Friday, October 9, 2026

How to Suggest Reviewers for a Scientific Manuscript

 

A practical guide to identifying appropriate reviewers, avoiding conflicts, using AI responsibly, and predicting who is most likely to accept

Suggesting reviewers is one of the most delicate parts of a journal submission.

It can be tempting to treat it as a strategic exercise:

"Who will give us a favourable review?"

That is the wrong starting point.

The appropriate question is:

Who is sufficiently knowledgeable, sufficiently independent, and sufficiently likely to evaluate this manuscript fairly?

A good reviewer list helps the editor find qualified experts quickly. A poor list can raise concerns about conflicts of interest, reviewer manipulation, or attempts to influence the editorial process.

The ideal reviewer-suggestion process therefore combines scientific expertise, independence, diversity, availability and editorial judgment.


1. What is the purpose of suggesting reviewers?

When a journal asks authors to suggest reviewers, it is generally not asking:

"Who do you want to review your paper?"

It is asking:

"Who could competently and independently evaluate this work?"

The editor remains responsible for choosing the reviewers.

Your suggestions are therefore recommendations, not nominations.

A strong reviewer list gives the editor several useful options.


2. The first principle: choose expertise, not friendliness

The most important rule is:

Never start by asking who likes your work. Start by asking who understands your work.

Suppose your paper contains:

  • comparative genomics,
  • phylogenetics,
  • gene-loss analysis,
  • transcriptomics,
  • evolutionary modelling,
  • and functional interpretation.

You may need reviewers with different strengths.

For example:

ReviewerPrimary expertise
AComparative genomics
BMolecular evolution
CGene-loss/pseudogene evolution
DTranscriptomics
EFunctional genomics

You don't necessarily need five people who work on exactly the same gene.

You need a group capable of evaluating the different claims made by the paper.


3. Start by identifying the manuscript's "reviewer needs"

Before searching for names, make a list of the expertise required.

For example:

Scientific question

Who studies the biological phenomenon?

Methodology

Who understands the main analytical approach?

Data type

Who understands the underlying dataset?

Interpretation

Who works on the broader biological/evolutionary question?

Specialized methods

Who understands the unusual method or model?

This produces a reviewer expertise matrix.

For example:

Manuscript componentRequired expertise
Gene lossComparative genomics
OrthologyGenome evolution
PhylogenyMolecular phylogenetics
Selection testsEvolutionary modelling
TranscriptomicsGene-expression analysis
Functional interpretationMolecular biology

Now search for people who collectively cover these areas.


4. Where should reviewer candidates come from?

There are many legitimate sources.

A. Recent papers

Probably the best starting point.

Search for researchers who published papers addressing the same scientific problem within approximately the last 3–5 years.

Look at:

  • authors of key papers
  • authors of recent methodological papers
  • authors of competing interpretations
  • authors of high-quality reviews

5. Follow the citation network

Start with your manuscript's most important references.

For each important paper:

  1. Who wrote it?
  2. Who cited it?
  3. Who subsequently challenged or extended it?
  4. Who publishes repeatedly in this area?
  5. Who developed the methods you use?

This creates a much better reviewer pool than simply searching Google for:

"gene X expert."


6. Look at recent papers rather than reputation alone

A famous scientist may be an excellent expert but a poor practical reviewer candidate.

Possible problems:

  • no longer active in the field
  • too senior and overloaded
  • moved into a different research area
  • does not review manuscripts anymore
  • lacks expertise in the specific methods

A researcher publishing three relevant papers in the last two years may be a better candidate than a famous scientist who published one relevant paper ten years ago.


7. Examine the authors' recent publications

For each candidate, ask:

How recently did they publish on the topic?

How often do they publish in the area?

Are they methodologically relevant?

Do they publish independently?

Are they likely to understand the manuscript?

Are they currently active?

This is much more informative than citation count alone.


8. Build a reviewer candidate spreadsheet

A lab should ideally maintain one.

For example:

CandidateInstitutionExpertiseRecent relevant paperConflict?Likely expertiseAvailabilityRecommendation
AUniv XGene evolution2025NoVery highHighYes
BUniv YPhylogenomics2026NoHighMediumYes
CUniv ZFunctional biology2024Recent collaboratorHighUnknownNo
DUniv QGene loss2026CompetitorVery highUnknownMaybe

This is far better than producing five names at the last minute.


9. Conflict of interest is the critical filter

Before suggesting anyone, investigate conflicts.

Potential conflicts include:

Recent collaboration

Someone who recently co-authored a paper with you is generally inappropriate.

Same institution

A researcher at your institution is usually unsuitable.

Recent student-supervisor relationship

Avoid former supervisors, students and close academic relationships where the journal's policies consider them conflicts.

Family/personal relationships

Obviously avoid these.

Financial relationships

Avoid people with relevant financial interests.

Direct professional conflicts

If there is an ongoing dispute, competition or formal conflict, be cautious.

Manuscript overlap

A person working on an extremely similar unpublished project may present a competing-interest problem.


10. Scientific disagreement is not automatically a conflict

This distinction is important.

Suppose your manuscript challenges Professor X's published interpretation.

Should Professor X automatically be excluded?

