Why I never wanted to break inwards Molecular Phylogenetics & Evolution (MPE)
All journals receive got ameliorate in addition to worse newspaper (science in addition to the publishing procedure depend on humans, in addition to except for the pope, nosotros are fallible), but MPE was i of the start journals on my personal dark list. Not because of its scientific content (there receive got been some rattling goodness papers inwards MPE), but the peer review procedure I experienced when submitting my rattling start ain newspaper there, in addition to what followed.In 2004, I chose the magazine as publication platform for my rattling start first-author paper. It dealt amongst a molecular phylogeny of Acer based on some 200 cloned ITS sequences roofing c. 50 species in addition to all its primary intrageneric lineages (sections, series).
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| My start 2003/2004 Acer tree (the 'all-compat' output of MrBayes; encounter also Grimm 2003), utterly flawed (according to our reviewers dorsum then). Feel gratuitous to depository fiscal establishment check out works life phylogenetic papers published dorsum so inwards MPE. |
After iv or to a greater extent than months of review, nosotros got dorsum a determination ("reject") amongst the anonymous experts pointing out that my analyses were rubbish – mainly Bayesian tree inference (see above; i reviewer told us to rely on maximum parsimony instead because "Bayesian analysis may discovery incorrect trees in addition to needs farther tests") spiced amongst some in-detail sequence motif analyses of to a greater extent than ofttimes than non length-polymorphic in addition to indel regions (Forest of Reviews is non only shrouded past times the Impermeable Fog, it is a nighttime in addition to deep i harbouring many dissimilar sorts of beasts.
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| An instance for the ITS motif analysis included inwards the newspaper (the "n" used to live filled squares representing the nucleotides/site polymorphism, but I lost the proper font) |
But what puzzled me in addition to seat MPE on my never-submit-there-again-list was that before long after my/our piece of work was judged flawed in addition to I was told that I'm needing assist to practice proper phylogenetics (see Denk et al. 2002, where I also did the molecular phylogenetic analyses on my own), I was asked to review two works life phylogenetic papers submitted to MPE. I wrote dorsum that I'm honoured to human activity as a reviewer of such a prestiguous journal, but can't assist to wonder how I managed to live upgraded from a know-nothing to a phylogenetic proficient inwards such small fourth dimension (and without having published anything in-between).
Another information to non-scientists: Many journals require ii reviews, but it tin live hard (or impossible) for an editor to larn one. So, yous shipping the newspaper to a Ph.D. or inexperienced post-doc knowing they can't afford to say no, as they may desire to break inwards your magazine inwards the future. And in that location piddling risk, the immature researcher volition either create a rattling careful in addition to constructive review (and pass a lot of fourth dimension doing it) or a harmless i for the bin.
I didn't larn an invitation to review a MPE paper in i lawsuit to a greater extent than for quite a time. And when I got i again, a decade later, I thankfully declined for to a greater extent than than i argue (all of which I pointed out to the editor). [PS I got the invitation shortly after nosotros published Chen et al. (2015) inwards MPE, because J. Biogeogr. didn't desire it — a tip: if J. Biogeogr. turns your downwardly your biogeographic newspaper amongst non so bad reviews, MPE will belike convey it.]
