Editing Fern (section)

== Taxonomy ==

[[Carl Linnaeus]] (1753) originally recognized 15 genera of ferns and fern allies, classifying them in class [[Cryptogamia]] in two groups, Filices (e.g. ''[[Polypodium]]'') and [[Musci]] (mosses).{{sfn|Underwood|1903}}{{sfn|Linnaeus|1753}}{{sfn|Schuettpelz et al|2018}} By 1806 this had increased to 38 genera,{{sfn|Swartz|1806}} and has progressively increased since (''see {{harvtxt|Schuettpelz et al|2018}}''). Ferns were traditionally classified in the [[class (biology)|class]] Filices, and later in a [[phylum|Division]] of the Plant Kingdom named [[Pteridophyta]] or Filicophyta. Pteridophyta is no longer recognised as a valid [[taxon]] because it is [[paraphyletic]]. The ferns are also referred to as Polypodiophyta or, when treated as a subdivision of [[Tracheophyta]] (vascular plants), Polypodiopsida, although this name sometimes only refers to leptosporangiate ferns. Traditionally, all of the spore producing [[vascular plant]]s were informally denominated the [[pteridophyte]]s, rendering the term synonymous with ferns and [[fern allies]]. This can be confusing because members of the division Pteridophyta were also denominated pteridophytes (''sensu stricto'').

Traditionally, three discrete groups have been denominated ferns: two groups of eusporangiate ferns, the families [[Ophioglossaceae]] ([[Ophioglossum|adder's tongues]], [[moonwort]]s, and grape ferns) and [[Marattiaceae]]; and the leptosporangiate ferns. The Marattiaceae are a primitive group of tropical ferns with large, fleshy rhizomes and are now thought to be a [[sister group|sibling taxon]] to the leptosporangiate ferns. Several other groups of species were considered fern allies: the [[clubmoss]]es, [[spikemoss]]es, and [[Isoëtes|quillworts]] in [[Lycopodiophyta]]; the whisk ferns of [[Psilotaceae]]; and the horsetails of [[Equisetaceae]]. Since this grouping is [[Polyphyly|polyphyletic]], the term fern allies should be abandoned, except in a historical context.{{sfn|Christenhusz|Chase|2014}} More recent genetic studies demonstrated that the Lycopodiophyta are more distantly related to other [[vascular plant]]s, having radiated evolutionarily at the base of the vascular plant [[clade]], while both the whisk ferns and horsetails are as closely related to leptosporangiate ferns as the [[ophioglossoid fern]]s and [[Marattiaceae]]. In fact, the whisk ferns and ophioglossoid ferns are demonstrably a [[clade]], and the [[horsetail]]s and [[Marattiaceae]] are arguably another clade.

=== Molecular phylogenetics ===

Smith et al. (2006) carried out the first higher-level pteridophyte classification published in the [[molecular phylogenetic]] era, and considered the ferns as monilophytes, as follows:{{sfn|Smith et al.2006}}
* [[Division (botany)|Division]] [[Tracheophyta]] (tracheophytes) – vascular plants
** [[Subdivision (botany)|Sub division]] [[Euphyllophytina]] (euphyllophytes)
*** Infradivision [[Moniliformopses]] ('''monilophytes''')
*** Infradivision [[Spermatophyta]] – seed plants, ~260,000 species
** Subdivision [[Lycopodiophyta]] (lycophytes) – less than 1% of extant vascular plants

Molecular data, which remain poorly constrained for many parts of the plants' phylogeny, have been supplemented by morphological observations supporting the inclusion of Equisetaceae in the ferns, notably relating to the construction of their sperm and peculiarities of their roots.{{sfn|Smith et al.2006}}

