EMBRYOPSIDA Pirani & Prado
Gametophyte dominant, independent, multicellular, initially ±globular; showing gravitropism; acquisition of phenylalanine lysase [PAL], phenylpropanoid metabolism [lignans +, flavonoids + (absorbtion of UV radiation)], xyloglucans in primary cell wall with distinctive side chains; plant poikilohydrous [protoplasm dessication tolerant], ectohydrous [free water outside plant physiologically important]; thalloid, leafy, with single-celled apical meristem, tissues little differentiated, rhizoids +, unicellular; chloroplasts several per cell, pyrenoids 0; glycolate metabolism in leaf peroxisomes [glyoxysomes]; centrioles/centrosomes in vegetative cells 0, interphase microtubules form hoop-like system; metaphase spindle anastral, predictive preprophase band of microtubules [where cell plate will join parental cell wall], phragmoplast + [cell wall deposition spreading from around the spindle fibres], plasmodesmata +; antheridia and archegonia jacketed, surficial; blepharoplast +, centrioles develop de novo, bicentriole pair coaxial, separate at midpoint, centrioles rotate, associated with basal bodies of cilia, multilayered structure + [4 layers: L1, L4, tubules; L2, L3, short vertical lamellae] (0), spline + [tubules from L1 encircling spermatid], basal body 200-250 nm long, associated with amorphous electron-dense material, microtubules in basal end lacking symmetry, stellate array of filaments in transition zone extended, axonemal cap 0 [microtubules disorganized at apex of cilium]; male gametes [spermatozoids] with a left-handed coil, cilia 2, lateral; oogamy; sporophyte multicellular, cuticle +, plane of first cell division horizontal [with respect to long axis of archegonium/embryo sac], early embryo developing towards the archegonial neck [from epibasal cell, exoscopic], with at least transient apical cell [?level], initially surrounded by and dependent on gametophyte, placental transfer cells +, in both sporophyte and gametophyte, wall ingrowths develop early; suspensor/foot +, cells at foot tip somewhat haustorial; sporangium +, single, terminal, dehiscence longitudinal; meiosis sporic, monoplastidic, MTOC [MTOC = microtubule organizing centre] associated with plastid, sporocytes 4-lobed, cytokinesis simultaneous, preceding nuclear division, quadripolar microtubule system +; wall development both centripetal and centrifugal, sporopollenin + laid down in association with trilamellar layers [white-line centred lamellae; tripartite lamellae], >1000 spores/sporangium; nuclear genome size <1.4 pg, main telomere sequence motif TTTAGGG, LEAFY and KNOX1 and KNOX2 genes present, ethylene involved in cell elongation; chloroplast genome with close association between trnLUAA and trnFGAA genes, precursor for starch synthesis in plastid.
Many of the bolded characters in the characterization above are apomorphies of subsets of streptophytes along the lineage leading to the embryophytes, not apomorphies of crown-group embryophytes per se.
All groups below are crown groups, nearly all are extant. Characters mentioned are those of the immediate common ancestor of the group,  contains explanatory material, () features common in clade, exact status unclear.
Abscisic acid, L- and D-methionine distinguished metabolically; sporophyte with polar transport of auxins, class 1 KNOX genes expressed in sporangium alone; sporangium wall 4≤ cells across [≡ eusporangium], tapetum +, secreting sporopollenin, which obscures outer white-line centred lamellae, columella +, developing from endothecial cells; stomata +, on sporangium, anomocytic, cell lineage that produces them with symmetric divisions [perigenous]; underlying similarities in the development of conducting tissue and of rhizoids/root hairs; spores trilete; shoot meristem patterning gene families expressed; MIKC, MI*K*C* genes, post-transcriptional editing of chloroplast genes; gain of three group II mitochondrial introns, mitochondrial trnS(gcu) and trnN(guu) genes 0.
[Anthocerophyta + Polysporangiophyta]: xyloglucans in the primary cell wall with fucosylated subunits; gametophyte leafless; archegonia embedded/sunken [on;y neck protruding]; sporophyte long-lived, chlorophyllous; cell walls with xylans.
Sporophyte dominant, branched, branching apical, dichotomous, potentially indeterminate; vascular tissue +; stomata on stem; sporangia several, each opening independently; spore walls not multilamellate [?here].
EXTANT TRACHEOPHYTA / VASCULAR PLANTS
Sporophyte with photosynthetic red light response; (condensed or nonhydrolyzable tannins/proanthocyanidins +); plant homoiohydrous [water content of protoplasm relatively stable]; control of leaf hydration passive; plant endohydrous [physiologically important free water inside plant]; (condensed or nonhydrolyzable tannins/proanthocyanidins +); xylans in secondary walls of vascular and mechanical tissue; root hairs +; lignins +; tracheids +, in both protoxylem and metaxylem, G- and S-types; sieve cells + [nucleus degenerating]; endodermis +; leaves/sporophylls spirally arranged, blades with mean venation density ca 1.8 mm/mm2 [to 5 mm/mm2], all epidermal cells with chloroplasts; sporangia adaxial, columella 0; tapetum glandular; ?position of transfer cells; MTOCs not associated with plastids, basal body 350-550 nm long, stellate array in transition region initially joining microtubule triplets; root lateral with respect to the longitudinal axis of the embryo [plant homorhizic].[MONILOPHYTA + LIGNOPHYTA]
Sporophyte endomycorrhizal [with Glomeromycota]; root cap +, protoxylem exarch, lateral roots +, endogenous; stem apex multicellular, G-type tracheids +, with scalariform-bordered pits; leaves with apical/marginal growth, venation development basipetal, growth determinate; sporangium dehiscence by a single longitudinal slit; cells polyplastidic, MTOCs diffuse, perinuclear, migratory; blepharoplasts +, paired, with electron-dense material, centrioles on periphery, male gametes multiciliate; chloroplast long single copy ca 30kb inversion [from psbM to ycf2]; LITTLE ZIPPER proteins.