Over a twelvemonth afterwards after my failed start in addition to only submission to MPE, I happened to live recruited as a co-author on a newspaper on a moss genus, Isothecium, amongst quite complex information signals in addition to (pseudo-)cryptic species. Our start writer needed the deport upon that MPE provides, branding should non live but is of import inwards scientific discipline in addition to MPE is a solid ranking mid-tier magazine amongst a sufficient deport upon ingredient for those of us that are non booked on Nature, Science etc. Review took ages, as my start writer seat it "a trip to hell": nosotros submitted Dec 2005, in addition to waited total nine months for the determination (the editor existence clearly annoyed amongst her peers, in addition to I got the impression, amongst MPE's peer review inwards general). No large surprise, MPE usually published cladograms (standard so in addition to still, although phylograms should live obligatory, also inwards molecular phylogenetic studies), in addition to nosotros came running fatty amongst networks. One anonymous review was so badly done that the editor decided it's non fifty-fifty worth sending along. The 2nd (also anonymous) was mixed but quite comprehensive helping to streamline our manuscript. Our editor wrote "Although the reviewer expresses involvement inwards the full general patch of study expanse of the paper, the reviewer also expresses a serial of reservations that forestall publication of the newspaper inwards MPE." The newspaper (Draper, Hedenäs & Grimm 2007), which was quite a unique (and cool) slice for the fourth dimension in addition to initiated some involvement inwards networks inwards bryology inwards full general (GoogleScholar gives 49 citations), was published nonetheless, thank yous to our editor. She decided to curvature a fleck the journal's rules "However, if yous experience that yous tin suitably address the concerns in addition to issues raised past times the reviewer, I would live willing to consider a revised manuscript. Also, delight live advised that the revised manuscript may live patch of study to re-review." It was not, our revision in addition to response missive of the alphabet was submitted halt of September, nosotros tryied in i lawsuit to a greater extent than the route to hell in addition to were prepared to human face upwards a few to a greater extent than months of re-review. But precisely ii days later, she accepted-as-is, in addition to I silent call upwards our editor made a goodness choice.
Why yous should non break inwards MPE
First, it's an Elsevier journal, in addition to as a scientist yous don't desire to back upwards the Coalition for Responsible Sharing.
Also, if yous belong to those utopian left-ish people, publishing inwards an Elsevier magazine equals stabbing Karl Marx (who precisely turned 200 in addition to is increasingly actual again) inwards the back: RELX is i of the most profitable companies inwards the how-to-make-the-public-hand-pay-for-shareholder-profits business.
In fact, yous should non piece of work inwards whatsoever capacity for an Elsevier magazine until they start in i lawsuit to a greater extent than to seat their "stakeholders" (that's the scientists doing all the piece of work for free) non start (the shareholders must live first, naturally, scientific publishing is pure oligopolistic capitalism, folks!) but at to the lowest degree essay to create their alive easier, non to a greater extent than difficult.
Second, providing access to the used phylogenetic data, the basic information demand to verify claims in addition to reconstructions inwards a paper, is editorial board of Palaeo^3, MPE's editorial board (or its reviewers, pers. obs. 2014) doesn't enforce to break crucial primary inquiry data.
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| Information non rarely works life nether the heading "Research data" of a MPE newspaper (or other Elsevier journals) |
This is also what yous discovery nether "Research data" for the recent MPE paper past times Liu et al. (2018).
Their phylogenetic data, the used information matrix, could perchance live made available on asking ... but only if yous inquire nicely the right person, namely the 4th out of vii authors.
[Note to non-scientists: inwards biological papers the of import people are inwards the front end or back, middle-authorships tin live awarded to people who receive got non truly done anything, or done a lot but don't demand a prominent writer position. Influenza A virus subtype H5N1 typical award-point organization is 5 points for a first-authorship, or asterisk-authorship (= equal contribution), 3 points for the "senior" (last) seat or corresponding author, in addition to 1 points for whatsoever other place.]
It's ok to criticise others, but non to live criticised
The newspaper of Liu et al. is non a peculiarly bad paper, I crossed worse biogeographic papers inwards MPE during my active time. |
| Extract of Fig. 1 inwards Liu et al. (2018) – showing the phylogenetic framework for their study: a cladogram masking the substantially varying branch-lenghts (between in- in addition to outgroup in addition to inside the ingroup) in addition to a topology pretty identical to the according subtree inwards Su et al. (2015) using a somewhat dissimilar cistron in addition to taxon sampling. See also this post regarding the seat of the outgroup-inferred root. |
That they downplayed or ignored most of what I pointed out, documented in addition to discussed during review (one to ii of the reviewers of our 2016–2017 Loranthaceae papers were co-authors of Liu et al.) inwards our papers regarding signal issues inwards the electrical flow molecular information (inevitable ingroup-outgroup long-branch-attraction in addition to banknote the number of silent ambiguously supported branches despite using a five-gene information laid amongst 85% gene/taxon coverage) is also non surprising. In contrast to Liu et al., our analyses (example provided below, information in addition to papers are opened upwards access) were non mentored in addition to guided past times the nigh-expert on the group, the paper's forth writer (out of seven), hence, tin live considered to live irrelevant.
