The newspaper (Wanntorp et al. 2014) stumbled quite a fourth dimension through the Forest of Reviews. The outset mag nosotros tried (J. Biogeogr.) was uninterested, mainly because nosotros did non include an explicit biogeographic inference in addition to a molecular dating. Which would pick out been pretty much chasing ghosts in addition to generating house-numbers nether the given circumstances. Nevertheless, since chasing ghosts using house-number is non uncommon inwards (plant) biogeography, they pointed it out as a deficit of import plenty to spend upwardly the newspaper (among other things, naturally). So nosotros added those, in addition to the adjacent mag (BMC Evol. Biol.) allowed us 2 rounds, but finally turned downwards the newspaper because ... well, nether the occupation ... the added biogeographic inference in addition to molecular dating didn't adapt the instant journal's reviewers. So, our brain-and-pain tike was shipping a tertiary fourth dimension into the Forest, finally finding a journal, Taxon, that would seat out the study. With a catch. Because going “too far” for their readership, the editor advised us (for non-scientists: editorial suggest inwards confidential peer review way exercise it or respect but about other journal) to driblet all my squeamish network figures. Figures in addition to reconstructions that were considered “a squeamish touch” past times a reviewer judging our newspaper before, in addition to a argue that editor allowed a revision. To protest, I was well-nigh to driblet out, too. I did not, in addition to however regret it to brand a point. Had invested also much time, work, in addition to passion into this slice (like the outset author); I couldn't. But when they tried this a instant fourth dimension several years later, inwards illustration of a newspaper on another asclepid, Cynanchum (Khanum et al. 2016), I retreated from the co-authorship. Which had the positive lawsuit that my co-authors were allowed publishing our bootstrap consensus networks. Influenza A virus subtype H5N1 sacrifice worth it (compare both papers).
The background: complex genetic differentiation patterns
The genetic information of my outset writer (comprising the nuclear-encoded 5'-ETS, ITS1 in addition to ITS2 spacers of the 35S rDNA; in addition to the plastid intergenic trnH-psbA and trnT-trnL spacer) were complex, why she ended upwardly amongst me as a co-author. But, inwards the complexity was structure, but waiting to live distilled. Several principal clades emerged, supported past times nuclear in addition to plastid factor regions, in addition to i could convey them inwards a quite sensible geographic framework (per hand-and-eye, non actually per inference). Because of the signal issues, a total analysis was done: single-gene trees, trees for nuclear vs. plastid data, combined analysis, analysis amongst restricted taxon laid in addition to outgroup, in addition to bootstrap back upwardly consensus networks highlighted signal issues, in addition to identified rogues – the taxa jumping across the tree – in addition to the occasional local incongruences. The only figure that passed through concluding editorial scrutiny was a tanglegram. |
| The plastid (left tree)-nuclear (right tree) simplified tanglegram, a graphic deemed publishable past times Taxon's editors. Colours refer to principal intra-generic lineages amongst lineage-specific nuclear in addition to plastid signatures. Trees are rooted against a few species of Dischidia, a closely related (possibly partly co-generic) genus of the Marsdenidae. |
And a (quite ordinary) tree, naturally, based on the combined information in addition to amongst but about critical depression supported branches. The electronic supplement at the journal's homepage but includes the voucher information in addition to a tabulation of the figure above. An archive (1.6 MB) including the tree inference in addition to bootstrapping results but non the primary information (first author's call, non mine), too, tin live flora here.
Why bootstrap consensus networks should live obligatory
In illustration of complex genetic data, trees may be- biased, showing a topology that prefers branches over improve supported, competing alternatives
- incomprehensive, showing only the back upwardly for the branch inwards the tree, it cannot live assessed whether a depression back upwardly is due to a conflicting alternative, or weak but unambiguous signal
 |
| Bootstrap consensus networks for the combined plastid (A; trnH-psbA + trnT-trnL) in addition to nuclear (B; 5'-ETS+ITS) data, included inwards the version for mag #2, in addition to the master version submitted to mag #3 (Taxon). And lost to the editorial streamlining. Terminal clades collapsed for improve visibility. Labels in addition to colours same as inwards the (reduced) tanglegram above. |
Bootstrap consensus networks are rarely seen inwards phylogenetic literature in addition to may live quite alien to reviewers, editors in addition to – later on – readers. Hence, the figure higher upwardly was preceeded past times a figure that included portions of the (full) bootstrap consensus networks at the relevant branches inwards the combined tree.
 |
| Combined (plastid + nuclear) tree amongst phylogenetic "weak spots" addressed using competing bootstrap (BS) back upwardly patterns. Colours in addition to labels as before. Values at tree branches in addition to border bundles give the non-parametric BS back upwardly using K pseudoreplicates computed from the combined matrix. |
The bootstrap consensus networks tin seat how rogues cause topological ambiguity. Moreover, they present whether depression branch back upwardly (e.g. BS <50) relates
- only to the lack of decisive signal – all alternatives amongst real depression to diminishing support, or
- conflicting signal – two, iii competing every bit valid alternatives sharing ample (low) back upwardly (usually the illustration here, when it comes to inter-lineage relationships).
- just two-third of the information (segregating sites) supporting this split, the balance beingness uninformative, or
- one tertiary of the information back upwardly a conflicting split?
