EMBRYOPSIDA Pirani & Prado
Gametophyte dominant, independent, multicellular, initially ±globular, not motile, branched; showing gravitropism; acquisition of phenylalanine lysase* [PAL], flavonoid synthesis*, microbial terpene synthase-like genes +, triterpenoids produced by CYP716 enzymes, CYP73 and phenylpropanoid metabolism [development of phenolic network], 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; mblepharoplast +, 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, growth 3-dimensional*, 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 [= MicroTubule Organizing Centre] associated with plastid, sporocytes 4-lobed, cytokinesis simultaneous, preceding nuclear division, quadripolar microtubule system +; wall development both centripetal and centrifugal, 1000 spores/sporangium, sporopollenin in the spore wall* laid down in association with trilamellar layers [white-line centred lamellae; tripartite lamellae]; plastid transmission maternal; nuclear genome [1C] <1.4 pg, main telomere sequence motif TTTAGGG, KNOX1 and KNOX2 [duplication] and LEAFY genes present, ethylene involved in cell elongation; chloroplast genome with close association between trnLUAA and trnFGAA genes [precursors for starch synthesis], tufA, minD, minE genes moved to nucleus; mitochondrial trnS(gcu) and trnN(guu) genes +.
Many of the bolded characters in the characterization above are apomorphies of more or less inclusive clades of streptophytes along the lineage leading to the embryophytes, not apomorphies of crown-group embryophytes per se.
All groups below are crown groups, nearly all are extant. Characters mentioned are those of the immediate common ancestor of the group,  contains explanatory material, () features common in clade, exact status unclear.
Sporophyte well developed, branched, branching dichotomous, potentially indeterminate; hydroids +; stomata on stem; sporangia several, terminal; spore walls not multilamellate [?here].
II. TRACHEOPHYTA / VASCULAR PLANTS
Sporophyte long lived, cells polyplastidic, 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]; PIN[auxin efflux facilitators]-mediated polar auxin transport; (condensed or nonhydrolyzable tannins/proanthocyanidins +); xyloglucans with side chains uncharged [?level], in secondary walls of vascular and mechanical tissue; lignins +; roots +, often ≤1 mm across, root hairs and root cap +; stem apex multicellular [several apical initials, no tunica], with cytohistochemical zonation, plasmodesmata formation based on cell lineage; vascular development acropetal, tracheids +, in both protoxylem and metaxylem, G- and S-types; sieve cells + [nucleus degenerating]; endodermis +; stomata numerous, involved in gas exchange; leaves +, vascularized, 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; archegonia embedded/sunken [only neck protruding]; 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].[MONILOPHYTA + LIGNOPHYTA]
Sporophyte growth ± monopodial, branching spiral; roots endomycorrhizal [with Glomeromycota], 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; cells polyplastidic, MTOCs diffuse, perinuclear, migratory; blepharoplasts +, paired, with electron-dense material, centrioles on periphery, male gametes multiciliate; nuclear genome size [1C] = 7.6-10 pg [mode]; 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.
Sporophyte woody; stem branching lateral, meristems axillary; lateral root origin from the pericycle; cork cambium + [producing cork abaxially], vascular cambium bifacial [producing phloem abaxially and xylem adaxially].
SEED PLANTS† / SPERMATOPHYTA†
Growth of plant bipolar [plumule/stem and radicle/root independent, roots positively geotropic]; plants heterosporous; megasporangium surrounded by cupule [i.e. = unitegmic ovule, cupule = integument]; pollen lands on ovule; megaspore germination endosporic [female gametophyte initially retained on the plant].
EXTANT SEED PLANTS
Plant evergreen; nicotinic acid metabolised to trigonelline, (cyanogenesis via tyrosine pathway); microbial terpene synthase-like genes 0; primary cell walls rich in xyloglucans and/or glucomannans, 25-30% pectin [Type I walls]; lignin chains started by monolignol dimerization [resinols common], particularly with guaiacyl and p-hydroxyphenyl [G + H] units [sinapyl units uncommon, no Maüle reaction]; roots often ≥1 mm across, stele diarch to pentarch, xylem and phloem originating on alternating radii, cork cambium deep seated; stem apical meristem complex [with quiescent centre, etc.], plasmodesma density in SAM 1.6-6.2[mean]/μm2 [interface-specific plasmodesmatal network]; eustele +, protoxylem endarch, endodermis 0; wood homoxylous, tracheids and rays alone, tracheid/tracheid pits circular, bordered; mature sieve tube/cell lacking functioning nucleus, sieve tube plastids with starch grains; phloem fibres +; cork cambium superficial; leaf nodes 1:1, a single trace leaving the vascular sympodium; leaf vascular bundles amphicribral; guard cells the only epidermal cells with chloroplasts, stomatal pore with active opening in response to leaf hydration, control by abscisic acid, metabolic regulation of water use efficiency, etc.; axillary buds +, exogenous; prophylls two, lateral; leaves with petiole and lamina, development basipetal, lamina simple; sporangia borne on sporophylls; spores not dormant; microsporophylls aggregated in indeterminate cones/strobili; grains monosulcate, aperture in ana- position [distal], primexine + [involved in exine pattern formation with deposition of sporopollenin from tapetum there], exine and intine homogeneous, exine alveolar/honeycomb; ovules with parietal tissue [= crassinucellate], megaspore tetrad linear, functional megaspore single, chalazal, sporopollenin 0; gametophyte ± wholly dependent on sporophyte, development initially endosporic [apical cell 0, rhizoids 0, etc.]; male gametophyte with tube developing from distal end of grain, male gametes two, developing after pollination, with cell walls; female gametophyte initially syncytial, walls then surrounding individual nuclei; embryo cellular ab initio, suspensor short-minute, embryonic axis straight [shoot and root at opposite ends], primary root/radicle produces taproot [= allorhizic], cotyledons 2; embryo ± dormant; chloroplast ycf2 gene in inverted repeat, trans splicing of five mitochondrial group II introns, rpl6 gene absent; ??whole nuclear genome duplication [ζ - zeta - duplication], 2C genome size (0.71-)1.99(-5.49) pg, two copies of LEAFY gene, PHY gene duplications [three - [BP [A/N + C/O]] - copies], 5.8S and 5S rDNA in separate clusters.bipolar [plumule/stem and radicle/root independent, roots positively geotropic];
EXTANT GYMNOSPERMS / PINOPHYTA / ACROGYMNOSPERMAE
Biflavonoids +; cuticle wax tubules with nonacosan-10-ol; ferulic acid ester-linked to primary unlignified cell walls, silica usu. low; root apical meristem organization?, protophloem not producing sieve tubes, with secretory cells, sieve area of sieve tube with small pores generally less than 0.8 µm across that have cytoplasm and E.R., joining to form a median cavity in the region of the middle lamella, Strasburger/albuminous cells associated with sieve tubes [the two not derived from the same immediate mother cell], phloem fibres +; sclereids +, ± tracheidal transfusion tissue +, rays uniseriate [?here]; stomatal poles raised above pore, no outer stomatal ledges or vestibule, epidermis lignified; buds perulate/with cataphylls; lamina development marginal; plants dioecious; parts of strobili spirally arranged; microsporangia abaxial, dehiscing by the action of the epidermis [= exothecium]; pollen tectate, endexine lamellate at maturity, esp. intine with callose; ovules aggregated into strobili, erect, pollen chamber formed by breakdown of nucellar cells, nucellus massive; ovules increasing considerably in size between pollination and fertilization, but aborting unless pollination occurs; ovule with pollination droplet; pollen grain germinates on ovule, usu. takes two or more days, tube with wall of pectose + cellulose microfibrils, branched, growing at up to 10(-20) µm/hour, haustorial, breaks down sporophytic cells; male gametophyte of two prothallial cells, a tube cell, and an antheridial cell, the latter producing a sterile cell and 2 gametes; male gametes released by breakdown of pollen grain wall, with >1000 cilia, basal body 800-900 nm long; fertilization 7 days to 12 months or more after pollination, to ca 2 mm from receptive surface to egg; female gametophyte initially with central vacuole and peripheral nuclei plus cytoplasm, cellularization/alveolarization by centripetal formation of anticlinal walls, the inner periclinal face open, with nuclei connected to adjacent nuclei by spindle fibres; seeds "large" [ca 8 mm3], but not much bigger than ovule, with morphological dormancy; testa mainly of coloured sarcoexotesta, scleromesotesta, and ± degenerating endotesta; first zygotic nuclear division with chromosomes of male and female gametes lining up on separate but parallel spindles, embryogenesis initially nuclear, embryo ± chlorophyllous; gametophyte persists in seed; plastid and mitochondrial transmission paternal; genome size [1C] 10< pg [1 pg = 109 base pairs]; two copies of LEAFY gene [LEAFY, NEEDLY] and three of the PHY gene, [PHYP [PHYN + PHYO]], chloroplast inverted repeat with duplicated ribosomal RNA operons, mitochondrial rps3 gene with second intron [group II, rps3i2].
