View source for Evolutionary history of plants

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{{further|Evolutionary history of life}}
[[File:Trilete spores.png|thumb|right |A [[late Silurian]] [[sporangium]], artificially colored. ''Green'': A spore tetrad. ''Blue'': A spore bearing a trilete mark&nbsp;– the ''Y''-shaped scar. The spores are about 30–35&nbsp;μm across.]]

The [[evolution]] of [[plant]]s has resulted in a wide range of complexity, from the earliest [[algal mat]]s of unicellular [[archaeplastid]]s evolved through [[endosymbiosis]], through multicellular [[marine habitat|marine]] and [[freshwater]] [[green algae]], to [[spore]]-bearing terrestrial [[bryophyte]]s, [[lycopod]]s and [[fern]]s, and eventually to the complex [[seed]]-bearing [[gymnosperm]]s and [[angiosperm]]s ([[flowering]] plants) of today. While many of the earliest groups continue to thrive, as exemplified by [[red algae|red]] and green algae in marine environments, more recently derived groups have displaced previously ecologically dominant ones; for example, the ascendance of flowering plants over gymnosperms in terrestrial environments.<ref name="Stewart-1993">{{cite book |last1=Stewart |first1=W.N. |last2=Rothwell |first2=G.W. |date=1993 |title=Paleobotany and the evolution of plants |edition=2 |publisher=Cambridge University Press |isbn=978-0-521-23315-6 }}</ref>{{rp |498}}

There is evidence that [[cyanobacteria]] and multicellular [[Thallus|thalloid]] eukaryotes lived in freshwater communities on land as early as 1 billion years ago,<ref name="Strother-2011">{{cite journal |first1=Paul K. |last1=Strother |first2=Leila |last2=Battison |first3= Martin D. |last3=Brasier |first4=Charles H. |last4=Wellman |date=2011 |title=Earth's earliest non-marine eukaryotes |journal=Nature |volume=473 |issue=7348 |pages=505–509 |doi=10.1038/nature09943 |pmid=21490597 |bibcode=2011Natur.473..505S |s2cid=4418860 |url=https://www.researchgate.net/publication/51048998}}</ref> and that communities of complex, multicellular photosynthesizing organisms existed on land in the late [[Precambrian]], around {{Ma |850}}.<ref name="Knauth-2009">{{cite journal |first1=L. Paul |last1=Knauth |first2=Martin J. |last2=Kennedy |date=2009 |title=The late Precambrian greening of the Earth |journal=Nature |volume=460 |issue=7256 |pages=728–732 |doi=10.1038/nature08213 |pmid=19587681 |bibcode=2009Natur.460..728K |s2cid=4398942 }}</ref>

Evidence of the emergence of [[embryophyte]] land plants first occurs in the middle [[Ordovician]] (~{{ma |470}}). By the middle of the [[Devonian]] (~{{ma |390}}), fossil evidence has shown that many of the features recognised in land plants today were present, including roots and leaves. More recently geochemical evidence suggests that around this time that the terrestrial realm had largely been colonized which altered the global terrestrial weathering environment.<ref>{{Cite journal |last=Waldeck |first=Anna R. |last2=Olson |first2=Haley C. |last3=Crockford |first3=Peter W. |last4=Couture |first4=Abby M. |last5=Cowie |first5=Benjamin R. |last6=Hodgin |first6=Eben B. |last7=Bergmann |first7=Kristin D. |last8=Dewing |first8=Keith |last9=Grasby |first9=Stephen E. |last10=Clark |first10=Ryan J. |last11=Macdonald |first11=Francis A. |last12=Johnston |first12=David T. |date=2025-03-01 |title=Marine sulphate captures a Paleozoic transition to a modern terrestrial weathering environment |url=https://www.nature.com/articles/s41467-025-57282-y?utm_source=rct_congratemailt&utm_medium=email&utm_campaign=oa_20250301&utm_content=10.1038/s41467-025-57282-y |journal=Nature Communications |language=en |volume=16 |issue=1 |pages=2087 |doi=10.1038/s41467-025-57282-y |issn=2041-1723|pmc=11873193 }}</ref> By the late Devonian (~{{ma |370}}) some free-sporing plants such as ''[[Archaeopteris]]'' had [[vascular cambium|secondary vascular tissue]] that produced [[wood]] and had formed forests of tall trees. Also by the late Devonian, ''Elkinsia'', an early [[Pteridospermatophyta|seed fern]], had evolved seeds.<ref name="Rothwell-1989">{{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 |journal=Botanical Gazette |volume=150 |issue=2 |pages=170–189 |s2cid=84303226 }}</ref>
Evolutionary innovation continued throughout the rest of the [[Phanerozoic]] eon and still continues 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 [[Poaceae|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}}.

{{anchor |Land |land}}
==Colonization of land==
===Divergence===
[[Land plant]]s evolved from a group of freshwater [[green algae]], perhaps as early as 850 mya,<ref name="Knauth-2009"/> but algae-like plants might have evolved as early as 1 billion years ago.<ref name="Strother-2011"/> The closest living relatives of land plants are the [[charophyte]]s, specifically [[Charales]]; if modern Charales are similar to the distant ancestors they share with land plants, this means that the land plants evolved from a branched, filamentous alga dwelling in shallow fresh water,<ref name="Kenrick-1997">{{cite book |last1=Kenrick |first1=P. |last2=Crane |first2=P.R. |title=The origin and early diversification of land plants. A cladistic study |isbn=978-1-56098-729-1 |year=1997 |publisher=Smithsonian Institution Press |location=Washington}}</ref> perhaps at the edge of seasonally desiccating pools.<ref name="Raven-2001"/> However, some recent evidence suggests that land plants might have originated from unicellular terrestrial [[charophyte]]s similar to extant [[Klebsormidiophyceae]].<ref name="Del-Bem-2018">{{cite journal |doi=10.1111/nph.15191 |pmid=29851097 |last1=Del-Bem |first1=L. E. |year=2018 |title=Xyloglucan evolution and the terrestrialization of green plants |journal=New Phytologist |volume=219 |issue=4 |pages=1150–1153 |doi-access=free |hdl=1843/36860 |hdl-access=free }}</ref> 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]] that 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="Heckman-2001">{{Cite journal |title=Molecular evidence for the early colonization of land by fungi and plants |journal=Science |volume=293 |issue=5532 |pages=1129–1133 |date=August 2001 |pmid=11498589 |doi=10.1126/science.1061457 |last1=Heckman |first1=D. S. |last2=Geiser |first2=D. M. |last3=Eidell |first3=B. R. |last4=Stauffer |first4=R. L. |last5=Kardos |first5=N. L. |last6=Hedges |first6=S. B. |s2cid=10127810 }}</ref>

[[File:Devonianscene-green.jpg|thumb|left |200px |The Devonian marks the beginning of extensive land colonization by plants, which – through their effects on erosion and sedimentation – brought about significant climatic change.]]

===Challenges to land colonization===
Plants were not the first photosynthesisers on land. Weathering rates suggest that organisms capable of photosynthesis were already living on the land {{Ma |1200}},<ref name="Raven-2001"/> 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="Knauth-2009"/> These organisms, although phylogenetically diverse,<ref name="Battistuzzi-2004">{{Cite journal |last1=Battistuzzi |first1=F. U. |last2=Feijao |first2=A. |last3=Hedges |first3=S. B. |title=A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land |journal=BMC Evolutionary Biology |volume=4 |pages=44 |year=2004 |doi=10.1186/1471-2148-4-44 |pmid=15535883 |pmc=533871 |doi-access=free }}</ref> were probably small and simple, forming little more than an algal scum.<ref name="Raven-2001"/>

Since [[lichen]]s initiate the first step in primary [[ecological succession]] in contemporary contexts, one hypothesis has been that lichens came on land first and facilitated colonization by plants; however, both molecular phylogenies and the fossil record seem to contradict this.<ref>{{cite journal |last1=Nelsen |first1=Matthew P. |last2=Lucking |first2=Robert |last3=Boyce |first3=C. Kevin |last4=Lumbsch |first4=H. Thorsten |last5=Ree |first5=Richard H. |title=No support for the emergence of lichens prior to the evolution of vascular plants |journal=Geobiology |date=2019 |volume=18 |issue=1|pages=3–13 |doi=10.1111/gbi.12369 |pmid=31729136 }}</ref>

There are multiple potential reasons for why it took so long for land plants to emerge. It could be that atmospheric 'poisoning' prevented eukaryotes from colonising the land prior to the emergence of land plants,<ref name="Kump-2005">{{Cite journal |first1=L. R. |last2=Pavlov |first2=A. |first3=M. A. |title=Massive release of hydrogen sulfide to the surface ocean and atmosphere during intervals of oceanic anoxia |journal=Geology |volume=33 |issue=5 |last1=Kump |pages=397 |year=2005 |last3=Arthur |doi=10.1130/G21295.1 |bibcode=2005Geo....33..397K }}</ref> or it could simply have taken a great time for the necessary complexity to evolve.<ref name="Butterfield-2009">{{Cite journal |last1=Butterfield |first1=N. J. |title=Oxygen, animals and oceanic ventilation: An alternative view |doi=10.1111/j.1472-4669.2009.00188.x |journal=Geobiology |volume=7 |issue=1 |pages=1–7 |year=2009 |pmid=19200141 |bibcode=2009Gbio....7....1B |s2cid=31074331 }}</ref> A major challenge to land adaptation would have been the absence of appropriate [[soil]].<ref>{{cite journal |last1=Dahl |first1=Tais W. |last2=Arens |first2=Suzanne K.M. |title=The impacts of land plant evolution on Earth's climate and oxygenation state – An interdisciplinary review |journal=Chemical Geology |date=2020 |volume=547|doi=10.1016/j.chemgeo.2020.119665 |bibcode=2020ChGeo.54719665D |doi-access=free }}</ref> Throughout the fossil record, soil is preserved, giving information on what early soils were like. Before land plants, the soil on land was poor in resources essential for life like [[nitrogen]] and [[phosphorus]] and had little capacity for holding water.

===Adaptations to land colonization===
Evidence of the earliest land plants occurs at about {{Ma|470}}, in lower middle Ordovician rocks from [[Saudi Arabia]]<ref name="Strother-1996">{{cite journal |last1=Strother |first1=P.K. |last2=Al-Hajri |first2=S. |last3=Traverse |first3=A. |date=1996 |title=New evidence for land plants from the lower Middle Ordovician of Saudi Arabia |journal=Geology |volume=24 |issue=1 |pages=55–59 |bibcode=1996Geo....24...55S |doi=10.1130/0091-7613(1996)024<0055:NEFLPF>2.3.CO;2}}</ref> and [[Gondwana]]<ref name="Rubinstein-2010">{{cite journal |first1=C. V. |last1=Rubinstein |first2=P. |last2=Gerrienne |first3=G. S. |last3=de la Puente |first4=R. A. |last4=Astini |first5=P. |last5=Steemans |date=2010 |title=Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana) |journal=New Phytologist |volume=188 |issue=2 |pages=365–369 |doi=10.1111/j.1469-8137.2010.03433.x |pmid=20731783 |doi-access=free|hdl=11336/55341 |hdl-access=free }}</ref> in the form of spores known as [[cryptospores]]. These spores have walls made of [[sporopollenin]], an extremely decay-resistant material that means they are well-preserved by the fossil record.
These spores were produced either singly (monads), in pairs (dyads) 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="Wellman-2003">{{cite journal |last1=Wellman |first1=Charles H. |last2=Osterloff |first2=Peter L. |last3=Mohiuddin |first3=Uzma |title=Fragments of the earliest land plants |journal=Nature |volume=425 |issue=6955 |pages=282–285 |year=2003 |doi=10.1038/nature01884 |pmid=13679913 |bibcode=2003Natur.425..282W |s2cid=4383813 |url=http://eprints.whiterose.ac.uk/106/1/wellmanch1.pdf }}</ref> Their walls contain [[sporopollenin]]&nbsp;– further evidence of an embryophytic affinity.<ref name="Steemans-2010">{{cite journal |last=Steemans |first=P. |author2=Lepota K. |author3=Marshallb, C.P. |author4=Le Hérisséc, A. |author5=Javauxa, E.J. |title=FTIR characterisation of the chemical composition of Silurian miospores (cryptospores and trilete spores) from Gotland, Sweden |journal=Review of Palaeobotany and Palynology |date=2010 |volume=162 |issue=4 |pages=577–590 |doi=10.1016/j.revpalbo.2010.07.006 |bibcode=2010RPaPa.162..577S |s2cid=128900940 |url=https://hal-insu.archives-ouvertes.fr/insu-00558990}}</ref>