Why using median-networks, a population genetic method, for interspecies relationships
The score of intra-lineage departure inwards each factor part Hoya was quite low. Furthermore, I tabulated the sequences (included inwards the master supplement, but non inwards the concluding "edited" version) in addition to checked their mutation patterns. Mutation patterns that revealed but about other score of ambiguous signal: ancestral sequence variants coexisting amongst champaign derived ones.Lack of departure tin live a occupation for probabilistic tree inferences, since the likelihood surface of the tree infinite – the magical airplane that decides whether i tree is improve than but about other – is quite flat, to a greater extent than similar a lake than a mount chain. Under these weather Bayesian inference falters (posterior probabilities, PP << 1.00), in addition to ML tree-inferences struggle, but parsimony tin work. The occupation amongst parsimony tree-building was inwards illustration of our information the amount of stochastic signal, its complexity. And all tree inferences autumn brusk inwards the appear upwardly of actual ancestor-descendant relationships: an ancestor would demand to live placed at an internal node, non at a tip [first phylogenetic trees, stacking neighbour-nets, why networks are inevitable, also inwards cladistics].
Countering both issues, median networks are a vivid tool:
- They include all parsimony trees, the parsimonious solutions that tin explicate the data.
- In contrast to ordinary parsimony trees, which care for all taxa as tips, median networks allow placing a taxon at an internal node, the median.
Noticing the resolution issues visible from the single-gene bootstrap consensus networks (towards the tips of the trees) in addition to the quite obvious mutation patterns emerging from the information tabulation, I decided using median-joining networks as vehicle to
- make a telephone phone well-nigh ancestry in addition to derivedness of sequence variants, in addition to see
- how retentivity of ancestral variants inwards i or several factor regions affects the tree inference in addition to explains conflicting bootstrap back upwardly patterns.
 |
| Simplified median-joining networks based on group-informative sites. A–C. Relatively variable/discriminative spacer regions: nuclear-encoded 5'-ETS (A), ITS1 (B), in addition to plastid trnT-trnL (C). D–E. Conserved/rather indiscriminative regions: nuclear-encoded ITS2 (currently advocated as barcode inwards every bit or worse differentiated groups) in addition to plastid trnH-psbA (length-heterogenous spacer, only unambiguously alignable nucleotide were considered). Note that the isolated micro-lineages (cyan, pink, white) are oft ancestral inwards their basic sequence compared to the diversified in addition to probable to a greater extent than of late radiated clades V (blue) in addition to VI (red). |
Despite non welcomed past times the editors, the network-based findings (largely undocumented then far) however play a purpose inwards the published paper. They were the principal footing for the discussed hypothesis(-es).
Confidential peer review hinders out-of-the-box-thinking
Median-joining networks are parsimony-based graphs; in addition to that I had to omit them did non lack irony. One of the recurrent reviewer critiques was that nosotros did non include a parsimony analysis to dorsum upwardly our maximum likelihood-based analysis framework. Grace to the Impermeable Fog shrouding the Forest of Reviewers, peers (rarer editors) judging the character of a newspaper are costless to human action similar imbeciles (on a case-to-case basis). Only authors in addition to editors read their reports. Authors, who are non only boundary past times confidentiality, but pick out to live friendly in addition to wilful to non lose the peril to seat out their paper. Facing editors who may cry upwardly real highly of their (anonymous to the authors) catholic (all-encompassing in addition to champaign infallible) peers, in addition to non rarely lack competence inwards the same fields. Naturally, none of Taxon's editors, a systematic-botanical journal, or our concluding reviewers, tin live considered an skilful of phylogenetic inference in addition to comprehensive analysis of non-trivial information patterns. Editing a low/mid-tier mag tin live tedious, the editor may live but happy having flora anyone reporting on the submitted run (which tin live hard enough, inwards detail for drafts roaming inwards the Forest of Reviews for quite but about time). So that mortal should live kept happy for the adjacent time(s) his/her services are needed. But since the review procedure is confidential, the reader (or whatever 3rd party) cannot know well-nigh the fights in addition to fiddles surrounding the publication of a paper. And thank yous to Taxon's editorial wisdom, which shields their readers from reconstructions going "too far", the to a greater extent than to a greater extent oft than non interested reader may respect it hard to empathise where the ideas of the authors come upwardly from. Because the principal reconstructions were stripped from the principal newspaper (and supplement) during review. Like inwards this case.Open information in addition to graphics (free to re-use)
The lost figures in addition to supplementary information tables pick out been uploaded to figshare (including the primary information files) in addition to tin live referenced as:- Grimm GW. 2017. Over-the-edge tables in addition to reconstructions linked to the slimmed-down newspaper of Wanntorp et al. (2014), published inwards Taxon. figshare https://doi.org/10.6084/m9.figshare.5688181
Further links in addition to references
- Grimm, GW. Using consensus networks to empathise pathetic roots. The Genealogical World of Phylogenetic Networks (ed. past times D. Morrison). http://www.rachelteodoro.com/search?q=
- Khanum R, Surveswaran S, Meve U, Liede-Schumann S. 2016. Cynanchum (Apocynaceae: Asclepiadoideae): Influenza A virus subtype H5N1 pantropical Asclepiadoid genus revisited. Taxon 65:467–486. — http://www.rachelteodoro.com/search?q=
- Wanntorp L, Grudinski M, Forster PI, Muellner-Riehl AN, Grimm GW. 2014. Wax plants (Hoya, Apocynaceae) evolution: epiphytism drives successful radiation. Taxon 63:89–102. — Official link; — electronic supplement archive @ palaegrimm.org/data (1.6MB); — PDF amongst the master laid of figures (including total legends)
- Network 5 – costless network software past times Fluxus to grip information in addition to compute median, median-joining in addition to reduced median networks: http://www.fluxus-engineering.com/sharenet.htm
- RAxML 8 – the electrical flow touchstone of maximum likelihood analysis, ideal to run a total laid of analyses (tree inference + bootstrapping using a batch/shell file) on minor information sets similar this i (also standalone; no demand for a processor grid)
- SplitsTree 4 – the costless in addition to classic software past times Huson in addition to colloborators to generate consensus networks in addition to gear upwardly them for publication
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