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| The phylogenetic framework nosotros used inwards our 2017 (online) pollen newspaper (Grímsson et al. 2018): a rooted (with Nuytsia, based on before outgroup-rooted trees) bootstrap consensus network showing the best-supported in addition to farther (using maximum likelihood bootstrapping) topological alternatives for the relationships inside the Loranthaceae. Boxes reverberate competing alternatives supported past times the underlying information (here: strict genus consensus sequences based on all information available inwards cistron banks halt of 2014; same cistron sample as used past times Liu et al. 2018) |
And given the time-constraints of peers in addition to editors (who practice non larn paid for this piece of work past times Elsevier or whatsoever other publisher), i cannot aspect whoever reviewed in addition to edited Liu et al. (such information is confidential; didn't James Bond boost a Ph.D., too?) to receive got read ii opened upwards access papers published inwards the twelvemonth before that plainly triggered Liu et al.'s study (Grímsson, Grimm & Zetter 2017 [2018 inwards print]; Grímsson et al. 2017) in addition to browse through their quite large online supplements [GGZ'18, G&al'17] which include supplementary tables, figures, extented methods, in addition to primary information in addition to analysis files. Maybe, the i or other peer fifty-fifty did, but his/her comments regarding the results of the before papers got lost or were rebutted past times the authors? No reviewer contribution is mentioned inwards the acknowledgements of Liu et al. (which commonly means, they were non-existent, negative or annoying). And because of peer review confidentiality, nosotros volition never know what they said, suggested or criticised.
MPEalso doesn't give the call of the editor treatment a manuscript, something works life inwards many Elsevier journals to shield the editors responsible for accepting a newspaper from nasty criticism. On the journal's homepage, the editors are listed, but no contact details (why, did yous larn besides many complaints?)
But what truly bugged me was that the authors criticised our piece of work (especially my portion of it) including misleading or precisely incorrect statements in addition to without substantiating them or documenting their information matrix.
Which would allow me to respond in addition to laid things right. In this context, encounter also this overnice Berkeley Q&A page for students: Misconceptions close science.
Whereas our start newspaper (GGZ'18) that provided such access already during the review phase, enjoyed a fierce, largely uninformed regarding the methodological-phylogenetic portion but highly useful regarding systematic aspects, in addition to long battle fought behind the drapery of peer review confidentiality amongst i anonymous reviewer (likely the above-mentioned forth writer in addition to nigh-expert) over ii rounds. And all for nothing, when yous read Liu et al. [PS: The much smoother but notwithstanding productive review procedure of our 2nd paper, G&al'17, published inwards PeerJ and the solid soil for Liu et al. tin live viewed past times everyone interested at the paper's page. Peer review transparency works, in addition to gives committed reviewers in addition to editors due credit.]
Grímsson et al. (2018) was submitted February, the 2nd, 2016, 73 days nether review (it's a long paper, in addition to if it would non live against rules inwards scientific publishing, i could receive got awarded our reviewers a co-authorship for their contribution), revision handed inwards a calendar week afterwards (having corrected everything what reviewer #1 in addition to #2 told us; in addition to having explained reviewer #1 the basic information province of affairs in addition to what our graphs demo in addition to don't show). Second review circular equalled some other 89 days "under review" because a tertiary reviewer, an "expert of phylogeny" (anonymous, of course) was added since #1 silent rejected the newspaper in addition to #2 works life it cook to publish. The tertiary reviewer's written report for which nosotros had to hold off iii months was a data-situation ignorant slice filled amongst common-place statements that would convey other experts inwards phylogenetics iii minutes to write, as an according colleague ensured me; my responses to it were simple: inwards principle, yes, but delight depository fiscal establishment check in addition to run our freely accessible for anonymous download information matrix yourself when yous don't believe what nosotros write in addition to show. Our concluding revision in addition to re-analysis of Su et al. (2015; File S6 to Grímsson et al. 2018 [PDF]) to explicate the information in addition to signal province of affairs to reviewer #1 (and the phylogenetic proficient #3), who kept expressing some rattling naive believes regarding Su et al.'s analysis in addition to data, was handed inwards after 50 days (due to holidays in addition to us existence sick of responding again) in addition to was finally accepted for publication a calendar month afterwards (October, tenth 2017) without a farther comment.