Not necessarily.

If Professor X is an independent expert and the journal permits author-suggested reviewers, they may actually be an excellent reviewer.

But there is a difference between:

"This researcher has a different scientific interpretation."

and:

"This researcher is involved in an active personal/professional dispute with us."

The former can be scientifically valuable.

The latter may constitute a genuine conflict.


11. Competitors require careful judgment

Direct competitors are complicated.

A direct competitor may be:

  • highly qualified,
  • completely independent,
  • scientifically ideal,

but may also have:

  • unpublished competing work,
  • a strong personal stake in the outcome,
  • access to your ideas before publication.

Do not automatically exclude competitors.

Instead ask:

Would a reasonable editor consider this person capable of providing an independent review without a significant competing interest?

If the answer is uncertain, disclose the issue rather than attempting to manipulate the reviewer pool.


12. How many reviewers should you suggest?

Follow the journal's instructions.

If it asks for:

3 reviewers

provide three strong candidates.

If it asks for:

5–8

provide a broader but carefully screened pool.

Do not submit 20 names merely to increase the chance that your preferred person is selected.

Quality matters more than quantity.


13. Don't suggest only your friends

This is one of the most obvious warning signs.

A suspicious list might consist of:

  • former collaborators,
  • close colleagues,
  • former supervisors,
  • people from your academic network,
  • researchers who cite you frequently.

Even if none technically violates a conflict rule, the pattern can look inappropriate.


14. Don't suggest only famous scientists

The opposite mistake is also common.

A list of five Nobel-level or field-leading researchers may look impressive but be practically useless.

Very senior researchers may:

  • receive enormous numbers of invitations,
  • have heavy administrative responsibilities,
  • decline most reviews,
  • delegate some reviewing,
  • have limited time.

A mid-career researcher with exactly the right expertise may be much more likely to accept.


15. Which reviewers are most likely to accept?

There is no reliable way to predict an individual's decision.

However, reviewer acceptance tends to be more plausible when the candidate:

Is actively publishing

Someone currently publishing in the area is more likely to see the manuscript as relevant.

Has reviewed before

Researchers who regularly review for journals are accustomed to the process.

Is at an appropriate career stage

Mid-career researchers and established early-career investigators may have both expertise and motivation, although this varies enormously.

Has a close topical match

A manuscript directly aligned with their research is more attractive than a peripheral connection.

Has the methodological expertise

Researchers are more likely to accept when they can confidently evaluate the work.

Is not overloaded

A person with a huge administrative workload may decline even if they are the perfect scientific match.

Is not conflicted

Obvious conflicts reduce the likelihood of a legitimate invitation.


16. A useful way to think about reviewer acceptance

You can conceptualize reviewer availability as:

Expertise × relevance × independence × availability

rather than:

fame × citation count.

A candidate with moderate fame but excellent topical fit may be a much better reviewer than a superstar.


17. Early-career researchers can be excellent reviewers

Do not restrict your list to professors.

A postdoctoral researcher, assistant professor, research scientist or newly independent investigator may have:

  • extremely current expertise,
  • detailed methodological knowledge,
  • time and motivation,
  • experience with the exact analytical techniques.

However, check whether the journal permits the person and whether the invitation should instead go to their PI or supervisor.

Never assume that someone should review simply because they are a coauthor's former student.


18. Geographic diversity

If appropriate candidates exist, avoid selecting everyone from:

  • one country,
  • one institution,
  • one academic network.

A geographically diverse reviewer pool can help reduce network bias.

However, expertise should come first.

Do not select a weaker reviewer merely to satisfy geographic diversity.


19. Gender and other diversity considerations

Where multiple equally qualified candidates exist, diversity can be a useful consideration.

But diversity should not become a substitute for expertise.

The priority remains:

  1. competence
  2. independence
  3. relevance
  4. availability

with diversity considered among otherwise appropriate candidates.


20. Search systematically

A robust search strategy might look like this:

Step 1

Identify 10–20 relevant recent papers.

Step 2

Extract authors.

Step 3

Remove:

  • your authors,
  • recent collaborators,
  • institutional colleagues,
  • obvious conflicts.

Step 4

Rank the remaining candidates by expertise.

Step 5

Check recent publication activity.

Step 6

Check methodological relevance.

Step 7

Check current affiliation.

Step 8

Check whether they are plausibly independent.

Step 9

Select the strongest candidates.

Step 10

Verify contact details from authoritative sources.


21. Use multiple discovery routes

Do not rely on one database.

Useful sources can include:

  • PubMed
  • Google Scholar
  • Web of Science
  • Scopus
  • Crossref
  • ORCID
  • institutional websites
  • journal articles
  • conference programs
  • field-specific databases

The objective is not to find the biggest list.

It is to verify the identity, expertise and independence of candidates.


22. AI can help—but it should not make the final decision

AI can be very useful for generating a candidate pool.

For example, give an AI system:

  • title
  • abstract
  • keywords
  • methods
  • major references
  • research question

and ask it:

Identify researchers who have published peer-reviewed work in the last five years on the specific scientific questions and methods represented in this manuscript.

This can produce useful candidates.