The leptosporangiate ferns are sometimes called "true ferns".<ref>{{Cite book |last=Stace |first=Clive |author-link = Clive Stace |year=2010b |title=New Flora of the British Isles |edition=3rd |location=Cambridge, UK |publisher=Cambridge University Press |isbn=978-0-521-70772-5 |page=xxviii}}</ref> This group includes most plants familiarly known as ferns. Modern research supports older ideas based on morphology that the Osmundaceae diverged early in the evolutionary history of the leptosporangiate ferns; in certain ways this family is intermediate between the eusporangiate ferns and the leptosporangiate ferns. Rai and Graham (2010) broadly supported the primary groups, but queried their relationships, concluding that "at present perhaps the best that can be said about all relationships among the major lineages of monilophytes in current studies is that we do not understand them very well".<ref name=RaiGraham2010>{{Cite journal |last1=Rai |first1=Hardeep S. |last2=Graham |first2=Sean W. |year=2010 |title=Utility of a large, multigene plastid data set in inferring higher-order relationships in ferns and relatives (monilophytes) |journal=American Journal of Botany |volume=97 |issue=9 |pages=1444–1456 |doi=10.3732/ajb.0900305 |name-list-style=amp |pmid=21616899}}, p. 1450</ref> Grewe et al. (2013) confirmed the inclusion of horsetails within ferns ''sensu lato'', but also suggested that uncertainties remained in their precise placement.<ref name=Grew13/> Other classifications have raised Ophioglossales to the rank of a fifth class, separating the whisk ferns and ophioglossoid ferns.<ref name=Grew13/>

=== Phylogeny ===

The ferns are related to other groups as shown in the following cladogram:{{sfn|Christenhusz|Chase|2014}}{{sfn|Cantino et al|2007}}{{sfn|Chase|Reveal|2009}}{{sfn|Pteridophyte Phylogeny Group|2016}}
{{clade |style=line-height:140%;font-size:100%;
|label1= [[Tracheophyta]] |sublabel1= (vascular plants) 
|1={{clade
   |1= [[Lycopodiophyta|Lycophytes]] [[File:2021-03_Amsterdam_Island_-_lycopodium_clavatum_10.jpg|50px]]
   |label2= [[Euphyllophyta]] 
   |2={{clade
      |1='''Ferns''' [[File:California_Arena_Point_fern.jpg|70px]]
      |label2= [[Spermatophyta]] |sublabel2=(seed plants)
      |2={{clade
         |1=[[Gymnosperm]]s [[File:Flore_des_serres_v15_147a.jpg|50px]]
         |2=[[Angiosperm]]s [[File:160 Ranunculus repens.jpg|50px]]
         }}
      }}
   }}
}}

=== Nomenclature and subdivision ===

{{further|List of fern families}}

The classification of Smith et al. in 2006 treated ferns as four classes:{{sfn|Smith et al.2006}}{{sfn|Schuettpelz|2007|loc=Table I}}

* [[Equisetidae|Equisetopsida]] (Sphenopsida) – 1 order, [[Equisetales]] ([[Horsetail]]s) ~ 15 species
* [[Ophioglossidae|Psilotopsida]] – 2 orders ([[Psilotaceae|whisk ferns]] and [[ophioglossoid fern]]s) ~92 species 
* [[Marattiidae|Marattiopsida]] – 1 order, [[Marattiales]] ~ 150 species
* [[Polypodiidae (plant)|Polypodiopsida]] (Filicopsida) – 7 orders ([[leptosporangiate fern]]s) ~ 9,000 species

In addition they defined 11 orders and 37 families.{{sfn|Smith et al.2006}} That system was a consensus of a number of studies, and was further refined.<ref name=Grew13>{{cite journal |last=Grewe |first=Felix |title=Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes |journal=BMC Evolutionary Biology |year=2013 |volume=13 |issue=1 |pages=1–16 |doi=10.1186/1471-2148-13-8 |issn=1471-2148 |display-authors=etal |pmid=23311954 |pmc=3553075 |doi-access=free |bibcode=2013BMCEE..13....8G }}</ref><ref>{{cite journal |last=Karol |first=Kenneth G. |title=Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages |journal=BMC Evolutionary Biology |year=2010|volume=10 |pages=321–336 |doi=10.1186/1471-2148-10-321 |issn=1471-2148 |pmid=20969798|pmc=3087542|issue=1|display-authors=etal |doi-access=free |bibcode=2010BMCEE..10..321K }}</ref> The phylogenetic relationships are shown in the following [[cladogram]] (to the level of orders).{{sfn|Smith et al.2006}}<ref>{{cite journal |last1=Li |first1=F-W |last2=Kuo |first2=L-Y |last3=Rothfels |first3=CJ |last4=Ebihara |first4=A |last5=Chiou |first5=W-L |display-authors=etal |year=2011 |title=rbcL and matK Earn Two Thumbs Up as the Core DNA Barcode for Ferns |journal=PLOS ONE |volume=6 |issue=10|page=e26597 |doi=10.1371/journal.pone.0026597 |pmid=22028918 |pmc=3197659|bibcode=2011PLoSO...626597L |doi-access=free }}</ref><ref name=Grew13/> This division into four major clades was then confirmed using [[plant morphology|morphology]] alone.{{sfn|Schneider et al|2009}}