Trilete spores similar to those of [[Tracheophytes|vascular plants]] appear soon afterwards, in Upper Ordovician rocks about 455 million years ago.<ref name="Steemans-2009">{{Cite journal |last3=Melvin |first1=P. |first2=L. |last2=Herisse |first3=J. |first4=A. |last5=Paris |last4=Miller |last7=Wellman |first5=F. |first6=J. |last1=Steemans |first7=H. |title=Origin and Radiation of the Earliest Vascular Land Plants |last6=Verniers |journal=Science |volume=324 |issue=5925 |pages=353 |date=Apr 2009 |issn=0036-8075 |pmid=19372423 |doi=10.1126/science.1169659 |bibcode=2009Sci...324..353S |s2cid=206518080 |url=https://biblio.ugent.be/publication/697223 |hdl=1854/LU-697223 |hdl-access=free}}</ref><ref name="Rubinstein-2019">{{cite journal |first1=Claudia |last1=Rubinstein |first2=Vivi |last2=Vajda |date=2019 |title=Baltica cradle of early land plants? Oldest record of trilete spores and diverse cryptospore assemblages; evidence from Ordovician successions of Sweden |journal=GFF (Journal of the Geological Society of Sweden) |volume=141 |issue=3 |doi=10.1080/11035897.2019.1636860 |pages=181–190 |doi-access=free |bibcode=2019GFF...141..181R |hdl=11336/124409 |hdl-access=free }}</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="Gray-1985">{{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 |doi-access= }}</ref> 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="Gray-1985"/> 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 they are, because the spores disperse before they are compressed enough to develop the mark or do not fit into a tetrahedral tetrad.<ref name="Gray-1985"/>

The earliest megafossils of land plants were [[Thallus|thalloid]] organisms, which dwelt in fluvial wetlands and are found to have covered most of an [[Llandovery epoch|early Silurian]] flood plain. They could only survive when the land was waterlogged.<ref>{{cite book |last1=Tomescu |first1=A. M. F. |chapter= Wetlands before tracheophytes: Thalloid terrestrial communities of the Early Silurian Passage Creek biota (Virginia) |chapter-url=http://www.humboldt.edu/biosci/docs/faculty/TomescuRothwell2006.pdf |access-date=2014-05-28 |journal=Wetlands Through Time |year=2006 |doi=10.1130/2006.2399(02) |isbn=9780813723990}}</ref> There were also microbial mats.<ref name="Tomescu-2008">{{Cite journal |last1=Tomescu |first1=A. M. F. |last2=Honegger |first2=R. |last3=Rothwell |first3=G. W. |title=Earliest fossil record of bacterial–cyanobacterial mat consortia: the early Silurian Passage Creek biota (440 Ma, Virginia, USA) |journal=Geobiology |volume=6 |issue=2 |pages=120–124 |year=2008 |pmid=18380874 |doi=10.1111/j.1472-4669.2007.00143.x |bibcode=2008Gbio....6..120T |s2cid=10555223 }}</ref>

Once plants had reached the land, there were two approaches to dealing with desiccation. Modern bryophytes either 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, as in the liverwort genus ''[[Targionia (plant)|Targionia]]''. [[Tracheophytes]] resist desiccation by controlling the rate of water loss. They all bear a waterproof outer [[plant cuticle|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 tracheophytes use variable openings, the [[stomata]], to regulate the rate of 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 ultimately also facilitated upright growth without the support of water and paved the way for the evolution of larger plants on land.{{citation needed|date=June 2024}}

===Consequences===
A global [[ice age|glaciation event]] called [[Snowball Earth]], from around 720-635 mya in the [[Cryogenian]] period, is believed to have been at least partially caused by early photosynthetic organisms, which reduced the concentration of carbon dioxide and decreased the [[greenhouse effect]] in the atmosphere,<ref>{{cite web |url=http://science.psu.edu/news-and-events/2001-news/Hedges8-2001.htm |title=First Land Plants and Fungi Changed Earth's Climate, Paving the Way for Explosive Evolution of Land Animals, New Gene Study Suggest |work=science.psu.edu |access-date=9 April 2018 |archive-date=15 December 2019 |archive-url=https://web.archive.org/web/20191215115624/http://science.psu.edu/news-and-events/2001-news/Hedges8-2001.htm/ |url-status=dead }}</ref> leading to an [[icehouse Earth|icehouse climate]]. Based on [[molecular clock]] studies of the previous decade or so, a 2022 study observed that the estimated time for the origin of the ''multicellular'' [[streptophyta|streptophytes]] (all except the unicellular basal clade [[Mesostigmatophyceae]]) fell in the cool Cryogenian while that of the subsequent separation of streptophytes fell in the warm [[Ediacaran]], which they interpreted as an indication of [[selective pressure]] by the glacial period to the photosynthesizing organisms, a group of which succeeded in surviving in relatively warmer environments that remained habitable, subsequently flourishing in the later Ediacaran and [[Phanerozoic]] on land as embryophytes. The study also theorized that the unicellular morphology and other unique features of the [[Zygnematophyceae]] may reflect further adaptations to a [[cryophilic|cold loving]] life style.<ref name="Žárský-2022">{{cite journal |last1=Žárský |first1=J. |last2=Žárský |first2=V. |last3=Hanáček |first3=M. |last4=Žárský |first4=V. |title=Cryogenian Glacial Habitats as a Plant Terrestrialisation Cradle – The Origin of the Anydrophytes and Zygnematophyceae Split |journal=[[Frontiers in Plant Science]] |publisher=[[Frontiers Media|Frontiers]] |volume=12 |date=2022-01-27 |page=735020 |issn=1664-462X |doi=10.3389/fpls.2021.735020 |pmid=35154170 |pmc=8829067 |doi-access=free }}</ref> The establishment of a land-based flora increased the rate of accumulation of oxygen in the atmosphere, as the land plants produced oxygen as a waste product. When this concentration rose above 13%, around 0.45 billion years ago,<ref>{{cite journal |title=The rise of atmospheric oxygen |journal=Nature |date=2008-01-16 |last=Kump |first=Leo R. |volume=451 |issue=7176 |pages=277–278 |doi=10.1038/nature06587 |pmid=18202642 |bibcode=2008Natur.451..277K |s2cid=5505876 |doi-access=free }}</ref> wildfires became possible, evident from charcoal in the fossil record.<ref>{{cite journal |last1=Glasspool |first1=I.J. |last2=Edwards |first2=D. |last3=Axe |first3=L. |title=Charcoal in the Silurian as evidence for the earliest wildfire |journal=Geology |date=2004 |volume=32 |issue=5 |pages=381–383 |doi=10.1130/G20363.1 |bibcode=2004Geo....32..381G}}</ref> Apart from a controversial gap in the Late Devonian, charcoal has been present ever since.

Charcoalification is an important [[taphonomy|taphonomic]] mode. Wildfire or burial in hot volcanic ash drives off the volatile compounds, leaving only a residue of pure carbon. This is not a viable food source for fungi, herbivores or detritovores, so it is prone to preservation. It is also robust and can withstand pressure, displaying exquisite, sometimes sub-cellular, detail in remains.{{citation needed|date=June 2024}}

In addition to the advent of charcoal in the rock record, the terrestrialization of plants has made significant contributions to changes in geology and landscapes. The Ordovician and Silurian show a 1.4 times greater proportion of mudrock in the geologic record than the previous 90% of earth's history and this increase in mudrock is considered to be a result of land plants retaining muds in a terrestrial setting.<ref>{{Cite journal |last=McMahon |first=William J. |last2=Davies |first2=Neil S. |date=2018-03-02 |title=Evolution of alluvial mudrock forced by early land plants |url=https://www.science.org/doi/10.1126/science.aan4660 |journal=Science |language=en |volume=359 |issue=6379 |pages=1022–1024 |doi=10.1126/science.aan4660 |issn=0036-8075}}</ref>

{{anchor |phases}}{{anchor |life cycles}}
==Evolution of life cycles==

{{Further |Alternation of generations}}

[[File:Angiosperm life cycle diagram-en.svg|thumb|upright=1.5 |[[Angiosperm]] life cycle]]

All multicellular plants have a life cycle comprising two generations or phases. The [[gametophyte]] phase has a single set of chromosomes (denoted&nbsp;''1n'') and produces gametes (sperm and eggs). The [[sporophyte]] phase has paired chromosomes (denoted&nbsp;''2n'') and produces spores. The gametophyte and sporophyte phases may be homomorphic, appearing identical&nbsp;in some algae, such as ''[[Ulva lactuca#Life history|Ulva lactuca]]'', but are very different&nbsp;in all modern land plants, a condition known as [[Gametophyte#Heterospory|heteromorphy]].{{citation needed|date=June 2024}}

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="Stewart-1993"/> Two trends are apparent: [[bryophyte]]s ([[Marchantiophyta|liverwort]]s, [[moss]]es and [[hornwort]]s) have developed the gametophyte as the dominant phase of the life cycle, with the sporophyte becoming almost entirely dependent on it; [[vascular plant]]s have developed the sporophyte as the dominant phase, with the gametophytes being particularly reduced in the [[seed plant]]s.{{citation needed|date=June 2024}}

It has been proposed as the basis for the emergence of the diploid phase of the life cycle as the dominant phase that diploidy allows masking of the expression of deleterious mutations through [[Complementation (genetics)|genetic complementation]].<ref>{{cite journal |last1=Bernstein |first1=H. |last2=Byers |first2=G.S. |last3=Michod |first3=R.E. |year=1981 |title=Evolution of sexual reproduction: Importance of DNA repair, complementation, and variation |journal=The American Naturalist |volume=117 |issue=4 |pages=537–549 |doi=10.1086/283734 |s2cid=84568130 }}</ref><ref>{{cite journal |last1=Michod |first1=R.E. |last2=Gayley |first2=T.W. |year=1992 |title=Masking of mutations and the evolution of sex |journal=The American Naturalist |volume=139 |issue=4 |pages=706–734 |doi=10.1086/285354 |s2cid=85407883 }}</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="Szövényi-2013">{{Cite journal |last1=Szövényi |first1=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 |volume=30 |issue=8 |pages=1929–39 |doi=10.1093/molbev/mst095 |pmid=23686659 |doi-access=free}}<!-- |access-date=2013-06-20 --></ref>

There are two competing theories to explain the appearance of a diplobiontic lifecycle.{{citation needed|date=June 2024}}

The ''[[interpolation theory]]'' (also known as the antithetic or intercalary theory)<ref name="Boyce-2008"/> holds that the interpolation of a multicellular sporophyte phase between two successive gametophyte generations was an innovation caused by preceding meiosis in a freshly germinated zygote with one or more rounds of mitotic division, thereby producing some diploid multicellular tissue before finally meiosis produced spores. This theory implies that the first sporophytes bore a very different and simpler morphology to the gametophyte they depended on.<ref name="Boyce-2008"/> This seems to fit well with what is known of the bryophytes, in which a vegetative thalloid gametophyte nurtures a simple sporophyte, which consists of little more than an unbranched 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="Stewart-1993"/> 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="Boyce-2008">{{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=179–194 |s2cid=36688488 }}</ref>