[CUPRESSALES [GNETALES + PINALES]]: tree, branched; compression wood + [reaction wood - much-thickened/lignified fibres on abaxial side of branch-stem junction]; wood pycnoxylic; torus:margo pits + [tracheid side walls], pits bordered; phloem with scattered fibres alone [Cycadales?], resin ducts/cells in phloem [and elsewhere]; lignins with guaiacyl units (G-lignin) [lacking syringaldehyde, Mäule reaction negative]; cork cambium ± deep seated; bordered pits on tracheids round, opposite; nodes 1:1; axillary buds + (0); leaves with single vein, fasciculate, needle-like or flattened; plants monoecious; microsporangiophore/filament simple, hyposporangiate; dehiscing by the action of the hypodermis [endothecium]; pollen saccate, exine thick [³2 µm thick], granular; ovulate strobilus compound, erect, ovuliferous scales flattened, ± united with bract scales; ovules lacking pollen chamber, inverted [micropyle facing axis]; pollen buoyant, not wettable, pollen tube unbranched, growing towards the ovule, wall with arabinogalactan proteins; gametes non-motile, lacking walls, siphonogamy [released from the distal end of the tube]; female gametophyte lacking chlorophyll, seed coat dry, not vascularized; embryo initially with 2 to 4 free-nuclear divisions, with upper tier or tiers of cells from which pro- or secondary suspensor develops, elongated primary suspensor cells and basal embryonal cells [or some variant]; germination phanerocotylar, epigeal, (seedlings green in the dark); one duplication in the PHYP gene line; germination phanerocotylar, epigeal, (seedlings green in the dark).
[GNETALES + PINALES]: tracheid side wall pits with torus:margo construction, bordered; phloem fibres 0; microsporangiophore/filament simple with terminal microsporangia; microsporangia abaxial, dehiscing by the action of the hypodermis [endothecium]; lhcb 3 and 6 genes not functional/lost [light harvesting genes], chloroplast ndh genes lost/pseudogenized, rpl16 gene lost.
PINALES Link / Conifers I - Main Tree.
Ectomycorrhizal association +; xylem resin ducts +, inducible, (also constitutive); sieve cells with nacreous walls, sieve tube plastids also with protein fibres; lamina vascular bundle surrounded by sheath; 2 microsporangia/microsporophyll, sporangia superficial, pollen saccate, exine thin [2³ µm] except distally, alveolar/honeycomb; bracts free from the ovuliferous scale, ovules 2/bract scale; free-nuclear stage with only four nuclei [= embryo tetrad]; seeds winged, wing terminal, developing from adaxial side of scale, cotyledons (2-)4-11(-20); chloroplast IRb copy lost. - 1 family, 11 genera, 231 species.
Phylogeny. For information on and relationships between the other major seed plant groups, see also angiosperms, Cupressales, Cycadales, Ginkgoales and Gnetales.
Synonymy: Abietales Link - Pinidae Cronquist, Takhtajan, & Zimmermann - Pinopsida Burnett - Pinophytina Reveal
PINACEAE F. Rudolphi - Back to Pinales
(Plant deciduous), (short shoots +); specialized resin diterpenes, e.g. with abietane/pimarane skeletons, biflavonoids 0; sieve cells with nacreous walls, sieve tube plastids also with protein fibres; phloem resin ducts +, constitutive or inducible; phloem fibres 0; sclereids with intracellular calcium oxalate crystals, etc.; axillary buds common, (producing short shoots, spur shoots); pollen saccate, exine thin [2³ µm] except distally, alveolar/honeycomb; (pollination droplet 0); seed cones terminal (axillary), persistent; seeds 2/scale, dry, wing (developing from integument), (0); (integument with resin canals); n = 12, nuclear genome size [1C] 9-36 pg; chloroplast transmission maternal, PHYP gene duplicated.
11 [list]/231. North Temperate (map: from Florin 1963; Farjon 1984, 1990a). [Photos - Collection.]
Age. Magallón et al. (2013) suggested an age of (161.2-)153.8-153.1(-150.1) Ma for crown Pinaceae, He et al. (2012) an age of around 237 Ma. Various divergence estimates were provided by Gernandt et al. (2008), e.g. dates of ca 184 Ma (Jurassic) or ca 136 Ma, while around 175 Ma is the estimate in Leslie et al. (2012) similar to the estimate of ca 172 Ma in Ran et al. (2018a), not that different from the estimate of (226.6-)187.2(-155.2) Ma in Leslie et al. (2018); crown and stem ages of 100 and 263 Ma respectively were suggested by Quirk et al. (2012); see also Tedersoo and Brundrett (2017). Ca 48 Ma is the estimate in Evkaikina et al. (2017), (266.9-)206.3(-168) Ma in Ran et al. (2018b), 220-191.4 Ma in Semerikova et al. (2018) and (233.4-)183.3(-150) m.y. (Lutzoni et al. 2018).
Fossils assigned to Pinaceae have been dated to around 155 Ma (Rothwell et al. 2012; see also Miller 1999).
1. Abietoideae Sweet
Taproot with a single central resin canal; (resin canals in wood); lamina (apically with 2 small teeth/lobes); two-year reproductive cycle (three-year, fertilization in 3rd year - Cedrus); (pollen with circular inflated frill - Tsuga, not buoyant, wettable); seed cones usu. erect, (not persistent); resin vesicles in seed coat; (germination hypogeal - Keteleeria); (n = 22 - Pseudolarix).
5/64: Abies (48). North temperate to boreal, mountains, Central America, North Africa.
Age. He et al. (2012) suggested an age of ca 200 Ma, Gernandt et al. (2008) ages of ca 172 or ca 109 Ma, Ran et al. (2018b) ages of (232.2-)170.2(-117.2) Ma, Lutzoni et al. (2018) ages of (233.4-)183.2(-150) Ma and Leslie et al. (2018) ages of (185.3-)140.4(-92.7) Ma for the beginning of Abietoideae diversification.
