Taxonomy of Allium
The precise taxonomy of the genus Allium is still poorly understood with incorrect descriptions being widespread. With over 850 species distributed over the Northern Hemisphere Allium is the sole genus in the Allieae, one of four tribes of subfamily Allioideae. New species continue to be described and Allium is both highly variable and one of the largest monocotyledonous genera, but the precise taxonomy of Allium is poorly understood, with incorrect descriptions being widespread. The difficulties arise from the fact that the genus displays considerable polymorphism and has adapted to a wide variety of habitats. Furthermore, traditional classifications had been based on homoplasious characteristics. However, the genus has been shown to be monophyletic, containing three major clades, although some proposed subgenera are not. Some progress is being made using molecular phylogenetic methods, and the internal transcribed spacer 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.
Allium includes a number of taxonomic groupings previously considered separate genera 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.
Description
The genus Allium are herbaceous geophytes is characterised by bulbs enclosed in membranous tunics, that may become fibrous and may be carried on rhizomes, with tepals that are free or almost free, and a subgynobasic style. The majority of species produce cysteine sulphoxides that are the source of their distinctive garlic and onion odor and taste. About twenty species are grown as edible crops, such as onions, garlic and leeks, while others are foraged from the wild, such as ramps. Many species are xerophytic and the over 850 species are found almost exclusively in the Northern Hemisphere, being particularly diverse in the warm dry summers and cool wet winters of the Mediterranean. The main 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.History
Descriptions of Allium taxonomy date back at least as far as Carolus Clusius' Rariarum plantarum historia. When Linnaeus formerly described the genus Allium in his Species Plantarum, there were thirty species with this name. He placed Allium in a grouping he referred to as Hexandria monogynia containing 51 genera in all. In 1763, Michel Adanson, who proposed the concept of families of plants, included Allium and related genera as a grouping within 'Liliaceae' as Section IV, Les Oignons, or Cepae in Latin. De Jussieu is officially recognised as the first formal establishment of the suprageneric grouping into families in 1789. In this system Allium was one of fourteen genera in Ordo VI, Asphodeles, of the third class of Monocots. Jean Henri Jaume Saint-Hilaire, who developed the concept of Amaryllidaceae, continued Jussieu's treatment of Allium under Asphodeli. He placed Allium in an unnamed monotypic section of Asphodeli defined as Fleurs en ombelle, racine bulbeuse. Calice à six parties egales.Subsequently, de Candolle reverted the family name back to Liliaceae from Asphodeli. He divided the Liliaceae into a series of Ordres, and the second ordre was named Asphodèles, based on Jussieus' family of that name, in which he placed Allium. The term 'Alliaceae' then reappeared in its subfamilial form, Allieae, in Dumortier's Florula Belgica, with six genera. The 'Alliaceae' have been treated as Allieae within the family Liliaceae by most authorities since.
Regel produced a major monograph of the genus in 1875, and this remained the major reference work for over 100 years till the molecularly based study of Friesen and colleagues in 2006. Despite recent advances the precise taxonomy of Allium remains still poorly understood with incorrect descriptions being widespread.
Phylogeny
Subdivision
Linnaeus originally grouped his 30 species into three alliances, e.g. ''Foliis caulinis planis and as the number of recognised species increased, so did the number of subgroups. Since then, many attempts have been made to divide the growing number of recognised species into infrageneric subgroupings, initially as sections, and then as subgenera further divided into sections. For a brief history, see Friesen et al. and Li et al. Regel's 1875 treatise on Allium divided his 262 species between the six sections proposed by Don, in his 1832 monograph on the genus. Stearn described 14 subgenera. Traub described 3 subgenera, 36 sections and subsections and about 600 species. By 1992 there were 6 sub-genera, 50 sections and subsections and 600–700 species. The situation was further confused by the presence of over 1,000 taxonomic names, many of which turned out to be synonyms.The modern era of phylogenetic analysis dates to 1996. In 2006 Friesen, Fritsch, and Blattner described a new classification with 15 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 included in the Gilliesieae. 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. 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. These alliances are usually referred to as the Ownbey alliances, after Marion Ownbey and were also used by Traub. A number of classification schemes have chosen to retain these, the Traub system not being universally accepted.
Subsequent molecular phylogenetic studies have shown the 2006 classification is a considerable improvement over previous classifications, but some of its subgenera and sections are probably not monophyletic. Meanwhile, the number of new species continued to increase, reaching 800 by 2009, 900 by 2016 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. Subgenus Melanocrommyum has also been the subject of considerable study, 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.
The major evolutionary lineages or lines correspond to the three major clades. Line one with three subgenera is predominantly bulbous, the second, with five subgenera and the third with seven subgenera contain both bulbous and rhizomatous taxa. Banfi and colleagues have suggested that the phylogenetic trichotomy of this genus Allium sensu lato is sufficiently distinct as to warrant splitting it into three separate genera. Banfi's scheme thus proposes the restoring the three originally separate genera Nectaroscordum Lindl., Caloscordum Herb. and Allium L. sensu stricto'' to correspond to lines 1-3.
Evolutionary lines and subgenera
The three evolutionary lineages and 15 subgenera here represent the classification schemes of Friesen et al. and Li, and subsequent additional species and revisions.;Evolutionary lines and subgenera
- [|First evolutionary line]
- # Nectaroscordum Asch. et Graebn Type: Allium siculum Mediterranean bells, Sicilian honey garlic
- # Microscordum N. Friesen Type: Allium monanthum
- # Amerallium Traub Type: Allium canadense
- [|Second evolutionary line]
- # Caloscordum R. M. Fritsch Type: Allium neriniflorum
- # Anguinum N. Friesen Type: Allium victorialis
- # Porphyroprason R. M. Fritsch Type: Allium oreophilum
- # Vvedenskya R. M. Fritsch Type: Allium kujukense
- # Melanocrommyum Rouy Type: Allium nigrum
- [|Third evolutionary line]
- # Butomissa N. Friesen Type: Allium ramosum fragrant garlic
- # Cyathophora R. M. Fritsch Type: Allium cyathophorum
- # Rhizirideum Wendelbo s.s Type: Allium senescens
- # Allium L. Type: Allium sativum
- # Reticulatobulbosa N. Friesen Type: Allium lineare
- # Polyprason Radic Type: Allium moschatum
- # Cepa Radic ́ Type: Allium cepa onion, garden onion, bulb onion, common onion
First evolutionary line
Subgenus ''Nectaroscordum''
, involving the western Mediterranean and southwest Asia- Section Nectaroscordum Gren. & Godr.
- * Allium siculum Ucria Type
- * Allium tripedale Trautv.