EVOLUTION OF LAND PLANTS (UNDER CONSTRUCTION)
Background. As little as thirty years ago our understanding of the evolution of land plants was very different from what it is now. Then it was usually thought that Psilotum represented a very ancient group, often being compared with plants from the Devonian Rhynie Chert; that horsetails were also ancient (but not immediately related), and were linked to the fossil Sphenophyllum and its relatives; and that Lycopodium, Selaginella and relatives formed a group, after which came ferns, gymnosperms, and seed plants. Bryophytes, that is mosses, liverworts and hornworts, represented the earliest land plants. Relationships between the bryophytes was unclear, but they seemed to form a group, while the aquatic Characeae (inc. Nitella) with their quite complex haploid plant bodies were thought to be the algal group most closely related to land plants (e.g. Graham 1993). Evolution seemed to have resulted in a fairly straightforward increase in complexity, but this comforting sequence has been severely challenged over the last twenty years or so.
Relatives of Land Plants. Land plants or Embryopsida are members of a clade embedded in a largely aquatic paraphyletic group, the "green algae" (paraphyletic groups will be denoted by scare quotes); the two together make up Viridiplantae. Viridiplantae can be divided into two main groups, Chlorophyta s. str. and Streptophyta, the latter including "Charophyta s.l." within which Embryopsida are embedded. For general information on the evolution of Chlorophyta and the streptophytes, see e.g. Lemieux et al. (2000), Turmel et al. (2002), Sanders et al. (2003), Waters (2003), Delwiche et al. (2004), Lewis and McCourt (2004), Becker et al. (2009), and Leliaert et al. (2012, a great deal of information, 2016). Lewis and McCourt (2004) emphasize that many clades of "green algae" have terrestrial representatives, of which Embryopsida are merely the most prominent. Leliaert et al. (2016) note a number of similarities in the chloroplast genome between their Palmophyllophyceae, perhaps sister to other chlorophyta, and Mesostigma, de Vries et al. (2016) note numerous features common in/characteristic of embryophytes that are also to be found in streptophytes, and they discuss changes in the chloroplast in partticular, and Buschmann and Zachgo (2016) looks at the evolution of the distinctive embryophyte mode of cell division from a similar point of view (see also below).
Within Chlorophyta s. str. there are several algae that are involved in lichen formation (Trebouxia and its relatives) as well as several ecologically very important marine algae. Volvox, Caulerpa, Ulva and Acetabularia are other Chlorophyta.
These include land plants (= embryophytes or Embryopsida) and a subset of freshwater green algae like Mesostigma viride (biciliate), Chlorokybus, Klebsormidium, Spirogyra, Coleochaete, and Chara.
Age. Stem streptophytes have been dated to 1200-725 m.y. (Yoon et al. 2004: Chaetosphaeridium vs. the rest), while Zimmer et al. (2007) give an age of (963-)725(-587) m.y. for the divergence of Chlamydomonas from the streptophytes.
Evolution: Divergence & Distribution. It is becoming increasingly clear that what appear to be land plant innovations may first appear more basally in the streptophyte clade (e.g. Becker & Marin 2009; Popper & Tuohy 2010; Wodniok et al. 2011). Lang et al. (2010) noted that a considerable number of transcription-associated protein families evolved in the basal land plants or their immediate aquatic ancestors, many more than subsequently, but exactly where subsequent changes occur is unclear since nothing between Selaginella and angiosperms was included in this study. For the synthesis of the cell wall polysaccharides so important in land plants, but also found here, see Mikkelsen et al. (2014). Boot et al. (2012) found that there was polar auxin transport in Chara; it is known from the sporophytic generation in mosses, etc., but not liverworts. A number of streptophytes have phragmoplasts (Brown & Lemmon 2007 and references).
There are several other features common in streptophytes. The zoospores are covered with small square scales and have paired cilia that are laterally inserted, joining a multilayered structure (Mattox & Stewart 1984; Simon et al. 2006). The photorespiratory glycolate pathway occurs in peroxisomes rather than in mitochondria (Stabenau & Winkler 2005). The BIP multigene family is prominent (Friedl & Rybalka 2012). The duplication yielding the important GAPA/B gene pair occurred around here, and streptophytes have a particular isoform of glyceraldehyde-3-phosphate dehydogenase, GAPDH B (Peterson et al. 2006). For characters of streptophytes and some of their subgroups, see Leliaert et al. (2012: esp. Fig 4). Buschmann and Zachgo (2016) discuss the evolution of cell division. In basal streptophytes there is a cleavage furrow and the new transverse wall develops centripetally while in embryophytes the cell plate develops centrifugally where the preprophase band (p.p.b.) of microtubules had been, and basal streptophytes have a centrosome from which radiating microtubules develop and are involved in pulling the dividing chromosomes apart while in most embryophytes neither centrosome nor radiating microtubules develop. These changes are complex. Many of them are evident in various groups of streptophytes close to the embryophytes, although some show parallelism and even loss there (Buschmann & Zachgo 2016). Thus Mougeotia, in the clade sister to Embryopsida, lacks centrioles and has a p.p.b., while Coleochaete (same clade, or next clade down) has monoplastidic meiosis and centrioles (e.g. Brown & Lemmon 1993, 2011b).
Genes & Genomes. Leliaert et al. (2012) summarize variation in the plastid and mitochodrial genomes in streptophytes and compare it with that in land plants, and some of this may convert to apomorphies when comparative data improve. A possible synapomorphy for the node that includes Mesostigma viride and the rest is the presence of the ndh and rps15 and the loss of the rps9 chloroplast genes, although Chara has the rps9 but not the rps15 genes (Martín & Sabater 2010); the presence of introns in the ndhA and ndhB genes may also be apomorphies around here. Both Zygnema and the desmid Staurastrum secondarily lack the chloroplast inverted repeat, present in other streptophytes (Turmel et al. 2007), indeed, evidence now suggests that the IR may have been lost several times in the [Zygnematales + Desmidales] clade as well as in Coleochaete (Civán et al. 2014; Lemieux et al. 2016). Indeed, in general the chloroplast genome in the [Zygnematales + Desmidales] is very labile, group II introns frequently being lost, and some phage/viral genes have been gained, although overall the genes it contains are much less labile (see esp. Lemieux et al. 2016). For similarities in the organisation of the chloroplast genome in particular between basal streptophytes and basal green algae, see Leliaert et al. (2016).
Phylogeny. Resolving the relationship of the polyphyletic prasinophytes, mostly Chlorophyta, has been important (e.g. Lewis & McCourt 2004; Niklas & Kutschera 2010; esp. Leliaert et al. 2016 and references). Mesostigma viride, the only streptophyte with an eye spot, used to be included in that group, but along with Chlorokybus it is sister to the other streptophytes, as is indicated by nuclear and some, but by no means all, organellar genes (Kim et al. 2006: isoprenoid synthesis pathways and glycolate oxidizing enzymes agree). Its zoospores have scales but lack a cellulose cell wall (J. Petersen et al. 2006) and it links with the non-motile Chlorkybus (Simon et al. 2006).
It was often thought that Characeae (inc. Nitella) were the immediate sister group of land plants (e.g. Graham 1993: still useful and readable; Karol et al. 2001; Turmel et al. 2003; Delwiche et al. 2004; Qiu et al. 2007: quite strong support), partly because they seemed to be intermediate in a progression between simple "algal"-like morphologies and the more complex land plants - they are filamentous, growth is by an apical cell, and they are oogamous. However, Turmel et al. (2006, 2007) found Zygnematales to occupy this position in a number of analyses based on complete chloroplast genome sequences - a commonly-found set of relationships was [Chara [Chaetosphaeridium [[Zygnema + Staurastrum] + Embryopsida]]] (see also Chang & Graham 2011: Staurastrum not included). Similar relationships are commonly recovered, e.g. [Nitella [[Spirogyra, Closterium, Chaetosphaeridium, etc.] [Coleochaete + Embryopsida]]], (Finet et al. 2010), while B. Zhong et al. (2013a, b; c.f. Springer & Gatesy 2014; Zhong et al. 2014a) found the variant relationships [Charales [Coleochaetales (inc. Chaetosphaeridium) [[Zygnematales + Desmidales] + Embryopsida]]] or [[Coleochaetales + Zygnematales] Embryopsida], and similar relationships were found by Simon et al. (2006) and Sayou et al. (2014). Although Springer and Gatesy (2014) found different topologies using other methods to analyse the data of Zhong et al. (2013a), Charales were never sister to embryophytes, and the relationships recovered around here are most often [[Chlorokybus + Mesostigma] [Klebsormidium [Nitella [[Coleochaete + Chaetosphaeridium] [[Penium + Spirogyra] + embryophytes]]]]], e.g. as found by Laurin-Lemay et al. (2012: q.v. for details) in a reanalysis of the data used by Finet et al. (2010) i.a. excluding contaminated data such as rotifer and diatom sequences; see also Cooper (2014).
Evidence for the sister group relationships of embryophytes and Spirogyra and its relatives is now quite strong (Leliaert et al. 2012: literature; Timme et al. 2012; see also Wodniok et al. 2011; Ruhfel et al. 2014; Wickett et al. 2014: transcriptome analyses), and chloroplast genome analyses of Davis et al. (2014a), Civán et al. (2014) and Lemieux et al. (2016). The [Penium + Spirogyra] clade has a number of apomorphies, including the loss of cilia and also the loss of morphological complexity (Wodniok et al. 2011; Timme et al. 2012).
For divergence within Coleochaete and its morphological variation, see Delwiche et al. (2002). Many genera of Desmidaceae are polyphyletic (Friedl & Rybalka 2012 and references).
Clarifying the relationships of and within Zygnematales is clearly critical. However, whatever the sister-group relationships of embryophytes might be, Chara et al. are no longer likely candidates. Although this topology questions a scenario involving the evolution of ever more complex plant bodies, it is in line with chloroplast genome evolution, including that of the tufA gene, which has moved to the nucleus, although it is present, if very odd, in Coleochaete (e.g. Baldauf et al. 1990; de Vries et al. 2016). The chloroplast ultrastructure of Coleochaete is in some ways similar to that of hornworts (Vaughn et al. 1992).
Classification. For a classification of life, see Ruggiero et al. (2015).
EMBRYOPSIDA Pirani & Prado
Gametophyte dominant, independent, multicellular, not motile, initially ±globular; showing gravitropism; acquisition of phenylalanine lysase [PAL], microbial terpene synthase-like genes +, phenylpropanoid metabolism [lignans +, flavonoids + (absorbtion of UV radiation)], xyloglucans in primary cell wall, side chains charged; 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, microtubules with γ-tubulin along their lengths [?here], interphase microtubules form hoop-like system; metaphase spindle anastral, predictive preprophase band + [with microtubules and F-actin; where new cell wall will form], phragmoplast + [cell wall deposition centrifugal, from around the anaphase spindle], 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 transverse [with respect to long axis of archegonium/embryo sac], sporangium and upper part of seta developing from epibasal cell [towards the archegonial neck, 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 +; >1000 spores/sporangium, sporopollenin in the spore wall laid down in association with trilamellar layers [white-line centred lamellae; tripartite lamellae]; mitochondrial trnS(gcu) and trnN(guu) genes +; 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 introns (not: Mesostigma), close association between trnLUAA and trnFGAA genes [precursors for starch synthesis], tufA gene moved to nucleus.
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).
All groups below are crown groups, nearly all are extant.
Age. Clarke et al. (2011: other estimates, too) suggested an age for crown Embryopsida of (815-)670(-568) m.y., Cooper et al. (2012) estimated its age at (519-)493(-469) m.y., and Magallón et al. (2013: including temporal constraints) an age of around (480.4-)475.3-474.6(-471) m.y. (see the constraint age in Heinrichs et al. 2007) and a stem age of around (962.5-)913, 911(-870) m.y.; the lowest crown date is around 439 m.y. (Magallón & Hilu 2009). An age of (629.5-)530(-449) m.y. is suggested in B. Zhong et al. (2014b: fossil calibration); see also P. Soltis et al. (2002: variety of ages, depend on calibrations).
Evolution: Divergence & Distribution. Many of the bolded characters in the characterization above are apomorphies of clades of subsets of streptophytes + embryophytes along the lineage leading to the embryophytes, not apomorphies of crown-group embryophytes per se, and these latter are indicated by asterisks. Characters supporting relationships between Embryopsida and subsets of streptophytes include many details of cell division, occurrence of an apical cell in the gametophyte (perhaps), numbers and types of introns in the chloroplast DNA, cilium ultrastructure, occurrence of sporopollenin (but in lower streptophytes it is associated with the inner wall of the zygote, not the walls of the spores - e.g. Wallace et al. 2011), retention of the zygote on the haploid plant, and nrDNA in a single array; see also above.
Laenen et al. (2014) give ages and diversification rates for well over 150 major clades throughout land plants.
The sporophytic generation can be thought of as being interpolated into a life cycle that was entirely haploid/gametophytic, with the exception of the zygote, rather than being the result of the divergence of initially morphologically similar diploid sporophytic and haploid gametophytic generations (e.g. Haig 2008, 2015; Gerrienne & Gonez 2011). The BELL1 homeobox gene may be involved in the interpolation of mitotic cell divisions between zygote formation and meiosis in early land plants (Horst & Reski 2016: the gene is also known from Chlamydomonas, but this is not close). The more complex plant body would allow the production of spores, meiospores, the immediate products of meiosis, in larger numbers (e.g. Brown & Lemmon 2011a; Qiu et al. 2012; Edwards et al. 2014). This change may have been driven by the unpredictability of fertilization (Haig 2015). (Interestingly, in Coleochaete the large, maternally-provisioned zygote may produce up to 32 zoospores, although exactly when meiosis occurs is unclear - Haig 2015.) Thus there may have been an initial development of a diploid spore-producing sporangium (= sporogonium), with the later elaboration of a full-blown free-living sporophyte in the polysporangiophyta, the vegetative body being an interpolation into the life cycle (e.g. Kaplan 1997: chap. 19; Kato & Akiyama 2005; Qiu et al. 2012: extensive discussion; Ligrone et al. 2012b), the sporophyte becoming independent of the parental gametophyte (Haig 2015; Qiu et al. 2012). Some streptophytes and nearly all land plants have placental transfer cells or their equivalents either on the sporophytic or gametophytic sides or both; these have labyrinthine wall ingrowths that mediate an initial transfer of nutrients from the gametophyte to the sporophyte (see Gunning & Pate 1969; Ligrone et al. 1993: much detail; Kendrick & Crane 1997; Hilger et al. 2002; Carapa et al. 2003; Vaughn & Bowling 2008; Renzaglia & Whittier 2013 for a tree). In both mosses and liverworts gene families involved in meiosis are early expressed in the sporophyte, hence, perhaps, the lack of its extended growth (Frank & Scanlon 2014); this is discussed further later. However, our lack both of reliable knowledge of life cycles in most charophyte algae (Haig 2010, 2015) and of the phylogenetic relationships of bryophytes, mosses, liverworts and hornworts (see below), hamper our understanding of the events that led to the development of the alternation of generations in land plants.
A variety of spores, including permanent tetrads, may have been produced by protoembryophytic plants whose sporophyte was little more that these spores alone. Cryptospores, initially largely defined by what they were not (Strother 1991; Volkova et al. 2016 for meiosis), are known from the mid-Cambium onwards, and cryptospores that are like bryophyte spores appear in the middle Ordovician, about 40 m.y. later and ca 476 m.y.a. (e.g. Gray 1993; Wellman 2004a; Brown & Lemmon 2011a; Gerienne et al. 2016 and references; for the evolution of the spore walls of land plants, see also Blackmore & Barnes 1987). Fragments of plant bodies of very early land plants, perhaps liverworts, appear in late Ordovician rocks from Oman (Kenrick 2000; Wellman et al. 2003), while Sphagnum-like fossils, the earliest embryophyte vegetative remains discovered so far, have been found in Ordovician rocks ca 455 m.y.o. in North America (Graham et al. 2013, esp. Cardona-Correa et al. 2016). Edwards et al. (2014) discuss what they call cryptophytes, plants that cannot be confidently assigned to any extant group, from this period, and their cryptospores, which were hilate monads, dyads, and permanent tetrads.
For a detailed study of the morphology of early land plants placed in a phylogenetic context, although some aspects of this are now dated, see Kenrick and Crane (1997), and for many apomorphies of bryophyte groups and the early polysporangiophytes, see Ligrone et al. (2012a). Gerienne et al. (2016) characterize many embryophyte clades up to and including spermatophytes (but note that details of the topologies of both trees in their Fig. 2 differ from the topology of the relationships accepted here). Other features can be added to the characterization. L and D isomers of methionine are treated identically metabolically in liverworts, almost alone in land plants (Kenrick & Crane 1997). Members of Klebsormidiales, Coleochaetales, Desmidaceae and Zygnematales have pyrenoids, and so the loss of pyrenoids may be an apomorphy for embryophytes (Cook 2004a, b).
For the evolution of cell division, see the useful summary by Buschmann and Zachgo (2016). Brown and Lemmon (e.g. 1990, 2007; Brown et al. 2010) and others have unravelled some of the complexity of both mitotic and meiotic cell divisions in land plants, particularly extreme in liverworts; for meiosis, see also Renzaglia and co-workers (e.g. Renzaglia et al. 2000a, Renzaglia & Garbary 2001). Although centrosomes and centrioles, which show vertical inheritance, are lost (Murata et al. 2007), similar structures (but they are not inherited) may develop during meiosis from microtubule organizing centres (MTOCs), and these vary considerably (Brown & Lemmon 2007). Indeed, in Marchantia polymorpha the nature of the MTOC changes during meiosis (Brown et al. 2007). In general, γtubulin, involved in the nucleation of microtubules, is highly migratory. Brown and Lemmon (1997, see also 2008) reviewed the distribution of the quadripolar microtubule system in land plants; it occurs in all three bryophyte groups, in lycophytes, and in Marattiales, at least. This system is linked with monoplastidy, the MTOC being associated with the plastid. For variation in plastid number and possible correlations with patterns of microspore division, see Rudall and Bateman (2007). In streptophytes as a whole basal bodies develop de novo immediately prior to the formation of motile sperm cells (Wastenays 2002). Interestingly, the p.p.b. is sometimes absent, as in the protonema of at least some mosses, and even in megaspore development and in the endosperm of flowering plants, but in such situations elements of the preprophasic band apparatus may be present (Webb & Gunning 1991;Buschmann & Zachgo 2016 and references).
Hodges et al. (2012) survey the evolution of land plant cilia in part focussing on the ciliome and the role it continues to play in land plant gametes even after the cilia are lost.
Pires and Dolan (2010) found that basic helix-loop-helix proteins, a class of transcription factors, diversified very early, at least as early as [mosses + the rest], while Volokita et al. (2010) discuss the GDSL-lipase gene family and its evolution. RNA editing in which the organelle-targeted pentatricopeptide repeat proteins play an important role is restricted to Embryopsida (Rüdinger et al. 2008).
Sayou et al. (2014, the subsequent discussion should also be read) looked at the evolution of the LEAFY gene, usually in a single copy in embryophytes (but two in gymnosperms), yet variously involved in cell division and specification of floral identity. Its binding specificity is notably variable (promiscuous) in the hornworts, and although the evolutionary scenario suggested by Sayou et al. (2014) is based on the rather unlikely topology [hornworts [mosses [liverworts + vascular plants]]] (see also below), they suggest that whatever the topology, this promiscuity hypothesis is likely (see their Fig. S9).
In mosses, at least, the great majority - ca 95% - of genes are expressed in both generations (Szövényi et al. 2010; c.f. in part O'Donoghue et al. 2013), in line with the proposal by Banks et al. (2011) that some of the genes involved in the patterning and differentiation of vascular tissue were present in the ancestral (gametophyte dominant) land plant and were recruited by the sporophytic generation. Similarly, in the fern Polypodium ca 97% of the genes are expressed in both generations, only 10% of the genes differing in transcription levels between the two (Gigel et al. 2016). Frank and Scanlon (2014) proposed a model for sporophyte evolution that is similar to that for vascular tissue evolution. There do seem to be substantial differences between the two generations in expression of genes controlling apical meristem growth and auxin polarity (e.g. Fujita et al. 2008; Sakakibara et al. 2008), and other studies found that over 12% of the transcriptome of the moss Physcomitrella switched in the transition from gametophyte to sporophyte, especially those genes involved in carbohydrate and energy metabolism (O'Donoghue et al. 2013; see also Szovenyi et al. 2010). It is only in angiosperms that a substantial proportion (ca 25%) of genes are expressed in the sporophyte alone (Szövényi et al. 2010). Interestingly, in both angiosperms and Physcomitrella genes expressed in the gametophyte were younger than those expressed in the sporophyte (O'Donoghue et al. 2013; Cui et al. 2015; Gossmann et al. 2016). Floyd and Bowman (2007) discuss developmental changes possibly occurring at this node, and Friedman et al. (2004) the evolution of plant development.
Much of interest is likely to come from the study of individual metabolic pathways and their control. Thus important signaling intermediates, the G-protein complex, is known from Chara and land plants (but not the green alga Micromeris), although elements of the pathway seem to be missing in some mosses and liverworts (Hackenberg et al. 2013). C3HDZ (class III homeodomain leucine zipper) genes, very important in development in euphyllophytes, etc., are also found in Chara (Prigge & Clark 2006; Floyd et al. 2006; Vasco et al. 2016). Recently it has been found that microbial-type terpene synthase-like genes are commonly found in all embryophytes except seed plants (at 3/7, hornworts have the lowest proportion of such genes), and they are not found in streptophytes; all land plants also have another class of terpene synthase genes (Jia et al. 2016). Some microbial terpene synthase genes are similar to those of fungi and others to bacterial genes (Jia et al. 2016), but other than the distinctive distribution of these genes, little is known about their evolution. Various classes of phosphoprotein phosphatases also have interesting distributions, with the ApaH phosphatases currently being known from streptophytes only, while the ALPH class is absent from land plants (Uhrig et al. 2012). Several copies of LATERAL ORGANS BOUNDARIES DOMAIN genes are to be found in bryophytes, and they are also also known from Coleochaete and Spirogyra (Chanderbali et al. 2015). KNOX1 and KNOX2 genes are unique to land plants, and KNOX1 regulates sporophytic meristems while KNOX2 suppresses the gametophytic developmental program in the sporophyte (Sakakibara et al. 2013). Two copies each of the plant homeobox KNOX genes, involved in meristem activity in vascular plants, and the MADS-box MIKC genes, functioning i.a. as floral identity genes, are found in mosses; subsequent duplication generated the diversity of these gene classes found in flowering plants in particular (Theißen et al. 2001). I am not sure where these should be placed on the tree...
Yue et al. (2012) suggested that numerous genes, including those involved in many embryophyte functions like cuticle and lateral root formation, had been acquired by lateral transfer from fungi and bacteria (see also Emiliani et al. 2009).
If a monophyletic bryophyte clade is sister to the polysporangiophytes/vascular plants (see below), then much of the above will need reevaluation, as will the evolution of stomata and the complex sporophyte. A bryophyte clade could be characterized by having a single terminal sporangium, a proximal extension of the basal body, basal body length, and the angle of the spline with respect to the lamellar strip (= MTOC), etc. (for details, see e.g. Hodges et al. 2012, esp. Table 1), i.e. some embryophyte apomorphies become bryophyte apomorphies. The story as told with bryophytes being paraphyletic - as here - emphasizes the progressive acquisition of features of vascular plants, e.g. of stomatal functions (Field et al. 2015b) and aspects of sporophyte development.
See Mishler and Churchill (1984, 1985) for important early morphological phylogenetic analyses; Graham (1993) and Finet et al. (2010), both general; Graham et al. (2000), body plan; Stabenau & Winkler (2005), glycolate metabolism, from mitochondria to cytoplasmic; Becker & Marin 2009, Domozych et al. 2010, Popper & Tuohy 2010, Sørensen et al. (2010), distinctive cell wall polysaccharide polymers evolved in charophyceans or before; Comparot-Moss and Denyer (2009), evolution of starch synthesis. For other possible apomorphies, see e.g. Goffinet (2000), Renzaglia et al. (2000), Schneider et al. (2002: much useful information), Johnson and Renzaglia (2009) and Doyle (2013). Carothers and Duckett (1982: bryophytes) and Renzaglia and Garbary (2001) discussed the evolution of the male gametes in land plants in some detail. For information on bryophyte body form easily placed in a phylogenetic context, see Goffinet and Buck (2013), and see e.g. Timme et al. (2012) for apomorphies immediately below the embryophyte node.