Sporophyte woody; stem branching lateral, meristems axillary; lateral root origin from the pericycle; cork cambium + [producing cork abaxially], vascular cambium bifacial [producing phloem abaxially and xylem adaxially].
Plants heterosporous; megasporangium surrounded by cupule [i.e. = unitegmic ovule, cupule = integument]; pollen lands on ovule; megaspore germination endosporic [female gametophyte initially retained on the plant].
EXTANT SEED PLANTS / SPERMATOPHYTA
Plant evergreen; nicotinic acid metabolised to trigonelline, (cyanogenesis via tyrosine pathway); primary cell walls rich in xyloglucans and/or glucomannans, 25-30% pectin [Type I walls]; lignins particularly with guaiacyl and p-hydroxyphenyl [G + H] units [sinapyl units uncommon, no Maüle reaction]; root stele with xylem and phloem originating on alternate radii, cork cambium deep seated; stem apical meristem complex [with quiescent centre, etc.], mitochondrial density in SAM 1.6-6.2[mean]/μm2 [interface-specific mitochondrial network]; eustele +, protoxylem endarch, endodermis 0; wood homoxylous, tracheids and rays alone, tracheid/tracheid pits circular, bordered; mature sieve tube/cell lacking functioning nucleus, sieve tube plastids with starch grains; phloem fibres +; cork cambium superficial; leaf nodes 1:1, a single trace leaving the vascular sympodium; leaf vascular bundles amphicribral; guard cells the only epidermal cells with chloroplasts, stomatal pore with active opening in response to leaf hydration, control by abscisic acid, metabolic regulation of water use efficiency, etc.; axillary buds +, exogenous; prophylls two, lateral; leaves with petiole and lamina, development basipetal, lamina simple; sporangia borne on sporophylls; spores not dormant; microsporophylls aggregated in indeterminate cones/strobili; grains monosulcate, aperture in ana- position [distal], primexine + [involved in exine pattern formation with deposition of sporopollenin from tapetum there], exine and intine homogeneous, exine alveolar/honeycomb; megasporangium indehiscent; ovules with parietal tissue 2+ cells across, megaspore tetrad linear, functional megaspore single, chalazal, sporopollenin 0; gametophyte ± wholly dependent on sporophyte, development initially endosporic [apical cell 0, rhizoids 0, etc.]; male gametophyte with tube developing from distal end of grain, male gametes two, developing after pollination, with cell walls; female gametophyte initially syncytial, walls then surrounding individual nuclei; embryo cellular ab initio, plane of first cleavage of zygote transverse, shoot apex developing away from micropyle [i.e. away from archegonial neck; from hypobasal cell, endoscopic], suspensor +, short-minute, embryonic axis straight [shoot and root at opposite ends; plant allorhizic], cotyledons 2; embryo ± dormant; plastid transmission maternal; ycf2 gene in inverted repeat, whole nuclear genome duplication [ζ - zeta - duplication], two copies of LEAFY gene, PHY gene duplications [three - [BP [A/N + C/O]] - copies], nrDNA with 5.8S and 5S rDNA in separate clusters; mitochondrial trans- nad2i542g2 and coxIIi3 introns present.
ANGIOSPERMAE / MAGNOLIOPHYTA
Lignans, O-methyl flavonols, dihydroflavonols, triterpenoid oleanane, apigenin and/or luteolin scattered, [cyanogenesis in ANA grade?], lignin also with syringyl units common [G + S lignin, positive Maüle reaction - syringyl:guaiacyl ratio more than 2-2.5:1], hemicelluloses as xyloglucans; root apical meristem intermediate-open; stele di- to pentarch [oligarch], pith relatively inconspicuous, lateral roots arise opposite or immediately to the side of [when diarch] xylem poles; origin of epidermis with no clear pattern [probably from inner layer of root cap], trichoblasts [differentiated root hair-forming cells] 0, hypodermis suberised and with Casparian strip [= exodermis]; shoot apex with tunica-corpus construction, tunica 2-layered; starch grains simple; primary cell wall mostly with pectic polysaccharides, poor in mannans; tracheid:tracheid [end wall] plates with scalariform pitting, wood parenchyma +; sieve tubes enucleate, sieve plate with pores (0.1-)0.5-10< µm across, cytoplasm with P-proteins, not occluding pores of plate, companion cell and sieve tube from same mother cell; sugar transport in phloem passive; nodes 1:?; stomata brachyparacytic [ends of subsidiary cells level with ends of pore], outer stomatal ledges producing vestibule, reduction in stomatal conductance with increasing CO2 concentration; lamina formed from the primordial leaf apex, margins toothed, development of venation acropetal, overall growth ± diffuse, secondary veins pinnate, fine venation hierarchical-reticulate, (1.7-)4.1(-5.7) mm/mm2, vein endings free; flowers perfect, pedicellate, ± haplomorphic, protogynous; parts free, numbers variable, development centripetal; P +, ?insertion, members each with a single trace, outer members not sharply differentiated from the others, not enclosing the floral bud; A many, filament not sharply distinguished from anther, stout, broad, with a single trace, anther introrse, tetrasporangiate, sporangia in two groups of two [dithecal], each theca dehiscing longitudinally by a common slit, ± embedded in the filament, walls with at least outer secondary parietal cells dividing, endothecium +, cells elongated at right angles to long axis of anther; tapetal cells binucleate; microspore mother cells in a block, microsporogenesis successive, walls developing by centripetal furrowing; pollen subspherical, tectum continuous or microperforate, ektexine columellate, endexine lamellate only in the apertural regions, thin, compact, intine in apertural areas thick, pollenkitt +; nectary 