Note to the reader: This is a post, non a scientific paper. Hence, my pick of literature is biased, together with I may easily take away hold overlooked something crucial. Admittedly, I used this chance to set out some reconstructions that never saw the low-cal of solar daytime (so to say), for diverse reasons (like my reluctance to shoosh my brain-child into the obscurity of the Forest of Reviews so it may live judged yesteryear the Wizards of the Forest).
You are gratis to rectify or comment: the comment choice is anonymous (only Google together with maybe the NSA volition live able to delineate you lot down). I do non encourage anonymous comments: scientists should live able to openly limited their persuasion on scientific matters but the reality of confidential peer-review (in together with beyond palaeobotany) demonstrates that this is non the case. As a affair of course, none of the authors of papers cited hither take away hold interacted with me regarding the content of this post. I am solely to blame 😈
Quicklinks
- Wang's “critique” of Herendeen et al. (2017)
- “Palaeobotanical Redux” ... would take away hold been nice
- Angiosperms must root deep
- The thing nigh dating
- Late Jurassic is a goodness guess for the flowering plant crown age
- The (cryptic) sis lineages of angiosperms
- What a palaeobotanical redux on the historic menses of angiosperms could human face like
Wang’s newspaper is a comment to a review on the flowering plant fossil tape yesteryear Herendeen et al. (2017) with the promising championship "Palaeobotanical Redux: Revisiting the Age of Angiosperms"; published inward March inward 1 of Nature’s many online (this 1 is non opened upwards access) off-shots, Nature Plants, a "natureresearch journal"[1].
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| Price of access to Nature Plants |
Five bucks is a fleck inexpensive for a Springer-Nature publication, though (probably non truly a seller, yet, this Nature Plants).
Furious together with entertainingly unprofessional with a truthful core: Wang's critique of Herendeen et al. (2017)
Not interested, fountain to adjacent sectionThe foremost judgement of Wang's abstract summarises good the content of his – good – persuasion piece: “A lately published review yesteryear Herendeen et al. is misleading, self-centered, self-praising, together with self-conflicting.” You wouldn’t teach this declaration yesteryear the High Wizards of the Forest of Review, but it is truthful to a worrying degree. It is fifty-fifty to a greater extent than truthful for Wang’s small but fiery piece. Seems to live a commonly shared designing alongside palaeobotanists interested inward early on angiosperms (never has been my loving cup of tea; curious but spurious data, specially when it comes to analysis, example provided below).
On the half-dozen pages, Wang ...
- ... shows the usual not-showing-much pictures (see also Herendeen et al. figs 3, 4; annotation the dark together with bluish arrows inward fig. 3A) that create many palaeobotanical papers solely uninteresting to non-experts. The purpose of the figures is to dorsum upwards some overly detailed intelligence of why the interpretation of shadows, bulges together with grooves yesteryear others were wrong culminating into dissection of phrases together with descriptions inward the literature that are seemingly inward conflict with themselves.[2]
- ... identified a "formidable tendency inward electrical current palaeobotany ... misinterpreting information according to their ain academics needs". Funny, because this has been done since the dawn of palaeobotanical enquiry (compare e.g. Nathorst’s published drawings with the original, photo-realistic pencil drawings of his illustrator; Denk et al. 2011) together with applies equally much to Herendeen et al. equally it applies to Wang's papers, or papers of other leading palaeobotanists (e.g. Rothwell & Nixon 2006; Rothwell et al. 2009; Crepet & Stevenson 2010). Although based on stones, palaeontology is, inevitably, the softest of all naturals sciences.
- ... gets to a greater extent than oft than non lost, criticising Herendeen et al. beingness biased yesteryear their ain research, rejecting results of others, together with overlooking or downplaying of import finds from other fields of scientific discipline – yesteryear doing just the same.
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| The motto of Herendeen et al.'s review newspaper |
"Palaeobotanial redux: revisiting the historic menses of the angiosperms" ... would take away hold been nice, indeed
Not interested, fountain to adjacent sectionHerendeen et al. write (abstract): "Their [the angiosperms] evolutionary together with ecological appearance is thus of considerable involvement together with has important implications for understanding patterns of diversification inward other lineages, including insects together with other animals." together with dot out (here together with there) the importance of the fossil tape for other biological disciplines such equally dating. Cited are only negative dating examples, of course, together with non e.g. this one: Magallón et al. (2015). Which does much to a greater extent than for reviving palaeobotany than Herendeen et al.'s review newspaper together with would take away hold fully fit inward their line of argumentation[3]. And the 4 authors, acting equally the Horsemen of Palaeobotany[4], are non only "... leaving the impression that they were only authoritative on the root together with early on history of angiosperms" (Wang's abstract), they effectively are (for rattling goodness together with some bad reasons[5]). So, the minimum 1 could await – regarding the championship together with with the authors' expertise together with decades of enquiry on early on angiosperms – would have been a tabular array or electronic supplement listing all the fossils that may stand upwards for early on angiosperms or take away hold falsely (according to the authors) live addressed equally such.