Ecology & Physiology. Problems of dealing with life on land centre on water loss, movement of water through the plant, protection from ultraviolet (UV-B) radiation (especially important for bryophytes), plant support, etc., and have shaped the evolution of both gametophyte and sporophyte (e.g. Watkins et al. 2007a, b; Del Bem & Vincentz 2010; McAdam & Brodribb 2011; Willis & McElwain 2014; Graham et al. 2014; Proctor 2014; Raven & Edwards 2014; Robinson & Waterman 2014). See also Bateman et al. (1998) and Hemsley and Poole (2004) for the physiology and ecology of early land plants.
One of the major changes, or better, complex of changes, that facilitated the spread of land plants may have been the evolution of sporopollenin-covered spores from the sporopollenin-covered zygotes of their aquatic ancestors (Gray 1993; Blackmore & Barnes 1987; Brown & Lemmon 2011a). Sporopollenin, known from streptophytes like Coleochaete (Delwiche et al. 1989), became associated with the walls of the haploid spores by a complex process involving precocious initiation of cytokinesis (hence the often quadrilobed, quadripolar microtubule system of many bryophytes), acceleration of meiosis, delay in wall deposition, etc., a mixture of heterochrony and heterotopy (Brown & Lemmon 2011a). The composition of sporopollenin is remarkably stable in land plants, and the sporopollenin of the walls around lycophyte fossil spores ca 310 m.y.o., of extant lycophytes and the embryos in some Charales is quite similar (Fraser et al. 2012), although the sporopollenin of conifers, at least, may differ. Homologues of just about all genes involved in pollen wall development in Arabdiopsis are to be found in Selaginella and Physcomitrella, emphasising the fundamental similarity of angiosperm pollen and moss spores (Wallace et al. 2011). Wellman (2004b) noted that sporopollenin deposition was associated with white line-centred lamellae.
Lignin, integral to the support and water-conducting facilities of vascular plants in particular, and flavonoids, involved in protection againt UV radiation, are synthesised by pathways that both use phenylalanine lysase (PAL) in an early step. Emiliani et al. (2009) suggested that embryophytes acquired this gene via lateral transfer from a bacterium; they found that it was also present in fungi, but absent from Nostoc. Delwiche et al. (1989) record lignin-like compounds (positive Maule reaction) from Coleochaete and Ligrone et al. (2008) lignin-related compounds from Nitella, so exactly where PAL moved into the streptophyte clade is uncertain. Much of the pathway by which lignin is synthesized in vascular plants is found already in mosses (Gómez-Ros et al. 2007; Z. Xu et al. 2009, see also Guo et al. 2010), but in some cases pathways in mosses and liverworts may differ (see below under stomatophytes). S lignin, made up of syringyl units, has been found in some liverworts and is scattered elsewhere in vascular plants; in flowering plants it is very common (Z. Xu et al. 2008Li & Chapple 2010; Espiñeira et al. 2010; see also Gómez-Ros et al. 2007). Isoprenoids (xanthophylls and tocopherols) that protect against photo-oxidation and other insults of a dry, high light environment are widely distributed in land plant and in some of their aquatic relatives, although some carotenoids involved in these functions may have evolved in land plants (Esteban et al. 2009).
Raven and Edwards (2014) list estimates of the net photosynthetic rates for bryophytes and other early land plants. It has recently been suggested that back in the Late Ordovician ca 450 m.y.a. and with an atmospheric CO2 concentration about eight times today's levels, land plants, bryophytes and lichens, supported a level of chemical weathering two to three times that of today's vegetation (Porada et al. 2016). Such high levels are likely to have been temporary as embryophytes spread and nutrients became limited and nutrient recycling in the developing soil/humus layers increased, but they may have helped precipitate glaciation (Porada et al. 2016). For photosynthesis in bryophytes and early embryophytes, see Graham et al. (2014) and other articles in Hanson and Rice (2014).
Reproductive Biology. For a discussion about various aspects of sexual and asexual reproduction in bryophytes, the latter very common and occuring in a variety of ways, see Maciel-Silva and Pôrto (2014). Chlorophyllous spores are found in a few bryophytes, and garmination in such spores is precocious (endosporic).
Plant-Animal Interactions. Some caterpillars of Micropterigidea, a jawed, lepidopteran clade that is perhaps Jurassic in age and sister to all other leps, are detritivores, but others eat mosses (e.g. Atrichum) and especially liverworts (Imada et al. 2011; Regier et al. 2015 and references; see also Hosts, consulted iii.2014), although they also eat angiosperms (Davis & Landry 2012 and references). On balance, evidence suggests that the Araucaria-eating jawed moths, Agathiphagidae, are sister to Micropterigidae (Regier et al. 2015; Kristiansen et al. 2015; c.f. Heikkilä et al. 2015). For the host plants of other jawed moths, see also Nothofagaceae. Caterpillars of Mnesarchaeidae, members on a basal glossatan clade, live in silk tunnels and eat mosses and liverworts, as well as fern sporangia, etc., their sister taxon, Hepialoidea, much more species rich, also are concealed feeders, but they eat just about everything (Regier et al. 2015).
Bacterial/Fungal Associations. Associations between embryophytes and fungi, initially with the gametophytes of the former, were established very early in the Silurian/Devonian (Selosse & Tacon 1998; Redecker et al. 2000b; Nebel et al. 2004; Köttke & Nebel 2005; see also Strullu-Derrien et al. 2014b). At least three genes involved in the establishment of mycorrhizae were found in the common ancestor of land plants, although the DM13 gene in particular seems to have other functions in many mosses (B. Wang et al. 2010, commentary by Bonfante & Selosse 2010). Strigolactones, involved in the establishment of vesicular-arbuscular mycorrhizal associations at least, are known from some streptophytes (Charales) and seem initially to have been involved the control of rhizoid elongation (Delaux et al. 2012); a number of other genes involved in mycorrhizal establishment have a similar ancestry (Delaux et al. 2015). A karrikin receptor complex is involved in the initial interaction between plant and fungus (karrikin and strigolactone both have a butenolide element), and this complex is found widely in embryophytes (DeLaux et al. 2012; Gutjahr et al. 2015).
Glomeromycota, Mucoromycotina, Ascomycota and Basidiomycota (especially a clade in Sebacinales-Serendipitaceae), the major groupings of fungi that form mycorrhizal associations with embryophytes, are all associated with liverworts (Read et al. 2000; Duckett et al. 2006b; Pressel et al. 2010; Bidartondo et al. 2011; Weiß et al. 2016). Bidartondo et al. (2011; see also Pressel et al. 2010) found that Endogone-like fungi (Mucoromycotina) also formed associations with Treubia, Haplomitrium, some hornworts, etc., and surmised that this might be the original land plant-fungus association (see also Rimington et al. 2014); associations between liverworts and basidiomycetes (especially Serendipitaceae) and ascomycetes are likely to be secondary (Bidartondo & Duckett 2009; Weiß et al. 2016). Even if Mucoromycotina were the first fungal associates of liverworts, the establishment of plant-fungus relationships there may be independent of those in other plants. Others have suggested that arbuscular mycorrhizal Glomeromycota were found in the earliest land plants (literature in van der Heijden et al. 2015). The fungus may move to the liverwort from a tracheophyte (Ligrone et al. 2007) or in the opposite direction (Pressel et al. 2010: see also Bidartondo & Duckett 2009). For the (mostly ascomycetous) endophytic fungi to be found in mosses and liverworts, see Stenroos et al. (2010) and Pressel et al. (2010).
There are similarities in the microbiomes of streptophytes and bryophytes, in particular, similar nitrogen-fixing and methanotrophic organisms occur in both, and this has implications both for the evolution of the atmosphere and for the organisms involved (Knack et al. 2015).
Genes & Genomes. Details of gene and genome evolution in embryophyte plastids are given by Jansen et al. (2007), A. M. Magee et al. (2010), Wicke et al. (2011), Civán et al. (2014) and Lemieux et al. (2016). Compared with their sister groups, the [Zygnematales + Desmidales] clade, the chloroplast genome in basal land plants is relatively stable (e.g. Lemieux et al. 2016). The trnLUAA and trnFGAA genes are not associated in other green plants (Quandt et al. 2004). Details of the evolution of the chloroplast trnS and trnN genes in embryophytes are complex (Knie et al. 2014).
Most bryophytes have small mitochondrial genomes and little variation in gene order compared with mitochondria in vascular plants (Y. Liu et al. 2014a); for the evolution of the mitochondrial genome in basal land plants, see Knoop (2013). For intron distributions in mitochondrial genes, see Dombrovska and Qiu (1994), Qiu et al. (1998), and Regina et al. (2005). trnS(gcu) and trnN(guu) genes occur in the mitochondria of many streptophytes and also in liverworts; the former gene is also found in the mitochondria of the [monilophyte + lignophyte] clade, but not in Gnetales.
See Wicke et al. (2011) for nuclear ribosomal DNA organization and Leitch and Leitch (2013) for the small nuclear genomes of bryophytes (club mosses not sampled).
Chemistry, Morphology, etc. For xyloglucans (hemicelluloses) in the primary cell wall, see Del Bem and Vincentz (2010), Scheller and Ulvskov (2010) and Zabotina (2012). Komatsu et al. (2014; see also Doi et al. 2006) discuss chloroplast movement, mediated by a single copy of the blue-light sensitive phototropin gene, in land plants. For the evolution of rhizoids and rhizoid-like structures, see Duckett et al. (2014), also below. The sporangium develops from tiers of four cells (quadrants) which divide periclinally producing an outer amphithecium and an inner endothecium; the major groups of bryophytes differ in how the capsule wall and spores develop from these cells (Ligrone et al. 2012a for a summary).
See also Kenrick (2000) and Ligrone et al. (2012a), both morphology, O'Donoghue et al. (2013: xyloglucans), O'Rorke et al. (2015: sugars of pectic polysaccharides, interpretation of change depends very much on phylogeny), Taylor et al. (2009: fossils, inc. those of fungi associated with plants), Blackmore and Crane (1998: spore/pollen apertures), Brown and Lemmon (1990: callose and spore development, mono/polyplastidy, 2013 and references: sporogenesis), Brown et al. (2015: spore walls of basal members of the bryophyte clades), Wallace et al. (2011: spore and pollen wall development in land plants), Renzaglia and Garbary (2001: male gametes), Wastenays (2002: microtubules), Tomescu et al. (2014: apical cells of sporophyte), Waters (2003: molecular adaptation), Hedges et al. (2004: timing), Hodges et al. (2012: cilia), Doyle (2013: reproductive features) and de Vries et al. (2016: plastid evolution). Goffinet and Shaw (2009) and Shaw et al. (2011) provide much general information about the "bryophytes" as a whole.
Phylogeny. See Kenrick and Crane (1997), Nishiyama and Kato (1999) and Shaw and Renzaglia (2004) for early literature on bryophyte relationships. The three groups are usually found to be monophyletic, although this was sometimes not so for liverworts (Bopp & Capesius 1998; Quandt & Stech 2003, and references). There are four competing hypotheses of relationships between bryophytes, and relationships here are currently somewhat problematic (see also Cooper 2014).
1. Many studies support the set of relationships [liverworts [mosses [hornworts + vascular plants]]] (e.g. Kenrick & Crane 1997; Goffinet & Shaw 2009; Shaw et al. 2011 for literature); Qiu et al. (2006) confirmed these relationships using three different data sets. This may be the most supported hypothesis of relationships at present (see also Lewis et al. 1997; Kelch et al. 2004; Wolf et al. 2006: many analyses, whole chloroplast genomes]; Qiu et al. 2007; S. Li et al. 2013; Y. Liu et al. 2014b: mitochondrial nucleotide and amino acid data, all other relationships very poorly supported; Magallón et al. 2013, 2016), and it is tentatively followed here. Dombrovska and Qiu (1994) had earlier outlined several lines of evidence such as the content of the inverted repeat and intron distributions that were consistent with the idea that liverworts are sister to all other land plants (see also Qiu et al. 1998b for mitochondrial introns; Antonov et al. 2000: cp rDNA ITS). Kelch et al. (2004), using structural characters of the plastome, and Groth-Malonek et al. (2004, not all analyses; see also Knoop 2005), looking at trans-splicing mitochondrial introns, also suggested the same position for liverworts (see also Rydin & Källersjö 2002 and Karol et al. 2010, but neither in all analyses). Consistent with this hypothesis, the distribution of an extension of the chloroplast inverted repeat placed hornworts as sister to tracheophytes, as did the distribution of cell wall xylans (Carafa et al. 2005), and this position is also favoured by an analysis of cpITS spacer sequences (Samigullin et al. 2002) and a complete plastome analysis (Karol et al. 2010).
2. In an analysis of whole chloroplast genomes, the relationships [liverworts, mosses [hornworts + vascular plants]] were obtained, although a [liverwort + moss] clade was sometimes found (Ruhfel et al. 2014). This latter clade was also recovered in the study by Finet et al. (2010: hornworts not sampled), in some analyses in Karol et al. (2010) and in B. Zhong et al. (2013b), where Anthoceros was sometimes sister to tracheophyta, sometimes sister to Lycopodiales, u.s.w.. In the chloroplast proteome analysis of Shanker et al. (2011: c.f. position of Huperzia) this group was part of a monophyletic bryophytes. Nishiyama et al. (2004) also proposed that the three bryophyte groups form a single clade; 51 genes from the entire chloroplast sequence were included, but taxon sampling was poor, e.g., no lycophytes were included. A similar grouping was also found in an analysis of the trnL intron (Quandt et al. 2004) and in another study that looked at many genes but with very skimpy sampling, that of Goremykin and Hellwig (2005). In the chloroplast genome Bayesian MCMC analysis of Civán et al. (2014) relationships were [[hornworts [mosses + liverworts]] [clubmosses, etc. + the rest]], although in a concensus tree [liverworts + hornworts] were sister to other embryophytes, within which relationsdhips were pretty much scrambled. In a more extensive analysis of chloroplast genomes, Lemieux et al. (2016) recovered the relationships [[mosses + liverworts] [hornworts + the rest], although support for the position of the sole hornwort included, Anthoceros, was weak.
Cox et al. (2014) noticed that trees based on protein coding sequences and trees based on the proteins they coded differed in their topologies, and they suggested that there may have been synonymous substitutions in the sequences; they, too, argued strongly for the monophyly of bryophytes. A [liverwort + moss] clade was also recovered by Wickett et al. (2014) in transcriptome analyses, and in many analyses there, too, bryophytes (as [hornworts [mosses + liverworts]]) were monophyletic; the topology in hypothesis 1 was never recovered.
3. Mitochondrial sequence data sometimes placed hornworts as sister to all other land plants (for references, see Stech et al. 2003); Sayou et al. (2014) found this position in their analysis of the LEAFY gene, and it also appeared in the analyses of Rai and Graham (2010), but it may be a rooting issue there. Renzaglia and Garbary (2010) considered that the evidence for the hornwort basal hypothesis was compelling, and several other studies have recovered this topology (Shanker et al. 2011 for references).
4. Mosses are sister to all other land polants in the analyses of Floyd et al. (2006, 2014) and Vasco et al. (2016), with either liverworts (Floyd et al. 2006) or hornworts (Vasco et al. 2016) sister to vascular plants, although basal land plant relationships were not the focus of these studies.
MARCHANTIOPHYTA / LIVERWORTS
Gametophyte thallus simple; lunularic acid +; rhizoids smooth, living, (pegged, dead); perforate water conducting cells +; membrane-surrounded oil bodies + (0); microtubule organizing centres + [MTOCs polar organizers]; cell walls with relatively little cellulose; sporophyte with apolar auxin transport, foot ± conical to spheroidal, cell divisions uniform, seta [stalk] evanescent, forming by cell elongation after the sporangium develops; sporangium columella 0, wall 1(2-4) cell layers across, opening by four slits; endothecial cells producing archesporial tissue; (sporogenesis polyplastidic); elaters +, unicellular; mitosis with polar MTOCs; spore walls with more or less continuous parallel lamellae at maturity [?level]; genome size (0.21-)1.2(-7.97) pg. (1C).
Ca 4,000-7,486 spp. (see Söderström et al. 2016).
Age. The crown group is dated to (509-)484(-452) m.y. by Cooper et al. (2012) and 509-486 m.y. by Laenen et al. (2014), although Heinrichs et al. (2007) suggested an age of (410.5-)407.6(-404.7) m.y., very much younger.
From fossil evidence, liverworts or liverwort-like plants were present by the Ordovician, and liverworts may have been common through the Silurian and Devonian (Graham et al. 2011); see also Heinrichs et al. (2007) for an evaluation of the identity of fossils purported to be liverworts.
1. Haplomitriopsida Stotler & Crandall-Stotler
Gametophyte axial; symbiont mucuromycotes; thallus apical cell tetrahedral, (stem anatomy complex - Treubia), mucilage copious [stalked slime papillae], leaves lacking costa; (rhizoids 0 - Hapolomitrium); (spores in diads); embryo haustorium?; distinctive blepharoplast.
3/16. More or less world-wide, scattered.
Age. Crown-group Haplomitriopsida are dated to (396-)353(-316) m.y.a. (Newton et al. 2007) or (469-)414(-352) m.y.a. (Cooper et al. 2012).
[Marchantiopsida + Jungermanniopsida]: gametophyte dorsiventral; leaves 0; late development of placental wall ingrowths.
Age. This node is dated to before the Middle Devonian (475-)442(-408) m.y.a. (Cooper et al. 2012), while Heinrichs et al. (2007) suggest an age of (382.8-)372.6(-362.4) m.y. (similar ages also in Newton et al. 2007) and B. Zhong et al. (2014b) an age of (569.7-)375.8(-172.5) m.y., which pretty much covers the waterfront.
2. Marchantiopsida Cronquist
Symbiont mucoromycote or glomeromycote (none); thallus complex, branching truly dichotomous; ventral scales in two rows; gemmae in receptacles [?level]; paraphyses +; sporocytes often lacking lobing, (MTOCs at nuclear envelope); placental transfer cells variable; no RNA editing in organellar genomes.
Ca 340 spp.
Age. Crown-group Marchantiopside are estimated to be (322-)284(-251) m.y.o. (Cooper et al. 2012), (268-)248(-231) m.y.o. (Newton et al. 2007), 269-207 m.y. (Laenen et al. 2014) or (365-)295(-250) m.y. (Villareal A. et al. 2015b).
There are fossils of complex thalloid liverworts from the Triassic and mid-Cretaceous (references in Villareal A. et al. 2015b).
2a. Blasiidae He-Nygrén
2b. Marchantiidae Engler: sporogenesis variable, inc. polyplastidic.
Age. The age of this clade is (328-)263(-226) m.y. (Villareal A. et al. 2015b).
2b1. Neohodgsoniales D. G. Long
Thallus with compound air pores; rhizoids dimorphic, some dead [all smooth]; archegoniophore/carpocephalum +, branched.
2b2. Sphaerocarpales Caveo
2b3. The Rest: ?
(Plant annual); thallus differentiated (not), air chambers +, photosynthetic filaments + (0); air pores +, simple or compound; rhizoids dimorphic, some pegged, dead; archegoniophore/carpocephalum +, simple, with furrows in which there are pegged rhizoids.
(Plant epiphytic); symbiont mucuromycote, dikaryan or glomeromycote (0); fructan sugars accumulated; thallus simple, or plant radial, leafy; cutting faces of apical cell at 120o, leaves (2-)3-ranked; placental haustorium +, transfer cells only in sporophyte (0); sporogenesis polyplastidic.Ca >4,000 spp.
Age. Differences in suggested ages for crown-group Jungermanniopsida are rather great, almost 100 m.y.: e.g. (425-)390(-353) m.y. (Cooper et al. 2012), (335-)328.5(-322) m.y. (Heinrichs et al. 2007) or (331-)292(-262) m.y. (Newton et al. 2007).
Evolution: Divergence and Distribution. Villarreal A. et al. (2015b: q.v. for dates) discuss evolution in the complex-thalloid clade, i.e. Marchantiopsoda; overall molecular evolution (plastid and mitochondria) was slow compared to that of other hepatics, except in Cyathodium, an annual (a reversal), but morphological evolution was less so. Given the topology of the tree (e.g. the position of Neohodgsonia is important), where features of the carpocephalium and those involved in the differentiation of the thallus - the variation is extensive - are to be paced on the tree is unclear, but the pattern of gains and losses will be complex (Villareal A. et al. 2015b). Heinrichs et al. (2007) discussed the evolution of the ca 4,500 species of leafy liverworts, suggesting possible divergence times for the clades (see also Newton et al. 2007; Coooper et al. 2012), and Wilson et al. (2007a, b) discuss the diversification of Lejeuneaceae in particular. Much of the diversification of Porellales and Jungermanniales, both leafy liverworts epiphytic on bark and leaves of flowering plants, has occurred since the evolution of angiosperms (Ahonen et al. 2003; Forrest & Crandall-Stotler 2004), although the clades involved are (much) older (Cooper et al. 2012). Indeed, although many liverwort families had diverged by the end of the Cretaceous, they have diversified considerably since (Cooper et al. 2012). Note that although ages in Newton et al. (2007), Heinrichs et al. (2007) and Cooper et al. (2012) can differ greatly, the overall conclusions of the authors differ less; additional dates may be found in these publications.
For characters of Haplomitriopsida, see Duckett et al. (2006a).
Ecology & Physiology. Understanding the ecophysiology of the first liverworts is a challenge. Field et al. (2012, 2014 and references) discuss details of the nature of the mutualistic association between fungus and plant in some liverworts, including Haplomitriopsida (see also Ligrone et al. 2007). The association of Mucoromycotina with Haplomitrium benefits both partners, and since Haplomitrium lacks rhizoids the fungus is particularly important in nutrient uptake here (Field et al. 2014). Interestingly, a clade of Sebacinales-Serendipitaceae is involved in liverwort mycorrhizae (Weiß et al. 2016: Fig 3G). Extant Marchantia, at least, is mixotrophic (Hata et al. 2000; Graham et al. 2010). The echlorophyllous Aneura mirabilis is the only mycoheterotrophic liverwort, indeed, it is the only mycoheterotrophic bryophyte. It may grow up to 20 cm below the surface of Sphagnum-dominated peat bogs, and it is associated with hyphae of the ectomycorrhizal basidiomycete Tulasnella which is simultaneously associated with Betula or Pinus and from which the liverwort imdirectly obtains its carbon (Wickett et al. 2008 and references; Merckx et al. 2013a).
Quite a number of liverworts, including epiphytes, are dessication tolerant, although most lack internal water-conducting cells (Ligrone et al. 2000).
Reproductive Biology. The dead, pegged rhizoids to be found in marchantialean liverworts with complex thalli may help ensure the water supply to the stalked carpocephala (Duckett et al. 2014).
Plant-Animal Interactions. For a summary of herbivory and galling, including examples from the Middle Devonian where some cells of the fossils perhaps contained oil and represent defence against herbivory, see Labandeira et al. (2013). Caterpillars of Micropterigidae, a basal, jawed, lepidopteran clade, are common on Conocephalum conicum in Japan, but this group also includes species eating liverworts elsewhere, angiosperms, detritus, etc. (Imada et al. 2011; Ragier et al. 2015 and references).
Bacterial/Fungal Associations. All the major groupings of fungi that form mycorrhizal associations with plants are associated with liverworts (Read et al. 2000; Duckett et al. 2006b; Pressel et al. 2010; Bidartondo et al. 2011; Field et al. 2014). Liverworts in the basal pectinations are associated with Glomeromycotina (Kottke & Nebel 2005; Field et al. 2014; Rimington et al. 2014), but this association may subsequently have been lost (Duckett et al. 2006b).