0; carpels present, superior, free, several, ascidiate [postgenital occlusion by secretion], stylulus at most short [shorter than ovary], hollow, cavity not lined by distinct epidermal layer, stigma ± decurrent, carinal, dry, extragynoecial compitum +; ovules few [?1]/carpel, marginal, anatropous, bitegmic, micropyle endostomal, outer integument 2-3 cells across, often largely subdermal in origin, inner integument 2-3 cells across, often dermal in origin, parietal tissue 1-3 cells across [crassinucellate], nucellar cap?; megasporocyte single, hypodermal, functional megaspore lacking cuticle; female gametophyte lacking chlorophyll, not photosynthesising, four-celled [one module, nucleus of egg cell sister to one of the polar nuclei]; ovule not increasing in size between pollination and fertilization; pollen grains land on stigma, bicellular at dispersal, mature male gametophyte tricellular, germinating in less than 3 hours, pollen tube elongated, unbranched, growing between cells, growth rate (20-)80-20,000 µm/hour, apex of pectins, wall with callose, lumen with callose plugs, penetration of ovules via micropyle [porogamous], whole process takes ca 18 hours, distance to first ovule 1.1-2.1 mm; male gametes lacking cell walls, ciliae 0, siphonogamy; double fertilization +, ovules aborting unless fertilized; P deciduous in fruit; mature seed much larger than fertilized ovule, small , dry [no sarcotesta], exotestal; endosperm +, cellular, development heteropolar [first division oblique, micropylar end initially with a single large cell, divisions uniseriate, chalazal cell smaller, divisions in several planes], copious, oily and/or proteinaceous, embryo short [<¼ length of seed]; dark reversal Pfr → Pr; Arabidopsis-type telomeres [(TTTAGGG)n]; nuclear genome very small [1C = <1.4 pg, 1 pg = 109 base pairs], whole nuclear genome duplication [ε/epsilon - duplication]; protoplasm dessication tolerant [plant poikilohydric]; ndhB gene 21 codons enlarged at the 5' end, single copy of LEAFY and RPB2 gene, knox genes extensively duplicated [A1-A4], AP1/FUL gene, palaeo AP3 and PI genes [paralogous B-class genes] +, with "DEAER" motif, SEP3/LOFSEP and three copies of the PHY gene, [PHYB [PHYA + PHYC]]; chloroplast chlB, -L, -N, trnP-GGG genes 0.
[NYMPHAEALES [AUSTROBAILEYALES [[CHLORANTHALES + MAGNOLIIDS] [MONOCOTS [CERATOPHYLLALES + EUDICOTS]]]]]: wood fibres +; axial parenchyma diffuse or diffuse-in-aggregates; pollen monosulcate [anasulcate], tectum reticulate-perforate [here?]; ?genome duplication; "DEAER" motif in AP3 and PI genes lost, gaps in these genes.
[AUSTROBAILEYALES [[CHLORANTHALES + MAGNOLIIDS] [MONOCOTS [CERATOPHYLLALES + EUDICOTS]]]]: vessel elements with scalariform perforation plates in primary xylem; essential oils in specialized cells [lamina and P ± pellucid-punctate]; tension wood + [reaction wood: with gelatinous fibres, g-fibres, on adaxial side of branch/stem junction]; tectum reticulate; anther wall with outer secondary parietal cell layer dividing; nucellar cap + [character lost where in eudicots?]; 12BP [4 amino acids] deletion in P1 gene.
[[CHLORANTHALES + MAGNOLIIDS] [MONOCOTS [CERATOPHYLLALES + EUDICOTS]]] / MESANGIOSPERMAE: benzylisoquinoline alkaloids +; sesquiterpene synthase subfamily a [TPS-a] [?level], polyacetate derived anthraquinones + [?level]; outer epidermal walls of root elongation zone with cellulose fibrils oriented transverse to root axis; P more or less whorled, 3-merous [?here]; pollen tube growth intra-gynoecial [extragynoecial compitum 0]; carpels plicate [?here]; embryo sac bipolar, 8 nucleate, antipodal cells persisting; endosperm triploid. Back to Main Tree
Age. Clarke et al. (2011: see other estimates) suggested an age of (179-)152(-133) m.y. for this clade, N. Zhang et al. (2012) an age of (163-)145(-133) m.y., Xue et al. (2012) an age of ca 146.4 m.y., Naumann et al. (2013) an age of about 148.5 m.y., and Magallón et al. (2013) an age of around (180.7-)158.7-151.6(-137.7) m.y.. Some other estimates are older, ranging from (200-)174(-153) m.y. (with eudicot calibration) to (210-)184(-160) m.y. (without: Smith et al. 2010). Looking at the pattern of duplication of SEPALLATA genes, Yockteng et al. (2013) dated this node to around 187-137.4 m.y.a. and Magallón et al. (2015) to around 135.9 m.y.a.; (216, 197-)191, 154(-141) and ca 217 m.y. are the somewhat older spread of ages on Zheng et al. (2014) and Z. Wu et al. (2014) respectively, and ca 219 m.y. in Tank et al. (2015: Table S1). Bell et al. (2010: Chloranthaceae sister to [Magnoliidae + everything else], but not monocots) suggested ages for this node of (152-)140(-128) or (135-)127(-119) m.y. depending on the method used.
The age of this branching point is estimated at (190-)167(-47) m.y. (95% HPD, Smith et al. 2010, Table S3), while a fossil-based estimate is ca 100 m.y. (Crepet et al. 2004). [Check]
Evolution. Divergence & Distribution. Tank et al. (2015) suggest that an increase in net diversification at this node might be linked to the ε/epsilon whole genome duplication that characterises all angiosperms. If [Chloranthales + Ceratophyllales] are sister to all other mesangiosperms, this increase will have to be placed at the node above their place of departure.
For the distribution of isoquinoline alkaloids, alternatively known as 1-benzyltetrahydroisoquinoline or 1-btiq alkaloids, see Waterman (1999, 2007). How to optimise them on the tree is unclear. They are known from Chloranthaceae, the magnoliids, and eudicots, so if there is a clade [[Chloranthaceae + magnoliids] [monocots [Ceratophyllaceae + eudicots]]], as is recognized above, or some variation of this, they may be best optimised here.