- Names, electrical current together with original, with the appropriate references (original description, emendation);
- currently accepted ages, non a few fossil strata take away hold been re-dated;
- botanical affinity according to the master authors together with the persuasion of the authors equally experts on the topic.
Age. The historic menses of crown-group Nymphaeales is around 125 m.y. (Magallón et al. (2015), (133.2-)126.7(-120.6) m.y.a. (Iles et al. 2014), equally fiddling equally (176.6-)97.7(-42.8) m.y.a. (Zhou et al. 2014), or equally much equally ca 164 (Z. Wu et al. 2014), ca 188 m.y. (Tank et al. 2015) or ca 209 m.y. (Foster et al. 2016a: q.v. for details). The curious fossil Archaefructus, in all likelihood an aquatic industrial plant life together with nigh 124 m.y. old, has been linked with Hydatellaceae inward morphological analyses (Doyle & Endress 2007, 2010; Doyle 2008b). Although they take away hold rattling fiddling inward mutual inward price of overall appearance, Archaefructus may live some other early on aquatic flowering plant with rattling unconventional floral morphology. Hydatellaceae may live represented inward the pollen tape from the Isle of Wight inward rocks of some 130 m.y. of historic menses (Hoffmann & Zetter 2010). Numerous other fossils [Stevens' listing all Herendeen et al.'s fossils] take away hold been identified equally members of Nymphaeales; these are discussed below nether Cabombaceae together with Nymphaeaceae [here you'll observe Monetianthus].
In Herendeen you lot just tin read: "The dubiety over the phylogenetic seat of Archaefructus provides a illustration inward point." for "...the possibility that such fossils were truly on the flowering plant stalk grouping rather than inward the crown group" together with citing 3 papers, but only 1 (Doyle & Endress 2014, the add-on to Doyle & Endress 2010 cited yesteryear Stevens, showing the same) that tried to house Archaefructus in an explicit phylogenetic context. Whereas the (neo)botanist Stevens (2001 onwards) provides a review of the earliest fossil tape and, hence, demonstrates the usage of palaeobotanical research, the skilful palaeobotanists are busy to dot out that fossils are so hard to house (too many uncertainties around them) that they are essentially useless to neighbouring scientific fields. Not truly a "redux", but what you'd await from the Four Horsemen. |
| Possible classification concepts for angiosperms. Blue cloud: non truly (crown) angiosperms according to Herendeen et al.'s definition: "...crowngroup angiosperms, defined equally the most recent mutual ancestors [plural? Hybrid or multiple origin(s) or mistype?] of all living angiosperms together with its derivatives". Later inward the text, Herendeen et al. combat that whatever fossil that cannot live reliably assigned to 1 of the modern, crown-group lineages (i.e. Amborellales to magnoliids), should also non live considered equally a crown-group angiosperm, inward violation of their ain node-based Definition (red cloud). Grey bar, Hennig's cladistic paradox (discrepancy betwixt phylogenetic together with cladistic classification systems; meet also this recent postal service yesteryear D. Morrison) |
- Since none of the pre-Cretaceous fossils tin live reliably associated with crown (!) angiosperms, they are probable non angiosperms at all.
PS Something Wang over-read (or did desire to over-read) and, I may humbly add, a near-literal quote of what I told Horseman #2–#4 nigh a decade ago, when #2 made me a co-author (Friis et al. 2007; to the growing despair of #4, who prevented us from publishing this nonsense[6]).
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| A graphic depiction Herendeen et al.'s fuzzy logic: Why pre-Cretaceous pollen cannot live flowering plant pollen |
Angiosperms take away hold no closed living relatives, hence must root deep
Not interested, fountain to adjacent sectionThe basic province of affairs is pretty simple. Molecular information clearly showed (and from the rattling start) that the flowering plant crown node (the Horsemen's preparation field) is far away from the flowering plant stalk (root) node (which the Horsemen non truly bother about); the flowering plant root length covers most of the crown-tip distances inward all-angiosperm or all-spermatophyte (all living seed plants) trees. The figure below shows a ML tree inferred from a curated (much updated[7]) information subset (same cistron sample, less taxa) of Soltis et al. (2011), the molecular-phylogenetic newspaper cited inward the Herendeen et al. H5N1 tree, I inferred nigh 5 years agone for an abandoned fiddling projection with a total-evidence dater[8] together with that I showed Horseman #2[9] (and others on occasion).
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| A non-comprehensive molecular-based flowering plant tree inferred from a curated, taxon-reduced version of the Soltis et al. (2011) matrix (the matrix includes coding genes from all 3 genomes, mostly plastid genes, hence the Gne-Pine branching artefact inward the outgroup; meet also Goremykin et al. 2015). All main clades of angiosperms (colours) are unambiguously supported. The flowering plant backbone lacks back upwards at some places. And the flowering plant root, the branch conncting the flowering plant stalk together with crown nodes, is to a greater extent than prominent than anything else. |
Even when nosotros assume massive charge per unit of measurement shifts (which are likely, annotation the branch-length imbalance inward the ML tree above; meet also Magallón et al. 2015), it is clear that the foremost fellow member of the flowering plant lineage – the ancestor of modern angiosperms together with their putative, so far cryptic sis lineages (but meet below) equally defined yesteryear the flowering plant stem (root) node – lived long before the final mutual ancestor of all modern (living) angiosperms – defined yesteryear the flowering plant crown node.
