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[[File:Trilete spores.png|thumb|right|A late [[Silurian]] [[sporangium]]. '''Green''': A spore tetrad. '''Blue''': A spore bearing a trilete mark&nbsp;– the <math>Y</math>-shaped scar. The spores are about 30-35&nbsp;μm across]]
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[[File:Plant Diversity (2).svg|thumb|Cladogram of plant evolution]]
{{further|Evolutionary history of life}}
The '''evolution of [[plant]]s''' has resulted in increasing [[Evolutionary grade|levels of complexity]], from the earliest [[algal mat]]s, through [[bryophyte]]s, [[lycopod]]s, [[fern]]s to the complex [[gymnosperm]]s and [[angiosperm]]s of today. While many of the groups which appeared earlier continue to thrive, especially in the environments in which they evolved, for a time each new grade of organisation became more "successful" than its predecessors.
 
In the [[Ordovician]] period, around {{Ma|450}}, the first land plants appeared.<ref>"The oldest fossils reveal evolution of non-vascular plants by the middle to late Ordovician Period (~450-440 m.y.a.) on the basis of fossil spores" [http://www.clas.ufl.edu/users/pciesiel/gly3150/plant.html Transition of plants to land]</ref> These began to diversify in the late [[Silurian Period]], around {{Ma|420}}, and the results of their diversification are displayed in remarkable detail in an early [[Devonian]] fossil assemblage from the [[Rhynie chert]]. This chert preserved early plants in cellular detail, petrified in volcanic springs.<ref>{{cite book |last=Barton |first=Nicholas |authorlink=Nick Barton |year=2007 |title=Evolution |edition= |pages=273–274|url=http://books.google.com/?id=mMDFQ32oMI8C&printsec=frontcover#v=onepage&q&f=false |accessdate=September 30, 2012|isbn=9780199226320}}</ref>
 
By the middle of the Devonian Period, most of the features recognised in plants today are present, including roots, leaves and secondary wood; and, by late Devonian times, seeds had evolved.<ref name="Rothwelletal989">{{cite journal | doi = 10.1086/337763 | last1 = Rothwell | first1 = G. W. | last2 = Scheckler | first2 = S. E. | last3 = Gillespie | first3 = W. H. | year = 1989 | title = ''Elkinsia'' gen. nov., a Late Devonian gymnosperm with cupulate ovules | url = | journal = Botanical Gazette | volume = 150 | issue = 2| pages = 170–189 }}</ref> Late Devonian plants had thereby reached a degree of sophistication that allowed them to form forests of tall trees.
 
Evolutionary innovation continued into the [[Carboniferous]] period and is still ongoing today. Most plant groups were relatively unscathed by the [[Permo-Triassic extinction event]], although the structures of communities changed. This may have set the scene for the appearance of the flowering plants in the Triassic (~{{ma|200}}), and their later diversification in the Cretaceous and [[Paleogene]]. The latest major group of plants to evolve were the grasses, which became important in the mid-Paleogene, from around {{Ma|40}}. The grasses, as well as many other groups, evolved new mechanisms of metabolism to survive the low {{co2}} and warm, dry conditions of the tropics over the last {{Ma|10|million&nbsp;years}}.
 
==Colonization of land{{anchor|land}}==
[[File:Devonianscene-green.jpg|thumb|The Devonian period marks the beginning of extensive land colonization by plants, which through their effects on erosion and sedimentation brought about significant climatic change.]]
Land plants evolved from [[chlorophyte]] algae, perhaps as early as {{Ma|510}};<ref name=Raven2001/> some molecular estimates place their origin even earlier, as much as {{Ma|630}}.<ref name="Clarke2011">{{cite doi|10.1111/j.1469-8137.2011.03794.x}}</ref> Their closest living relatives are the [[charophyte]]s, specifically [[Charales]]; assuming that the Charales' habit has changed little since the divergence of lineages, this means that the land plants evolved from a branched, filamentous alga dwelling in shallow fresh water,<ref name="KCbook
">{{cite book|author=P. Kenrick, P.R. Crane (1997) |title=The origin and early diversification of land plants. A cladistic study. Smithsonian Institution Press, Washington & London|isbn=1-56098-729-4|year=1997|publisher=Smithsonian Inst. Press|location=Washington}}</ref> perhaps at the edge of seasonally desiccating pools.<ref name=Raven2001/> The alga would have had a [[Biological life cycle#Haplontic life cycle|haplontic life cycle]]: it would only very briefly have had paired [[chromosome]]s (the [[Polyploidy#diploid|diploid]] condition) when the [[Ovum|egg]] and [[sperm]] first fused to form a [[zygote]]; this would have immediately divided by [[meiosis]] to produce cells with half the number of unpaired chromosomes (the [[Polyploidy#haploid|haploid]] condition). [[symbiosis|Co-operative interactions]] with [[fungi]] may have helped early plants adapt to the stresses of the terrestrial realm.<ref name=Heckman2001>{{cite pmid|11498589}}</ref>
 
Plants were not the first photosynthesisers on land; weathering rates suggest that organisms were already living on the land {{Ma|1200}},<ref name=Raven2001/> and microbial fossils have been found in freshwater lake deposits from {{Ma|1000}},<ref>{{Walcott 2009|Brasier-1}}</ref> but the [[Isotopic signature#Carbon isotopes|carbon isotope record]] suggests that they were too scarce to impact the atmospheric composition until around {{Ma|850}}.<ref name='Knauth2009'>{{cite doi | 10.1038/nature08213 }}</ref> These organisms, although phylogenetically diverse,<ref name="Battistuzzi2004">{{cite doi|10.1186/1471-2148-4-44}}</ref> were probably small and simple, forming little more than an "algal scum".<ref name=Raven2001/>
 
The first evidence of [[plant]]s on land comes from spores of Mid-Ordovician age (early Llanvirn, ~{{Ma|470}}).<ref name=Gray1985>{{cite journal
| author = Gray, J.
| year = 1985
| last2 = Chaloner
| first2 = W. G.
| last3 = Westoll
| first3 = T. S.
| title = The Microfossil Record of Early Land Plants: Advances in Understanding of Early Terrestrialization, 1970-1984
| journal = [[Philosophical Transactions of the Royal Society B]]
| volume = 309
| issue = 1138
| pages = 167–195
| doi = 10.1098/rstb.1985.0077
| jstor=2396358
| bibcode=1985RSPTB.309..167G
}}</ref><ref name=Wellman2000>{{cite doi |10.1098/rstb.2000.0612}}</ref><ref name="Rubinstein2010">{{cite doi| 10.1111/j.1469-8137.2010.03433.x}}</ref> These spores, known as [[cryptospore]]s, were produced either singly (monads), in pairs (diads) or groups of four (tetrads), and their microstructure resembles that of modern [[Marchantiophyta|liverwort]] spores, suggesting they share an equivalent grade of organisation.<ref name="Wellman2003">{{cite doi|10.1038/nature01884}}</ref> They are composed of sporopollenin&nbsp;– further evidence of an embryophytic affinity.<ref name="Steemans2010">{{cite doi|10.1016/j.revpalbo.2010.07.006 }}</ref> It could be that atmospheric 'poisoning' prevented eukaryotes from colonising the land prior to this,<ref name=Kump2005>{{cite doi|10.1130/G21295.1}}</ref> or it could simply have taken a great time for the necessary complexity to evolve.<ref name=Butterfield2009>{{cite doi|10.1111/j.1472-4669.2009.00188.x}}</ref>
 
Trilete spores similar to those of [[Tracheophytes|vascular plants]] appear soon afterwards, in Upper Ordovician rocks.<ref name='Steemans2009'>{{cite doi | 10.1126/science.1169659 }}</ref> Depending exactly when the tetrad splits, each of the four spores may bear a "trilete mark", a Y-shape, reflecting the points at which each cell squashed up against its neighbours.<ref name=Gray1985/> However, this requires that the spore walls be sturdy and resistant at an early stage. This resistance is closely associated with having a desiccation-resistant outer wall—a trait only of use when spores must survive out of water. Indeed, even those [[embryophytes]] that have returned to the water lack a resistant wall, thus don't bear trilete marks.<ref name=Gray1985/> A close examination of algal spores shows that none have trilete spores, either because their walls are not resistant enough, or in those rare cases where it is, the spores disperse before they are squashed enough to develop the mark, or don't fit into a tetrahedral tetrad.<ref name=Gray1985/>
 
The earliest megafossils of land plants were [[Thallus|thalloid]] organisms, which dwelt in fluvial wetlands and are found to have covered most of an early Silurian flood plain. They could only survive when the land was waterlogged.<ref>{{cite doi|10.1130/2006.2399(02)}}</ref> There were also microbial mats.<ref name="Tomescu2008">{{cite doi|10.1111/j.1472-4669.2007.00143.x}}</ref>
 
Once plants had reached the land, there were two approaches to dealing with desiccation. The bryophytes avoid it or give in to it, restricting their ranges to moist settings, or drying out and putting their metabolism "on hold" until more water arrives. [[Tracheophytes]] resist desiccation: They all bear a waterproof outer cuticle layer wherever they are exposed to air (as do some bryophytes), to reduce water loss, but—since a total covering would cut them off from {{co2}} in the atmosphere—they rapidly evolved stomata, small openings to allow gas exchange. Tracheophytes also developed vascular tissue to aid in the movement of water within the organisms (see [[#xylem|below]]), and moved away from a gametophyte dominated life cycle (see [[#Changing life cycles|below]]). Vascular tissue also facilitated upright growth without the support of water and paved the way for the evolution of larger plants on land.
 
The establishment of a land-based flora caused increased accumulation of oxygen in the atmosphere, as the plants produced oxygen as a waste product. When this concentration rose above 13%, wildfires became possible. This is first recorded in the early Silurian fossil record by charcoalified plant fossils.<ref name=Scott2006>{{cite doi|10.1073/pnas.0604090103}}</ref> Apart from a controversial gap in the Late Devonian, charcoal is present ever since.
 
Charcoalification is an important [[taphonomy|taphonomic]] mode. Wildfire drives off the volatile compounds, leaving only a shell of pure carbon. This is not a viable food source for herbivores or detritovores, so is prone to preservation; it is also robust, so can withstand pressure and display exquisite, sometimes sub-cellular, detail.
 
==Evolution of life cycles{{anchor|phases}}{{anchor|life cycles}}==
{{further|Alternation of generations}}
[[File:Angiosperm life cycle diagram.svg|thumb|[[Angiosperm]] life cycle]]
All multicellular plants have a life cycle comprising two generations or phases. One is termed the '''[[gametophyte]]''', has a single set of chromosomes (denoted&nbsp;'''1N'''), and produces gametes (sperm and eggs). The other is termed the '''[[sporophyte]]''', has paired chromosomes (denoted&nbsp;'''2N'''), and produces spores. The gametophyte and sporophyte may appear identical&nbsp;– homomorphy&nbsp;– or may be very different&nbsp;– heteromorphy.
 
The pattern in plant evolution has been a shift from homomorphy to heteromorphy. The algal ancestors of land plants were almost certainly [[wikt:haplobiontic|haplobiontic]], being haploid for all their life cycles, with a unicellular zygote providing the 2N stage. All land plants (i.e. [[embryophytes]]) are [[wikt:diplobiontic|diplobiontic]]&nbsp;– that is, both the haploid and diploid stages are multicellular.<ref name=StewartRothwell>Stewart, W.N. and Rothwell, G.W. 1993. ''Paleobotany and the evolution of plants'', Second edition. Cambridge University Press, Cambridge, UK. ISBN 0-521-38294-7</ref> Two trends are apparent: [[bryophyte]]s ([[Marchantiophyta|liverwort]]s, [[moss]]es and [[hornwort]]s) have developed the gametophyte, with the sporophyte becoming almost entirely dependent on it; [[vascular plant]]s have developed the sporophyte, with the gametophyte being particularly reduced in the [[seed plant]]s.
 
It has been proposed that the basis for the emergence of the diploid phase of the life cycle as the dominant phase, is that diploidy allows masking of the expression of deleterious mutations through [[Complementation (genetics)|genetic complementation]].<ref>Bernstein H, Byers GS, Michod RE. (1981).  Evolution of sexual reproduction: Importance of DNA repair, complementation, and variation" ''The American Naturalist'' 117(4)  537-549.</ref><ref>Michod RE, Gayley TW. (1992). Masking of mutations and the evolution of sex" ''The American Naturalist'' 139(4)  706-734.</ref> Thus if one of the parental genomes in the diploid cells contains [[mutation]]s leading to defects in one or more [[gene product]]s, these deficiencies could be compensated for by the other parental genome (which nevertheless may have its own defects in other genes).  As the diploid phase was becoming predominant, the masking effect likely allowed [[genome size]], and hence information content, to increase without the constraint of having to improve accuracy of replication.  The opportunity to increase information content at low cost is advantageous because it permits new adaptations to be encoded.  This view has been challenged, with evidence showing that selection is no more effective in the haploid than in the diploid phases of the lifecycle of mosses and angiosperms.<ref name=SzövRiccHockShaw13>{{Cite journal |last=Szövényi |first=Péter |last2=Ricca |first2=Mariana |last3=Hock |first3=Zsófia |last4=Shaw |first4=Jonathan A. |last5=Shimizu |first5=Kentaro K. |last6=Wagner |first6=Andreas |year=2013 |title=Selection is no more efficient in haploid than in diploid life stages of an angiosperm and a moss |journal=Molecular Biology and Evolution |accessdate=2013-06-20 |doi=10.1093/molbev/mst095 |lastauthoramp=yes }}</ref>
 
There are two competing theories to explain the appearance of a diplobiontic lifecycle.
 