Ecology & Physiology. Foliar primary xylem with simple perforation plates in both protoxylem and metaxylem has evolved several times within this clade (Feild & Brodribb 2013); ceteris paribus, such vessels conduct water well. This then allowed the miniaturization of the foliar vein reticulum through the development of veins that are narrow yet still conduct water adequately, in turn allowing dense leaf venation and all that this entails in terms of high rates of photosynthesis and evaporation, etc.; see also .
Chemistry, Morphology, etc. The betalains of core Caryophyllales have biosynthetic similarities with benzylisoquinoline alkaloids. For the sesquiterpene synthase subfamily a, see the Amborella Genome Project (2013); not in Amborellaceae. For the orientation of cellulose fibrils in the outer epidermal walls of root elongation zone, see Kerstens and Verbelen (2002); I do not know what happens in the ANITA grade and in gymnosperms, and magnoliids and eudicots are very poorly sampled. This is perhaps the best place to put triploid endosperm on the tree; the other would be as a synapomorphy for all angiosperms, but in that case it would subsequently be lost twice, or lost once and then regained.
I largely follow Ronse De Craene et al. (2003) on the insertion of floral organs. To add where?: A whorled.
Phylogeny. Relationships between the major clades mmediately above the basal pectination, the ANITA grade (Amborellales, Nymphaeales and Austrobaileyales), remain unclear (see also Zeng et al. 2014; Wickett et al. 2014 for a summary). Pending further studies, apomorphies for a topology [[Chloranthales + magnoliids] [monocots [Ceratophyllales + eudicots]]] are suggested, but the main tree shows a polytomy, the relationships of these five groups being unresolved (see also P. Soltis et al. 1999; D. Soltis et al. 2005b; c.f. A.P.G. IV 2016, and in particular A.P.G. III 2006). A variety of other topologies have also been described. For further details of the clades involved, see eudicots, magnoliids, Ceratophyllales, Chloranthales and monocots.
In the following discussion, the ANA grade is considered fixed, as is the monophyly of the magnoliids, monocots and eudicots. However, in Goremykin et al. (2005) the monocots did not always form a monophyletic group, a rather unlikely result that has been obtained in some studies where the nuclear 18S gene has been included (Troitsky et al. 1991: see Duvall et al. 2006 for references).
The questions to be addressed are, what are the relationships between the magnoliids, monocots and eudicots, and where in particular are Chloranthales and Ceratophyllum to be placed (see Zeng et al. 2014: suppl. Fig 1 for various hypotheses of relationships)? These two sets of questions are linked, for example, Graham et al. (2005) found that the inclusion of Ceratophyllum and Chloranthaceae could destabilise relationships among other early branching clades, e.g., the position of the monocots became labile. Over the years, the positions of Ceratophyllaceae and Chloranthaceae have been particularly uncertain, and Piperales have also tended to wander around the tree, so now analyses trying to tease apart relationships in this area that do not include both Ceratophyllaceae and Chloranthaceae in particular must be considered to be incomplete. One of the issues here is the role of aquatics in early angiosperm evolution. How diverse and/or abundant were these two aquatic clades, Nymphaeales and Ceratophyllalaceae and whatever else with which the latter are to be associateds, in the earlier Cretaceous?
As data sets increase in size and sampling of some clades is necessarily constrained - perhaps more Chloranthaceae could be included, but addition of more Ceratophyllaceae is unlikely to affect the issue - the analytical techniques used will become increasingly important (e.g. Jarvis et al. 2014). Thus different seed plant topologies were obtained from analyses using single genes or the same number of sites chosen from twelve separate loci (Burleigh & Mathews 2007a); maximum likelihood and maximum parsimony analyses might show systematic error (Burleigh & Mathews 2007b). Below only more frequently found relationships are discussed, but in more comprehensive analyses such as Moore et al. (2010) and Sun et al. (2014) other "minority" relationships can usually be found.
Chloranthaceae and Ceratophyllaceae. 1. Not immediately related [next two paragraphs to be folded together]. Hilu et al. (2003: a matK analysis alone), suggested that Ceratophyllaceae were sister to eudicots (see also D. Soltis et al. 2000; Borsch et al. 2005: three rapidly evolving genes, 62% jacknife, 96% posterior probabilities; Müller et al. 2006: 96% posterior probability; some analyses in Saarela et al. 2007; Soltis et al. 2007a: support weak; Qiu & Estabrook 2008; most analyses in Drew et al. 2014). A [Chloranthaceae + magnoliid] clade was recovered by Jansen et al. (2006b) and Hansen et al. (2007). In line with both these previous groupings, Ruhfel et al. (2014: whole chloroplast genomes, support not strong) found that Chloranthaceae tended to be sister to Magnoliales and Ceratophyllaceae to the eudicots; see also most analyses in Drew et al. (2014). Similarly, Ceratophyllum, with quite a long branch, was sister to eudicots (in some reconstructions, Piper, with a very long branch, was also involved), and Chloranthus was sister to the magnoliids (Jansen et al. 2007: moderate to strong support), a position also found by Saarela et al. (2007), many analyses in Moore et al. (2007, 2010), Smith et al. (2010) and Magallón et al. (2015). The relationships [eudicots [Ceratophyllaceae + Piperaceae]] were found by Xue et al. (2012: ML analysis of whole chloroplast genomes), although relationhips around here not the focus of the study, nor were they in a PHYC analysis in Hertweck et al. (2015) in which the relationships [Chloranthaceae [[Ceratophyllum + some of the Magnoliales included] [[Acorus + Eudicots] other monocots]]] were obtained.