The thing with dating
(why palaeobotanists should partake inward it instead of ranting nigh it)
Not interested, fountain to adjacent sectionThe combination of an extremely long-root, a condensed proximal part, together with partly inflated distal part, explains the work inward dating stalk (root) together with crown ages together with their vulnerability to sampling bias. Why it would take away hold been crucial that the Horsemen would take away hold set some endeavour inward evaluating the fossil historic menses constraints used for the many molecular dating studies when revisiting the historic menses (crown and stem) of angiosperms. Who else is qualified to dot to problematic constraints?
Let me illustrate the work with a rattling unsmooth dating experiment using Monetianthus, the fossil Wang gets lost about. Monetianthus has been character-wise together with phylogenetically placed inside the Nymphaeales, it's closed to the Nymphaeaceae (Friis et al. 2009; meet also Stevens 2010 onwards) together with is in all likelihood (and "provisionally" equally nosotros write on p. 1091) belatedly Aptian-early Albian, i.e. 113 Ma (Cohen et al. 2013, updated). Ultrametrising the ML tree higher upwards together with assuming a uncomplicated strict clock, nosotros would infer
- a minimum flowering plant crown historic menses of 270 Ma, mid-Permian, implausible together with probable wrong, but a crown historic menses non also far from the dating papers cited yesteryear the Horsemen (and published inward peer-reviewed journals, probable without beingness reviewed yesteryear palaeobotanists);
- an flowering plant stem (root) historic menses beyond the possible: c. 580 Ma; the fourth dimension of the Ediacara biota, the foremost complex biocoenosis (marine naturally, the solid ground was soundless barren).
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| Crude, strict-clock estimates for root (stem; "Origin") together with crown historic menses ("MRCA") of the flowering plant lineage using Monethianthus' phylogenetic seat inside the Nymphaeales (Friis et al. 2009) |
- Obviously at that topographic point were charge per unit of measurement shifts betwixt the Nymphaeaceae crown together with root together with deeper branches, so applying a strict clock is fundamentally flawed.
- If nosotros could sample the deoxyribonucleic acid of Monetianthus, we would probable observe sequences much closer to the MRCA (tree distance = cumulative branch-length) than seen inward the ultrametrised tree (same would apply for coeval members of the Trithuria and Amborella lineages).
- fix a minimum flowering plant crown historic menses of 113 Ma; together with nosotros would
- estimate a Middle Triassic stalk (root) historic menses of 245 Ma.
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| Same equally above, but fixing the historic menses of the MRCA of modern angiosperms to the historic menses of Monetianthus. |
- wind-dispersed – animal-dispersed pollen is to a greater extent than oft than non rare(r), together with oft has patchy fossil records (even post-Early Cretaceous, when angiosperms already dominated the world);
- did non evolve their pollen sculpture inward 50–100 Ma – which is something traditional palaeobotanists similar to pass upwards equally possibility inward to a greater extent than recent context per se when beingness confronted with > 50 Ma former pollen just looking similar (lineage-diagnostic) modern counterparts[10].
Monetianthus is non the foremost angiosperm, at that topographic point are older ones, but – the Horsemen's objective is devastation non revitalisation – Herendeen et al. prefer to non introduce them inward a concise fashion (again meet Magallón et al. 2015: fig. 1; much older clock-based estimates inward contrast to the rule: node-based estimates should live – yesteryear regulation – also young). In fact, the "redux" doesn't fifty-fifty furnish or speak over candidates for the rattling earliest (crown or stem) angiosperms (but meet Friis et al. 2011). Maybe because these candidates take away hold been described yesteryear their competitors (Wang's opinion), maybe because they take away hold just no idea, maybe they are afraid to limited it (my opinion; it could live wrong equally inward the illustration of Friis et al. 2001, what an chance for their enemies to teach old-testimonial). Errare humanum est, but non an choice for the demi-gods inward their ivory towers.
Just for fun, let's assume Monetianthus is the foremost representative of the Nymphaeales s.str. (excluding the long-branched, potentially first-diverged together with strongly derived Hydratellaceae; meet also this postal service on misleading, long-branched roots). Result: crown historic menses > 150 Ma, i.e. Late Jurassic; stalk historic menses > 320 Ma (mid-Carboniferous).
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| One more, treating Monetianthus equally the oldest tape of the Nymphales s.str |
This does, however, non hateful that Monetianthus is the foremost mutual ancestor of all Nymphaeales s.str., but that placing it at that topographic point gives 1 to a greater extent than realistic root-crown-tip distances (i.e. compensates to some storey for the charge per unit of measurement change). Fossils together with molecular clocks tin live co-informative together with used to essay hypothesis (and interpretations; meet e.g. Bomfleur et al. 2015). Would maybe take away hold been an of import dot to create inward a "palaeobotanical redux" ...