The '''interpolation theory''' (also known as the antithetic or intercalary theory)<ref name=Boyce2008/> holds that the sporophyte phase was a fundamentally new invention, caused by the mitotic division of a freshly germinated zygote, continuing until meiosis produces spores. This theory implies that the first sporophytes bore a very different morphology to the gametophyte they depended on.<ref name=Boyce2008/> This seems to fit well with what is known of the bryophytes, in which a vegetative thalloid gametophyte is parasitised by simple sporophytes, which often comprise no more than a sporangium on a stalk. Increasing complexity of the ancestrally simple sporophyte, including the eventual acquisition of photosynthetic cells, would free it from its dependence on a gametophyte, as seen in some hornworts (''[[Anthoceros]]''), and eventually result in the sporophyte developing organs and vascular tissue, and becoming the dominant phase, as in the tracheophytes (vascular plants).<ref name=StewartRothwell/> This theory may be supported by observations that smaller ''[[Cooksonia]]'' individuals must have been supported by a gametophyte generation. The observed appearance of larger axial sizes, with room for photosynthetic tissue and thus self-sustainability, provides a possible route for the development of a self-sufficient sporophyte phase.<ref name=Boyce2008>{{cite journal|title=How green was ''Cooksonia''? The importance of size in understanding the early evolution of physiology in the vascular plant lineage
|author=Boyce, C. K. |doi=10.1666/0094-8373(2008)034[0179:HGWCTI]2.0.CO;2|year=2008|journal=Paleobiology|volume=34|issue=2|pages=179|issn=0094-8373
}}</ref>
 
The alternative hypothesis is termed the '''transformation theory''' (or homologous theory). This posits that the sporophyte appeared suddenly by a delay in the occurrence of meiosis after the zygote germinated. Since the same genetic material would be employed, the haploid and diploid phases would look the same. This explains the behaviour of some algae, which produce alternating phases of identical sporophytes and gametophytes. Subsequent adaption to the desiccating land environment, which makes sexual reproduction difficult, would result in the simplification of the sexually active gametophyte, and elaboration of the sporophyte phase to better disperse the waterproof spores.<ref name=StewartRothwell/> The tissue of sporophytes and gametophytes preserved in the Rhynie chert is of similar complexity, which is taken to support this hypothesis.<ref name=Boyce2008/><ref name=Kerpetal2004>{{cite journal|title=New gametophytes from the Early Devonian Rhynie chert
|author=Kerp, H., Trewin, N. H. & Hass, H.|year=2004|journal=Transactions of the Royal Society of Edinburgh|volume=94|pages=411–428
}}</ref><ref name=Tayloretal2005>{{cite journal|doi=10.1073/pnas.0501985102|title=Life history biology of early land plants: deciphering the gametophyte phase|author=Taylor, T. N., Kerp, H. & Hass, H.|year=2005|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=102|issue=16|pages=5892–5897|pmid=15809414|pmc=556298
|bibcode = 2005PNAS..102.5892T }}</ref>
 
==Evolution of morphology==
 
===Xylem{{anchor|xylem}}===
{{further|Xylem}}
To photosynthesise, plants must absorb {{co2}} from the atmosphere. However, this comes at a price: while stomata are open to allow {{co2}} to enter, water can evaporate.<ref name=Sperry2003>{{cite jstor|3691719}}</ref> Water is lost much faster than {{co2}} is absorbed, so plants need to replace it, and have developed systems to transport water from the moist soil to the site of photosynthesis.<ref name=Sperry2003/> Early plants sucked water between the walls of their cells, then evolved the ability to control water loss (and {{co2}} acquisition) through the use of a waterproof [[plant cuticle|cuticle]] perforated by stomata. Specialised water transport tissues soon evolved in the form of hydroids, tracheids, then secondary xylem, followed by an endodermis and ultimately vessels.<ref name=Sperry2003/>
 
The high {{co2}} levels of Silurian-Devonian times, when plants were first colonising land, meant that the need for water was relatively low. As {{co2}} was withdrawn from the atmosphere by plants, more water was lost in its capture, and more elegant transport mechanisms evolved.<ref name=Sperry2003/> As water transport mechanisms, and waterproof cuticles, evolved, plants could survive without being continually covered by a film of water. This transition from [[poikilohydry]] to [[homoiohydry]] opened up new potential for colonisation.<ref name=Sperry2003/> Plants then needed a robust internal structure that contained long narrow channels for transporting water from the soil to all the different parts of the above-soil plant, especially to the parts where photosynthesis occurred.
 
During the Silurian, {{co2}} was readily available, so little water needed to be expended to acquire it. By the end of the Carboniferous, when {{co2}} levels had lowered to something approaching today's, around 17 times more water was lost per unit of {{co2}} uptake.<ref name=Sperry2003/> However, even in these "easy" early days, water was at a premium, and had to be transported to parts of the plant from the wet soil to avoid desiccation. This early water transport took advantage of the '''cohesion-tension''' mechanism inherent in water. Water has a tendency to diffuse to areas that are drier, and this process is accelerated when water can be [[capillary action|wick]]ed along a fabric with small spaces. In small passages, such as that between the plant cell walls (or in tracheids), a column of water behaves like rubber&nbsp;– when molecules evaporate from one end, they literally pull the molecules behind them along the channels. Therefore transpiration alone provided the driving force for water transport in early plants.<ref name=Sperry2003/> However, without dedicated transport vessels, the cohesion-tension mechanism cannot transport water more than about 2&nbsp;cm, severely limiting the size of the earliest plants.<ref name=Sperry2003/> This process demands a steady supply of water from one end, to maintain the chains; to avoid exhausing it, plants developed a waterproof [[plant cuticle|cuticle]]. Early cuticle may not have had pores but did not cover the entire plant surface, so that gas exchange could continue.<ref name=Sperry2003/> However, dehydration at times was inevitable; early plants cope with this by having a lot of water stored between their cell walls, and when it comes to it sticking out the tough times by putting life "on hold" until more water is supplied.<ref name=Sperry2003/>
 
[[File:banded tube.jpg|thumb|A [[banded tube]] from the late Silurian/early Devonian. The bands are difficult to see on this specimen, as an opaque carbonaceous coating conceals much of the tube. Bands are just visible in places on the left half of the image&nbsp;– click on the image for a larger view. Scale bar: 20&nbsp;μm]]
To be free from the constraints of small size and constant moisture that the [[Ground tissue#Parenchyma|parenchymatic]] transport system inflicted, plants needed a more efficient water transport system. During the early Silurian, they developed specialized cells, which were [[lignin|lignified]] (or bore similar chemical compounds)<ref name=Sperry2003/> to avoid implosion; this process coincided with cell death, allowing their innards to be emptied and water to be passed through them.<ref name=Sperry2003/> These wider, dead, empty cells were a million times more conductive than the inter-cell method, giving the potential for transport over longer distances, and higher {{co2}} diffusion rates.
 
The earliest macrofossils to bear water-transport tubes are Silurian plants placed in the genus ''[[Cooksonia]]''.<ref name=Edwards1992>{{Cite journal |last=Edwards |first=D. |last2=Davies |first2=K.L. |last3=Axe |first3=L. |year=1992 |title=A vascular conducting strand in the early land plant ''Cooksonia'' |journal=Nature |volume=357 |issue=6380 |pages=683–685 |doi=10.1038/357683a0 |bibcode=1992Natur.357..683E }}</ref> The early Devonian pretracheophytes ''[[Aglaophyton]]'' and ''[[Horneophyton]]'' have structures very similar to the '''[[hydroid (botany)|hydroids]]''' of modern mosses.
 
Plants continued to innovate new ways of reducing the resistance to flow within their cells, thereby increasing the efficiency of their water transport. Thickened bands on the walls of tubes are apparent from the early Silurian onwards<ref name=Niklas1983>{{cite jstor|2400461}}</ref> are adaptations to ease the flow of water.<ref name=Niklas1985/> Banded tubes, as well as tubes with pitted ornamentation on their walls, were lignified<ref name=Niklas1980>{{cite pmid |17747811}}</ref> and, when they form single celled conduits, are referred to as '''[[tracheids]]'''. These, the "next generation" of transport cell design, have a more rigid structure than hydroids, preventing their collapse at higher levels of water tension.<ref name=Sperry2003/> Tracheids may have a single evolutionary origin, possibly within the hornworts,<ref name="Qiu2006
">{{cite journal
| author = Qiu, Y.L.
| coauthors = Li, L.; Wang, B.; Chen, Z.; Knoop, V.; Groth-malonek, M.; Dombrovska, O.; Lee, J.; Kent, L.; Rest, J.; Others,
| year = 2006
| title = The deepest divergences in land plants inferred from phylogenomic evidence
| journal = Proceedings of the National Academy of Sciences
| pmid = 17030812
| volume = 103
| issue = 42
| pmc = 1622854
| pages = 15511–6
| doi = 10.1073/pnas.0603335103
|bibcode = 2006PNAS..10315511Q }}</ref> uniting all tracheophytes (but they may have evolved more than once).<ref name=Sperry2003/>
 
Water transport requires regulation, and dynamic control is provided by [[stoma]]ta.<ref name=gk>{{cite book|author=Stewart, W.N.; Rothwell, G.W.|title=Paleobiology and the evolution of plants|year=1993|publisher = Cambridge University Press|pages=521pp}}</ref>
By adjusting the amount of gas exchange, they can restrict the amount of water lost through transpiration. This is an important role where water supply is not constant, and indeed stomata appear to have evolved before tracheids, being present in the non-vascular hornworts.<ref name=Sperry2003/>
 
An [[endodermis]] probably evolved during the Silu-Devonian, but the first fossil evidence for such a structure is Carboniferous.<ref name=Sperry2003/> This structure in the roots covers the water transport tissue and regulates ion exchange (and prevents unwanted pathogens etc. from entering the water transport system). The endodermis can also provide an upwards pressure, forcing water out of the roots when transpiration is not enough of a driver.
 
Once plants had evolved this level of controlled water transport, they were truly homoiohydric, able to extract water from their environment through root-like organs rather than relying on a film of surface moisture, enabling them to grow to much greater size.<ref name=Sperry2003/> As a result of their independence from their surroundings, they lost their ability to survive desiccation&nbsp;– a costly trait to retain.<ref name=Sperry2003/>
 
During the Devonian, maximum xylem diameter increased with time, with the minimum diameter remaining pretty constant.<ref name=Niklas1985>{{cite jstor|2408738}}</ref> By the mid Devonian, the tracheid diameter of some plant lineages<ref>Zosterophyllophytes</ref> had plateaued.<ref name=Niklas1985/> Wider tracheids allow water to be transported faster, but the overall transport rate depends also on the overall cross-sectional area of the xylem bundle itself.<ref name=Niklas1985/> The increase in vascular bundle thickness further seems to correlate with the width of plant axes, and plant height; it is also closely related to the appearance of leaves<ref name=Niklas1985/> and increased stomatal density, both of which would increase the demand for water.<ref name=Sperry2003/>
 
While wider tracheids with robust walls make it possible to achieve higher water transport pressures, this increases the problem of cavitation.<ref name=Sperry2003/> Cavitation occurs when a bubble of air forms within a vessel, breaking the bonds between chains of water molecules and preventing them from pulling more water up with their cohesive tension. A tracheid, once cavitated, cannot have its embolism removed and return to service (except in a few advanced angiosperms{{Verify source|gymnosperms too?|date=April 2008}} that have developed a mechanism of doing so). Therefore, it is well worth plants' while to avoid cavitation occurring. For this reason, pits in tracheid walls have very small diameters, to prevent air entering and allowing bubbles to nucleate.<ref name=Sperry2003/> Freeze-thaw cycles are a major cause of cavitation.<ref name=Sperry2003/> Damage to a tracheid's wall almost inevitably leads to air leaking in and cavitation, hence the importance of many tracheids working in parallel.<ref name=Sperry2003/>
 
Cavitation is hard to avoid, but once it has occurred plants have a range of mechanisms to contain the damage.<ref name=Sperry2003/>
Small pits link adjacent conduits to allow fluid to flow between them, but not air&nbsp;– although ironically these pits, which prevent the spread of embolisms, are also a major cause of them.<ref name=Sperry2003/> These pitted surfaces further reduce the flow of water through the xylem by as much as 30%.<ref name=Sperry2003/> Conifers, by the Jurassic, developed an ingenious improvement,<ref name=Pittermann2005>{{Cite journal|author=Pittermann J.; Sperry J.S.; Hacke U.G.; Wheeler J.K.; Sikkema E.H. |title=Torus-Margo Pits Help Conifers Compete with Angiosperms | journal=Science Magazine | volume=310 | issue=5756 | pages=1924 |date=December 2005 | url=http://www.sciencemag.org/content/310/5756/1924.full | doi=10.1126/science.1120479}}</ref> using valve-like structures to isolate cavitated elements. These torus-margo<ref>[http://www.physorg.com/news9298.html Why Christmas trees are not extinct]</ref> structures have a blob floating in the middle of a donut; when one side depressurises the blob is sucked into the torus and blocks further flow.<ref name=Sperry2003/> Other plants simply accept cavitation; for instance, oaks grow a ring of wide vessels at the start of each spring, none of which survive the winter frosts. Maples use root pressure each spring to force sap upwards from the roots, squeezing out any air bubbles.
 
Growing to height also employed another trait of tracheids&nbsp;– the support offered by their lignified walls. Defunct tracheids were retained to form a strong, woody stem, produced in most instances by a secondary xylem. However, in early plants, tracheids were too mechanically vulnerable, and retained a central position, with a layer of tough [[sclerenchyma]] on the outer rim of the stems.<ref name=Sperry2003/> Even when tracheids do take a structural role, they are supported by sclerenchymatic tissue.
 
Tracheids end with walls, which impose a great deal of resistance on flow;<ref name=Niklas1985/> vessel members have perforated end walls, and are arranged in series to operate as if they were one continuous vessel.<ref name=Niklas1985/> The function of end walls, which were the default state in the Devonian, was probably to avoid [[embolism]]s. An embolism is where an air bubble is created in a tracheid. This may happen as a result of freezing, or by gases dissolving out of solution. Once an embolism is formed, it usually cannot be removed (but see later); the affected cell cannot pull water up, and is rendered useless.
 
End walls excluded, the tracheids of prevascular plants were able to operate under the same hydraulic conductivity as those of the first vascular plant, ''Cooksonia''.<ref name=Niklas1985/>
 
The size of tracheids is limited as they comprise a single cell; this limits their length, which in turn limits their maximum useful diameter to 80&nbsp;μm.<ref name=Sperry2003/> Conductivity grows with the fourth power of diameter, so increased diameter has huge rewards; '''vessel elements''', consisting of a number of cells, joined at their ends, overcame this limit and allowed larger tubes to form, reaching diameters of up to 500&nbsp;μm, and lengths of up to 10&nbsp;m.<ref name=Sperry2003/>
 
Vessels first evolved during the dry, low {{co2}} periods of the late Permian, in the horsetails, ferns and [[Selaginellales]] independently, and later appeared in the mid Cretaceous in angiosperms and gnetophytes.<ref name=Sperry2003/>
Vessels allow the same cross-sectional area of wood to transport around a hundred times more water than tracheids!<ref name=Sperry2003/> This allowed plants to fill more of their stems with structural [[Ground tissue#Fibres|fibres]], and also opened a new niche to vines, which could transport water without being as thick as the tree they grew on.<ref name=Sperry2003/> Despite these advantages, tracheid-based wood is a lot lighter, thus cheaper to make, as vessels need to be much more reinforced to avoid cavitation.<ref name=Sperry2003/>
 
<!--Expand to detail: Angiosperms; patterns in gymnosperm wood & rings; palms; 'clicks'-->
<!--*Note: Raven & Edwards (2001) has a brief but noteworthy review on [[homoiohydry]] which may come in useful.-->
 
===Leaves{{anchor|leaves}}===
{{Further|Ecology}}
[[File:Illustration Isoetes lacustris0.jpg|thumb|The lycopod ''[[Isoetes]]'' bears microphylls with a single vascular trace.]]
[[File:Vein sceleton hydrangea ies.jpg|thumb|The branching pattern of megaphyll veins may belie their origin as webbed, dichotomising branches.]]
[[File:Leaf 1 web.jpg| thumb | 250px | right | Leaf lamina. The [[leaf]] architecture probably arose multiple times in the plant lineage]]
 
[[Leaves]] today are, in almost all instances, an adaptation to increase the amount of sunlight that can be captured for [[photosynthesis]]. Leaves certainly evolved more than once, and probably originated as spiny outgrowths to [[plant defence against herbivory|protect]] early plants from herbivory.
 
