Publishing: where, why, and how
Outline
• Why it matters where you publish
• What journals should you try and publish in?
• How to publish in the top tier journals
• An outline for a major article in a top-tier journal
• How the review process works
Why it matters where you publish
• For university faculty jobs, your publication record
will likely have a strong impact on your eventual
teaching load, and if you get a job at all
• Many publications in top tier journals  low
teaching load, higher probability of getting a job
• Few publications, and/or publications only in lower
tier journals  high teaching load, lower probability
of getting a job
Why it matters where you publish
• Given that you are going to spend the next few
years doing research, it only makes sense to do it
in a way that will give you more opportunities and
choices in the future
• Ergo, you should write your papers and design
your research such that it can be published in top
tier journals
Outline
• Why it matters where you publish
• What journals should you try and publish in?
• How to publish in the top tier journals
• An outline for a major article in a top-tier journal
• How the review process works
What are “top tier journals”?
• What follows will be my highly subjective opinion
(but based partly on hard data and the opinions of
many fellow evolutionary biologists and ecologists)
• Varies somewhat between subdisciplines of
ecology and evolution
What are top tier journals?
• Best: Nature, Science (duh!)
• Second best: PNAS, PLOS Biology
• Third best: Proceedings of the Royal Society of
London/Biology Letters, Current Biology
• (Not clear to me that this third tier is necessarily
better than top tier journals within a field…)
What are top tier journals?
For Evolutionary Biology (not an exhaustive
list)
• Top (in alphabetical order only): American Naturalist,
AREES, Evolution, Genetics, Molecular Biology and
Evolution, Systematic Biology, TREE
• Uncertain (first or second): Molecular Ecology, Heredity,
Journal of Molecular Evolution, BMC Evolutionary
Biology
• Second tier: Biological Journal of the Linnean Society,
Genetica, Journal of Evolutionary Biology, Journal of
Heredity, Molecular Phylogenetics & Evolution
What are top tier journals?
For Ecology (not an exhaustive list)
• Top (in alphabetical order only): American
Naturalist, AREES, Ecology, Ecology Letters,
Ecological Monographs, TREE
• Uncertain (first or second): Animal Behavior,
Conservation Biology, Ecological Applications
• Second tier: Ecography, Journal of Ecology,
Journal of Animal/Plant Ecology, Oecologia, Oikos
The bottom line
• You should design your dissertation research such
that you will have multiple, first-authored major
articles in the best and/or top tier journals
• You can bet that the other people applying for jobs
in evolution and ecology will...
Outline
• Why it matters where you publish
• What journals should you try and publish in?
• How to publish in the top tier journals
• An outline for a major article in a top-tier journal
• How the review process works
How to get published in the best/top tier
journals?
Based primarily on serving as Associate Editor for:
•
•
•
•
American Naturalist
Ecology Letters
Evolution
Systematic Biology
How to get published in the best/top tier
journals?
• Most important ingredient for publishing in top tier
journals = single ingredient lacking in most papers
that get rejected
How to get published in the best/top tier
journals?
• You generally need to have something to say that
is both new and conceptually broad
• From the “Instructions to authors” from the journal
Evolution: “Demonstrating a well-established
phenomenon in another taxon or context may fall
short of being acceptable.”
How to get published in the best/top tier
journals?
Examples of what these journals are looking for:
• New hypothesis to explain well known phenomenon
• New way to test old hypothesis (new method, new type
of data)
• Show a new phenomenon
• Test a previously untested theory or major assumption
of theory
How do I come up with something new to
say?
• Subscribe to journals that you want to publish in
• Read the articles; find articles that you like
• Become an expert on a topic
• Once you know a topic, you’ll see that nobody has
convincingly demonstrated almost anything, and
that most of the really interesting topics are still
wide open!
Outline
• Why it matters where you publish
• What journals should you try and publish in?
• How to publish in the top tier journals
• An outline for a major article in a top-tier journal
• How the review process works
Outline of a paper in a top-tier journal
• Going to focus on how to publish in a top-tier journal
of the type for which I have served as Associate Editor
(e.g., Evolution, Am. Nat., Syst. Biol.)
But wait!
• Wouldn’t it be better to know how to get things
published in Science or Nature?
But wait!
• Wouldn’t it be better to know how to get things
published in Science or Nature?
• No shit.
But wait!
• Wouldn’t it be better to know how to get things
published in Science or Nature?
• No shit.