But the output should be treated as:

a discovery tool, not a reviewer recommendation.


23. A good AI reviewer-search workflow

A robust workflow is:

MANUSCRIPT
     ↓
AI identifies scientific themes
     ↓
AI generates candidate researchers
     ↓
Human verifies publications
     ↓
Human checks conflicts
     ↓
Human checks current affiliation
     ↓
Human evaluates independence
     ↓
Human ranks candidates
     ↓
Final reviewer suggestions

The human verification stage is essential.


24. What AI is particularly good at

AI can help with:

Identifying subfields

For example:

comparative genomics + molecular evolution + pseudogenization

Finding expertise gaps

AI may recognize that your manuscript actually requires:

  • phylogenetics expertise,
  • statistical modelling,
  • functional genomics,
  • genome annotation.

Expanding candidate pools

It can identify researchers you may not have encountered through your immediate academic network.

Comparing expertise

You can ask AI to summarize:

What aspects of this manuscript could researcher X evaluate particularly well?

Detecting obvious conflicts

AI can flag potential coauthorship relationships—but these must be independently verified.


25. What AI should NOT be trusted to do

Do not blindly accept AI-generated:

  • researcher names,
  • affiliations,
  • email addresses,
  • publication histories,
  • conflicts,
  • claims about expertise.

AI systems can hallucinate.

A nonexistent paper or incorrect affiliation can easily make its way into a reviewer list.

Therefore:

Every suggested reviewer should be verified against primary or authoritative sources.


26. Don't ask AI "Who will give me a favourable review?"

That is a problematic objective.

A better prompt is:

"Identify independent researchers who are highly qualified to evaluate the scientific claims and methodology of this manuscript."

The distinction is important.

The goal should be appropriate review, not favorable review.


27. Don't use AI to predict personal bias

Be particularly cautious with prompts such as:

"Which researchers are likely to agree with our conclusions?"

or:

"Find reviewers who will be sympathetic to our paper."

This moves the process away from identifying independent expertise and toward attempting to influence peer review.

Instead ask:

"Which researchers have published evidence supporting, challenging, or independently investigating the scientific question?"

That produces a more balanced reviewer pool.


28. Use AI to identify both sides of a scientific debate

This can actually improve reviewer selection.

For example:

Identify researchers who have independently published evidence supporting the prevailing model and researchers who have published evidence challenging it.

Then:

  • verify the candidates,
  • remove conflicts,
  • assess expertise,
  • let the editor choose.

This is particularly useful when your manuscript challenges an established interpretation.


29. AI can help build a reviewer matrix

For example:

CandidateExpertiseMethodsRecent workIndependencePotential conflictOverall
AVery highHigh2026HighNoneExcellent
BHighVery high2025HighNoneExcellent
CVery highMedium2026LowCompetitorAvoid
DMediumHigh2026HighNoneGood

This is a much better use of AI than asking:

"Give me five reviewers."


30. Verify every candidate manually

For every final candidate, check:

Identity

Is this actually the person you think they are?

Current affiliation

Has the person moved?

Expertise

Do their recent papers actually match your manuscript?

Recent publication

Have they published recently in the area?

Conflicts

Have they coauthored with your authors?

Institution

Are they independent?

Relationship

Do you have a close professional relationship?

Contact details

Is the email address from an authoritative source?


31. Be careful with email addresses

Do not obtain reviewer emails from questionable databases.

Prefer:

  • university profile
  • laboratory website
  • ORCID-associated information
  • journal publication
  • institutional directory

And if the journal can identify the reviewer from their name and affiliation without requiring an email, do not invent one.


32. What about people who cited your work?

They can be appropriate.

But citation alone does not make someone a good reviewer.

A person who cited your paper once in passing is not necessarily an expert.

Conversely, someone who never cited you may be an excellent reviewer.

Expertise should be determined from the body of relevant work, not citation relationships.


33. What about authors of papers you cite?

They are often excellent candidates.

But there are two possibilities:

They are independent experts.

Excellent.

Your manuscript directly attacks their published conclusion.

Potentially still appropriate, but consider whether there is a genuine conflict and whether the editor should know about the relationship.

Scientific disagreement itself is not a reason to manipulate the reviewer pool.


34. What about reviewers who reviewed your previous paper?

Potentially excellent candidates if:

  • they are independent,
  • their expertise remains appropriate,
  • there is no conflict,
  • the journal allows it.

But do not attempt to reconstruct anonymous reviewers through clues.

If a reviewer was anonymous, you should not try to identify them simply because you liked or disliked their review.


35. What about suggesting the same reviewers to multiple journals?

There is nothing inherently wrong with recommending an appropriate expert to another journal if the manuscript is subsequently submitted elsewhere.

But don't maintain a rigid list of "my five favourite reviewers."

The appropriate reviewer pool should be rebuilt based on:

  • the manuscript,
  • the target journal,
  • the current literature,
  • current conflicts.

36. A particularly useful concept: reviewer complementarity

Instead of asking:

Who are the five best experts?

ask:

What five perspectives would provide the strongest independent evaluation?