Within Jungermanniopsida, epiphytic Porellales lack fungus associations, and in general epiphytic or epilithic liverworts are often not associated with fungi (Pressel et al. 2010), a tendency also ecident in angiosperms. In Jungermanniales associations with ascomycetes are more than 250 m.y.o. (Pressel et al. 2008), and the fungus may move from these liverworts to seed plants (Pressel et al. 2010: see also Bidartondo & Duckett 2009). The ascomycete Rhizoscyphus [= Hymenoscyphus] ericae is very commonly an associate of the hair roots of North Temperate Ericaceae, and it also forms mycorrhizal associations with Jungermanniales-Schistochilaceae and other leafy liverworts; colonization of the liverwort is by their rhizoids (Duckett & Read 1995; Upson et al. 2007; Pressel et al. 2008). These indirect associations with seed plants have little necessarily to do with early liverwort-fungus associations (e.g. Duckett & Read 1995) Members of a clade of Sebacinales-Serendipitaceae are associated with liverworts (Weiß et al. 2016), and this is also likely to be a relatively recent connection.
The mycoheterotrophic Cryptothallus [= Aneura] mirabilis is associated with the ectomycorrhizal basidiomycete Tulasnella (Kottke & Nebel 2005; Wickett & Goffinet 2008; Wickett et al. 2008; Imhof et al. 2013). Cryptothallus may be nested within Aneura, and the latter is also associated with basidiomycetes (Pressel et al. 2010).
Blasia (Marchantiopsida) fixes nitrogen by virtue of of its association with Nostoc (Rai et al. 2000).
Genes & Genomes. Endopolyploidy has rarely been detected in liverwort nuclei (Bainard & Newmaster 2010a, b), although the nuclei of the smooth rhizoids of at least some liverworts are highly endopolyploid (Duckett et al. 2014).
Marchantiopsida have lost to ability to carry out RNA editing of the organellar genes (Rüdinger et al. 2008). There is also substantial variation in the size of the nuclear genome, that of Marchantiopsida being particularly small, but few species have been examined (Villareal A. et al. 2015b).
For the chloroplast genome of Aneura mirabilis, see Wickett et al. (2008). The genome is more or less normal in size, although it has functionally lost around 25 genes, in line with gene losses in parasitic angiosperms (see also Bellot & Renner 2015).
Chemistry, Morphology, etc. Details of meiosis, whether there is one or more chloroplasts, etc., vary considerably in liverworts, and some derived taxa are quite like vascular plants in these respects (Brown & Lemmon 2008, 2013). There is monoplastidic meiosis in Monoclea, Haplomitrium and Blasia (Brown & Lemmon 2011a), but there is also polyplastidic meiosis as well as intermediates. Buschmann et al. (2016) discuss microtubles and cell division in Marchantia.
For apical cell division, see Piatkowski et al. (2013), for the development of the unicellular elaters, see Renzaglia et al. (1997) and Crandall-Stotler and Stotler (2000), for spore walls, see Wellman et al. (2003), and for rhizoids, see Duckett et al. (2014).
Phylogeny. Morphological studies indicated that Sphaerocarpos might be sister to all other liverworts (Crandall-Stotler & Stotler 2000). However, molecular data suggest rather different relationships, and it is now included in Marchantiopsida (see also Forrest & Crandall-Stotler 2004, 2005; He-Nygrén et al. 2004; Qiu et al. 2006), although the long branches associated with Haplomitrium and Treubia cause their position in the tree to be somewhat migratory. He-Nygrén et al. (2006: 3 chloroplast and 1 nuclear genes, morphology) outline the phylogeny and classification of liverworts, finding a basic structure [Treubiopsida [Marchantiopsida + Jungermanniopsida]]. This basic topology is confirmed by Forrest et al. (2006: five genes, all three compartments, good sampling, esp. of thalloid liverworts), Volkmar and Knoop (2010) and Cooper et al. (2012). N.B.: Treubiopsida = Haplomitriopsida.
Marchantiopsida include Blasia, Sphaerocarpos, etc., although support for the inclusion of the former in this clade could be improved (but c.f. some analyses in Forrest & Crandall-Stotler 2004, esp. 2005; Qiu et al. 2007: Blasia sister to other Marchantiopsida; see also He-Nygrén et al. 2004). Cooper et al. (2012) also found Blasia - with Cavicularia - to be sister to the other Marchantiopsida.
Within Jungermanniopsida, simple-thallus groups are paraphyletic with respect to the speciose and monophyletic leafy liverworts, within which Pleurozia is sister to the rest (e.g. He-Nygrén et al. 2004; Davis 2004: grouped with some simple-thalloid genera; Cooper et al. 2012: extensive study). These general relationships were also recovered by Qiu et al. (2007). Leafy liverworts have been studied by Cooper et al. (2011: the speciose Lepidoziaceae), and Gradstein et al. (2003) and Yu et al. (2013), both Lejeunaceae.
Classification. See Crandall-Stotler et al. (2009) for a formal phylogeny-based classification of Marchantiophyta and Söderström et al. (2016) for a classification (followed above) that goes down to species.
Abscisic acid, L- and D-methionine distinguished metabolically; pro- and metaphase spindles acentric; 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.
Age. Clarke et al. (2011) suggested an age for this clade of (750-)632(-548) m.y., Magallón et al. (2013) an age of around 458.3 m.y.; other estimates are (748-)703(-658) m.y. (Heckman et al. 2001: protein sequence analysis), a little over 500 m.y. (Villarreal & Renner 2014), (580-)496(-412) m.y. (Zimmer et al. 2007), ca 450 m.y. (Theißen et al. 2001), and (550.8-)487.6(-435.6) m.y. (B. Zhong et al. 2014b) and ca 470 m.y.a. (Y. Liu et al. 2014a); see also Hedges et al. (2004) and P. Soltis et al. (2002).
Evolution: Divergence & Distribution. When mosses were thought to be sister to vascular plants the conducting tissue in the centre of the stem in some moss gametophytes was homologized with the vascular tissue in the sporophytes of vascular plants (e.g. Mishler & Churchill 1984, 1985; Mishler et al. 1994). However, this was in part due to the way in which characters describing conductive tissue were conceptualized; there may be little reason to consider the conductive tissues of mosses and those of polysporangiophytes as having much similarity other than that due to their similar functions (e.g. Ligrone et al. 2000, 2002). Ligrone et al. (2002) found no great similarity between the water conducting cells of Takakia, the hydroids of other mosses, and the conducting tissues in Haplomitrium and metzgerialean liverworts (see also Doyle 2013).
However, recent work may modify such interpretations. Thus B. Xu et al. (2014) found that similar NAC transcription factor family genes were expressed during the development of hydroids of mosses and xylem of vascular plants, despite the difference in the generation in which they were expressed and in morphology (neither pitting nor lignification in hydroids), i.a. inducing cell death in both. Such NAC genes are uncommon in liverworts. Similarly, the formation of both sporophytic root hairs in Arabidopsis and gametophytic rhizoids in Physcomitrella involves the same regulatory gene network, perhaps independent recruitment and/or some kind of heterochrony/topy (Menand et al. 2007; Pires & Dolan 2010; Pires et al. 2013; see also Szövényi et al. 2010); Jones and Dolan (2012), Kenrick and Strulla-Derrien (2014) and Tam et al. (2015) also discuss the evolution of root hairs and rhizoids. The latter found that the development of "tip-growing" cells like rhizoids, caulonema cells and root hairs was controlled by a similar auxin-regulated network. Whether such findings can be extended to liverworts is of considerable interest.
If the three groups of bryophytes form a clade (see above), then interpretating the evolution of such features as stomata, cell division and the sporophyte shoot meristem becomes challenging (e.g. Frank & Scanlon 2014, see below). That aside, optimization of such distinctive and important features as the presence of a sporangium with a seta and columella, stomata, trilete spores, etc., is not easy even if bryophytes are a paraphyletic group. Stomata, although placed at the node above, are absent from some of the basal clades of mosses, and their morphology can be quite distinctive (see below; Merced & Renzaglia 2013; Haig 2013), perhaps suggesting their independent origin within mosses. The pores of the mucilage clefts of hornwort gametophytes are probably not homologous with stomata (Adams 2002; Adams & Duggan 2008).
Ecology & Physiology. Stomata may not be involved in gas exchange in the context of photosynthesis in either mosses or hornworts, rather, they may facilitate the drying out of the capsule and hence aid in spore dispersal (Duckett et al. 2009; Pressel et al. 2011; see also Merced & Renzaglia 2013; Merced 2015). If this was the original function of stomata (McAdam & Brodribb 2012a, b), then the central role that stomata now play in photosynthesis in vascular plants becomes a spectacular exaption. Stomata may also originally have increased transpiration and so improved the supply of nutrients to the sporangium (e.g. Haig 2013).
It has been suggested that the stomatal behaviour of vascular plants differs from that of bryophytes (McAdam & Brodribb 2011, esp. Fig. 4), for instance, abscisic acid plays a crucial role in control of stomatal opening only in seed plants, even if similar genes involved in abscisic acid metabolism are found throughout land plants (McAdam & Brodribb 2012; McAdam et al. 2016). On the other hand, Chater et al. (2011) suggested that stomata of the moss Physcomitrella responded to at least some environmental stimuli rather like those of flowering plants (O'Donoghue et al. 2013), abscisic acid being involved in both (see also Beerling & Franks 2009; Chater et al. 2014; references in Raven & Edwards 2014; Lind et al. 2015). Genes involved in the signalling pathway in guard cell opening/closing are known from liverworts (Chater et al. 2014; Lind et al. 2015), but McAdam et al. (2016) suggest that in bryophytes such genes are primarily involved in spore dormancy. Similar genes are involved in stomatal development in both vascular plants and some mosses (see also O'Donoghue et al. 2013), although whether the stomata of Sphagnum are like those of other mosses in such respects is unclear (Merced 2015). Field et al. (2015b) found that stomatal density and aperture size in taxa from mosses and hornworts were largely unresponsive to changing CO2 concentrations. However, the physiology of stomatal functioning is unclear (Roelfsema & Hedrich 2016). For the literature on stomatal patterning, i.e. the development of stomata and their associated/surrounding cells, of extant and extinct stomatophytes, see Rudall et al. (2013a), and for the molecular basis of stomatal development, see Peterson et al. (2010). There is more discussion about stomata under extant tracheophytes, but again, the absence of a firm phylogeny for bryophytes makes understanding stomatal evolution difficult/impossible (see also Lind et al. 2015).
Genes & Genomes. For post-transcriptional editing of the chloroplast genes, see Martín and Sabater (2010). Knie et al. (2015) note that the cis- state of the nad2i542g2 intron of the mitochondrial genome is likely to be the ancestral condition for land plants.
For the loss of the loss of the mitochondrial trnS(gcu) and trnN(guu) genes at this node, see Knie et al. (2014).
Chemistry, Morphology, etc. Poli et al. (2003), Sakakibara et al. (2008), Fujita et al. (2008) and Fujita and Hasebe (2009) discuss sporophyte growth and polar auxin transport in land plants, although sampling needs to be improved (what about liverworts?), and polar transport is not well develop in hornworts. Boot et al. (2012) have demonstrated polar auxin transport in the gametophyte of Chara.
For spore morphology, see Qiu et al. (2012) and Blackmore et al. (2012) and references (correlation: monolete spores, successive sporogenesis, tetrads tetragonal/decussate, simultaneous sporogenesis).
Several gametophytes developing from a single spore; gametophyte leafy, radial, axial, cutting faces of apical cell at 136o [most]; cells ± differentiated, leaves +, spiral, unistratose; perichaetium +; early embryo spindle-shaped, foot ± elongate-tapering-pointed, seta developing from basal meristem [between epibasal and hypobasal cells], indurated, tissues differentiated; calyptra +, persistent; endothecium also producing archesporial tissue; placenta with transfer cells in sporophyte alone; MTOC from plastids, becoming diffuse, perinuclear; perine + [?level]; endopolyploidy widespread; genome size (0.17-)0.5(-2.05) pg. (1C).
Age. Crown-group mosses may be (400-)379(-362) m.y.o. (Newton et al. 2009).
The separation of Takakia and Sphagnum is dated to 319-129 m.y.a. (Shaw et al. 2010a).
Gametophyte initially ?thalloid, mycorrhizal; rhizoids 0;; vegetative cells monoplastidic; cutting faces of apical cell at 120o; leaves forked, ± 3-ranked; perforate water conducting cells +; plant acrocarpous; capsule dehiscence spiral; stomata 0; sporocytes unlobed, spores not trilete; n = 4.
1/2. East Asia, west North America.
[Sphagnopsida [Andreaeopsida + The Rest]]: gametophyte initially a filamentous persistent protonema; rhizoids multicellular [septate]; cp ITS3 differences.
Age. The crown-group age of this clade is (360-)352(-344) m.y.a. (Y. Liu et al. 2014a), but see below.
Fructan sugars accumulated; leaf cells dimorphic [groups of empty and hyaline cells surrounded by strands of chloroplast-containing cells]; rhizoids on protonema only; capsule ?position; foot from hypobasal cell, bulbous, placental transfer tissue 0; capsule sessile, borne on gametophytic pseudopodium; stomata +, stomium 0; dehiscence subapical and transverse ["operculate"], explosive; columella massive, overarched by spores; placental transfer tissue 0; amphithecium producing archesporial tissue; sporocytes unlobed, spore wall multilayered.
Age. Crown-group Sphagnopsida are around 104-30 m.y.o. (Shaw et al. 2010a) or a mere ca 25 or even 14 m.y.o. (Shaw & Devos 2014).
[Andreaeopsida + The Rest]: ?
Gametophyte initially thalloid; plant acrocarpous; leaf costa +/0; capsule sessile, borne on gametophytic pseudopodium; stomata 0; columella overarched by spores; (calyptra 0); sporangium dehisces down four (eight) vertical slits; spores not trilete; exine initiated as globules, white-line centred lamellae 0.
2/110: Andreaea (110). World-wide, rather scattered, esp. cool southern/circum-Antarctic.
4. The Rest.
(L and D isomers of methionine identical metabolically - Mnium); (rhizoids 0 - Haplomitrium); hydroids + [cells dead, no contents], leptoids containing refractive spherules; paraphyses + [multicellular chlorenchymatous hairs mixed with gametangia] (0 - Buxbaumia); plant acrocarpous or pleurocarpous; (first division of zygote longitudinal - Funaria); stomata + (0); capsule dehiscence transverse, peristome +; spores hilate; PEP α subunit rpoA gene 0 (+).
Age. The crown-group age of this clade is perhaps 602-488 m.y.o. (Laenen et al. 2014) - none of the first three clades above was included.
Evolution: Divergence & Distribution. Fossils of leaves with distinctive cell structure remarkably similar to that of extant Sphagnum are known from the Ordovician deposits in Wisconsin - they are the earliest known vegetative remains of an embryophyte and are dated at 455-454 m.y. (Cardona-Correa et al. 2016).
Mosses in China showed weaker latitudinal diversity gradients than did liverworts, perhaps because the former can handle a wider diversity of enviornments than the latter, a number of which are epiphyllous and need humid conditions; moss diversity was linked in part to local habitat heterogeneity (S.-B. Chen et al. 2015).
Polytrichopsida/Dicranidae/haplolepidious taxa are a diverse but species-poor group compared to the ca 12,000 species of Hypnanae/hypnalian pleurocarpous/arthrodontous mosses (Cox et al. 2010); Newton et al. (2007, 2009; see also B. Zhong et al. 2014b) give dates for many clades. There is strong geographical signal in the phylogeny of Polytrichopsida, clades being largely south or north temperate (Bell & Hyvönen 2010: intergeneric hybridization?). Within the speciose pleurocarpous mosses - about 40% of all mosses - diversification seems to have been early and rapid, clades diverging in the early Cretaceous, but since then there has been semi-stasis (Kürschner & Parolly 1999; Shaw et al. 2003b; Newton et al. 2006, 2007), although there may also have been more recent ([post-]Cretaceous) diversification as well.
Since some combination of Andreaea, Takakia and Sphagnum and immediate relatives are at the base of the moss phylogenetic tree and all have distinctive morphologies, apomorphies for mosses as a whole are unclear. Huttunen et al. (2013: focus on Plagiothecaceae) optimize the evolution of a number of features in both Hypnales and Hookeriales.
Ecology & Physiology. Dessication tolerance is common in mossses, even in taxa like Sphagnum. The antheridia remain functional if they were dried slowly and then were subsequently rehydrated (Stark et al. 2016 and references).
Mosses are important components of tundra and boreal forest biomes (for the bryosphere, see Lindo & Gonzalez 2010) and can make up a substantial proportion of the biomass in boreal forests (Wardle et al. 2013). Hummock-forming Sphagnum in particular is a major element of the boggy vegetation in such areas in communities from poor fens to the forest floor. Indeed, rich fens in such areas commonly progress from so-called brown mosses like Drepanocladus and Calliergon and a pH of ca 6 to Sphagnum-dominated bogs with a pH of 4 or a little more - oligotrophification and acidification is mediated by Sphagnum, a process that proceeds fastest in cool, wet conditions (Kuhry et al. 1993).
The ecophysiology of Sphagnum, often dominant in in tundra and boreal biomes, has been studied in some detail. Particularly in exposed areas, damage from high-light conditions becomes important, as with other mosses, and drying out may also occur - but water reduces CO2 diffusion by a factor of 104. However, methanotropic bacteria live in the hyaline cells in the leaf, and they prefer damper conditions; they oxidize methane from decomposing peat, producing CO2 which is then utilized by the plant. This can provide up to a third of its CO2 supply. All 23 of the species of Sphagnum in a site in Finland could convert methane into a source of CO2, so this capability may be ubiquitous in the genus (in Scorpidium scorpioides, which grows in similar habitats, the figure is up to 70% - Larmola et al. 2010; Hájek 2014.) For the microbiome of Sphagnum, integral to the functioning of the organism and its ecosystem, see Bragina et al. (2014).
Different species of Sphagnum tend to grow in hummocks and in hollows of the bogs, and these preferences correlate with different growth rates, rates of peat breakdown (Turetsky et al. 2008), phylogeny, etc., while the differences in the rate of peat breakdown can be linked to variation in carbohydrate metabolism within the genus (Turetsky et al. 2008). There is also extensive pH variation in these bogs, and different species prefer different pHs, but here there is no large-scale correlation with phylogeny (Johnson et al. 2015).
Sphagnum-dominated fens in northern Alberta may not be very productive in terms of gross primary productivity. However, respiration tends to be low, the plants start photosynthesizing early in the year, etc., so overall net carbon productivity may be higher than in, for example, Carex-dominated rich fens (Flanagan 2014; see also Ragoebarsing et al. 2005). Breakdown of moss peat in general, and Spagnum peat in particular, tends to be slow (Turetsky et al. 2008).
The discovery of Sphagnum-like fossils in Ordovician rocks ca 455 m.y.o. suggests that the ecological equivalents of modern Sphagnum peatlands may have been around for a long time, and this has considerable implications for carbon fixation and sequestration in general, the evolution of the biota associated with the moss in particular, etc. (Graham et al. 2013, esp. Cardona-Correa et al. 2016). Carpenter et al. (2015) found spores of Stereisporites to be very common in fire-prone heathlands in Central Australia 75-65.5 m.y.a., and they linked them with Sphagnum, while Daly et al. (2011) suggest that Sphagnum-type mosses were components of peats produced by mire vegetation in northern Alaska ca 60 m.y.a. that later were converted to coal. However, the beginning of the diversification that gave rise to extant species of peat-forming Sphagnum has been dated to as late as the mid-Miocene ca 14 m.y.a. (Shaw et al. 2010a; Shaw & Devos 2014), indeed, the major accumulators of peat today make up only a clade, albeit major, within Sphangum, i.e. not including either subgenus Rigida or the segregate genera (Shaw et al. 2016). A genome duplication in Sphagnum dated to (221-)197(-173) m.y.a. might have been involved is its rise to dominance in peatlands (Devos et al. 2016) - and this gets us back to the dating of Sphagnum diversification, the fossil record of the genus, and where it might grow when the earth was much warmer than it is now - even at the poles.
In northern ecosystems a few species of feather mosses, pleurocarpous Hypnales like Hylocomium splendens and Pleurozium schreberi, form close associations with the cyanobacterium Nostoc, nitrogen moving from the latter into the former (Bay et al. 2013). However, details of further movement of nitrogen in the ecosystem are unclear (Rousk et al. 2013; Lindo et al. 2013).
Gametophyte vascularization is particularly well developed in Polytrichopsida, and the leptoids apparently transport organic molecules (Ligrone et al. 2000).
Reproductive Biology. For the recurrent evolution of dioecy in mosses - at least 133 times - see McDaniel et al. (2013). Dioecy may be accompanied by sexual dimorphism of the plants. Reversal to hermaphroditism is less common, but diversification may be higher in hermaphroditic clades (McDaniel et al. 2013).
When the antheridium dehisces, the contents are released as a single sperm mass, and subsequently the individual sperm disperse (Stark et al. 2016 and references). Very small arthropods are attracted to volatile compounds produced by Ceratodon purpureus and are involved in the transfer of sperm to the archegonia (Rosenstiel et al. 2012; see also Cronberg et al. 2006).
For a comprehensive study of the evolution of capsule shape in mosses, see Rose et al. (2016). At least sometimes shape changes are associated with changed speciation rates, as is the adoption of the pleurocarpous habit.
The stomata of Sphagnum lack both pores and airspaces immediately under the guard cells; the stomata help the capsule to dry out, and as it buckles the stomium pops off and the spores are shot into the air (Duckett et al. 2009).
Bacterial/Fungal Associations. Bay et al. (2013) discuss associations between Nostoc and some pleurocarpous mosses in boreal forests; other blue-green algae are also involved (Rousk et al. 2013 for a review). Functional mycorrhizal associations, i.e. associations that are involved in the exchange of nutrients, are very rare in mosses, and most moss-fungus associations involve parasitic fungi (Read et al. 2000; Davey & Currah 2006). Fot the possibility that Buxbaumia is mycoheterotrophic, see Imhof et al. (2013). Other endophytic fungi may also affect moss growth and ecology (Read et al. 2000; Davey & Currah 2006).
Genes & Genomes. Genomes in mosses are small, 1C values being less than 1.4 pg (Bennett & Leitch 2005); I do not know what the sizes are in liverworts, etc.. The rate of molecular evolution is slow in the three genes from all three compartments examined (Stenøien 2008: liverworts, hornworts, and lycophytes not examined).
Endopolyploidy is widespread in mosses, although not occuring in Sphagnum (Bainard & Newmaster 2010a, b). However, genome duplications are reported from this genus, (Devos et al. 2016). Aside from suggesting that such duplications might have been involved is its rise to dominance in peatlands, as in many other land plants, the genes retained after this event are similar to those retained after similar events - i.e. involved in ion channels or signal transduction pathways, although Physcomitrella differs somewhat in this respect (Szövényi et al. 2015; Devos et al. 2016, and references).
There is a very large (ca 71 kb) inversion of the chloroplast genome in Funariaceae (which includes Physcomitrella), Disceliaceae, and Encalyptaceae, all Funariidae, although Gigaspermaceae lack this inversion (Goffinet et al. 2007). For the loss of the PEP α subunit-encoding rpoA gene in many mosses, see Goffinet et al. (2005); it is absent in Tetraphis and Diphyscium, present in Buxbaumia and Polytrichum.
Yue et al. (2012) found a number of genes in Physcomitrella patens that had moved there by lateral transfer from fungi and bacteria; how widely they might be distributed in mosses is unknown.
Chemistry & Morphology. The stomata of Sphagnum lack a stomium (), while in those of Funaria, at least, the stomium is encircled by a single cell that has two nuclei (Sack & Paolillo 1983; Merced & Renzaglia 2016: spacing), however, in other mosses the stomata have two guard cells (Merced & Renzaglia 2013). For spore wall morphology of Sphagnum, see Brown et al. (1982); some layers, e.g. the translucent layer, may be unique.
For a general entry into the literature, see Goffinet et al. (2004) and for information about pleurocarp mosses, see Newton and Tangney (2007); for sporogenesis, see Brown and Lemmon (1984: Andreaea, 2013), for apical cell division, see Piatkowski et al. (2013), for sieve elements/leptoids, see Scheirer (1990), and for placental tissue, see Carapa et al. (2003).