Synonymy: Abietaceae Gray, Cedraceae Vest
2. Pinoideae W. Hochst.
Branchlets ultimately abscise [cladoptosis] or not: taproot with resin canals associated with protoxylem poles; resin canals in wood; leaves petiolate, lamina (apparently with two vascular bundles); two-year reproductive cycle (three-year, fertilization in 3rd year - Pinus); (pollen not saccate, atectate, exine granular - Larix, Pseudotsuga); pollen chamber formed by breakdown of nucellar tissue [Pinus, Picea]; (pollen not buoyant, pollination drop 0, exine shed during microgametophyte germination - Larix, Pseudotsuga); seed cones often pendulous; (n = 13 - Pseudotsuga); chromosomes large, 4.4-16.2 μm long; plastid transmission biparental; (mitochondrial transmission maternal - Pinus).
5/167: Pinus (113), Picea (38). North temperate to Boreal, mountains, to West Malesia.
Age. Approximate ages for crown-group Pinoideae are ca 168 or ca 133 Ma (Gernandt et al. 2008), ca 155 Ma (He et al. 2012), (203.7-)170(-145.7) Ma (Leslie et al. 2018) and (236.2-)185.4(-154-5) Ma (Ran et al. 2018b).
Synonymy: Piceaceae Gorozhankin
Evolution: Divergence & Distribution. For more ages, see Leslie et al. (2018), and these authors also evaluate the rich fossil record which, however, shows only limited congruence with the ages they suggest. There may have been extinction after initial diversification, generic-level crown-group diversification taking place within the last 50 Ma or so - and Pinaceae themselves have a stem ca 110 Ma (Les;lie et al. 2018: no Gnetales). Similarly, despite the Triassic-Jurassic crown-group age for Pinaceae suggested by Semerikova et al. (2018), these authors thought that diversification began around the Palaeogene-Neogene transition, a mere ca 23 Ma, while Crisp and Cook (2011) estimated.
Pinus yorkshirensis, a cone associated with needles in Lower Cretaceous deposits 131-129 Ma, formed a polytomy with extant and some other fossil species of the genus in morphological analyses (Ryberg et al. 2012), indeed, in morphological analyses, there was no strong support for Cretaceous fossils ascribed to the genus to nest within it (Klymiuk et al. 2011; Ryberg et al. 2011, and see Hilton et al. 2016 and references in Saladin et al. 2017). However, Gernandt et al. (2018b) found that P. yorkshirensis nested within crown-group Pinus, albeit with little support, as did a number of other fossils.
However, ages suggested for the diversification of Pinus in particular are all over the clock. Thus stem ages for Pinus are around 95 or 73 Ma (B. Wang & Wang 2014), ca 126 Ma (He et al. 2012), ca 140 Ma (X.-Q. Wang et al. (2000), ca 123 or 155 Ma (Gernandt et al. 2008) or ca 180 Ma (Lockwood et al. 2013: Picea is sister). On the other hand, Naumann et al. (2013) date the Pinus/Picea split to around 33.1-29.3 Ma, although angiosperms were the focus of this study. More: A stem-group age for Pinus of (132-)128(-124) Ma was suggested by Eckert and Hall (2006), while Crisp and Cook (2011) suggested that Pinus and Picea diverged around the K/C boundary ca 65 Ma. Turning to crown Pinus, estimates in Gernandt et al. (2008) are ca 87-72 Ma, and here and elsewhere its stem can be very long - in this case, ca 70 and 50 Ma respectively. Other estimates are much older, 165-148 Ma, or (144-)125, 112(-5) Ma (Saladin et al. 2017: another estimate, not favoured, ca 90 Ma) and others younger (85-)45(-25) Ma in Stevens et al. (2016: c.f. p. 1614 and Fig. 1A). Willyard et al. (2007) estimated upper (permineralized wood) and lower dates for divergence of the two subgenera of 85 and 45 Ma respectively (for the latter, see also Magallón & Sanderson 2005), although there were bouts of speciation much later. On the other hand, Millar (1998) suggested that this divergence and that of some of the sections had occurred by the middle of the Cretaceous. Crown-group Pinus is estimated to be (96-)89(-80)Ma by He et al. (2012; age rather similar in Gallien et al. 2015); the age of (80.1-)58.8(-45) Ma was suggested by B. Wang and Wang (2014: some estimates older), with most BEAST crown-group ages for both subgenera being 22-20 Ma, although some are as much as 50 Ma. Fossils of crown-group Pinus have been dated to 140-133 Ma (Ryberg et al. 2012; Falcon-Lang et al. 2016a, b, c.f. Hilton 2016) and those of Picea, at ca 136 Ma (Klymiuk & Stockey 2012), are similar in age. For other divergence times within Pinaceae, see also X.-Q. Wang et al. (2000), Lin et al. (2010), Saladin et al. (2017), Semerikova et al. (2018), and Ran et al. (2018b) and references.
For a discussion on the biogeography of the family, see X.-Q. Wang and Ran (2014). Pinus seems to have been a mid-latitude (30-50o N) plant in the Cretaceous, but in the warm Palaeocene and Eocene it retreated to higher latitudes, although also persisting near the equator. With the climatic deterioration of the Late Eocene-Oligocene, it moved back to mid latitudes while remaining at higher latitudes (Miller 1993), so Pinaceae could be quite common in high latitude Canadian Eocene floras (N. McIver & Basinger 1999). He at al. (2012) looked at the origin of fire-associated traits in Pinus, and found that thick bark characterised the whole genus, with its origin being somewhere between 126-89 Ma (age spreads greater), while very thick bark, branch shedding and serotiny were common in subgenus Pinus, whose diversification was dated at (96-)89(-80) Mya; grass-like seedlings were uncommon (He at al. 2012 noted that thick bark and serotiny were found in a few other Pinales). In the mid Cretaceous the presence of shrubby angiosperms and ferns may have increased the prevalence of intense and rapidly-spreading fires that seriously affected conifer forests, indeed, traits for various aspects of fire resistance in Pinus seem to have evolved then, even if some conifer groups may have been driven to extinction (Gernandt et al. 2008; Belcher & Hudspith 2016). Le Page (2003; see also X.-Q. Wang et al. 2000) thought that there was an episode of diversification in Pinaceae in the Palaeocene, while Klaus et al. (2017) suggested that ca 4.4 Ma is the estimated median node age in the genus. Pinus now has a centre of diversity in Mexico and Central America, almost 50 species being native there, and of which ca 3/4 are endemic or practically so; Cupressaceae are also quite speciose (Farjon & Styles 1997; Perry et al. 1998; Gernandt & Pérez-de la Rosa 2014).
Lockwood et al. (2013) dated diversification of Picea to beginning in the middle Oligocene, only (37-)28(-21) Ma, however, the oldest fossils in this clade are ca 130 Ma (Klymiuk & Stockey 2012) - a ca 100 Ma stem (see also Leslie et al. 2018)? In Abies there is weak support for the Californian endemic A. bracteata being sister to the rest of the genus, and section Balsamea may be of hybrid origin (Xiang et al. 2014); A. bracteata tended to be associated with a New World clade, the rest of the genus being a largely Old World clade and movement from the New to the Old World being responsible for the topological conflicts between the mitochondrial and the chloroplast plus nuclear trees (Semerikova et al. 2018). Crown-group Abies is estimated to be (73.4-)48.6(-33.7) Ma (Xiang et al. 2014) or (24.5-)17.7, 16.2(-13.5) Ma (Semerikova et al. 2018)...
Ran et al. (2018b) outline the distributions of a number of features within the two subfamilies; these have been incorporated into the characterizations.