Angiosperm crown-age? Late Jurassic is a goodness guess
Not interested, fountain to adjacent sectionH5N1 Late Jurassic crown-age, inferred yesteryear non a few former but also recent dating studies – none of which the Horsemen cite, next the 10th of the Holy Commandments of True Palaeobotany: Thou shalt non travel out Thy Ivory Tower – makes sense when 1 tries to arrange belatedly Early/early Late Cretaceous flowering plant fossils inward a phylogenetic framework, e.g. using a Bayesian total-evidence approach.
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| A Bayesian (majority-rule) counterpart of the ML tree before, but based on a combined molecular-morphological matrix (Grimm 2018) together with including early on crown angiosperms (stars; morphological division = matrix of Doyle & Endress, 2010). Note that most fossils (filled stars) create longer terminal branches than their modern (extant) sis taxa: the analysis resolves them equally to a greater extent than derived. When running this information laid using the total-evidence dating approach (Ronquist et al. 2012), the conflict betwixt the terminal branch lengths of the fossils together with their assumed historic menses (all Early/mid-Cretaceous independent of their positions inward the tree), forces the MCMC chain to optimise indefinitely to higher ages until the root historic menses of the tree hits the a priori defined maximum possible historic menses (analysed together with tested yesteryear S. Klopfstein, Feb./March 2013). Side note: Some branches with high, near-unambiguous ML-BS back upwards are collapsed (PP < 0.5) indicating that the added morphological division truly messes upwards some things. |
All major lineages of extant angiosperms are known from the Early (mid-)Cretaceous, including sublineages relatively high-up inward the currently accepted flowering plant tree. Herendeen et al. cite a twain of them (mostly those they described themselves for natural reasons[12]). The root-proximal small branches (in molecular or combined trees) bear witness that the initial radiations together with diversification of the flowering plant crown grouping was fast. But, no flowering plant lineage evolved, radiated, together with diversified inside a few 1 1000 m years (see e.g. Magallón et al. 2015), thus, it is unlikely that the lineage including the mutual ancestor of all modern angiosperms, was a near-contemporary of the known, derived fossils.
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| Estimated flowering plant crown-ages taken from Stevens' (2001 onwards) introduction to the angiosperms mapped on our final dating experiment above. Oldest estimates at top, youngest at bottom, because he's right inward pointing out that "It is amusing to meet a graph of suggested flowering plant ages against the publication dates of these ages...". Green, Magallón et al.'s (2015) appointment using a meta-calibrated (fully constrained) chronogram. H5N1 graphic comparing estimates together with earlies crown-group flowering plant fossils would take away hold been obligatory for a "palaeobotanical redux" to "revisit the historic menses of (crown) angiosperms" (title of Herendeen et al.'s review paper). |
The (cryptic) sis lineages are crucial to speak over historic menses of angiosperms
Not interested, fountain to final sectionAnother way to define to a greater extent than sensible flowering plant root ages is to seat their sistergroup(s), inward companionship to add together informed "shadow-nodes" to the flowering plant root. Nodes that dissever the root branch into the actual flowering plant root together with the stalk branch(es) of angiosperms together with their putative sis clades.
The Horsemen dot to "Caytonia [is] a well-known case", without providing whatever reference (the compass of Nature Plants is all plant-related research, so their reader may non live familiar with the well-known – inward palaeobotany – case). Maybe to avoid citing their enemies (?) such equally this written report (officially peer-reviewed, but non yesteryear someone experienced inward phylogenetic reconstructions): Rothwell, Crepet & Stockey (2009). Caytonia was resolved together with well-supported (signal-wise) equally sis of the angiosperms (Hilton & Bateman 2006; meet also supplement to Friis et al. 2007). Fiercely disagreeing with Friis et al. (2007)’s conclusions together with interpretations, Rothwell et al. set a lot of endeavour inward re-coding the before matrix together with re-scoring Caytonia to demonstrate that Caytonia is non a sis of the angiosperms. While doing so, they also decreased the aAmplitude of discriminating signal inward the matrix (Grimm 2017a, 2017c), which Pb (in their consensus trees) to a collapse of several unchallenged clades.
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| Two neighbour-nets based on hateful morphological distances inferred from Rothwell et al.'s 'matrix 5' (A, including the debated Erdtmanithecales) together with their preferred ‘matrix 3’ (B). Values exhibit non-parametric bootstrap (BS) back upwards nether the least-squares (via neighbour-joining) together with parsimony optimality criteria (10,000 BS replicates) for compatible together with competing phylogenetic splits. Green = splits inward understanding with ..., bluish = best-supported but non resolved inward ..., together with scarlet = inward conflict with the strict-consensus trees shown yesteryear the authors (see also this postal service on the principal work with such matrices). |
This was collateral harm equally Rothwell et al. mainly aimed to destroy the Erdtmanithecales, which linked the Bennettitales to the Gnetales[13]. The Erdtmanithecales is the taxon Herendeen et al. usage equally illustration that pollen originally associated with angiosperms occurs inward groups non related to angiosperms.
