Taxonomy of Allium

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The precise

clades, although some proposed subgenera are not.[2] Some progress is being made using molecular phylogenetic methods, and the internal transcribed spacer (ITS) region, including the 5.8S rDNA and the two spacers ITS1 and ITS2, is one of the more commonly used markers in the study of the differentiation of the Allium species.[1]

Allium includes a number of taxonomic groupings previously considered separate genera (Caloscordum Herb., Milula Prain and Nectaroscordum Lindl.) Allium spicatum had been treated by many authors as Milula spicata, the only species in the monospecific genus Milula. In 2000, it was shown to be embedded in Allium.[3]

Description

The

centre of diversity is the Old World with species rich areas in Central Asia as well as the Mediterranean Basin. A second centre, in the New World, is western North America.[4][5]

History

Linnaeus' description of Allium, Species Plantarum 1753

Descriptions of Allium taxonomy date back at least as far as

calyx of six equal parts).[14]

Subsequently,

de Candolle reverted the family name back to Liliaceae from Asphodeli.[15] He divided the Liliaceae into a series of Ordres, and the second ordre was named Asphodèles, based on Jussieus' family of that name,[16] in which he placed Allium.[16] The term 'Alliaceae' then reappeared in its subfamilial form, Allieae, in Dumortier's Florula Belgica (1827),[17]
with six genera. The 'Alliaceae' have been treated as Allieae within the family Liliaceae (or Aspholecaceae, a partial synonym) by most authorities since.

Regel produced a major monograph of the genus in 1875,[18] and this remained the major reference work for over 100 years till the molecularly based study of Friesen and colleagues in 2006.[19] Despite recent advances the precise taxonomy of Allium remains still poorly understood with incorrect descriptions being widespread.[20][2][1]

Phylogeny

Amaryllidaceae: Subfamily Allioideae

Tribe

monogeneric
, Allium)

Tribe Tulbaghieae

Tribes

Leucocoryneae

Subdivision

Linnaeus originally grouped his 30 species into three

Traub (1968) described 3 subgenera, 36 sections and subsections and about 600 species.[23] By 1992 there were 6 sub-genera, 50 sections and subsections and 600–700 species.[24] The situation was further confused by the presence of over 1,000 taxonomic names, many of which turned out to be synonyms.[25][20]

The modern era of

subgenera, 56 sections, and about 780 species based on the nuclear ribosomal gene internal transcribed spacers. Some of the subgenera correspond to the once separate genera (Caloscordum, Milula, Nectaroscordum) included in the Gilliesieae.[2][27]
The terminology has varied with some authors subdividing subgenera into Sections and others Alliances.

The term alliance has been used for both subgroupings within species, e.g. Allium nigrum, as well as infrageneric subsections. These alliances are informal groupings based on morphological similarity and reflecting hypotheses of evolutionary relationship. and can be used between any two formal ranks.[28] For instance the some 70 North American species were divided into nine well-defined species alliances, of which the largest was the Allium falcifolium alliance with 31 taxa.[29] These alliances are usually referred to as the Ownbey alliances, after Marion Ownbey[20] and were also used by Traub.[23] A number of classification schemes have chosen to retain these, the Traub system not being universally accepted.[19][5]

Subsequent

monophyletic. Meanwhile, the number of new species continued to increase, reaching 800 by 2009, 900 by 2016[30] and the pace of discovery has not decreased. Detailed studies have focused on a number of subgenera, including Amerallium. Amerallium is strongly supported as monophyletic.[31] Subgenus Melanocrommyum has also been the subject of considerable study (see below), while work on subgenus Allium has focused on section Allium, including Allium ampeloprasum, although sampling was not sufficient to test the monophyly of the section.[32]

The major

sensu stricto (type: A. sativum) to correspond to lines 1-3.[33]

Evolutionary lines and subgenera

The three evolutionary lineages and 15 subgenera here represent the classification schemes of Friesen et al. (2006)[19] and Li (2010),[2] and subsequent additional species[34][31][35][30] and revisions.[36]

Cladogram of evolutionary lines in Allium[19]
Allium

First evolutionary line

Second evolutionary line

Third evolutionary line

Evolutionary lines and subgenera (number of sections/number of species)[37]