Nuclear genome size in Pinus directly or indirectly correlates with a number of other features. Smaller genomes are associated with small seeds, wind (not animal) dispersal, invasiveness, fast growth, etc.; larger genomes are commoner in subgenus Strobus, which has genomes averaging ca 32.8 pg compared to those of subgenus Pinus at 27 pg (Grotkopp et al. 2004). In gymnosperms in general, rates of genome change are low, as are speciation rates, the two being correlated; Pinaceae have overall the lowest speciation rates among land plants (Puttick et al. 2015) in clades of any size.
Ecology & Physiology. For general information, see papers in Richardson (1998: Pinus), Andersson (2005), and especially Brodribb et al. (2012) and Augusto et al. (2014); the ecology of Pinaceae along with that of other conifers is discussed briefly above and that of ECM Pinaceae in particular is also discussed elsewhere. The environmental impact of these ECM relationships is of considerable interest. Thus Augusto et al. (2014) date confirmed ECM symbioses in gymnosperms - these would be largely Pinaceae - to the mid-Cretaceous some 115 Ma, probable ECM symbioses are dated to over 200 Ma in the Late Triassic, while possible ECM symbioses are dated to the Permian, over 250 Ma. At the same time Augusto et al. (2014) warn about extrapolating from the ecophysiological proclivities of modern gymnosperms to those of early gymnosperms.
Pinaceae are a noted ectomycorrhizal (ECM) clade and they dominate huge areas of mostly cool-temperate and boreal forests in the northern hemisphere. They are the major component of the boreal forest/taiga biome in particular, a very young biome that has formed within the last 12 Ma as warm temperate broadleaf evergreen and mixed forests contracted, the climate drying and cooling (Taggart & Cross 2009; Pound et al. 2012). However, in suitable conditions Pinus-dominated forests in particular occur much further south, the plants tolerating nutrient-poor soils and also quite dry climates, hence their current diversity in Mexico, their dominance in parts of the Mediterranean, and they also grow in Costa Rica (Janzen 1983) and even south of the equator, as in montane Sumatra (Maps in White et al. 2000; Andersson 2005; see also Richardson & Rundel 1998 for Pinus). For the most part Pinaceae are unable to compete in tropical broad-leaved rain forests (but see the relatively broad-leaved P. krempfii: Brodribb & Feild 2008).
The association with ECM fungi is central to understanding the ecology of Pinaceae. As Read (1998: p. 328) noted, "pine roots are simply food bases which nourish an extremely dense mycelial system", the mycelium:root ratio being something like 200,000:1 on a soil volume basis. The ectomycorrhizae aid in the uptake of both phosphorus and nitrogen, as well as helping the plants deal with the solubilization of toxic metals in the low pH soils that develop in pine-dominated communities (Read 1998; see also Scholes & Nowicki 1998). For the complex interactions between fungal composition, species diversity, productivity, soil moisture and carbon content in Pinus sylvestris forests, see Hiiesalu et al. (2017). Pinaceae thrive in high-light conditions; they have high leaf mass per unit area and also a very high leaf area index, and although their seedlings have lower photosynthetic rates than those of angiosperms they tolerate leaf water stress better (Fu et al. 2012; see also Rundel & Yoder 1998). Longevity of pine and spruce needles increases in colder, northern latitudes (Picea needles may live for 12 years or more - Reich et al. 2014a). W. Chen et al. (2016) noted that the three ECM Pinaceae included in their study of nutrient uptake from the soil had thick to very thick first-order roots compared with other ECM plants and showed little response in terms of either ECM or rootlet proliferation in an environment where nitrogen was patchily distributed. They suggested that this may be because in places where Pinaceae normally grow the soil is more homogeneous and has large amounts of persistent leaf litter. N derived directly from rock can greatly increase ecosystem C storage in coniferous forests, and such forests grow in parts of the globe where relative increase in total N coming from rock breakdown is highest, sometimes over 100% (Morford et al. 2011; Houlton et al. 2018).
Many Pinaceae tolerate burning, indeed, fossils of Pinus mundayi, 140-133 Ma, consist of charcoalified remains (Falcon-Lang et al. 2016a). Fires open the forest canopy, so making conditions suitable for Pinus in particular, many species of which are adapted to fire-prone environments (Brodribb et al. 2012; see also Agee 1998; Schwilk & Ackerley 2001; Keeley 2012; Pausas 2015). He et al. (2012; see also Bond & Midgley 2012) thought that thick bark resistant to low intensity fires and the shedding of dead lower branches that would tend to prevent crown fires evolved in Pinus around (147-)126(-105) Ma; this is the age of stem Pinus, so it assumes that evolution of these features occurred as the genus split from the [Picea + Cathaya] clade. Very thick bark and serotinous cones are an ecological syndrome adapted to high intensity (crown) fires, and this syndrome is dated to (96-)89(-80) Ma, the age of crown-group Pinus (He at al. 2012). Those juveniles that have long and very dense needles covering the growing point (the grass stage) can also tolerate burning. Interestingly, although Pinus with its long needles has relatively well-aerated and very flammable litter like that of many/most other gymnosperms, leaves/needles of many other Pinaceae are smaller and the litter is compact and much less flammable (Cornwell et al. 2015). When the phylogeny of Pinaceae settles down, one can start thinking about the evolution of this set of traits - small needles and non-flammable litter are probably derived, but what about the situation in Pinus?
Estimates of live above-ground biomass in Pinaceae-dominated forests are in the order of 0.8-0.9 x 106 kg ha-1, Pseudotsuga menziesii perhaps even reaching 1.6 x 106 kg ha-1 (see Franklin & Dryness 1973). Figures for the total above + below ground carbon in boreal forests are about 505 PgC, ca 34.2 kgC m-2, and a mean turnover time of (45.4-)53.3(-73.4) years (Carvalhais et al. 2014: tables S1 and S2). The fraction of biomass in the foliage decreases with latitude, that in the root tends to increase, both changes connected with the increased longevity of the needles and associated low values of new leaves produced annually in far northern conifers (Reich et al. 2014a: p. 13705 has it backwards; see Reich 2014b: fig. 2). Accumulation of non-flammable litter under genera like Tsuga and Picea can be massive, and it can also protect the trees against ground fires, while litter of Pinus, much more flammable, accumulates less (Cornwell et al. 2015 and references). Wood of Pinaceae, as in other conifers, is broken down mostly by brown rot fungi. These fungi cannot degrade lignin, but readily break down cellulose and hemicellulose, leaving behind brown, crumbly detritus that is very rich in lignin and resistant to decay (Boddy & Watkinson 1995; see above).
Associated with the tolerance of many Pinaceae to burning is the fact that a number of species of Pinus in particular are pioneer plants that regenerate soon after a burn, and they can also be invasive species. Particularly in such situations, an association between Pinaceae and ECM suilloid basidiomycetes (including genera like Rhizopogon and Gomphidium; see also below) is evident; Suillus in particular is noted for its association with Pinus, and its spores seem to be very widely dispersed (Hayward et al. 2015).
Complex ECM connections and networks can be built up, for example, fungi associated with Ericaceae-Arbutoideae in western North America may also be ECM associates of Pinus (Bruns et al. 2002; Kennedy et al. 2012 and references), and such connections have important implications for forest regeneration. ECM associates of Picea may simultaneously be ericoid mycorrhizal associates on Ericaceae, with carbon and nitrogen moving between the two plants (Grelet et al. 2009, 2010), and fungi that form ericoid mycorrhizae can be endophytic in Picea (Vohnik et al. 2013). The oldest and the youngest individuals in Pseudotsuga menziesii forests may be linked by ECM networks (Belier et al. 2010), although this may preferentially benefit the larger individuals (see Weremijewicz et al. 2016: there are similar phenomenon in AM associations).