Drew et al. (2014) also found topologies like [Chloranthaceae [monocots [Ceratophyllaceae + Piperaceae]]], while there was fairly good support for a clade [monocots + Ceratophyllaceae] in a compartmentalised 6-gene analysis (Zanis et al. 2003; see also Qiu et al. 1999; some analyses in Saarela et al. 2007). Qiu et al. (2005; see also Löhne & Borsch 2005) found initial rather strong bootstrap support for a [monocot + Ceratophyllaceae] clade in a 9-gene analysis being vitiated by the failure to obtain much support in any of the subanalyses and by details of the topology obtained in the 9-gene analysis itself (e.g. Acorus sister to the Alismatales included) that are rather improbable. Goloboff et al. (2009) found a [Chloranthaceae + monocot] clade. Moore et al. (2010) i.a. found Ceratophyllum, or [Ceratophyllum + Piper] to be sister to monocots and Chloranthaceae sister to a clade including magnoliids, monocots, and eudicots; the latter pair of relationships with moderate jacknife support were found by Davis et al. (2013) in their comprehensive chloroplast analysis focussing on monocots. Indeed, a [Ceratophyllaceae + Piperaceae] clade is not uncommonly found, as by Petersen et al. (2015), and there Chloranthaceae were sister to all angiosperms apart from the ANITA grade (see also P. S. Soltis et al. 2015) - but neither position had much support. Goremykin et al. (2009b: Chloranthaceae not included) found a [Ceratophyllum + magnoliid] clade after removing 2,500 highly variable positions from an analysis of chloroplast genome data; with the removal of 1,000 positions Ceratophyllum was sister to a [monocot + eudicot] clade. Some analyses have suggested a sister taxon relationship between Chloranthaceae and eudicots (Borsch et al. 2003; P. S. Soltis et al. 2015), and this relationship was favoured in several concatenation-based transcriptome analyses by Wickett et al. (2014; no Ceratophyllaceae). Other studies show no clear pattern (e.g. Jansen et al. 2006a; Qiu et al. 2006b). One alignment of 18S/26S nuclear ribosomal data suggested a clade [Ceratophyllaceae + Tofieldiaceae] embedded within the monocots, but thankfully with little support (Maia et al. 2014).
Finally, Morton (2011) found weak support for Ceratophyllaceae as sister to all other angiosperms, while in the massive parsimony analysis of Goloboff et al. (2009) the relationships [Ceratophyllum [[Amborella + Nymphaeales] all other angiosperms]] were recovered.
2. Sister taxa. A [Chloranthales + Ceratophyllales] clade is quite often obtained. The analyses in Mathews (2006a) preferred an unresolved position for this clade somewhere above the Austrobaileyales. Duvall et al. (2006) and Qiu et al. (2010: chloroplast data, support weak) again found a [Chloranthales + Ceratophyllales] clade, as did N. Zhang et al. (2012); see also Huang et al. 2010, weak support using the ycf2 gene; Moore et al. 2011, very weak support In the comprehensive analyses of Sun et al. (2014) this clade was also frequently recovered, although in a variety of positions. Of course, if there is a there is [Chloranthales + Ceratophyllales] clade, the question is then where is it to be placed? Usually it is associated with magnoliids, monocots or core eudicots (so see below), but sometimes it is placed sister to all other angiosperms except the ANITA grade (e.g. Endress & Doyle 2009; Doyle & Endress 2010; Doyle & Upchurch 2014).
Members of the two groups have fascinating morphologies, although florally both are very reduced, and they may suggest a relationship between the two. Analyses of morphological data gave a [Ceratophyllum + Chloranthaceae] clade with quite strong support (Endress & Doyle 2009). Kvacek et al. (2012) linked Pseudoasterophyllites, vegetatively quite like Ceratophyllum, with Tucanopollis, an abundant palynomorph from Africa-South America over 125 m.y. ago, and Pseudoasterophyllites tends to link Chloranthaceae and Ceratophyllum (Doyle et al. 2015). Similarly, the recently-described Montsechia is either Ceratophyllales or to be placed in a [Chloranthaceae + Ceratophyllum] clade (Gomez et al. 2015) while the fossil chloranthalean Canrightiopsis goes with Ceratophyllum - and with the odd magnolian plant - in a splits-graph analysis (Friis et al. 2015a). If the staminate flower of Ceratophyllum is interpreted as being simply a single stamen, then much of this reduction must have occured in the common ancestor of Chloranthaceae and Ceratophyllaceae - which was terrestrial (Endress & Doyle 2015). Zeng et al. (2014) optimised the distribution of a large number of characters on a tree with a clade [Ceratophyllum + Chloranthaceae] (see also below).
Relationships Between the Three Major Groups. 1. [Monocots [magnoliids + eudicots]]. Zanis et al. (2002) analysed 11 genes from all genomes and found some support for the magnoliids (strong support for this clade) as being sister to eudicots, with Chloranthaceae, and [monocots + Ceratophyllaceae] occurring as successively more basal branches (see also Graham & Olmstead 2000; Borsch et al. 2003). Support for some of these nodes depended on the method of analysis (see also Borsch et al. 2000; Graham & Olmstead 2000; Hilu et al. 2001; Whitlock et al. 2001) or the particular gene studied (see Duvall & Bricker 2002: nuclear 18s; Hilu et al. 2003: matK; Duvall et al. 2006: nuclear 18S in particular causes problems). Soltis et al. (2007a) found very weak support for monocots as sister to [magnoliids, Chloranthaceae, eudicots, etc.]. Lee et al. (2011: Chloranthales and Ceratophyllales not included) found a clade [monocots [magnoliid + eudicot], and with strong support (see also Duarte et al. 2010), and they initially looked at almost 23,000 sets of orthologues from nuclear genomes of 101 genera of land plants (most taxa represented by ESTs, genes included if represented in as few as 4 taxa). Such relationships were strongly supported in the 59 low-copy nuclear gene analysis of Zeng et al. (2014: see also some analyses in Moore et al. 2011), and there sampling is not obviously a problem, Ceratophyllum, Sarcandra and Chloranthus being included. The [Ceratophyllum + Chloranthaceae] clade also recovered by these two groups was placed sister to eudicots (c.f. also Zeng et al. 2014: Table 2, p. 7 etc., conflict between single-copy and IR genes). In the nuclear and mitochondrial analyses by M. Sun et al. (2014) [Chloranthales + Ceratophyllales] were sister to monocots [check]. In an early study the relationships [Monocots [Ceratophyllum [[magnoliids + Chloranthus] eudicots]]] were obtained (Barkman et al. 2000b), although support was poor, while Zanis et al. (2002) and Qiu et al. (2005: other topologies also recovered) found Ceratophyllum to be sister to monoocots and Chloranthus sister to the [eudicot + magnoliid] clade. Wickett et al. (2014) found that [Magnoliids + Chloranthaceae] were sister to eudicots in coalescent transcriptome analyses, other topologies (2 and 3 below) being rejected.