For example:

Reviewer 1 → Biological question
Reviewer 2 → Evolutionary theory
Reviewer 3 → Computational methodology
Reviewer 4 → Statistical analysis
Reviewer 5 → Functional interpretation

This can be much stronger than five people who all work on exactly the same biological system.


37. The ideal reviewer profile

A particularly good candidate often has:

  • recent publications in the topic,
  • direct methodological expertise,
  • sufficient independence,
  • active research,
  • experience reviewing,
  • no obvious conflicts,
  • an appropriate career stage,
  • a professional connection to the scientific problem rather than to the authors.

That combination is much more valuable than prestige alone.


38. A practical ranking system

A lab could score candidates:

CriterionScore
Scientific expertise0–5
Methodological expertise0–5
Recent activity0–3
Independence0–5
Relevance to manuscript0–5
Availability likelihood0–3
Conflict risk−5 to 0
Overall—

But do not turn this into an algorithm that automatically selects reviewers.

The scoring system is a decision aid.


39. An important warning: don't optimize for acceptance probability

You might be tempted to build:

"Reviewer X = 80% chance of accepting invitation."

That is not really knowable from public information.

Instead, use qualitative categories:

Likely to be feasible

  • active researcher
  • strong topical fit
  • regular publication activity
  • not obviously overloaded

Possibly difficult

  • extremely senior
  • major administrative role
  • exceptionally high-profile
  • already serving on many editorial boards

Poor candidate

  • conflict
  • weak expertise
  • inactive in field
  • insufficient independence

40. Never contact a reviewer asking them to review your paper

Unless the journal explicitly permits pre-submission reviewer contact, do not send someone:

"We have suggested you as a reviewer. Please accept if invited."

That undermines the independence of the process.

Similarly, do not send them the manuscript privately with the expectation that they will review it.

Let the journal handle the invitation.


41. Don't ask colleagues to create fake reviewer identities

This is an obvious but important ethical boundary.

Never:

  • create fake email accounts,
  • provide personal addresses pretending to be institutional,
  • nominate yourself under another identity,
  • ask a friend to review under a different identity,
  • manipulate reviewer databases.

These practices can constitute serious publication misconduct.


42. Don't suggest people who cannot reasonably review the manuscript

For example, don't recommend:

  • a graduate student who has no independent reviewing role unless the journal permits it,
  • a retired researcher who has completely left the field,
  • someone working in an unrelated field simply because they are famous,
  • a person whose expertise is only tangentially related.

43. Reviewer suggestions should help—not control—the editor

The healthiest attitude is:

"Here are several people who could competently evaluate this manuscript."

not:

"Here are the people we want you to select."

The editor may select none of them.

That is completely normal.


44. A recommended laboratory workflow

For every manuscript:

Stage 1 — Identify expertise

Create the reviewer-needs matrix.

Stage 2 — Generate candidates

Use:

  • recent papers,
  • citation networks,
  • databases,
  • editorial boards,
  • conferences,
  • AI-assisted discovery.

Stage 3 — Create 10–20 candidates

Do not immediately select five.

Stage 4 — Verify candidates

Check:

  • publications,
  • affiliation,
  • conflicts,
  • independence.

Stage 5 — Rank

Identify the strongest candidates.

Stage 6 — Create a balanced final list

Provide the number requested by the journal.

Stage 7 — Record the rationale

Maintain the internal reviewer-selection record.


45. Keep a reviewer-selection record

For your lab's publication archive, I would create:

Reviewer_Selection/
├── Candidate_List.xlsx
├── Expertise_Assessment.xlsx
├── Conflict_Check.xlsx
├── AI_Assisted_Search_Record.txt
└── Final_Reviewer_List.pdf

This is particularly useful if a question later arises about why a reviewer was suggested.


46. A useful AI prompt

A responsible AI-assisted workflow might use a prompt like:

"Analyze the following manuscript abstract, key claims, methods and references. Identify the scientific subfields and methodological expertise required to independently evaluate the manuscript. Then generate a candidate pool of researchers who have published recent peer-reviewed work in those areas. For each candidate, explain which aspect of the manuscript they are qualified to assess. Do not rank candidates according to whether they are likely to support the manuscript's conclusions. Do not infer personal relationships or conflicts without evidence. Clearly mark any information that requires independent verification."

Then provide:

  • title
  • abstract
  • key claims
  • methods
  • major references

After AI produces the candidate list, independently verify every candidate.


47. An even better AI workflow

Instead of asking AI for names immediately:

Prompt 1

Identify the five most important scientific expertise areas needed to review this manuscript.

Prompt 2

Identify the major scientific debates relevant to the manuscript.

Prompt 3

Identify researchers who have published recent work representing the different perspectives in those debates.

Prompt 4

Compare these candidates by topical expertise and methodological relevance.

Prompt 5

Identify information that must be independently verified before any candidate is suggested to a journal.

This reduces hallucination and confirmation bias.


48. The final reviewer-selection checklist

Before submitting the names:

Expertise

  • Can this person genuinely understand the manuscript?
  • Have they published recently in the relevant area?
  • Do they understand the key methodology?

Independence

  • No recent collaboration?
  • No institutional conflict?
  • No close personal/professional relationship?
  • No inappropriate financial relationship?