The alternative hypothesis, called the ''transformation theory'' (or homologous theory), posits that the sporophyte might have appeared suddenly by delaying the occurrence of meiosis until a fully developed multicellular sporophyte had formed. Since the same genetic material would be employed by both the haploid and diploid phases, they would look the same. This explains the behaviour of some algae, such as ''Ulva lactuca'', which produce alternating phases of identical sporophytes and gametophytes. Subsequent adaption to the desiccating land environment, which makes sexual reproduction difficult, might have resulted in the simplification of the sexually active gametophyte, and elaboration of the sporophyte phase to better disperse the waterproof spores.<ref name="Stewart-1993"/> The tissue of sporophytes and gametophytes of vascular plants such as ''[[Rhynia]]'' preserved in the [[Rhynie chert]] is of similar complexity, which is taken to support this hypothesis.<ref name="Boyce-2008"/><ref name="Kerp-2004">{{cite journal |title=New gametophytes from the Early Devonian Rhynie chert |last1=Kerp |first1=H. |last2=Trewin |first2=N.H. |last3=Hass |first3=H. |year=2004 |journal=Transactions of the Royal Society of Edinburgh |volume=94 |issue=4 |pages=411–428 |doi=10.1017/s026359330000078x |s2cid=128629425}}</ref><ref name="Taylor-2005b">{{cite journal |doi=10.1073/pnas.0501985102 |title=Life history biology of early land plants: deciphering the gametophyte phase |last1=Taylor |first1=T.N. |last2=Kerp |first2=H. |last3=Hass |first3=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 |doi-access=free}}</ref> By contrast, modern vascular plants, with the exception of ''Psilotum'', have heteromorphic sporophytes and gametophytes in which the gametophytes rarely have any vascular tissue.<ref name="Holloway-1939">{{cite journal |last1=Holloway |first1=John E. |title=The gametophyte, embryo, and young rhizome of ''Psilotum triquetrum'' (Swartz) |journal=Annals of Botany |date=1939 |volume=3 |issue=2 |pages=313–336 |doi=10.1093/oxfordjournals.aob.a085063 }}</ref>

==Evolution of plant anatomy==

===Arbuscular mycorrhizal symbiosis===

There is no evidence that early land plants of the Silurian and early Devonian had roots, although fossil evidence of rhizoids occurs for several species, such as ''[[Horneophyton]]''. The earliest land plants did not have vascular systems for transport of water and nutrients either. ''[[Aglaophyton]]'', a rootless vascular plant known from Devonian fossils in the [[Rhynie chert]]<ref name="Kidston-1920">{{Citation |last1=Kidston |first1=R. |last2=Lang |first2=W.H. |year=1920 |title=On Old Red Sandstone plants showing structure, from the Rhynie Chert Bed, Aberdeenshire. Part II. Additional notes on ''Rhynia gwynne-vaughani'', Kidston and Lang; with descriptions of ''Rhynia major'', n.sp. and ''Hornea lignieri'', n.g., n.sp |journal=Transactions of the Royal Society of Edinburgh |volume=52 |issue=3 |pages=603–627 |name-list-style=amp |doi=10.1017/s0080456800004488 |s2cid=130329822 |url=https://zenodo.org/record/1428662 }}</ref> was the first land plant discovered to have had a [[symbiotic]] relationship with fungi <ref name="Remy-1994">{{cite journal |last1=Remy |first1=W. |last2=Taylor |first2=T.N. |last3=Hass |first3=H. |last4=Kerp |first4=H. |year=1994 |title= 4 hundred million year old vesicular-arbuscular mycorrhizae |journal= Proceedings of the National Academy of Sciences of the United States of America |volume=91 |issue=25 |pages=11841–11843 |doi=10.1073/pnas.91.25.11841 |pmid=11607500 |pmc=45331 |bibcode=1994PNAS...9111841R |doi-access=free }}</ref> which formed [[arbuscular mycorrhiza]]s, literally "tree-like fungal roots", in a well-defined cylinder of cells (ring in cross section) in the cortex of its stems. The fungi fed on the plant's sugars, in exchange for nutrients generated or extracted from the soil (especially [[phosphate]]), to which the plant would otherwise have had no access. Like other rootless land plants of the Silurian and early Devonian ''Aglaophyton'' may have relied on arbuscular mycorrhizal fungi for acquisition of water and nutrients from the soil.<ref>{{Cite journal |last1=Bonfante |first1=Paola |last2=Genre |first2=Andrea |date=September 2008 |title=Plants and arbuscular mycorrhizal fungi: an evolutionary-developmental perspective |url=https://doi.org/10.1016/j.tplants.2008.07.001 |journal=Trends in Plant Science |volume=13 |issue=9 |pages=492–498 |doi=10.1016/j.tplants.2008.07.001 |pmid=18701339 |bibcode=2008TPS....13..492B |issn=1360-1385|url-access=subscription }}</ref>

The fungi were of the phylum [[Glomeromycota]],<ref name="Schussler-2001">{{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|url-access=subscription }}</ref> a group that probably first appeared 1 billion years ago and still forms arbuscular mycorrhizal associations today with all major land plant groups from bryophytes to pteridophytes, gymnosperms and angiosperms and with more than 80% of vascular plants.<ref name="Smith-2008"/>

Evidence from DNA sequence analysis indicates that the arbuscular mycorrhizal mutualism arose in the common ancestor of these land plant groups during their transition to land<ref name="Simon-1993b">{{cite journal |last1=Simon |first1= L. |first2= J. |last2= Bousquet |first3= R.C. |last3= Lévesque |first4= M. |last4=Lalonde |date=1993 |title=Origin and diversification of endomycorrhizal fungi and coincidence with vascular land plants |journal=Nature |volume=363 |issue= 6424 |pages= 67–69 |bibcode=1993Natur.363...67S |doi=10.1038/363067a0 |s2cid= 4319766 }}</ref> and it may even have been the critical step that enabled them to colonise the land.<ref name="Simon-1993a">{{Cite journal |doi=10.1038/363067a0 |last1=Simon |first1=L. |last2=Bousquet |first2=J. |last3=Lévesque |first3=R. C. |last4=Lalonde |first4=M. |title=Origin and diversification of endomycorrhizal fungi and coincidence with vascular land plants |journal=Nature |volume=363 |pages=67–69 |year=1993 |bibcode=1993Natur.363...67S |issue=6424 |s2cid=4319766 }}</ref> Appearing as they did before these plants had evolved roots, mycorrhizal fungi would have assisted plants in the acquisition of water and mineral nutrients such as [[phosphorus]], in exchange for organic compounds which they could not synthesize themselves.<ref name="Smith-2008">{{cite book  |last1=Smith |first1=Sally E. |last2=Read |first2=David J. |date=2008 |title= Mycorrhizal symbiosis |publisher= Academic Press |edition=3 |isbn= 9780123705266 }}</ref> Such fungi increase the productivity even of simple plants such as liverworts.<ref name="Humphreys-2010">{{Cite journal |doi=10.1038/ncomms1105 |last1=Humphreys |first1=C. P. |last2=Franks |first2=P. J. |last3=Rees |first3=M. |last4=Bidartondo |first4=M. I. |last5=Leake |first5=J. R. |last6=Beerling |first6=D. J. |author-link6=David Beerling |title=Mutualistic mycorrhiza-like symbiosis in the most ancient group of land plants |journal=Nature Communications |volume=1 |issue=8 |pages=103 |year=2010 |bibcode=2010NatCo...1..103H |pmid=21045821 |doi-access=free }}</ref><ref name="Brundrett-2002">{{Cite journal |doi=10.1046/j.1469-8137.2002.00397.x |last1=Brundrett |first1=M. C. |title=Coevolution of roots and mycorrhizas of land plants |journal=New Phytologist |volume=154 |issue=2 |pages=275–304 |year=2002 |pmid=33873429 |doi-access=free }}</ref>

===Cuticle, stomata and intercellular spaces===

To photosynthesise, plants must absorb {{co2}} from the atmosphere. However, making the tissues available for {{co2}} to enter allows water to evaporate, so this comes at a price.<ref name="Sperry-2003">{{Cite journal |last1=Sperry |first1=J. S. |title=Evolution of Water Transport and Xylem Structure |jstor=3691719 |journal=International Journal of Plant Sciences |volume=164 |issue=3 |pages=S115–S127 |year=2003 |doi=10.1086/368398 |s2cid=15314720}}</ref> Water is lost much faster than {{co2}} is absorbed, so plants need to replace it. Early land plants transported water [[apoplast]]ically, within the porous walls of their cells. Later, they evolved three anatomical features that provided the ability to control the inevitable water loss that accompanied  {{co2}} acquisition.  First, a waterproof outer covering or [[plant cuticle|cuticle]] evolved that reduced water loss. Secondly, variable apertures, the [[stomata]] that could open and close to regulate the amount of water lost by evaporation during {{CO2}} uptake and thirdly intercellular space between photosynthetic parenchyma cells that allowed improved internal distribution of the {{CO2}} to the chloroplasts. This three-part system provided improved homoiohydry, the regulation of water content of the tissues, providing a particular advantage when water supply is not constant.<ref name="Raven-1977">{{cite journal |first=John |last=Raven |date=1977 |title=The evolution of vascular land plants in relation to supracellular transport processes |journal=Advances in Botanical Research |volume=1977 |pages=153–219 |doi=10.1016/S0065-2296(08)60361-4 |isbn=9780120059058 }}</ref> The high {{co2}} concentrations of the Silurian and early Devonian, when plants were first colonising land, meant that they used water relatively efficiently. As {{co2}} was withdrawn from the atmosphere by plants, more water was lost in its capture, and more elegant water acquisition and transport mechanisms evolved.<ref name="Sperry-2003"/> Plants growing upwards into the air needed a system for transporting water from the soil to all the different parts of the above-soil plant, especially to photosynthesising parts. By the end of the [[Carboniferous]], when {{co2}} concentrations had been reduced to something approaching that of today, around 17 times more water was lost per unit of {{co2}} uptake.<ref name="Sperry-2003"/> However, even in the "easy" early days, water was always at a premium, and had to be transported to parts of the plant from the wet soil to avoid desiccation.<ref name="Raven-1977"/>

Water can be wicked by [[capillary action]] along a fabric with small spaces. In narrow columns of water, such as those within the plant cell walls or in tracheids, when molecules evaporate from one end, they pull the molecules behind them along the channels. Therefore, evaporation alone provides the driving force for water transport in plants.<ref name="Sperry-2003"/>  However, without specialized transport vessels, this [[Xylem#Cohesion-tension theory|cohesion-tension]] mechanism can cause negative pressures sufficient to collapse water conducting cells, limiting the transport water to no more than a few cm, and therefore limiting the size of the earliest plants.<ref name="Sperry-2003"/>

[[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. Scale bar: 20&nbsp;μm]]

===Xylem<span class="anchor" id="xylem"></span>===
{{Further |Xylem}}

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.  As plants grew upwards, specialised water transport [[vascular tissue]]s evolved, first in the form of simple [[hydroid (botany)|hydroids]] of the type found in the setae of moss sporophytes. These simple elongated cells were dead and water-filled at maturity, providing a channel for water transport, but their thin, unreinforced walls would collapse under modest water tension, limiting the plant height.  [[Xylem]] [[tracheid]]s, wider cells with [[lignin]]-reinforced cell walls that were more resistant to collapse under the tension caused by water stress, occur  in more than one plant group by mid-Silurian, and may have a single evolutionary origin, possibly within the hornworts,<ref name="Qiu-2006">{{cite journal |author=Qiu, Y.L. |author2=Li, L. |author3=Wang, B. |author4=Chen, Z. |author5=Knoop, V. |author6=Groth-malonek, M. |author7=Dombrovska, O. |author8=Lee, J. |author9=Kent, L. |author10=Rest, J. |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 |display-authors=etal |doi-access=free }}</ref> uniting all tracheophytes.  Alternatively,  they may have evolved more than once.<ref name="Sperry-2003"/>  Much later, in the Cretaceous, tracheids were followed by [[vessel element|vessels]] in [[flowering plant]]s.<ref name="Sperry-2003"/> 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="Sperry-2003"/><ref name="Raven-1977"/>