2. [Eudicots [monocots + magnoliids]]. This topology was recovered by Hertweck et al. (2015: eight genes), with a [Ceratophyllum + Chloranthaceae] clade sister to the monocots. Eudicots were sister to an unresolved clade including monocots, magnoliids, and Chloranthaceae (D. Soltis et al. 2000; P. Soltis et al. 2000; Wu et al. 2007; Qiu & Estabrook 2008: compatibility analysis; Doyle & Endress 2010). Hilu et al. (2003) in a matK analysis, suggested that magnoliids were sister to monocots, although the support was weak in parsimony analyses if with 100% posterior probabilities in Bayesian analyses, furthermore, in the latter case only, [Chloranthacaeae + monocots] were sister to magnoliids, although the probabilities there were low. Davis et al. (2004) found magnoliids to be sister to monocots and that Chloranthaceae and Ceratophyllaceae were successively sister to a clade including the few eudicots in the analysis, but support was not exactly overwhelming (the best supported topology in Duvall et al. 2006 is somewhat similar). Müller et al. (2006) found very poorly supported relationships between Chloranthaceae and monocots, which together linked with the magnoliids. Whitlock et al. (2002) recovered largely similar groupings, but support was only moderate; the exact position of Chloranthaceae remained unclear. Duvall et al. (2006: four genes, three compartments) also preferred a relationship between magnoliids and monocots, as did N. Zhang et al. (2012), Doyle and Upchurch (2014) and Doyle and Endress (2014). Wickett et al. (2014) rejected a clade [monocots [Chloranthaceae + magnoliids]] in their transcriptome study.
3. [Magnoliids [monocots + eudicots]]. A [monocot + eudicot] grouping has quite often been recovered, as in Jansen et al. (2006b: 37 whole chloroplast genomes, see also Zhengqiu et al. 2006), Cai et al. (2006: 35 whole chloroplast genomes, no Chloranthaceae, Ceratophyllaceae, or Austrobaileyales), Duvall et al. (2006: four genes, three compartments, nuclear PHYC gene, 18S being excluded), Mathews (2006a: three PHY genes, 105 taxa), Hansen et al. (2007: 61 protein-coding chloroplast genes), Goloboff et al. (2009), and Xue et al. 2012: whole chloroplast genomes). Graham et al. (2005) found a rather weakly supported (73% bootstrap) [monocot + eudicot] grouping, but this was still more weakly supported when Chloranthaceae and Ceratophyllaceae were included. When sequences of complete chloroplast genomes are analysed, an association between monocots and eudicots may be more strongly suggested. Thus Jansen et al. (2007) found good support for a [monocot + eudicot] grouping, a number of alternative topologies being excluded, but support in Moore et al. (2007) was somewhat less strong; see also Magallón et al. (2015). However, the possibility of a [monocot + eudicot] grouping was rejected by Wickett et al. (2014: transcriptome analyses).
Evolution of some floral developmental genes, e.g. in the C and D lineages, are also consistent with a [monocot + eudicot] clade (Kramer et al. 2004), as is the distribution of taxa in which DEF-like proteins cannot form heterodimers (Melzer et al. 2014). The positional relationships between members of the androecium and the perianth, the stamens being individually opposite perianth members, and trimery of some floral whorls occur in a number of taxa, and their distribution is broadly consistent with all three sets of relationships. Variation in how calcium oxalate is synthesized may also be of phylogenetic interest, although sampling is very poor; neither members of the ANITA grade nor magnoliids have been examined. Vacuolar crystal formation associated with membranes and paracrystalline bodies with widely spaced subunits are found in eudicots (crystals seem also to be formed in other ways here), while in monocots there are no membrane complexes and the paracrystalline bodies have closely spaced subunits (Horner & Wagner 1995; Evert 2006). Some patterns of RNA editing may be phylogenetically informative at this level (Logacheva et al. 2008).
4. Other Relationships. Analysis of morphological data in particular has quite often grouped more or less herbaceous clades in magnoliids and the ANITA grade, i.e. Piperales, Chloranthaceae, and Nymphaeales, with monocots; this is the pal(a)eoherb hypothesis (see e.g. Donoghue & Doyle 1989; Taylor & Hickey 1992; Endress 2000). Analysis of combined morphological and molecular data suggested that Piperales weresister to monocots (Doyle & Endress 2000: support weak), Tamura et al. (2011: 6 plastid, 7 mitochondrial, and 1 nuclear genes sequenced) found some support for this clade, as did Barrett and Davis (2011: or [Piperales + Ceratophyllales] the sister group). However, although quite popular in the latter years of the last century, the palaeoherb support comes from homoplasies associated with the adoption of the herbaceous habit. Indeed, Piperales are now firmly (usually!) embedded in the magnoliid clade, suggestions like that of Parkinson et al. (1999) of a [Piperales + eudicot] and by Ruhfel et al. (2014: amino acid analyses) of a [Piperales + Ceratophyllaceae] clade being exceptions, while Nymphaeales are very near the base of the whole angiosperm clade.