{{Fern cladogram.show(Orders & Outgroups)}}

Subsequently, [[Mark W. Chase|Chase]] and [[James L. Reveal|Reveal]] considered both lycopods and ferns as subclasses of a class Equisetopsida ([[Embryophyta]]) encompassing all land plants. This is referred to as [[Equisetopsida sensu lato|Equisetopsida]] ''[[sensu lato]]'' to distinguish it from the narrower use to refer to horsetails alone, [[Equisetopsida]] ''sensu stricto''. They placed the lycopods into subclass Lycopodiidae and the ferns, keeping the term monilophytes, into five subclasses, Equisetidae, Ophioglossidae, Psilotidae, Marattiidae and Polypodiidae, by dividing Smith's Psilotopsida into its two orders and elevating them to subclass (Ophioglossidae and Psilotidae).{{sfn|Chase|Reveal|2009}} Christenhusz et al.{{efn|President, International Association of Pteridologists}} (2011) followed this use of subclasses but recombined Smith's Psilotopsida as Ophioglossidae, giving four subclasses of ferns again.{{sfn|Christenhusz et al|2011}}

[[Christenhusz]] and [[Mark Chase|Chase]] (2014) developed a new classification of ferns and lycopods. They used the term Polypodiophyta for the ferns, subdivided like Smith et al. into four groups (shown with equivalents in the Smith system), with 21 families, approximately 212 genera and 10,535 species;{{sfn|Christenhusz|Chase|2014}}
* [[Equisetidae]] (=Equisetopsida) – [[monotypic]] (Equisetales, [[Equisetaceae]], ''[[Equisetum]]'') horsetails ~ 20 species)
* [[Ophioglossidae]] (=Psilotopsida) – 2 monotypic orders ~ 92 species
* [[Marattiidae]] (=Marattiopsida) – 1 monotypic order (Marattiales, [[Marattiaceae]], 2 subfamilies) ~ 130 species
* [[Polypodiidae (plant)|Polypodiidae]] (=Polypodiopsida) – 7 orders

This was a considerable reduction in the number of families from the 37 in the system of Smith et al., since the approach was more that of [[lumping]] rather than splitting. For instance a number of families were reduced to subfamilies. Subsequently, a [[Scientific consensus|consensus]] group was formed, the [[Pteridophyte Phylogeny Group]] (PPG), analogous to the [[Angiosperm Phylogeny Group]], publishing their first complete classification in November 2016. They recognise ferns as a class, the Polypodiopsida, with four subclasses as described by Christenhusz and Chase, and which are phylogenetically related as in this cladogram:

