What Is An Angiosperm? Business Office 1: The Deviation Betwixt Cladistic Together With Phylogenetic Classification

The “age of angiosperms” is withal a affair of debate. But piffling give-and-take revolves some a to a greater extent than key question. What is an angiosperm? The respond is trivial, from a modern-day perspective. Influenza A virus subtype H5N1 flowering plant. But when it comes to dated trees too phylogenetics, nosotros clash with semantics too non-congruent philosophical frameworks. Because too then it's non necessarily nearly producing a flower, but pure concepts.
In the last post, I provided some critical comments of a ‘review’ newspaper published past times initiative of all palaeobotanists (Herendeen et al. 2017) inward Nature Plants (a closed-access online magazine past times Springer Nature with apparently relaxed peer review), which triggered a fiery ‘reply’ past times Wang (2017) published inward a pseudo-scientific, non-reviewed open-access magazine (Natural Science by SCIRP) that he edits. Herendeen et al. preferred a cladistic node-based definition of the flowering plants: whatever descendant of the ‘most recent mutual ancestor’ (MRCA) of all living angiosperms is an flowering plant (they subsequently refine it to a poly-phyletic Definition past times excluding all descendants of this MRCA that cannot live assigned to whatever of the modern lineages). Wang, on the other hand, seemed to follow a cladistic branch-based definition: all members of the clade including the modern-day angiosperms are angiosperms. The foreign thing hither is that all authors are palaeobotanists with piffling thought or dearest for molecular-dating approaches, but withal utilization the conceptual framework of molecular dating too phylogenetics. The alternative would receive got been to utilization a phylogenetic classification next Hennig's concept of monophyla, groups of inclusive mutual origin, linked to synapomorphies: uniquely shared, derived traits.

Phylogenetic too cladistic classifications

It is of import to realise that 1 should distinguish betwixt Hennig too cladistics (see also Felsenstein 2001, 2004; too this shipping service on clades, cladograms, cladistics too networks). Hence, a curt recapitulation too explanation.

Phylogenetic classification was formalised past times Hennig (1950). Nearly a century before Haeckel (1866) coined the term monophyletisch (monophyletic) for a grouping of organisms sharing a mutual source inward contrary to polyphyletisch (polyphyletic): un-natural, artificial groups not sharing a mutual source (until into the 20^th century, many classifications were only based on shape too ignored the evolutionary thought that 1 organism evolves from another; similar non a few modern-day phylogenetic studies). In principle, phylogenetic classification is a natural final result of accepting evolution, the thought that goes dorsum to Darwin too Wallace. We alone desire to form groups that are role of the same evolutionary lineage.
Whereas Haeckel too the offset phylogenetic classifications (e.g. Pojárkova 1933 for Acer, maples; Schwarz 1936 for Quercus, oaks) where quite flexible (and combat nebulous) on how to define too recognise a mutual origin, Hennig set upwards a dominion prepare too added a novel category: paraphyletisch (paraphyletic).
Hennig (1950, 1982; — & Schlee 1978) differentiated betwixt

• monophyla inward a strict sense, groups of an inclusive common source – all descendants of the mutual ancestor – ideally defined past times uniquely shared, derived traits (synapomorphomies); the alone valid dry reason for defining a taxon;
• paraphyla, groups of an exclusive common source – some but non all descendants of the mutual ancestor – that may portion primitive traits retained from their mutual ancestor, so-called ‘symplesiomorphies’;
• polyphyla, artificial groups with multiple origins.

To avoid confusion, a paraphylum is monophyletic per before definition, Ashlock (1971) proposed to telephone phone Hennig's monophyla ‘holophyletic’ (which semantically makes feel given the pregnant of mono- and holo-, but has non been widely adopted). When working with fossils too aiming for holistic classifications (e.g. Bomfleur et al. 2017), it tin live rattling handy to receive got monophyletic as collective term for paraphyletic too holophyletic as it may live impossible to discern betwixt the latter 2 based on the available data. Influenza A virus subtype H5N1 fossil grouping may live a precursor, hence, paraphyletic, or an extinct sis lineage, hence, reciprocally holophyletic.

From phylogeny (here: the truthful evolutionary tree) to Hennig's phylogenetic classification.
Each lineage (here = clade) has at to the lowest degree 1 synapomorphy, too the fossils (lower-case letters) equal the MRCAs of the modern taxa (upper-case latters). Taxonomic classes (rank) named after their offset representative.