Leaves are the primary [[photosynthetic]] organs of a plant. Based on their structure, they are classified into two types: [[microphylls]], which lack complex venation patterns, and [[megaphylls]], which are large and have complex [[Leaf#Venation .28arrangement of the veins.29|venation]]. It has been proposed that these structures arose independently.<ref>{{cite journal | author=Crane and Kenrick | title = Diverted development of reproductive organs: A source of morphological innovation in land plants | journal=Plant System. And Evol. | volume=206 | issue=1 | pages=161–174 | year=1997 | doi = 10.1007/BF00987946 | last2=Kenrick | first2=Paul}}</ref> Megaphylls, according to Walter Zimmerman's telome theory,<ref>Zimmermann, W. 1959. ''Die Phylogenie der Pflanzen''. 2nd edition. Stuutgart: Gustav Fischer Verlag.</ref> have evolved from plants that showed a three dimensional branching architecture, through three transformations—'''overtopping''', which led to the lateral position typical of leaves, '''planation''', which involved formation of a planar architecture, '''webbing''' or '''fusion''', which united the planar branches, thus leading to the formation of  a proper [[leaf]] lamina. All three steps happened multiple times in the evolution of today's leaves.<ref>{{cite journal | author=Piazza P | title = Evolution of leaf developmental mechanisms | journal=New Phytol. | volume=167 | pages=693–710 | year=2005 | doi=10.1111/j.1469-8137.2005.01466.x | pmid=16101907 | issue=3 | url=http://www.blackwell-synergy.com/doi/abs/10.1111/j.1469-8137.2005.01466.x | author-separator=, | display-authors=1 | last2=Jasinski | first2=Sophie | last3=Tsiantis | first3=Miltos}}</ref>
 
It is widely believed that the telome theory is well supported by fossil evidence. However, Wolfgang Hagemann questioned it for morphological and ecological reasons and proposed an alternative theory.<ref>Hagemann, W. 1976. Sind Farne Kormophyten? Eine Alternative zur Telomtheorie.
Plant Systematics and Eveolution 124: 251-277.</ref><ref>Hagemann, W. 1999. Towards an organismic concept of land plants: the marginal blastozone and the development of the vegetation body of selected frondose gametophytes of liverworts and ferns. Planr Systematics and Evolution 216: 81-133.</ref> Whereas according to the telome theory the most primitive land plants have a three-dimensional branching system of radially symmetrical axes (telomes), according to Hagemann's alternative the opposite is proposed: the most primitive land plants that gave rise to vascular plants were flat, thalloid, leaf-like, without axes, somewhat like a liverwort or fern prothallus. Axes such as stems and roots  evolved later as new organs. Rolf Sattler proposed an overarching process-oriented view that leaves some limited room for both the telome theory and Hagemann's alternative and in addition takes into consideration the whole continuum between dorsiventral (flat) and radial (cylindrical) structures that can be found in fossil and living land plants.<ref>Sattler, R. 1992. Process morphology: structural dynamics in development and evolution. Canadian Journal of Botany 70: 708-714.</ref><ref>Sattler, R. 1998. On the origin of symmetry, branching and phyllotaxis in land plants. In: R.V. Jean and D.  Barabé (eds) Symmetry in Plants. World Scientific, Singapore, pp. 775-793.</ref> This view is supported by research in molecular genetics. Thus, James (2009)<ref>James, P. .J. 2009. 'Tree and Leaf': A different angle. The Linnean 25, p. 17.</ref> concluded that "it is now widely accepted that... radiality [characteristic of axes such as stems] and dorsiventrality [characteristic of leaves] are but extremes of a continuous spectrum. In fact, it is simply the timing of the KNOX gene expression!"
 
From the point of view of the telome theory, it has been proposed that before the evolution of [[leaves]], plants had the [[photosynthetic]] apparatus on the stems. Today's megaphyll leaves probably became commonplace some 360mya, about 40my after the simple leafless plants had colonized the land in the [[early Devonian]] period. This spread has been linked to the fall in the atmospheric [[carbon dioxide]] concentrations in the Late [[Paleozoic]] era associated with a rise in density of [[stomata]] on leaf surface. This must have allowed for better [[transpiration]] rates and gas exchange. Large leaves with less stomata would have gotten heated up in the sun's heat, but an increased stomatal density allowed for a better-cooled leaf, thus making its spread feasible.<ref>{{cite journal | author=Beerling D. | title = Evolution of leaf-form in land plants linked to atmospheric CO<sub>2</sub> decline in the Late Palaeozoic era | journal=Nature | volume=410 | pages=352–354 | year=2001 | doi = 10.1038/35066546 | pmid=11268207 | issue=6826 | author-separator=, | display-authors=1 | last2=Osborne | first2=C. P. | last3=Chaloner | first3=W. G.}}</ref><ref>[http://www.corante.com/loom/archives/004766.html A perspective on the CO<sub>2</sub> theory of early leaf evolution]</ref>
 
The rhyniophytes of the Rhynie chert comprised nothing more than slender, unornamented axes. The early to middle Devonian [[trimerophyte]]s  may be considered leafy. This group of vascular plants are recognisable by their masses of terminal sporangia, which adorn the ends of axes which may bifurcate or trifurcate.<ref name=gk/> Some organisms, such as ''[[Psilophyton]]'', bore [[wikt:enation|enation]]s. These are small, spiny outgrowths of the stem, lacking their own vascular supply.
 
Around the same time, the [[zosterophyllophytes]] were becoming important. This group is recognisable by their kidney-shaped sporangia, which grew on short lateral branches close to the main axes. They sometimes branched in a distinctive H-shape.<ref name=gk/> The majority of this group bore pronounced spines on their axes. However, none of these had a vascular trace, and the first evidence of vascularised enations occurs in the Rhynie genus ''[[Asteroxylon]]''. The spines of ''Asteroxylon'' had a primitive vascular supply&nbsp;– at the very least, [[leaf trace]]s could be seen departing from the central protostele towards each individual "leaf". A fossil known as ''[[Baragwanathia]]'' appears in the fossil record slightly earlier, in the late Silurian.<ref name=Rickards2000>{{cite journal
| author = Rickards, R.B.
| year = 2000
| title = The age of the earliest club mosses: the Silurian Baragwanathia flora in Victoria, Australia
| journal = Geological Magazine
| volume = 137
| issue = 2
| pages = 207–209
| url = http://geolmag.geoscienceworld.org/cgi/content/abstract/137/2/207
| accessdate = 2007-10-25
| doi = 10.1017/S0016756800003800
| format = abstract
}}</ref> In this organism, these leaf traces continue into the leaf to form their mid-vein.<ref name=Kaplan2001>{{cite journal
| author = Kaplan, D.R.
| year = 2001
| title = The Science of Plant Morphology: Definition, History, and Role in Modern Biology
| journal = American Journal of Botany
| volume = 88
| issue = 10
| pages = 1711–1741
| doi = 10.2307/3558347
| jstor = 3558347
| pmid=21669604
}}</ref> One theory, the "enation theory", holds that the leaves developed by outgrowths of the protostele connecting with existing enations, but it is also possible that microphylls evolved by a branching axis forming "webbing".<ref name=gk/>
 
''Asteroxylon''<ref name=Taylor2005>{{cite journal
| author = Taylor, T.N.
| coauthors = Hass, H.; Kerp, H.; Krings, M.; Hanlin, R.T.
| year = 2005
| title = Perithecial ascomycetes from the 400 million year old Rhynie chert: an example of ancestral polymorphism
| journal = Mycologia
| volume = 97
| issue = 1
| pmid = 16389979
| pages = 269–285
| url = http://www.mycologia.org/cgi/content/abstract/97/1/269
| accessdate = 2008-04-07
| format = abstract
| doi = 10.3852/mycologia.97.1.269
}}</ref> and ''Baragwanathia'' are widely regarded as primitive lycopods.<ref name=gk/> The [[lycopod]]s are still [[wikt:extant|extant]] today, familiar as the [[quillwort]] ''Isoetes'' and the [[club moss]]es. Lycopods bear distinctive [[microphylls]]&nbsp;– leaves with a single vascular trace. Microphylls could grow to some size&nbsp;– the [[Lepidodendrales]] boasted microphylls over a meter in length&nbsp;– but almost all just bear the one vascular bundle. (An exception is the branching ''[[Selaginella]]'').
 
The more familiar leaves, [[megaphylls]], are thought to have separate origins&nbsp;– indeed, they appeared four times independently, in the ferns, horsetails, progymnosperms, and seed plants.<ref name=Boyce2002>{{cite journal
| author = Boyce, C.K.
| coauthors = Knoll, A.H.
| year = 2002
| title = Evolution of developmental potential and the multiple independent origins of leaves in Paleozoic vascular plants
| journal = Paleobiology
| volume = 28
| issue = 1
| pages = 70–100
| doi = 10.1666/0094-8373(2002)028<0070:EODPAT>2.0.CO;2
| issn = 0094-8373
}}</ref> They appear to have originated from [[dichotomising]] branches, which first overlapped (or "overtopped") one another, and eventually developed "webbing" and evolved into gradually more leaf-like structures.<ref name=Kaplan2001/> So megaphylls, by this "teleome theory", are composed of a group of webbed branches<ref name=Kaplan2001/>&nbsp;– hence the "leaf gap" left where the leaf's vascular bundle leaves that of the main branch resembles two axes splitting.<ref name=Kaplan2001/> In each of the four groups to evolve megaphylls, their leaves first evolved during the late Devonian to early Carboniferous, diversifying rapidly until the designs settled down in the mid Carboniferous.<ref name=Boyce2002/>
 
The cessation of further diversification can be attributed to developmental constraints,<ref name=Boyce2002/> but why did it take so long for leaves to evolve in the first place? Plants had been on the land for at least 50&nbsp;million years before megaphylls became significant. However, small, rare mesophylls are known from the early Devonian genus ''[[Eophyllophyton]]''&nbsp;– so development could not have been a barrier to their appearance.<ref name="Hao2003
">{{cite journal
| author = Hao, S.
| coauthors = Beck, C.B.; Deming, W.
| year = 2003
| title = Structure of the Earliest Leaves: Adaptations to High Concentrations of Atmospheric {{co2}}
| journal = International Journal of Plant Sciences
| volume = 164
| issue = 1
| pages = 71–75
| doi = 10.1086/344557
}}</ref> The best explanation so far incorporates observations that atmospheric {{co2}} was declining rapidly during this time&nbsp;– falling by around 90% during the Devonian.<ref name="Berner2001
">{{cite journal
| author = Berner, R.A.
| coauthors = Kothavala, Z.
| year = 2001
| title = Geocarb III: A Revised Model of Atmospheric {{co2}} over Phanerozoic Time
| journal = American Journal of Science
| volume = 301
| issue = 2
| pages = 182
| url = http://ajsonline.org/cgi/content/abstract/301/2/182
| accessdate = 2008-04-07
| doi = 10.2475/ajs.301.2.182
| format = abstract
}}</ref> This corresponded with an increase in stomatal density by 100 times. Stomata allow water to evaporate from leaves, which causes them to curve. It appears that the low stomatal density in the early Devonian meant that evaporation was limited, and leaves would overheat if they grew to any size. The stomatal density could not increase, as the primitive steles and limited root systems would not be able to supply water quickly enough to match the rate of transpiration.<ref name=Beerling2001>{{cite journal
| author = Beerling, D.J.
| coauthors = Osborne, C.P.; Chaloner, W.G.
| year = 2001
| title = Evolution of leaf-form in land plants linked to atmospheric CO2 decline in the Late Palaeozoic era
| journal = Nature
| pmid = 11268207
| volume = 410
| issue = 6826
| pages = 287–394
| doi = 10.1038/35066546
}}</ref>
 
Clearly, leaves are not always beneficial, as illustrated by the frequent occurrence of secondary loss of leaves, famously exemplified by [[cacti]] and the "whisk fern" ''[[Psilotum]]''.
 
Secondary evolution can also disguise the true evolutionary origin of some leaves. Some genera of ferns display complex leaves which are attached to the pseudostele by an outgrowth of the vascular bundle, leaving no leaf gap.<ref name=Kaplan2001/> Further, horsetail (''[[Equisetum]]'') leaves bear only a single vein, and appear for all the world to be microphyllous; however, both the fossil record and molecular evidence indicate that their forbears bore leaves with complex venation, and the current state is a result of secondary simplification.<ref name=Taylor1993>{{cite journal
| author = Taylor, T.N.
| coauthors = Taylor, E.L.
| year = 1993
| title = The biology and evolution of fossil plants
}}</ref>
 
[[Deciduous]] trees deal with another disadvantage to having leaves. The popular belief that plants shed their leaves when the days get too short is misguided; evergreens prospered in the [[Arctic circle]] during the [[PETM|most recent]] [[greenhouse earth]].<ref name=Shellito2006>{{cite journal
| author = Shellito, C.J.
| coauthors = Sloan, L.C.
| year = 2006
| title = Reconstructing a lost Eocene paradise: Part I. Simulating the change in global floral distribution at the initial Eocene thermal maximum
| journal = Global and Planetary Change
| volume = 50
| issue = 1–2
| pages = 1–17
| url = http://linkinghub.elsevier.com/retrieve/pii/S0921818105001475
| accessdate = 2008-04-08
| doi = 10.1016/j.gloplacha.2005.08.001
|bibcode = 2006GPC....50....1S }}</ref> The generally accepted reason for shedding leaves during winter is to cope with the weather&nbsp;– the force of wind and weight of snow are much more comfortably weathered without leaves to increase surface area. Seasonal leaf loss has evolved independently several times and is exhibited in the [[ginkgoales]], [[pinophyta]] and angiosperms.<ref name=Aerts1995>{{cite journal
| author = Aerts, R.
| year = 1995
| title = The advantages of being evergreen
| journal = Trends in Ecology & Evolution
| volume = 10
| issue = 10
| pages = 402–407
| doi = 10.1016/S0169-5347(00)89156-9
}}</ref> Leaf loss may also have arisen as a response to pressure from insects; it may have been less costly to lose leaves entirely during the winter or dry season than to continue investing resources in their repair.<ref name=Labandeira1994>{{cite journal
| author = Labandeira, C.C.
| coauthors = Dilcher, D.L.; Davis, D.R.; Wagner, D.L.
| year = 1994
| title = Ninety-seven million years of angiosperm-insect association: paleobiological insights into the meaning of coevolution
| journal = Proceedings of the National Academy of Sciences of the United States of America
| pmid = 11607501
| volume = 91
| issue = 25
| pmc = 45420
| pages = 12278–12282
| doi = 10.1073/pnas.91.25.12278
| bibcode=1994PNAS...9112278L
}}</ref>
 
====Factors influencing leaf architectures====
 
Various physical and physiological forces like [[light]] intensity, [[humidity]], [[temperature]], [[wind speeds]] etc. are thought to have influenced evolution of leaf shape and size. It is observed that high trees rarely have large leaves, owing to the obstruction they generate for winds. This obstruction can eventually lead to the tearing of leaves, if they are large. Similarly, trees that grow in [[temperate]] or [[taiga]] regions have pointed leaves, presumably to prevent nucleation of ice onto the leaf surface and reduce water loss due to transpiration. [[Herbivory]], not only by large mammals, but also small [[insects]] has been implicated as a driving force in leaf evolution, an example being plants of the genus ''Aciphylla'', that are commonly found in [[New Zealand]]. The now extinct [[Moas]] fed upon these plants, and its seen that the leaves have spines on their bodies, which probably functioned to discourage the moas from feeding on them. Other members of ''Aciphylla'', which did not co-exist with the moas, do not have these spines.<ref>{{cite journal | author=Brown V | title = Herbivory and the Evolution of Leaf Size and Shape | journal=[[Philosophical Transactions of the Royal Society B]] | volume=333 | issue=1267 | pages=265–272 | year=1991 | doi = 10.1098/rstb.1991.0076 | author-separator=, | display-authors=1 | last2=Lawton | first2=J. H. | last3=Grubb | first3=P. J.}}</ref>
 
At the genetic level, developmental studies have shown that repression of the KNOX genes is required for initiation of the [[leaf]] [[primordium]]. This is brought about by ''ARP'' genes, which encode [[transcription factors]]. Genes of this type have been found in many plants studied till now, and the mechanism i.e. repression of KNOX genes in leaf primordia, seems to be quite conserved. Interestingly, expression of KNOX genes in leaves produces complex leaves. It is speculated that the ''ARP'' function arose quite early in [[vascular plant]] evolution, because members of the primitive group [[Lycophytes]] also have a functionally similar gene <ref>{{cite journal | author= Harrison C. J. | title = Independent recruitment of a conserved developmental mechanism during leaf evolution | journal=Nature | volume=434 | issue= 7032 | pages=509–514 | year=2005 | pmid= 15791256 | doi=10.1038/nature03410|bibcode = 2005Natur.434..509H | author-separator= , | display-authors= 1 | last2= Corley | first2= Susie B. | last3= Moylan | first3= Elizabeth C. | last4= Alexander | first4= Debbie L. | last5= Scotland | first5= Robert W. | last6= Langdale | first6= Jane A. }}</ref> Other players that have a conserved role in defining leaf primordia are the phytohormone [[auxin]], [[gibberelin]] and [[cytokinin]].
 
