Neither mode changes the scientific text.
  • Main and supplementary references. A shared bibliography feeds two independent reference lists. Optional macros count entries in each list; a source cited in both counts once in each.
  • Consistent S numbering. Supplementary sections, equations, figures, tables, mathematical statements and pages have S prefixes, with a local contents list and distinct hyperlink targets.
  • Mathematics that travels with the argument. Examples cover aligned equations, a proposition, a proof and a supplementary lemma. Cross-references generate the object name and number together.
  • Replies tied to manuscript labels. The response letter imports page, line, section and equation labels from the review manuscript. Comments are numbered within each reviewer’s section; excerpts distinguish additions and deletions.
  • Word-count scope is explicit. An optional helper estimates abstract and main-text prose separately, excluding the supplement, captions, headings and mathematics. It is an estimate to check against the journal’s rules.
  • Fewer hidden dependencies. The example figure is a vector illustration built inside LaTeX. No shell escape, external images or automatic embedding of source files is required.

Start writing

In Overleaf

  1. Download the ZIP and upload it as a new project.
  2. Select main.tex as the main document, with pdfLaTeX and TeX Live 2024 or newer.
  3. Edit metadata.tex: title, author block, journal, revision date and keywords.
  4. Replace the examples in sections/abstract.tex, sections/manuscript.tex and sections/supplement.tex. Add your references to references.bib.
  5. Compile main.tex for review, or select reading.tex for the compact copy.
  6. Compile main.tex before switching to response.tex, so the response can read the manuscript’s current labels.

On your computer

An up-to-date TeX installation with pdfLaTeX, latexmk and Biber is sufficient for the PDFs. Python and TeXcount are needed only for the optional count helper.

python3 count-words.py
latexmk -pdf main.tex
latexmk -pdf reading.tex
latexmk -pdf response.tex

The full README explains the file structure, reference counts, word-count scope and customization. The example PDFs were compiled and checked before being added here.

A response letter that stays connected

Place line labels at the start and end of a passage in the review manuscript:

\linelabel{line:question-start}
The revised paragraph begins here ...
... and ends here.\linelabel{line:question-end}

Then use the labels in the reply:

\wherechanged{line:question-start}{line:question-end}
\cref{m-eq:logistic}

The m- prefix identifies a label imported from the manuscript. Rebuild the review manuscript before rebuilding the response, and check the printed locations against the exact PDF you submit. The response’s PDF links work when the review PDF is kept alongside it; line numbers from a different revision should never be reused.

Reviewer comments, replies and excerpts use separate environments. The comment boxes can break across pages, and each comment has a stable place in the reviewer’s sequence. The sample comments are newly written examples, not correspondence from a real review.

References and revision tools

This version uses biblatex and Biber, retaining familiar \citep and \citet syntax through its natbib compatibility option. It does not use the old journal-specific .bst files. A journal requiring BibTeX or a special document class may need a different bibliography setup; its submission instructions take precedence over this template. See the biblatex documentation.

For line numbers around mathematics, the template uses the current lineno package, rather than manually redefining the equation and align environments. Use a current TeX distribution and check the rendered equations after changing the setup.

For revision diffs, keep named copies or use Git. A modular project needs both versions flattened, or an appropriate version-control workflow, before running latexdiff. Overleaf now documents a latexdiff workflow; the old statement that it was unavailable is no longer useful guidance. Always inspect the diff PDF, especially its equations, citations and floats.

Why I still use LaTeX

For quantitative work, I find LaTeX particularly useful when equations, references, proofs and supplementary material need to stay consistent through many revisions. Keeping formatting tools separate from the scientific text also makes collaboration and reuse easier.

This is a practical starting point, not a claim that LaTeX is the best tool for every project. Use the tool that helps your collaborators write clearly, and use the target journal’s requirements when preparing the final submission. The template has writing defaults; it is not a journal-approved submission class or an anonymization tool.

Earlier version

The original Overleaf project and earlier ZIP remain available for existing users. They are the earlier template; the updated version is the v2.0 download at the top of this page.