{|class="wikitable"
|-
! colspan=1 |Christenhusz and Chase 2014{{sfn|Pteridophyte Phylogeny Group|2016}}
! colspan=1 |Nitta et al. 2022<ref name="Polypodiopsida"/> and Fern Tree of life<ref>{{cite web |year=2024 |title=Tree viewer: interactive visualization of FTOL |url=https://fernphy.github.io/viewer.html |version=FTOL v1.7.0 |access-date=1 May 2025}}</ref>
|- 
|style="vertical-align:top|
{{Clade |style=font-size:90%;line-height:80%
|label1='''Polypodiopsida'''
|1={{clade
  |label1=[[Equisetidae]]
  |1=[[Equisetales]]
  |2={{clade
    |label1=[[Ophioglossidae]]
    |1={{clade
       |1=[[Ophioglossales]]
       |2=[[Psilotales]]
       }}
    |2={{clade
      |label1=[[Marattiidae]]
      |1=[[Marattiales]]
      |label2=[[Polypodiidae (plant)|Polypodiidae]]
      |2={{clade
        |1=[[Osmundales]]
        |2={{clade
          |1=[[Hymenophyllales]]
          |2={{clade
            |1=[[Gleicheniales]]
            |2={{clade
              |1=[[Schizaeales]]
              |2={{clade
                |1=[[Salviniales]]
                |2={{clade
                  |1=[[Cyatheales]]
                  |2=[[Polypodiales]]
                   }}
                 }}
               }}
             }}
           }}
         }}
       }}
     }}
   }}
}}
|
{{Clade |style=font-size:90%;line-height:80%
|1={{clade
  |1={{clade
    |label1=[[Equisetidae]]
    |1=[[Equisetales]]
    |label2=[[Ophioglossidae]]
    |2={{clade
      |1=[[Psilotales]]
      |2=[[Ophioglossales]]
       }}
     }}
  |2={{clade
    |label1=[[Marattiidae]]
    |1=[[Marattiales]]
    |label2=[[Polypodiidae (plant)|Polypodiidae]]
    |2={{clade
      |1=[[Osmundales]]
      |2={{clade
        |1=[[Hymenophyllales]]
        |2={{clade
          |1=[[Gleicheniales]]
          |2={{clade
            |1=[[Dipteridales]]
            |2={{clade
              |1=[[Schizaeales]]
              |2={{clade
                |1={{clade
                  |1=[[Salviniales]]
                  |2=[[Cyatheales]]
                   }}
                |2=[[Polypodiales]]
                 }}
               }}
             }}
           }}
         }}
       }}
     }}
   }}
}}
|}

In the Pteridophyte Phylogeny Group classification of 2016 (PPG I), the Polypodiopsida consist of four subclasses, 11 orders, 48 families, 319 genera, and an estimated 10,578 species.{{sfn|Christenhusz|Byng|2016}} Thus Polypodiopsida in the broad sense (''sensu lato'') as used by the PPG (Polypodiopsida ''sensu'' PPG I) needs to be distinguished from the narrower usage (''sensu stricto'') of Smith et al. (Polypodiopsida ''sensu'' Smith et al.){{sfn|Pteridophyte Phylogeny Group|2016}} Classification of ferns remains unresolved and controversial with competing viewpoints ([[splitting vs lumping]]) between the systems of the PPG on the one hand and Christenhusz and Chase on the other, respectively. In 2018, Christenhusz and Chase explicitly argued against recognizing as many genera as PPG I.{{sfn|Schuettpelz et al|2018}}{{sfn|Christenhusz |Chase|2018}}

{|class="wikitable" style= "font-size: 87%"
|+ Comparison of fern subdivisions in some classifications
|-
! Smith et al. (2006){{sfn|Smith et al.2006}} !! Chase & Reveal (2009){{sfn|Chase|Reveal|2009}} !! Christenhusz et al. (2011){{sfn|Christenhusz et al|2011}} !! Christenhusz & Chase (2014, 2018){{sfn|Christenhusz|Chase|2014}}{{sfn|Christenhusz et al|2018}} !! PPG I (2016){{sfn|Pteridophyte Phylogeny Group|2016}}
|-
|'''ferns'''<br/>(no rank) ||'''monilophytes'''<br/>(no rank) ||'''ferns (monilophytes)'''<br/>(no rank) ||'''ferns (Polypodiophyta)'''<br/>(no rank) ||&nbsp;'''Class Polypodiopsida'''
|-
|Class Equisetopsida ||&nbsp;&nbsp;Subclass Equisetidae ||&nbsp;&nbsp;Subclass Equisetidae ||&nbsp;&nbsp;Subclass Equisetidae ||&nbsp;Subclass [[Equisetidae]]
|-
|Class Psilotopsida ||&nbsp;&nbsp;Subclass Ophioglossidae<br/>&nbsp;&nbsp;Subclass Psilotidae ||&nbsp;&nbsp;Subclass Ophioglossidae ||&nbsp;&nbsp;Subclass Ophioglossidae ||&nbsp;Subclass [[Ophioglossidae]]
|-
|Class Marattiopsida ||&nbsp;&nbsp;Subclass Marattiidae ||&nbsp;&nbsp;Subclass Marattiidae ||&nbsp;&nbsp;Subclass Marattiidae ||&nbsp;Subclass [[Marattiidae]]
|-
|Class Polypodiopsida ||&nbsp;&nbsp;Subclass Polypodiidae ||&nbsp;&nbsp;Subclass Polypodiidae ||&nbsp;&nbsp;Subclass Polypodiidae ||&nbsp;Subclass [[Polypodiidae (plant)|Polypodiidae]]
|}