Nonetheless, the Erdtmanithecales, goodness taxon or not, together with pollen associated with them, require farther studies. Is it identical to the monosulcate pollen of living angiosperms? Is it possible that non-related gymnosperms together with angiosperms (monosulcate pollen is typically institute inward 5 of the half-dozen main flowering plant lineages) evolved inward parallel? Or is it an bear witness for a shared mutual origin, a deep synapomorphy?
Remember: fifty-fifty reasonable clocks together with fully constrained dated trees prefer a Carboniferous flowering plant stalk age. Surely these foremost members of the angiosperm-lineage (from a modern-day, molecular perspective) were non only the ancestors of the angiosperms but probable some other, quite distinct, together with extinct (Permian and) Mesozoic seed plants.
The association of Erdtmanithecales with Gnetales together with Bennettitales is just 1 hypothesis. Horseman #2–#4 could take away hold informed their foremost writer that the matrix nosotros used (Friis et al. 2007) prefers a BEG clade ("Erdtmanithecales-Bennettitales-Gnetales"; a goodness hypothesis based on the data), but that the signal was (and is; Grimm 2017b) also faint to dominion out whatever other possibility. No affair which matrix I usage (Friis et al.'s or Rothwell et al.'s), I tin set the Erdtmanithecales also at the root of the angiosperms without inflicting also much pain. This would invalidate Herendeen et al.'s entire anti-angiosperm pollen argumentation, but opened upwards the avenue to care for conspicuously sculptured monosulcate pollen equally unique to the angiosperm-lineage. Maybe it is fifty-fifty the only unique characteristic of modern angiosperms together with their extinct precursors together with direct sis lineages that tin live institute (traced) inward the fossil record. Thus, invaluable for dating.
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| Lee et al.'s (2011) phylogenomic tree showing angiosperms equally sis to the gymnosperms (see also Magallón et al. 2015). Note the branch-length pattern: the flowering plant root is relatively small inward comparing to within-angiosperm diversification. Based on the seen designing a middle Carboniferous flowering plant stalk historic menses makes sense. But this may non live equivalent with the historic menses of the foremost (stem) flowering plant equally defined yesteryear the dot where the lineage leading to the modern angiosperms diverged from its final extinct sis lineage. Age for gymnosperms taken from Earle's introductory page (see at that topographic point for references). Earle cites a Late Triassic historic menses for the so-far unplaced, extinct Bennettitales (235–202 Ma), (co-)dominant seed plants of the Mesozoic. With observe to electrical current seed industrial plant life phylogenies (dated or undated), they are either component division of the same lineage than the angiosperms or the (monophyletic) gymnosperms, or belong to a 3rd lineage that diverged before the modern seed plants, i.e. before the mid-Carboniferous (unlikely). |
An of import grouping – interacting betwixt the unambiguous modern seed industrial plant life clades (angiosperms vs. gymnosperms) are the enigmatic together with 1 time dominant (mid- to high-latitudes) Bennetittales, a grouping severely under- together with mis-represented inward all all-spermatophyte matrices so far; a grouping hard to house inward a phylogenetic context together with with unsculptured monosulcate pollen (similar to cycads, but non "angiosperm-like"; e.g. Pott, Fischer & Ashauer 2017)
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| A neighbour-net based on hateful morphological distances (matrix of Crepet & Stevenson 2010). The matrix is identical to the Rothwell et al.'s (2009) 'matrix 3' (no Erdtmanithecales), except that the Bennettitales (usually treated equally 1 taxon inward all-spermatophyte matrices) are differentiated into 4 taxa. Numbers dot NJ-based together with parsimony bootstrapping support: Green = splits resolved ...; bluish = splits non resolved but best-supported ..., scarlet = splits conflicting with Crepet & Stevenson's shown strict-consensus tree (their "analysis 1"); cyan (replacing green) together with majestic (replacing red) announce branches collapsed inward the strict-consensus tree of "analysis 2" (one recoded character!) APO = Angiosperm point-of-origin; ASNA = flowering plant stalk node expanse (defined yesteryear the adjacent extant seed plants: hither (probably wrong) Gnetidae (Gnetales); B = Bennettitales root; POMSP = point-of-origin of modern seed plants (the purpose of the matrix was to link Bennetittales with cycads, Cycadidae/Cycadales; yesteryear the way). |
With Caytonia out of the race together with Bennetittales beingness also unique, a novel candidate emerged lately that could live of usage to inform the actual flowering plant (s.str.) stalk node. But neither the acting Horsemen of Palaeobotany nor Wang comment on the Triassic – again, coincidence or consistent pattern? – Petriellales (Bomfleur et al. 2014). According to the most-recent phanerogam morphological matrix (Rothwell & Stockey 2016), the Petriellales are a candidate for an (ancient) flowering plant sistergroup. If so, it would live some other palaeobotanical bear witness that the actual flowering plant lineage diverged yesteryear the Triassic (or before) together with a dot to create inward a redux-review paper. Rothwell together with co-workers' matrices are notoriously depleted of tree-like together with discriminating signal (see this Genealogical World of Networks post), but the 2016 matrix is the foremost – when analysed using up-to-date methods (Coiro, Chomicki & Doyle 2017) – that prefers a placement of the Gnetidae (Gnetales) equally sis to the remaining gymnosperms (Ginkgoidae, Pinidae together with extinct relatives, including or excluding Cycadidae). H5N1 placement inward understanding to e.g. phylogenomic analyses (e.g. Lee et al. 2011, figure above; the principal inter-seed industrial plant life relationships are a long-standing issue, meet e.g. Mathews 2009; Mathews, Clements & Beilstein 2010). And the 2016 matrix places the Petriellales – their pollen is so far non known – firmly equally sis to the angiosperms (Coiro et al. 2017; Grimm 2017a, b; meet also the intelligence inward the master newspaper of Bomfleur et al. 2014).