First evolutionary line

Although this lineage consists of three subgenera, nearly all the species are attributed to subgenus Amerallium, the third largest subgenus of Allium. The lineage is considered to represent the most ancient line within Allium, and to be the only lineage that is predominantly bulbous, the other two having both bulbous and rhizomatous taxa. Nectaroscordum and Microscordum are bulbous, but Amerallium contains some rhizomatous elements. Within this lineage Amerallium is a sister group to the other two subgenera (Microscordum+Nectaroscordum).[2]

Subgenus Nectaroscordum
Type species: Allium siculum

Disjunct distribution, involving the western Mediterranean (type species) and southwest Asia

Subgenus Microscordum

East Asia

Subgenus Amerallium
Type species: Allium canadense

This large monophyletic subgenus is extremely diverse, both morphologically and ecologically and is characterised by leaves with one row of

chromosome number x=7.[2]

Taxonomy

Amerallium is a relatively large subgenus with about 120–140 species. Under the alliance system of classification proposed by Ownbey (1966), species north of Mexico and two Mexican

endemics were treated as eight informal alliances: the A. acuminatum, A. campanulatum, A. canadense, A. cernuum, A. falcifolium, A. kunthii, A. sanbornii, and A. validum alliances.[20] Traub (1968) then arranged the New World alliances into four sections: Amerallium Traub, Caulorhizideum Traub, Lophioprason Traub, and Rhopetoprason Traub. In addition he arranged the Old World species into 6 sections.[23]

Since Traub's revision of the subgenus, two biogeographical sister clades (or alliances) have been recognised. The Old World clade is represented by two relatively small groups from the Mediterranean and East Asia. The larger New World clade by all North American species of Allium. The New World sections are Lophioprason, Amerallium, and Rhophetoprason, while the Old World is represented by sections Arctoprasum, Briseis, Narkissoprason, Molium, Bromatorrhiza and Rhynchocarpum.[19]

The subgenus is thought to originate in the Old World, with a later split, and to have its origin in the higher latitudes of East Asia, at the time of transition from Cretaceous to Tertiary, dispersing to western North America. Twelve sections were subsequently recognized, with sections Amerallium and Molium further split into two subsections.[19][2][5]

Distribution

Amerallium is widely distributed within North America, Europe, north Africa, Ethiopia, the Caucasus, northern Iran, southeast Tibet, and southwest China.[5] The greatest species diversity occurs in North America with 81 species recognized in the 2002 Flora of North America (north of Mexico)[38] and a further 13 are unique to Mexico,[39] and a total of 26 species recognised there.[5] Within N America, the genus covers most of the area south of the 53rd parallel, including the oak hillsides of California and Oregon, deserts of Nevada and Texas, alpine meadows of Utah and Idaho, prairies of Nebraska and Manitoba, and forest glades of Missouri and Arkansas.[5]

Uses

Both bulbous and rhizomatous species occur in both Old World and New World alliances. The subgenus includes both ornamentals, such as A. moly, A. roseum, A. unifolium and A. neapolitanum, and culinary species such as A. ursinum.[19][5]

15 Sections[5]

Section Amerallium
Section Arctoprasum
  • Section Arctoprasum Kirschl.
Arctoprasum: A. ursinum
    • Allium ursinum L. ramsons, buckrams, wild garlic, broad-leaved garlic, wood garlic, bear's garlic
Section Briseis
Section Bromatorrhiza
  • Section Bromatorrhiza Ekberg
Bromatorrhiza: A. wallichii
Section Caulorhizideum
  • Section Caulorhizideum Traub
Caulorhizideum: A. validum
Section Chamaeprason
Section Lophioprason
  • Section Lophioprason Traub
Lophioprason: A. acuminatum
Section Molium
  • Section Molium G.Don ex Koch
Molium: A. roseum
Section Narkissoprason
  • Section Narkissoprason Hermann
Narkissoprason: A. narcissiflorum
Other

Second evolutionary line

Nearly all the species in this lineage of five subgenera are accounted for by subgenus Melanocrommyum, which is most closely associated with subgenera Vvedenskya and Porphyroprason, phylogenetically. These three genera are late-branching whereas the remaining two subgenera, Caloscordum and Anguinum are early branching.[2] Of the five subgenera, the large Melanocrommymum and the oligo- or monotypic Caloscordum, Vvedenskya and Porphyroprason are bulbous and the remaining small subgenus Anguinum is rhizomatous.[28]