Is it irresponsible to part data?
Testing Liu et al. claims would receive got been slowly for them, they precisely would receive got needed to re-do amongst their information what nosotros (I) did before amongst the information I could access. But they didn't. And I receive got no number amongst that. For professional person scientists, it's break or perish. One is good advised to only practice the necessary for a paper, thus, minimising the per-paper-effort.
Each peer may asking something else, in addition to yous cannot perchance anticipate all requests eventually seat frontward past times experts inwards the i or other aspect of your study or the other peers. My ain experience inwards the concern was, the to a greater extent than yous invest in addition to demo inwards a paper, the higher the run a jeopardy it volition neglect or live cutting downwardly (an example) during the widely applied single-blind confidential peer review. In the best case, it precisely increases the fourth dimension "under review". And i is to a greater extent than ofttimes than non ill-advised to advert whatsoever problems amongst one's data. And in i lawsuit a newspaper is published, its analyses in addition to information are rarely revisited (Using consensus networks to empathise pathetic roots. Showing why phylograms in addition to consensus networks are obligatory when i faces ambiguous back upwards patterns.
He also informed me that they receive got "more in addition to better" information "in hand":
... Over the in conclusion few weeks I receive got assembled a 5-gene dataset for all Santalales - 146 of the 163 genera inwards the guild ... All nodes inwards the tree are resolved, except some along the spine [surprise, surprise] of Loranthaceae. And during this process, I discovered uncorrected sequences from my lab that were submitted to Genbank years agone [which will] live corrected shortly.
Therefore, in that location is no argue for yous to live focusing so heavily upon sequences obtained from Genbank [if it would live obligatory to break phylogenetic data, I would non receive got needed to harvest the cistron banks at all] – we receive got to a greater extent than in addition to ameliorate character [?!?] sequences inwards manus now in addition to many of these volition live submitted inside the twelvemonth when the manuscripts are submitted for publication. ...
Therefore, in that location is no argue for yous to live focusing so heavily upon sequences obtained from Genbank [if it would live obligatory to break phylogenetic data, I would non receive got needed to harvest the cistron banks at all] – we receive got to a greater extent than in addition to ameliorate character [?!?] sequences inwards manus now in addition to many of these volition live submitted inside the twelvemonth when the manuscripts are submitted for publication. ...
I'm non only certainly why Dan felt obliged writing me this. But it has a certainly logic to upload only mediocre information to publicly accessible cistron banks (where everyone tin larn in addition to plunder the fruits of your hard work) in addition to job it for some emergency quick-shot paper, spell keeping to a greater extent than in addition to ameliorate information for the adjacent publication already inwards the pipage (where i tin claim a ameliorate identify inwards the writer list?) in addition to maybe inwards a ameliorate magazine than MPE. By the way, Liu et al. was "Received xiv Nov 2017; Received inwards revised cast 3 March 2018; Accepted 7 March 2018" (see also One appointment that is missing inwards many scientific publications). Publish or perish, i cannot hold off some other half-a-year to closed all gaps in addition to using the "more in addition to ameliorate character sequences", which according to Dan (and the authors) volition resolve the backbone.
... As I receive got seen recently, many phylogeny issues are resolved in i lawsuit i has accurate in addition to consummate sequences....
