Peer Review Process – Journal Articles

1. Peer Review Process – Journal Articles Step 1 – submit manuscript (ms) with permission of all authors through journal website Step 2 – ms is initially assigned to a subject editor with expertise in the appropriate field, who decides if it is worthy of being sent out for review Step 3 – the subject editor chooses 2-3 reviewers, usually a combination of individuals you suggest and ones the editor comes up with …the reviewers you suggest can have a major impact on the odds of getting a paper accepted (politics & personality) …so does the number of reviewers (2 versus 3)

2. Peer Review Process – Journal Articles Step 4 – reviewers evaluate your manuscript and recommend: - publish as-is - publish after minor revision - possibly acceptable after major revision; reviewer(s) wants to see it again to check corrections - this could involve asking for new experiments, new analyses of data, or a major re-write to answer questions the reviewer(s) has - rejected

3. Peer Review Process – Journal Articles Step 4 – the reviewers evaluate your manuscript Step 5 – the editor sends you the reviewers’ comments, and any of their own, and then makes a ruling based on what the reviewers say - editor can decide to reject a paper even if all reviewers liked it, usually if it is not “important enough” - editor may also accept a paper even if one or more reviewers says it has fatal flaws … this is another place where politics can come into play

4. Peer Review Process – Journal Articles Step 4 – the reviewers evaluate your manuscript Step 5 – the editor sends you the reviewers’ comments, and any of their own, and then makes a ruling based on what the reviewers say Step 6 – you prepare a line-by-line rebuttal to all reviewer comments you don’t agree with, and list of all changes you made to your manuscript Step 7 – the editor sends it back out for re-review, if necessary Step 8 – the editor ultimately decides if you have adequately addressed all reviewer concerns, and if the final version is “important” enough for that particular journal

5. Peer Review Process – Journal Articles Step 9 – you upload a properly formatted version of all text, figures, tables, references, supplementary data files Step 10 – journal’s copy editor sends you a marked-up PDF of your paper, now in the journal format, but with all the corrections and questions you need to address for clarity and formatting, not for science reasons Step 11 – you get the page proofs to inspect, which is where you have to catch all the mistakes and changes that were made during the copy editting and page setting processes Step 12 – you get the bill for publishing your work: often over $1,000, more if you have color figures or want your paper to be open access so anyone can read it

6. How do you pick a journal? You’ve just spent 2 years of life on your project. What journal do you submit your manuscript to? What criteria are important to you in choosing a journal?

7. How do you pick a journal? One popular measure (among many) used to compare the importance of different journals is impact factor Total # of citations published in 2011 that reference papers in Journal X from the previous 2 years, divided by the total # of “citable” papers published in Journal X (judged by Thompson Scientific) Idea: papers have the most “impact” on a field when they are cited more by other papers Journals are more prestigious if on average, their papers get more citations

8. Journal Impact Factor = journal that covers all areas of science = review articles, notprimary literature (data-based papers)

9. Journal Impact Factor

10. Journal Impact Factor

11. total cites to journal # of “citable” papers Journal Impact Factor = Problems with the impact factor approach: - ethical conduct - are all papers equally “citable” ? During the course of discussions with Thompson Scientific, PLoS Medicine’s potential impact factor – based on the same articles published in the same year – see-sawed between 3 and 11 !! Current Biology had an impact factor of 7.00 in 2002 but 11.91 in 2003. The denominator somehow dropped from 1032 in 2002 to 634 in 2003, although total # of papers published went up

12. total cites to journal # of “citable” papers Journal Impact Factor = Problems with the impact factor approach: - ethical conduct - are all papers equally “citable” ? - what does a “mean” mean?... blockbusters vs average papers Nature noted that 89% of their citations came from only 25% of the papers published, highly cited “blockbusters” Thompson Sci. has been asked to provide the median, as well as the mean score, for each journal; so far, will not

13. Journal Impact Factor Other problems with the impact factor approach: - evaluating journals vs scientists - bad papers cited by rebuttals - some fields cite older literature more, or cite less in general - journal limits on citations - show me the data! - proprietary data of Thompson Sci. - for-profit motives of this private company

14. My results ImpactCitations 0.9 24 2.5 53 2.0 30 5.4 33 5.2 24 2.5 41 9.4 59 2.2 61 Krug 2011. Amer Malacological Bull 29: 169-186. Handeler et al. 2009. Frontiers in Zoology 6: 28. Krug 2009. Biol Bull 132: 483-494. Ellingson & Krug 2006. Evolution 60: 2293-2310. Zimmer et al. 2006. EcolMonogr 76: 585-600. Botello and Krug. 2006. MEPS 312: 149-159. Riffell, Krug, Zimmer, 2004. PNAS 101: 4501-4506. Krug 2001. Mar Ecol Prog Ser 213: 177-192.

15. Alternatives for Judging Impact Other algorithms have been proposed to judge journals, papers 1) PageRank (Google): impactful journal citations count more  if you link from a more popular site, your visit counts more  citations in more population journals count more 2) user-ratings (PLoS ONE) – the Yelp of science

16. Alternatives for Judging Impact Personal metrics of “impactful-ness” a) total citations b) h-index: largest # h such that h papers have at least hcitations -- "recent" version only covers the last 5 years I have 16 papers that have been cited at least 16 times each c) i10-index: # of papers with at least 10 citations I have 22 papers that have been cited at least 10 times

17. My results ImpactCitations 0.9 15 2.5 30 2.0 22 5.4 27 5.2 22 2.5 35 9.4 52 2.2 56 Krug 2011. Amer Malacological Bull 29: 169-186. Handeler et al. 2009. Frontiers in Zoology 6: 28. Krug 2009. Biol Bull 132: 483-494. Ellingson & Krug 2006. Evolution 60: 2293-2310. Zimmer et al. 2006. EcolMonogr 76: 585-600. Botello and Krug. 2006. MEPS 312: 149-159. Riffell, Krug, Zimmer, 2004. PNAS 101: 4501-4506. Krug 2001. Mar Ecol Prog Ser 213: 177-192.

18. Recent paper’s journey population genetics of an invasivemarinemussel – where to send it?? Initially submitted to Molecular Ecology (6.5) - accepted by 2 of 3 reviews - rejected by one reviewer because of scope of sampling Then Proceedings of the Royal Society (5.1) - editor would not send out for review, not “important” enough Then Marine Ecology Progress Series (2.5) - three rounds of review with 2 reviewers making numerous technically incorrect demands and comments - 3rd editor brought in to evaluate my rebuttal to reviewers; rejected because I “didn’t properly consider” their comments Then Biological Invasions (3.5) - accepted without change

19. Assignment 1) Identify the names and impact factors of: (a) the top journal in your field of study (b) a second-tier journal in your sub-discipline 2) For one journal, identify a subject editor with expertise in your specific area of study, who would be the person you’d want handling your manuscript submission 3) Find the correct citation format for this journal. This should be the citation format you follow for the references in your prospectus and thesis.