The early Devonian pretracheophytes ''[[Aglaophyton]]'' and ''[[Horneophyton]]'' have unreinforced water transport tubes with wall structures very similar to moss hydroids, but they grew alongside several species of [[tracheophytes]], such as ''[[Rhynia]] gwynne-vaughanii'' that had xylem tracheids that were well reinforced by bands of lignin. The earliest macrofossils known to have xylem tracheids are small, mid-Silurian plants of the genus ''[[Cooksonia]]''.<ref name="Edwards-1992">{{Cite journal |last1=Edwards |first1=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 |s2cid=4264332 }}</ref> However, thickened bands on the walls of isolated tube fragments are apparent from the early Silurian onwards.<ref name="Niklas-1983">{{Cite journal |last1=Niklas |first1=K. J. |last2=Smocovitis |first2=V. |s2cid=35550235 |title=Evidence for a Conducting Strand in Early Silurian (Llandoverian) Plants: Implications for the Evolution of the Land Plants |jstor=2400461 |journal=Paleobiology |volume=9 |issue=2 |pages=126–137 |year=1983 |doi=10.1017/S009483730000751X|bibcode=1983Pbio....9..126N }}</ref>

Plants continued to innovate ways of reducing the resistance to flow within their cells, progressively increasing the efficiency of their water transport and to increase the resistance of the tracheids to collapse under tension.<ref name="Niklas-1985"/><ref name="Niklas-1980">{{Cite journal |last1=Niklas |first1=K. |last2=Pratt |first2=L. |title=Evidence for lignin-like constituents in Early Silurian (Llandoverian) plant fossils |journal=Science |volume=209 |issue=4454 |pages=396–397 |year=1980 |pmid=17747811 |doi=10.1126/science.209.4454.396 |bibcode=1980Sci...209..396N |s2cid=46073056}}</ref> During the early Devonian, maximum tracheid diameter increased with time, but may have plateaued in the [[zosterophyll]]s by mid-Devonian.<ref name="Niklas-1985">{{Cite journal |last1=Niklas |first1=K. J. |title=The Evolution of Tracheid Diameter in Early Vascular Plants and Its Implications on the Hydraulic Conductance of the Primary Xylem Strand |jstor=2408738 |journal=Evolution |volume=39 |issue=5 |pages=1110–1122 |year=1985 |doi=10.2307/2408738 |pmid=28561493}}</ref>  Overall transport rate also depends on the overall cross-sectional area of the xylem bundle itself, and some mid-Devonian plants, such as the Trimerophytes, had much larger steles than their early ancestors.<ref name="Niklas-1985"/> While wider tracheids provided higher rates of water transport, they increased the risk of cavitation, the formation of air bubbles resulting from the breakage of the water column under tension.<ref name="Sperry-2003"/> Small pits in tracheid walls allow water to by-pass a defective tracheid while preventing air bubbles from passing through<ref name="Sperry-2003"/> but at the cost of restricted flow rates. By the Carboniferous, Gymnosperms had developed [[Pit (botany)#Types of pits|bordered pits]],<ref name="Pitterman-2005">{{Cite journal |author1=Pittermann J. |author2=Sperry J.S. |author3=Hacke U.G. |author4=Wheeler J.K. |author5=Sikkema E.H. |title=Torus-Margo Pits Help Conifers Compete with Angiosperms |journal=Science Magazine |volume=310 |issue=5756 |pages=1924 |date=December 2005 |doi=10.1126/science.1120479 |pmid=16373568 |doi-access= |s2cid=28339481 }}</ref><ref>{{Cite web|url=https://phys.org/news/2005-12-christmas-trees-extinct.html|title=Why Christmas trees are not extinct|website=phys.org}}</ref> valve-like structures that allow high-conductivity  pits to seal when one side of a tracheid is depressurized.

Tracheids have non-perforated end walls with pits, which impose a great deal of resistance on water flow,<ref name="Niklas-1985"/> but may have had the advantage of isolating air embolisms caused by cavitation or freezing. 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 gnetophytes and angiosperms.<ref name="Sperry-2003"/>  Vessel members are open tubes with no end walls, and are arranged end to end to operate as if they were one continuous vessel.<ref name="Niklas-1985"/> Vessels allowed the same cross-sectional area of wood to transport much more water than tracheids.<ref name="Sperry-2003"/> 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="Sperry-2003"/> 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="Sperry-2003"/> Once plants had evolved this level of control over water evaporation and water transport, they were truly [[Homoiohydry|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="Raven-1977"/><ref name="Sperry-2003"/> but as a result of their increased independence from their surroundings, most vascular plants lost their ability to survive desiccation&nbsp;- a costly trait to lose.<ref name="Sperry-2003"/> In early land plants, support was mainly provided by turgor pressure, particularly of the outer layer of cells known as the sterome tracheids, and not by the xylem, which was too small, too weak and in too central a position to provide much structural support.<ref name="Sperry-2003"/>  Plants with [[secondary xylem]] that  had appeared by mid-Devonian, such as the [[Trimerophytes]] and [[Progymnosperms]] had much larger vascular cross sections producing strong woody tissue.{{citation needed|date=June 2024}}

===Endodermis===
An [[endodermis]] may have evolved in the earliest plant roots during the Devonian, but the first fossil evidence for such a structure is Carboniferous.<ref name="Sperry-2003"/> The endodermis in the roots surrounds the water transport tissue and regulates ion exchange between the groundwater and the tissues 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.

==Evolution of plant morphology==

===Leaves{{anchor |leaves}}===
[[File:Illustration Isoetes lacustris0.jpg|thumb |The lycopod ''[[Isoetes]]'' bears [[microphyll]]s (leaves with a single vascular trace).]]

[[File:Vein sceleton hydrangea ies.jpg|thumb|The branching pattern of megaphyll veins may indicate their origin as webbed, dichotomising branches.]]

[[File:Leaf 1 web.jpg|thumb |250px |right |Leaf lamina. The megaphyllous [[leaf]] architecture arose multiple times in different plant lineages]]

Leaves are the primary [[photosynthetic]] organs of a modern plant. The origin of [[leaves]] was almost certainly triggered by falling concentrations of atmospheric {{CO2}} during the Devonian period, increasing the efficiency with which carbon dioxide could be captured for [[photosynthesis]].<ref name="Kenrick-2001">{{cite journal |first=Paul |last=Kenrick |date=2001 |title=Turning over a new leaf |journal=Nature |volume=410 |issue=6826 |pages=309–310 |bibcode=2001Natur.410..309K |doi=10.1038/35066649 |pmid=11268183 |s2cid=4335355}}</ref><ref name="Beerling-2001"/>

Leaves evolved more than once. Based on their structure, they are classified into two types: [[microphylls]], which lack complex venation and may have originated as spiny outgrowths known as enations, and [[megaphylls]], which are large and have complex [[Leaf#Venation|venation]] that may have arisen from the modification of groups of branches. It has been proposed that these structures arose independently.<ref name="Crane-1997">{{cite journal |last1=Crane |first1=P.R. |last2=Kenrick |first2=P. |title=Diverted development of reproductive organs: A source of morphological innovation in land plants |journal=Plant Systematics and Evolution |volume=206 |issue=1 |pages=161–174 |year=1997 |doi=10.1007/BF00987946 |bibcode=1997PSyEv.206..161C |s2cid=23626358}}</ref> Megaphylls, according to Walter Zimmerman's telome theory,<ref name="Zimmermann-1959">{{cite book |last=Zimmermann |first=W. |date=1959 |title=Die Phylogenie der Pflanzen |edition=2 |location=Stuttgart |publisher= 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 |last1=Piazza |first1=P. |title=Evolution of leaf developmental mechanisms |journal=New Phytologist |volume=167 |pages=693–710 |year=2005 |doi=10.1111/j.1469-8137.2005.01466.x |pmid=16101907 |issue=3 |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 Evolution 124: 251–277.</ref><ref>{{cite journal |last1=Hagemann |first1=W. |year=1999 |title=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 |journal=Plant Systematics and Evolution |volume=216 |issue=1–2 |pages=81–133 |doi=10.1007/bf00985102 |bibcode=1999PSyEv.216...81H |s2cid=21483458 }}</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>{{cite journal |last1=Sattler |first1=R. |year=1992 |title=Process morphology: structural dynamics in development and evolution |journal=Canadian Journal of Botany |volume=70 |issue=4 |pages=708–714 |doi=10.1139/b92-091}}</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>{{cite journal |last1=James |first1=P.J. |year=2009 |title='Tree and Leaf': A different angle |journal=The Linnean |volume=25 |page=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".

Before the evolution of [[leaves]], plants had the [[photosynthetic]] apparatus on the stems, which they retain albeit leaves have largely assumed that job. Today's megaphyll leaves probably became commonplace some 360mya, about 40my after the simple leafless plants had colonized the land in the [[Early Devonian]]. 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.<ref name="Kenrick-2001"/> This would have resulted in greater [[transpiration]] rates and gas exchange, but especially at high {{CO2}} concentrations, large leaves with fewer stomata would have heated to lethal temperatures in full sunlight. Increasing the stomatal density allowed for a better-cooled leaf, thus making its spread feasible, but increased {{CO2 |link=yes}} uptake at the expense of decreased water use efficiency.<ref name="Beerling-2001">{{cite journal |author=Beerling D. |author-link=David Beerling |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 |last2=Osborne |first2=C. P. |last3=Chaloner |first3=W. G. |bibcode=2001Natur.410..352B |s2cid=4386118 |url=http://eprints.whiterose.ac.uk/59/1/osbornecp2.pdf }}</ref><ref>{{Cite web |url=http://www.corante.com/loom/archives/004766.html |title=A perspective on the CO<sub>2</sub> theory of early leaf evolution |access-date=2011-03-08 |archive-url=https://web.archive.org/web/20110629184105/http://www.corante.com/loom/archives/004766.html |archive-date=2011-06-29 |url-status=dead }}</ref>

The rhyniophytes of the Rhynie chert consisted only of 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="Stewart-1993"/> Some organisms, such as ''[[Psilophyton]]'', bore [[wikt:enation|enation]]s. These are small, spiny outgrowths of the stem, lacking their own vascular supply.{{citation needed|date=June 2024}}

The [[zosterophyll]]s were already important in the late Silurian, much earlier than any rhyniophytes of comparable complexity.<ref name="Kotyk-2002">{{cite journal |first1=M.E. |last1=Kotyk |first2=J.F. |last2=Basinger |first3=P.G. |last3=Gensel |first4=T.A. |last4=de Freitas |date=2002 |title=Morphologically complex plant macrofossils from the late Silurian of arctic Canada |journal=American Journal of Botany |volume=89 |issue=6 |pages=1004–1013 |doi= 10.3732/ajb.89.6.1004 |pmid=21665700 |doi-access=free }}</ref> This group, recognisable by their kidney-shaped sporangia which grew on short lateral branches close to the main axes, sometimes branched in a distinctive H-shape.<ref name="Stewart-1993"/> Many zosterophylls bore enations (small tissue outgrowths on the surface with variable morphologies) on their axes but none of these had a vascular trace. The first evidence of vascularised enations occurs in a fossil clubmoss known as ''[[Baragwanathia]]'' that had already appeared in the fossil record in the Late Silurian.<ref name="Rickards-2000">{{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 |access-date=2007-10-25 |doi=10.1017/S0016756800003800 |format=abstract |bibcode=2000GeoM..137..207R |s2cid=131287538 |url-access=subscription }}</ref> In this organism, these leaf traces continue into the leaf to form their mid-vein.<ref name="Kaplan-2001">{{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 |doi-access= }}</ref> One theory, the "enation theory", holds that the microphyllous leaves of clubmosses developed by outgrowths of the protostele connecting with existing enations<ref name="Stewart-1993"/> The leaves of the Rhynie genus ''[[Asteroxylon]]'', which was preserved in the Rhynie chert almost 20 million years later than ''Baragwanathia'', had a primitive vascular supply&nbsp;– in the form of [[leaf trace]]s departing from the central protostele towards each individual "leaf".<ref name="Taylor-2005a">{{cite journal |author=Taylor, T.N. |author2=Hass, H. |author3=Kerp, H. |author4=Krings, M. |author5=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
 |doi=10.3852/mycologia.97.1.269 |hdl=1808/16786 |hdl-access=free }}</ref> ''Asteroxylon'' and ''Baragwanathia'' are widely regarded as primitive lycopods,<ref name="Stewart-1993"/> a group still [[wikt:extant|extant]] today, represented by the [[Isoetes|quillworts]], the [[Selaginella|spikemosses]] and the [[club moss]]es. Lycopods bear distinctive [[microphylls]], defined as leaves with a single vascular trace. Microphylls could grow to some size, those of [[Lepidodendrales]] reaching over a meter in length, but almost all just bear the one vascular bundle. An exception is the rare branching in some ''[[Selaginella]]'' species.