[[File:Leaf diversity.jpg|thumb | 250px | right |The diversity of leaves]]
One interesting feature of a plant is its [[phyllotaxy]]. The arrangement of leaves on the plant body is such that the plant can maximally harvest light under the given constraints, and hence, one might expect the trait to be genetically [[Robustness (evolution)|robust]]. However, it may not be so. In [[maize]], a mutation in only one gene called ''ABPHYL'' ''(ABnormal PHYLlotaxy)'' was enough to change the phyllotaxy of the leaves. It implies that sometimes, mutational adjustment of a single locus on the [[genome]] is enough to generate diversity. The ''abphyl'' gene was later on shown to encode a [[cytokinin]] response regulator protein.<ref>{{cite journal | author=Jackson D., Hake S. | title = Control of Phyllotaxy in Maize by the ABPHYL1 Gene | journal=Development | volume=126 | pages=315–323 | year=1999 | pmid=9847245 | issue=2}}</ref>
 
Once the leaf primordial cells are established from the SAM cells, the new [[Cartesian coordinate system|axes]] for leaf growth are defined, one important (and more studied) among them being the abaxial-adaxial (lower-upper surface) axes. The genes involved in defining this, and the other axes seem to be more or less conserved among higher plants. Proteins of the ''HD-ZIPIII'' family have been implicated in defining the adaxial identity. These proteins deviate some cells in the leaf [[primordium]] from the default [[abaxial]] state, and make them [[adaxial]]. It is believed that, in early plants with leaves, the leaves just had one type of surface&nbsp;— the abaxial one. This is the underside of today's leaves. The definition of the adaxial identity occurred some 200 million years after the abaxial identity was established.<ref>{{cite journal | author=Cronk Q. | title = Plant evolution and development in a post-genomic context | journal=Nature Reviews Genetics  | volume=2 | pages=607–619 | year=2001 | url=http://www.nature.com/nrg/journal/v2/n8/abs/nrg0801_607a.html | issue=8 | doi=10.1038/35084556 | pmid=11483985}}</ref> One can thus imagine the early leaves as an intermediate stage in evolution of today's leaves, having just arisen from spiny stem-like outgrowths of their leafless ancestors, covered with [[stomata]] all over, and not optimized as much for [[photosynthesis|light harvesting]].
 
How the infinite variety of plant leaves is generated is a subject of intense research. Some common themes have emerged. One of the most significant is the involvement of KNOX genes in generating [[compound leaves]], as in the [[tomato]] ''(see above)''. But, this again is not universal. For example, the [[pea]] uses a different mechanism for doing the same thing.<ref>{{cite journal | author=Tattersall | title = The Mutant crispa Reveals Multiple Roles for PHANTASTICA in Pea Compound Leaf Development | journal=Plant Cell | volume=17 | issue=4 | pages=1046–1060 | year=2005 | pmid=15749758 | last2=Turner | first2=L | last3=Knox | first3=MR | last4=Ambrose | first4=MJ | last5=Ellis | first5=TH | last6=Hofer | first6=JM | doi=10.1105/tpc.104.029447 | pmc=1087985 | display-authors=1 }}</ref><ref>{{cite journal | author=Bharathan and Sinha | title = The Regulation of Compound Leaf Development | journal=Plant Physiol. | volume=127 | issue=4 | pages=1533–1538 | date=Dec 2001 | pmid=11743098 | last2=Sinha | first2=NR | pmc=1540187 | url=http://www.plantphysiol.org/cgi/content/full/127/4/1533#B18 | doi=10.1104/pp.010867}}</ref> Mutations in genes affecting leaf [[curvature]] can also change leaf form, by changing the leaf from flat, to a crinky shape,<ref>{{cite journal | author=Nath U | title = Genetic Control of Surface Curvature | journal=Science | volume=299 | issue=5611 | pages=1404–1407 | year=2003 | doi = 10.1126/science.1079354 | pmid=12610308 | author-separator=, | display-authors=1 | last2=Crawford | first2=BC | last3=Carpenter | first3=R | last4=Coen | first4=E}}</ref> like the shape of [[cabbage]] leaves. There also exist different [[morphogen]] gradients in a developing leaf which define the leaf's axis. Changes in these morphogen gradients may also affect the leaf form. Another very important class of regulators of leaf development are the [[microRNAs]], whose role in this process has just begun to be documented. The coming years should see a rapid development in comparative studies on leaf development, with many [[Expressed Sequence Tag|EST]] sequences involved in the process coming online.
 
===Tree form===
[[File:Psaronius double section.JPG|thumb|The trunk of early tree fern ''[[Psaronius]]'', showing internal structure. The top of the plant would have been to the left of the image]]
[[File:LepidodendronOhio.jpg|thumb|External mold of ''[[Lepidodendron]]'' trunk showing leaf scars from the [[Upper Carboniferous]] of [[Ohio]]]]
The early Devonian landscape was devoid of vegetation taller than waist height. Without the evolution of a robust vascular system, taller heights could not be attained. There was, however, a constant evolutionary pressure to attain greater height. The most obvious advantage is the harvesting of more sunlight for photosynthesis&nbsp;– by overshadowing competitors&nbsp;– but a further advantage is present in spore distribution, as spores (and, later, seeds) can be blown greater distances if they start higher. This may be demonstrated by ''[[Prototaxites]]'', thought to be a late Silurian fungus reaching eight metres in height.<ref name="Boyce2007
">{{Cite journal|author=Boyce, K.C.; Hotton, C.L.; Fogel, M.L.; Cody, G.D.; Hazen, R.M.; Knoll, A.H.; Hueber, F.M. |title =Devonian landscape heterogeneity recorded by a giant fungus | journal =[[Geology (journal)|Geology]] | volume =35 | issue =5 | pages =399–402 |date=May 2007 | url=http://geology.geoscienceworld.org/cgi/reprint/35/5/399.pdf|format=PDF|doi= 10.1130/G23384A.1|bibcode = 2007Geo....35..399B }}</ref>
 
To attain [[wikt:arborescence|arborescence]], early plants had to develop [[wood]]y tissue that provided support and water transport. The stele of plants undergoing "secondary growth" is surrounded by the [[vascular cambium]], a ring of cells which produces more xylem (on the inside) and phloem (on the outside). Since xylem cells comprise dead, lignified tissue, subsequent rings of xylem are added to those already present, forming wood.
 
The first plants to develop this secondary growth, and a woody habit, were apparently the ferns, and as early as the middle Devonian one species, ''[[Wattieza]]'', had already reached heights of 8&nbsp;m and a tree-like habit.<ref name=Stein2007>{{cite journal
| author = Stein, W.E.
| coauthors = Mannolini, F.; Hernick, L.V.; Landing, E.; Berry, C.M.
| year = 2007
| title = Giant cladoxylopsid trees resolve the enigma of the Earth's earliest forest stumps at Gilboa
| journal = Nature
| pmid = 17443185
| volume = 446
| issue = 7138
| pages = 904–7
| doi = 10.1038/nature05705
|bibcode = 2007Natur.446..904S }}</ref>
 
Other clades did not take long to develop a tree-like stature; the late Devonian ''[[Archaeopteris]]'', a [[progymnosperm|precursor]] to [[gymnosperm]]s which evolved from the trimerophytes,<ref name=Retallack1985>{{cite journal
| author = Retallack, G.J.
| coauthors = Catt, J.A.; Chaloner, W.G.
| year = 1985
| title = Fossil Soils as Grounds for Interpreting the Advent of Large Plants and Animals on Land [and Discussion]
| journal = [[Philosophical Transactions of the Royal Society B]]
| volume = 309
| issue = 1138
| pages = 105–142
| doi = 10.1098/rstb.1985.0074
| jstor=2396355
|bibcode = 1985RSPTB.309..105R }}</ref> reached 30&nbsp;m in height. These progymnosperms were the first plants to develop true wood, grown from a bifacial cambium, of which the first appearance is in the mid Devonian ''[[Rellimia]]''.<ref name=Dannenhoffer1989>{{cite journal
| author = Dannenhoffer, J.M.
| coauthors = Bonamo, P.M.
| year = 1989
| title = ''Rellimia thomsonii'' from the Givetian of New York: Secondary Growth in Three Orders of Branching
| journal = American Journal of Botany
| volume = 76
| issue = 9
| pages = 1312–1325
| doi = 10.2307/2444557
| jstor = 2444557
}}</ref> True wood is only thought to have evolved once, giving rise to the concept of a "lignophyte" clade.
 
These ''Archaeopteris'' forests were soon supplemented by lycopods, in the form of [[lepidodendrales]], which topped 50m in height and 2m across at the base. These lycopods rose to dominate late Devonian and Carboniferous coal deposits.<ref name="Davis2004
">{{cite book|author=Davis, P; Kenrick, P.
|title=Fossil Plants
|publisher = Smithsonian Books, Washington D.C.
|year=2004|isbn=1-58834-156-9}}</ref> Lepidodendrales differ from modern trees in exhibiting determinate growth: after building up a reserve of nutrients at a lower height, the plants would "bolt" to a genetically determined height, branch at that level, spread their spores and die.<ref name=Donoghue2005>{{cite journal
| author = Donoghue, M.J.
| year = 2005
| title = Key innovations, convergence, and success: macroevolutionary lessons from plant phylogeny
| journal = Paleobiology
| volume = 31
| issue = 2
| pages = 77–93
| url = http://paleobiol.geoscienceworld.org/cgi/content/abstract/31/2_Suppl/77
| accessdate = 2008-04-07
| doi = 10.1666/0094-8373(2005)031[0077:KICASM]2.0.CO;2
| format = abstract
| issn = 0094-8373
}}</ref> They consisted of "cheap" wood to allow their rapid growth, with at least half of their stems comprising a pith-filled cavity.<ref name=gk/> Their wood was also generated by a unifacial vascular cambium&nbsp;– it did not produce new phloem, meaning that the trunks could not grow wider over time.{{Verify source|date=April 2008}}
 
The [[horsetail]] ''[[Calamites]]'' was next on the scene, appearing in the [[Carboniferous]]. Unlike the modern horsetail ''[[Equisetum]]'', ''[[Calamites]]'' had a unifacial vascular cambium, allowing them to develop wood and grow to heights in excess of 10&nbsp;m. They also branched multiple times.
 
While the form of early trees was similar to that of today's, the groups containing all modern trees had yet to evolve.
 
The dominant groups today are the gymnosperms, which include the coniferous trees, and the angiosperms, which contain all fruiting and flowering trees. It was long thought that the angiosperms arose from within the gymnosperms, but recent molecular evidence suggests that their living representatives form two distinct groups.<ref name="Bowe2000
">{{cite journal
| author = Bowe, L.M.
| coauthors = Coat, G.; Depamphilis, C.W.
| year = 2000
| title = Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers
| journal = Proceedings of the National Academy of Sciences
| volume = 97
| issue = 8
| pages = 4092–7
| doi = 10.1073/pnas.97.8.4092
| pmid=10760278
|bibcode = 2000PNAS...97.4092B
| pmc=18159}}</ref><ref name=Chaw2000>{{cite journal
| author = Chaw, S.M.
| coauthors = Parkinson, C.L.; Cheng, Y.; Vincent, T.M.; Palmer, J.D.
| year = 2000
| title = Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers
| journal = Proceedings of the National Academy of Sciences
| volume = 97
| issue = 8
| pages = 4086–91
| doi = 10.1073/pnas.97.8.4086
| pmid=10760277
|bibcode = 2000PNAS...97.4086C
| pmc=18157}}</ref><ref name=Soltis2002>{{cite journal
| author = Soltis, D.E.
| coauthors = Soltis, P.S.; Zanis, M.J.
| year = 2002
| title = Phylogeny of seed plants based on evidence from eight genes
| journal = American Journal of Botany
| volume = 89
| issue = 10
| pages = 1670–81
| url = http://amjbot.org/cgi/content/abstract/89/10/1670
| accessdate = 2008-04-08
| doi = 10.3732/ajb.89.10.1670
| format = abstract
| pmid = 21665594
}}</ref> The molecular data has yet to be fully reconciled with morphological data,<ref name=Friis2006>{{cite journal
| author = Friis, E.M.
| coauthors = Pedersen, K.R.; Crane, P.R.
| year = 2006
| title = Cretaceous angiosperm flowers: Innovation and evolution in plant reproduction
| journal = Palaeogeography, Palaeoclimatology, Palaeoecology
| volume = 232
| issue = 2–4
| pages = 251–293
| doi = 10.1016/j.palaeo.2005.07.006
}}</ref><ref name=Hilton2006>{{cite journal
| author = Hilton, J.
| coauthors = Bateman, R.M.
| year = 2006
| title = Pteridosperms are the backbone of seed-plant phylogeny
| journal = The Journal of the Torrey Botanical Society
| volume = 133
| issue = 1
| pages = 119–168
| doi = 10.3159/1095-5674(2006)133[119:PATBOS]2.0.CO;2
| issn = 1095-5674
}}</ref><ref name=Bateman2006>{{cite journal
| author = Bateman, R.M.
| coauthors = Hilton, J.; Rudall, P.J.
| year = 2006
| title = Morphological and molecular phylogenetic context of the angiosperms: contrasting the 'top-down' and 'bottom-up' approaches used to infer the likely characteristics of the first flowers
| journal = Journal of Experimental Botany
| pmid = 17056677
| volume = 57
| issue = 13
| pages = 3471–503
| doi = 10.1093/jxb/erl128
}}</ref> but it is becoming accepted that the morphological support for paraphyly is not especially strong.<ref name=Frohlich2007/>
This would lead to the conclusion that both groups arose from within the pteridosperms, probably as early as the [[Permian]].<ref name=Frohlich2007/>
 
The angiosperms and their ancestors played a very small role until they diversified during the Cretaceous. They started out as small, damp-loving organisms in the understory, and have been diversifying ever since the mid{{Verify source|date=April 2008}}-Cretaceous, to become the dominant member of non-[[wikt:boreal|boreal]] forests today.
 
===Roots===
{|align=right class="wikitable" width=300 style="margin:0 0 0 1em; text-align:center"
|-
|[[File:Lepidodendron aculeatum2.jpg|frameless]]
|-
|[[File:Lepido root top.jpg|frameless]]
|-
|The roots (bottom image) of lepidodendrales are thought to be functionally equivalent to the stems (top), as the similar appearance of "leaf scars" and "root scars" on these specimens from different species demonstrates.
|}
Roots are important to plants for two main reasons: Firstly, they provide anchorage to the substrate; more importantly, they provide a source of water and nutrients from the soil. Roots allowed plants to grow taller and faster.
 