Recent work is showing that one species of ascomycete can form ERM (ericoid mycorrhizal), endophytic or ECM associations, the latter two in particular with Pinaceae (e.g. Vrålstad et al. 2000, 2002; Grelet et al. 2009; Perotto et al. 2018; Martino et al. 2018), growing in the same habitat, indeed, Ericaceae and Pinaceae often grow together. Furthermore, dark septate endophytes, ECM and ERM commonly have melanin, a substance particularly resistant to degradation, in their hyphae (e.g. Butler & Day 1998; Read et al. 2004; Bardgett et al. 2014; Clemmensen et al. 2014; Peter et al. 2016; Lindahl & Clemmensen 2017; Martino et al. 2018), and so C in these hyphae turns over more slowly than that in AM hyphae (Phillips et al. 2013; Fernandez et al. 2013, 2016; Fernandez & Kennedy 2018). Fernandez and Koide (2014) found that amounts of melanin, along with those of N, determined the rate of hyphal breakdown, suggesting that from this point of view melanin was an analogue of lignin, being notably decay-resistant (see also Fernandez et al. 2016). Bjorbækmo et al. (2010) and Timling & Taylor (2012) noted the high frequency of melanized fungi and dark septate endophytes in high northern latitudes where Pinaceae often dominate, melanin being an important component of the sequestered carbon in at least some older boreal forests (Read et al. 2004; Clemmensen et al. 2014; Fernandez et al. 2014, 2016; Lindahl & Clemmensen 2017).
Interestingly, the particular ECM fungal associates of individuals of a spermatophyte ECM species may depend on the genotype of the latter. Thus the genotypes of seedlings of pinyon pines (Pinus edulis) varied, but resembled those of their parents, which were either drought-tolerant, the basidiomycete Rhizopogon roseolus being prominent in their ECM community, or drought-intolerant, two species of the ascomycete Geopora then being prominent (Gehring et al. 2017a). There may be extensive mortality of ECM conifers, including Pinus edulis, under drought conditions (McDowell et al. 2016), and under such conditions P. edulis, for instance, would be replaced by the arbuscular mycorrhizal Juniperus (Gehring et al. 2017b). This has additional consequences, since litter of the AM juniper has a lower C:N ratio than that of the ECM Pinus edulis and decomposes faster (Gehring et al. 2017b and references), and there are also differences in root characteristics, e.g. in fine root diameter - rather narrower in ECM plants here (Valverde-Barrantes et al. 2017). Furthermore, the pinyon jay is closely associated with P. edulis whose seeds make up an important component of its diet (Ligon 1978 - see also below).
Given the close association of ECM fungi and Pinaceae, knowledge of the age of the clades of both is of interest. Crown group ages for the origins of ECM clades of Agaricales were split about equally between the Late Cretaceous and Eocene, and for nearly all a Jurassic origin could be rejected; Pinaceae-associated fungi were linked with both the Eocene and the Late Cretaceous dates (Ryberg & Matheny 2012). The ECM \sebacina clade (= Sebacinaceae - Weiß et al. 2016) in Sebacinales seems to have evolved on North American temperate Pinaceae (87-)57, 45(-30) Ma (Tedersoo et al. 2014a: stem and crown fungal ages). Diversification rates in the basidiomycete Russula are highest in extratropical lineages/those associated with Pinaceae (Looney et al. 2015). However, many estimates suggest that Pinaceae had begun diverging long before these fungal dates (see above). Given current uncertainties over details of crown Pinaceae diversification, the relation between the evolution of ECM fungi and Pinaceae remains unclear, although the ECM association can be thought of as an apomorphy for the family.
Large stems of some Pinaceae are quite frequently found very close together, whether because of vegetative growth or because of the germination and establishment of seeds from an overlooked animal cache (Tomback & Linhart 1990 and references).
For aging and the bristlecone pine, Pinus longaeva, see Munné-Bosch (2014 and references).
Pollination Biology & Seed Dispersal. See above. Pollination mechanisms are quite diverse (Little et al. 2014). Doyle and O'Leary (1935b) described the distinctive pollination in Larix and Pseudotsuga where the pollen, which lacks sacci, lands on an almost stigmatic extension of the integument, the margins of which tend to inroll; contact with the nucellus may (Larix) or may not (Pseudotsuga) be needed for pollen tubes to develop. The time from pollination to fertilization may be over a year and pollen germination can take months (Little et al. 2014 and references). Comparing the young seed cones of Picea and Abies, Losada and Leslie (2018) found differences in appearance of the cones could be understood in terms of variation in the rate of cone scale development, but it seemed to have little to do with how effective pollination was.
The female cones of several genera of Pinaceae seem to be thermogenic, being up to 150 C warmer than the needles, and as a consequence they emit infrared radiation (Takács et al. 2017) - and for the consequence of that, see below...
For details of seed morphology, dispersal types, etc., and their evolution, see Contreras et al. (2016) and Leslie et al. (2017). The shape of the wings in seeds of Pinaceae is largely determined by the shape of the cone scales (Diedrich & Leslie 2016). A number of species of pine are serotinous, particularly those susceptible to crown fires (e.g. Hernández-Serrano et al. 2013 and literature, see also above). Seeds of ca 20 species of Pinus (nearly all subgenus Strobus) lack wings and are primarily dispersed by nutcrackers and other corvids, and such seeds tend to be larger than those of their winged relatives - from which they have evolved four to twelve times (Contreras et al. 2016; see also Tomback & Linhart 1990; Leslie et al. 2017). One nutcracker may store some 3,200 seeds/hectare - and this is just for one species of pine in one season (Tomback & Linhart 1990); for the relationship between pinyon pines, Pinus edulis, and Clark's nutcracker, see Vander Wall and Balda (1977), and for that between the pine and the pinyon jay, a flock of 250 of which can cache around 4.5 million pine seeds per year (close to 20,000/individual), see Ligon (1978).
Pinaceae tend to show (weak) masting behaviour (Koenig & Knops 2000).