Scientific balance

  • Are different relevant perspectives represented?
  • Is the list dominated by one academic network?
  • Have we avoided selecting people simply because they are likely to agree?

Practicality

  • Are they currently active?
  • Is their current affiliation correct?
  • Are contact details verified?
  • Is the suggested number consistent with journal instructions?

AI

  • Was AI used only as a discovery/organization aid?
  • Were all candidates independently verified?
  • Were no AI-generated claims about conflicts accepted without verification?
  • Was AI used to identify expertise rather than favorable reviewers?

49. The central principle

The best reviewer-selection strategy is not:

"Find people who will like our paper."

It is:

"Find people who would be capable of finding the weaknesses in our paper, while being sufficiently independent to evaluate those weaknesses fairly."

That mindset has an interesting advantage.

If your manuscript survives scrutiny from people who genuinely understand its weaknesses, the paper is usually stronger.


50. The final reviewer-selection philosophy

A good reviewer list should make an editor think:

These are credible, independent experts who understand the science and can evaluate this manuscript properly.

It should not make the editor think:

These authors appear to be trying to engineer a favourable review.

The strongest reviewer-selection process therefore follows a simple sequence:

Understand the manuscript → identify the expertise required → find active experts → verify their work → eliminate conflicts → ensure appropriate breadth → suggest the strongest independent candidates.

AI can make the search and organization much faster.

It should not replace the scientific and ethical judgment involved in deciding who is an appropriate reviewer.

And perhaps the most important rule of all:

Choose reviewers you would still consider appropriate if you had no idea whether they would recommend acceptance or rejection.

That is a good test of whether the reviewer-selection process is genuinely about obtaining an independent scientific assessment rather than attempting to control the outcome.

Thursday, October 8, 2026

The Myth of the Single “Cradle of Agriculture”

Maps of agricultural origins often contain neat circles.

The Fertile Crescent.

China.

Mesoamerica.

The Andes.

West Africa.

These are useful, but the paper argues that domestication increasingly looks less like a collection of points and more like a collection of landscapes.

Vavilov's centres of origin

Nikolai Vavilov famously recognised geographical regions containing unusually high diversity of crop plants and their relatives.

These became associated with major centres of domestication.

Later research expanded and subdivided the centres.

Figure 4 of the article maps many of these regions alongside crops following different domestication pathways.

But modern archaeology and genomics have complicated the picture.

Different crops emerged at different places and times

Even within one broad region, crops were not necessarily domesticated together.

Different species may show evidence of cultivation or domestication at different locations and different times.

A “centre” may therefore encompass many separate interacting processes.

Even one crop can have a mosaic history

Genome sequencing has made matters even more interesting.

Barley and emmer wheat contain genetic contributions from wild populations distributed across broad areas.

Their domesticated genomes resemble mosaics.

That makes it difficult to identify one tiny location as “the place” where domestication happened.

The crop population may have been assembled gradually through gene flow across landscapes.

Bananas provide an even more spectacular example.

Important cultivated banana groups contain ancestry derived from different species, subspecies and populations distributed across New Guinea and Southeast Asia.

Human movement brought plant populations into contact that might otherwise have remained separated.

The crop emerged partly from those new biological encounters.

Domestication as a network

The resulting picture resembles a network rather than a birthplace.

Plants move.

People move.

Seeds are exchanged.

Wild and cultivated populations interbreed.

Useful varieties are transported.

Different communities contribute genetic material and cultivation practices.

The question therefore changes from:

“Where was this crop domesticated?”

to:

“What landscape-scale processes assembled this domesticated population?”

That is a much richer question.

###################################################################################

Further reading: This post is inspired by and draws on Dorian Q. Fuller, Tim Denham, and Robin Allaby, “Plant domestication and agricultural ecologies,” Current Biology 33, no. 11 (2023): R636–R649, doi:10.1016/j.cub.2023.04.038. Read the original article in Current Biology
For a classic and highly readable perspective on why plant domestication arose in some regions but not others, see Jared Diamond, Chapter 8, “Apples or Indians: Why Did Peoples of Some Regions Fail to Domesticate Plants?”, in Guns, Germs, and Steel: The Fates of Human Societies (W. W. Norton, 1997), pp. 131–156. Read “Apples or Indians” View Guns, Germs, and Steel on Google Books

###################################################################################

 

Writing the Ideal Cover Letter for a Scientific Manuscript

 

What editors actually need to know—and how to make your paper difficult to reject at the editorial stage

A cover letter is one of the most underestimated components of a journal submission.

Researchers often treat it as a formality: they copy the manuscript title, paste the abstract, write “We believe this manuscript will be of interest to the readers of your journal”, and submit.

That is a missed opportunity.

A good cover letter is not a miniature version of the paper. It is an editorial document whose primary purpose is to help the handling editor answer four questions quickly:

  1. What is this paper about?
  2. What is genuinely new about it?
  3. Why is it appropriate for this particular journal?
  4. Why should the editor send it for peer review?

The ideal cover letter therefore sits at the intersection of science, editorial strategy, journal fit, and research integrity.


1. What is the cover letter actually for?

The manuscript is written primarily for the scientific record and eventual readers.