The onset of roots also had effects on a global scale. By disturbing the soil, and promoting its acidification (by taking up nutrients such as nitrate and phosphate{{Verify source|date=April 2008}}), they enabled it to weather more deeply, promoting the draw-down of {{co2}}<ref name=Mora1996>{{cite journal
| author = Mora, C.I.
| coauthors = Driese, S.G.; Colarusso, L.A.
| year = 1996
| title = Middle to Late Paleozoic Atmospheric {{co2}} Levels from Soil Carbonate and Organic Matter
| journal = Science
| volume = 271
| issue = 5252
| pages = 1105–1107
| doi = 10.1126/science.271.5252.1105
|bibcode = 1996Sci...271.1105M }}</ref> with huge implications for climate.<ref name=Berner1994>{{cite journal
| doi = 10.2475/ajs.294.1.56
| author = Berner, R.A.
| year = 1994
| title = GEOCARB II: A revised model of atmospheric {{co2}} over Phanerozoic time
| journal = Am. J. Sci
| volume = 294
| issue = 1
  | pages = 56–91
}}</ref> These effects may have been so profound they led to [[Late Devonian extinction|a mass extinction]].<ref name=Algeo1995>{{cite journal
| author = Algeo, T.J.
| coauthors = Berner, R.A.; Maynard, J.B.; Scheckler, S.E.; Archives, G.S.A.T.
| year = 1995
| title = Late Devonian Oceanic Anoxic Events and Biotic Crises: "Rooted" in the Evolution of Vascular Land Plants?
| journal = GSA Today
| volume = 5
| issue = 3
| url = http://www.geosociety.org/pubs/gsatoday/archive/toc9503.htm
}}</ref>
 
But, how and when did roots evolve in the first place? While there are traces of root-like impressions in fossil soils in the late Silurian,<ref name="Retallack1986
">{{cite book|author=Retallack, G. J. |title=Paleosols: their Recognition and Interpretation|editor=Wright, V. P.|publisher=Blackwell|location=Oxford|year=1986}}</ref> body fossils show the earliest plants to be devoid of roots. Many had tendrils that sprawled along or beneath the ground, with upright axes or [[wikt:thalli|thalli]] dotted here and there, and some even had non-photosynthetic subterranean branches which lacked stomata. The distinction between root and specialised branch is developmental; true roots follow a different developmental trajectory to stems. Further, roots differ in their branching pattern, and in possession of a [[root cap]].<ref name=Raven2001/> So while Silu-Devonian plants such as ''[[Rhynia]]'' and ''[[Horneophyton]]'' possessed the physiological equivalent of roots, roots&nbsp;– defined as organs differentiated from stems&nbsp;– did not arrive until later.<ref name=Raven2001/> Unfortunately, roots are rarely preserved in the fossil record, and our understanding of their evolutionary origin is sparse.<ref name=Raven2001/>
 
Rhizoids&nbsp;– small structures performing the same role as roots, usually a cell in diameter&nbsp;– probably evolved very early, perhaps even before plants colonised the land; they are recognised in the [[Characeae]], an algal sister group to land plants.<ref name=Raven2001/> That said, rhizoids probably evolved more than once; the rhizines of [[lichen]]s, for example, perform a similar role. Even some animals (''[[Lamellibrachia]]'') have root-like structures!<ref name=Raven2001/>
 
More advanced structures are common in the Rhynie chert, and many other fossils of comparable early Devonian age bear structures that look like, and acted like, roots.<ref name=Raven2001/> The rhyniophytes bore fine rhizoids, and the trimerophytes and herbaceous lycopods of the chert bore root-like structure penetrating a few centimetres into the soil.<ref name=Algeo1998/> However, none of these fossils display all the features borne by modern roots.<ref name=Raven2001/> Roots and root-like structures became increasingly more common and deeper penetrating during the [[Devonian]] period, with lycopod trees forming roots around 20&nbsp;cm long during the Eifelian and Givetian. These were joined by progymnosperms, which rooted up to about a metre deep, during the ensuing Frasnian stage.<ref name=Algeo1998/> True gymnosperms and zygopterid ferns also formed shallow rooting systems during the Famennian period.<ref name=Algeo1998/>
 
The rhizomorphs of the lycopods provide a slightly different approach to rooting. They were equivalent to stems, with organs equivalent to leaves performing the role of rootlets.<ref name=Raven2001/> A similar construction is observed in the extant lycopod ''Isoetes'', and this appears to be evidence that roots evolved independently at least twice, in the lycophytes and other plants,<ref name=Raven2001/> a proposition supported by studies showing that roots are initiated and their growth promoted by different mechanisms in lycophytes and euphyllophytes.<ref name=Coudert2012>{{Cite journal | doi = 10.1093/molbev/mss250| issn = 0737-4038| last = Coudert| first = Yoan| coauthors = Anne Dievart, Gaetan Droc, Pascal Gantet| year=2012 |title = ASL/LBD Phylogeny Suggests that Genetic Mechanisms of Root Initiation Downstream of Auxin Are Distinct in Lycophytes and Euphyllophytes| journal = Molecular Biology and Evolution | volume = 30 | issue = 3 | pages = 569–72 | pmid = 23112232 }}</ref>
 
A vascular system is indispensable to rooted plants, as non-photosynthesising roots need a supply of sugars, and a vascular system is required to transport water and nutrients from the roots to the rest of the plant.<ref name=KCbook/> These plants are little more advanced than their Silurian forbears, without a dedicated root system; however, the flat-lying axes can be clearly seen to have growths similar to the rhizoids of bryophytes today.<ref name=KCpaper>{{cite journal
| author = Kenrick, P.
| coauthors = Crane, P.R.
| year = 1997
| title = The origin and early evolution of plants on land
| journal = Nature
| volume = 389
| issue = 6646
| pages = 33
| doi = 10.1038/37918
| bibcode=1997Natur.389...33K
}}</ref>
 
By the mid-to-late Devonian, most groups of plants had independently developed a rooting system of some nature.<ref name=KCpaper/> As roots became larger, they could support larger trees, and the soil was weathered to a greater depth.<ref name=Algeo1995/> This deeper weathering had effects not only on the aforementioned drawdown of {{co2}}, but also opened up new habitats for colonisation by fungi and animals.<ref name=Algeo1998/>
 
Roots today have developed to the physical limits. They penetrate many{{Quantify|date=April 2008}} metres of soil to tap the water table.{{Verify source|date=April 2008}} The narrowest roots are a mere 40&nbsp;μm in diameter, and could not physically transport water if they were any narrower.<ref name=Raven2001>{{cite journal
| author = Raven, J.A.
| coauthors = Edwards, D.
| year = 2001
| title = Roots: evolutionary origins and biogeochemical significance
| journal = Journal of Experimental Botany
| volume = 52
| issue = 90001
| pages = 381–401
| url=http://jxb.oxfordjournals.org/cgi/content/full/52/suppl_1/381
| doi = 10.1093/jexbot/52.suppl_1.381
| language = active DOI due to publisher error (2008-04-30)
| pmid=11326045
}}</ref>
The earliest fossil roots recovered, by contrast, narrowed from 3&nbsp;mm to under 700&nbsp;μm in diameter; of course, [[taphonomy]] is the ultimate control of what thickness can be seen.<ref name=Raven2001/>
 
====Arbuscular mycorrhizae====
The efficiency of many plants' roots is increased via a [[wikt:symbiotic|symbiotic]] relationship with a fungal partner. The most common are [[arbuscular mycorrhizae]] (AM), literally "tree-like fungal roots". These comprise fungi that invade some root cells, filling the cell membrane with their [[wikt:hypha|hypha]]e. They feed on the plant's sugars, but return nutrients generated or extracted from the soil (especially phosphate), which the plant would otherwise have no access to.
 
This symbiosis appears to have evolved early in plant history. AM are found in all plant groups, and 80% of extant vascular plants,<ref name=schuessler>{{cite journal | author = Schüßler, A. | year=2001 | title=A new fungal phylum, the ''Glomeromycota'': phylogeny and evolution | journal=Mycol. Res. | volume=105 | issue=12 | pages=1416 | url=http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=95091 | doi=10.1017/S0953756201005196 | display-authors = 1 | last2 = Schwarzott | first2 = Daniel | last3 = Walker | first3 = Christopher}}</ref> suggesting an early ancestry; a "plant"-fungus symbiosis may even have been the step that enabled them to colonise the land,.<ref name="simon">{{cite doi|10.1038/363067a0}}</ref> Such fungi increase the productivity even of simple plants such as liverworts.<ref name="Brundrett2002a">{{cite doi|10.1038/ncomms1105}}</ref> Indeed, AM are abundant in the Rhynie chert;<ref name="remy">{{cite doi|10.1073/pnas.91.25.11841}}</ref> the association occurred even before there were true roots to colonise, and some have suggested that roots evolved to provide a more comfortable habitat for mycorrhizal fungi.<ref name=Brundrett2002>{{cite doi|10.1046/j.1469-8137.2002.00397.x
}}</ref>
 
===Seeds===
[[File:Trigonocarpus.jpg|thumb|The fossil seed ''[[Trigonocarpus]]'']]
[[File:Runcaria megasporangium and cupule drawing.jpg|thumb|75px|The transitional fossil ''Runcaria'']]
Early land plants reproduced in the fashion of ferns: spores germinated into small gametophytes, which produced sperm. These would swim across moist soils to find the female organs (archegonia) on the same or another gametophyte, where they would fuse with an ovule to produce an embryo, which would germinate into a sporophyte.<ref name=Algeo1998>{{cite journal
| author = Algeo, T.J.
| coauthors = Scheckler, S.E.
| year = 1998
| title = Terrestrial-marine teleconnections in the Devonian: links between the evolution of land plants, weathering processes, and marine anoxic events
| journal = [[Philosophical Transactions of the Royal Society B]]
| volume = 353
| issue = 1365
| pages = 113–130
| doi = 10.1098/rstb.1998.0195
}}</ref>
 
Heterosporic organisms, as their name suggests, bear spores of two sizes&nbsp;– microspores and megaspores. These would germinate to form microgametophytes and megagametophytes, respectively. This system paved the way for seeds: taken to the extreme, the megasporangia could bear only a single megaspore tetrad, and to complete the transition to true seeds, three of the megaspores in the original tetrad could be aborted, leaving one megaspore per megasporangium.
 
The transition to seeds continued with this megaspore being "boxed in" to its sporangium while it germinates. Then, the megagametophyte is contained within a waterproof integument, which forms the bulk of the seed. The microgametophyte&nbsp;– a pollen grain which has germinated from a microspore&nbsp;– is employed for dispersal, only releasing its desiccation-prone sperm when it reaches a receptive megagametophyte.<ref name=gk/>
 
Lycopods go a fair way down the path to seeds without ever crossing the threshold. Fossil lycopod megaspores reaching 1&nbsp;cm in diameter, and surrounded by vegetative tissue, are known&nbsp;– these even germinate into a megagametophyte ''in situ''. However, they fall short of being seeds, since the nucellus, an inner spore-covering layer, does not completely enclose the spore. A very small slit remains, meaning that the seed is still exposed to the atmosphere. This has two consequences&nbsp;– firstly, it means it is not fully resistant to desiccation, and secondly, sperm do not have to "burrow" to access the archegonia of the megaspore.<ref name=gk/>
 
A middle [[Devonian]] [[transitional fossil|precursor]] to seed plants from Belgium has been identified predating the earliest [[seed plants]] by about 20 million years. ''[[Runcaria]]'', small and radially symmetrical, is an integumented [[megasporangium]] surrounded by a cupule. The [[megasporangium]] bears an unopened distal extension protruding above the multilobed [[integument]]. It is suspected that the extension was involved in anemophilous [[pollination]]. ''Runcaria'' sheds new light on the sequence of character acquisition leading to the seed. ''Runcaria'' has all of the qualities of seed plants except for a solid [[seed coat]] and a system to guide the pollen to the seed.<ref>{{Cite web | title = Science Magazine | work = Runcaria, a Middle Devonian Seed Plant Precursor | publisher = American Association for the Advancement of Science | year = 2011 | url = http://www.sciencemag.org/content/306/5697/856.abstract | accessdate = March 22, 2011 }}</ref>
 
The first spermatophytes (literally: "seed plants")&nbsp;– that is, the first plants to bear true seeds&nbsp;– are called '''[[pteridosperm]]s''': literally, "seed ferns", so called because their foliage consisted of fern-like fronds, although they were not closely related to ferns. The oldest fossil evidence of seed plants is of Late Devonian age and they appear to have evolved out of an earlier group known as the [[progymnosperms]]. These early seed plants ranged from trees to small, rambling shrubs; like most early progymnosperms, they were woody plants with fern-like foliage. They all bore ovules, but no cones, fruit or similar. While it is difficult to track the early evolution of seeds, the lineage of the seed ferns may be traced from the simple trimerophytes through homosporous [[Aneurophytes]].<ref name=gk/>
 
This seed model is shared by basically all gymnosperms (literally: "naked seeds"), most of which encase their seeds in a woody or fleshy (the [[Taxus|yew]], for example) cone, but none of which fully enclose their seeds. The angiosperms ("vessel seeds") are the only group to fully enclose the seed, in a carpel.
 
Fully enclosed seeds opened up a new pathway for plants to follow: that of [[seed dormancy]]. The embryo, completely isolated from the external atmosphere and hence protected from desiccation, could survive some years of drought before germinating.
Gymnosperm seeds from the late Carboniferous have been found to contain embryos, suggesting a lengthy gap between fertilisation and germination.<ref name="Mapes1989
">{{cite journal
| author = Mapes, G.
| coauthors = Rothwell, G.W.; Haworth, M.T.
| year = 1989
| title = Evolution of seed dormancy
| journal = Nature
| volume = 337
| issue = 6208
| pages = 645–646
| doi = 10.1038/337645a0
|bibcode = 1989Natur.337..645M }}</ref> This period is associated with the entry into a [[greenhouse earth]] period, with an associated increase in aridity. This suggests that dormancy arose as a response to drier climatic conditions, where it became advantageous to wait for a moist period before germinating.<ref name=Mapes1989/> This evolutionary breakthrough appears to have opened a floodgate: previously inhospitable areas, such as dry mountain slopes, could now be tolerated, and were soon covered by trees.<ref name=Mapes1989/>
 
Seeds offered further advantages to their bearers: they increased the success rate of fertilised gametophytes, and because a nutrient store could be "packaged" in with the embryo, the seeds could germinate rapidly in inhospitable environments, reaching a size where it could fend for itself more quickly.<ref name=Algeo1998/> For example, without an endosperm, seedlings growing in arid environments would not have the reserves to grow roots deep enough to reach the water table before they expired from dehydration.<ref name=Algeo1998/> Likewise, seeds germinating in a gloomy understory require an additional reserve of energy to quickly grow high enough to capture sufficient light for self-sustenance.<ref name=Algeo1998/>
A combination of these advantages gave seed plants the ecological edge over the previously dominant genus ''Archaeopteris'', thus increasing the biodiversity of early forests.<ref name=Algeo1998/>
 
Despite these advantages, it is common for fertilized ovules to fail to mature as seeds.<ref>Bawa KS, Webb CJ (1984). Flower, fruit and seed abortion in tropical forest trees. Implications for the evolution of paternal and maternal reproductive patterns" ''American Journal of Botany'' 71(5)  736-751.</ref> Also during seed dormancy (often associated with unpredictable and stressful conditions) DNA damages accumulate.<ref>{{cite journal |author=Cheah KS, Osborne DJ |title=DNA lesions occur with loss of viability in embryos of ageing rye seed |journal=Nature |volume=272 |issue=5654 |pages=593–9 |date=April 1978 |pmid=19213149 |doi=  10.1038/272593a0|url=|bibcode = 1978Natur.272..593C }}</ref><ref>{{cite journal |author=Koppen G, Verschaeve L |title=The alkaline single-cell gel electrophoresis/comet assay: a way to study DNA repair in radicle cells of germinating Vicia faba |journal=Folia Biol. (Praha) |volume=47 |issue=2 |pages=50–4 |year=2001 |pmid=11321247 |doi= |url=}}</ref><ref>{{cite journal |author=Bray CM, West CE |title=DNA repair mechanisms in plants: crucial sensors and effectors for the maintenance of genome integrity |journal=New Phytol. |volume=168 |issue=3 |pages=511–28 |date=December 2005 |pmid=16313635 |doi=10.1111/j.1469-8137.2005.01548.x |url=}}</ref>  Thus DNA damage appears to be a basic problem for survival of seed plants, just as [[DNA damage (naturally occurring)#DNA damages are a major problem for life|DNA damages are a major problem for life in general]].<ref>Bernstein C, Bernstein H. (1991) Aging, Sex, and DNA Repair. Academic Press, San Diego. ISBN 0120928604  ISBN 978-0120928606</ref> (Bernstein and Bernstein, 1991).
 