The more familiar leaves, [[megaphylls]], are thought to have originated four times independently: in the ferns, horsetails, progymnosperms and seed plants.<ref name="Boyce-2002">{{cite journal |author=Boyce, C.K. |author2=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 |bibcode=2002Pbio...28...70B |s2cid=1650492 }}</ref> They appear to have originated by modifying [[dichotomising]] branches, which first overlapped (or "overtopped") one another, became flattened or planated and eventually developed "webbing" and evolved gradually into more leaf-like structures.<ref name="Kaplan-2001"/> Megaphylls, by [[Walter Max Zimmermann|Zimmerman's]] [[Microphyll#Leaf vasculature|telome theory]], are composed of a group of webbed branches<ref name="Kaplan-2001"/> and hence the "leaf gap" left where the leaf's vascular bundle leaves that of the main branch resembles two axes splitting.<ref name="Kaplan-2001"/> 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="Boyce-2002"/>

The cessation of further diversification can be attributed to developmental constraints,<ref name="Boyce-2002"/> raising the question of why it took so long for leaves to evolve in the first place. Plants had been on 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="Hao-2003">{{cite journal |author=Hao, S. |author2=Beck, C.B. |author3=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 |s2cid=84741832 }}</ref> The best explanation so far is that atmospheric {{co2}} was declining rapidly during this time&nbsp;– falling by around 90% during the Devonian.<ref name="Berner-2001">{{cite journal |author=Berner, R.A. |author2=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=182–204 |url=http://ajsonline.org/cgi/content/abstract/301/2/182 |access-date=2008-04-07 |doi=10.2475/ajs.301.2.182 |format=abstract |bibcode=2001AmJS..301..182B |citeseerx=10.1.1.393.582 |archive-url=https://web.archive.org/web/20090129172708/http://www.ajsonline.org/cgi/content/abstract/301/2/182 |archive-date=2009-01-29 |url-status=dead }}</ref> This required an increase in stomatal density by 100 times to maintain the rate of photosynthesis. When stomata open to allow water to evaporate from leaves it has a cooling effect, resulting from the loss of [[latent heat]] of evaporation. It appears that the low stomatal density in the early Devonian meant that evaporation and evaporative cooling were limited, and that leaves would have overheated 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="Beerling-2001" /> Clearly, leaves are not always beneficial, as illustrated by the frequent occurrence of secondary loss of leaves, exemplified by [[cacti]] and the "whisk fern" ''[[Psilotum]]''.

Secondary evolution can 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="Kaplan-2001"/>

[[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="Shellito-2006">{{cite journal |author=Shellito, C.J. |author2=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 |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]], some [[pinophyta]] and certain angiosperms.<ref name="Aerts-1995">{{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 |pmid=21237084 |bibcode=1995TEcoE..10..402A }}</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="Lababdeira-1994">{{cite journal
 |author=Labandeira, C.C. |author2=Dilcher, D.L. |author3=Davis, D.R. |author4=Wagner, D.L. |year=1994 |title=Ninety-seven million years of angiosperm-insect association: paleobiological insights into the meaning of coevolution |journal=PNAS |pmid=11607501 |volume=91 |issue=25 |pmc=45420 |pages=12278–12282 |doi=10.1073/pnas.91.25.12278 |bibcode=1994PNAS...9112278L |doi-access=free }}</ref>

===Roots===
{{multiple image
 | align = right
 | direction = vertical
 | width = 200
 | image1 = Lepidodendron aculeatum2.jpg
 | image2 = Lepido root top.jpg
 | footer = The rhizomes (''[[Stigmaria]]'') (bottom image) of lycopsids (including the Carboniferous [[Lepidodendrales]]) are thought to be developmentally equivalent to the stems (top), as the similar appearance of "leaf scars" and "root scars" on these specimens from different species demonstrates.
}}

The evolution of roots had consequences on a global scale. By disturbing the soil and promoting its acidification (by taking up nutrients such as nitrate and phosphate<ref>{{cite journal |last1=de Souza |first1=Rocheli |last2=Ambrosini |first2=Adriana |last3=Passaglia |first3=Luciane M.P. |title=Plant growth-promoting bacteria as inoculants in agricultural soils |journal=Genetics and Molecular Biology |date=December 2015 |volume=38 |issue=4 |pages=401–19 |doi=10.1590/S1415-475738420150053 |pmid=26537605 |pmc=4763327}}</ref>), they enabled it to weather more deeply, injecting carbon compounds deeper into soils<ref name="Mora-1996">{{cite journal |author=Mora, C.I. |author2=Driese, S.G. |author3=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 |s2cid=128479221 }}</ref> with huge implications for climate.<ref name="Berner-1994">{{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 |bibcode=1994AmJS..294...56B |doi-access=free }}</ref> These effects may have been so profound they led to [[Late Devonian extinction|a mass extinction]].<ref name="Algeo-1995">{{cite journal |author=Algeo, T.J. |author2=Berner, R.A. |author3=Maynard, J.B. |author4=Scheckler, S.E. |author5=GSA Today Archives |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=https://www.geosociety.org/pubs/gsatoday/archive/toc9503.htm |access-date=2019-08-29 |archive-date=2015-05-01 |archive-url=https://web.archive.org/web/20150501170048/http://geosociety.org/pubs/gsatoday/archive/toc9503.htm |url-status=dead }}</ref>

While there are traces of root-like impressions in fossil soils in the Late Silurian,<ref name="Retallack-1986">{{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 prostrate branches that sprawled along the ground, with upright axes or [[wikt:thalli|thalli]] dotted here and there, and some even had non-photosynthetic subterranean branches which lacked stomata. Roots have a [[root cap]], unlike specialised branches.<ref name="Raven-2001"/> So while Siluro-Devonian plants such as ''[[Rhynia]]'' and ''[[Horneophyton]]'' possessed the physiological equivalent of roots,<ref>{{Cite web |url=http://palaeos.com/plants/tracheophyta/tracheophyta2.html |title=Tracheophyta - 2 |website=Paleos - Life Through Deep Time.}}</ref><ref>{{Cite journal |title=EARLY EVOLUTION OF LAND PLANTS: Phylogeny, Physiology, and Ecology of the Primary Terrestrial Radiation |last=Richard M. Bateman, Peter R. Crane, William A. DiMichele, Paul R. Kenrick, Nick P. Rowe, Thomas Speck, and William E. Stein |journal=Annual Review of Ecology and Systematics |s2cid=44508826 |date=1998 |volume=29 |pages=263–292 |doi=10.1146/annurev.ecolsys.29.1.263}}</ref> roots&nbsp;– defined as organs differentiated from stems&nbsp;– did not arrive until later.<ref name="Raven-2001"/> Unfortunately, roots are rarely preserved in the fossil record.<ref name="Raven-2001"/>

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="Raven-2001"/> That said, rhizoids probably evolved more than once; the [[rhizine]]s of [[lichen]]s, for example, perform a similar role. Even some animals (''[[Lamellibrachia]]'') have root-like structures.<ref name="Raven-2001"/> Rhizoids are clearly visible in the Rhynie chert fossils, and were present in most of the earliest vascular plants, and on this basis seem to have presaged true plant roots.<ref>{{cite journal |doi=10.1098/rstb.2017.0042 |pmid=29254968 |pmc=5745339 |title=Bilaterally symmetric axes with rhizoids composed the rooting structure of the common ancestor of vascular plants |journal=Philosophical Transactions of the Royal Society B: Biological Sciences |volume=373 |issue=1739 |pages=20170042 |year=2017 |last1=Hetherington |first1=Alexander J |last2=Dolan |first2=Liam}}</ref>

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="Raven-2001"/> 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="Algeo-1998"/> However, none of these fossils display all the features borne by modern roots,<ref name="Raven-2001"/> with the exception of ''Asteroxylon'', which has recently been recognized as bearing roots that evolved independently from those of extant vascular plants.<ref>{{cite journal |doi=10.1038/s41586-018-0445-z |pmid=30135586 |pmc=6175059 |title=Stepwise and independent origins of roots among land plants |journal=Nature |volume=561 |issue=7722 |pages=235–238 |year=2018 |last1=Hetherington |first1=Alexander J. |last2=Dolan |first2=Liam |bibcode=2018Natur.561..235H}}</ref> Roots and root-like structures became increasingly common and deeper penetrating during the [[Devonian]], 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="Algeo-1998"/> True gymnosperms and zygopterid ferns also formed shallow rooting systems during the Famennian.<ref name="Algeo-1998"/>

The rhizophores 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="Raven-2001"/> 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="Raven-2001"/> a proposition supported by studies showing that roots are initiated and their growth promoted by different mechanisms in lycophytes and euphyllophytes.<ref name="Coudert-2012">{{Cite journal |doi=10.1093/molbev/mss250 |issn=0737-4038 |last=Coudert |first=Yoan |author2=Anne Dievart |author3=Gaetan Droc |author4=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 |doi-access=free}}</ref>

Early rooted plants are little more advanced than their Silurian forebears, 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="Kenrick-1997b">{{cite journal |author=Kenrick, P. |author2=Crane, P.R. |year=1997 |title=The origin and early evolution of plants on land |journal=Nature |volume=389 |issue=6646 |pages=33–39 |doi=10.1038/37918 |bibcode=1997Natur.389...33K |s2cid=3866183 }}</ref>

By the Middle to Late Devonian, most groups of plants had independently developed a rooting system of some nature.<ref name="Kenrick-1997b"/> As roots became larger, they could support larger trees, and the soil was weathered to a greater depth.<ref name="Algeo-1995"/> 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="Algeo-1998"/>

The narrowest roots of modern plants are a mere 40&nbsp;μm in diameter, and could not physically transport water if they were any narrower.<ref name="Raven-2001">{{cite journal |author=Raven, J.A. |author2=Edwards, D. |year=2001 |title=Roots: evolutionary origins and biogeochemical significance |journal=Journal of Experimental Botany |volume=52 |issue=90001 |pages=381–401 |doi=10.1093/jexbot/52.suppl_1.381 |pmid=11326045 |doi-access=free  }}</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="Raven-2001"/>

===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. Greater height provided a competitive advantage in the harvesting of sunlight for photosynthesis,&nbsp;overshadowing of competitors&nbsp;and in spore distribution, as spores (and later, seeds) could be blown for greater distances if they started higher. An effective vascular system was required in order to achieve greater heights. To attain [[wikt:arborescence|arborescence]], plants had to develop [[wood]]y tissue that provided both support and water transport, and thus needed to evolve the capacity for [[secondary growth]]. The stele of plants undergoing secondary growth is surrounded by a [[vascular cambium]], a ring of meristematic 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. Fossils of plants from the early Devonian show that a simple form of wood first appeared at least 400 million years ago, at a time when all land plants were small and herbaceous.<ref name="Gerrienne-2011">{{cite journal |first1=Philippe |last1=Gerrienne |first2=Patricia G. |last2=Gensel |first3=Christine |last3=Strullu-Derrien |first4=Hubert |last4=Lardeux |first5=Philippe |last5=Steemans |first6=Cyrille |last6=Prestianni |date=2011 |title=A simple type of wood in two early Devonian plants |journal=Science |volume=333 |issue=6044 |page=837 |doi=10.1126/science.1208882 |pmid=21836008 |bibcode=2011Sci...333..837G |hdl=2268/97121 |s2cid=23513139 |hdl-access=free }}</ref> Because wood evolved long before shrubs and trees, it is likely that its original purpose was for water transport, and that it was only used for mechanical support later.<ref>{{cite news |last=Kinver |first=Mark |title='Early wood' samples reshape plant history |url=https://www.bbc.co.uk/news/science-environment-14543120 |work=BBC News |date=16 August 2011}}</ref>

The first plants to develop 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="Stein-2007">{{cite journal |author=Stein, W.E. |author2=Mannolini, F. |author3=Hernick, L.V. |author4=Landing, E. |author5=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=904–907 |doi=10.1038/nature05705 |bibcode=2007Natur.446..904S |s2cid=2575688 }}</ref>

[[File:Givetianwood.jpg|thumb |A piece of fossilized driftwood from the Middle Devonian ([[Givetian]]) of New York State.]]