Plant-Animal Interactions. For a summary of insect-pine interactions, see also de Groot and Turgeon (1998). Ambrosia and bark beetles (Curculionidae-Scolytinae: see Wood 1982; Wood & Bright 1992; Six 2012; Huler & Stelinski 2016), highly derived weevils, have a very close association with conifers (Jordal et al. 2011; see also Gohli et al. 2017: Fig. 1). Bark beetles, some 3,700 species, make their gallery systems in the phloem, and members of genera like the North American Dendroctonus and the Northern Hemisphere Ips can be very noxious pests, and a few invade living pines (e.g. Franceschi et al. 2005; Six 2012: for the southern pine beetle, D. frontalis, see Sullivan 2011; Lesk et al. 2017: future spread), interestingly, their gut microbiota is similar to that of other bark beetles like Hylobius (see below), sawflies, etc., all in similar niches (Berasategui et al. 2017 and references). Although the beetles tend to attack relatively few species of conifers, outbreaks can be devastating, colonizing beetles being attracted to trees by pheromones produced by beetles that are already there, and in such situations they may be able to overwhelm the defences of even healthy trees (Kelley & Farrell 1998 for host specificity; Franceschi et al. 2005; Sullivan 2011; Raffa 2014). Drought conditions may also make the trees more susceptible to attack, but other factors must also be involved (Netherer et al. 2015); unhealthy trees have fewer rewards for the beetles than do healthy trees. Bristlecone pine, Pinus longaeva, has high levels of constitutive expression of potential defensive compounds like (+)-α-pinene in its phloem unlike the other pines growing with it - it has over twenty times the amount in limber pine, P. flexilis, for example - and it is not attacked by Dendroctonus (Bentz et al. 2016). However, as Raffa (2014) notes, the relationships between the mountain pine beetle D. ponderosae and pine, for instance, are extremely complex and context-dependent, and how the beetle will react to pines such as the white pine, P. albicaulis, that it encounters as its range changes is not easy to predict. Many aspects of these relationship are mediated by terpenoids, whether produced by the weevil as pheromones or pine, importantly, terpenoid concentrations are affected by a variety of bacteria which metabolize particular terpenoids, apparently using them as a carbon source. Furthermore, enemies of the beetles are attracted by plant volatiles induced by hebivores and by beetle pheromones (Raffa 2014). The pine weevil Hylobius is an important pest of conifers in Europe, the adult in particular killing seedlings and saplings, and its gut microbiota, too, thrive on the diterpenes the weevil ingests, increasing the number of eggs it can lay (Berasategui et al. 2017).
Ambrosia beetles are associated with blue-stain fungi, mostly ascomycetes such as Ophiostoma, Ceratocystis (immediately unrelated) and some yeasts (e.g. Rivera et al. 2009 for the variety of yeasts involved) as well as a few basidiomycetes (there have been at least five origins of being farmed in ascomycetes, two or more in basidiomycetes - Hulcr & Stelinski 2016), and these grow into the sapwood and help hasten the death of the infected tree (Franceschi et al. 2005). The beetles, some 3,400 species, mostly tunnel in dead or dying wood, although early-branching members of the ambrosia beetle clade may live in phloem; both larvae and adults obtain all their nutrition from the fungi. Adult beetles have intricate cuticular invaginations in which they carry a fungus inoculum that infects the trees, and the beetle larvae eat yeast-like bodies proliferating from the cultivated fungi in the galleries (Jordal et al. 2000; Cognato et al. 2011 and references); the mouth-parts of the weevil are also much modified. Interestingly, females of the beetle Xylosandrus germanus preferentially attack trees that have high ethanol, a product of anaeroic respiration that is particularly abundant in stressed plant tissue. Its fungal associates like Raffaelea and Ambrosiella can detoxify alcohol, and they also produce it. However, ethyl alcohol is toxic to the possible competitors of these fungi such as Aspergillus in the beetle galleries (Ranger et al. 2018). Not only beetles and fungi, but bacteria (some nitrogen-fixing, as in Dendroctonus - Berasategui 2017 and references), parasitoids of the beetles, and fungus-eating nematodes all form part of a very complex association. Trees suffering from stress, as well as recently-sawn timber, are the prime targets of the weevils (Hulcr & Stelinski 2016). Overall, angiosperm hosts are more common, and the evolution of the ambrosia feeding habit, which happened 8 times or more (ca 15< times - Hulcr & Stelinski 2016), is associated with shifts to angiosperms (Six 2012); development of fungus cultivation is unreversed (Beaver 1989; Farrell et al. 2001; Jordal et al. 2008 and references, 2011; Gohli et al. 2017).
Understanding the details of the evolution of the defence system against such weevils depends on our knowledge of conifer phylogeny (e.g. Hudgins et al. 2004), and this is currently unclear. Hudgins et al. (2003, 2004) examined the diversity of bark beetles in conifers in the context of various plant structures that might be defences against such beasts. The beetles eat the wood despite the resin ducts in both phloem and xylem in Pinaceae (e.g. Hudgins et al. 2004), although paradoxically other Pinales, which have resin ducts only in the xylem, nevertheless harbour a lower diversity of these beetles. There are also intracellular crystals, phenolics in phloem-associated cells, etc., which could be protective. Keeling and Bohlmann (2006a, esp. b) describe terpenoid diversity and conifer defence mechanisms, a complex subject; it is unclear just what is responsible for the considerable diversity of terpenoids here, although multisubstrate and multifunctional enzymes involved in terpenoid synthesis in Picea sitchensis (Sitka Spruce), for example, may well be responsible (Hamberger et al. 2011).
Despite these defences, blue-stain fungi, species from a few unrelated ascomycete genera that are carried by the beetles, can quickly invade the sapwood and render it non-functional, basically clogging it up and killing the plant surprisingly quickly. Some, at least, of these fungi (e.g. Endoconidiophora polonica on Picea abies, Norway spruce), detoxify the plant's defences against the weevil Ips typographus by beginning the breakdown of stilbenes (in the phenolic defences) and flavonoids (in the resin defences), i.e. the two major components of the plant's defences (S.-H. Li et al. 2012; Keeling & Bohlmann 2006a). Genes involved in the synthesis of such compoounds are expressed in the infected pine, but nevertheless the amount of the products decline in the pine as they are used up by the fungus (Wadke et al. 2016), so neutralizing these defences against the weevil (DiGuistini et al. 2011; Wadke et al. 2016). See also Wood (1982) and Wood and Bright (1992) for the weevils.
The tortricid moth Choristoneura has twice moved from angiosperms, where it is a generalist feeder, on to Pinales, where pines and spruce are its favourites and where it can cause serious damage. These shifts have been dated to ca 11 Ma, although divergence in the North American spruce budworm complex, one of the clades involved, has been dated to to a mere ca 3.5 Ma (Fagua et al. 2018). Endophytes of Picea (spruce) produce several metabolites toxic to the eastern spruce budworm (J. D. Miller et al. 2002; Findlay et al. 2003; Sumarah et al. 2010).
Iason et al. (2011) tested monoterpenes, common in pines, for protection against herbivory by capercaillie, bank voles, slugs, or red deer; some, but not all, worked (see also Hamberger et al. 2011: defensive properties of diterpene resin acids). Pine needle phenolics and pine stem resins are constitutively more abundant in Nearctic than in Palaearctic Pinus, but there was no difference between the two groups in how inducible these defences were (Carrillo-Gavilán et al. 2014: seedlings examined). Mumm and Hilker (2006) discuss the chemical defence of pines against foliovores in particular; for conifer exudates, see Lambert et al. (2007a).
The female cones of several genera of Pinaceae, apparently thermogenic and up to 150 C warmer than the needles, emit infrared radiation, so making the cones very conspicuous and attracting a hemipteran bug, Leptoglossus occcidentalis, which has IR receptors - it is a seed predator (Takács et al. 2017). Turgeon et al. (1994) noted that ca 85% of the insects recorded as eating conifer cones had been recorded from Pinaceae, but that was probably due to the economic importance of the family; they also noted that almost as many hymenopteran parasitoids of these insects had also been recorded.
Some 70 species of Adelgidae (aphids) are restricted to Pinaceae, and include Adelges piceae and A. tsugae, serious introduced pests in North America, the wooly adelgid, Adelges tsugae, being a major pest of hemlock, Tsuga canadense (Havill et al. 2007). There are five different generations in a single life cycle, the sexual, gall-forming generation being on Picea; as with other aphids, vertically transmitted bacteria are part of this ecosystem (Havill & Foottit 2007). Cinara, a genus of lachnine aphids with about 250 species, radiated on conifers beginning ca 50 Ma (Meseguer et al. 2015; ) or (88.5-)78.5(-68.5) Ma (R. Chen et al. 2016). It and other eulachnines (all told, ca 290 species) grow only on conifers, but they are embedded in a clade in which the original host may have been angiosperms (R. Chen et al. 2016). Cinara itself is found mainly on Pinus, perhaps its original host, and also Abies and Picea, although some species feed on Cupressaceae (Meseguer et al. 2015; R. Chen et al. 2016). Cinara species live mosstly in the bark while other eulachnines feed on needles of Pinaceae alone (R. Chen et al. 2016). For speciation of Cinara, where closely-related species are found on different hosts, see Favret and Voegtlin (2004).