===Flowers{{anchor|Flowers}}===
''For a more ecological discussion on the evolution of flowers, go to [[Flower]]''
[[File:Crossotheca nodule.JPG|thumb|right|The pollen bearing organs of the early "flower" ''[[Crossotheca]]'']]
Flowers are modified leaves possessed only by the [[angiosperm]]s, which are relatively late to appear in the fossil record; the group originated and diversified during the Early Cretaceous and became ecologically significant thereafter.<ref name="Feild2011">{{cite doi|10.1073/pnas.1014456108}}</ref> Flower-like structures first appear in the [[fossil]] records some ~130 mya, in the [[Cretaceous]] period.<ref name="Lawton-Rauh">{{cite journal | author=Lawton-Rauh A. | title = Molecular evolution of flower development | journal=Trends in Ecology and Evolution | volume=15 | issue=4 | pages=144–149 | year=2000 | doi=10.1016/S0169-5347(99)01816-9 | pmid=10717683 | last2=Alvarez-Buylla | first2=ER | last3=Purugganan | first3=MD}}</ref>
Colourful and/or pungent structures surround the cones of plants such as [[cycads]] and [[gnetales]], making a strict definition of the term "flower" elusive.<ref name=Bateman2006/>
 
The main function of a flower is [[reproduction]], which, before the evolution of the flower and [[angiosperms]], was the job of microsporophylls and megasporophylls. A flower can be considered a powerful evolutionary [[innovation]], because its presence allowed the plant world to access new means and mechanisms for reproduction.
[[File:syncarp evolution.svg|thumb|left|The evolution of syncarps. <br>a: sporangia borne at tips of leaf<br>
b: Leaf curls up to protect sporangia
<br>c: leaf curls to form enclosed roll<br>
d: grouping of three rolls into a syncarp]]
 
The flowering plants have long been assumed to have evolved from within the [[gymnosperms]]; according to the traditional morphological view, they are closely allied to the [[gnetales]]. However, as noted above, recent molecular evidence is at odds to this hypothesis,<ref name=Chaw2000/><ref name=Soltis2002/> and further suggests that gnetales are more closely related to some gymnosperm groups than angiosperms,<ref name=Bowe2000/> and that [[wikt:extant|extant]] gymnosperms form a distinct clade to the angiosperms,<ref name=Chaw2000/><ref name=Soltis2002/><ref name=Bowe2000/> the two clades diverging some {{Ma|300}}.<ref name=Nam2003>{{cite journal | url=http://mbe.oxfordjournals.org/cgi/content/full/20/9/1435 |title=Antiquity and Evolution of the MADS-Box Gene Family Controlling Flower Development in Plants | first4=M | last4=Nei | first3=H | last3=Ma | journal=Mol. Biol. Evol. | first2=CW | volume=20 | issue=9 | last2=Depamphilis | pages=1435–1447 | year=2003 | pmid=12777513 | doi = 10.1093/molbev/msg152 |author=Nam, J.}}</ref>
 
{{further|Gnetophyta#Classification}}
 
The relationship of [[stem group]]s to the [[angiosperms]] is important in determining the evolution of flowers. stem groups provide an insight into the state of earlier "forks" on the path to the current state. Convergence increases the risk of misidentifying stem groups. Since the protection of the [[megagametophyte]] is evolutionarily desirable, probably many separate groups evolved protective encasements independently. In flowers, this protection takes the form of a [[carpel]], evolved from a leaf and recruited into a protective role, shielding the ovules. These ovules are further protected by a double-walled [[wikt:integument|integument]].
 
Penetration of these protective layers needs something more than a free-floating [[microgametophyte]]. [[Angiosperms]] have pollen grains comprising just three cells. One cell is responsible for drilling down through the integuments, and creating a conduit for the two sperm cells to flow down. The megagametophyte has just seven cells; of these, one fuses with a sperm cell, forming the nucleus of the egg itself, and another joins with the other sperm, and dedicates itself to forming a nutrient-rich [[endosperm]]. The other cells take auxiliary roles.{{Clarify|date=April 2008}} This process of "[[double fertilisation]]" is unique and common to all angiosperms.
 
[[File:Bennettitales-cycadeoidaceae.jpg|thumb|right|The inflorescences of the [[Bennettitales]] are strikingly similar to flowers]]
In the fossil record, there are three intriguing groups which bore flower-like structures. The first is the [[Permian]] pteridosperm ''[[Glossopteris]]'', which already bore recurved leaves resembling carpels. The [[Triassic]] ''[[Caytonia]]'' is more flower-like still, with enclosed ovules&nbsp;– but only a single integument. Further, details of their pollen and stamens set them apart from true flowering plants.
 
The [[Bennettitales]] bore remarkably flower-like organs, protected by whorls of [[wikt:bract|bract]]s which may have played a similar role to the petals and sepals of true flowers; however, these flower-like structures evolved independently, as the Bennettitales are more closely related to [[cycad]]s and [[ginkgo]]s than to the angiosperms.<ref name=Crepet2000>{{cite journal|url=http://www.pnas.org/cgi/reprint/97/24/12939
| doi = 10.1073/pnas.97.24.12939|pmc=34068
| title = Progress in understanding angiosperm history, success, and relationships: Darwin's abominably "perplexing phenomenon"|pmid=11087846
| year = 2000
| author = Crepet, W. L.
| journal = Proceedings of the National Academy of Sciences
| volume = 97|issue=24
| pages = 12939–41|bibcode = 2000PNAS...9712939C }}</ref>
 
However, no true flowers are found in any groups save those extant today. Most morphological and molecular analyses place ''[[Amborella]]'', the [[nymphaeales]] and [[Austrobaileya]]ceae in a basal clade dubbed "ANA". This clade appear to have diverged in the early Cretaceous, around {{Ma|130}}&nbsp;– around the same time as the [[Archaeofructus|earliest fossil angiosperm]],<ref name="Sun2002
">{{cite journal
| author = Sun, G.
| coauthors = Ji, Q.; Dilcher, D.L.; Zheng, S.; Nixon, K.C.; Wang, X.
| year = 2002
| title = Archaefructaceae, a New Basal Angiosperm Family
| journal = Science
| pmid = 11988572
| volume = 296
| issue = 5569
| pages = 899–904
| doi = 10.1126/science.1069439
|bibcode = 2002Sci...296..899S }}</ref><ref name=Friis2003>In fact, ''Archaeofructus'' probably didn't bear true flowers: see
*{{cite journal
| author = Friis, E.M.
| coauthors = Doyle, J.A.; Endress, P.K.; Leng, Q.
| year = 2003
| title = Archaefructus--angiosperm precursor or specialized early angiosperm?
| journal = Trends in Plant Science
| pmid = 12927969
| volume = 8
| issue = 8
| pages = 369–373
| doi = 10.1016/S1360-1385(03)00161-4
}}</ref> and just after the [[Clavatipollenites|first angiosperm-like pollen]], 136 million years ago.<ref name=Frohlich2007>{{cite journal
| author = Frohlich, M.W.
| coauthors = Chase, M.W.
| year = 2007
| title = After a dozen years of progress the origin of angiosperms is still a great mystery
| journal = Nature
| pmid = 18097399
| volume = 450
| issue = 7173
| pages = 1184–9
| doi = 10.1038/nature06393
|bibcode = 2007Natur.450.1184F }}</ref>
The [[magnoliids]] diverged soon after, and a rapid radiation had produced eudicots and monocots by {{Ma|125}}.<ref name=Frohlich2007/> By the end of the Cretaceous {{Ma|{{period end|Cretaceous}}}}, over 50% of today's angiosperm orders had evolved, and the clade accounted for 70% of global species.<ref name=Wing1998>{{cite journal
| author = Wing, S.L.
| coauthors = Boucher, L.D.
| year = 1998
| title = Ecological Aspects Of The Cretaceous Flowering Plant Radiation
| journal = Annual Reviews in Earth and Planetary Sciences
| volume = 26
| issue = 1
| pages = 379–421
| doi = 10.1146/annurev.earth.26.1.379
|bibcode = 1998AREPS..26..379W }}</ref>
It was around this time that flowering trees became dominant over [[conifer]]s <ref>Wilson Nichols Stewart & Gar W. Rothwell‏, '''Paleobotany and the evolution of plants''', 2nd ed., Cambridge Univ. Press 1993, p. 498</ref>
 
The features of the basal "ANA" groups suggest that angiosperms originated in dark, damp, frequently disturbed areas.<ref name="Feild2004
">{{cite journal
| author = Feild, T.S.
| coauthors = Arens, N.C.; Doyle, J.A.; Dawson, T.E.; Donoghue, M.J.
| year = 2004
| title = Dark and disturbed: a new image of early angiosperm ecology
| journal = Paleobiology
| volume = 30
| issue = 1
| pages = 82–107
| url=http://paleobiol.geoscienceworld.org/cgi/content/abstract/30/1/82
| accessdate = 2008-04-08
| doi = 10.1666/0094-8373(2004)030<0082:DADANI>2.0.CO;2
| format = abstract
| issn = 0094-8373
}}</ref> It appears that the angiosperms remained constrained to such habitats throughout the Cretaceous&nbsp;– occupying the niche of small herbs early in the successional series.<ref name=Wing1998/> This may have restricted their initial significance, but given them the flexibility that accounted for the rapidity of their later diversifications in other habitats.<ref name=Feild2004/>
{{anthophyta}}
 
====Origins of the flower====
[[File:Amborella.jpg| thumb | 200px | left | ''[[Amborella trichopoda]]'' : [[Amborellaceae]] is considered the sister family of all other flowering plants ''(magnified image of male flower)'']]
The family [[Amborellaceae]] is regarded as being the sister [[cladistics|clade]] to all other living flowering plants. The complete genome of ''Amborella trichopoda'' is still being sequenced {{as of|2012|March|lc=yes}}. By comparing its genome with those of all other living flowering plants, it will be possible to work out the most likely characteristics of the ancestor of ''A. trichopoda'' and all other flowering plants, i.e. the ancestral flowering plant.<ref>{{Cite journal |author=Zuccolo, A. |year=2011 |title=A physical map for the ''Amborella trichopoda'' genome sheds light on the evolution of angiosperm genome structure |journal=Genome Biology |volume=12 |issue=5 |page=R48 |doi=10.1186/gb-2011-12-5-r48 |display-authors=1 |last2=Bowers |first2=John E |last3=Estill |first3=James C |last4=Xiong |first4=Zhiyong |last5=Luo |first5=Meizhong |last6=Sebastian |first6=Aswathy |last7=Goicoechea |first7=José |last8=Collura |first8=Kristi |last9=Yu |first9=Yeisoo }}</ref>
 
It seems that on the level of the organ, the [[leaf]] may be the ancestor of the flower, or at least some floral organs. When some crucial genes involved in flower development are [[mutate]]d, clusters of leaf-like structures arise in place of flowers. Thus, sometime in history, the developmental program leading to formation of a leaf must have been altered to generate a flower. There probably also exists an overall robust framework within which the floral diversity has been generated. An example of that is a gene called ''[[LEAFY]] (LFY)'', which is involved in flower development in ''[[Arabidopsis thaliana]]''. The [[homology (biology)|homologs]] of this gene are found in [[angiosperms]] as diverse as [[tomato]], [[Antirrhinum|snapdragon]], [[pea]], [[maize]] and even [[gymnosperms]]. Expression of ''Arabidopsis thaliana'' LFY in distant plants like [[poplar]] and [[citrus]] also results in flower-production in these plants. The ''LFY'' gene regulates the expression of some genes belonging to the [[MADS-box]] family. These genes, in turn, act as direct controllers of flower development.
 
====Evolution of the MADS-box family====
The members of the [[MADS-box]] family of transcription factors play a very important and evolutionarily conserved role in flower development. According to the [[The ABC Model of Flower Development|ABC Model of flower development]], three zones&nbsp;— A,B and C&nbsp;— are generated within the developing flower primordium, by the action of some [[transcription factors]], that are members of the [[MADS-box]] family. Among these, the functions of the B and C domain genes have been evolutionarily more conserved than the A domain gene. Many of these genes have arisen through [[gene duplication]]s of ancestral members of this family. Quite a few of them show redundant functions.
 
The evolution of the [[MADS-box]] family has been extensively studied. These genes are present even in [[pteridophytes]], but the spread and diversity is many times higher in [[angiosperms]].<ref>{{cite journal | author=Medarg NG and Yanofsky M | title = Function and evolution of the plant MADS-box gene family | journal=Nature Reviews Genetics  | volume=2 | pages=186–195 |date=March 2001 | url=http://www.nature.com/nrg/journal/v2/n3/full/nrg0301_186a.html | issue=3 | doi=10.1038/35056041}}</ref> There appears to be quite a bit of pattern into how this family has evolved. Consider the evolution of the C-region gene ''[[AGAMOUS]] (AG)''. It is expressed in today's flowers in the [[stamens]], and the [[carpel]], which are reproductive organs. Its ancestor in [[gymnosperms]] also has the same expression pattern. Here, it is expressed in the [[Strobilus|strobili]], an organ that produces [[pollen]] or ovules.<ref>{{cite journal | author=Jager | title = MADS-Box Genes in Ginkgo biloba and the Evolution of the AGAMOUS Family | journal=Mol. Biol. And Evol. | volume=20 | issue=5 | pages=842–854| year=2003 | doi = 10.1093/molbev/msg089 | pmid=12679535 | last2=Hassanin | first2=A | last3=Manuel | first3=M | last4=Le Guyader | first4=H | last5=Deutsch | first5=J | url=http://mbe.oxfordjournals.org/cgi/content/full/20/5/842 | display-authors=1}}</ref> Similarly, the B-genes' ''(AP3 and PI)'' ancestors are expressed only in the male organs in [[gymnosperms]]. Their descendants in the modern angiosperms also are expressed only in the [[stamens]], the male reproductive organ. Thus, the same, then-existing components were used by the plants in a novel manner to generate the first flower. This is a recurring pattern in [[evolution]].
 