The cover letter is written primarily for the editor.

That distinction matters.

The manuscript might spend several pages establishing:

Previous studies have reported A, B and C. However, the relationship between X and Y remains unclear. We therefore investigated...

The cover letter should instead communicate:

We demonstrate X, which changes the interpretation of Y. This is particularly relevant to your journal because...

The editor does not need the entire story.

They need the editorially relevant story.


2. The cover letter should answer five questions

A strong cover letter should allow an editor to identify the following almost immediately:

Question 1 — What did you discover?

One or two sentences.

Question 2 — Why does it matter?

What changes because of this paper?

Question 3 — What is genuinely new?

Not merely that you used a new dataset or method.

Question 4 — Why this journal?

This should be specific to the journal.

Question 5 — Is there any reason the editor should be cautious?

For example:

  • related preprint
  • previous submission
  • manuscript transfer
  • overlapping publication
  • unusual authorship issue
  • competing interests
  • related manuscript under consideration
  • reviewer conflict

A good cover letter handles these transparently rather than leaving the editor to discover them later.


3. Start with the journal—not with the manuscript

One of the biggest mistakes is writing one generic cover letter and sending it to every journal.

Instead, prepare a journal-specific cover letter.

Before writing it, examine:

  • journal scope
  • article type
  • readership
  • recent publications
  • editorial priorities
  • methodological preferences
  • whether the journal emphasizes mechanism, broad significance, resources, methods, evolution, clinical relevance, etc.
  • whether the journal publishes similar studies
  • whether the journal has recently published papers addressing related questions

You should be able to complete this sentence:

This paper belongs in this journal because ________.

If you cannot fill that blank with something specific, the journal may not be the right target.


4. The opening paragraph

The opening should immediately identify the submission.

For example:

Dear Editor,
We are pleased to submit our manuscript, “TITLE,” for consideration as an Article in Journal X.

Then briefly identify the scientific problem.

Do not spend half the first paragraph thanking the editor for considering the manuscript.

Get to the science.


5. The most important paragraph: the scientific contribution

This is the heart of the cover letter.

It should answer:

What does this paper actually contribute?

A useful structure is:

Problem → approach → finding → consequence

For example:

We investigated whether the apparent conservation of gene X across mammals reflects retention of a functional gene or persistence of a degraded genomic remnant. By integrating comparative genomics, synteny, transcriptomic evidence and evolutionary analyses across XXX species, we find that...

Then:

These results challenge the prevailing interpretation that...

And finally:

Our findings therefore suggest...

Notice that this is not simply an abstract.

It emphasizes the intellectual consequence of the work.


6. Distinguish "new" from "important"

These are not the same thing.

A manuscript can be technically novel but scientifically unimportant.

For example:

We analyzed 230 genomes using a newly developed pipeline.

That tells the editor what you did.

It does not tell them why they should care.

Compare:

Our analysis reveals that a widely assumed conserved gene has been independently lost in multiple mammalian lineages, requiring a reassessment of previous functional interpretations.

The second statement tells the editor why the observation matters.


7. Do not oversell novelty

Editors see exaggerated claims constantly.

Avoid:

This is the first study ever to...

unless you are genuinely certain.

Similarly, avoid:

This groundbreaking study completely overturns...

unless the evidence genuinely supports that conclusion.

Better language is:

  • "provides evidence that..."
  • "reveals..."
  • "demonstrates..."
  • "supports a reinterpretation of..."
  • "challenges the prevailing view that..."
  • "provides a framework for..."
  • "suggests that..."

Strong scientific writing does not require inflated adjectives.


8. Explain why the paper belongs in this journal

This is where many otherwise good cover letters become generic.

Bad:

We believe this manuscript will be of interest to the broad readership of your journal.

Almost every submission says this.

Better:

The manuscript fits Journal X because it addresses the evolution of gene loss across vertebrates while combining comparative genomics with functional interpretation, areas that are central to the journal's interest in evolutionary mechanisms and genome biology.

Even better is a reference to the journal's actual recent content:

Recent articles in Journal X have highlighted the evolutionary consequences of lineage-specific genomic change. Our study extends this theme by...

Now the editor can see that you understand the journal.


9. Show the appropriate level of generality

A cover letter should make clear whether the finding matters beyond your specific system.

For example:

Although our analysis focuses on GPRC6A in mammals, the broader implication is that apparent protein-level evidence should not automatically be interpreted as evidence for an intact ortholog when comparative genomic evidence indicates lineage-specific gene degradation.

This is particularly valuable for journals with broad readership.

The editor needs to understand the general lesson.


10. Explain why the result matters now

Sometimes the scientific contribution becomes stronger when placed in the context of an active debate.

For example:

Several recent studies have interpreted detection of GPRC6A-related protein signals in bovine tissues as evidence that the gene remains functional in cattle. Our comparative genomic analysis provides an independent test of this assumption and identifies...

This tells the editor:

There is an existing scientific question, and this paper addresses it directly.

That can be more compelling than simply saying that the gene is "interesting."


11. If your manuscript challenges published work, be especially careful

This is particularly important.

If your paper disputes another group's findings, the cover letter should not sound like a personal attack.