Phylogeny. Relationships between clades at the base of the moss tree remain unclear. Sphagnum, Andreaea and Takakia, the latter initially thought to be a liverwort (see Renzaglia et al. 1997), are all in this area, Sphagnum and Takakia perhaps being sister taxa and Andreaea sister to remaining mosses (e.g. Cox et al. 2004; Qiu et al. 2006, 2007: rather strong support; Volkmar & Knoop 2010; Shaw et al. 2010b [perhaps]; S. Li et al. 2013: 9 loci; Rose et al. 2016). However, Takakia has a region in the cpITS3 sequence that is very like that of all other land plants but is deleted in other mosses, from this evidence alone, Takakia might be sister to all other mosses (Samigullin et al. 2002). Indeed, recent work suggests relationships may be [Takakia [Sphagnum [[Andreaea + Andreaeobryum] [Oedopodium [[Polytrichopsida + Tetraphidopsida] Bryopsida]]]]] (Chang & Graham 2009, esp. 2011, 2014; Rose et al. 2016: but c.f. in part above); a [Takakia + Sphagnum] clade was recovered only in some reconstructions. The odd, almost leafless Buxbaumia may be sister to all other Bryopsida.
See Shaw et al. (2010b; also Shaw et al. 2003a for morphology, 2010a, 2016) for relationships in the Sphagnum et al. clade. The very distinctive Sphagnum leucobryoides (= Ambuchanania) was described only some twenty five years ago (Yamaguchi et al. 1990), and it and a very few other species of Sphagnum (placed in genera like Flatbergia) are outside Sphagnum s. str., the bulk of the clade.
Within the remaining mosses, Chang and Graham (2009, esp. 2011) and S. Li et al. (2013) found Oedopodium to be sister to the others. See Cox et al. (2010) for a phylogenetic study of mosses focusing on genera and families. Wahrmund et al. (2010) used a new mitochondrial locus to investigate relationships among mosses; the position of Timmia was particularly unclear.
For relationships in Dicranidae (haplolepidious mosses), see Stech et al. (2012). Bell et al. (2007) discuss the phylogeny of the early diverging pleurocarp clades, and adjust their taxonomy accordingly, while Buck et al. (2005) discuss the phylogeny of Hookeriales. Most branch lengths in the speciose Hypnales are short (Huttunen et al. 2012).
Classification. For a classification of mosses based on phylogeny, see Shaw and Goffinet (2000, also Goffinet & Buck 2004), and for an (over)classification of Sphagnum s.l., see Shaw et al. (2010b).
[Anthocerophyta + Polysporangiophyta]: gametophyte leafless; archegonia embedded/sunken [only neck protruding]; sporophyte long-lived, chlorophyllous.
Age. Clarke et al. (2011: other estimates, but all old) suggested that this clade was (596-)524(-475) m.y.o., an age of around 440 m.y. was offered by Magallón et al. (2013), an age of (501.5-)454.4(-413.6) m.y. by B. Zhong et al. (2014b) and of around 460 m.y.a. by Villarreal and Renner (2012); see also P. Soltis et al. (2002).
Evolution: Divergence & Distribution. Qiu et al. (2006a, 2007 and references) note a number of features of hornworts, particularly of the sporophyte, that suggest similarities with polysporangiophytes, and they may be synapomorphies of the two. For the evolution of trilete spores, see e.g. J. A. Doyle (2012b) and Brown et al. (2015). I had>primary cell walls with xylans (xyloglucans with fucosylated subunits) as an apomorphy here pior to July 2016, but Xyland seem to be an apomorphy of land plants, although the nature of their side chains (charged vs uncharged) varies (Scheller & Ulvskov 2010).
Chemistry & Morphology. Zabotina (2012 and references) discussed the composition of the xyloglucans in the primary cell wall.
ANTHOCEROPHYTA Stotler & Crandall-Stotler / HORNWORTS
Gametophyte thalloid, (leafy), closely associated with N-fixing Nostoc; flavonoids 0; apical cell wedge-shaped, with four cutting faces; branching truly dichotomous; rhizoids unicellular; ventral mucilage clefts/cavities, opening by stoma-like pore; vegetative cells monoplastidic, microtubules axial; antheridia in chambers [endogenous]; bicentriole pair formed in cell generation before spermatogenous cells; stellate array in basal body of cilium absent; male gametes bilaterally symmetrical, with a right-handed coil; placenta with haustorial cells in sporophyte, transfer cells in gametophyte; sporophyte lacking apical cell, foot ovoid-bulbous; (stomata 0 if sporophytes more or less enclosed); basal meristem active for an extended period, seta short; sporangium dehiscing by 2 longitudinal slits; amphithecium producing archesporial tissue; elaters +, spirally thickened, multicellular; xylans in walls of spores and elaters; ?genome size; mitochondrial rpl2 gene 0.
Age. The age of this clade has been estimated at around 290 m.y. (Villarreal & Renner 2012), or ca 170 m.y.a., the overall variation being (245.2-)228.9, 160.2(-107.1) m.y. (Villarreal et al. 2015a).
LEIOSPOROCEROTOPSIDA Stotler & Crandall-Stotler
Mucilage clefts only in young uninfected plants, Nostoc in branching schizogenous strands in the centre of the thallus; antheridia up to 70/chamber; spore tetrads bilateral alterno-opposite, spores "minute", monolete, surface smooth.
1/1: Leiosporoceros dussii.
Neochrome +; chloroplast grana lack highly curved end membranes, channel thylakoids connect adjacent granal stacks; gametophyte plastids (>1/cell, division still monoplastidic), pyrenoids +/0; mucilage clefts persist, Nostoc in spherical colonies; antheridia 1-6/chamber; (first division of zygote vertical - Anthoceros); 1-many chloroplasts/cell; white line-centred lamellae 0?; spores ornamented, (chlorophyllous); phototropins lack introns; elevated rate of RNA editing.
Age. The age of this clade may be (399-)306, 248(-173) m.y. (Villarreal & Renner 2012) or 261-186 m.y. (Laenen et al. 2014).
Evolution: Divergence and Distribution. Most diversification within Anthocerotopsida has taken place within the last 100 m.y. or so, or even within the Caenozoic (Villarreal & Renner 2012; Villarreal et al. 2015a, q.v. for dates, etc.).
Ecology & Physiology. Neochromes, a chimaeric photoreceptor in which red-sensing phytochrome and blue-sensing phototropin are fused into a single molecule, have been found in all hornworts sampled (Leiosporoceros not studied: F.-W. Li et al. 2014).
Pyrenoids (for which, see Hanson et al. 2014) vary considerably in morphology and have evolved five times or more in the hornworts between 101 and 18 m.y.a. (and also subsequently been lost); their repeated evolution in Anthocerotopsida seems to be another example of a "tendency" (Villarreal & Renner 2012). I.a. they increase the concentration of CO2 around the chloroplasts and so increase the efficiency of photosynthesis (E. Smith & Griffiths 1996).
For the association of hornworts with the nitrogen-fixing Nostoc, see Rai et al. (2000), and for what is known about Nostoc and nitrogen fixation, see Santi et al. (2013).
Bacterial/Fungal Associations. Endogone-like fungi (Mucoromycotina) are associated with some hornworts (Bidartondo et al. 2011; Rimington et al. 2014), and are quite common there, as are Glomeromycota (Pressel et al. 2010). The two may form mycorrhizal associations with the same species, but whether either or both mycorrhizal association was ancestral in the group is unclear (Desirò et al. 2013); the latter association, at least, seems rather casual (Pressel et al. 2010).
In most taxa Nostoc enters the gametophyte through mucilaginous clefts (Adams 2002; Adams & Duggan 2008).
Genes & Genomes. The extensive RNA editing in Anthoceros and its relatives is at codon positions that are otherwise universally conserved in land plants (Duff et al. 2007). There seems to have been between 1-6 duplications in each of the three groups of GDSL lipases somewhere around here (Volokita et al. 2010).
Anthoceros has lost the chloroplast rps15 gene (Martín & Sabater 2010) and the IR has expanded somewhat (Villarreal et al. 2013).
There has been extensive loss of protein-coding genes in the mitochondrion, i.e. ca 1/2, versus less than 1/3 in other land plants (Y. Liu et al. 2014b). Leiosporoceros has an intron in the mitochondrial nad5 gene, as do Anthoceros and immediate relatives (Villarreal et al. 2013).
Chemistry, Morphology, etc. The cell walls of spores and their elaters contain xylans, an important polysaccharide in secondary cells walls of vascular plants, but unknown in other bryophytes (Carafa et al. 2005). The elaters are multicellular structures of tapetal origin, quite unlik those of ,i>Equisetum(Pacini & Franchi 1991).
See also Ligrone et al. (2000) for general information, Villarreal et al. (2010) for a summary of our understanding of hornworts, Vaughn et al. (1992) for the distinctive and variable chloroplasts and Brown and Lemmon (2013) for sporogenesis; for antheridia, see Duff et al. (2004) and Cargill et al. (2005).
Phylogeny. Relationships within hornworts are still unclear in part. Leiosporoceros may be sister to all other hornworts, although the extensive RNA editing in other members of the clade obscures this position in some analyses (e.g. Duff et al. 2007); it has many distinctive features (see above). See also Stech et al. (2003), Duff et al. (2004) and Villarreal and Renner (2012) for relationships. Anthoceros and its possible segregate Folioceros are sister to remaining hornworts, and they have black or dark spores, etc. (in this they are like Leiosporoceros). Villarreal and Renner (2014) discussed the limits of and relationships around Nothoceros.
Classification. Several classifications of this clade have appeared recently (Frey & Stech 2005; Stotler & Crandall-Stotler 2005; Duff et al. 2007); they tend to be rather elaborate; see Söderström et al. (2016) for a classification down to the level of species.
Sporophyte well developed, branched, branching apical, dichotomous, potentially indeterminate; hydroids +; stomata on stem; sporangia several, terminal; spore walls not multilamellate [?here].
Evolution: Divergence & Distribution. Note that the number of spores produced per sporangium is roughly the same here as in bryophytes (Qiu et al. 2012). For a comprehensive study of the early evolution of land plants with apomorphies at all levels and incorporating fossil members, see e.g. Kenrick and Crane (1997; also Kenrick et al. 2004; Doyle 2013; etc.). Characters that can be pegged to this node and those to be linked with the tracheophyte node need to be separated.
The exact relationship between the sporophytes of polysporangiophytes and bryophytes is unclear (e.g. Shaw et al. 2011), especially given the uncertainties in the phylogeny. The stalk of a moss capsule may not be strictly homologous to the branching sporophyte axis of the polysporangiophytes (Kato & Akiyama 2005; Qiu et al. 2012). Sterilization of the sporangial axis or simple elaboration of a bryophyte sporangium leading to the evolution of a branched sporophyte are ideas that have been suggested, but prolongation of embryonic growth is perhaps more likely (Tomescu et al. 2014). Frank and Scanlon (2014) found that there was expression of meiosis gene families early in the development of both Physcomitrella (see also O'Donoghue et al. 2013: carbohydrate metabolism genes) and Marchantia sporophytes, which would perhaps make their extended growth unlikely, however, in the stem apex of maize and in the gametophyte apex of mosses, but not liverworts, similar patterning gene families were upregulated (see also Fujita et al. 2008; Sakakibara et al. 2008). A scenario for the evolution of a complex sporophyte may involve delayed expression of genes involved in meiosis, which would allow for indeterminate development of a sporophyte in which these patterning genes were expressed (Frank & Scanlon 2014). Genes expressed in the gametophyte may be essential for the subsequent elaboration of the sporophyte.
Some sporophytes of early polysporangiophytes were very small. Those of the Silurian cooksonioids in particular are 1 mm or substantially less across and were probably dependent physiologically on the gametophyte (Rothwell 1995; Boyce 2008b; see also Edwards et al. 2014). Conversely, some early gametophytes were quite elaborate structures, although different in morphology from the sporophytes, and they even had conducting tissue, stomata, a cuticle, and were apparently homoiohydric (Remy & Haas 1991; Edwards 1993; Edwards & Richardson 2004; Taylor et al. 2005; Gerrienne & Gonez 2011; Ligrone et al. 2012a). A stage in the evolution of vascular plants may involve an ancestor in which the generations were pretty much isomorphic. Indeed, a largely isomorphic alternation of generations represented by some of the plants from the Lower Devonian Rhynie Chert of some 410 m.y.a. figures largely in attempts to understand the evolution of land plant life cycles (Niklas & Kutschera 2009, 2010). Some early vascular plants had multicellular stem apices (Hueber 1992). The sequence may be as follows: Gametophyte only free living, sporophyte unbranched, dependent on the gametophyte → gametophyte only free living, sporophyte branched, dependent on the gametophyte → generations ± isomorphic, both free living → sporophyte dominant, gametophyte free-living → sporophyte dominant, gametophyte dependent on sporophyte (see also Tomescu et al. 2014; c.f. Qiu et al. 2012).
Bacterial/Fungal Associations. Vesicular arbuscular mycorrhizae have been found in the axes of Aglaophyton major from the early Devonian ca 400 m.y.a. (Remy et al. 1994). A variety of fungal associations have been found in fossils of early polysporangiophytes, whether in gametophyte or sporophyte, and sometimes the fungi pervade the whole plant (e.g. Strullu-Derrien et al. 2014b). Because true roots had not yet evolved, they are best called paramycorrhizal associations (Kenrick & Strullu-Derrien 2014).
Vascular tissue + [tracheids, walls with bars of secondary thickening].
Age. Silvestro et al. (2015) estimate that vascular plants are (449-)433.5(-424 )m.y.o., and other estimates are broadly similar, e.g. 454-416 m.y. (Clarke et al. 2011) and (463.5-)429(-400) m.y. (B. Zhong et al. 2013b).
Evolution: Divergence & Distribution. Pryer et al. (2004b) provide a useful summary of the evolution of vascular plants; see also e.g. Kenrick and Crane (1997; also Doyle 2013; etc.).
Ecology & Physiology. Proctor (2014: p. 66) emphasized that the endohydrous and homoiohydrous vascular plant clearly did not evolve as such (c.f. the birth of Athena), but that elements of the "vascular-plant package" were to be found in extant ecto- and poikilohydrous plants.
Edwards (1993; Edwards & Richardson 2004; see also Niklas 2015 for some cautionary comments) reviewed the anatomy of the vegetative parts of sporophytes of early land plants. For the evolution of xylem and the relation between details of cell anatomy and cell wall chemistry and water transport, plant support, etc., see Sperry (2003 and references); lignin may initially helped in keeping tracheary elements open, only later becoming involved in plant support. Cichan (1986) and Wilson (2015) and references relate details of xylem anatomy and water transport, linking extinct and extant plants; woods of early vascular plants may have been quite efficient in conducting water, although susceptible to embolism/cavitation. Tracheophytes all have some kind of roots, although these have almost certainly evolved more than once (e.g. Raven & Edwards 2001; Pires & Dolan 2012). Tomescu et al. (2014) and Proctor (2014) also discuss the evolution of roots in vascular plants; roots would allow plant size to increase by providing stability and facilitating increased water uptake. For the evolution of root hairs, see the discussion above.
Classification. Note that Polysporangiophyta technically lack vascular tissue of any sort, and so they include tracheophytes; for the two broken out (and protracheophytes, with hydroid and leptoid conducting cells, paratracheophytes and eutracheophytes also separated), see Gerienne et al. (2016).
EXTANT TRACHEOPHYTA / VASCULAR PLANTS
Sporophyte with photosynthetic red light response, stomata open in response to blue light; 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 +); xyloglucans with side chains uncharged [?level], in secondary walls of vascular and mechanical tissue; lignins +; stem apex multicellular, with cytohistochemical zonation, plasmodesmata formation based on cell lineage; 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; suspensor +, shoot apex developing away from micropyle/archegonial neck [from hypobasal cell, endoscopic], root lateral with respect to the longitudinal axis of the embryo [plant homorhizic].
Age. Clarke et al. (2011) suggested an age for the clade of (456-)446(-425) m. years. Somewhat younger ages for vascular plants, (434.3-)424-421.6(-416.2), can be found in Magallón et al. (2013), (492.9-)428.8(-400.1) m.y. in B. Zhong et al. (2014b), while Larsén and Rydin (2015) suggest ages of ca 432 m.y., largely in line with fossil-based ages (Kenrick et al. 2012) which were used in the calibrations (a similar age in Villarreal & Renner 2014). However, P. Soltis et al. (2002: variety of estimates) suggested an older crown age of (813-)603(-393) m.y. ago.
Hilate/trilete spores that do not remain as tetrads appear in the Early Silurian ca 443 m.y.a. and may mark the origin of vascular plants (Steemans et al. 2009; Kenrick et al. 2012; Gerienne et al. 2016 and references), but note that the first appearance of trilete spores is placed at the stomatophyte node here.
Evolution: Divergence & Distribution. Rothfels et al. (2015a) suggested that lycopods, ferns and other plants with abiotically mediated fertilization evolved reproductive incompatability only slowly, hence they have an intrinsically slow rate of speciation.
The basic pattern of early development of the sporophyte, exoscopic or endoscopic, is outlined by Niklas and Kutschera (2009). Their scenario involves both gains and losses of endoscopic development; the optimisation here involves parallel gains, but is equally parsimonious. For sporopollenin in land plants, see above. Baucher et al. (2007) discuss vascular evolution, Johnson and Renzaglia (2009) that of the embryo, while Arens et al. (1998: Virtual paleobotany laboratory) is a valuable web resource.
As Ambrose and Vasco (2015) emphasize, apical meristems of vascular plants as a whole are best thought of as being multicellular structures with cytohistochemical zonation (for plasmodesmata, see Imaichi & Hiratsuka 2007, c.f. interpretation of apical meristems there). However, there is some discussion as to the occurrence of apical cells in polysporangiophytes. Stems have an apical meristem, either of a single cell or group of cells (e.g. Kato & Akiyama 2005), and it is commonplace to make a distinction between tracheophytes with meristems of a single cell and those with meristems of several cells (Imaichi 2008). Interestingly, the expression patterns in the single apical cells of Selaginella and Equisetum are quite different (Frank et al. 2015). This may suggest that the apical cells in ferns s.l. and Selaginella evolved independently - or that the differences between the two reflect the long period they have been separated, some 400 m.y. or more (see above for ages; Frank et al. 2015). Details of the construction of the apical meristem varies within lycophytes (see below) but not in the other main groups, and they correlate with the richness of plasmodesmatal connections between the cells: many plasmodesmata - meristem a single cell, few plasmodesmata - meristem a group of cells (Imaichi & Hiratsuka 2007). Fern apical meristems for the most part are multicellular, the apical initial(s) only rarely dividing (Ambrose & Vasco 2015; Vasco et al. 2016). D'Amato and Avanzi (1968; see also Gifford 1985) noted that the apical cells of Equisetum early became polyploid and did not divide (c.f. in part Gifford et al. 1979). See also elsewhere. Interestingly, even in fern gametophytes the apical cell is functional for a short while only, and then the apical region converts to a multicellular meristem (Takahashi et al. 2009, 2015 and references).
Roots are thought to have evolved two or more times in vascular plants (e.g. Raven & Edwards 2001). Within angiosperms, gene families involved in root development are conserved, the great majority being found in all six angiosperms studied, and this is true of genes involved in root development in Arabidopsis in particular (Huang & Schiefelbein 2015). Remarkably, around 82% of the gene families expressed in all angiosperm roots are also expressed in Selaginella, even root cap-associated genes. Although details of the functional similarities of these genes is unknown, there may have been parallel evolution of root-associated genes in lycophytes and other vascular plants, or the dissimilarity of roots of lycophytes and other vascular plants was, at one time at least, not that great, some sort of roots occuring in the ancestor of extant vascular plants (Huang & Schiefelbein 2015; see also Hetherington et al. 2016).
Floyd and Bowman (2006), Boyce (2008a), Boyce and Leslie (2012) and others emphasize the diversity of leaf morphologies, growth forms, etc., to be found in non-angiospermous plants in general. However, all leaves, whether megaphylls or microphylls, can be thought of as structures with "a determinate growth programme [added] to the indeterminate apical growth programme" (Harrison et al. 2005b: p. 509). Similar but independently recruited developmental mechanisms may be involved in the evolution of microphylls and megaphylls (Harrison et al. 2005b), as in many other aspects of evolution in land plants (Pires & Dolan 2012).
Zimmermann's (1930, see also 1952, 1965) telome theory that euphylls are the result of overtopping, planation and webbing of a stem/branch system, has been influential, although in detail it is no longer tenable (Kenrick 2002; Beerling & Fleming 2007). It has been suggested that the development of euphylls or megaphylls, often quite large structures the vascular supply of which is associated with gaps in the central stele, is quite different from that of microphylls, vascularized structures, but not associated with leaf gaps in the central steele (e.g. Bower 1935; Floyd & Bowman 2006). The leaves of lycophytes are characterized by having an intercalary meristem and being supplied by a single vein that does not leave a gap in the central stele when it departs (see Kaplan 1997, vol. 2: chap. 16, vol. 3: chap. 19, 2001 for leaf morphology), while megaphylls are determinate organs with ad/abaxial identities; vascular bundles supplying them leave "gaps" in the central stele when they depart (see e.g. Sporne 1965, but c.f. Kaplan 1997, vol. 3: chap. 19, 2001 in particular, see also Harrison et al. 2005; Boyce 2005a: summary of earlier literature, 2008; Tomescu 2008, 2009; Sanders et al. 2007, 2009; Corvez et al. 2012).
However, details of the evolution of the euphylls that are supposed to characterise the [Monilophyta + Lignophyta] clade are unclear. Schneider et al. (2009: p. 461 and references) suggest that mega/euphylls arose once, and can be characterized by apical/marginal growth, apical origin of the venation, determinate growth, etc., or independently in seed plants and monilophytes, and an estimated 3-6 times in the latter alone, and perhaps elsewhere as well (Floyd & Bowman 2007), or four independent origins of megaphylls in ferns/monilophytes, progymnosperms, and seed plants by the end of the Devonian (D.-M. Wang et al. 2015; see also Kenrick & Crane 1997; Boyce & Knoll 2002; Osborne et al. 2004; Gensel & Kenrick 2007; Tomescu 2009; Niklas & Kutschera 2009; Sanders et al. 2009; Galtier 2010; Corvez et al. 2012: at least two origins; Tomescu et al. 2014).
Indeed, Harrison et al. (2005b), Floyd et al. (2014), Vasco et al. (2016) and others are chipping away at understanding the developmental background of euphylls or megaphylls or whatever they are called, indeed, of leaves in general. Some of the genes involved in megaphyll formation may have evolved long before megaphylls appeared, but with different functions then, (e.g. Beerling 2005a, b; Floyd 2006; Vasco et al. 2016 and references). Floyd et al. (2014) place the origin of the post-translational negative regulators of apical meristem and leaf development, the LITTLE ZIPPER (ZPR) proteins, at the [Monilophyta + Lignophyta] node; they are part of the C3HDZ (class III homeodomain leucine zipper) stable of genes, which may initially have been expressed in sporangia in embryophytes im btyophytes on up (Vasco et al. 2016 and references). After gene duplication of the C3HDZ gene in the [Monilophyta + Lignophyta] clade, one of the copies degenerated and became the ZPR gene, and it and C3HDZ genes together were involved in the evolution of euphylls. Floyd et al. (2014) could not find ZPR genes in lycophytes.
However, there may be more commonality between microphylls and megaphylls than might appear, and Vasco et al. (2016) suggest that C3HDZ genes may have been coopted in both megaphyll and microphyll development. Both megaphylls and microphylls can be thought of as modified sporangia. In lycophytes one of a pair of sporangia became a microphyll (see also Crane & Kenrick 1997) with C3HDZ genes being expressed in their development, while in the [Monilophyta + Lignophyta] clade more complex telome systems make up the leaf and C3HDZ genes are involved in leaf dorsiventrality, being expressed throughout the young primordium, but only on the adaxial surface and involved in the development of dorsiventrality later on (a neofunctionalization - Vasco et al. 2016; see also Scarpella & Meijer 2004 for the radial/dorsiventral sequence). Overall, there is a very complex pattern of gains, modifications, and losses of genes (Vasco et al. 2016).