No, it won't. In cases similar this, i tin larn only larn higher resolution (unambiguous branch support) past times reducing the taxon laid in addition to increasing the cistron sample. Cut downwardly the bush to a information laid providing trivial-as-possible signal.And if it does, would i non live well-advised to job that ameliorate information for reconstructing the "Historical biogeography of Loranthaceae (Santalales)"? Accuracy of the dating in addition to the biogeographic inferences relies on well-defined branch-lengths. We precisely pushed dorsum the primary radiations at to the lowest degree xx Ma in addition to linked it to the Eocene warm-phase, which Liu et al. re-reconstruct in addition to verbalize over at large as their result. So why the hurry? To avoid that besides many people cite in addition to encounter our dating study in addition to realise i tin study Loranthaceae without Dan Nickrent inwards the helm?!
Dan's total post service (he also pointed out that former sequences may live of lower quality, hence, may inflict topological problems during tree inference in addition to that I could pay for filling information gaps) in addition to my answer to it, quite a read (Being a natural-born constructivist, I naturally included a serial of tips in addition to links, in addition to used the chance to bespeak out in i lawsuit to a greater extent than where I encounter problems but also how to bargain amongst them) can live works life here. It's clear that no-one exterior the His Majesty's Court volition larn the actual inquiry information used inwards publications. And Limin's promise that in that location volition live a response from his co-authors to the actual issues I raised inwards my ResearchGate comment to their newspaper has (so far) non been fulfilled, too.
Elsevier's responsible sharing of scientific information inwards the 21st century
The liberty of science. Influenza A virus subtype H5N1 retired proficient who is neither the start or 2nd author, the ii primary authors that contributed every bit to the newspaper according to the championship page, nor i of the ii corresponding ("senior") authors of a seven-author paper, decides who deserves access to the used data.This may explain, why in that location has been so piddling progress (phylogenetically speaking) inwards an former (pre-Eocene initial radiation), widespread in addition to interesting works life grouping similar the Loranthaceae. It would non live the start fief inwards systematic phytology in addition to similarly soft natural sciences existence controlled past times an former homo thriving on restricted access to cloth in addition to information (it's commonly a manlike soul at the top, fifty-fifty when it comes to flowers...). Someone, who should live a benevolent instructor (when yous are retired, your career is over) using his noesis to facilitate in addition to propagate research, in addition to non comprise in addition to command it.
Instead, the Lord of the Realm comfortably robes himself inwards the Impermeable Fog, making inquiry endorsed past times His Majesty unassailable (Su et al. 2015, amongst an online supplement challenging results reported inwards the primary text in addition to a tree riddled past times obvious signal issues in addition to information holes; Liu et al. 2018), spell existence able to line the strings as hard as possible against everyone daring to larn inwards his Very Own Realm.
But tin yous blame him? No, the job lies solely amongst journals similar MPE and publishers like Elsevier. Above all scientific petty kingdoms lies the Great Cloud: Elsevier's lax policies when it comes to information access in addition to documentation, but strict policies when it comes to peer review intransparence (sorry, confidentiality). Share, but part responsibly.
Sancho, laid upwards the mount. Time to ride against the windmills.
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| Source: Wikimedia Commons, past times רנדום |
Any (science) post should receive got a positive ending
Hence, a tip for those searching for challenging, freely accessible in addition to ready-to-use information matrices to play precisely about with. Once I had my homepage running, I started to upload all my information for anonymous download (mainly because most journals publishing our papers didn't render an according service).
Downloadable data
Find below a (alphabetically ordered) listing of archives including primary data, analyses in addition to results files used inwards our evolutionary in addition to other studies. For details refer to the master literature in addition to text files included inwards each archive. Anyone is invited to job these information for whatever purpose, fifty-fifty if yous desire to demo that nosotros were wrong, but inwards whatsoever case, yous job it at your ain risk: Archives receive got been tested in addition to should live gratuitous of viruses, trojans, worms, cladistics, etc., but inwards today's unsafe world, yous never know.