Avoid:

We expose serious errors in the work of Smith et al.

Prefer:

Our findings raise questions about the interpretation of the observations reported by Smith et al. and provide an independent comparative framework for evaluating those conclusions.

The distinction is important.

You are submitting a scientific argument, not a complaint about another researcher.


12. Explain methodological strength briefly

Do not reproduce the Methods section.

Instead, identify the feature that makes the conclusion credible.

For example:

We combine independent lines of evidence—including genome assemblies, conserved synteny, transcriptomic data and evolutionary constraint analyses—to distinguish true gene retention from pseudogenization and annotation artefacts.

This is much more useful to an editor than listing every software package used.


13. Mention the strongest result, not every result

A cover letter should usually have one central message and perhaps two or three supporting findings.

Think:

If the editor remembers only one sentence tomorrow morning, what should it be?

That sentence should appear near the beginning.


14. Include the broader significance

A useful paragraph is:

Why should anyone outside this specific subfield care?

For example:

Beyond the specific gene examined here, our results illustrate how apparently conflicting molecular and comparative-genomic evidence can arise when degraded genomic loci, transcript fragments or cross-reactive proteins are interpreted as evidence of functional gene retention.

This transforms a specialist observation into a broader scientific message.


15. Address article type

Explicitly state the article category if relevant:

We submit this work as a Research Article.

or:

We believe this manuscript is appropriate as a Methods Article because...

This avoids ambiguity.


16. Mention preprints

If a preprint exists, disclose it.

For example:

An earlier version of this manuscript is available as a preprint at bioRxiv (DOI: ...). The manuscript submitted here has been substantially revised to incorporate additional analyses and clarifications.

Do not hide a preprint.

A preprint is normally part of the publication history, not something that needs to be concealed.


17. Mention related manuscripts

This is particularly important for laboratories producing multiple papers from related datasets.

If another manuscript is:

  • published,
  • accepted,
  • under review,
  • or being prepared,

and it overlaps substantially, explain the relationship.

For example:

A related manuscript from our group examines the evolutionary distribution of APOBEC1 in birds. The present manuscript addresses a distinct question concerning...

This prevents editors from wondering whether there is duplicate publication or salami slicing.


18. Address previous submissions

Suppose the manuscript was rejected by another journal and is now being submitted elsewhere.

Usually you do not need to volunteer:

Journal A rejected this manuscript.

But if the current submission is a transfer, or the journal explicitly asks about previous submissions, disclose it accurately.

For a transferred manuscript:

This manuscript was previously considered by Journal X and is being submitted here following transfer through the publisher's manuscript-transfer process.

For a substantially revised manuscript after rejection:

The present manuscript has been substantially revised following editorial and reviewer feedback received during an earlier submission.

Honesty is preferable to creating ambiguity.


19. Reviewer suggestions

If the journal requests reviewers, suggest people who are:

  • scientifically appropriate
  • genuinely independent
  • knowledgeable about the subject
  • not recent collaborators
  • not close personal colleagues
  • not from your institution
  • not conflicted through an ongoing dispute

Before recommending someone, verify:

  • current affiliation
  • email address
  • expertise
  • recent publications

Do not suggest a famous scientist simply because they are famous.

The best reviewer is someone who can competently evaluate the central claim.


20. Reviewer exclusions

If exclusions are permitted, use them sparingly.

Legitimate reasons can include:

  • recent collaboration
  • current institutional relationship
  • direct personal conflict
  • clear competing interests
  • involvement in a closely competing project

Avoid language such as:

Professor X should not review this because they disagree with us.

Scientific disagreement is not necessarily a conflict of interest.


21. Conflict-of-interest disclosure

The cover letter should not contradict the manuscript or submission system.

If there is a relevant conflict, disclose it clearly.

For example:

The authors declare no competing interests.

or, where necessary, explain the relationship.

Never assume that an editor will interpret an unusual situation correctly without explanation.


22. Authorship issues

If the authorship situation is unusual, explain it.

Potential examples:

  • author added after initial submission
  • author removed
  • equal contribution
  • consortium authorship
  • deceased author
  • corresponding-author change
  • institutional change

Do not leave unusual authorship arrangements unexplained.


23. Funding

The cover letter can briefly mention funding where useful, particularly if it relates to the journal's policies.

However, don't turn the cover letter into a funding report.

The detailed funding statement belongs in the manuscript/submission system.


24. AI use

This is increasingly relevant.

If the journal requires AI disclosure, follow its specific instructions.

The cover letter should not make claims that conflict with the manuscript's AI declaration.

If necessary:

Any use of generative AI in manuscript preparation was limited to language editing and was reviewed and verified by the authors.

But this should only be stated if accurate and consistent with the journal's policy.

Do not imply that AI performed scientific reasoning or validation if it did not.


25. Ethical and regulatory information

For studies involving:

  • human participants
  • patient data
  • animals
  • clinical trials
  • sensitive datasets
  • field sampling
  • indigenous/community-held biological resources

the relevant ethical approvals should be clearly documented.

The full details belong in the manuscript and submission system.

The cover letter can simply reassure the editor that the relevant requirements have been met.