===Factors influencing floral diversity===
{{wikiversity-bc|Linaria vulgaris}}
There is enormous variation in the developmental programs of plants. For example, grasses possess unique floral structures. The carpels and stamens are surrounded by scale-like [[monocot|lodicules]] and two bracts: the lemma and the palea. Genetic evidence and morphology suggest that lodicules are homologous to [[eudicot]] petals.<ref name="Thompsom">[http://www.plantphysiol.org/content/149/1/38.full Translational Biology: From Arabidopsis Flowers to Grass Inflorescence Architecture. Beth E. Thompson* and Sarah Hake, 2009], Plant Physiology 149:38-45.</ref> The palea and lemma may be homologous to sepals in other groups, or may be unique grass structures. The genetic evidence is not clear.
 
Variation in floral structure is typically due to slight changes in the MADS-box genes and their expression pattern.
 
Another example is that of ''[[Linaria vulgaris]]'', which has two kinds of flower symmetries-[[Symmetry in biology#Radial symmetry|radial]] and [[Symmetry in biology#Bilateral symmetry|bilateral]]. These symmetries are due to [[epigenetic]] changes in just one gene called ''CYCLOIDEA''.<ref name="Lawton-Rauh A. et al. 2000 144–149">{{cite journal | author=Lawton-Rauh A. | title = Molecular evolution of flower development | journal=Trends in Ecol. And Evol. | volume=15 | issue=4 | pages=144–149 | year=2000 | url=http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VJ1-40D6284-X&_user=1111158&_coverDate=04%2F01%2F2000&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000051676&_version=1&_urlVersion=0&_userid=1111158&md5=c9e34ee50c60723d79efd0441b1be815 | doi=10.1016/S0169-5347(99)01816-9 | author-separator=, | display-authors=1 | last2=Alvarez-Buylla | first2=Elena R. | last3=Purugganan | first3=Michael D. | pmid=10717683}}</ref>
[[File:Pink rose albury botanical gardens.jpg| thumb | 200px | right | Large number of [[petals]] in [[rose]]s is the result of human selection]]
''Arabidopsis thaliana'' has a gene called ''[[AGAMOUS]]'' that plays an important role in defining how many [[petals]] and [[sepals]] and other organs are generated. Mutations in this gene give rise to the floral [[meristem]] obtaining an indeterminate fate, and many floral organs keep on getting produced. [[Rose]]s, [[carnations]] and [[morning glory]], for example, that have very dense floral organs. These flowers have been selected by horticulturists for increased number of [[petals]]. Researchers have found that the morphology of these flowers is because of strong [[mutations]] in the ''AGAMOUS'' homolog in these plants, which leads to them making a large number of petals and sepals.<ref>{{cite journal | author=Kitahara K and Matsumoto S. | title = Rose MADS-box genes 'MASAKO C1 and D1' homologous to class C floral identity genes | journal=Plant Science | volume=151| pages=121–134 | year=2000 | pmid=10808068 | issue=2 | url=http://www.ingentaconnect.com/content/els/01689452/2000/00000151/00000002/art00206 | doi=10.1016/S0168-9452(99)00206-X}}</ref> Several studies on diverse plants like [[petunia]], [[tomato]], [[Impatiens]], [[maize]] etc. have suggested that the enormous diversity of flowers is a result of small changes in [[genes]] controlling their development.<ref>{{cite journal | author=Kater M | title = Multiple AGAMOUS Homologs from Cucumber and Petunia Differ in Their Ability to Induce Reproductive Organ Fate | journal=Plant Cell | volume=10| pages=171–182 | year=1998 | doi = 10.1105/tpc.10.2.171 | pmid=9490741 | issue=2 | pmc=143982 | url=http://www.plantcell.org/cgi/content/full/10/2/171 | author-separator=, | display-authors=1 | last2=Colombo | first2=L | last3=Franken | first3=J | last4=Busscher | first4=M | last5=Masiero | first5=S | last6=Van Lookeren Campagne | first6=MM | last7=Angenent | first7=GC}}</ref>
 
Some of these changes also cause changes in expression patterns of the developmental genes, resulting in different [[phenotypes]]. The [[Floral Genome Project]] looked at the [[Expressed sequence tag|EST]] data from various tissues of many flowering plants. The researchers confirmed that the [[ABC Model of flower development]] is not conserved across all [[angiosperms]]. Sometimes expression domains change, as in the case of many [[monocots]], and also in some basal angiosperms like ''[[Amborella]]''. Different models of flower development like the ''Fading boundaries model'', or the ''Overlapping-boundaries model'' which propose non-rigid domains of expression, may explain these architectures.<ref>{{cite journal | author=Soltis D | title = The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression | journal=Trends in Plant Sci. | volume=12 | issue=8 | pages=358–367 | year=2007 | url=http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD1-4P77GFC-2&_user=1111158&_coverDate=08%2F31%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000051676&_version=1&_urlVersion=0&_userid=1111158&md5=36555b3b2c6bcb8eae785961b010f2c9 | doi=10.1016/j.tplants.2007.06.012 | author-separator=, | display-authors=1 | last2=Ma | first2=Hong | last3=Frohlich | first3=Michael W. | last4=Soltis | first4=Pamela S. | last5=Albert | first5=Victor A. | last6=Oppenheimer | first6=David G. | last7=Altman | first7=Naomi S. | last8=Depamphilis | first8=Claude | last9=Leebens-Mack | first9=Jim}}</ref> There is a possibility that from the basal to the modern angiosperms, the domains of floral architecture have gotten more and more fixed through evolution.
 
====Flowering time====
Another floral feature that has been a subject of [[natural selection]] is flowering time. Some plants flower early in their life cycle, others require a period of [[vernalization]] before flowering. This decision is based on factors like [[temperature]], [[intensity (physics)|light intensity]], presence of [[pollinators]] and other environmental signals: genes like ''CONSTANS (CO)'', ''[[Flowering Locus C]]'' (''FLC'') and ''FRIGIDA'' regulate integration of environmental signals into the pathway for flower development. Variations in these loci have been associated with flowering time variations between plants. For example, ''[[Arabidopsis thaliana]]'' ecotypes that grow in the cold, [[temperate]] regions require prolonged vernalization before they flower, while the [[tropical]] varieties, and the most common lab strains, don't. This variation is due to mutations in the ''FLC'' and ''FRIGIDA'' genes, rendering them non-functional.<ref>{{cite journal | author=Putterhill | title = It's time to flower: the genetic control of flowering time | doi=10.1002/bies.20021 |pmid=15057934 | journal=BioEssays | volume=26 | issue=4 | pages=353–363 | year=2004 | url=http://www3.interscience.wiley.com/cgi-bin/abstract/107640082/ABSTRACT | display-authors=1 | last2=Laurie | first2=Rebecca | last3=MacKnight | first3=Richard}}</ref>
 
Quite a few players in this process are conserved across all the plants studied. Sometimes though, despite genetic conservation, the mechanism of action turns out to be different. For example, [[rice]] is a short-day plant, while ''[[Arabidopsis thaliana]]'' is a long-day plant. Now, in both plants, the proteins ''CO'' and ''FLOWERING LOCUS T (FT)'' are present. But, in ''Arabidopsis thaliana'', ''CO'' enhances ''FT'' production, while in rice, the ''CO'' homolog represses ''FT'' production, resulting in completely opposite downstream effects.<ref>{{cite journal | author=Blazquez | title = Flowering on time: genes that regulate the floral transition | journal=EMBO Reports | volume=2 | issue=12 | pages=1078–1082 | year=2001 | pmid=11743019 | last2=Koornneef | first2=M | last3=Putterill | first3=J | doi=10.1093/embo-reports/kve254 | pmc=1084172 | url=http://www.nature.com/embor/journal/v2/n12/full/embor267.html | display-authors=1}}</ref>
 
====Theories of flower evolution====
There are many theories that propose how flowers evolved. Some of them are described below.
 
The ''Anthophyte Theory'' was based on the observation that a gymnospermic group [[Gnetae|Gnetales]] has a flower-like [[ovule]]. It has partially developed [[vessel element|vessels]] as found in the [[angiosperms]], and the [[megasporangium]] is covered by three envelopes, like the [[ovary]] structure of angiosperm flowers. However, many other lines of evidence show that Gnetales is not related to angiosperms.<ref name=Crepet2000>{{cite journal|url=http://www.pnas.org/cgi/reprint/97/24/12939
| doi = 10.1073/pnas.97.24.12939
| title = Progress in understanding angiosperm history, success, and relationships: Darwin's abominably "perplexing phenomenon"
| year = 2000
| author = Crepet, W. L.
| journal = Proceedings of the National Academy of Sciences
| volume = 97
| pages = 12939–41|pmid=11087846|issue=24|pmc=34068|bibcode = 2000PNAS...9712939C }}</ref>
{{Further|anthophyta}}
 
The ''Mostly Male Theory'' has a more genetic basis. Proponents of this theory point out that the gymnosperms have two very similar copies of the gene ''LFY'', while angiosperms just have one. [[Molecular clock]] analysis has shown that the other ''LFY'' paralog was lost in angiosperms around the same time as flower fossils become abundant, suggesting that this event might have led to floral evolution.<ref>{{cite journal | author=Lawton-Rauh A. | title = The Mostly Male Theory of Flower Evolutionary Origins: from Genes to Fossils | journal=Sys.Botany | volume=25 | issue=2 | pages=155–170 | year=2000 | doi = 10.2307/2666635 | publisher=American Society of Plant Taxonomists | jstor=2666635 | author-separator=, | display-authors=1 | author2=<Please add first missing authors to populate metadata.>}}</ref> According to this theory, loss of one of the ''LFY'' [[paralog]] led to flowers that were more male, with the [[ovules]] being expressed ectopically. These ovules initially performed the function of attracting [[pollinators]], but sometime later, may have been integrated into the core flower.
 
==Evolution of photosynthetic pathways==
[[File:HatchSlackpathway2.svg|thumb|300px|The C<sub>4</sub> carbon concentrating mechanism]]
{{main|Evolution of photosynthesis}}
The [[C4 carbon fixation|C<sub>4</sub> metabolic pathway]] is a valuable recent evolutionary innovation in plants, involving a complex set of adaptive changes to [[physiology]] and [[gene expression]] patterns.<ref name = "williamsjohnston">{{cite journal | author = Williams BP, Johnston IG, Covshoff S, Hibberd JM | title = Phenotypic landscape inference reveals multiple evolutionary paths to C₄ photosynthesis | journal = eLife | volume = 2 | pages = e00961 |date=September 2013 | doi = 10.7554/eLife.00961}}</ref>
 
[[Photosynthesis]] is not quite as simple as adding water to {{co2}} to produce sugars and oxygen. A complex chemical pathway is involved, facilitated along the way by a range of [[enzymes]] and co-enzymes. The [[enzyme]] [[RuBisCO]] is responsible for "fixing" {{co2}}&nbsp;– that is, it attaches it to a carbon-based molecule to form a sugar, which can be used by the plant, releasing an oxygen molecule along the way. However, the enzyme is notoriously inefficient, and just as effectively will also fix oxygen instead of {{co2}} in a process called [[photorespiration]]. This is energetically costly as the plant has to use energy to turn the products of photorespiration back into a form that can react with {{co2}}.
 
===Concentrating carbon===
C<sub>4</sub> plants evolved carbon concentrating mechanisms. These work by increasing the concentration of {{co2}} around RuBisCO, thereby facilitating photosynthesis and decreasing photorespiration. The process of concentrating {{co2}} around RuBisCO requires more energy than allowing gases to [[diffusion|diffuse]], but under certain conditions&nbsp;– i.e. warm temperatures (>25°C), low {{co2}} concentrations, or high oxygen concentrations&nbsp;– pays off in terms of the decreased loss of sugars through photorespiration.
 
One type of C<sub>4</sub> metabolism employs a so-called [[Kranz anatomy]]. This transports {{co2}} through an outer mesophyll layer, via a range of organic molecules, to the central bundle sheath cells, where the {{co2}} is released. In this way, {{co2}} is concentrated near the site of RuBisCO operation. Because RuBisCO is operating in an environment with much more {{co2}} than it otherwise would be, it performs more efficiently.
 
A second mechanism, [[CAM photosynthesis]], temporally separates photosynthesis from the action of RuBisCO. RuBisCO only operates during the day, when stomata are sealed and {{co2}} is provided by the breakdown of the chemical [[malate]]. More {{co2}} is then harvested from the atmosphere when stomata open, during the cool, moist nights, reducing water loss.
 
===Evolutionary record===
These two pathways, with the same effect on RuBisCO, evolved a number of times independently&nbsp;– indeed, C<sub>4</sub> alone arose 62 times in 18 different plant [[family (biology)|families]].  A number of 'pre-adaptations' seem to have paved the way for C4, leading to its clustering in certain clades: it has most frequently been innovated in plants that already had features such as extensive vascular bundle sheath tissue.<ref name="Christin2012">{{cite doi|10.1073/pnas.1216777110 }}</ref> Many potential evolutionary pathways resulting in the {{c4}} [[phenotype]] are possible and have been characterised using [[Bayesian inference]],<ref name = "williamsjohnston">{{cite journal | author = Williams BP, Johnston IG, Covshoff S, Hibberd JM | title = Phenotypic landscape inference reveals multiple evolutionary paths to C₄ photosynthesis | journal = eLife | volume = 2 | pages = e00961 |date=September 2013 | doi = 10.7554/eLife.00961}}</ref> confirming that non-photosynthetic adaptations often provide evolutionary stepping stones for the further evolution of {{c4}}.
 