Subgenus Caloscordum

East Asia

Sections
Subgenus Anguinum

Two distinct distributions: 1. Eurasian-American (A. victorialis alliance, including A. tricoccum) 2. East Asia (A. prattii, A. ovalifolium)

Sections
Subgenus Porphyroprason
Sections
    • Section Porphyroprason Ekberg 1 sp.
Subgenus Vvedenskya
Sections
Subgenus Melanocrommyum
Type species: Allium nigrum

This

clades, although their exact relationships remained not fully resolved. Consequently, traditional sections required considerable re-alignment. Eventually 160 species and subspecies were recognised in 20 sections and 22 subsections.[1][28][40]

Description: The subgenus is characterised by true tunicated bulbs, annual roots, leaves that are mostly broad and flat with subterranean sheath parts that are barely visible above the ground, scapes that are strong and most often strictly upright and of varying length, and large, fasciculate to globular inflorescences. The latter are composed of many moderately small to large, often star-like, flowers, and some of which have a sweet or noticeable odor.[28][2]

History: Early (prior to 1950) classifications of Allium included many of the members of this subgenus within the bulbous section, Mollium based on morphological characteristics. Mollium was later raised to subgenus level (and then again reduced to a section of Amerallium after transferring many species to Melanocrommyum. The subgenus was then divided into sections in 1969. Molecular methods in the 1990s confirmed the identity of Melanocrommyum as a distinct monophyletic group, together with the presence of several subgroups, but the deeper relationships remained inconsistent.[28]

Subdivision: Subdivision of the subgenus was first proposed by

Wendelbo in 1966,[41] proposing section Regeloprason Wendelbo, followed in 1969 by Melanocrommyum Webb & Berthel., Kaloprason K. Koch, Acanthoprason Wendelbo, Megaloprason Wendelbo, and Thaumasioprason Wendelbo.[42] Kamelin (1973) provided an alternative arrangement of sections,[43] which was supplanted by the Gatersleben Allium Group classification (1992) which used a broad range of variables.[24]

The use of molecular markers to develop phylogeny began in the 1990s and showed that the subgenus was a well separated taxon with a number of subgeneric groupings. Friesen and colleagues (2006) carried out an extensive molecular phylogenetic study

oligogotypic
with 2–8 species (Compactoprason, Pseudoprason, Miniprason, Brevicaule, Thaumasioprason, Verticillata) or monotypic (Acaule, Aroidea, Popovia).

In a more focused study in 2010 this was expanded to 20 sections and 22 subsections, or in some cases, e.g. section Melanocrommyum (type: A. nigrum) into nine alliances and Acanthoprason into seven.

basal clade. Although Li et al. (2010) included three sections, their study was confined to species endemic to China.[2]

Uses: The subgenus also contains many species grown as

isoalliin.[44]

15 sections

  • Section Acanthoprason Type A. akaka
  • Section Acaule Type A. hexaceras
  • Section Acmopetala Type A. backhousianum
    • 7 subsections
  • Section Aroidea Type A. aroides
  • Section Asteroprason Type A. elburzense
    • 2 subsections
  • Section Brevicaule Type A. sergii
  • Section Compactoprason Type A. giganteum
    • 3 subsections
  • Section Decipientia Type A. decipiens
  • Section Kaloprason Type A. caspium
    • 3 subsections
  • Section Longibidentata Type A. fetisowii
  • Section Megaloprason Type A. rosenbachianum
    • 4 subsections
  • Section Melanocrommyum Type A. nigrum
  • Section Miniprason Type A. karataviense
  • Section Popovia Type A. gypsaceum
  • Section Procerallium Type Allium stipitatum
    • 2 subsections
  • Section Pseudoprason Type A. koelzii
  • Section Regeloprason Type A. regelii
    • 3 subsections
  • Section Stellata Type A. taeniopetalum
  • Section Thaumasioprason Type A. mirum
  • Section Verticillata Type A. verticillatum
Sections[28]
  • Section Acanthoprason
    Wendelbo
Acanthoprason: A. akaka
Kaloprason: A. cristophii
Compactoprason: A. giganteum
Melanocrommyum: A. atropurpureum
Miniprason: A. karataviense
    • Allium karataviense Regel (Syn. Allium cabulicum Baker, Allium singulifolium Rech. f.; ? incl. subsp. henrikii Ruksans)
  • Section Popovia Khass. & R.M.Fritsch
  • Section Procerallium R. M. Fritsch
  • Section Pseudoprason (Wendelbo) K.Persson & Wendelbo
  • Section Regeloprason Wendelbo
Regeloprason: A. regelii