Find below a (alphabetically ordered) listing of archives including primary data, analyses in addition to results files used inwards our evolutionary in addition to other studies. For details refer to the master literature in addition to text files included inwards each archive. Anyone is invited to job these information for whatever purpose, fifty-fifty if yous desire to demo that nosotros were wrong, but inwards whatsoever case, yous job it at your ain risk: Archives receive got been tested in addition to should live gratuitous of viruses, trojans, worms, cladistics, etc., but inwards today's unsafe world, yous never know.
I e'er felt that providing a link to information matrix in addition to one's analysis results already during review stage could assist to avoid the i or other misunderstanding betwixt authors in addition to reviewers as e.g. inwards the instance of my start essay to break an Acer phylogeny inwards MPE.
And I e'er sent anyone my matrices when existence contacted or shared them when people were interested inwards them (published or not). It got me quite a fleck extra citation for my papers, in addition to fifty-fifty a few novel collaborations (after the start shock, that somebody sends information in addition to a ready-to-run matrix without asking for anything, non fifty-fifty a co-authorship).
Not only ideas in addition to thoughts, but also basic scientific information should live free.
And when it comes to (molecular) phylogenies, these basic information are small-scale in addition to uncomplicated files, ideally NEXUS-formatted (with the cistron regions annotated).
Related posts in addition to links
- The correspondance regarding my asking (so far) as PDF
- My comment on ResearchGate to the Liu et al.'s paper.
- Elsevier needs my help: The 10 ... no, non Commandments, precisely questions by a high-profit science-publisher that sets out to explore the wonderous globe of opened upwards science; amongst some links on their concern model (which is: you build the house, pay for all materials in addition to workers, create the check-up in addition to finish, in addition to inwards the end, they rent out your line of piece of work solid to you for a reasonable price).
- The Kraken awakes – Elsevier increases pressure level on ResearchGate (through the backdoor) inwards instance yous haven't heard yet of the Coalition for Responsible Sharing.
- We desire to break our phylogenetic information – including networks, but where? David Morrison in addition to I advocate in addition to scrap for opened upwards phylogenetic information in addition to providing some storage tips.
- Trivial but illogical – reconstructing the biogeographic history of the Loranthaceae
Chen L-Y, Grimm GW, Wang Q-F, Renner SS. 2015. A novel phylogeny for the aquatic household unit of measurement Aponogetonaceae, combined amongst northern hemisphere fossils, rejects the hypothesized Australian root of the family. Molecular Phylogenetics in addition to Evolution 82:111–117.
Denk T, Grimm G, Stögerer K, Langer M, Hemleben V. 2002. The evolutionary history of Fagus in western Eurasia: Evidence from genes, morphology in addition to the fossil record. Plant Systematics in addition to Evolution 232:213-236.
Draper I, Hedenäs L, Grimm GW. 2007. Molecular in addition to morphological incongruence inwards European species of Isothecium (Bryophyta). Molecular Phylogenetics in addition to Evolution 42:700-716.
Göker M, Grimm GW. 2008. General functions to transform associate information to host data, in addition to their job inwards phylogenetic inference from sequences amongst intra-individual variability. BMC Evolutionary Biology 8:86.
Grimm GW. 2003. Tracing the way in addition to speed of intrageneric development - a instance study of genus Acer L. in addition to Fagus L. D.Sc. thesis. Eberhard-Karls University.
Grimm GW, Renner SS, Stamatakis A, Hemleben V. 2006. Influenza A virus subtype H5N1 nuclear ribosomal deoxyribonucleic acid phylogeny of Acer inferred amongst maximum likelihood, splits graphs, in addition to motif analyses of 606 sequences. Evolutionary Bioinformatics 2:279–294.
Grímsson F, Grimm GW, Zetter R. 2018 [2017 online]. Evolution of pollen morphology inwards Loranthaceae. Grana 57:16–116.
Grímsson F, Kapli P, Hofmann C-C, Zetter R, Grimm GW. 2017. Eocene Loranthaceae pollen pushes dorsum departure ages for major splits inwards the family. PeerJ 5:e3373 [e-pub].
Vidal-Russell R, Nickrent DL. 2007. The biogeographic history of Loranthaceae. Darwiniana 45:52–54.
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