What a palaeobotanical redux on the historic menses of angiosperms could human face like
When you lot read Herendeen et al. (2017), it is obvious that this review newspaper was non scrutinised during peer-review, but some sentences similar those nigh Triassic "stem angiosperms" human face similar reluctant additions made during (quick) revision. It is clearly non a "redux", but a demonstration of we-will-stay-firm-and-ignorant-of-anything-else. This is a pity. Molecular dating done inward ignorance of the fossil tape is oft for the bin. And to a greater extent than together with to a greater extent than dater realised this.Palaeobotanists would take away hold a lot to offering together with to throw inward the band since node dating depends strongly on placing the fossil on the right node, together with using the oldest representative of a lineage. But that is only the get-go of what could teach a dream-story of inter-disciplinary research.
In the final 5 years, 2 novel methodologies take away hold been proposed for which palaeobotanical expertise similar that of the Four Horsemen of Palaeobotany or the Triumvirate of Hell[6] would live crucial. Both approaches are theoretically (and inward practise) superior to the traditional node dating: One is total-evidence dating (Ronquist et al. 2012), which volition e'er live hard using industrial plant life information sets (above[11]; supplement to Grimm et al. 2015), together with the fossilised-birth decease (FBD) dating, which provided rattling overnice (sensible) results fifty-fifty for apartment together with deep industrial plant life phylogenies (Grimm et al. 2015; Renner et al. 2016; see/cf. Denk et al. 2005; Denk & Grimm 2009; Bomfleur et al. 2015; Grímsson et al. 2016).
- Total-evidence dating needs a morphological division that includes the fossils – something only palaeobotanists tin furnish (pers. experience, I can’t).
- FBD dating needs a comprehensive compilation of the fossil tape – together with you’ll live damned if you lot essay to do that just yesteryear re-create & glue from literature without whatever prior palaeobotanical knowledge.
And regarding “Palaeobotanical redux: revisiting the historic menses of angiosperms” this should live done (not yesteryear a unmarried individual though; PB = palaeobotanists, NB = (neo)botanists, BI = (bio)informaticians):
- PB: Compile the entire Mesozoic fossil tape of seed plants (taxon – historic menses – assumed botanical affinity).
- BI (assisted yesteryear NB together with PB): Select a laid of molecular-phylogenetic hypotheses (based on recent studies, non six-year-old ones based on a information laid that – partly – has been assembled 20–25 years agone together with never been updated since then) together with recruit a molecular information laid providing sensible (on the backdrop of morphological together with genetic diversity, together with the fossil record) branch lengths.
- BI: Map the development of fossil-relevant traits onto the molecular tree(s) using a probabilistic approach to seat conserved together with quick-evolving traits, together with – eventually – diagnostic graphic symbol suites (I'll elaborate the work with synapomorphies inward a follow-up post).
- PB + NB: Recruit together with re-train a grouping of (systematic) botanists to delineate dorsum these traits inward the fossil record, together with give them unrestricted access to the material. When 2 doctors suggest 2 rattling different treatments (like electrical current palaeobotanical debate), teach a third, fresh opinion!
- BI: Do a fossilised-birth decease dating on a taxon laid that includes the least-diverged representatives of all main seed industrial plant life together with flowering plant clades; if at that topographic point is to a greater extent than than 1 alternative, essay all of them. [I would e'er recruit (bio)informaticians for this job, who take away hold no thought nigh the organism, hence, tin piece of work solely unbiased]
- BI for PB: Make a serial of node-dating tests to farther reconcile the fossil record, the interpretation of fossils, with the molecular hypotheses – meet e.g. Grimm & Renner 2013 for such an experiment together with farther references; together with Hubert et al. (2014) for historic menses estimates inward oaks (Quercus) that fit good afterward palaeobotanical finds (Grímsson et al. 2015, 2016; I call back both papers are examples of “palaeobotanical redux”; the only argue why at that topographic point is no FBD dating yet for all Fagaceae (or all Fagales) – much needed inward my persuasion – is just the lack of human resources).
But equally long equally the few palaeobotanists with prominent positions together with (obviously) enquiry money (see acknowledgements inward Herendeen et al. together with Wang) pass their fourth dimension (and review papers) criticising the piece of work of others (and each other; e.g. Rothwell, Crepet & Stockey 2009; Crepet & Stevenson 2010; Herendeen et al. 2017; Wang 2017) rather than come upwards together, haggle it out, together with create a telephone telephone to furnish something useful for non-palaeobotanists … well, create an appointment with the undertaker.