• If you figure out how to do this, please let me know.
Quick Digression:
How to get published in Science or Nature
• Work very, very hard on your cover letter; ~90% of
papers get rejected without review
• Need to convince the non-specialist editors why the
paper is incredibly important and possibly interesting
to general public
• After you do that, your chances are rumored to be
~50% (twice as good as Am. Nat.)
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
The title page
• Authorship
• Another quick digression!!!
Authorship
• As a grad student or postdoc, you need to get
multiple first-authored papers
• When you start a collaboration, be clear about
authorship up front (don’t expect things to just work
out in your favor after the work is done)
• Limit major time investments in junior authored
papers (unless you are RAing to pay the bills)
Authorship
• In theory, established researchers should be
generous about granting first authorship to more
junior people (on the other hand, they will expect
you to do more of the work!)
• If you are collaborating with friends at a similar
career level as you, you should expect to get (or
feel) screwed sometimes--but a little altruism now
can pay off later
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
Abstract
• Most important part of the paper; will determine
whether anyone reads it or not
• Introduce the topic, what is lacking in the current
approach to it, what you will do, what you found, and
the general significance of the results for the field
• Mini-version of introduction and discussion, but not
Materials & Methods or Results!
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
Introduction (each point = separate paragraph[s])
• What the topic is and why the topic is important
• What is lacking in the current approach to the topic
• How the current approach could be improved upon
• What people have done that is similar (and how it is
different from what you are doing)
• Introduce what you will do, your study system, and
maybe a little about what you will find
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
Materials and Methods
• Be transparent and concise
• Anticipate every possible criticism of your data and
methods (use your imagination) and briefly address it
• Don’t try to sweep weaknesses of your study “under
the rug”; mention them and clearly explain why they
are not fatal
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
Results
• Tell people what you found
• Only provide results that are relevant to the main point
of your study
• Should be little or no interpretation of the results or
comparison to other studies (i.e., no citations); save
that for discussion
• Check for same order of analyses in M&M and Results
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
Discussion (each point = separate paragraph)
• What did your study show (interpret and summarize
the results)
• Where does this new approach/new hypothesis take
us in understanding the topic?
• How do your results relate to prior work?
• Where do we go next in research on this topic?
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
Discussion
• Common but very serious flaw in discussion of many
papers: discussion is focused solely on the study
system and not on the general topic
• Many papers bring up an interesting general question
in the Introduction, but never really return to answer it
in the Discussion
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
Literature Cited
• Carefully follow the exact format of the journal
• Make sure that every paper cited in the text is in the
Literature Cited and that every paper in the Literature
Cited is cited in the text
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
A comment on sloppiness
• Huge amount of trust involved in review process
• Reviewers routinely assume that you can competently
collect data and analyze data
• If you are sloppy and careless in the things that
reviewers can see (i.e., manuscript format), why
should they trust you for the things that they can’t?
(i.e., data collection)
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
A comment on sloppiness
• Check spelling
• Check “Guide for Authors” of journal and follow very
carefully
• Check recent articles in the journal for anything not
covered explicitly in the “Guide for Authors”
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
Figures
• The second most important part of the paper? (after
the abstract)
• Should tell the story of the paper and should look
great
• Good to be creative (but simple often works fine)
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
Introduction/Discussion
• The fatal flaw of most papers is that they fail to put
their work in the broader context of the field to show
the novelty and importance
• Why not? Probably because it is easier and more fun
to collect and analyze data than to figure out the broad
context of the field and figure out something new to
say
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
Introduction/Discussion--Walking the tightrope
• It is important to show limitations of prior studies
• It is also very important to not piss people off
• Assume that everyone you cite is a potential reviewer
• You need to walk a tightrope of showing prior research
to be flawed/limited, without angering authors of that
research
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
Introduction/Discussion--Walking the tightrope
• Be very sure to cite all the relevant people in the topic
• If you cite someone, they will have at least some
motivation to favor acceptance of your paper, even if
your research convincingly demonstrates that they are
a complete idiot
• But miss-citing papers can make you look like an idiot
Outline of a paper in a top-tier specialist
journal (e.g., American Naturalist, Evolution)
Introduction/Discussion--Walking the tightrope
• Important to make it clear that your work is important
• Also very important to not sound pretentious, arrogant,
cocky, etc.