Theoretically perfect – nosotros tin alone assay for holophyly but non paraphyly – Hennig's phylogenetic classification has a key short-coming when it comes to application: the issue of ranks tin easily travel rattling large or the systematic groups also large to brand whatever sense. And it doesn't run good with Linné's binominal code to advert organisms, inward item when fossils should receive got binominals, too.

Two to a greater extent than unproblematic examples.

In the examples above, it would live practical to give the paraphyla a name: the X-aceae portion a mutual source too tin live unambiguously diagnosed with abide by to the holophyla inward both examples, but they are non inclusive.

Let's assume all terminals (modern-day taxa: B, C, E, F, G) inward the to a higher house examples are genera. Using the Hennigian dominion set, all fossils beingness the actual ancestors of 2 or to a greater extent than genera, would involve to rest nameless or nosotros would involve to redefine the modern genera. In praxis, nosotros would assign each fossil its ain genus, as they all differ from the modern-day genera past times missing a synapomorphy or the genus' autapomorphy. But since the fossil genera are ancestors of modern genera, they are paraphyletic per definition. Under certainly conditions, nosotros would fifty-fifty live tempted to utilization the same genus advert for a fossil too modern taxon (because they are visibly rattling similar) with the final result that a today holophyletic genus (or higher taxon) becomes paraphyletic. [Cladists receive got occasionally argued that all fossil taxa must correspond extinct sis taxa to bypass this problem. But come upwards on: how probable is it that nosotros never observe the ancestors of today (and inward the past) dominating organisms, too alone their less successful, hence, extinct, sis lineages?]

Inevitability of paraphyla when aiming at fully inclusive classifications.
No affair whether nosotros start wit a molecular tree too modern-day relationships, a top-down classification, or including all available show from the historical tape (when, what, where), a bottom-up classification, nosotros receive got to bargain with paraphyletic (morpho)taxa. The modern-day molecular information volition brand us realise that the X-aceae paraphyletic, collecting all X-ales that are non role of the holophyletic A-/B-aceae too F-aceae/-oideae. The fossil tape indicates that the morphospace characterising E-oideae too E-aceae, including quondam (d) too oldest X-ales (x), equals a paraphyletic group.

Noting the impracticability of Hennig's organisation {Mayr Bock 2001} argued, inward a somewhat convolute point-of-view, that nosotros should convey too advert (diagnose) also paraphyla inward what they labelled an “evolutionary classification” (an ill-advised move) to distinguish it from Hennig's “phylogenetic classification”. Both classifications are based on the evolution-derived (phylogenetic) regulation of assuming a mutual origin. Furthermore, nosotros tin alone define paraphyla worth naming via the recognition of holophyla (see illustration above), so it is mainly a semantic alteration of Hennig's concept. I would rather telephone phone it a Haeckelian phylogenetic classification as it names groups that Haeckel would receive got recognised as monophyletic. 



For cladistic classification, we receive got 2 principal options once nosotros inferred a tree (!): node-based or branch-based. At this dot neontological practice diverges: dating papers ever beak nearly the “angiosperm stalk age” too the “angiosperm crown age”. The stalk historic menses is defined past times dot at which the flowering plant lineage diverged, its dot of origin. The crown historic menses is the historic menses of the MRCA of all extant (living) angiosperms. So they implicitly define angiosperms branch-based. But inward systematic phytology (and palaeobotany, officially, but come across Herendeen et al. 2017), nosotros define the angiosperms essentially node-based assuming that the MRCA was also the offset organism showing all characteristics of an angiosperm.

For our unproblematic examples above, cladistic classification (node- or branch-based) volition recognise the same taxa than (Hennigian) phylogenetic classification.

Cladistic classification systems for the 3 examples before.
Upper row: node-based; lower row: branch-based.

Since our information are costless of homoplasy, all inferred clades correspond holophyletic groups. Since all our fossils inward the illustration equal the MRCA, at that spot is no difference betwixt node- too branch-based definition. The alone cost nosotros pay is that our classification tin live imprecise because some lineages lack the necessary issue of diagnostic traits to resolve all holophyla. Total-evidence that uses molecular information to resolve modern-day relationships too a morphological sectionalization for placing the fossils, is a double-edged sword. Keep inward heed that missing information are treated as 'N' (= Influenza A virus subtype H5N1 or C or G or T) inward a phylogenetic analysis. As final result a total-evidence tree likes to house a fossil as sis to a non-inclusive (paraphyletic), inward a historical context, clade comprising alone the modern taxa, its descendants. Influenza A virus subtype H5N1 node-based modern-day-derived classification volition inevitably include paraphyletic groups.

Total-evidence approaches volition non run for node-based cladistic classifications.