References (bold font = opened upwards access)
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Footnotes (background info, tin live politically wrong or completely harmless)
[1]Info to non-scientists: Nature is THE magazine to set out something dealing with organisms, together with the flagship publication of Springer-Nature, 1 of the globally leading scientific discipline publishers; fifty-fifty for veteran Nature authors it has teach quite hard to teach a newspaper into Nature, so Nature launched a soundless growing number of spin-offs, to give Nature authors or prospective futurity Nature authors a dissemination platform for papers rejected yesteryear Nature. The create call ensures a certainly fame; for instance, if you lot published something inward Nature Whatever, the PR-department of your academy volition teach an information direct from Nature publishing squad together with contact you. If you lot set out the same inward a non-Nature offspring, you lot ordinarily take away hold to travel to them. Go dorsum to section[2] The work palaeobotanists human face when describing novel taxa is that they are supposed to create a diagnosis that fulfil the requirements of the Botanical Code. On the other hand, it is the dominion that whatever fossil beyond a certainly age, gets its ain genus, together with non rarely the genus diagnosis is identical to that of the novel described species. So fifty-fifty similar fossils volition teach novel generic epithets, or the authors take away hold to emend the genus (which tin live rattling tricky). Another complication is that each fossil lacks certainly features, including 1 of the few synapomorphies. But may live indistinguishable from already described taxa. In extreme cases, the seeds together with pollen institute in-situ inward a blossom volition take away hold different generic names, together with each organ volition teach a novel species. H5N1 few palaeobotanists follow mutual sense, when it looks the same, give it the same name, but when you lot do so at that topographic point is a high likelihood that the anonymous reviewer volition essay to shoot downwards your paper. Which is the argue (beyond uncomplicated sloppiness) that diagnosis together with description tin differ inward detail. Furthermore, inward the few illustration morphological matrices take away hold been used to house fossils, you lot ordinarily volition take away hold to generalise further, adding superficial inconsistencies (like some that Wang points out regarding Monetianthus). Go dorsum to section
[3] Magallón et al. (2015) aim at identifying rates shifts inside the flowering plant tree. To do so they usage a “meta-calibrated” dated tree, effectively a fully constrained tree. Relying only on to a greater extent than oft than non excepted fossils (a lot from Friis et al. 2011) but also the Triassic “angiosperm-like” pollen equally minimum historic menses for the flowering plant root, the infer an Early Cretaceous crown-age for the angiosperms. Go dorsum to section
[4] The Horsemen of the Apocalypse also include, according to rattling reliable sources (see T Pratchett, due north Gaiman, Good Omens), 1 woman. Go dorsum to section
[5] Palaeontology is in all likelihood the softest of all natural sciences. H5N1 lot is interpretation, but it also depends a lot on skills together with sense that cannot live quantified together with are hard to select around. For instance, an experienced palynologist volition recognise certainly pollen grains on sight, but to depict them inward a way that a reader tin reproduce the identification tin live rattling difficult. The same applies to mesofossils described yesteryear the Horsemen. When you lot worked with a fossil group, you lot notice of import feats nearly subconsciously (human designing recognition capacity is soundless non matched yesteryear computers). But since opinions are rattling of import together with the peer-review is confidential, it tin live rattling harsh inward palaeobotany. You don’t fuck with prominent people, but they tin fuck you lot equally much equally they want. On diverse occasions inward my career people similar together with including Herendeen (in illustration of my foremost phylogenetic paper; Denk et al. 2002) tried to kill off our papers during review. The editors, ordinarily also palaeobotanists (it’s a niche science), cannot afford to create enemies, together with – equally writer – you lot only take away hold hints who it was this fourth dimension (confidentiality). Since the review procedure is confidential, at that topographic point is no way to say how many innovative ideas take away hold been killed off during peer-review. Go dorsum to section
[6] An interesting fiddling story to tell (a human face behind the thick drape of confidential peer-review). The paper, well-done from my perspective, was submitted to Nature together with fits the journal’s needs: the imaging methodology together with the fossil is spectacular, the authors are leading inward their diverse fields, and, non surprisingly, the newspaper has been already cited to a greater extent than than 150 times, including dental medicine papers. One of the reviews, however, anonymous of course of written report but probable from 1 of the sworn-enemies (scientifically) of the authors (Crepet, Nixon, Rothwell), allow me to telephone telephone them the ‘Hellish Triumvirate of Palaeobotany’ (see e.g. Rothwell et al. 2009; Crepet & Stevenson 2010; together with N. Gaiman, Sandman Vol. 1, for who-is the Hellish Triumvirate), did non belief the Horsemen’s interpretation unless they would furnish an explicit phylogenetic reconstruction supporting their assessment. Which, from my humble perspective, wasn’t needed at all together with stupid to inquire for; but Einem geschenkten Gaul schaut human being nicht ins Maul (German saying). Probably hoping the Horsemen wouldn’t live able to do it – the Triumvirate considers themselves (still) experts inward “cladistics”, together with the only ones inward palaeobotany. So, Horseman #2 asked 1 of her trusted colleagues to do it (at the fourth dimension the only palaeobotanist with properly done