Ecology & Physiology. Kenrick et al. (2012) discussed the effect of vascular plants on the carbon cycle. There are broad correlations between atmospheric CO2 concentration and stomatal size that have important implications for plant productivity, transpiration, and rock weathering. When the CO2 concentration of the atmosphere is low, leaves tend to have higher densities of smaller stomata, allowing more CO2 to diffuse into the leaf, when concentrations increase, relationships are the reverse (e.g. Franks & Beerling 2009). It has also been suggested that CO2 concentration, guard cell size, and genome size can be linked, the first and last being broadly correlated over the last 400 m.y. (Haworth et al. 2011), although genome size reconstructions (Fig. 4) and some other aspects of this story (see also Franks et al. 2012) are difficult to understand. Within vascular plants there is a great range of relative pore area (pore area/total guard cell + pore area), that of Huperzia and Nephrolepis being much lower than that of flowering plants, and there is even greater variation in the rate of stomatal opening (Franks & Farquhar 2006). For water use efficiency throughout the Phanerozoic, see Franks and Beerling (2009a) and Assouline and Or (2013: a different interpretation for higher CO2 concentrations). The carbon cycle was further affected by the evolution of vascular plants with well developed secondary thickening, whether producing mostly bark or both bark and wood (see elsewhere).
The response of photosynthesis to red light and passive stomatal control of leaf hydration are perhaps best tagged to this node (see above: McAdam & Brodribb 2011). Thus the mechanism of stomatal closure in ferns is like that of lycophytes rather than that of seed plants (McAdam & Brodribb 2011, 2012, 2013; see also Haworth et al. 2011, 2013; McAdam et al. 2016); it is passive, and abscisic acid is not immediately involved. Watkins and Cardelús (2012) noted that in some respects epiphytic ferns, at least, are ecologically more like angiosperms than terrestrial ferns, using water quite efficiently (and having very low hydraulic conductivity). However, one of the ways in which ferns and lycophytes, whether gametophyte or sporophyte, can grow in drier conditions is by being dessication tolerant, even if the mechanism of stomatal control is overall similar to that in ferns growing in more mesic conditions (McAdam & Brodribb 2013). Note that there seems to be no movement of the stomatal aperture in Equisetum, where it is permanently closed, and this may also be the case in Psilotum - although there is movement in Lycopodiales (Cullen & Rudall 2016; Roelfsema & Hedrich 2016). Indeed, in ferns, at least, part of the pathway involved in stomatal closing in seed plants is involved in spore dormancy (as perhaps in bryophytes) and in the determination of the sex of the gametophyte, and there, too, there is antagonism between giberellic acid and abscisic acid (McAdam et al. 2016).
Ferns, gymnosperms and lycophytes tolerate nutrient-poor (but sometimes rich in non-essential minerals) conditions, perhaps the ancestral conditions for many of them (Page 2004). The evolution of some genes in plants involved in mycorrhizal associations that facilitate phosphorus uptake by the plant may be pegged to this node (Delaux et al. 2015). Note, however, that advantages to plants in which mycorrrhizae were first established and advantages to extant plants may differ (Maherali et al. 2016).
Bacterial/Fungal Associations. Mycorrhizal associations with VAM Glomus are common in members of this clade, and the basic kind of mycorrhizal associations seems to be the Paris type where the hyphae are intercellular, forming coiled structures between the plant cells (F. A. Smith & Smith 1997; Winther & Friedman 2008). In Ophioglossum and Botrychium, some Lycopodiaceae, Psilotum, and a few ferns and angiosperms, etc., associations are variously with the echlorophyllous gametophytic and/or sporophytic stages (Winther & Friedman 2007, 2008, 2009; Hynson et al. 2013). Around 10% of all vascular plants are mycoheterotrophic for all or part of their life cycles (Leake & Cameron 2010), a nuber driven by the number of species in Orchidaceae ( 27,800) nearly all of which have such associations with fungi; there are perhaps 1,000 species in the Lycopodiales and Monilophytes combined (Winther & Friedman 200). Full mycoheterotrophy, known from ca 880 species (this number includes ferns, etc., that have echlorophyllous gametophytes alone), has evolved 46 or more times, including some cases in liverworts (Merckx et al. 2013a).
Genes & Genomes. Chromosome numbers in heterosporous vascular plants seem to be lower than those of homosporous plants. Thus in pteridophytes (including lycophytes) n = 57 on average, but in heterosporous water ferns n = 13.7, in angiosperms n = 16, in homosporous Lycopodium chromosome numbers are higher than in heterosporous Isoetes and Selaginella, and chromosome numbers in cymnosperms are on average also low (Barker 2013). Not that some flowering plants in particular do not have high chromosome numbers, but the average is low. In ferns, genome duplication followed by gene selencing but not chromosome loss may be responsible (Haufler 1987; Barker 2013 and references), in angiosperms in particular there is extensiv gene and genome remodelling after polyploidization events (see elsewhere).
Three new families of transcription-associated proteins may have evolved somewhere in this general area (Lang et al. 2010: hornworts not included; see also Zhu et al. 2012, Lang et al. not cited). For genome sizes in monilophytes and lycophytes, see Nakazato et al. (2008) and Leitch and Leitch (2013).
For the evolution of the chloroplast genome in other than seed plants, see Wolf and Karol (2012). Chloroplast genomes seem particularly labile in taxa ouside the angiosperms (Guisinger et al. 2011 for references). The order of genes in the mitchondrion is relatively invariable in bryophytes but much more variable in vascular plants (Y. Liu et al. 2014a).
Chemistry, Morphology, etc. Condensed tannins are polymerized in a chloroplast thylakoid-derived tannosome (Brillouet et al. 2013). In extant vascular plants, lignins are rich in guaiacyl units (Harris 2005), and the evolution of the cinnamyl/sinapyl alcoholase gene family involved in the synthesis of the hydroxycinnamyl alcohol monomer units (p-coumaryl, guaiacyl, syringyl) that ultimately constitute lignin can perhaps be pegged to this node (Guo et al. 2010; c.f. Gómez-Ros et al. 2007; Zu et al. 2009). Some xylans may be restricted to the sporophyte (Eeckhout et al. 2014).
For programmed cell death in vascular plants, which is involved in tracheid development, for instance, see van Hautegem et al. (2015). Edwards (2003) and Edwards et al. (2003) examined conducting cells of early tracheophytes and compared the morphologies of the cells involved with those of the bryophytes. For a general discussion on the evolution of water-conducting cells, with particular attention to wall sculpturing and its nature, see especially Kenrick and Crane (1991, 1997), Cook and Friedman (1997), Friedman and Cook (2000) and Edwards et al. (2006). However, understanding the fossil record is difficult in part because our knowledge of the development and nature of the wall thickening even of extant vascular plants is surprisingly poor, and exactly where in the wall lignin is deposited affects water conductance (Sperry 2003). The developmental control of conducting tissue in moss gametophytes and vascular plant sporophytes suggests that at one level they may not be that much different (see also above). For a general comparison of tracheary cells, see Bailey and Tupper (1918).
Secondary thickening has evolved more than once and the pattern of secondary growth varies considerably. The vascular cambium is usually unifacial, producing xylem internally only, and there are usually no anticlinal divisions of the cambial cells. Sphenophyllales alone outside the seed plant lineage may have developed a bifacial vascular cambium (e.g. Rothwell et al. 2008b; Spicer & Groover 2010; Hoffman & Tomescu 2011). Strullu-Derrien et al. (2014a) examined the hyudraulic properties of a very early wood with secondary thickening. It is unclear exactly when/in what clade an endodermis evolves (Raven & Edwards 2001: p. 385).
Kaplan (1997; vol. 3, 2001) provides an extensive discussion and analysis of the basic morphology of lycophytes and monilophytes in particular.
Phylogeny. The relationships [lycophytes [monilophytes + lignophytes]] are commonly found (although not in some analyses of chloroplast genomes in Ruhfel et al. 2014 or in the mostly chloroplast gene analysis of Z.-D. Chen et al. 2016).
Classification. Lycophytes and monilophytes or ferns have traditionally been called pteridophytes.
LYCOPODIALES Berchtold & J. Presl / LYCOPODIOPHYTA / LYCOPHYTES / LYCOPSIDS
Root-bearing stems from angles of branches, branching dichotomous, protoxylem endarch, positively geotropic; fine roots plagiotropic, dichotomising; mitosis monoplastidic; stem with protostele [= actinostele], protoxylem exarch, endodermis +; leaves small, with a single vein, phloem surrounding xylem; sporangia lateral, in strobili, 1/leaf, adaxial, often heart-shaped, dorsiventrally flattened, dehiscence transverse, along line of conspicuously thickened cells; MTOC on nuclear membrane; zygote with variable plane of first cell division, elongating, with quadrant/octant formation, shoot developing towards the archegonial neck [from hypobasal cell, endoscopic], embryonic axis reorients during development, root lateral with respect to its longitudinal axis [plant homorhizic]; nuclear genome size?; mitochondrion with loss/pseudogenisation of 6 genes [inc. all 4 ccm genes], some group II introns lost. - 3 families, 5 genera, ca 1300 species.
Age. Larsén and Rydin (2015) estimated an age of about 407 m.y., Magallón et al. (2013) an age of around 383.7 m.y., Laenen et al. (2014) an age of ca 303.1 m.y., B. Zhong et al. (2014b) an age of (403-)386.3(-377.4) m.y., and Villarreal and Renner (2014) an age of only around 270 m.y. for crown-group lycophytes; see also P. Soltis et al. (2002).
Evolution: Divergence & Distribution. For the early evolution of lycophytes, which have a rich fossil record, see Gensel and Berry (2001), Wellman et al. (2009), Ambrose (2013), Gerienne et al. (2016 and references) and Xue et al. (2016: Drepanophycus rhizomes ca 410 m.y.o.). Lycophytina include the three families below and their fossil relatives, and these latter include zosterophylls, which have circinately-coiled stems and sporangia in two rows (e.g. Gensel 1992; Kenrick & Crane 1997; Gonez & Gerienne 2010; Gerienne et al. 2016 and references). Zosterophylls and some other genera may form a clade with Lycopodiaceae (Gomez & Gerienne 2010).
Laenen et al. (2014) give some crown-group ages for genera.
Ecology & Physiology. Green (2010) described photosynthesis in this clade, focussing on the tree-like extinct lycopsids and the extant Isoetaceae. Tree lycopsids flourished for around 100 m.y. from the end of the Carboniferous to the beginning of the Permian, a time when atmospheric CO2 concentrations were low and oxygen concentrations were high. Air canals/aerenchyma permeated both above- and below-ground parts of the plants, i.e. they had a parichnos system. This enabled oxygen to move to the roots, where it was used up in respiration, while CO2 produced by the plant remained in the plant and also moved into the plant from the anoxic CO2-rich soil, ultimately going to the leaves, where it was used up in photosynthesis; this is the lycopsid photosynthetic pathway, LPP (Green 2010, esp. p. 2258). However, although movement of oxygen within the plant may have been facilitated, a pad of tissue at the base of the rootlets cut off their air spaces from those of the stigmarian roots, so overall CO2 movement and photosynthesis in the plant are likely to have been little affected (Boyce & DiMichele 2015).
Some lycopsids reached perhaps 50 m tall, 2 m d.b.h., and had dichotomously branching stigmarian roots, but they had little secondary or even primary phloem. Cork and a little xylem were all that was produced by the cambium, and the plants seem to have undergone a period of establishment growth (c.f. palms) when the stigmarian root system became established and the apical meristem of the stem enlarged so that when the stem finally began to elongate, it was the "adult" thickness (e.g. Phillips & DiMichele 1992). The phloem, in which the sieve cells may have had degenerate nuclei (c.f. palms: no nuclei at all) is likely to have been very long lived (Boyce & DiMichele 2015).
Such trees are in the same immediate clade as the lowly Isoetes and were dominant in Carboniferous peat swamps. Indeed, rootlets on Carboniferous stigmarian roots have the same branching pattern as in extant Isoëtes; branching is dichotomous, the roots are narrower each dichotomy, but there is otherwise no tapering, and there are root hairs - add similarities in anatomy, and Isoëtes is pracically identical (Hetherington et al. 2016). From the analysis of vascular tissue, it seems that auxin travelled from the base to the apex of the stigmarian root, the "wrong" direction for a stem - which it is morphologically - but the "right" direction for a root - which it is functionally (Sanders et al. 2011).
Bacterial/Fungal Associations. There are various associations of fungi with lycophyte sporophytes, although they may quite often be absent (Rimington et al. 2014; c.f. Winther & Friedman 2008).
Genes & Genomes. Leitch and Leitch (2013) found that lycophytes had rather small nuclear 1C genome sizes - (0.086-)1.7(11.96) pg - but sampling was poor. For the loss of various mitochondrial genes and the distribution of introns - ca 11 cis-splicing introns seem to have been gained - in this clade, see W. Guo et al. (2016b). The ccm genes that have been lost represent the loss of the mitochondrial cytochrome c maturation pathway.
Chemistry, Morphology, etc. Lycopodiales may contain fair amounts of silica (Trembath-Reichert et el. 2015). Root-bearing axes of many taxa in this group appear to be modified branches and branch dichotomously, while the rootlets/true roots are modified leaves (Pigg 1992; Rothwell & Erwin 1985; Rothwell 1995) or organs sui generis (Matsunaga & Tomescu 2016; see also Tomescu et al. 2014). Crane and Kendrick (1997) suggested that all appendicular structures in lycophytes - microphylls, ligules, sporangia, and stigmarian rootlets - were equivalent, i.e., consistent with the former hypothesis. In Isoetes the roots are exogenous (Rothwell & Erwin 1985) and this is also true of the K-branching that produces root-bearing axes in other lycophytes, as in a drepanophycalean lycophyte (i.e. in the same immediate clade as Lycopodium) where one branch of a dichotomy becomes a root-bearing axis and which may have a few leaves along its upper part, the other, an erect leafy stem (Matsunaga & Tomescu 2016). Are such roots characteristic of the whole clade? The small, dichotomising roots s. str. (Matsunaga & Tomescu 2016) may have a root cap, and this is reported from other lycophytes (Friedman et al. 2004, q.v. for caveats over roots in tracheophytes in general). Stubblefield and Rothwell (1981) discuss embryogenesis in lycophytes. Rothwell and Erwin (1965) described the roots of Lycopodium and Selaginella as being adventitious.
Meiosis is poyplastidic and anastral.
For general information, see also Kenrick and Crane (1997) Boyce (2005a) and Ranker and Haufler (2008), for fossil members, see Gensel et al. (2013), for sporophytes and their placentae, see Hilger et al. (2002), for details of phloem, see Evert (1990a), and for meiosis, MTOCs, etc., see Brown and Lemmon (2008).
Classification. For families and genera, see Christenhusz et al. (2011a). Each family is sometimes put in a monofamilial order...
LYCOPODIACEAE Mirbel Back to Lycophyta
Terrestrial or epiphytic; root ?hairs, endodermis 0; apical meristem complex, plasmodesmatal density in whole SAM 0.4-4.2[mean]/μm2; (strobili 0); pollen tapetum 0; (spermatogenesis polyplastidic); (gametophyte mycoheterotrophic); n = 34 [quite often; lots of other numbers].
3-4 [list]/400+: Huperzia (300), Lycopodiella (60). ± World-wide, esp. South America>
Age. The age of crown-group Lycopodiaceae is about 265 m.y. (Laenen et al. 2014: crown age of Huperzia) or 167 m.y. (Larsén & Rydin 2015).
Evolution: Divergence & Distribution. Wikström and Kenrick (1997, 2001) and Wikström (2001) discuss diversification and phylogeny of extant Lycopodium s.l. and relatives. Although diversification in Lycopodium s.l. may have begun some 200 or more m.y.a. when there are fossils with the distinctive plectostele that characterises Lycopodium s. str., most páramo species are probably derived from epiphytic species within the last 15 m.y. (Wikström et al. 1999; Sklenár et al. 2011).
Ecology & Physiology. About two thirds of the species of Huperzia, and all told around 200 species in the family, are epiphytic (Wikström et al. 1999; Schuettpelz & Pryer 2009; Zotz 2013).
Glomales are associated with the echlorophyllous gametophytic and subterranean sporophytic stages in lycophytes (Winther & Friedman 2008; Merckx et al. 2013a; Imhof et al. 2013). A member of Sebacinales-Sebacinaceae from Diphasiastrum alpinum was also found on Calluna vulgaris growing nearby, and nutrients moved from Calluna to the echlorophyllous lycopod gametophyte (Horn et al. 2013).
Bacterial/Fungal Associations. The Glomus involved in the mycoheterotrophic association forms a clade with "species" involved in similar associations in Arachnitis (Corsiaceae) and Botrychium (Ophioglossaceae) (Winther & Friedman 2007, 2008); together, they are part of the Glomus A group (Schußler et al. 2001).
Genes & Genomes. The trnL and trnS genes in the mitochondrial genome of Huperzia, but not in those of other lycophytes, may have come from chlamydial bacteria by lateral gene transfer (Knie et al. 2015).
Chemistry, Morphology, etc. For general information, see Ølgaard (1990), for spermatogenesis, see Renzaglia et al. (1994).
Phylogeny. For relationships in the family, see Field et al. (2016) and Burnard et al. (2016); Phylloglossum is sister to one main clade, the other. The bulbiferous Huperzia selago group is sister to the rest of the genus, which is mostly epiphytic; there are New and Old World clades (Wikström et al. 1999).
Classification. For genera, see Field et al. (2016).
[Isoetaceae + Selaginellaceae]: leaves with adaxial ligule; plant heterosporous; megaspore wall with much silica, outer and inner exine separated by discontinuity; gametophyte development endosporic, intraplacental space +, transfer cells 0; mitochondrion with loss of 15 genes.
Age. The age of this node is around 209 m.y. (Laenen et al. 2014) or 381 m.y. (Larsén & Rydin 2015).
Evolution: Divergence & Distribution. Blackmore et al. (2000) score the cells of this pair as not being monoplastidic, but c.f. Brown and Lemmon (1990), etc.. For spore wall ultrastructure in fossil members of this clade (homosporous!), see e.g. Wellman et al. (2009).
Genes & Genomes. W. Guo et al. (2016b) found that a total of 21/46 mitochondrial genes were absent from or pseudogenised in Isoetes and Selaginella.
Chemistry, Morphology, etc. For embryo development, see Renzaglia and Whittier (2013).
ISOËTACEAE Reichenbach Back to Lycophyta
Terrestrial or aquatic herb; roots arising from beneath the corm/rhizome, branching dichotomous, with a central air space, vascular bundle single, excentric, xylem abaxial to phloem; stem cormose, unbranched (elongated, dichotomously branching - I. andicola), vascular cambium +; SAM with mean plasmodesmatal density 2.2-4.1/μm2 [cell interface-specific plasmodesmatal network]; xylem mesarch; ?cambium; leaves with several vascular strands; megasporangia indehiscent, decaying, trabeculate; 50-300 megaspores/megasporangium; megaspores tuberculate; microsporogenesis successive, tetrads decussate, blepharoplast branched; (microspores monolete); male gametes with many cilia [10-20]; embryo lacking suspensor; n = (10) 11.
1 [list]/80(-150?). More or less world-wide.
Age. The age of crown-group Isoëtes is (235-)165, 147(-96) m.y. (Larsén & Rydin 2015) or ca 251 m.y. (Kim & Choi 2016).
Evolution: Divergence & Distribution. For the evolution of the whole group, including arborescent members and fossils that have been linked with Isoëtes, see Retallack (1997c), Grauvogel-Stamm and Lugardon (2001), Pigg (1992, 2001) and above; Pleuromeia may not have been the "ancestor" of Isoëtes.
Ecology & Physiology. Some species of Isoëtes take up CO2 from the mud in which they grow via their very well developed roots, Stylites (= I. andicola) and submerged individuals of other species of Isoëtes even lacking stomata - I. andicola never has stomata (Bristow 1975; Keeley 1998; Raven et al. 1998 and references). Photosynthesis is by a sort of modified CAM pathway, the lycopsid photosynthetic pathway (see above), and this has a substantially more ancient origin than does the CAM pathway in flowering plants (Edwards & Ogburn 2012).
Chemistry, Morphology, etc. The growth and anatomy of Isoëtes is poorly understood (e.g. Gifford & Foster 1988). Doyle (2013) described the vascular cambium as producing both xylem and phloem to the inside and parenchyma to the outtside (c.f. Kaplan 1997, vol. 3: chap. 19).
Strobili are not obvious; all leaves may be fertile. Isoëtes, at least, has placental cells with thickened, nacreous walls.
For general information, see also Jermy (1990); for megaspore morphology, quite diverse, see Hickey (1986).
Phylogeny. For relationships within Isoëtes, see Rydin and Wikström (2002), Hoot et al. (2006: ?rooting) and especially Larsén and Rydin (2015); a clade widely distributed on Gondwanan continents is sister to the rest (Larsén & Rydin 2015, q.v. for dates, etc.)..
SELAGINELLACEAE Willkommen Back to Lycophyta
Usu. terrestrial; Si02 accumulation common; syringyl lignin +; (rhizophores +), rhizophores and roots growing in length via intercalary meristems, calyptra +; root ?hairs, hypodermis suberized/with Casparian strip; stele in central cavity surrounded by trabeculate endodermal cells; (vessels +); stem with single apical cell[?}, plasmodesmatal density in whole SAM 27-44[mean]/μm2 [cell lineage-specific plasmodesmatal network]; stem mono-(-4-)stelic, ± actinostelic); leaves (often 4-ranked), (often anisophyllou; sporophylls (often 4-ranked); sporangia ± spherical, megaspores 4/megasporangium, surface with solitary protrusions (scabrate, reticulate); microspores (in tetrads), often echinate; n = (7-)9(10, 12), nuclear genome size [1C] 0.16-0.24 pg; trans splicing of some mitochondrial group II introns.
1 [list]/ca 800. World-wide.
Age. The crown-group age of this clade is ca 328 m.y. (Larsén & Rydin 2015).
Evolution: Divergence & Distribution. The small subgenus Selaginella is sister to the rest of the genus and is relatively undistinguished vegetatively, not even having rhizophores, the S. sanguinolenta clade may be sister to the remainder, although its position is as yet unclear (Zhou et al. 2015a; Zhou & Zhang 2015; Westrand & Korall (2016a). Both clades have more or less monomorphic sterile leaves, and details of their morphology, especially those of subgenus Selaginella, affect character polarization.
Ecology & Physiology. Selaginella grows in habitats varying from very humid and in considerable shade to open and xeric; plants in the latter habitats reconstitute quite nicely when water is added (Pampurova & van Dijck 2014).
Genes & Genomes. Selaginella has a highly reorganized chloroplast genome (Tsuji et al. 2007).
Chemistry, Morphology, etc. For the synthesis of syringyl lignin in Selaginella, see J.-K. Weng et al. (2010); details of the synthetic pathway are quite different from those in angiosperms. Root and rhizophore growth is distinctive, not proceeding by divisions of the immediate derivates of the apical cell but by the activity of an intercalary meristem that is some way behind the apex (Otreba & Gola 2011). See Damus et al. (1997) for the root hypodermis.
Zhou et al. (2015b) and Zhou and Zhang (2015 and references) illustrate the sometimes baroque morphology of the micro- and megaspores of the genus; Hemsley et al. (1998 and references) describe hpow self-assembly in involved in putting together the exine.
Phylogeny. Zhou et al. (2015a) and especially Westrand and Korall (2016a) provide a comprehensive phylogeny of the genus. As in other studies, the Selaginella selaginoides clade is sister to the rest of the genus, and the S. sanguinolenta clade may be sister to the remainder, although its position is as yet unclear (Zhou et al. 2015a; Westrand & Korall (2016a).
Classification. See Westrand and Korall (2016b) for an infrageneric classification.[MONILOPHYTA + LIGNOPHYTA] / EUPHYLLOPHYTA
Sporophyte endomycorrhizal [with Glomeromycota]; growth ± monopodial, branching spiral; roots +, endogenous, positively geotropic, root hairs and root cap +, protoxylem exarch, lateral roots +, endogenous; G-type tracheids +, with scalariform-bordered pits; leaves with apical/marginal growth, venation development basipetal, growth determinate; sporangium dehiscence by a single longitudinal slit; meiosis 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]; mitochondrion with loss of 4 genes, absence of numerous group II introns; LITTLE ZIPPER proteins + [see below].