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="Retallak-1985">{{cite journal |author=Retallack, G.J. |author2=Catt, J.A. |author3=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 |doi-access= }}</ref> reached 30&nbsp;m in height. The progymnosperms were the first plants to develop true wood, grown from a bifacial cambium. The first appearance of one of them, ''[[Rellimia]]'', was in the Middle Devonian.<ref name="Dannenhoffer-1989">{{cite journal |author=Dannenhoffer, J.M. |author2=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.{{citation needed |date=April 2018}}

''Archaeopteris'' forests were soon supplemented by arborescent lycopods, in the form of [[Lepidodendrales]], which exceeded 50m in height and 2m across at the base. These arborescent lycopods rose to dominate Late Devonian and Carboniferous forests that gave rise to [[coal]] deposits.<ref name="Davis-2004">{{cite book |author1=Davis, P |author2=Kenrick, P. |title=Fossil Plants |publisher=Smithsonian Books, Washington D.C. |year=2004 |isbn=978-1-58834-156-3}}</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" as a single trunk to a genetically determined height, branch at that level, spread their spores and die.<ref name="Donoghue-2005">{{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 |doi=10.1666/0094-8373(2005)031[0077:KICASM]2.0.CO;2 |s2cid=36988476 |url-access=subscription }}</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="Stewart-1993"/> 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]]'' appeared 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 and to branch repeatedly.

While the form of early trees was similar to that of today's, the [[Spermatophytes]] or seed plants, the group that contain all modern trees, had yet to evolve. The dominant tree groups today are all seed plants, the gymnosperms, which include the coniferous trees, and the angiosperms, which contain all fruiting and flowering trees. No free-sporing trees like ''Archaeopteris'' exist in the extant flora. 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="Bowe-2000">{{cite journal |author=Bowe, L.M. |author2=Coat, G. |author3=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=4092–4097 |doi=10.1073/pnas.97.8.4092 |pmid=10760278 |bibcode=2000PNAS...97.4092B |pmc=18159 |doi-access=free }}</ref><ref name="Chaw-2000">{{cite journal |author=Chaw, S.M. |author2=Parkinson, C.L. |author3=Cheng, Y. |author4=Vincent, T.M. |author5=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 |doi-access=free }}</ref><ref name="Soltis-2002">{{cite journal
 |author=Soltis, D.E. |author2=Soltis, P.S. |author-link3=Pamela S. Soltis |author3=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 |doi=10.3732/ajb.89.10.1670 |pmid=21665594 |doi-access=  }}</ref> The molecular data has yet to be fully reconciled with morphological data,<ref name="Friis-2006">{{cite journal |author=Friis, E.M. |author2=Pedersen, K.R. |author3=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 |bibcode=2006PPP...232..251F}}</ref><ref name="Hilton-2006">{{cite journal |author=Hilton, J. |author2=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 |s2cid=86395036 }}</ref><ref name="Bateman-2006">{{cite journal |author=Bateman, R.M. |author2=Hilton, J. |author3=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 |doi-access=free }}</ref> but it is becoming accepted that the morphological support for paraphyly is not especially strong.<ref name="Frohlich-2007"/>
This would lead to the conclusion that both groups arose from within the pteridosperms, probably as early as the [[Permian]].<ref name="Frohlich-2007"/>

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 understorey, and have been diversifying ever since the Cretaceous,<ref>{{cite journal |title=Angiosperm diversification through time |journal=American Journal of Botany |date=2009-01-01 |last1=Magallón |first1=Susana |last2=Castillo |first2=Amanda |volume=96 |issue=1 |pages=349–365 |pmid=21628193 |doi=10.3732/ajb.0800060 |url=https://bsapubs.onlinelibrary.wiley.com/doi/full/10.3732/ajb.0800060 |access-date=2021-04-27 |url-access=subscription }}</ref> to become the dominant member of non-[[wikt:boreal|boreal]] forests today.

===Seeds===

[[File:Trigonocarpus.jpg|thumb |The fossil seed ''[[Trigonocarpus]]'']]

[[File:Runcaria megasporangium and cupule drawing.jpg|thumb|upright=0.4|The transitional fossil ''[[Runcaria]]'']]

Early land plants reproduced in the fashion of ferns: spores germinated into small gametophytes, which produced eggs and/or sperm. These sperm would swim across moist soils to find the female organs (archegonia) on the same or another gametophyte, where they would fuse with an egg to produce an embryo, which would germinate into a sporophyte.<ref name="Algeo-1998">{{cite journal |author=Algeo, T.J. |author2=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 |pmc=1692181 }}</ref>

Heterosporic plants, 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 ovules and seeds: taken to the extreme, the megasporangia could bear only a single megaspore tetrad, and to complete the transition to true ovules, three of the megaspores in the original tetrad could be aborted, leaving one megaspore per megasporangium.{{citation needed|date=June 2024}}

The transition to ovules continued with this megaspore being "boxed in" to its sporangium while it germinated. Then, the megagametophyte was contained within a waterproof integument, which enclosed the seed. The pollen grain, which contained a microgametophyte germinated from a microspore&nbsp;, was employed for dispersal of the male gamete, only releasing its desiccation-prone flagellate sperm when it reached a receptive megagametophyte.<ref name="Stewart-1993"/>

Lycopods and sphenopsids got a fair way down the path to the seed habit without ever crossing the threshold. Fossil lycopod megaspores reaching 1&nbsp;cm in diameter, and surrounded by vegetative tissue, are known&nbsp;(Lepidocarpon, Achlamydocarpon);– these even germinated into a megagametophyte ''in situ''. However, they fell short of being ovules, since the nucellus, an inner spore-covering layer, does not completely enclose the spore. A very small slit (micropyle) remains, meaning that the megasporangium 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="Stewart-1993"/>

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 ovule.<ref>{{Cite journal |title=Science Magazine |journal=Runcaria, A Middle Devonian Seed Plant Precursor |publisher=American Association for the Advancement of Science |year=2011 |volume=306 |issue=5697 |pages=856–858 |doi=10.1126/science.1102491 |url=https://www.science.org/doi/abs/10.1126/science.1102491 |last1=Gerrienne |first1=P. |last2=Meyer-Berthaud |first2=B. |last3=Fairon-Demaret |first3=M. |last4=Streel |first4=M. |last5=Steemans |first5=P. |pmid=15514154 |s2cid=34269432 |url-access=subscription }}</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="Stewart-1993"/>
The seed plants underwent their first major evolutionary radiation in the [[Famennian]] era.<ref>{{cite journal | doi=10.1038/srep10736 | title=A Late Devonian Fertile Organ with Seed Plant Affinities from China | year=2015 | last1=Wang | first1=Deming | last2=Liu | first2=Le | last3=Guo | first3=Yun | last4=Xue | first4=Jinzhuang | last5=Meng | first5=Meicen | journal=Scientific Reports | volume=5 | page=10736 | pmid=26022973 | pmc=4448223 | bibcode=2015NatSR...510736W }}</ref>

This seed model is shared by basically all gymnosperms (literally: "naked seeds"), most of which encase their seeds in a woody cone or fleshy aril (the [[Taxus|yew]], for example), but none of which fully enclose their seeds. The angiosperms ("vessel seeds") are the only group to fully enclose the seed, in a carpel.{{citation needed|date=June 2024}}

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="Mapes-1989">{{cite journal |author=Mapes, G. |author2=Rothwell, G.W. |author3=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 |s2cid=4358761 }}</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="Mapes-1989"/> 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="Mapes-1989"/>

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="Algeo-1998"/> 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="Algeo-1998"/> 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="Algeo-1998"/>
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="Algeo-1998"/>

Despite these advantages, it is common for fertilized ovules to fail to mature as seeds.<ref>{{cite journal |last1=Bawa |first1=K.S. |last2=Webb |first2=C.J. |year=1984 |title=Flower, fruit and seed abortion in tropical forest trees. Implications for the evolution of paternal and maternal reproductive patterns |journal=American Journal of Botany |volume=71 |issue=5 |pages=736–751 |doi=10.2307/2443371 |jstor=2443371 }}</ref> Also during seed dormancy (often associated with unpredictable and stressful conditions) DNA damage accumulates.<ref>{{cite journal |last1=Cheah |first1=K.S. |last2=Osborne |first2=D.J. |title=DNA lesions occur with loss of viability in embryos of ageing rye seed |journal=Nature |volume=272 |issue=5654 |pages=593–599 |date=April 1978 |pmid=19213149 |doi= 10.1038/272593a0 |bibcode=1978Natur.272..593C |s2cid=4208828 }}</ref><ref>{{cite journal |last1=Koppen |first1=G. |last2=Verschaeve |first2=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=50–54 |year=2001 |pmid=11321247 }}</ref><ref>{{cite journal |last1=Bray |first1=C.M. |last2=West |first2=C.E. |title=DNA repair mechanisms in plants: crucial sensors and effectors for the maintenance of genome integrity |journal=New Phytologist |volume=168 |issue=3 |pages=511–28 |date=December 2005 |pmid=16313635 |doi=10.1111/j.1469-8137.2005.01548.x |doi-access= }}</ref> Thus DNA damage appears to be a basic problem for survival of seed plants, just as DNA damage is a [[DNA damage (naturally occurring)#A major problem for life|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>

===Flowers{{anchor |Flowers}}===
{{For |a more ecological discussion on the evolution of flowers and earliest flower |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="Feild-2011">{{Cite journal |last1=Feild |first1=T. S. |last2=Brodribb |first2=T. J. |last3=Iglesias |first3=A. |last4=Chatelet |first4=D. S. |last5=Baresch |first5=A. |last6=Upchurch |first6=G. R. |last7=Gomez |first7=B. |last8=Mohr |first8=B. A. R. |last9=Coiffard |first9=C. |last10=Kvacek |doi=10.1073/pnas.1014456108 |first10=J. |last11=Jaramillo |first11=C. |title=Fossil evidence for Cretaceous escalation in angiosperm leaf vein evolution |journal=Proceedings of the National Academy of Sciences |volume=108 |issue=20 |pages=8363–8366 |year=2011 |pmid=21536892 |pmc=3100944 |bibcode=2011PNAS..108.8363F |doi-access=free }}</ref> Flower-like structures first appear in the [[fossil]] records some ~130 mya, in the [[Cretaceous]].<ref name="Lawton-Rauh-2000">{{cite journal |last1=Lawton-Rauh |first1=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=E.R. |last3=Purugganan |first3=M.D.}}</ref> However, in 2018, scientists reported the finding of a fossil [[flower]] from about 180 million years ago, 50 million years earlier than previously thought.<ref name="Chinese Academy of Sciences-2018">{{cite news |author=Chinese Academy of Sciences |title=Flowers originated 50 million years earlier than previously thought |url=https://www.eurekalert.org/pub_releases/2018-12/caos-fo5121818.php |date=18 December 2018 |work=[[EurekAlert!]] |access-date=18 December 2018 |author-link=Chinese Academy of Sciences }}</ref> The interpretation has been however highly disputed.<ref>{{Cite journal |last1=Coiro |first1=Mario |last2=Doyle |first2=James A. |last3=Hilton |first3=Jason |date=2019-01-25 |title=How deep is the conflict between molecular and fossil evidence on the age of angiosperms? |journal=New Phytologist |volume=223 |issue=1 |pages=83–99 |language=en |doi=10.1111/nph.15708 |pmid=30681148 |doi-access=free}}</ref>

Colorful 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="Bateman-2006"/>

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.{{citation needed|date=June 2024}}

[[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 with this hypothesis,<ref name="Chaw-2000"/><ref name="Soltis-2002"/> and further suggests that Gnetales are more closely related to some gymnosperm groups than angiosperms,<ref name="Bowe-2000"/> and that [[wikt:extant|extant]] gymnosperms form a distinct clade to the angiosperms,<ref name="Bowe-2000"/><ref name="Chaw-2000"/><ref name="Soltis-2002"/> the two clades diverging some {{Ma |300}}.<ref name="Nei-2003">{{cite journal |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. |doi-access=free }}</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 |The inflorescences of the [[Bennettitales]] are strikingly similar to flowers, but evolved independently.]]