• Reviewers can and do complain about the tone of
your paper
Being a good (scientific) writer
• Scientific writing is very structured and disciplined
• But there are still good scientific writers and bad
scientific writers
• Good writers are clear and understandable, and make
the paper interesting and exciting to read (even when
the general format is set in stone)
• Try to find papers in your area that you think are wellwritten and think about what it is that you like about
the writing...
Being a good (scientific) writer
Other tips
• When in doubt, write short, simple declarative
sentences
• Avoid redundant phrasing and structure “However,…”
• Think about your paper as telling a story, and make
sure that everything in the paper helps tell that story
and makes it convincing
• Think about the impact that you want your paper to
have on the field and write it accordingly
Outline
• Why it matters where you publish
• What journals should you try and publish in?
• How to publish in the top tier journals
• An outline for a major article in a top-tier journal
• How the review process works
How does the publication process work?
(most journals)
• Submit to journal office/Editor
• Editor makes initial decision about suitability (some
journals reject many papers at this stage)
• Editor assigns an AE (Associate Editor)
• AE picks reviewers
• Reviewers make recommendation to AE  AE
makes recommendation to Editor  Editor makes
final decision  you get an e-mail from the Editor
How does the publication process work?
(most journals)
What are the possible outcomes?
• Accept without revision
• Accept pending minor revision
• Accept pending major revision
• Rejection without prejudice/resubmission possible
• Rejection (no resubmission)
How does the publication process work?
(most journals)
• Reviewers often disagree, and often disagree
wildly (e.g., accept pending minor + reject without
resubmission)
• Decision typically rests with AE
• AE can also disagree wildly with reviewers
(reviewers like it, AE hates it, or vice versa)
How does the publication process work?
(most journals)
• In theory, AE protects authors from unfair
reviewers (good paper, bad reviews), and protects
journal from combination of incompetent authors
and incompetent reviewers (bad paper, good
reviews)
• BUT: AE typically handle at least some papers
outside their area of expertise (can expect AEs to
be incompetent also, at least some of the time)
How does the publication process work?
(most journals)
• Will the Editor protect you from an incompetent
AE?
• Hardly ever: if the Editor routinely ignores or
overrides the AE, the AE can simply quit
• Some Editors have little or no actual input on the
decisions
On getting rejected...
• Assume that it will happen sometimes, no matter how
important the paper is
• If you have anything important to say, you can assume
that someone will find it threatening
• Reviewers and AEs are often lazy, incompetent, and
self-serving
• Don’t get too discouraged if you do get rejected, but
do pay close attention to the substance of the
negative reviews (they’re not always stupid)
Revising your paper
• Most papers require some revision, and for most
acceptance hinges upon details of that revision
• You must write a cover letter that accompanies
your revision
• Many comments by the reviewers and AE are
completely moronic
• May be good idea not to point this out to them
explicitly
Revising your paper
• You should assume that every stupid comment
made by the reviewers and editors is your fault
(i.e., they misunderstood because you didn’t
explain things clearly enough)
• In general, you should respond to all or almost all
reviewer and AE comments with some change in
the manuscript itself
• (Don’t just say that the reviewers and editors are
wrong, even if they obviously are)
Manipulating the review process
• You can influence who your paper is sent to or not
sent to; many journals ask authors for preferred (or
“not preferred”) reviewers and AE
• AEs often appreciate suggestions as to who to send
the paper to (especially if paper is outside their area)
• People in the acknowledgements are usually out
• But you can ask them to send it to your friends,
collaborators, Aunt Jody, etc.
Manipulating the review process
• You can also ask that they not send it to someone
• They may or may not ask you why
• If you do this, be careful about the “why” (don’t make
questionable accusations; you could get sued)
• Too many non-preferred reviewers may also be a “red
flag”
• But keep this option in mind...
Final Advice
• Start submitting parts of your dissertation/postdoc
research long before you finish
• Get feedback on your manuscripts from your
labmates, advisors, and committee members
Final Advice
• Stony Brook E&E students have done great things in
the distant and recent past.
• Don’t assume that you can’t do the same.
Some Accomplishments of Recent E&E
Graduates/Graduate Students
•
Lacey Knowles (graduated 1999; now tenured professor at Univ. Michigan);
lead author of most cited paper in Ecology and Evolution in 2003!
•
Patrick Stephens (graduated 2005)--interviewed for Assistant Professor
position at Yale while still a graduate student here
•
Dusty Brisson (graduated 2006)--interviewed and got position as Assistant
Professor at Univ. Pennsylvania while still a graduate student here