Age. The divergence of the monilophytes and lignophytes may date to 401-380 m.y.a. (Leebens-Mack et al. 2005); Theißen et al. (2001) suggested an age of ca 400 m.y., Clarke et al. (2011: also other estimates) an age of (452-)434(-410) m.y. and Magallón et al. (2013) estimated an age of around (422-)411-404(-394) m.y.; (463.5-)428.9(-400.1) m.y. are the ages in B. Zhong et al. (2014b) and (478.4-)447.4(-415.2) m.y. in Rothfels et al. (2015b). See also Pryer et al. (1995, 2000, 2001a, 2004), P. Soltis et al. (2002: a variety of ages, some very old), Schneider et al. (2002), Stein et al. (2012) and Larsén and Rydin (2015).
Evolution: Divergence & Distribution. For possible apomorphies of crown members of this clade, see Raubeson and Jansen (1992b), Kenrick and Crane (1997), and Schneider et al. (2009).
Extra-floral nectaries are scattered throughout [Monilophyta + Lignophyta], and Weber and Agrawal (2014) found that their evolution was often - but not always - associated with an increase in diversification of the clades in which they occurred; they indirectly facilitated diversification. Cyanogenic glycosides, α-hydroxynitrile glucosides that release hydrogen cyanide when acted upon by plant β-glucosides, are similarly scattered, and Bak et al. (2006) suggest they may be an apomorphy at this level. They note that ferns and gymnosperms have aromatic cyanogenic glucosides (derived from tyrosine or phenylalanine) and angiosperms have both aliphatic and aromatic glucosides (derived from leucine, isoleucine or valine), the latter group being derived - parallel evolution at different levels perhaps seems as likely.
The leaves of this clade, often called megaphylls, vary considerably. The leaf supply in monilophytes seems to have evolved by dissection of an amphiphloic siphonostele, although the vascular system of the rhizome in some true ferns consists of sympodia (Karafit et al. 2005), while leaf gaps in seed plants are also associated with a stele that consists of a series of sympodia of collateral vascular strands. From this point of view the leaves with large blades in the two groups may represent parallelisms rather than a synapomorphy and leaf gaps are not equivalent; the term "megaphyll" can thus be used in a descriptive sense only (Namboodiri & Beck 1968c; Beck et al. 1982). Furthermore, the growth of fern leaves is accompanied by proliferation at the apex of the blade and that of angiosperms by proliferation at the base (Nardmann & Werr 2013), while Boyce (2005b, 2008a) noted the prevalence of marginal leaf growth in non-angiospermous leaf blades and of diffuse growth in angiosperm leaf blades - these may be oversimplifications, but they suggest differences between the two. Relating such differences to a common pattern of leaf development that includes that of the Lycopodiales/lycophytes is a challenge. For further details of the development/evolution of euphylls, which may well have evolved more than once, see above.
Ecology & Physiology. Osborne et al. (2004) provide an ecological explanation for the origin of mega/euphylls based on falling CO2 levels in the latter part of the Devonian.
Support for the stem in monilophytes is provided largely by the lignified stereome, in the outer cortex, while the tracheids are relatively thin walled. In gymnosperms thick-walled tracheids provide much of this support, and in angiosperms, too, it is various elements of the vascular tissue that provide support (e.g. Rowe et al. 2004; Pitterman et al. 2011; Klepsch et al. 2015).
Genes & Genomes. For the absence of numerous group II introns at this node, see W. Guo et al. (2016b); depending of how characters are otimized, 12-21 introns may have been lost here.
Chemistry, Morphology, etc. For microtubules, see Scmit (2002), for roots and their evolution, see Kenrick and Strullu-Derrien (2014), and for lamina morphology and venation development, see Boyce (2005b).
Phylogeny. Ferns and their relatives, the monilophytes or Moniliformopses, and lignophytes, the extant members of which are seed plants or spermatophytes, are both well supported clades.
Classification. The clade [monilophytes + lignophytes] is sometimes called Euphyllophyta/the euphyllophytes.
MONILOPHYTA / FERNS s.l. Back to Main Tree
Roots with a single apical cell, originating from the pericycle, lateral roots from the endodermis; stem with apical initial(s), plasmodesmatal density in whole SAM 19-56[mean]/μm2 [lineage-specific mitochondrial network]; stem with hypodermal and outer-cortical band of fibres [= stereome]; amphiphloic siphonostele +, discontinuities in stele in t.s. caused by frond gaps; protoxylem restricted to lobes of central xylem strand [giving a beaded appearance, hence monilophytes], xylem mesarch, tracheids with scalariform pits, G-type tracheids in protoxylem; phloem with refractive spherules in sieve tubes, phloem fibres rare; stem endodermis and pericycle +; leaves megaphyllous [ad/abaxial symmetry evolved first, then determinancy], development acropetal; petiole with multiple leaf traces coming from a U-shaped bundle; frond veins not anastomosing; sporangia grouped in sori, sporangium stalk 6< cells across, walls two cells thick, dehiscence by an exothecium, tapetum ± amoeboid, spores/sporangium 1000<, white, globose-tetrahedral, with orbicules, wall development centrifugal, exospore 3-layered, pseudoendospore +; gametophyte thalloid; antheridium wall ³5 cells thick, male gametes with 30-150 cilia, with numerous plastids and mitochondria; root lateral with respect to the longitudinal axis of the embryo [plant homorhizic]; x = ca 121, genome size [1C] = ca 14.3 pg [averages], chloroplast rps4 gene with nine-nucleotide insertion, LSC inversion from trnG-GCC to trnT-GGU; loss of one group II mitochondrial intron.
Age. Oldest, at (482-)430(-420.5) m.y., is the estimate in Testo and Sundue (2016). Magallón et al. (2013) estimated a crown-group age of around (404-)394.3-389.9(-382) m.y. for this clade, ca 360 and ca 364 m.y. are the ages in Schuettpelz and Pryer (2007) and Y-L. Qiu et al. (2007) respectively, (390.7-)368.5(-354) m.y. in B. Zhong et al. (2014b) and around 330 m.y. in Villarreal and Renner (2014); see also P. Soltis et al. (2002) for suggestions.
Evolution: Divergence & Distribution. Schuettpelz and Pryer (2009, esp. Tables 2, 3 in the Supplement) and Rothfels et al. (2015b: Appendix S4) provide numerous clade ages in monilophytes, and for more ages of the major monilophyte clades see Y.-L. Qiu et al. (2007) and Schneider et al. (2004a). Schuettpelz and Pryer (2009) also list a number of fossil records (see also Rothwell & Stockey 2008).
Ferns as a whole shows little variation in disparity, that is, the amount/extent of morphological variation in a sample of taxa, over time (Oyston et al. 2016), although in leptosporangiate ferns in particular there has been a gradual increase in disparity over time. There have been several radiations of homosporous leptosporangiate ferns, the first in the Palaeozoic, giving rise to lineages that have since become extinct, and again in the Jurassic and the Cretaceous (Rothwell & Stockey 2008). General fern diversity decreased (along with that of the cycads) through the Cretaceous (Wing & Boucher 1998). Ferns appear to have temporarily dominated at least locally after the end-Cretaceous bolide impact/Deccan Traps eruptions (Schneider et al. 2004a). The eusporangiate Marattia and Angiopteris and the leptosporangiate royal and tree ferns are almost living fossils and show little molecular and even morphological evolution (P. Soltis et al. 2002; B. Zhong et al 2014b; Rothfels et al. 2015b; Bomfleur et al. 2014a, c.f. Schneider et al. 2015).
Some 98% of living ferns are leptosporangiate ferns, and their main radiation may have have been after the diversification of the angiosperms in the late Cretaceous-early Caenozoic; initially it was a largely terrestrial radiation (Lovis 1977; Schneider et al. 2004a; Rothwell & Stockey 2008; Schuettpelz & Pryer 2009; H.-M. Liu et al. 2014). Well over 70% of ferns are eupolypods, and about one third of these are epiphytes, amd these make up ca 10% of all vascular epiphytes. Diversification of epiphytic ferns in particular occurred during the Palaeogene, perhaps linked with the Palaeocene-Eocene thermal maximum (Schneider et al. 2004a, b; Schuettpelz 2007; esp. Schuettpelz & Pryer 2009: Supplemental Tables 2, 3; Watkins et al. 2010; c.f. Dubuisson et al. 2009, in part). An exception is Trichomanes and relatives (but not Hymenophyllum and its relatives, for which, see Dubuisson et al. 2009) which diversified in the early Cretaceous; they are commonly epiphytic on tree ferns, which themselves had begun diversifying in the Jurassic (Schuettpelz 2007; also Schuettpelz & Pryer 2009; Rothwell & Stockey 2008 for early radiations of leptosporangiate ferns).
A provisional hierarchy of characters taken from Smith et al. (2006, 2008), Pryer et al. (1996) and Rothfels et al. (2012b) is given below. For a first stab at apomorphies for members of the polypod II clade, see Sundue and Rothfels (2013); their suggestions are largely followed here, and problems with sampling, character state delimitation, and different apomorphies produced by different methods of character optimization are taken into account as far as possible. Only unambiguous synapomorphies (Sundue & Rothfels 2013) are flagged below (see also Pittermann et al. 2015 for petiolar vascular anatomy). Kaplan (1997, vol. 3: chap. 19) summarized the sporangium wall morphology of monilophyta; the annulus is an apomorphy of Polypodiopsida, the leptosporangiate ferns. For other possible apomorphies, see e.g. Schneider et al. (2009). More features need to be added, e.g. if the megaphyllous leaves of most ferns and those of seed plants have evolved independently, which seems likely (see above).
Understanding the evolution of the apparently very unfern-like plant body of Psilotales, particularly that of Psilotum itself, until fairly recently considered to be perhaps the most primitive extant vascular plant. When I was taught about Psilotum, it was compared with the Palaeozoic rhyniophytes, now thought to be entirely unrelated. This still presents difficulties; Kaplan (1997, vol. 3: chap. 10; Siegert 1973 and references) summarize the literature. As he noted, young leaves of Psilotum did have features of fronds (see also Kaplan 1977). Similarly, the leaves of Equisetum may be secondarily simple. Thus its fossil relative Sphenophyllum has much larger leaves with dichotomous venation; bifacial xylem has been found in this genus (Kenrick & Crane 1997; Doyle 2013 and references).
Takahashi et al. (2009, 2015 and references) describe gametophyte development in ferns. They note that even there the apical cell (there can be two, quite separate, on a single gametophyte) is functional for a short while only, and then the apical region converts to a multicellular meristem, which can divide - dichotomous branching - if cell division in the middle of the meristem stops.
Ecology & Physiology. The evolutionary physiology of ferns is repaying examination. Thinking about water transport, the tracheids of ferns tend to be long and wide, and the scalariform perforation plates may extend the length of the cell. As a result, water transport can be relatively efficient (Pittermann et al. 2015); conifers, another group without vessels and that also have quite efficent water transport at least has secondary thickening and bordered pits (Pittermann et al. 2011). Fern richness in Australia is correlated with precipitation, and depending on what aspect of diversity is emphasized, precipitation may be linked to equability, etc., bryophytes, but not flowering plants, showing rather similar patterns (Nagalingum et al. 2015).
Epiphytic ferns are concentrated in Hymenophyllaceae, Polypodiaceae, Pteridaceae (e.g. Vittaria) and Dryopteridaceae (e.g. Elaphoglossum) (Schuettpelz & Pryer 2009; Watkins & Cardelús 2012; Kato & Tsutsumi 2013; see also above). The gametophytes of these epiphytes are often strap-shaped and long-lived, and, like other fern gametophytes, are dessication-tolerant; as Watkins et al. (2007a: p. 716) observed, "fern gametophytes are, for all intents and purposes, bryophytes", and the epiphytic species they studied were the most tolerant of drying (see also Nayar & Kaur 1971: survey of gametophyte diversity; Dassler & Farrar 2001; Farrar et al. 2008; Watkins et al. 2007; Rothfels & Schuettpelz 2014; Farrar 2016). Gemmae on these gametophytes (e.g. Pryer et al. 2016; Farrar 1974, 2016) will further increase their longevity. (Moss gametophytes, even their antheridia, are also notably dessication-tolerant - Stark et al. 2016 and references.) Dessication tolerace is quite common in fern sporophytes, both epiphytic and terrestrial, and peltate scaless may play a central role in the uptake of water, rather as in Bromeliaceae (John & Hasenstein 2016). Ferns show a variety of other adaptations to the ecologically dry epiphytic habitat, including CAM photosynthesis (Keeley & Rundell 2003; Watkins & Cardelús 2012), and mycorrhizae are less frequent (e.g. B. Wang & Qiu 2006; Kato & Tsutsumi 2013); nutrients tend to be low in the epiphytic habitat. Testo and Sundue (2014) found that both terrestrial species and hemiepiphytes (where roots from the climbing plant establish a connection with the soil) were derived within a clade of epiphytic Polypodiaceae, while J. Clark et al. (2016) suggested that the epiphytic habit and increased genome size in eupolypods may be connected.
In seed plants, stomata open in response to both red and blue light. Stomata of those few ferns examined, all leptosporangiates (Pteris, Adiantum, Asplenium and Nephrolepis), lacked a blue light-specific opening response, although elements of the response, including the relevant phototropin, a blue right receptor protein kinase, were present (Doi et al. 2006). In the shaded understory environments that many ferns prefer, blue (and red) light has been preferentially absorbed by the canopy above; stomatal closure is mediated by red light. Doi et al. (2015) later found that there was a blue-light response in other ferns, lycophytes, cycads, etc., indeed, stomata of a few of these taxa, including Equisetum, did not respond to red light. Kawai et al. (2003; see also Suetsugu et al. 2005) noted that there was a distinctive chimaeric red/far red light photoreceptor (phy 3, = neochrome) in which red-sensing phytochrome and blue-sensing phototropin are fused into a single molecule (F.-W. Li et al. 2014) in some Polypodiales, possibly aiding in phototropic responses in the shaded conditions in which ferns have diversified; neochrome is very sensitive to white light (Wada 2008). Neochrome seems to have been acquired by polypod ferns from hornworts via lateral gene transfer around 179 m.y.a., which, perhaps not so coincidentally, is about the age of Polypodiales (Schneider et al. 2004a), and it may even have been acquired more than once (F.-W. Li et al. 2014); it is also known from Mougeoria, Zygnemataceae (Suetsugu et al. 2005). Veins in fern leaves are not the same distance from the epidermis as they are from each other, i.e., they are not hydraulically optimised. However, photosynthesis may proceed best in the low levels of diffuse light and so this hydraulic optimisation may not matter so much (Zwieniecki & Boyce 2014). (Note that in seed plants the effectiveness of the stomatal response is white/blue + red > blue > red > green light [Willmer & Fricker 1996] and in many flowering plants leaves are hydraulically optimised [Zwieniecki & Boyce 2014].)
Stomatal responses in non-flowering plants have been characterized as being passive, those of flowering plants, active. Thus it has been suggested that fern stomata do not respond to increased CO2 concentrations in the atmosphere (McAdam & Brodribb 2012a), although this has been questioned, such a response apparently being present in the common ancestor of extant vascular plants (Franks & Britton-Harper 2016). Furthermore, the synthesis of abscisic acid, involved in stomatal responses to this and other stimuli, is not triggered by changes in leaf turgor in non-flowering plants, but it is in flowering plants, although not all of the latter show the same sensitivity to turgor changes (McAdam & Brodribb 2016). Interestingly, the stomata of Equisetum seem to be permanently closed, and this may also be true for those of Psilotum (Cullen & Rudall 2016). However, details of the physiology of stomatal functioning is unclear and in part conflicting (Lind et al. 2015; Roelfsema & Hedrich 2016 and references).
Fertilization & Spore Dispersal. The distributions of the sporophytic and gametophytic plants of the one fern species may be quite different, particularly if the gametophyte is other than heart-shaped. Strap-shaped or filamentous gametophytes can live for a very long time and/or produce gemmae, and so they can persist in sites that are hundreds of miles from the nearest sporophytes (e.g. Farrar 1967; Ebihara et al. 2013). With the advent of the ability to identify gametophytes directly by molecular sequencing, rather than waiting for them to produce sporophytes, this phenomenon is turning out to be remarkably common (Ebihara et al. 2013), and it has interesting implications for the evolution of ferns (see e.g. Ebihara et al. 2009).
Noblin et al. (2012) describe the mechanics of how the annulus functions in sporangium dehiscence.
Plant-Animal Interactions. Overall, herbivory in ferns is about the same as that in angiosperms (Balick et al. 1978; Turcotte et al. 2014: see caveats). However, in the chemically well defended bracken, Pteridium aquilkinum, at least, herbivory is not associated with jasmonate-mediated regulation of VOC (volatile organic compound) emissions, which in flowering plants, for instance, can attract predatores of herbivores, etc. (Radhika et al. 2012). For herbivory by lithinine geometric moths, which has involved host shifts after a single colonization event, see Weintraub et al. (1995).
Bacterial/Fungal Associations. For mycorrhizae in ferns, see Lehnert et al. (2010 and references). Fine endophytes, with their distinctive fan-like arbuscules, are known from ferns; these endophytes are probably mucoromycotes, not Glomus (Orchard et al. 2016 and references). Equisetum is not known to form mycorrhizal associations (Read et al. 2000).
Genes & Genomes. For the evolution of the monilophyte chloroplast genome, see Karol et al. (2010), Grewe et al. (2013) and J. Clark et al. (2016). Within Polypodiopsida, some inversions in the chloroplast inverted repeat may be high-level synapomorphies (Gao et al. 2009). Grammitidaceae s. str. in particular (included in Polypodiaceae) have green spores and accelerated plastid genome evolution, a correlation found elsewhere in ferns, although it is not 100% (Schneider et al. 2004b), indeed, spores that less obviously contain chloroplasts are quite widespread (Sundue et al. 2011).
Ferns are noted for their high incidence of polyploidy, almost 1/3 (31%) of all speciation events being accompanied by polyploidy (Wood et al. 2009), and base chromosome numbers are also usually very high. There has been recent hybridization between clades (Cystopteris, Gymnocarpium) that diverged an estimated (76.2-)57.9(-40.2) m.y.a. (Rothfels et al. 2015a) while there is hybridization in Osmunda between clades that may have been separated for four times as long (Bomfleur et al. 2014b; Grimm et al. 2015).
For information on genome size, see Obermayer et al. (2002) and J. Clark et al. (2016); particularly large genomes occur in Psilotales and some Ophioglossales, and in a few polypods.
Chemistry, Morphology, etc. The xyloglucan composition of the primary cell wall varies substantially, that of Equisetum being particularly distinctive (Hsieh & Harris 2012); for cell wall polysaccharides, see also Silva et al. (2011).
Basic sporophyte morphology was outlined by Kaplan (1997, vol. 2: chap. 11, 18, vol. 3: chap. 19, 2001). For the organization of the apical meristem, see Amrbose and Vasco (2015). The stem has a siphonostele, the protoxylem being restricted to lobes of the central xylem strand, hence bringing to mind a necklace (development of the xylem is mesarch, although it is notably variable in the Ophioglossum/Psilotum clade). The protoxylem is described as having G-type tracheids (Edwards 1993). Hernández-Hernández et al. (2012) discuss the distribution of the circumendodermal band, tannin-containing cells with thickenings on in inner periclinal and also sometimes the anticlinal walls, that surround the petiolar vascular bundles and that have a common orgin with the endodermis; they also detail the distributions of a number of other vegetative/habit features. Vasco et al. (2013) summarize fern frond morphology and development, noting a number of shoot-like features. Details of leaf development in Equisetum are similar to those of other ferns and seed plants rather than of lycophytes (Ambrose & Vasco 2016), but it has paracytic stomata unlike those of any other land plants (Cullen & Rudall 2016). For aerophore distribution in ferns, see Davies (1991). The information on horizontal cell walls in early embryo development in ferns given by Philipson (1990) seems to be incorrect - the examples should be vertical?
For the stem apex of ferns, see above.
Takahashi et al. (2009, 2014 and references) describe gametophyte development in ferns. They note that the apical region converts to a multicellular meristem, which can divide - dichotomous branching - if cell division in the middle of the meristem stops; the branched, strap-shaped gametophytes of epiphytic ferns are simply an extreme variant of this morphology. Archegonia develop only after the formation of the multicellular meristem. For details of male gamete morphology and movement, etc., see e.g. Renzaglia et al. (2000b, 2002) and Schneider et al. (2002).
For information on pteridophytes in general (these have often - and still may - include lycophytes), see also Kato (2005) and Ranker and Haufler (2008). For other general information, see Raven and Edwards (2001), for comparative anatomy, see Ogura (1972), for vessels, see Sen and Mukhopadhyay (2014 and references), for phloem, see Evert (1990a), for venation, see Wagner (1979) and Boyce (2005b), for details of stelar morphology and evolution, see Beck et al. (1982), and for young sporophytes, etc., see Johnson and Renzaglia (2009 and references).
Phylogeny. The circumscription of this clade has only recently become clear. It includes the strongly supported [Psilotum + Ophioglossum] clade (Tmesipteris is sister to Psilotum) perhaps sister to all other ferns, as chloroplast data has broadly tended to suggest (Rothfels et al. 2015b for references). Wickett et al. (2014) obtained a [Marattiales + Psilotales] clade sister to leptosporangiate ferns, but this may be a sampling issue. The inclusion of morphology alone or in combination with molecular data also affects the relationships detected (Wikström & Pryer 2005 and references); see also Grand et al. (2013) for various morphological analyses. The position of Equisetum is uncertain.
1. Equisetum may be embedded in ferns, perhaps sister to Angiopteris, etc. (although support only moderate), the combined clade in turn being sister to remaining ferns (e.g. Pryer et el. 2001a, 2004a; Wikström & Pryer 2005; Qiu et al. 2007; Ebihara et al. 2011; c.f. in part Wolf et al. 1998). Z.-D. Chen et al. (2016) found that it was sister to the eusporangiate ferns, although support was not strong, indeed, there Marattiales were sister to all other ferns.
2. Equisetum may be sister to all other ferns, as in a rps4 analysis, and also 4- and 5-gene analyses, the latter two with strong support (Schuettpelz et al. 2006), analyses of several plastid genes (Rai & Graham 2010), and in a matK phylogeny (Kuo et al. 2011). Knie et al. (2015) also find good support for the relationships [Equisetum [[Psilotum + Ophioglossum] + The Rest]], as does Rothfels et al. (2015b) in their nuclear gene analysis and Testo and Sundue (2016) in their 4,000 species analysis. Interestingly, spore wall ultrastructure of Calamites, an extinct equisetaceous plant, is not so different from that of Ophioglossaceae and other ferns (Lugardon & Brousmiche-Delcambre 1994; Grauvogel-Stamm & Lugardon 2009). Equisetum has no mitochondrial atp1 intron, either a secondary (and parallel) loss or plesiomorphic absence, depending on the topology of the whole group (Wikström and Pryer 2005: see the character hierarchy below).
3. Schneider et al. (2009) noted potential morphological apomorphies such as simple leaf blade and stems with both radial and dorsiventral symmetries (= erect plus creeping stems...) suggesting a clade [Psilotales + Equisetales], consistent with some structural changes in the chloroplast genome (Grewe et al. 2013; see also some analyses in Karol et al. 2010; also Wolf & Karol 2012; Ruhfel et al. 2014; J.-M. Lu et al. 2015: chloroplast genomes).
This reorganisation of monilophytes has sometimes been severely criticised (Rothwell & Nixon 2006), but it is unclear how damning such criticism is. Since the evaluation of "support" values for particular topologies is integral to the approach adopted in these pages, the decision to exclude such values by those authors makes their work difficult (for me, at least) to interpret. Indeed, in several morphological cladistic analyses (e.g. Bremer 1985; Stevenson & Loconte 1996; Rothwell 1999: fossils included or not) Psilotum came out as sister to all other vascular plants. However, some morphological analyses (Schneider et al. 2009) do place Psilotum with other monilophytes, even if the same analyses also place flowering plants within a paraphyletic group of extant gymnosperms.
Classification. Smith et al. (2006, 2008) propose a phylogeny-based reclassification of the ferns, and they also include literature, ordinal and familial synonymy, and a list of accepted genera and some major synonyms; Prelli (2010) gives a nice account of European ferns. However, adjustments to this classification are being made as details of the phylogeny become better understood (Schuettpelz & Pryer 2007, 2008; Kuo et al. 2011; Rothfels et al. 2012b: reclassification of eupolypods II). A linear sequence of families and genera (Christenhusz et al. 2011a) is now dated, but more recently Christenhusz and Chase (2014) have proposed another classification. There are some differences between the hierarchy below and that used by e.g. Rothfels et al. (2015b), but they will be cleared up as things (hopefully) settle down.