Third evolutionary line

The third evolutionary line contains the most number of subgenera (seven) and also the largest subgenus of the genus Allium, subgenus Allium which includes the type species of the genus, Allium sativum. This subgenus also contains the majority of the species in the line. Within the lineage the phylogeny is complex. Two small subgenera Butomissa and Cyathophora form a sister clade to the remaining five subgenera, with Butomissa as the first branching group. Amongst the remaining five subgenera, Rhizirideum forms a medium-sized subgenus that is the sister to the other four larger subgenera. However, they may not be monophyletic.[2] Of the seven subgenera, the large subgenus Allium, represents the bulbous elelement.[28]

Subgenus Butomissa
Allium tuberosum

2 sections

  • Section Austromontana Type A. oreoprasum
  • Section Butomissa Type A. ramosum
Sections
  • Section Austromontana N.Friesen
Mountains from eastern to central Asia up to the borderline of the eastern Mediterranean
Siberian–Mongolian–North Chinese steppes
    • Allium ramosum L. (Syn. Allium odorum L., Allium tataricum L. f., Allium lancipetalum Y.P.Hsu, Allium potaninii Regel, Allium weichanicum Palibin) Type
    • Allium tuberosum Rottler ex Spreng Chinese chives
Subgenus Cyathophora
Type species: Allium cyathophorum

Asia (Tibet and the Himalayas)

3 sections

  • Section Coleoblastus Type A. mairei
  • Section Cyathophora Type A. cyathophorum
  • Section Milula Type A. spicatum
Sections
Subgenus Rhizirideum
Type species: Allium senescens

~ 37 species. Eurasian steppes, with greatest diversity in southern Siberia and Mongolia. Only a few species distributed in Europe, with Portugal as most western point. Some species occur also in Korea and far eastern Russia, and one in Japan.

5 sections

  • Section Caespitosoprason Type A. polyrhizum
  • Section Eduardia Type A. eduardii
  • Section Rhizirideum Type A. senescens
  • Section Rhizomatosa Type A. caespitosum
  • Section Tenuissima Type A. tenuissimum
Sections
Subgenus Allium
Type species: Allium sativum

Subgenus Allium, the youngest of the subgenera, is predominantly Mediterranean but its distribution extends east towards Central Asia. This very large subgenus is divided into 15 - 16 sections[a] and demonstrates two main groups. One has been referred to as classical Allium with tripartite inner filaments and only one thick storage cataphyll. The other is more diverse morphologically reflected in less closely related sections. A number of sections appear to be non-monophyletic, including Avulsea, Pallasia, Brevispatha and Kopetdagia.[32] It includes both ornamentals, such as A. sphaerocephalon, A. caeruleum, A. carinatum and A. flavum as well as food crops such as A. sativum and A. ampeloprasum.

16 Sections

  • Section Allium Type A. sativum
  • Section Avulsea Type A. rubellum
  • Section Brevidentia Type A. brevidens
  • Section Brevispatha Type A. parciflorum
  • Section Caerulea Type A. caeruleum
  • Section Codonoprasum Type A. oleraceum
  • Section Costulatae Type A. filidens
  • Section Crystallina Type A. crystallinum
  • Section Eremoprasum Type A. sabulosum
  • Section Kopetdagia Type A. kopedeganse
  • Section Longivaginata Type A. longivaginatum
  • Section Minuta Type A. minutum
  • Section Mediasia Type A. turkestanicum
  • Section Multicaulea Type A. lehmannianum
  • Section Pallasia Type A. pallasii
  • Section Spathulata Type A. spathulatum
Sections
Section Allium