In the instance of real-world data, cladistic classifications that rely on an inferred tree are mostly problematic inward palaeontology, because

1. fossils supply – for the most role – alone information nearly morphology;
2. most morphological traits receive got been evolved inward parallel or convergently, i.e. to a greater extent than than a unmarried fourth dimension inward the same (monophyletic [sensu Haeckel]) or unlike lineages (polyphyletic);
3. hence, clades inward trees are oftentimes with misfortunate support, tin receive got as valid alternatives, or are misleading. 

Illustrated inward a serial of posts I made for David Morrison's seed plants, dinosaurs, mosasaurs, insects, or using simple theoretical examples.

And this is the optimal case. In the worst case, our fossils do non supply plenty scorable characters to include them inward whatever explicit phylogenetic analysis at all. No tree, no cladistic classification.

What is an angiosperms depends on the classification system

When nosotros apply the 4 classification systems on the flowering plant problem, nosotros terminate upwards with 3 possible but unlike definitions of angiosperms – 2 cladistic ones (node-based, branch-based) too 1 phylogenetic one. 

• Cladistic node-based: all descendants of the hypothetical MRCA of all living angiosperms as defined past times the 'angiosperm crown node'
• Cladistic branch-based: all members of the flowering plant clade
• Phylogenetic: all plants that (originally) evolved the total prepare of flowering plant synapomorphies (we should non live overly picky here: because of the molecular phylogenies nosotros know that some lost/modified those traits subsequently on).

The 3 options to define angiosperms beyond present-day.

The terminal diamonds too triangles reverberate the known fossil tape (following Earle 2010, for gymnosperms; too Stevens 2001 [onwards] for angiosperms, since neither Herendeen et al. nor Wang did their chore too produced whatever listing of earliest records). The time-scaled tree is based on the chronogram produced past times Magallon (Magallón et al. 2015); it is a "meta-calibrated" (nearly-full constrained) tree fully inward business with Herendeen et al.'s philosophy of an Early Cretaceous flowering plant crown age. Note that lacking compensating constraints, the departure ages inward the outgroup/ sistergroup (gymnosperms) are much also young, too the topology is biased past times long-branch attraction betwixt Gnetidae too angiosperms. For the angiosperms, the Magallón et al.’s tree fits with Stevens' tree based on diverse literature. Regarding the flowering plant synapomorphies (ASA), I only assumed a immature historic menses to fall-in-line with electrical flow mainstream (will live discussed inward Part 2).

The alone difference betwixt Hennigian too Haeckelian phylogenetic classification (“evolutionary classification” of Mayr & Bock) is the rank of the taxon collecting the flowering plant precursors (and potential extinct sis lineages of angiosperms). For Hennigian it needs to live the next-higher rank, i.e. Magnoliopsida, since alone holophyla should live named; for Haeckelian, nosotros tin exactly define a paraphyletic shape (same rank as angiosperms, the Magnoliidae; Stevens 2001 onwards) that include(s) all plants that portion the same source than the angiosperms too are role of the same evolutionary lineage, the Magnoliopsida, but receive got non (yet) evolved the total prepare of flowering plant synapomorphies. Once the final diverging sis lineage of angiosperms is defined (see final post), this tin live accommodated inward Haeckelian classification past times additional paraphyletic taxa too inward Hennigian classification past times adding farther ranks.

The 2 flavours of phylogenetic classification

Now that the principles too basic options are set out, nosotros tin hash out them (see Part 2 of this post) too observe that only a Haeckelian phylogenetic classification too Definition of angiosperms is an pick (not surprising, I know). At this dot branch-based cladistic classifications volition live highly misleading, node-based cladistic impossible due to the FUZ – Farris’ Uncertainty Zone – too Hennigian phylogenetic impractical because of the undetermined extend of the HAZ – Hennig’s Ambiguity Zone. 


Cited literature
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Coiro M, Chomicki G, Doyle JA. 2017. Experimental signal dissection too method sensitivity analyses reaffirm the potential of fossils too morphology inward the resolution of seed institute phylogeny. bioRxiv DOI:10.1101/134262 http://www.rachelteodoro.com/search?q=age-of-angiosperms-may-palaeobotany
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Mayr E, Bock WJ. 2002. Classifications too other ordering systems. Journal of Zoological Systematics too Evolutionary Research 40:169-194.
Pojárkova AI. 1933. Botanico-geographical survey of the maples of the USSR inward connectedness with the history of the whole genus Acer L. Acta Inst Bot Acad Sci USSR, Ser 1 1:225-374.
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