To Conclude. There may be be differing signals in nuclear ([monocots [magnoliids + The Rest]]) and chloroplast ([magnoliids + [monocots + The Rest]]) genes (Xi et al. 2014: Ceratophyllum and Chloranthaceae not included) here. Sun et al. (2014) retrieved the latter set of relationships, but both nuclear and mitochondrial trees recovered a [eudicots [monocots + magnoliids]] topology. Wickett et al. (2014) in particular noted that chloroplast genes do not give consistent relationships. A pentatomy seems the best depiction of our current understanding of relationships. Since a clade [Chloranthaceae + Ceratophyllaceae] is quite commonly recovered, characters of that clade, several of which may be apomorphies are suggested below (in part from Zeng et al. 2014), but to which major clade it should be attached is unclear. I have also given character for a clade [Chloranthales + magnoliids] above; these relationships are quite comonly recovered.
[Ceratophyllum + Chloranthaceae]: leaves opposite, secondary veins pinnate; flowers dense, sessile, small [<5 mm across], monosymmetric by reduction; P 0; A 1, sporangia ± embedded in connective; G 1, ascidiate; ovule 1/carpel, apical, straight.
Age. The age for this node is estimated to be (174-)170, 126(-71) m.y.a. (Zeng et al. 2014).
[magnoliids [[Ceratophyllum + Chloranthaceae] + eudicots]]: Age. The age for this node was estimated to be (192-)187,148(-128) m.y. (Zeng et al. 2014).
[[Ceratophyllum + Chloranthaceae] + eudicots]: Age. This node is about (187-)182, 141(-132) m.y.o. (Zeng et al. 2014).
[CHLORANTHALES [[MAGNOLIALES + LAURALES] [CANELLALES + PIPERALES]]]: sesquiterpenes +; (microsporogenesis also simultaneous); seed endotestal.
Age. Moore et al. (2010) estimated an age of (141-)136(-129) m.y. for this node and Xue et al. (2012) an age of ca 143.2 or 141.3 m. years. Clarke et al. (2011) a somewhat older age of (176-)149(-128) m.y., Soltis et al. (2008) suggested (168-)131(-126) m.y., and Magallón et al. (2013) an age of around 149.1 m.y. and Naumann et al. (2013) an age of around 142.5 m.y.; see also Magallón (2009) for other dates around 140-150 m.y. ago, about 134.6 m.y. was estimated by Magallón et al. (2015) and ca 198.9 to 192 m.y. by Tank et al. (2015: Table S1, S2). The estimate in Z. Wu et al. (2014), at ca 210 m.y.a., is definitely the oldest.
Doyle and Endress (2010) thought that the Pennipollis plant, from ca 120-115 m.y.a. in Portugal and originally linked to the monocots (Petersen et al. 2000b), was sister to Chloranthaceae, a family they considered to be sister to all angiosperms apart from the ANA grade.
Evolution. Divergence & Distribution. Soltis et al. (2008) offer ages for a number of branching points within this clade based on the topology [monocots [Chloranthaceae, magnoliids [Ceratophyllaceae + eudicots]]].
The character, "endotesta palisade, crystaliferous", could perhaps be placed at this node.
Chemistry, Morphology, etc. Microsporogenesis is variable throughout this clade (Furness & Rudall 2004).
CHLORANTHALES Martius Main Tree.
Branching from the current flush; neolignans ?+; compression wood + [Sarcandra]; nodes often swollen; leaves opposite, joined by sheath, lamina margins toothed, teeth with lateral vein and others [hydathodal]; stipules +; flowers very small [<4 mm across], monosymmetric by reduction, parts whorled; P 0, A 1, abaxial; G 1, ascidiate, postgenital fusion by secretion; ovule 1/carpel, apical, pendulous, straight; antipodal cells proliferating; fruit fleshy; endotesta palisade, lignified, crystalliferous. - 1 family, 4 genera, 75 species.
Note: Boldface denotes possible apomorphies, (....) denotes a feature common in the clade, exact status uncertain, [....] includes explanatory material. Note that the particular node to which many characters, particularly the more cryptic ones, should be assigned is unclear. This is partly because homoplasy is very common, in addition, basic information for all too many characters is very incomplete, frequently coming from taxa well embedded in the clade of interest and so making the position of any putative apomorphy uncertain. Then there are the not-so-trivial issues of how character states are delimited and ancestral states are reconstructed (see above).
Synonymy: Chloranthineae Thorne & Reveal - Chloranthanae Doweld - Chloranthidae C. Y. Wu
CHLORANTHACEAE Sims, nom. cons. Back to Chloranthales
Evergreen; (vessels 0); primary stem with vascular cylinder; rays 6-10-seriate; nodes 1:1, 1:2, or ± 3:3, 2 traces from the central or all gaps, (+ split laterals); (sclereids - Hedyosmum); cuticle wax crystalloids 0; stomata variable, laterocytic, etc.; branching from current flush; lamina vernation conduplicate [Chloranthus], teeth with clear persistent swollen cap into which proceed higher order veins as well as secondaries or tertiaries; stipules small, paired, interpetiolar, usually on rim of sheath; (plants dioecious); inflorescence spicate (branched), flowers sessile; staminate flowers: A ± latrorse, lobed, or connective produced or not, (glandular); (pollen apertures star-shaped polychotomosulcate, pantocolpate, pantoporate); pistillode 0; carpellate flowers: (P +, uniseriate, ± connate, with windows - Hedyosmum); staminode 0; (ovary inferior), stigma ± expanded or not, dry ?or wet; ovules with outer integument 4-8 (2 - Ascarina) cells across, inner integument (3-)7-10 cells across, (micropyle bistomal), parietal tissue 6-8 cells across, nucellar cap +/0; fruit baccate or drupaceous, (bracts accrescent and succulent), (P persistent); coat ± tanniniferous, (mesotesta lignified - Chloranthus), endotesta palisade, containing crystals, tegmen ± crushed, (exo- and mesotegmen fibrous), endotegmen initially subpalisade; endosperm cellular, starchy, grains clustered); n = 8, 14, 15, chromosomes 1-4(-10: Hedyosmum) µm long.
4[list]/75: Hedyosmum (45). Tropics and subtropics, not Africa (Madagascar - Ascarina only) (map: from Verdcourt 1986; Todzia 1988; Leitman 2014). [Photo - Leaf, Flower.]