Cecidomyiid gall midges are quite common on North American members of the family (Gagné 1989). See Powell et al. (1999) for other insect-conifer associations.
Most species of the dwarf mistletoe Arceuthobium (Santalaceae-Visceae) parasitize Pinaceae, with a few species also growing on Juniperus (Cupressaceae - Farjon 2008); they can be serious pests of Pinus in particular (Unger 1992; Harrington & Wingfield 1998).
Bacterial/Fungal Associations. Ectomycorrhizal associations are common in Pinaceae, and appropriate ECM fungi may have to be introduced if Pinus, for instance, is to be grown successfully in areas in which it normally does not grow (see Hayward et al. 2015: not always necessary). The beneficial effects of the boletes Suillus and Rhizoderma is particularly evident (Hoeksema et al. 2019: meta-analysis), indeed, suilloid fungi are notably common on Pinaceae, perhaps because the fungi establish ECM asssociations in early successional situations (Bruns et al. 2002; Hayward et al. 2015). Overall ECM fungal diversity may be low in such situations, but this is by no means always so for pine ECM communities (D. L. Taylor et al. 2013; Anderson et al. 2013). Garcia et al. (2015 and references) suggest that the establishment of ECM associations may differ from those in flowering plants, genes of the common symbiotic signalling pathway (CSSP) (for both ECM and AM associations) not being involved. Pinus and Larix in particular may also form ectendomycorrhizal associations with an ascomycete (Peterson 2013). As in other ECM associations, the complexity of pine-ECM fungus networks may be considerable (Simard et al. 2012). Thus Simard et al. (1997) found that ca 6.6% of the carbon fixed by Betula papyrifera moved to Pseudotsuga menziesii via their common ECM associate, while 5-15% of fixed 15N2 moved from Alnus glutinosa to Pinus contorta (Ekblad & Huss-Danell 1995), although the ecological significance of the latter is unclear. See also Brundrett (2017a), Tedersoo (2017b) and Tedersoo and Brundrett (2017) for literature, etc., and there is more discussion under Ecology and Physiology above.
Bacteria associated with tuberculate ECM on Pinus contorta, a particular kind of ECM in which a cluster of root tips is surrounded by hyphae, are thought to fix nitrogen (Paul et al. 2007). Strains of Bradyrhizobium are the dominating bacteria in pine forests across North America, and although they are unable to fix nitrogen, they seem to be able to metabolize aromatic carbon sources (VanInsberghe et al. 2015). Some Pinaceae have foliar bacterial endophytes that fix nitrogen (Carrell & Frank 2014). In a final wrinkle of the story of how Pinaceae may acquire nitrogen, Laccaria bicolor, a brown rot fungus, took up nitrogen from springtails that it had first immobilized, and this nitrogen could be transferred to seedlings of Pinus strobus (Klironomos & Hart 2001).
A number of rusts, including those on ferns, have their aecial stages on Pinales, especially Pinaceae (Savile 1979b; Durrieu 1980). These include the white pine blister rust, Cronartium ribicola (alternate host Ribes, Grossulariaceae), introduced to North America around 1900 and now a very serious pathogen of white pine and its relatives (subgenus Strobus) (Harrington & Wingfield 1998; Stevens et al. 2016 and references).
In Pinus strobus endophytes synthesize antifungal metabolites, effective against Microbotryum violaceum, parasitic on some Caryophyllaceae (Sumarah et al. 2010, 2011), and endophyte metabolites in spruce may be toxic to insects (Findlay et al. 2003). However, on occasion dark septate endophytes can reduce the growth of their hosts, although the relationship between the two is complex, being affected by the identity of the host, temperature, whether or not the host has established a relationship with ECM fungi, etc. (Reininger & Sieber 2012 and references).
Harrington and Wingfield (1998) discuss a number of fungal diseases that can seriously affect the growth of species of Pinus.
Genes & Genomes. The rate of change of genome size is faster in Pinaceae than in other gymnosperm groups (Burleigh et al. 2012). Roa and Guerra (2018) note that 45S rDNA sites in Pinaceae tend to be in the middle of the short arms of the chromosomes, unlike other gymnosperms, where they tend to be at the end and the centromere, or angiosperms, where they tend to be near the end. For the nuclear karyotype, see Murray (2013); extensive synteny in Pinaceae persists for a long time. For genome size and evolution in Pinus, see Grotkopp et al. (2004). Genomes can be very large, and transposable elements (LTR - Long Terminal Repeats - retrotransposons, perhaps especially Gypsy elements) may make up around 75% or even more of the genome (Neale et al. 2014; Stevens et al. 2016); this large and extensive TE population may be (mostly) old, but lack mechanisms for its removal (Nystedt et al. 2013). There is extensive duplication of the knox-1 gene within Pinaceae, at least, although more general sampling is needed to pin down the point at which this duplication occurred (Guillet-Claude et al. 2004).
Nkongolo and Mehes-Smith (2012) discuss karyotype evolution in Pinaceae - i.a. they suggest that Pinus has a karyotype that is ancestral for the group as a whole.
The inverted repeat is very much reduced in size here (Jansen & Ruhlmann 2012 for references), and Labiak and Carol (2017) talk about its drastic reduction or complete loss. C. S. Wu et al. (2011a: p. 310 and references) noted that the cpDNAs of Pinaceae "have preserved a rather reduced pair of IRs (236-495 bp) containing only the 3'psbA and trnl-CAU genes", the ndh genes and one copy of the ycf2 gene being lost early on (Wu et al. 2011a); as in Cupressales, there are small inverted repeats (Guo et al. 2014). Braukmann et al. (2009) chart the extent of the loss of the ndh genes (see also Cronn et al. 2008; Hirao et al. 2008), and these genes are also lost in Gnetales - note that some details of the loss of nuclear transcripts encoding NDH proteins differ between the two, and there is also variation in Pinaceae themselves (Ruhlman et al. 2015). Associated with this loss, chloroplast genome rearrangements are notably extensive in Pinaceae (Lin et al. 2010; Wu et al. 2011a, b). For inversions (two) in the plastomes, see Wu et al. (2011a), c.f. Cupressaceae in particular (Wu & Chaw 2016). For biparental plastid inheritance, see references in Sullivan et al. (2017).
Mitochondrial transmission is maternal in Pinus (Neale & Sederoff 1989; X.-R. Wang 1996); B. Wang and Wang (2014) discuss the complex history of mitochondrial inheritance in the genus.
Economic Importance. The majority of the world's lumber comes from softwood, and the majority of that comes from members of Pinaceae (Mullin et al. 2011 and references). Interestingly, over 20% of the species of Pinus alone are invasives, P. radiata, with a narrow native range, being a good example, although it is also planted (Lavery & Mead 1998; Gallien et al. 2015), and this is facilitated by their ability to form ECM associations with Suillus species whose spores are very widely dispersed (Hayward et al. 2015; Peay 2016 and references).