26. Data and code availability

For computational papers, this can strengthen the submission.

For example:

All underlying sequence data, analysis code and processed datasets will be made available through [repository] upon publication.

If the data are already available:

The analysis code and processed datasets are available at...

Do not promise a repository release that does not actually exist.


27. What should NOT be in a cover letter?

Avoid:

A full abstract

The editor already has the abstract.

A long literature review

Not necessary.

Detailed methods

Not necessary.

Every result

Not necessary.

Excessive praise of your own work

Avoid:

revolutionary, unprecedented, paradigm-shifting, groundbreaking, highly significant...

unless genuinely justified.

Complaints about other scientists

Avoid.

Complaints about previous editors

Almost always avoid.

Emotional language

Avoid:

We strongly believe the reviewers were unfair...

That belongs nowhere in a new submission unless the journal explicitly provides an appeal mechanism.


28. The ideal length

For most research articles:

Approximately 500–800 words is a useful target.

A very strong cover letter can be shorter.

The objective is not to fill a page.

It is to communicate the editorial case efficiently.

A useful test:

Can the editor understand the novelty, significance and journal fit after reading the first 3–4 paragraphs?

If not, revise.


29. A useful five-paragraph structure

A highly effective default structure is:

Paragraph 1 — Submission

What are you submitting?

Paragraph 2 — Scientific problem

What important question does the paper address?

Paragraph 3 — Main discovery

What did you find, and why does it matter?

Paragraph 4 — Journal fit

Why does this belong in this journal and why will its readership care?

Paragraph 5 — Administrative declarations

Preprint, related manuscripts, conflicts, reviewers, author approval, data/code availability, etc.

This is usually enough.


30. The "editorial pitch" test

Before submitting, ask a colleague to read only the cover letter.

Then ask:

What do you think is the main discovery?

If they cannot answer, the letter has failed.

Ask:

Why does this belong in this journal?

If they say:

"Because it is interesting."

the journal-fit paragraph needs work.

Finally:

Would you send this out for peer review? Why?

This is one of the best internal tests you can perform.


31. A powerful way to write the central paragraph

Before writing the cover letter, complete these six sentences privately:

The problem is: ________

The gap is: ________

We did: ________

We found: ________

This changes: ________

This matters because: ________

Then compress those answers into two or three paragraphs.

This prevents the cover letter from becoming an abstract with a greeting attached.


32. Cover letter checklist

Before submission, check:

Scientific case

  • Main scientific question clearly stated
  • Knowledge gap identified
  • Main discovery clearly stated
  • Novelty clearly identified
  • Importance/significance explained
  • Broader implication stated
  • Claims are appropriately calibrated

Journal fit

  • Correct journal named throughout
  • Correct editor addressed
  • Article type specified
  • Journal scope considered
  • Specific readership identified
  • Recent relevant journal content considered
  • Generic "of interest to readers" language minimized

Transparency

  • Preprint disclosed
  • Related manuscripts disclosed if relevant
  • Previous submission/transfer disclosed where required
  • Conflicts disclosed
  • Reviewer exclusions justified
  • Funding information consistent with manuscript
  • AI disclosure consistent with journal requirements
  • Ethics information consistent with manuscript

Submission logistics

  • Title exactly matches manuscript
  • Author list exactly matches submission system
  • Corresponding author correct
  • Article type correct
  • Reviewer suggestions verified
  • Supplementary files correctly described
  • Data/code availability statements consistent

Writing

  • No spelling errors
  • No journal-name errors
  • No references to another journal
  • No exaggerated claims
  • No unnecessary technical detail
  • No unexplained acronyms
  • Professional and confident tone
  • Approximately 500–800 words unless journal guidance suggests otherwise

33. The most common cover-letter mistakes

If I had to identify the ten most common problems, they would be:

1. Writing a generic letter for every journal.

2. Repeating the abstract.

3. Failing to state the actual discovery.

4. Describing methods instead of scientific significance.

5. Saying the paper is "interesting" without explaining why.

6. Overclaiming novelty.

7. Ignoring the journal's readership.

8. Failing to disclose related work or a preprint.

9. Treating reviewer suggestions as a popularity contest.

10. Spending 700 words explaining the paper but never making the editorial case for why it should be reviewed.


34. The cover letter as an editorial decision aid

The best way to think about the cover letter is this:

The editor may have hundreds of manuscripts competing for attention.

Your manuscript arrives accompanied by:

  • a title,
  • an abstract,
  • figures,
  • a manuscript,
  • supplementary material,
  • and a cover letter.

The cover letter should make the editor's job easier.

It should effectively say:

Here is the scientific problem.

Here is what we discovered.

Here is why the discovery matters.

Here is what is genuinely new.

Here is why your journal is the right place for it.

Here are any circumstances you should know about before making the editorial decision.

That is the job.


35. The final principle

A cover letter should not try to convince the editor that your paper is the greatest paper ever written.

It should give the editor a clear, credible and compelling reason to send the manuscript to expert reviewers.

The ideal tone is therefore:

confident, specific, concise, transparent and scientifically restrained.

The manuscript demonstrates the science.

The cover letter explains why the editor should invest the time to have that science evaluated.