Previous Relationships. Psilotum and Equisetum were previously thought to represent independent lineages, with Psilotum and relatives considered to be the most primitive living vascular plants, and the latter do look superficially similar to some early fossils. Their association with ferns, now very largely accepted, was unexpected (but see Kenrick & Crane 1997). Although Bierhorst (1968, see also 1977) compared Psilotum with the extant fern Stromatopteris and found some morphological similarities, most of these have turned out to be parallelisms and the two are not at all close.
EQUISETOPSIDA / [Equisetales [Psilotales + Ophioglossales]]: plant with erect and creeping stems; ?vernation; tapetum plasmodial; embryo exoscopic, suspensor 0; chloroplast rps16 gene and rps12i346 intron lost.
Age. The clade that contains Equisetum has probably been separate from other monilophytes since the Permian, ca 250+ m.y.a. (Stanich et al. 2009); B. Zhong et al. (2014b) thought that this clade was (370.3-)296.2(-189.9) m.y. old.EQUISETALES Berchtold & Presl
EQUISETACEAE de Candolle
Plant with erect and creeping stems; roots triarch, with large central tracheid; cell wall also with (1→3),(1→4)-ß-D-MLGs [Mixed-Linkage Glucans], Si02 accumulation common; stem with intercalary meristem [at base of leaf sheath], ridged, photosynthetic, protoxylem mesarch, with central canal; protoxylem lacunae developing; stomata paracytic, maturing basipetally, mesogenous, subsidiary cells forming stomium; leaf vascular bundles amphicribral; leaves whorled, "axillary" buds +, alternating with the leaves, members of branch whorls alternating at each node; leaves small, simple, 1-veined, basally connate, not photosynthetic; sporangiophores peltate, aggregated into a strobilus; sporangial cell walls with helical secondary thickenings; tapetum plasmodial; spores with circular aperture [hilate], abapertural obturator +, green, wall with silica, elaters 4-6/spore, spatulate, helically-coiled; embryo exoscopic, plane of first cell division variable, suspensor 0; n = 108; mitochondrial atp1 intron 0.
1 [list] /15. ±World-wide, not the Antipodes.
Age. Extant species of Equisetum seem to have separated in the Caenozoic (77.5-)64.8(-52.1) m.y.a. (Des Marais et al. 2003, but c.f. Stanich et al. 2009).
Fossils with many of the apomorphies of crown group Equisetum are known from Upper Jurassic deposits from Patagonia some 150 m.y. or more old (Channing et al. 2011; see also Stanich et al. 2009); for still older Equisetum-like spores - but with trilete marks - and associated elaters from the Middle Triassic, see Schwendemann et al. (2010).
Evolution: Divergence & Distribution. Change in spore morphology from the Calamites type to the at first sight very different trilete spores of Equisetum is convincingly demonstrated by Grauvogel-Stamm and Lugardon (2009). Other fossils placed in this area include Sphenophyllum, which has megaphylls, and this suggests that the tiny leaves of Equisetum may be reduced rather than being microphylls; roots of fossils also differ in morphology and can be polyarch. For the long fossil record of Equisetum, see Channing et al. (2011).
Ecology & Physiology. Equistetum tends to grow in ecologically rather stressfull habitats, including hot springs (Channing et al. 2011 and literature; Husby 2012). There is pressurized gas flow, so-called convective ventilation, from the stems into the rhizomes in some extant species of Equisetum and probably in their fossil calamitalean relatives from the Carboniferous. Oxygen moves via interconnected air spaces into the rhizomes, so allowing them to penetrate deeply into the anoxic substrates commonly favoured by this group (Armstrong & Armstrong 2009). However, those species of Equisetum that lack interconnected air spaces - and this is accompanied by changes in position of the flow-resistant endodermis in the stem - have no convective ventilation (Armstrong & Armstrong 2011).
The stomata are likely to be immobile, especially when older, because of the rigid radiating rib-like silica thickenings of the subsidiary cells, and the stomata may even be permanently closed then; the chloroplasts can move from one guard cell to another (Cullen & Rudall 2016).
Reproductive Biology. Aided by their elaters, spores of Equisetum can either jump up to 1 cm in the air as they dry, or move by short random walk-type movements along the ground (Marmottant et al. 2013).
Genes & Genomes. For a genome duplication in Equisetum dated to (112.5-)92.4(-75.2) - or perhaps only 70-50 - m.y.a., see Vanneste et al. (2015).
Chemistry, Morphology, etc. For (1→3),(1→4)-ß-d-glucans, see Fry et al. (2008) and Xue and Fry (2012), and for Si concentration, etc., see Husby (2012). Cullen and Rudall (2016) discuss the development of the remarkable stomata in detail; they are mesogenous. The tapetum seems to be involved in the formation of the elaters (Uehara & Murakami 1995).
Phylogeny. Equisetum bogotense is sister to the rest of the genus (Guillon 2007).
[[Psilotales + Ophioglossales] [Marattiopsida + Polypodiopsida]]: (spore aperture proximal and monolete); indel in mitochondrial rpl2 coding region.
Age. Rothfels et al. (2015b) suggested an age of (390.4-)351.7(-309.7) m.y. for this node.
[Psilotales + Ophioglossales]: plant with erect and creeping stems; stem protoxylem development variable; embryo exoscopic, suspensor 0; gametophyte subterranean, axial, mycoheterotrophic [non-photosynthetic, mycorrhizal]; nuclear genome size 32.7-64.8 pg.
Age. Magallón et al. (2013) estimated an age of around 275.6 m.y. for this clade, and (316-)306(-267) m.y. is the age in Y. L. Qiu et al. (2007), ca 214.5 m.y. in Laenen et al. (2014) and (317.1-)250.5(-141.8) m.y. in Rothfels et al. (2015b); see also P. Soltis et al. 2002) for estimates.
Bacterial/Fungal Associations. For mycoheterotrophy in this clade, not yet confirmed for the small genera in Ophioglossaceae, see Merckx et al. (2013a).
Genes & Genomes. Both Psilotum and Ophioglossum have large genomes (Bennett & Leitch 2005; J. Clark et al. 2016).
For the mitochondrial genomes of Psilotum (very large) and Ophioglossum, seee W. Guo et al. (2016b); they are similar in terms of apomorphies with those of seed plants.PSILOTALES Prantl
PSILOTACEAE J. W. Griffith & Henfrey
Epiphytes; silica content slight; roots 0; ?leaf vascular bundles; leaves small, simple, (laterally flattened - Tmesipteris), veins 1 or 0; sporangia 2-3, forming synangium; tapetum glandular-amoeboid; spores kidney-shaped, monolete; gametophyte with septate rhizoids; (transfer cells in sporophyte only - Psilotum), n = 52, 208, genome size [1C] = ca 72.5 pg.
Age. B. Zhong et al. (2014b) estimated an age of (147.1-)72.3(-14.7) m.y. and Rothfels et al. (2015b) an age of (142.5-)78.9(-28.5) m.y.a. for this clade.
Evolution. Bacterial/Fungal Associations. Mycorrhizal associations in Psilotum in the echlorophyllous gametophytic and subterranean sporophytic stages are with glomalean Glomus group A fungi (Winther & Friedman 2009; Imhof et al. 2013).OPHIOGLOSSSALES Link
Root with 2-5 protoxylem poles; root hairs 0; cork mid cortical; vascular cambium +; stem stele sympodial; tracheids with circular bordered pits; frond vascular bundles collateral; (axillary buds +); fronds compound to simple, 1 produced/year, petiole vasculature U-shaped, venation reticulate, with internally directed veins, vernation nodding, bases sheathing, stipules +, thin; one or more sporophores associated with each tropophore; (gametophyte with septate rhizoids); (embryo endoscopic; first cell wall of the zygote vertical); n = (44) 45 (46 ...720), genome size [1C] = ca 28.35 pg.
Age. Rothfels et al. (2015b) suggested an age of (249.6-)161.7(-74) m.y. for crown-group Ophioglossaceae.
Ecology & Physiology. Glomeromycote mycorrhizae in Ophioglossum and Botrychium are associated with the echlorophyllous gametophyte and subterranean sporophytic stage, and also the photosynthesising sporophyte; the latter may obtain some of its carbon from conspecific or heterospecific plants with which the fungus is also associated (Winther & Friedman 2007; Field et al. 2015a). Botrychium gametophytes do not develop beyond the 8-celled phase without establishing this mycorrhizal association, and plants may spend the first ten years of their lives underground (Winther & Friedman 2007).
Bacterial/Fungal Associations.The Glomus involved in the mycoheterotrophic association is in the same immediate clade as species involved in similar associations in Arachnitis (Corsiaceae) and Lycopodiaceae (Winther & Friedman 2007, 2008; Imhof et al. 2013).
Takahashi and Kato (1988) describe the development of lateral meristems in the family.
Ophioglossum reticulatum, at n = 720, has the highest chromosome numbers of any plant.
See Hauk et al. (2003) for a phylogeny, Mankyua not included, also Shinohara et al. (2013), Mankyua included, but position unstable - sister to rest of family (also in the joint analysis), or to Ophioglossum s. str..
[Marattiopsida + Polypodiopsida]: frond vascular bundles amphicribral; frond compound, vernation circinate; scales +; sporangia abaxial; gametophyte green, surficial; shoot developing towards the archegonial neck [from hypobasal cell, endoscopic]; nuclear genome 3.5-14.0 pg [?here]; changed gene adjacencies at borders of chloroplast IR; mitochondrial atp1i361g2 intron gain.
Age. B. Zhong et al. (2014b) suggested an age of (378.8-)336.7(-291.5) and Rothfels et al. (2015b) an age of (364.1-)329(-289.2) m.y. for this clade.
P. Soltis et al. (2002) offer a variety of suggestions for ages of nodes in this clade.
Roots with several protoxylem poles; root hairs septate [?multicellular]; petiole vasculature polycyclic; stipules +, fleshy and starchy.MARATTIALES Link
Dictyostele +; mucilage canals +; rhizome with scales; aerophores linear, with lenticels; petiole vasculature polycyclic; fronds pulvinate, (divisions with internally directed reticulate venation - Christensenia); meiosis monoplastidic [?all}; spores bilateral or ellipsoid, monolete; transfer cells 0; x = 40. 5/150: Danaea (50).
For meiosis, see Brown and Lemmon (2001).
Evolution: Divergence & Distribution. For some comments on biogeography, see Christenhusz and Chase (2013). There seems to be a slow-down in the rate of evolution in this clade (Rothfels et al. 2015b and references).
Phylogeny. For a phylogeny, see Murdock (2008a), also Christenhusz et al. (2008); the fossil Psaronius seems to associate consistently with Marattia (e.g. Grand et al. 2013 and references).
Both Marattia and Angiopteris are paraphyletic, but they can easily be made monophyletic (Murdock 2008b). For Danaea, see Christenhusz (2010).
POLYPODIOPSIDA / leptosporangiate ferns.
Blue light stomatal opening response absent; primary cell walls poor in mannans and rich in tannins; roots with 2 protoxylem poles; primary xylem with scalariform bordered pits; leaf trace single; aerophores linear, on either side of the petiole, with stomata; sporangium derived from periclinal division of a single epidermal cell, wall one-layered, stalk 4-6 cells across [= leptosporangiate]; sporangium with exothecium forming an annulus, 64-800 spores/sporangium; antheridium ± exposed; gametophyte cordate [level?]; embryo prone [first cell wall of the zygote vertical, parallel to gravity], with quadrant/octant formation, suspensor 0.
Age. Magallón et al. (2013: with temporal constraints) estimated an age of around (267.8-)252.7-251.4(-246.1) m.y. for this clade; ca 299 m.y.a.is the age in Schuettpelz and Pryer (2009), (327.8-)301.3(-271.5) m.y. in Rothfels et al. (2015b), (330-)323(-310) m.y. in Y. L. Qiu et al. (2007), perhaps 350 m.y.a. in Schneider et al. (2004a), and (357.5-)357(-356) m.y. in Testo and Sundue (2016) - but only around 170 m.y.a. in Villarreal and Renner (2014). All told, a rather disconcerting spread.
Phylogeny. The large clade made up of leptosporangiate ferns has very strong support (see also Hasebe et al. 1994, 1995, Pryer et al. 1995; Wolf et al. 1998; Quandt et al. 2004; Schuettpelz et al. 2006; Rai & Graham 2010, etc.). Rothfels et al. (2015b) emphasized that their analyses of nuclear data broadly agreed with several plastid sequence analyses.
Within the leptosporangiates, Osmunda and relatives, the sporangia of which have some eusporangiate features, are strongly supported as being sister to the rest. There is further substantial resolution of relationships (e.g. Pryer et al. 2004a, b and references; Schuettpelz & Pryer 2007; c.f. in part Kuo et al. 2011: positions of Gleicheniaceae, Lindsaeaceae, Nephrolepis [previously in Lomariopsidaceae] uncertain). It is unclear whether or not there is a clade [Hymenophyllales + Gleicheniales] (Knie et al. 2015 for literature; Rothfels et al. 2015b: Gleicheniales paraphyletic, but with little support). J.-M. Lu et al. (2015: chloroplast genome, but sampling) found Dipteridaceae and Lygodiaceae to be successive branches along the leptosporangiate stem. Schizaeales and Salviniales (strong support) and Cyatheales (weak support) are successively sister to Polypodiales (e.g. Rothfels et al. 2015), and Rai and Graham (2010) suggest additional variants. For relationships with Schizaeales, see Labiak et al. (2015 and references).
Within Polypodiales, Lindsaeaceae are probably sister to all others (see also Rothfels et al. 2015b), but the genera Cystodium, ex Dicksoniaceae, and Lonchitis and Saccoloma, both ex Dennstaediaceae - the last as a separate family below - are also in this area (Lehtonen et al. 2012). Pteridaceae and Dennstaediaceae were well supported as successive sister taxa to the eupolypods (Rothfels et al. 2015b; J.-M. Lu et al. 2015). Davalliaceae and related taxa are sister to the polygrammoid ferns, and both include a number of epiphytes (for their evolution, see Tsutsumi & Kato 2006). Relationships suggested by structural changes in the chloroplast genome (Wolf & Roper 2008; Wolf et al. 2010, 2011) are consistent with those suggested by sequence analyses. Cystopteris and relatives form a clade that may be sister to the eupolypod II clade (Rothfels et al. 2009, esp. 2012a, 2013, 2015b).
OSMUNDALES LinkOSMUNDACEAE Martinov
Cataphylls [petiole bases] +; Si02 accumulation common; stem with ectophloic siphonostele, with a ring of conduplicate/twice conduplicate discrete bundles; leaves with stipules; petiole vasculature complex U-shaped; fronds with fertile and sterile portions (fertile and sterile fronds separate); annulus a lateral group of cells; spores green; (rhizoids septate), zygote elongating; n = 22. 4/20.
The Osmunda clade originated in the late Carboniferous, ca 323 or 305 m.y.a. (Phipps et al. 1998; Schneider et al. 2004a), and is very diverse from the Permian onwards, less so more recently. Fossils some 180 m.y.o. have anatomy that is remarkably like that of the extant Osmunda claytoniana, and probably the chromosome number and genome size of the fossil plant were similar, too (Bomfleur et al. 2014a). Schneider et al. (2015) reconstruct the history of genome size changes in Osmundaceae; there is some variation. Generation times in royal ferns are long, so genome change might be expected to be low, but whether or not there is "genomic stasis" (Bomfleur et al. 2014a; c.f. Schneider et al. 2015) is another issue; there has been some change.
Age. The age of this clade is estimated at around 199.6 m.y. (Schuettpelz & Pryer 2009); however, estimates from Carvalho et al. (2013) based on fossils that can be assigned to the leptosporangioid branch of the tree suggest an age in excess of ca 265 m.y.a., Late Permian (see also Wilf & Escapa 2014), while the preferred age in Grimm et al. (2015: comprehensive analysis, also incorporating fossils) is (264-)243(-233) m.y. ago.
Todea, hitherto known only from the other main southern land masses (except Antarctica) has been found in the early Eocene of Patagonia in rocks ca 53 m.y.o. (Carvalho et al. 2013).
It has been suggested that Osmunda is paraphyletic, with Osmunda (now = Osmundastrum) cinnamomea being sister to the rest of the family (Metzgar et al. 2008); relationships in Carvalho et al. (2013) are [Osmundastrum [Osmunda [Leptopteris, Todea, Todites]]]. However, Bomfleur et al. (2014b) argue for the monophyly of [Osmunda + Osmundastrum] based on extensive data from fossils and a re-evaluation of the molecular evidence, i.a. they note that O. cinnamomea is able to hybridize with some species of Osmunda, but not with other Osmundaceae. Given an estimated date of the split of the first two of (264-)238(-233) m.y.a., only a little less than the age of crown-group Osmundaceae as a whole (Grimm et al. 2015), they have been separated for far longer than any other vascular plants that hybridize.
[[Hymenophyllales + Gleicheniales] [Schizaeales [Salviniales [Cyatheales + Polypodiales]]]]: protostele +; sporangia in sori, annulus ± oblique, continuous; loss of chloroplast trnK gene and its intron.
Age. (297-)286(-272) m.y. is the age for this node in Y. L. Qiu et al. (2007), ca 280.1 m.y. in Schuettpelz and Pryer (2009: Hymenophyllales sister to the rest) (306.8-)278.7(-252.3) m.y. in Rothfels et al. (2015b).
[Hymenophyllales + Gleicheniales]: ?
Age. The age for this node in Y. L. Qiu et al. (2007) was estimated at (283-)273(-259) m.y. and in Rothfels et al. (2015b) at (276.7-)237.2(-192.4) m. years.
HYMENOPHYLLALES A. B. FrankHYMENOPHYLLACEAE Martinov
Epiphytes common; axillary buds +; petiole vasculature ; fronds 1 cell thick between veins, stomata 0; sporangia on ± elongated receptacle, maturation basipetal; spores globose, green; gametophyte filamentous or ribbon-like; embryo not with tetrad/octant formation; x = 36. 9/600.
Age. Crown Hymenophyllaceae are (190.4-)185.1(-174.7) m.y.o. (Schuettpelz & Pryer 2009).
For the rate of molecular evolution if Hymenophyllaceae, with an apparent slow-down in Hymenophyllum, see Schuettpelz and Pryer (2007).
Around half the family is epiphytic (Zotz 2013), and there are also climbing taxa (see Dubuisson et al. 2009 for growth forms in Hymenophyllum). Epiphytism in Trichomanes evolved before that in Hymenophyllum, the plants probably growing on the stems of Cyantheaceae on which species are still often to be found (Hennequin et al. 2008), indeed, diversification in Trichomanes is estimated to have begun in the middle of the Jurassic and that in Hymenophyllum in the middle of the Cretaceous (Schuettpelz & Pryer 2007), ca 147.3 versus ca 41.9 m.y.a. (Schuettpelz & Pryer 2009). See also Schuettpelz and Pryer (2007) and Hennequin et al. (2008) for other dates.
Despite the delicate fronds of Hymenophyllaceae, dessication tolerance is at least sometimes well developed - rather like mosses (Proctor 2003, 2012). Indeed, the sporophytes of some epiphytic trichomanoid ferns have lost both cuticle and roots ("regressive evolution" - Dubuisson et al. 2011), and may be functionally similar to bryophytes; the stem stele may have just a single vascular element (Dubuisson et al. 2013; see also Dubuisson et al. 2003b).
For the phylogeny of the family, see Pryer et al. (2001b) and Dubuisson et al. (2003a, 2013), for that of Trichomanes and relatives, see Ebihara et al. (2007), for that of Hymenophyllum, with a focus on the large subgenus Mecodium, which turns out to be polyphyletic but common in a number of basal clades, see Hennequin et al. (2006), and for a possible base chromosome number in the family - previous suggestions x = 6-9, 11, 13, but here = 36 - see Hennequin et al. (2010).
[Gleicheniales + The Rest]: (spores monolete, perine closely attached ro exine).
Age. The stem group age of this node is ca 276.4 m.y. (Schuettpelz & Pryer 2009).
Root steles with 3-5 protoxylem poles; rhizome with scales; frond veins anastomosing; sporangium maturation simultaneous; (gametophyte axial - Stromatopters), (rhizoids septate); antheridia with 6-12 narrow curved or twisted cells in walls; x = 20, ... 116, genome size [1C] = 2.96 pg [sampling].
Age. Crown-group Gleicheniales are ca 262.2 m.y. (Schuettpelz & Pryer 2009) or (252.4-)196.1(-134) m.y.o. (Rothfels et al. 2015b).
Synonymy: Dipteridales Doweld, Matoniales Reveal, Stromatoperidales RevealGLEICHENIACEAE C. Presl
Leaves indeterminate, pseudodichotomously forked (not - Stromatopteris); petiole vasculature incurved U-shaped; spores (bilateral), monoulcerate; (embryo exoscopic, cell wall vertical, gametophyte (axial, subterranean), with clavate hairs; x = 22, 34, etc.. 6/125.
There has been a chloroplast genome inversion in the family (Wolf & Roper 2008).
Stromatopteris has a mycoheterotrophic gametophyte, but the identity of the fungus is not known (Merckx et al. 2013a; Imhof et al. 2013).
[Dipteridaceae + Matoniaceae]: ?DIPTERIDACEAE Seward & E. Dale
Petiole vasculature inverted Ω-shaped bundle; frond veins reticulate, areoles with included veins, veins 4.4-5.6 mm/mm2; sporangia with "long" stalks, (spores bilateral, monolete); x = 33. 2/11. N.E. India to N.E. Australia, earlier in Caenozoic widespread.
Stems solenostelic, with two vascular cylinders and a central bundle; petiole vasculature ± inverted Ω-shaped bundle; fronds or pinnae ± dichotomously branched; sporangia in ring surrounding central "receptacle", sorus indusiate; x = 25, 26. 2/4. Malesia, previously widespread.
[Schizaeales [Salviniales [Cyatheales + Polypodiales]]]: plant with hairs; endospore 2-layered; antheridium wall ca 3 cells across; two overlapping inversions in chloroplast genome.
Age. (281-)266(-250) m.y. is the age for this node in Y. L. Qiu et al. (2007), ca 264.6 m.y. in Schuettpelz and Pryer (2009) and (289.4-)258.3(-235.2) m.y. in Rothfels et al. (2015b).SCHIZAEALES Schimper
Fronds differentiated into fertile/sterile portions [hemidimorphic]; petiole vasculature ?; annulus sub-apical; n = 28-504.
Age. The crown-group age of Schizaeales is estimated to be around 218.4 m.y. (Schuettpelz & Pryer 2009).LYGODIACEAE M. Roemer
Fronds indeterminate, climbing, pseudodichotomously branched, with a bud in angle of branch; one sporangium/sorus, subtended by antrorse indusium-like flange; x = 29, 30. 1/25.
Actinostachys has a mycoheterotrophic gametophyte, but it is not known what the fungus is (Merckx et al. 2013a; Imhof et al. 2013).
Rhizome with dictyostele or solenostele, (with pockets axillary to the fronds); spores tetrahedral, with parallel solid ridges (ridges hollow, centre spongy); x = 38. 1/100.
For a largely well-resolved phylogeny of the family and optimisation of characters on to the tree, see Labiak et al. (2015: spore morphology!).
Inner pericyclic cells 6, 8, thickened; fronds undivided or fan-shaped, veins dichotomizing; sporangia borne on marginal projections at blade tip; spores monolete, bilateral; gametophyte filamentous, (white, subterranean, tuberous), rhizoids septate, (embryo exoscopic, cell wall vertical); x = 77, 94, 103. 2/30.
There has been a chloroplast genome inversion somewhere around here (Wolf & Roper 2008); see also the next node up.
[Salviniales [Cyatheales + Polypodiales]]: sporangium stalk 1-3 cells across [?position]; two [more!] overlapping inversions in chloroplast genome.
Age. The age of this node is estimated to be around 234.7 m.y. (Schuettpelz & Pryer 2009) and (269.1-)231.6(-190.8) m.y. (Rothfels et al. 2015b).