This is the largest section with about 114 species, a number of which are economically important, such as A. sativum (garlic) and A. ampeloprasum (leek). This section also expresses frequent polyploidy and contains a number of species whose boundaries have been difficult to establish, notably A. ampeloprasum which includes a number of subspecies and varieties, as well as synonymous species, which have been labelled the "A. ampeloprasum complex". Horticulturally, it is represented by at least four groups, including leeks, whose exact ancestry has been considered uncertain. In the molecular phylogenetic study by Hirschegger and colleagues (2010) showed section Allium to be a well supported clade with two main subclades, one of which included two smaller clades. All of the tetraploid forms of A. ampeloprasum were resolved in a single clade, and leeks appeared to be more closely allied to A. iranicum and A. atroviolaceum than A. ampeloprasum. Restoration of A. porrum L. was therefore proposed for the tertraploid forms, reserving A. ampeloprasum for the forms known horticulturally as great headed garlic and A. ampeloprasum var. babingtonii.[32]

Section Avulsea
  • Section Avulsea F.O.Khass.
Section Brevidentia
Section Brevispatha
Section Caerulea
  • Section Caerulea (Omelcz.) F.O.Khass.
Section Codonoprasum

Section Codonoprason is strongly

Reichenbach in 1828.[46] The taxonomy of the section is complicated with inconsistent speciation. In 2005 the section was considered to consist of 58 species and 7 subspecies.[47] The section is characterised as large plants with multiflowered inflorescences, long pedicels, very long spathe valves and a cylindrical-campanulate perigon, with unequal and long-caudate spathe leaves.[48][45]

Historically the section has been considered to have a number of subsections. Friesen recognised 2,[19] while others have described 3, e.g.;[49]

Codonoprasum (Rchb.) Kamelin
Longistamineum Cheshm. ex Omelczuk
Haemoprason (F. Herm.) Cheshm.

Many species were previously included in a grouping referred to as the Paniculatum complex. Molecular studies demonstrate the presence of two clades within the section. Clade A contains the two autumn flowering species, Allium tardans and Allium parciflorum as a subclade. Clade B contains the smaller taxa within the section.

Section Costulatae
Other
Subgenus Reticulatobulbosa
Allium barsczewskii

The second largest subgenus in the third evolutionary line. 5 sections.

  • Section Campanulata Type A. xiphopetalum
  • Section Nigrimontana Type A. drobovii
  • Section Reticulatobulbosa Type A. lineare
  • Section Scabriscapa Type A. scabriscapum
  • Section Sikkimensia Type A. sikkimense
Sections
Kazakhstan
Southwestern and southern China
Subgenus Polyprason
Allium carolinianum

4 sections

  • Section Daghestanica Type A. daghestanicum
  • Section Falcatifolia Type A. carolinianum
  • Section Oreiprason Type A. saxatile
  • Section Scorodon Type A. moschatum
Sections
  • Section Daghestanica (Tscholok.) N.Friesen
2 geographical alliances
1. Caucasian species (A. daghestanicum, A. gunibicum)
2. European species from the eastern Alps to the Pyrenees
Montane to subalpine belt of Central Asian mountains
Subgenus Cepa
Type species: Allium cepa

Polyphyletic. 5 sections.[50]

  • Section Annuloprason Type A. fedschenkoanum
  • Section Cepa Type A. cepa
  • Section Condensatum Type A. condensatum
  • Section Sacculiferum Type A. sacculiferum
  • Section Schoenoprasum Type A. schoenoprasum
Sections
Eastern Siberia and Mongolia north to Korea and Japan

Species

Main article: List of Allium species

Etymology

The name Allium is ancient, and the plant was known to both the Romans and the Greeks.[51] The name is thought to be Celtic in origin, meaning "to burn", in reference to its taste and smell.[52] One of the earliest uses of the name in botany, was by Joseph Pitton de Tournefort (1656- 1708).