Age. Despite the age of the clade (see below), some estimates are that crown group diversification is quite recent, being mostly within the last 60-29 m.y. (Zhang & Renner 2003b; Soltis et al. 2008). However, Magallón and Castillo (2009) estimated the crown group age at ca 153.6 or 125 m.y., Wikström et al. (2001) at 131-121 m.y., Bell et al. (2010) at around 121 or around 98 m.y.a., depending on the analysis, Antonelli and Sanmartín (2011: fossil-based) suggested ages of (112-)111(-110) m.y. or thereabouts, while Zhang et al. (2011) provided another series of age estimates, some of which are dramatically older than the others depending on the calibration and the analytical methods used.
Fossils assignable to Chloranthaceae are already common, diverse, and world-wide in distribution in the early angiosperm fossil record (Friis et al. 2011, 2015a; Doyle & Upchurch 2014 for summaries). Distinctive fossil pollen grains, Asteropollis, are first known from the Barremian-Aptian of the early Cretaceous, some 125 m.y. before present (Friis et al. 1997; Doyle 1999; Eklund 1999, but c.f. Clarke et al. 2011, questions over dating); these grains have been identified as belonging to Hedyosmum (see also Crepet & Nixon 1996; Eklund et al. 2003; Friis et al. 2005; Martínez et al. 2013). Doyle and Endress (2007) and Clarke et al. (2011) discuss other palynomorphs that have been associated with Chloranthaceae; some fossil androecia assigned to the family have spiraperturate pollen that is in situ (Crane et al. 1989)!
Evolution. Divergence & Distribution. With older estimates of the family age, all genera had separated by ca 90 m.y.a. (e.g. Wikström et al. 2000; Antonelli & Sanmartín 2011). Diversification within Hedyosmum could be dated to (57.1-)43.3(-30.1) or (43-)35.6-(25.9) m.y.a. depending on the method used, and was in part associated with the Andean uplift, although the family as a whole showed a pattern of gradual extinction over time (Antonelli & Sanmartín 2011).
For general morphological evolution, living and fossil Chloranthaceae integrated, see Eklund et al. (2004). Endress (2001) emphasized what he considered to be the plesiomorphic floral morphology of the family. However, there is no evidence that it is a member of the ANA grade, and several aspects of its floral morphology and development, including the loss of any perianth, are clearly highly derived derived (e.g. Li et al. 2005). For the evolution of the chloranthaceous flower, integrating fossils into the scenario, see Doyle and Endress (2014); the flowers of Chloranthus and Sarcandra are secondarily perfect/bisexual (see also Doyle & Endress 2011), or imperfect flowers have evolved twice, or perfect flowers are really pseudanthia (Endress & Doyle 2015).... In the careful analysis of Friis et al. (2015a), Canrightiopsis, with a single carpel and three stamens borne on one side of semi-inferior gynoecium, shows similarities with Canrightia, which has a hypanthium, 2-5 carpels each with 2-5 seeds, and its stamens are radially arranged. The seeds of Canrightiopsis are very small, the embryo being about 1/4 the size of that of Sarcandra, with which it has been compared (Friis et al. 2015b).
Chemistry, Morphology, etc. Although benzylisoquinoline alkaloids apparently have not been detected in Chloranthaceae, (S)norcolaurine synthase activity is high, suggesting that they may be found here (Liscombe et al. 2005). Roots - presumably those of the seedlings and young plants - seem not have any secondary thickening (Blanc 1986)?
For some discussion of inflorescence morphology, see Doria et al. (2012). The perianth of Hedyosmum has unique, schizogenous apertures/windows (Doria et al. 2012 and references; c.f. Endress & Doyle 2015). Crane et al. (1989), Crepet and Nixon (1997), Eklund et al. (1997), Eklund (1999), and others discuss the nature of the androecium in the family, a matter over which there has been considerable controversy. In Chloranthus it has been suggested that the androecium is lobed, with 2 or 4 dithecal stamens(!!?), and that staminate flowers of Hedyosmum have hundreds of anthers, however, here as in most angiosperms the stamens seem to be dithecal (Kong et al. 2002, and references). Doria et al. (2012) illustrate a superior gynoecium in Hedyosmum. The stylulus is filled with secretion. Endress and Igersheim (1997) describe the stigma as being wet (c.f. Todzia 1988). The ovule in Chloranthus is not quite straight ("subatropous" - Yamada et al. 2001a). For variation in micropyle type, see Heo and Tobe (1995). Johri et al. (1992) noted that the endosperm stores oil, but there may also be starch. The cotyledonary nodes have split laterals (Bailey 1956).
For general information, see Swamy (1953), Todzia (1988, 1993) and Eklund (1999), for chemistry, see Hegnauer (1964, 1989), young plants, see Blanc (1986), general vegetative anaomy, see Metcalfe (1987), for wood anatomy, see Carlquist (1992a), for reaction wood, see Aiso et al. (2014), for embryology, see Vijayaraghavan (1964), and for floral development, see Endress (1987b) and G. S. Li et al. (2005).
Phylogeny. Within Chloranthaceae, morphological analyses, including details of wood anatomy, suggested the genus pairs [Ascarina + Hedyosmum], mainly woody, plant monoecious to dioecious, and [Chloranthus + Sarcandra], herbaceous to semi-shrubby, flowers perfect. In molecular work (Qiu et al. 1999), on the other hand, the relationships [Hedyosmum [Ascarina [Chloranthus + Sarcandra]]] were found. Although there was strong support, the sampling was rather minimal, but the same set of relationships were confirmed by Zhang and Renner (2003b) and Zhang et al. (2011), both with a much improved sampling. They have also been found in subsequent morphological analyses with constrained outgroups (Doyle et al. 2003; Eklund et al. 2004).
Previous Relationships. Cronquist (1981) included Chloranthaceae in his Piperales while Takhtajan (1997) placed Chloranthales after Calycanthales at the end of his Magnoliidae.
Synonymy: Hedyosmaceae Caruel