The C<sub>4</sub> construction is most famously used by a subset of grasses, while CAM is employed by many succulents and [[cacti]]. The trait appears to have emerged during the [[Oligocene]], around {{Ma|25|32}};<ref name=Osborne2006>{{cite journal
| author = Osborne, C.P.
| coauthors = Beerling, D.J.
| year = 2006
| title = Review. Nature's green revolution: the remarkable evolutionary rise of C<sub>4</sub> plants
| journal = [[Philosophical Transactions of the Royal Society B]]
| volume = 361
| pmid = 16553316
| issue = 1465
| pages = 173–194
| url = http://www.journals.royalsoc.ac.uk/index/YTH8204514044972.pdf
| pmc = 1626541
| accessdate = 2008-02-11
| doi = 10.1098/rstb.2005.1737
}}</ref> however, they did not become ecologically significant until the [[Miocene]], {{Ma|6|7}}.<ref name=Retallack1997/> Remarkably, some charcoalified fossils preserve tissue organised into the Kranz anatomy, with intact bundle sheath cells,<ref name=Thomasson1986>{{cite journal
| author = Thomasson, J.R.
| coauthors = Nelson, M.E.; Zakrzewski, R.J.
| year = 1986
| title = A Fossil Grass (Gramineae: Chloridoideae) from the Miocene with Kranz Anatomy
| journal = Science
| pmid = 17752216
| volume = 233
| issue = 4766
| pages = 876–878
| doi = 10.1126/science.233.4766.876
|bibcode = 1986Sci...233..876T }}</ref> allowing the presence C<sub>4</sub> metabolism to be identified without doubt at this time. Isotopic markers are used to deduce their distribution and significance.
C<sub>3</sub> plants preferentially use the lighter of two [[isotopes]] of carbon in the atmosphere, <sup>12</sup>C, which is more readily involved in the chemical pathways involved in its fixation. Because C<sub>4</sub> metabolism involves a further chemical step, this effect is accentuated. Plant material can be [[mass spectrometry|analysed]] to deduce the ratio of the heavier <sup>13</sup>C to <sup>12</sup>C. This ratio is denoted {{delta|13|C}}. C<sub>3</sub> plants are on average around 14‰ (parts per thousand) lighter than the atmospheric ratio, while C<sub>4</sub> plants are about 28‰ lighter. The {{delta|13|C}} of CAM plants depends on the percentage of carbon fixed at night relative to what is fixed in the day, being closer to C<sub>3</sub> plants if they fix most carbon in the day and closer to C<sub>4</sub> plants if they fix all their carbon at night.<ref name="isotope">{{cite journal|doi=10.2307/1310735|last=O'Leary|first=Marion|date=May 1988|title=Carbon Isotopes in Photosynthesis|journal=BioScience|volume=38|issue=5|pages=328–336|jstor=1310735}}</ref>
 
It's troublesome procuring original fossil material in sufficient quantity to analyse the grass itself, but fortunately there is a good proxy: horses. Horses were globally widespread in the period of interest, and browsed almost exclusively on grasses. There's an old phrase in isotope palæontology, "you are what you eat (plus a little bit)"&nbsp;– this refers to the fact that organisms reflect the isotopic composition of whatever they eat, plus a small adjustment factor. There is a good record of horse teeth throughout the globe, and their {{delta|13|C}} has been measured. The record shows a sharp negative inflection around {{Ma|6|7}}, during the Messinian, and this is interpreted as the rise of C<sub>4</sub> plants on a global scale.<ref name=Retallack1997>{{cite jstor|3515337}}</ref>
 
===When is C<sub>4</sub> an advantage?===
While C<sub>4</sub> enhances the efficiency of RuBisCO, the concentration of carbon is highly energy intensive. This means that C<sub>4</sub> plants only have an advantage over C<sub>3</sub> organisms in certain conditions: namely, high temperatures and low rainfall. C<sub>4</sub> plants also need high levels of sunlight to thrive.<ref name=Osborne2009>{{cite doi|10.1098/rspb.2008.1762}}</ref> Models suggest that, without wildfires removing shade-casting trees and shrubs, there would be no space for C<sub>4</sub> plants.<ref name=Bond2005>{{cite journal
| author = Bond, W.J.
| coauthors = Woodward, F.I.; Midgley, G.F.
| year = 2005
| title = The global distribution of ecosystems in a world without fire
| journal = New Phytologist
| pmid = 15720663
| volume = 165
| issue = 2
| pages = 525–538
| doi = 10.1111/j.1469-8137.2004.01252.x
}}</ref> But, wildfires have occurred for 400 million years&nbsp;– why did C<sub>4</sub> take so long to arise, and then appear independently so many times? The Carboniferous period (~{{ma|300}}) had notoriously high oxygen levels&nbsp;– almost enough to allow [[spontaneous combustion]]<ref>Above 35% atmospheric oxygen, the spread of fire is unstoppable. Many models have predicted higher values and had to be revised, because there was not a total extinction of plant life.</ref>&nbsp;– and very low {{co2}}, but there is no C<sub>4</sub> isotopic signature to be found. And there doesn't seem to be a sudden trigger for the Miocene rise.
 
During the Miocene, the atmosphere and climate were relatively stable. If anything, {{co2}} increased gradually from {{Ma|14|9}} before settling down to concentrations similar to the Holocene.<ref name=Pagani2005>{{cite journal
| author = Pagani, M.
| coauthors = Zachos, J.C.; Freeman, K.H.; Tipple, B.; Bohaty, S.
| year = 2005
| title = Marked Decline in Atmospheric Carbon Dioxide Concentrations During the Paleogene
| journal = Science
| pmid = 15961630
| volume = 309
| issue = 5734
| pages = 600–603
| doi = 10.1126/science.1110063
|bibcode = 2005Sci...309..600P }}</ref> This suggests that it did not have a key role in invoking C<sub>4</sub> evolution.<ref name=Osborne2006/> Grasses themselves (the group which would give rise to the most occurrences of C<sub>4</sub>) had probably been around for 60 million years or more, so had had plenty of time to evolve C<sub>4</sub>,<ref name=Piperno2005>{{cite journal
| author = Piperno, D.R.
| coauthors = Sues, H.D.
| year = 2005
| title = Dinosaurs Dined on Grass
| journal = Science
| pmid = 16293745
| volume = 310
| issue = 5751
| pages = 1126–8
| doi = 10.1126/science.1121020
}}</ref><ref name=Prasad2005>{{cite journal
| author = Prasad, V.
| coauthors = Stroemberg, C.A.E.; Alimohammadian, H.; Sahni, A.
| year = 2005
| title = Dinosaur Coprolites and the Early Evolution of Grasses and Grazers
| journal = Science(Washington)
| pmid = 16293759
| volume = 310
| issue = 5751
| pages = 1177–1180
| doi=10.1126/science.1118806
|bibcode = 2005Sci...310.1177P }}</ref> which, in any case, is present in a diverse range of groups and thus evolved independently. There is a strong signal of climate change in South Asia;<ref name=Osborne2006/> increasing aridity&nbsp;– hence increasing fire frequency and intensity&nbsp;– may have led to an increase in the importance of grasslands.<ref name=Keeley2005>{{cite journal
| author = Keeley, J.E.
| coauthors = Rundel, P.W.
| year = 2005
| title = Fire and the Miocene expansion of C4 grasslands
| journal = Ecology Letters
| volume = 8
| issue = 7
| pages = 683–690
| doi = 10.1111/j.1461-0248.2005.00767.x
}}</ref> However, this is difficult to reconcile with the North American record.<ref name=Osborne2006/> It is possible that the signal is entirely biological, forced by the fire- (and elephant?)-<ref name=Retallack2001/> driven acceleration of grass evolution&nbsp;– which, both by increasing weathering and incorporating more carbon into sediments, reduced atmospheric {{co2}} levels.<ref name=Retallack2001>{{cite journal
| author = Retallack, G.J.
| year = 2001
| title = Cenozoic Expansion of Grasslands and Climatic Cooling
| journal = The Journal of Geology
| volume = 109
| issue = 4
| pages = 407–426
| doi = 10.1086/320791
| bibcode=2001JG....109..407R
}}</ref> Finally, there is evidence that the onset of C<sub>4</sub> from {{Ma|9|7}} is a biased signal, which only holds true for North America, from where most samples originate; emerging evidence suggests that grasslands evolved to a dominant state at least 15Ma earlier in South America.
 
==Evolution of secondary metabolism==
[[File:Azadirachtin.png|thumb|right|250px|Structure of [[Azadirachtin]], a terpenoid produced by the [[Neem]] plant, which helps ward off microbes and insects. Many secondary metabolites have complex structures]]
[[Secondary metabolites]] are essentially low [[molecular weight]] compounds, sometimes having complex structures. They function in processes as diverse as [[immunity (medical)|immunity]], anti-herbivory, [[pollinator]] attraction, [[communication]] between plants, maintaining [[symbiotic]] associations with soil flora, enhancing the rate of [[fertilization]] etc., and hence are significant from the evo-devo perspective. The structural and functional diversity of these secondary metabolites across the plant kingdom is vast; it is estimated that hundreds of thousands of enzymes might be involved in this process in the entire of the plant kingdom, with about 15–25% of the genome coding for these enzymes, and every species having its unique arsenal of secondary metabolites.<ref>{{cite journal | author=Pichersky E. and Gang D. | title = Genetics and biochemistry of secondary metabolites in plants: an evolutionary perspective | journal=Trends in Plant Sci | volume=5 | issue=10 | pages=439–445 | year=2000 | url=http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD1-41FCH6C-S&_user=1111158&_coverDate=10%2F01%2F2000&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000051676&_version=1&_urlVersion=0&_userid=1111158&md5=9ed55aafae5e064b9217accec3a18258 | doi=10.1016/S1360-1385(00)01741-6}}</ref> Many of these metabolites are of enormous medical significance to humans.
 
What is the purpose of having so many secondary metabolites being produced, with a significant chunk of the [[metabolome]] devoted to this activity? It is hypothesized that most of these chemicals help in generating immunity and, in consequence, the diversity of these metabolites is a result of a constant war between plants and their parasites. There is evidence that this may be true in many cases. The big question here is the reproductive cost involved in maintaining such an impressive inventory. Various models have been suggested that probe into this aspect of the question, but a consensus on the extent of the cost is lacking.<ref>{{cite journal | author=Nina Theis and Manuel Lerdau | title = The evolution of function in plant secondary metabolites | journal=Int. J.Plant. Sci | volume=164 | issue=S3 | pages=S93–S102 | year=2003 | url=http://www.journals.uchicago.edu/IJPS/journal/issues/v164nS3/164708/164708.html | doi=10.1086/374190}}</ref> We still cannot predict whether a plant with more secondary metabolites would be better off than other plants in its vicinity.
 
Secondary metabolite production seems to have arisen quite early during evolution. In plants, they seem to have spread out using mechanisms including gene duplications, evolution of novel genes etc. Furthermore, studies have shown that diversity in some of these compounds may be positively selected for.
 
Although the role of novel gene evolution in the evolution of secondary metabolism cannot be denied, there are several examples where new metabolites have been formed by small changes in the reaction. For example, [[cyanogen glycosides]] have been proposed to have evolved multiple times in different plant lineages. There are several such instances of [[convergent evolution]]. For example, enzymes for synthesis of [[limonene]]&nbsp;– a [[terpene]]&nbsp;– are more similar between angiosperms and gymnosperms than to their own terpene synthesis enzymes. This suggests independent evolution of the limonene biosynthetic pathway in these two lineages.<ref>{{cite journal | author=Bohlmann J. | title = Plant terpenoid synthases: molecular and phylogenetic analysis | journal=Proc. Natl. Acad. Sci. U.S.A. | volume=95 | pages=4126–4133 | year=1998 | pmid=9539701 | issue=8 | pmc=22453 | doi=10.1073/pnas.95.8.4126 | url=http://www.pnas.org/cgi/content/abstract/95/8/4126|bibcode = 1998PNAS...95.4126B | author-separator=, | display-authors=1 | last2=Meyer-Gauen | first2=G | last3=Croteau | first3=R }}</ref>
 
==Mechanisms and players in evolution of plant form==
[[File:Microrna secondary structure.png|thumb|left|The [[stem-loop]] [[secondary structure]] of a pre-microRNA from [[Brassica oleracea]]]]
While environmental factors are significantly responsible for evolutionary change, they act merely as agents for [[natural selection]]. Change is inherently brought about via phenomena at the genetic level - [[mutations]], chromosomal rearrangements and [[epigenetic]] changes. While the general types of [[mutations]] hold true across the living world, in plants, some other mechanisms have been implicated as highly significant.
 
[[Genome doubling]] is a relatively common occurrence in plant evolution and results in [[polyploidy]], which is consequently a common feature in plants. It is believed that at least half (and probably all) plants have seen genome doubling in their history. Genome doubling entails [[gene duplication]], thus generating functional redundancy in most genes. The duplicated genes may attain new function, either by changes in expression pattern or changes in activity. Polyploidy and gene duplication are believed to be among the most powerful forces in evolution of plant form; though it is not known why [[genome]] doubling is such a frequent process in plants. One probable reason is the production of large amounts of [[secondary metabolites]] in plant cells. Some of them might interfere in the normal process of chromosomal segregation, causing genome duplication.
 
[[File:Maize-teosinte.jpg| thumb | right | 150px | Extreme left: [[teosinte]], Extreme right: [[maize]], middle: maize-teosinte hybrid]]
In recent times, plants have been shown to possess significant [[microRNA]] families, which are conserved across many plant lineages. In comparison to [[animal]]s, while the number of plant miRNA families are lesser than animals, the size of each family is much larger. The [[miRNA]] genes are also much more spread out in the genome than those in animals, where they are more clustered. It has been proposed that these miRNA families have expanded by duplications of chromosomal regions.<ref>{{cite journal | author=Li A and Mao L. | title = Evolution of plant microRNA gene families | journal=Cell Research| volume=17 | pages=212–218 | year=2007 | pmid=17130846 | issue=3 | doi=10.1038/sj.cr.7310113}}</ref> Many miRNA genes involved in regulation of [[plant development]] have been found to be quite conserved between plants studied.
 
[[Domestication]] of plants like [[maize]], [[rice]], [[barley]], [[wheat]] etc. has also been a significant driving force in their evolution. Some studies have tried to look at the origins of the [[maize]] plant and it turns out that maize is a domesticated derivative of a wild plant from [[Mexico]] called teosinte. [[Teosinte]] belongs to the [[genus]] ''Zea'', just as maize, but bears very small [[inflorescence]], 5-10 hard cobs and a highly branched and spread out stem.
[[File:Cauliflower.JPG| thumb | left | 150px | [[Cauliflower]] : ''Brassica oleracea var botrytis'']]
Interestingly, crosses between a particular teosinte variety and maize yields fertile offspring that are intermediate in [[phenotype]] between maize and teosinte. [[QTL]] analysis has also revealed some loci that, when mutated in maize, yield a teosinte-like stem or teosinte-like cobs. [[Molecular clock]] analysis of these genes estimates their origins to some 9,000 years ago, well in accordance with other records of maize domestication. It is believed that a small group of farmers must have selected some maize-like natural mutant of teosinte some 9,000 years ago in Mexico, and subjected it to continuous selection to yield the familiar maize plant of today.<ref>{{cite journal | author=Doebley J.F. | title = The genetics of maize evolution | journal=Ann. Rev. Gen| volume=38 | issue=1 | pages=37–59| year=2004 | doi=10.1146/annurev.genet.38.072902.092425 | pmid=15568971 | url=http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.38.072902.092425}}</ref>
 
Another interesting case is that of [[cauliflower]]. The edible cauliflower is a domesticated version of the wild plant ''[[Brassica oleracea]]'', which does not possess the dense undifferentiated [[inflorescence]], called the curd, that cauliflower possesses.
{{Wikispecies|Brassicaceae}}Cauliflower possesses a single mutation in a gene called ''CAL'', controlling [[meristem]] differentiation into [[inflorescence]]. This causes the cells at the floral meristem to gain an undifferentiated identity and, instead of growing into a [[flower]], they grow into a lump of undifferentiated cells.<ref>{{cite journal | author=Purugannan | title = Variation and Selection at the CAULIFLOWER Floral Homeotic Gene Accompanying the Evolution of Domesticated Brassica olerace | journal=Genetics| volume=155 | pages=855–862| year=2000 | pmid=10835404 | last2=Boyles | first2=AL | last3=Suddith | first3=JI | issue=2 | pmc=1461124 | display-authors=1}}</ref> This mutation has been selected through domestication since at least the [[Greeks|Greek]] empire.<!--9 'greek empires' are listed; with dates ranging from 477 BC to 1479 AD-->
 
==See also==
;Plants:
*[[Plant]]
*[[Flora]];
General evolution:
*[[Evolutionary history of life]]
*[[Timeline of plant evolution]]
 
;Study of plants:
*[[Paleobotany]]
*[[Plant evolutionary developmental biology]]
*[[Cryptospores]]
;Plant interactions:
*[[Herbivory#evolution|Evolution of herbivory]]
 
==References==
{{Reflist|2}}
 
{{Botany}}
{{evolution}}
 
{{DEFAULTSORT:Evolution Of Plants}}
[[Category:Plants]]
[[Category:Paleobotany]]
[[Category:Evolution by taxon]]
 
[[sv:Växt#Växternas evolution]]

Latest revision as of 11:04, 13 August 2014

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