Notes

  1. ^ Friesen et al. include section Costulatae within section Allium, while others treat it separately
  2. ^ The history of A. macrostemon is complex. Historically the species was included in subgenus Allium section Scorodon s.l.. When the species in the section were redistributed by Friesen et al. 2006[19] they were unable to allocate this species to a section and questioned whether a new section should be created. Nguyen et al. (2008)[31] found it most closely related to species within section Codonoprason. In contrast Li et al. (2010)[2] placed it in section Allium and Choi et al. (2012)[50] believed it belonged in section Caerulea, but did not recommend moving it on the basis of available information. It is therefore unplaced within subgenus Allium or considered the sole member of section Scorodon s.l.
  3. ^ In older classifications, such as Hanelt (1992)[24] section Scorodon was placed in subgenus Allium. It was a relatively large section with several subsections. In the study of Friesen et al. 2006[19] the section was shown not to be monophyletic, and most species were allocated to other sections. One subsection segregated with subgenus Polyprason and was elevated to section Scorodon. To distinguish between the two, the older section is designated Scorodon s.l. and the new section Scorodon s.s.
  4. ^ Whereas Friesen et al. 2006[19] treat A. taquetii as synonymous with the type species A. thunbergii, Choi and Oh 2011 present evidence as to why they should be treated separately[36]

References

  1. ^ a b c d e f Deniz et al. 2015.
  2. ^ a b c d e f g h i j k l m n o p q Li et al. 2010.
  3. ^ Friesen et al. 2000.
  4. ^ Dahlgren, Clifford & Yeo 1985, Tribus Allieae
  5. ^ a b c d e f g h Wheeler et al. 2013.
  6. ^ Clusius 1601.
  7. ^ Linnaeus 1753, Allium pp. 294–301
  8. ^ Linnaeus 1753, Hexandria monogynia pp. 285–332
  9. ^ Linnaeus Sexual System 2015.
  10. ^ Adanson 1763, VIII. Liliaceae. Part II. p. 42
  11. ^ Adanson 1763, VIII. Liliaceae Section IV. Cepae Part II. p. 50
  12. ^ Jussieu 1789, ordo VII Narcissi. pp. 51–53
  13. ^ Jaume Saint-Hilaire 1805, Asphodelées vol. 1. pp. 126–133
  14. ^ Jaume Saint-Hilaire 1805, Asphodelées Cinquième Section vol. 1. pp. 132–133
  15. ^ De Lamarck & De Candolle 1815, Vingtième Famille Liliacées Liliaceae pp. 198–255
  16. ^ a b De Lamarck & De Candolle 1815, Liliaceae Asphodèles CCXLII: Ail Allium pp. 218–228
  17. ^ Dumortier 1827, Fam. 104. Asphodeleae Juss. Trib. 1 Allieae pp. 139–140
  18. ^ von Regel 1875.
  19. ^ a b c d e f g h i j k l m n o Friesen, Fritsch & Blattner 2006.
  20. ^ a b c d Saghir et al. 1966.
  21. ^ Don 1832.
  22. ^ Stearn 1944.
  23. ^ a b c Traub 1968.
  24. ^ a b c Hanelt et al. 1992a.
  25. ^ Gregory et al. 1998.
  26. ^ von Berg et al. 1996.
  27. ^ Sykorova et al. 2006.
  28. ^ a b c d e f g h Fritsch et al. 2010.
  29. ^ Rieseberg et al. 1987.
  30. ^ a b Koçyiğıt et al. 2016.
  31. ^ a b c Nguyen et al. 2008.
  32. ^ a b c Hirschegger et al. 2010.
  33. ^ Banfi et al. 2011.
  34. ^ Brullo et al. 2003.
  35. ^ Tzanoudakis & Trigas 2015.
  36. ^ a b Choi & Oh 2011.
  37. ^ GRIN 2015, Allium
  38. ^ FNA 2008
  39. ^ Serna & López-Ferrari 1992.
  40. ^ Fragman-Sapir & Fritsch 2011.
  41. ^ Wendelbo 1966.
  42. ^ Wendelbo 1969.
  43. ^ Kamelin 1973.
  44. ^ a b Fritsch et al. 2006.
  45. ^ a b Salmeri et al. 2016.
  46. ^ Reichenbach 1828, Alliaceae p. 66
  47. ^ Seregin 2005.
  48. ^ Hanelt 1996.
  49. ^ Cesmedziev & Terzijski 1997.
  50. ^ a b Choi et al. 2012.
  51. ^ Jay 2016.
  52. ^ Motta & Motta 1962.

Bibliography

Books

Chapters

Articles and theses

Phylogenetics

Subgenera and sections
Line 1
Line 2
Line 3
subgen. Allium
sect. Codonoprasum

Websites

Databases

External links

  • Media related to Allium at Wikimedia Commons
  • Data related to Allium at Wikispecies
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