molecular-phylogenetic papers), who recommended me. I did a total phylogenetic analysis of the available information (largely heretic from the viewpoint of the Hellish Triumvirate together with Horseman #1, no thought what #4 truly thought nigh it, he’s 90% a politician/10% a scientist – inward stark contrast to all other major protagonists, who are full-blooded scientists with a lot of expertise together with knowledge inward their respective focus areas). Very fiddling of what I did sipped into the main-text, most ended upwards inward the supplement, together with the relaxation inward the bin. Because the reconstruction that was the most honest, most revealing, together with most innovative (first-timer, together with liked yesteryear Horseman #2) was considered yesteryear Horseman #4 to live also risky to fifty-fifty set into the supplement. He was afraid the Hellish reviewer may together with so live able to kill the paper, which, inward hind-sight, would take away hold been a peachy loss for keeping upwards Nature’s high (and inflated, personal opinion) touching factor; together with – much to a greater extent than importantly – I in all likelihood would non had gotten a four-year ‘forsass’ grant yesteryear the Swedish Research Council (so I’m soundless thankful to whoever the Hellish reviewer was). Go dorsum to section
[7] The Soltis et al. (2011) matrix, which is quite a deal, was the end-product of to a greater extent than than 2 decades of research. Unfortunately, the authors never institute it necessary to update/check the information of before versions of the matrix, they just added 1 gene/taxon after the other. As upshot the oldest component division of the matrix includes mediocre sequences, with to a greater extent than pseudomutations (editing/sequencing) artefacts than actual mutations confirmed yesteryear newer data. Also they never checked for additional information to fill upwards the blank spots. So when I filtered the matrix to fit it with the morphological division nosotros had (Doyle & Endress 2010), I pass nearly a calendar month with nada else than replacing outdated information together with filling the white spots, using e.g. information shape the consummate reference plastomes (the Amborella information has been completely exchanged) or, non rarely, information produced yesteryear the authors themselves together with used inward other studies. One upshot of the cleaning was that Amborella is preferred equally sis of the Nympheales (it is less distinct, hence, lesser chance for ingroup-outgroup long-branch attraction) but non of all angiosperms (moves 1 non up; a long debate betwixt Soltis et al. together with e.g. Goremykin together with co-workers (2003). Go dorsum to section
[8] I promised Seraina Klopfstein (Ronquist et al. 2012) to dig out a industrial plant life total bear witness matrix. So, I pruned downwards the Soltis et al. (2011) matrix to the taxa inward the matrix of Doyle & Endress (2010), together with – after heavy curation of the molecular information laid (see footnote 7) – she run a total-evidence dating. The outcome was rattling interesting, nosotros had an thought why total-evidence failed, but nada you lot could set out inward a wink without much to a greater extent than tests. See also footnote 11. Go dorsum to section
[9] Back then, Horseman #2 was quite happy nigh it, together with my explanations regarding instability of dating estimated together with topology (branching artefacts, sample bias). But in all likelihood also shy to dot it out to #1. After all, none of the Horsemen has notable competence regarding molecular information or phylogenetics. That is no shame, but together with so you lot should teach into contact with people who have. For instance, Magallón would patently take away hold been a natural co-author for the Horsemen’s review, with observe to the 2015 paper. Go dorsum to section
[10] For example, when reviewing papers showing e.g. lxxx Ma former (or older) pollen with just the same form, size together with sculpture than inward certainly modern counterparts. These pollen grains take away hold to live named using artificial pollen taxa because they may non come upwards from the same genus/family that produces them today. Go dorsum to section
[11] Which is probable the reason, why our foremost total bear witness dating run gave us a root historic menses of 4.5 billion years for the flowering plant root, when no maximum historic menses was defined (the historic menses of Earth is the in-built max. historic menses cut-off of MrBayes 3). Illustrating the work for MrBayes converging to max-possible ages using simulations would take away hold been quite a bargain (and hard to publish), so nosotros abandoned the project. Go dorsum to section
[12] Many reviews (also inward other fields of science) only take away hold 1 main objective: citing your ain stuff, advertise it, so people volition select inward the citations for their ain work. And teach an tardily foremost authorship again, for a alter (at a certainly level, you lot are covered inward admin etc.) Properly placed, such a review is worth dozens of actual scientific papers for the author. In contrast, well-done reviews select upwards all literature together with listing the pros together with contras to furnish an overview. Which agency a lot of work, together with touching points for your enemies/competitors (just cheque how many papers yesteryear the Hellish Triumvirate are cited. Go dorsum to section
[13] The according “cladistic test” yesteryear Rothwell et al. (separating the organs together with optimise the seat of each independently) is nonsense – whatever taxon inward their matrix except the angiosperms (very distinct from everything else) would neglect the essay including clearly monophyletic ones such equally the modern conifers (which their tree resolves equally paraphyletic to Gnetales together with angiosperms). H5N1 demonstration that they take away hold fiddling thought nigh the signal lineament of their matrices, permit lone the mechanics of phylogenetic reconstructions. Go dorsum to section
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