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 [[Mesozoic]] ''[[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="Crepet-2000"/>

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 called "ANA". This clade appear to have diverged in the early Cretaceous, around {{Ma |130}}&nbsp;– around the same time as the [[Archaefructus|earliest fossil angiosperm]],<ref name="Sun-2002">{{cite journal |author=Sun, G. |author2=Ji, Q. |author3=Dilcher, D.L. |author4=Zheng, S. |author5=Nixon, K.C. |author6= 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 |s2cid=1910388 }}</ref><ref name="Doyle-2003">In fact, ''[[Archaefructus]]'' probably didn't bear true flowers: see {{cite journal |author=Friis, E.M. |author2=Doyle, J.A. |author3=Endress, P.K. |author4=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="Frohlich-2007">{{cite journal  |author=Frohlich, M.W. |author2=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=1184–1189 |doi=10.1038/nature06393 |bibcode=2007Natur.450.1184F |s2cid=4373983 }}</ref> The [[magnoliids]] diverged soon after, and a rapid radiation had produced eudicots and monocots by {{Ma |125}}.<ref name="Frohlich-2007"/> 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="Wing-1998">{{cite journal |author=Wing, S.L. |author2=Boucher, L.D. |year=1998 |title=Ecological Aspects Of The Cretaceous Flowering Plant Radiation |journal=Annual Review of 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 name="Stewart-1993"/>{{rp |498}}

The features of the basal "ANA" groups suggest that angiosperms originated in dark, damp, frequently disturbed areas.<ref name="Feild-2004">{{cite journal |author=Feild, T.S. |author2=Arens, N.C. |author3=Doyle, J.A. |author4=Dawson, T.E. |author5=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 |doi=10.1666/0094-8373(2004)030<0082:DADANI>2.0.CO;2 |bibcode=2004Pbio...30...82F |s2cid=42855952 |url-access=subscription }}</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="Wing-1998"/> 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="Feild-2004"/>

{{anthophyta}}
Some propose that the Angiosperms arose from an unknown Seed Fern, Pteridophyte, and view Cycads as living Seed Ferns with both Seed-Bearing and sterile leaves (Cycas revoluta)<ref name="Hilton-2006" />

In August 2017, scientists presented a detailed description and 3D reconstruction of possibly the first [[flower]] that lived about 140 million years ago.<ref name="Gabbott-2017">{{cite news |last=Gabbott |first=Prof Sarah |title=Did the first flower look like this? |url=https://www.bbc.com/news/science-environment-40780491 |date=1 August 2017 |work=[[BBC News]] |access-date=1 August 2017 }}</ref><ref name="Sauquet-2017">{{cite journal |author=Sauquet, Hervé |display-authors=etal |title=The ancestral flower of angiosperms and its early diversification |date=1 August 2017 |journal=[[Nature Communications]] |volume=8 |pages=16047 |doi=10.1038/ncomms16047 |pmid=28763051 |pmc=5543309 |bibcode=2017NatCo...816047S }}</ref>

====Origins of the flower====

The family [[Amborellaceae]] is regarded as being the sister [[cladistics|clade]] to all other living flowering plants. A draft genome of ''Amborella trichopoda'' was published in December, 2013.<ref>{{cite journal |last1=Amborella Genome Project |date=20 Dec 2013 |title=The ''Amborella'' Genome and the Evolution of Flowering Plants |url=https://www.science.org/doi/10.1126/science.1241089 |journal=Science |volume=342 |issue=6165 |page= 1241089 |doi=10.1126/science.1241089 |access-date= 1 February 2020 |pmid=24357323 |s2cid=202600898 |url-access=subscription }}</ref> 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=3 |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 |pmid=21619600 |pmc=3219971 |doi-access=free }}</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 [[Populus|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.{{citation needed |date=December 2015}}

===Adaptive function of flowers===

[[Flower]]s likely emerged during plant evolution as an adaptation to facilitate cross-[[fertilization]] ([[outcrossing]]), a process that leads to the masking of recessive deleterious [[mutation]]s in progeny [[genome]]s.  This masking effect of expression  of deleterious mutations is referred to as [[complementation (genetics)|genetic complementation]].<ref name="Bernstein-1985">Bernstein H, Byerly HC, Hopf FA, Michod RE. Genetic damage, mutation, and the evolution of sex. Science. 1985 Sep 20;229(4719):1277–81. doi: 10.1126/science.3898363. PMID 3898363</ref>  This beneficial masking effect of cross-fertilization is also considered to be the basis of  [[hybrid vigour|hybrid vigor]] or [[heterosis]] in progeny.  Once flowers have become established in a lineage based on their adaptive function of promoting cross-fertilization, subsequent switching to inbreeding ordinarily then becomes disadvantageous, mainly because it permits expression of the previously masked deleterious recessive mutations, i.e. [[inbreeding depression]].  In addition, [[meiosis]], the process by which seed progeny are produced in flowering plants, provides a direct mechanism for [[DNA repair|repairing DNA]] through genetic recombination.<ref name="Hörandl-2024">Hörandl E. Apomixis and the paradox of sex in plants. Ann Bot. 2024 Mar 18:mcae044. doi: 10.1093/aob/mcae044. Epub ahead of print. PMID 38497809</ref>  Thus, in flowering plants, the two fundamental processes of sexual reproduction are cross-fertilization (outcrossing) and meiosis and these two processes appear to be maintained respectively by the advantages of genetic complementation and recombinational repair of DNA.<ref name="Bernstein-1985"/>

====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.{{citation needed|date=June 2024}}

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 |last1=Medarg |first1=N. G. |last2=Yanofsky |first2=M. |title=Function and evolution of the plant MADS-box gene family |journal=Nature Reviews Genetics |volume=2 |pages=186–195 |date=March 2001 |issue=3 |doi=10.1038/35056041 |pmid=11256070 |s2cid=7399106 }}</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 |last1=Jager |first1=Muriel |last2=Hassanin |first2=Alexandre |last3=Manuel |first3=Michael |last4=Le Guyader |first4=Hervé |last5=Deutsch |first5=Jean |display-authors=3 |title=MADS-Box Genes in Ginkgo biloba and the Evolution of the AGAMOUS Family |journal=Molecular Biology and Evolution |volume=20 |issue=5 |pages=842–854 |year=2003 |doi=10.1093/molbev/msg089 |pmid=12679535 |doi-access=free }}</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]].{{citation needed|date=June 2024}}

===Factors influencing floral diversity===

There is enormous variation in floral structure in plants, typically due to changes in the [[MADS-box]] genes and their expression pattern. 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, but genetic evidence and morphology suggest that lodicules are homologous to [[eudicot]] petals.<ref name="Thompson-2009">[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.{{citation needed |date=April 2018}} 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-2000" />

[[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 proliferation of floral organs in [[double-flowered]] forms of [[rose]]s, [[carnations]] and [[morning glory]]. These [[phenotypes]] have been selected by horticulturists for their increased number of [[petals]].<ref>{{cite journal |author1=Kitahara, K. |author2=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 |doi=10.1016/S0168-9452(99)00206-X|bibcode=2000PlnSc.151..121K }}</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 |display-authors=1 |last2=Colombo |first2=L. |last3=Franken |first3=J. |last4=Busscher |first4=M. |last5=Masiero |first5=S. |last6=Van Lookeren Campagne |first6=M.M. |last7=Angenent |first7=G.C.}}</ref>

The [[Floral Genome Project]] 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 Plant Sci. |volume=12 |issue=8 |pages=358–367 |year=2007 |doi=10.1016/j.tplants.2007.06.012 |pmid=17658290 |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|bibcode=2007TPS....12..358S }}</ref> There is a possibility that from the basal to the modern angiosperms, the domains of floral architecture have become more and more fixed through evolution.{{citation needed|date=June 2024}}

====Flowering time====

Another floral feature that has been a subject of [[natural selection]]<!--is there any feature that has not?!--> is flowering time. Some plants flower early in their life cycle, others require a period of [[vernalization]] before flowering. This outcome 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 |last1=Putterhill |first1=Jo |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 |archive-url=https://archive.today/20121216152310/http://www3.interscience.wiley.com/cgi-bin/abstract/107640082/ABSTRACT |url-status=dead |archive-date=2012-12-16 |last2=Laurie |first2=Rebecca |last3=MacKnight |first3=Richard |s2cid=43335309 |url-access=subscription }}</ref>

Many of the genes involved 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. Both plants have the proteins ''CO'' and ''FLOWERING LOCUS T (FT)'', 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 |display-authors=1}}</ref>

====Theories of flower evolution====

The [[Anthophyta|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="Crepet-2000"/>

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 |last1=Frohlich |first1=Michael W. |last2=Parker |first2=David S. |title=The Mostly Male Theory of Flower Evolutionary Origins: from Genes to Fossils |journal=Syst. Bot. |volume=25 |issue=2 |pages=155–170 |year=2000 |doi=10.2307/2666635 |jstor=2666635 |s2cid=85612923 }}</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.{{citation needed|date=June 2024}}

===Mechanisms and players in evolution of plant morphology===
[[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.{{citation needed|date=June 2024}}

[[Genome doubling]] is a relatively common occurrence in plant evolution and results in [[polyploidy]], which is consequently a common feature in plants. It is estimated 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.{{citation needed|date=June 2024}}

[[File:Maize-teosinte.jpg|thumb |right |150px |Top: [[teosinte]], bottom: [[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 |vauthors=Li A, 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 |doi-access=free }}</ref> Many miRNA genes involved in regulation of [[plant development]] have been found to be quite conserved between plants studied.{{citation needed|date=June 2024}}

[[Domestication]] of plants like [[maize]], [[rice]], [[barley]], [[wheat]] etc. has also been a significant driving force in their evolution. Research concerning the origin of maize has found that it 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'']]
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=Annu. Rev. Genet. |volume=38 |issue=1 |pages=37–59 |year=2004 |doi=10.1146/annurev.genet.38.072902.092425 |pmid=15568971 |url=https://zenodo.org/record/895359 }}</ref>

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.
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 dense mass of inflorescence meristem cells in arrested development.<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 |doi=10.1093/genetics/155.2.855 |pmc=1461124 |display-authors=1}}</ref> This mutation has been selected through domestication since at least the time of the [[Greeks|Greek]] empire.<!--9 'Greek empires' are listed; with dates ranging from 477 BC to 1479 AD-->

==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="Williams-2013">{{cite journal |last1=Williams |first1=Ben P. |last2=Johnston |first2=Iain G. |last3=Covshoff |first3=Sarah |last4=Hibberd |first4=Julian M. |title=Phenotypic landscape inference reveals multiple evolutionary paths to C4 photosynthesis |journal=eLife |publisher=eLife Sciences Publications |volume=2 |date=2013-09-28 |pages=e00961 |doi=10.7554/elife.00961 |pmid=24082995 |pmc=3786385 |s2cid=6552541 |doi-access=free }}</ref>

[[Photosynthesis]] is a complex chemical pathway facilitated 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. However, the enzyme is notoriously inefficient, and, as ambient temperature rises, will increasingly 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}}.{{citation needed|date=June 2024}}

===Concentrating carbon===

Broadly, the two main ways to concentrate carbon dioxide in plants are 1) biochemical {{co2}} concentrating mechanisms (CCM) and 2) biophysical {{co2}} concentrating mechanisms. Biochemical CCMs such as C<sub>4</sub> and [[CAM photosynthesis]] concentrate {{co2}} by using an enzyme, [[phosphoenolpyruvate carboxylase]], to bind inorganic carbon to an intermediate four carbon sugar, which can then be converted back to RuBP and {{co2}} for subsequent fixation by Rubisco. Biophysical CCMs like [[carboxysome]]s and [[pyrenoids]] concentrate {{co2}} in a particular locus through the coordination of [[carbonic anhydrase]]s and anion channels.