Genes & Genomes. The rate of evolution of the 18S nuclear gene was lower than in the other vascular plants examined (Stenøien 2008: lycophytes not included).
Aquatics, aerenchyma +; stems dichotomizing; veins ± anastomosing; sterile/fertile frond dimorphism; plant heterosporous, sporangia lacking annulus; megaspore single; gametophyte development endosporic; genome size [1C] = ca 2.38 pg; nrDNA with 5.8S and 5S rDNA in separate clusters.
Age. Crown-group Salviniales are estimated to be ca 186.8 m.y.o. (Schuettpelz & Pryer 2009) or (204.5-)153.5(-152) m.y. (Testo & Sundue 2016).
See Nagalingum et al. (2006, 2007: sporocarp structure) and Nagalingum et al. (2008: phylogeny).Synonymy: Marsileales von Martius, Pilulariales Berchtold & Presl
Froinds simple, or to 4 divisions/frond; sori in stalked bean-shaped sporocarps [folded pinnae]; megaspore with acrolamella over the exine aperture, perine gelatinous; female gametophyte with 1 archegonium; n = 10, genome size [1C] ca 0.8 pg [Azolla]. 3/75.
For the phylogeny of Marsilea and character evolution there, see Nagalingum et al. (2007).SALVINIACEAE Martinov
Plant free-floating; fronds sessile, 2-ranked, <2.5 cm long, simple; n = 9, 22. 2/16.
Azolla has Nostoc in its tissues and is an important nitrogen fixer in rice paddies, etc..
[Cyatheales + Polypodiales]: dictyostele +; hydathodes +; IR with several large inversions, ycf2 duplication.
Age. The age for this node is ca 211 m.y. in Y. L. Qiu et al. (2007), ca 223.2 m.y. in Schuettpelz and Pryer (2009), (270.1-)228.8(-187.5) m.y. in B. Zhong et al. (2014b) and (238.1-)204.6(-179) m.y. in Rothfels et al. (2015b).
CYATHEALES A. B. Frank
Petiole vasculature complex, ± inverted Ω-shaped; hairs +; sori terminal on veins, indusiate, indusium with outer and inner parts; sporangium stalk ca 5 cells across; antheridium walls ³5 cells across; genome size [1C] = ca 7.91 pg [?sampling].
Age. The crown-group age of Cyatheales is ca 186.7 m.y. (Schuettpelz & Pryer 2009) or rather younger, (167.8-)109.1(-56.8) m.y. (Rothfels et al. 2015b: Alsophila sister to the rest).
There seems to be a slow-down in the rate of evolution at the base of Cyatheales (Rothfels et al. 2015b and references).Synonymy: Dicksoniales Reveal, Hymenophyllopsidales Reveal, Loxsomatales Reveal, Metaxyales Doweld, Plagiogyriales Reveal
Indusium cup-shaped, receptacle columnar, clavate; x = ca 78. 1/1.
Petiole vasculature complex; indusium urceolate, receptacle elongate, often exserted; gametophyte with scale-like hairs; x = 46, 50. 2/2.
Petiole vasculature inverted Ω-shaped; outer indusium scarcely differentiated; sori with paraphyses; x = 66. 1/2.
Petiole vasculature with multiple traces coming from a U-shaped bundle; young fronds with dense, pluricellular, mucilage-secreting hairs; indusium 0; x = ?66. 1/15.
[Cibotiaceae + Cyatheaceae + Dicksoniaceae + Metaxyaceae]: petiole vasculature with multiple traces coming from a ± U-shaped bundle; paraphyses +.CIBOTIACEAE Korall
Stomata with three subsidiary cells; spores with equatorial flange, usu. parallel ridges on distal face; x = 68. 1/11.
[Cyatheaceae + Dicksoniaceae]: the crown-group age of this clade, if it exists, is ca 150 m.y.o. (Janssen et al. 2008).CYATHEACEAE Kaulfman
Stem with polycyclic dictyostele;Fronds with multiple traces coming from a U-shaped bundle; scales large (also small); fronds large; indusium 0 to completely surrounding sporangia); x = 69. 5/600.
Age. Crown-group Cyatheaceae are estimated to be ca 96 m.y.o. (Janssen et al. 2008).
The rate of chloroplast genome evolution has slowed down considerably here, probably because of the long generation time of tree ferns (P. Soltis et al. 2002; esp. B. Zhong et al. 2014b).
Korall and Pryer (2014) outline major biogeographic patterns in the group; initially Gondwanan vicariance seems to be involved, although crown-goup diversification did not begin until ca 96 m.y.a. with subsequent rather limited (for ferns) transoceanic long distance dispersal. The 100+ endemic species of Cyathea on Madagascar may represent a Pliocene ([4.24-]3.07> m.y) diversification of three separate clades each of which has a fairly lengthy sojourn on the island - thus there was around 30 m.y. in one Malagasy clade before diversification (Janssen et al. 2008, see also Korall & Pryer 2014). Bystriakova et al. (2011) discussed niche evolution.
See Korall et al. (2006, 2007) for a phylogeny.
[Dicksoniaceae + Metxyaceae]: the crown-group age of this clade, if it exists, is (172-)132(-94.5) m.y. (Testo & Sundue 2016).DICKSONIACEAE M. R. Schomburgk
Adaxial [outer!?] valve of sorus formed by reflexed frond segment margin and often differently coloured from the other; x = 56, 65. 3/30.
Indusium 0; x = 95, 96. 1/2.
Roots black, wiry [?level]; rhizome dorsiventral [?level]; petiole vasculature with a single bundle; sporangial maturation mixed; stalk 1-3 cells thick, annulus vertical, interrupted by stalk and stomium; neochrome/phy 3 +.
Age. This clade is estimated to be around 260 m.y.o. (Testo & Sundue 2016), (200-)176(-163) m.y.o. (Schneider et al. 2004a), ca 191 m.y.o. (Schuettpelz & Pryer 2009) or (220.1-)184.2(-149.2) m.y.(Rothfels et al. 2015b).Synonymy: Aspleniales Reveal, Athyriales Schmakov, Blechnales Reveal, Dennstaedtiales Doweld, Dryopteridales Schmakov, Lindseales Doweld, Negripteridales Reveal, Parkeriales A. B. Frank, Platyzomatales Reveal, Pteridales Doweld, Thelypteridales Doweld
For a discussion of characters for this clade, particularly the eupolypods II, see Sundue and Rothfels (2014).
Innermost cortical layer of root usu. of 6 large cells; stele protostelic, with internal phloem; petiolar vasculature V-shaped and then with two bundles; indusium opening towards margin; x = 34, 38, etc. 6/200. Pantropical (subtropical).
See Lehtonen et al. (2010) for a phylogeny and generic classification.
Age. (193.6-)165.4(-113.7) m.y. is a suggesttion for the age of this node by Rothfels et al. (2015b).CYSTODIACEAE J. R. Croft
Petiole vasculature with two complex bundles. 1/1: Cystodium sorbifolium. Malesia.LONCHITIDACEAE M. R. Schomburgk
Petiole vasculature with two bundles. 1/2. Tropical America and Africa, Madagascar.SACCOLOMATACEAE Doweld
Scales?; petiole vasculature with inverted Ω-shaped bundle; spores also with distinctive ± parallel branched ridges; x = ca 63. 1/12.[Dennstaedtiaceae + Pteridaceae]: Si02 accumulation common; petiole vasculature with inverted Ω-shaped bundle.
Age. B. Zhong et al. (2014b) suggested an age of (217-)154.3(-93.1) m.y. for this node ([Denn. + Pterid.]), Schuettpelz and Pryer (2009) an age of ca 110.8 m.y., and Schneider at al. (2016) ages somewhere around 137.4-95.6 m. years.
Chimaeric red/far red light photoreceptor [phy 3, neochrome]; stele?; hairs jointed; petiole bearing buds; x = 26, 29. 11/170.
Age. Crown-group Dennstaedtiaceae are estimated to be ca 72.2 m.y.o. (Schuettpelz & Pryer 2009) or around 98-66.2 m.y.o. (Schneider et al. 2016).
(Epiphytic), (xeric); indusium 0; (spores bilateral); (gametophyte ribbon-like); x = 29, 30. 50/950: Pteris (200-250), Adiantum (200), Vittaria (80). Worldwide.
Age. This clade is around 106.3 m.y.o. (Schuettpelz & Pryer 2009), 90 m.y.o. (Rothfels & Schuettpelz 2014), or about 99.9-87.4 m.y.o. (Schneider et al. 2016).
Kramopteris resinatus, in amber ca 100 m.y.o. from Myanmar, is placed at the split between Monachosorum and other Pteridaceae (Schneider et al. 2016).
Phylogeny. For phylogenies, see Crane et al. (1995), Prado et al. (2007), Schuettpelz (2007), Chao et al. (2014: Pteris, position of P. longifolia, the type, unclear), L. Zhang et al. (2015: Pteris somewhat expanded), and Schuettpelz et al. (2016: vittarioids). . Pryer et al. (2016) found that Adiantum is monophyletic and is sister to Vittaria and its relatives. For increased rates of molecular evolution, see Rothfels and Schuettpelz (2014). Cheilanthoid ferns, some 400 or more species, can grow in very dry conditions; generic limits are difficult here, but see also Grusz et al. (2014 and references) and Yesilyurt et al. (2015).Eupolypods: petiole vasculature V-shaped bundle, then two bundles, circum-endodermal band + (0); fronds to 1.5 times pinnate; spores monolete, reniform, perine distinct; x = 41.
Age. This clade, which includes most ferns, is (124-)105(-91) m.y.o. (Schneider et al. 2004a) or ca 116.7 m.y.o. (Schuettpelz & Pryer 2009).[Didymochlaenaceae [Hypodematiaceae [Lomariopsidaceae [Dryopteridaceae [Tectariaceae [Oleandraceae [Davalliaceae + Polypodiaceae]]]]]]] / eupolypod I: (plants epiphytic); rhizome scales persistent, dense; petiole vasculature complex, circular in t.s., also with abaxial semicircular arc of smaller bundles; perispore with thick tuberculate folds/wings.
Age. The age of this node is ca 98.9 m.y. (Schuettpelz & Pryer 2009) or (172.5-)170(-158.5) m.y. (Testo & Sundue 2016).
This is a largely epiphytic clade (e.g. Schuettpelz & Pryer 2009). For rhizome scales, perhaps protecting the plant against dessication and aiding in the absorbtion of water and nutrients, see Tsutsumi and Kato (2008); if they are not at this position on the tree, they should be placed at the next node up (with parallel evolution within Dryopteridaceae).
For relationships, see L.-B. Zhang and Zhang (2015); a couple more families may still be needed. Thus H.-M. Liu et al. (2014), as they placed the odd genera Pteridrys and Pleocnemia in Tectariaceae and Dryopteridaceae respectively, recognised an [Arthropteridaceae + Tectariaceae] clade (the former is synonymized under the latter here), but relationships are as suggested above.DIDYMOCHLAENACEAE L.-B. Zhang & L. Zhang
Rhizome erect, subarborescent; sori hippocrepiform, somewhat elongated. 1/?1. ± Pantropical.[Hypodematiaceae [Lomariopsidaceae [Dryopteridaceae [Tectariaceae [Oleandraceae [Davalliaceae + Polypodiaceae]]]]]]: ?
(n = 40).[Lomariopsidaceae + Nephrolepidaceae]: ?
For relationships in Lomariopsidaceae, see L. Zhang et al. (2016); it seems reasonable to adopt a broad circumscription of the family.
Synonymy: Nephrolepidaceae J. Agardh[Dryopteridaceae [Tectariaceae [Oleandraceae [Davalliaceae + Polypodiaceae]]]]: ?
(Epiphytic); fronds >3.5 times pinnate; perine winged; gametophyte strap-like; x= 41. 30-35/1700: Elaphoglossum (600), Polystichum (500). World-wide.
Age. Crown-group Dryopteridaceae are around 81.8 m.y.o. (Schuettpelz & Pryer 2009) or (94-)76(-58) m.y.o. (Le Péchon et al. 2016).
Elaphoglossum is the major epiphytic genus in the family - ca 400 species (ca 3/4 of the genus) are epiphytes (Zotz 2013). Diversification within the speciose Polystichum began in the Eocene, (60-)46(-32) m.y.a. (Le Péchon et al. 2016), that in Elaphoglussum began a bit more recently - that covers about 2/3 of the family.
For a phylogeny of the whole family, see H.-M. Liu et al. (2007, esp. 2015); three subfamilies are recognised, although two genera are unplaced. For a phylogeny of Elaphoglossum, see also Lóriga et al. (2014: 20-15 m.y.a. fossil of ?crown-group Elaphoglossum from Dominican amber). Rouhan et al. et al. (2004) and Vasco et al. (2015) discuss relationships within Elaphoglossum, where the Coast Rican E. amygdalifolia and the Cuban E. wrightii are successively sister to the rest of the genus. Moran et al. (2010a, b) investigate relationships within the bolbitidoid ferns focussing on variation in perispore morphology. Li and Lu (2006a, b), L.-B. Zhang et al. (2012), Sessa et al. (2012a), and McHenry and Barington (2014: exindusiate Andean species monphyletic, sister to Mexican spp.) have been working on relationships within Dryopteris itself, a genus whose limits are being clarified (e.g. Zhang & Zhang 2012) and which shows extensive hybridization at all levels (Sessa et al. 2012b). Le Péchon et al. (2016) examined phylogenetic and biogeographic relationships in Polystichum, while Labiak et al. (2014) looked at relationships around Lastreopsis, with movement to and fro between Australia and South America towards the middle of the Caenozoic.[Tectariaceae [Oleandraceae [Davalliaceae + Polypodiaceae]]]: frond veins free, parallel or pinnate.
(Climbers); (rhizome slender), (stipe and pinnae articulated); (frond veins free, parallel or pinnate), with jointed usually stubby hairs; n = 40-42: Tectaria (200). 8-19/320. Pantropical, inc. oceanic islands.
Age. Crown-group Tectariaceae (excluding Arthropteris) are around 50.4 m.y.o. (Schuettpelz & Pryer 2009).
Although in the analysis of H.-M. Liu et al. (2013) the position of Arthropteridaceae was uncertain, F. G. Wang et al. (2014a) found that they were embedded in Polypodiaceae-Tectarioideae, as were Lomariopsidaceae; the latter was in a separate clade in Schuettpelz and Pryer (2009). L.-B. Zhang and Zhang (2014) placed Arthropteridaceae sister to Tectariaceae, but with less than overwhelming support, Lomariopsidaceae were again separate. The circumscription of Tectariaceae as adopted here was also found by L. Zhang et al. (2016) and the monophyly of Tectaria s. str. confirmed.
Synonymy: Arthopteridaceae H. M. Liu, Hovenkamp & H. Schneider[Oleandraceae [Davalliaceae + Polypodiaceae]]: fronds abscising from rhizome.
Fronds abscising just above the base [so leaving phyllopodia], often simple; x = 41. 1/40.
The two diverged ca 42 m.y.a. (Sundue et al. 2015).DAVALLIACEAE M. R. Schomburgk
Fronds >3.5 times pinnate; spores warty, warts close, not constricted at their bases [= verrucate-colliculate]; x = 40. 1/65. South East Asia to Oceania, western Mediterranean and tropical Africa, both one species.
Age. Crown-group Davalliaceae are ca 19.4 m.y.o. (Schuettpelz & Pryer 2009).
F.-G. Wang et al. (2014b) optimize spore morphology on a phylogeny of the family. Tsutsumi et al. (2016) found seven major clades in the family (one monotypic), but relationships rather depended on the marker analysed. For a generic classification, see Kato and Tsutsumi (2008), however, Tsutsumi et al. (2016: sectional classification) suggest that only a single genus should be recognised, in part because of these phylogenetic uncertainties.POLYPODIACEAE J. Presl & C. Presl
(Rhizome polysmmetrical); (petiole with one or two vascular bundles - grammitids); indusium 0; (spores green, globose-tetrahedral, trilete - grammitids); (gametophyte strap-like); x = 35-37. 56/1200: Drynaria (50).
Age. Crown-group Dryopteridaceae (Loxogramme + The Rest) are about 55.8 m.y.o. (Schuettpelz & Pryer 2009).
For ages of splits of clades, see Schuettpelz and Pryer (2009) and Sundue et al. (2015). Ca 87% of the species of Polypodiaceae are epiphytic (Zotz 2013), making them the major epiphytic clade in the monilophytes, and diversification is associated with the uplift of the Andes (e.g.), clades with broad elevational ranges diversifying faster, speciation being related to climatic/environmental factors, less obviously associated with morphological features (Sundue et al. 2015: epiphytes in general; Kreier et al. 2008: Andean Serpocaulon; L. Wang et al. 2012: Qinghai-Tibet Lepisorus). Weber and Agrawal (2014) suggested that the evolution of extra-floral nectaries in Pleopeltis was associated with an increase in diversification.
For a phylogeny of microsoroid ferns, see Kreier et al. (2008), for that of grammitid ferns, see Sundue et al. (2010, 2015 and references: generic changes). For the phylogeny of grammitid ferns, see Sundue et al. (2014a, esp. b: Grammatis still polyphyletic).
Janssen et al. (2005) discussed the evolution of the diverse frond morphologies in Drynaria s.l.. For root anatomy, see Schneider (1996, 1997), and for petiole anatomy, see Sundue et al. (2014a, esp. b and references).
F.-G. Wang et al. (2014a) include a broadened but monophyletic Tectariaceae as a subfamily of Polypodiaceae.[Cystopteridaceae [[Rhachidosoraceae [Diplaziopsidaceae [Desmophlebiaceae [Hemidictyaceae + Aspleniaceae]]]] [Thelypteridaceae [Woodsiaceae [Athyriaceae [Blechnaceae + Onocleaceae]]]]]] / eupolypod II: petiole vasculature with V-shaped bundle changing to two, ± elongated/crescent-shaped [in t.s.]; rhachis sulcus wall confluent with the costa of pinna; sorus with 7-21 cells/annulus [?level].
Age. This node is ca 103.1 m.y.o. (Schuettpelz & Pryer 2009) or (196-)186(-184) m.y.o. (Testo & Sundue 2016).
For a discussion of apomorphies in this clade, see Sundue and Rothfels (2014).CYSTOPTERIDACEAE Schmakov
Rhizome long-creeping; veins reaching the frond margin; indusium 0 or hood-like; n = 40, etc.. 3/36: Cystopteris (27).
For phylogenetic relationships, see Rothfels et al. (2013). The genera are monophyletic, but there has been very extensive hybridization within Cystopteris and Gymnocarpidium (Rothfels et al. 2014).[[Rhachidosoraceae [Diplaziopsidaceae [Desmophlebiaceae [Hemidictyaceae + Aspleniaceae]]]] [Thelypteridaceae [Woodsiaceae [Athyriaceae [Blechnaceae + Onocleaceae]]]]]: ?
Rhizome scales clathrate; petiole bundels U-shaped; sori on one side of veinn = 41; 1/4-7.
Plant proliferous [producing plantlets by asexual reproduction]; roots pale, fleshy; fronds soft and fleshy; vein endings raised and thickened, forming a submarginal vein; sori elongated, only on one side of vein; n = 40, 41. 3/5.[Desmophlebiaceae [Hemidictyaceae + Aspleniaceae]]: ?
Rhizomes erect or decumbent; petiole bundles hippocampiform, U-shaped or free; fronds unequal-pinnate, veins free, forming submarginal vein; sori elongated; spores cristate; n = ? 1/2. Costa Rica to Brazil.
For information on Desmophlebiaceae, see Mynssen et al. (2016).[Hemidictyaceae + Aspleniaceae]: ?
Fronds unequal pinnate, with submarginal collecting vein and margins with broad membranous border; vein endings raised and thickened; n = 31. 1/1: Hemidictyum marginatum. S. Mexico to S.E. Brazil.
Epiphytes common; root pericyclic sclereids with excentric lumina; rhizome scales clathrate; frond trace single, circumendodermal band surrounding trace 0; petiole vasculature with bundles back-to-back, C-shaped, fusing and becoming X-shaped (V- or U-shaped), circumendodermal band 0; frond usu. 2-3 times pinnate, with small clavate hairs, margins decurrent and forming lateral ridge along rhachis; sori on one side of vein; indusia lateral, linear; sporangium stalk 1 cell across in the middle; spores with decidedly winged perine; x = 35, 36, 38, 39. 1-10/700. Widely distributed.
Asplenium s.l. includes a large number of epiphytic species (Zotz 2013). Helical, non-lignified wall thickenings (c.f. the velamen of monocots) occur in cortical cells of some Asplenium, mostly epiphytic species (Leroux et al. 2011).
Age. Crown-group Aspleniaceae are ca 57.7 m.y.o. (Schuettpelz & Pryer 2009).
For generic limits, see Bellefroid et al. (2010 and references); Asplenium s. str. is paraphyletic.[Thelypteridaceae [Woodsiaceae [Athyriaceae [Blechnaceae + Onocleaceae]]]]: (Si02 accumulation common [?Athy., Onocl.]); frond once-pinnate/pinnatifid.
Petiole vasculature with bundles uniting distally into a gutter shape; hairs acicular, whitish or hyaline, on fron, also on surface and/or margins of rhizome scales; first venation of frond lobe/pinnule develops on basiscopic side [catadromous]; n = 27-36. 8/950: Microsorium (600).
Age. The age of crown-group Thelypteridaceae is ca 68.5 m.y. (Schuettpelz & Pryer 2009).
For a careful evaluation of generic limits, which are best drawn broadly given the extensive generic polyphyly and highly homoplasious "generic" characters, especially within Cyclosorus s.l., see He and Zhang (2012) and also Almeida et al. (2016).[Woodsiaceae [Athyriaceae [Blechnaceae + Onocleaceae]]]: ?
Plant epipetric; rhizomes suberect; petiole bases persist; circumendodermal band 0; indusium basal, of many strap-shaped or filamentous segments, receptacle raised; n = 33, 38, 39, 41. 1/35. Mostly montane, northern hemisphere.[Athyriaceae [Blechnaceae + Onocleaceae]]: ?
Woodsia may be sister to this whole clade (Schuettpelz & Pryer 2009: Fig. S1).ATHYRIACEAE Alston
Mature frond with abundant anthocyanin; margins entire ["smooth"], petiole base swollen, (starch-containing), ± persistent [= trophopod]; corniculae/scales at adaxial junction of pinna costa with rachis; sori on both sides of vein, indusia opening to face away from vein [either two linear back to back sori, or J-shaped indusium wrapped around the vein], (on one side); n = 40, 41. 5/600: Diplazium (400). Mostly, terrestrial, understory.
Age. Crown-group Athyriaceae are around 78.4 m.y.o. (Schuettpelz & Pryer 2009).
Wei et al. (2013) evaluated relationships within Diplazium and found i.a. that species previously assigned to Allantodia in particular were scattered through the tree; they circumscribed Diplazium broadly and provided an infrageneric classification for it. For divergence dates and biogeography in Diplazium, perhaps a member of the boreotropical flora in the Eocene, see Wei et al. (2015).[Blechnaceae + Onocleaceae]]: fronds dimorphic [fertile and sterile].
Young fronds reddish; petiole vasculature complex, abaxially also with three to many round vascular bundles arranged in an arc; (fronds monomorphic), venation catadromous, veins forming narrow areoles near the costa [costular anastomoses]; sori linear, on subcostal commissural vein, indusia opening towards costa; perine winged; n = 34 [27, 28, 31-37, 40]. 4/200. Cosmopolitan
Age. Crown-group Blechnaceae are around 59.8 m.y.o. (Schuettpelz & Pryer 2009).
For relationships in Blechnaceae, with Blechnum circumscribed rather broadly, see Perrie et al. (2014).ONOCLEACEAE Pichi-Sermolli
Circumendodermal band 0; petiole basally ± swollen, vascular bundles uniting distally into a gutter shape; trophopods +; fronds dimorphic; sori enclosed by reflexed lamina margins; indusium deltate; sorus with 24-35 cells/annulus; spores chlorophyllous; n = 37, 39, 40. 4/5. Northern Hemisphere.
Age. Onoclea sensibilis is known fossil from Palaeocene North America 62-58 m.y.a., the fossils being remarkably similar to extant individuals (Rothwell & Stockey 1991).