Pinaceae, in North America species of Pinus and Tsuga in particular, can be very heavily infested by bark beetles, a variety of fungi, tortricid moths, dwarf mistletoes, etc. (see above: plant-animal interactions), that kill the plants, especially when they are stressed (e.g. de Groot & Turgeon 1998; Harrington & Wingfield 1998). The effects of these organisms are exacerbated by the tendency of conifers to be locally very abundant, and some herbivore- and pathogen-induced die-offs have been very extensive.
Chemistry, Morphology, etc. The diameter of first order roots seems to vary considerably (W. Chen et al. 2013: rather narrower than co-occuring angiosperms, China, 2016: rather broader than co-occuring angiosperms, U.S.A.). For seedling (?hypocotyl) anatomy of Pinus and Larix, see Miller and Johnson (2017); there is potentially interesting variation in features like the presence of cortical sclereids, pith lignification, and number of protoxylem poles. Schultz (1990) notes that there are no phloem fibres in Pinaceae. Pinus cuticular wax tubules look almost scalloped (c.f. commelinids!), but this is because the tubules are densely aggregated (Wilhelmi & Barthlott 1997). Dörken and Stützel (2012) discuss the anatomy of Pinus needles; needles of subgenus Pinus are often described as having two vascular bundles, but there is a single vascular bundles with two parts separated by a parenchymatic band, the whole being surrounded by a common bundle sheath. Adult plants of Pinus have scale leaves alone on their long shoots; seedings may bear needles directly on long shoots (see also Dörken et al. 2010).
The seed coat of Cedrus is vascularized. The seed wing of Pinaceae is derived from the middle or stony layer of the integument. Cleavage polyembryony is common, as is true polyembryony (more than one archegonium is formed), but the seed generally contains only a single embryo.
For Pinus, see e.g. Mirov (1967: monograph), Richardson (1998: ecology and biogeography), and Farjon (2005a: monograph); for Pinaceae more broadly, see Gernandt et al. (2011b), Farjon (1990, 2008, 2017) and the Gymnosperm Database, all general. For wood anatomy of Abietoideae, see Esteban and de Palacios (2009) and Esteban et al. (2009), for leaf anatomy, see Yao and Hu (1982), for details of reproduction, see Owens and Molder (1979), for aspects of ovuliferous cone morphology and anatomy, see Hu et al. (1989), Napp-Zinn and Hu (1989), and Gernandt et al. (2011a), for the embryo, see Buchholz (1931), for seed coat development, see Owens and Smith (1964).
Phylogeny. Relationships within Pinaceae suggested in the past have depended in part on the kind of data analysed (morphology, molecules) and methods of analysis (parsimony, Bayesian) - see Tsumura et al. (1995), X.-Q. Wang et al. (2000), Rydin and Källersjö (2002), Liston et al. (2006b), and Gernandt et al. (2008, 2016, 2018a, b). For instance, studying the mitochondrial rps3 gene, Ran et al. (2010) found that Larix and Pseudotsuga were sister to all other Pinaceae. However, the main problem is the position of Cedrus with respect to Abietoideae (Abies, Keteleeria, Nothotsuga, Pseudolarix, Tsuga) and Pinoideae (Cathaya, Larix, Picea, Pinus, Pseudotsuga) (Holman et al. 2010). Thus Wang et al. (2000) placed Cedrus sister to the rest of the entire family, Gernandt et al. (2008) and Z.-D. Chen et al. (2016) as sister to Abietoideae (see also C. Hou et al. 2015; Leslie et al. 2018), while Liu et al. (2010) retrieved the clade [Cedrus [Abies + Keteleeria]] as sister to the rest of the family, although Tsuga and Pseudolarix were not sampled; Cathaya and Pinus formed a clade. Holman et al. (2010) nicely summarize the morphological evidence that is compatible with the relationship of Cedrus to either of those groups, or as sister to the whole family; here it is included in Abietoideae.
In the various analyses in Gernandt et al. (2016: inc. morphological analysis with 158 characters, 2018b) the position of Cedrus was uncertain, and the immediate relationships around Pinus the same; fossils - the focus of this study - tended to be unstable in position. Note that fossils assigned to Pityostrobus are scattered through the family phylogeny (Klymiuk & Stockey 2012; Ryberg et al. 2012; Gernandt et al. 2016, 2018b). Gernandt et al. (2016) found that adding morphology to molecular data for extant taxa improved resolution and support, adding fossils to a morphology-only data set for extant taxa decreased support and resolution, when included in joint analyses they reduced support for other relationships in the tree, and using implied weighting (weighting in inverse proportion to homoplasy) improved things - one bottom line is that adding incomplete fossils helps little in phylogenetic analyses.
In a study with exhaustive sampling of conventional Pinaceae and all other Pinales except for Gnetum, etc., Leslie et al. (2012, 2018) found the set of relationships [[Cedrus [Pseudolarix [Nothotsuga + Tsuga]] [Abies + Keteleeria]] [[Pseudotsuga + Larix] [Pinus [Cathaya + Picea]]]]. The same two major groups were recovered by Lockwood et al. (2013), although major groupings were not the focus of that study and details of relationships within the two groups differed; see also He et al. (2012), Klimiuk and Stockey (2012: [Pinus [Cathaya + Picea]]), Ruhfel et al. (2014), C. Hou et al. (2015), Sudianto et al. (2016) and Stevens et al. (2016: [[Abies [Pseudotsuga + Larix]] [Pinus + Picea]]).
For the phylogeny of Pinus, see Price et al. (1998), Syring et al. (2005), Gernandt et al. (2005, 2008, 2011a, 2018a: some conflict between plastid and nuclear genes, b), Eckert and Hall (2006), Parks et al. (2012) and Gallien et al. (2015). Pinus has two subgenera (see Gernandt et al. 2005 for an infrageneric classification). Leaves of subgenus Pinus, the hard pines, apparently have two vascular bundles (but see above), the plesiomorphic condition, while those of subgenus Strobus, the soft pines, have but a single bundle (references in Gallien et al. 2015 for studies on individual subgenera). Lockwood et al. (2013) provide a detailed phylogeny of Picea, sister to Pinus, but Picea was found to be embedded in Pinus by Sen et al. (2016). The recovery of conflicting relationships in this genus may reflect ancient hybridization, mitochondrial introgression and plastome recombination (Ran et al. 2015; Sullivan et al. 2017). Analysis of nuclear ITS variation was largely uninformative in suggesting relationships between sections in Abies, but at lower levels was more useful (Xiang et al. 2009); in a more extensive study (genes from all three compartments), Xiang et al. (2014) largely resolved relationships in the genus.
Classification. If the topology suggested by Leslie et al. (2012) holds up, a two subfamily classification, Abietoideae and Pinoideae, the subfamilies being the two major clades recognized there, is reasonable (see above) - however, confirmation of this topology would be useful...
Fot a sectional classification of Abies, with section Balsamea of suspected hybrid origin, see Xiang et al. (2018). Haploxylon/white/soft pines, with (four to) five (to eight) needles = Pinus subgenus Strobus, Diploxylon/yellow/hard pines, with (one to) two to three needles = Pinus subgenus Pinus.
Botanical Trivia Living up to 4,700 years or more, the bristlecone pine, Pinus longaeva, is the longest-living non-clonal seed plant (Munné-Bosch 2014 and references); its needles, which can live for over 30 years (Hacke et al. 2015), are the longest-lived leaves of all land plants except Welwitschia - and the latter has very odd leaves. The plant does not seem to attract native mountain pine beetles (Dendroconus, see Bentz et al. 2016).