C<sub>4</sub> plants evolved carbon concentrating mechanisms that work by increasing the concentration of {{co2}} around RuBisCO, and excluding oxygen, thereby increasing the efficiency of photosynthesis by 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&nbsp;°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.

The third mechanism present in plants, pyrenoid-based CCMs, is found only in the [[hornwort]] lineage.<ref>{{cite journal | vauthors=((Robison, T. A.)), ((Oh, Z. G.)), ((Lafferty, D.)), ((Xu, X.)), ((Villarreal, J. C. A.)), ((Gunn, L. H.)), ((Li, F.-W.)) | journal=Nature Plants | title=Hornworts reveal a spatial model for pyrenoid-based CO2-concentrating mechanisms in land plants | pages=1–11 | publisher=Nature Publishing Group | date=3 January 2025 | issn=2055-0278 | doi=10.1038/s41477-024-01871-0}}
</ref> In this mechanism, RuBisCO is concentrated in the pyrenoid, a membraneless compartment, by importing inorganic carbon in the form of bicarbonate . This import is thought to be dependent on the coordination of carbonic anhydrases and anion channels, and takes advantage of the native pH differences between the [[cytosol]], [[chloroplast]] stroma, and [[thylakoid]] lumen.

===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="Christin-2012">{{Cite journal |last1=Christin |first1=P.-A. |last2=Osborne |first2=C. P. |last3=Chatelet |first3=D. S. |last4=Columbus |first4=J. T. |last5=Besnard |first5=G. |last6=Hodkinson |first6=T. R. |last7=Garrison |first7=L. M. |last8=Vorontsova |first8=M. S. |author8-link=Maria Vorontsova (botanist) |last9=Edwards |first9=E. J. |doi=10.1073/pnas.1216777110 |title=Anatomical enablers and the evolution of {{C4}} photosynthesis in grasses |journal=Proceedings of the National Academy of Sciences |volume=110 |issue=4 |pages=1381–1386 |year=2012 |pmid=23267116 |pmc=3557070 |bibcode=2013PNAS..110.1381C |doi-access=free }}</ref> Many potential evolutionary pathways resulting in the {{c4}} [[phenotype]] are possible and have been characterised using [[Bayesian inference]],<ref name="Williams-2013"/> confirming that non-photosynthetic adaptations often provide evolutionary stepping stones for the further evolution of {{c4}}.

The C<sub>4</sub> construction is used by a subset of grasses, while CAM is employed by many succulents and [[cacti]]. The C<sub>4</sub> trait appears to have emerged during the [[Oligocene]], around {{Ma |25 |32}};<ref name="Osborne-2006">{{cite journal  |author=Osborne, C.P. |author2=Beerling, D.J. |author-link2=David Beerling |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 |pmc=1626541 |doi=10.1098/rstb.2005.1737 }}</ref> however, they did not become ecologically significant until the [[Miocene]], {{Ma |6 |7}}.<ref name="Retallack-1997"/> Remarkably, some charcoalified fossils preserve tissue organised into the Kranz anatomy, with intact bundle sheath cells,<ref name="Thomasson-1986">{{cite journal |author=Thomasson, J.R. |author2=Nelson, M.E. |author3=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 |s2cid=41457488 }}</ref> allowing the presence C<sub>4</sub> metabolism to be identified. 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="O'Leary-1988">{{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>

Original fossil material in sufficient quantity to analyse the grass itself is scarce, but horses provide a good proxy. They were globally widespread in the period of interest, and browsed almost exclusively on grasses. There's an old phrase in isotope paleontology, "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}} record shows a sharp negative inflection around {{Ma |6 |7}}, during the Messinian that is interpreted as resulting from the rise of C<sub>4</sub> plants on a global scale.<ref name="Retallack-1997">{{cite journal |first=G. J. |title=Neogene Expansion of the North American Prairie |date=1 August 1997 |journal=PALAIOS |last=Retallack |volume=12 |issue=4 |pages=380–390 |doi=10.2307/3515337 |jstor=3515337 |bibcode=1997Palai..12..380R}}</ref>

===Advantage of C<sub>4</sub>===
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="Osborne-2009">{{Cite journal |last1=Osborne |first1=P. |last2=Freckleton |first2=P. |title=Ecological selection pressures for {{C4}} photosynthesis in the grasses |journal=Proceedings: Biological Sciences |volume=276 |issue=1663 |pages=1753–1760 |date=Feb 2009 |pmid=19324795 |pmc=2674487 |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="Bond-2005">{{cite journal |author=Bond, W.J. |author2=Woodward, F.I. |author3=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 |s2cid=4954178 }}</ref> But, wildfires have occurred for 400 million years. The Carboniferous (~{{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 no C<sub>4</sub> isotopic signature has been found. There also does not seem to be a sudden trigger for the Miocene rise.{{citation needed|date=June 2024}}

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="Pagani-2005">{{cite journal |author=Pagani, M. |author2=Zachos, J.C. |author3=Freeman, K.H. |author4=Tipple, B. |author5=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 |s2cid=20277445 |doi-access=free }}</ref> This suggests that it did not have a key role in invoking C<sub>4</sub> evolution.<ref name="Osborne-2006"/> 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="Piperno-2005">{{cite journal  |author=Piperno, D.R. |author2=Sues, H.D. |year=2005 |title=Dinosaurs Dined on Grass |journal=Science |pmid=16293745 |volume=310 |issue=5751 |pages=1126–1128 |doi=10.1126/science.1121020 |s2cid=83493897 }}</ref><ref name="Prasad-2005">{{cite journal |author=Prasad, V. |author2=Stroemberg, C.A.E. |author3=Alimohammadian, H. |author4=Sahni, A. |year=2005 |title=Dinosaur Coprolites and the Early Evolution of Grasses and Grazers |journal=Science |pmid=16293759 |volume=310 |issue=5751 |pages=1177–1180 |doi=10.1126/science.1118806 |bibcode=2005Sci...310.1177P |s2cid=1816461 }}</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="Osborne-2006"/> increasing aridity&nbsp;– hence increasing fire frequency and intensity&nbsp;– may have led to an increase in the importance of grasslands.<ref name="Keeley-2005">{{cite journal |author=Keeley, J.E. |author2=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|bibcode=2005EcolL...8..683K }}</ref> However, this is difficult to reconcile with the North American record.<ref name="Osborne-2006"/> It is possible that the signal is entirely biological, forced by the fire<ref name="Retallack-2001"/> driven acceleration of grass evolution&nbsp;– which, both by increasing weathering and incorporating more carbon into sediments, reduced atmospheric {{co2}} levels.<ref name="Retallack-2001">{{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 |s2cid=15560105 }}</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.{{citation needed|date=June 2024}}

==Evolution of transcriptional regulation==
Transcription factors and transcriptional regulatory networks play key roles in plant development and stress responses, as well as their evolution. During plant landing, many novel transcription factor families emerged and are preferentially wired into the networks of multicellular development, reproduction, and organ development, contributing to more complex morphogenesis of land plants.<ref name="Jin-2015">{{cite journal |last1=Jin |first1=JP |last2=He |first2=K |last3=Tang |first3=X |last4=Li |first4=Z |last5=Lv |first5=L |last6=Zhao |first6=Y |last7=Luo |first7=J |last8=Gao |first8=G |title= An Arabidopsis transcriptional regulatory map reveals distinct functional and evolutionary features of novel transcription factors |journal= Molecular Biology and Evolution |date=July 2015 |volume=32 |issue=7 |doi=10.1093/molbev/msv058 |url= |pmid=25750178 |pmc=4476157 |pages=1767–1773}}</ref>

==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, that are not essential for the normal processes of [[Cell growth|growth]], [[Biological development|development]], or [[reproduction]]. They function in processes as diverse as [[immunity (medical)|immunity]], anti-herbivory, [[pollinator]] attraction, [[communication]] between plants, maintaining [[symbiotic]] associations with soil flora, or enhancing the rate of [[fertilization]], and hence are significant from the evo-devo perspective. Secondary metabolites are structurally and functionally diverse, and it is estimated that hundreds of thousands of enzymes might be involved in the process of producing them, with about 15–25% of the genome coding for these enzymes, and every species having its unique arsenal of secondary metabolites.<ref>{{cite journal |author1=Pichersky E. |author2=Gang D. |title=Genetics and biochemistry of secondary metabolites in plants: an evolutionary perspective |journal=Trends Plant Sci. |volume=5 |issue=10 |pages=439–445 |year=2000 |doi=10.1016/S1360-1385(00)01741-6 |pmid=11044721|bibcode=2000TPS.....5..439P }}</ref> Many of these metabolites, such as [[salicylic acid]] are of medical significance to humans.{{citation needed|date=June 2024}}

The purpose of producing so many secondary metabolites, with a significant proportion of the [[metabolome]] devoted to this activity is unclear. It is postulated that most of these chemicals help in generating immunity and, in consequence, the diversity of these metabolites is a result of a constant [[evolutionary arms race|arms race]] between plants and their parasites. Some evidence supports this case. A central question involves the reproductive cost to maintaining such a large inventory of genes devoted to producing secondary metabolites. Various models have been suggested that probe into this aspect of the question, but a consensus on the extent of the cost has yet to be established;<ref>{{cite journal |author1=Nina Theis |author2=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 |s2cid=85705162 |url-access=subscription }}</ref> as it is still difficult to predict whether a plant with more secondary metabolites increases its survival or reproductive success compared to other plants in its vicinity.{{citation needed|date=June 2024}}

Secondary metabolite production seems to have arisen quite early during evolution. In plants, they seem to have spread out using mechanisms including gene duplications or the evolution of novel genes. Furthermore, research has 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 is clear, 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 |bibcode=1998PNAS...95.4126B |display-authors=1 |last2=Meyer-Gauen |first2=G |last3=Croteau |first3=R |doi-access=free }}</ref>

==Evolution of plant-microbe interactions==

The origin of microbes on Earth, tracing back to the beginning of life more than 3.5 billion years ago, indicates that microbe-microbe interactions have continuously evolved and diversified over time, long before plants started to colonize land 450 million years ago. Therefore, it is likely that both intra- and inter-kingdom intermicrobial interactions represent strong drivers of the establishment of plant-associated [[microbial consortia]] at the soil-root interface. Nonetheless, it remains unclear to what extent these interactions in the rhizosphere/phyllosphere and in endophytic plant compartments (i.e., within the host) shape microbial assemblages in nature and whether microbial adaptation to plant habitats drive habitat-specific microbe-microbe interaction strategies that impact plant fitness. Furthermore, the contribution of competitive and cooperative microbe-microbe interactions to the overall community structure remains difficult to evaluate in nature due to the strong environmental noise.<ref name="Hassani-2018">Hassani, M.A., Durán, P. and Hacquard, S. (2018) "Microbial interactions within the plant holobiont". ''Microbiome'', '''6'''(1): 58. {{doi |10.1186/s40168-018-0445-0|doi-access=free}}. [[File:CC-BY icon.svg|50px]] Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License].</ref>

==See also==
* [[Herbivory#evolution|Evolution of herbivory]]
* [[Evolutionary history of life]]
* [[Paleobotany]]
* [[Plant evolutionary developmental biology]]
* [[Timeline of plant evolution]]{{Clear}}

==References==

{{Reflist |30em}}

==External links==
{{Wikispecies |Brassicaceae}}
* [https://www.britannica.com/plant/plant/Evolution-of-seed-plants-and-plant-communities Evolution And Paleobotany] at [https://www.britannica.com/ Britannica]

{{Botany}}
{{Evolution}}
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[[Category:Evolution of plants|Evolution of plants]]
[[Category:Plant sexuality]]