=== Evolution and biogeography ===

Fern-like taxa (''[[Wattieza]]'') first appear in the fossil record in the middle [[Devonian]] period, ca. 390&nbsp;[[Mya (unit)|Mya]]. By the [[Triassic]], the first evidence of ferns related to several modern families appeared. The great fern radiation occurred in the late [[Cretaceous]], when many modern families of ferns first appeared.{{sfn|UCMP|2019}}{{sfn|Stein et al|2007}}{{sfn|Berry|2009}}{{sfn|Bomfleur et al|2014}} Ferns evolved to cope with low-light conditions present under the canopy of angiosperms.

Remarkably, the [[Photoreceptor protein|photoreceptor]] neochrome in the two orders Cyatheales and Polypodiales, integral to their adaptation to low-light conditions, was obtained via [[horizontal gene transfer]] from [[hornwort]]s, a [[bryophyte]] lineage.<ref>{{cite journal |last1=Li |first1=F.-W. |last2=Villarreal |first2=J. C. |last3=Kelly |first3=S. |last4=Rothfels |first4=C. J. |last5=Melkonian |first5=M. |last6=Frangedakis |first6=E. |last7=Ruhsam |first7=M. |last8=Sigel |first8=E. M. |last9=Der |first9=J. P. |last10=Pittermann |first10=J. |last11=Burge |first11=D. O. |last12=Pokorny |first12=L. |last13=Larsson |first13=A. |last14=Chen |first14=T. |last15=Weststrand |first15=S. |last16=Thomas |first16=P. |last17=Carpenter |first17=E. |last18=Zhang |first18=Y. |last19=Tian |first19=Z. |last20=Chen |first20=L. |last21=Yan |first21=Z. |last22=Zhu |first22=Y. |last23=Sun |first23=X. |last24=Wang |first24=J. |last25=Stevenson |first25=D. W. |last26=Crandall-Stotler |first26=B. J. |last27=Shaw |first27=A. J.|author28-link=Michael Deyholos |last28=Deyholos |first28=M. K. |last29=Soltis |first29=D. E. |last30=Graham |first30=S. W. |last31=Windham |first31=M. D. |last32=Langdale |first32=J. A. |last33=Wong |first33=G. K.-S. |last34=Mathews |first34=S. |last35=Pryer |first35=K. M. |display-authors=3 |title=Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns |journal=Proceedings of the National Academy of Sciences |date=6 May 2014 |volume=111 |issue=18 |pages=6672–6677 |doi=10.1073/pnas.1319929111|pmid=24733898 |pmc=4020063 |bibcode=2014PNAS..111.6672L |doi-access=free }}</ref>

Due to the very large genome seen in most ferns, it was suspected they might have gone through [[Paleopolyploidy|whole genome duplications]], but [[DNA sequencing]] has shown that their genome size is caused by the accumulation of mobile DNA like [[Transposable element|transposons]] and other genetic elements that infect genomes and get copied over and over again.<ref>[https://www.science.org/content/article/genes-seeds-arose-early-plant-evolution-ferns-reveal Genes for seeds arose early in plant evolution, ferns reveal]</ref>

Ferns appear to have evolved [[extrafloral nectaries]] 135 million years ago, nearly simultaneously with the trait's evolution in angiosperms. However, nectary-associated diversifications in ferns did not hit their stride until nearly 100 million years later, in the [[Cenozoic]]. There is weak support for the rise of fern-feeding arthropods driving this diversification.<ref>{{Cite journal |last1=Suissa |first1=Jacob S. |last2=Li |first2=Fay-Wei |last3=Moreau |first3=Corrie S. |date=2024-05-24 |title=Convergent evolution of fern nectaries facilitated independent recruitment of ant-bodyguards from flowering plants |journal=Nature Communications |language=en |volume=15 |issue=1 |pages=4392 |doi=10.1038/s41467-024-48646-x |issn=2041-1723|doi-access=free |pmid=38789437 |pmc=11126701 |bibcode=2024NatCo..15.4392S }}</ref>