Classification of the plant genus 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 (Amaryllidaceae). 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 classications had been based on homoplasious characteristics (what turn out to be independently evolved similar features in species from different lineages). 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 (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.
"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".
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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" (1601). When Linnaeus formerly described the genus "Allium" in his "Species Plantarum" (1753), there were thirty species with this name. He placed "Allium" in a grouping he referred to as "Hexandria monogynia" (i.e. six stamens and one pistil) 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" (Onions), or "Cepae" in Latin. De Jussieu is officially recognised as the first formal establishment of the suprageneric grouping into families (Ordo) in 1789. In this system "Allium" was one of fourteen genera in Ordo VI, "Asphodeles" (Asphodeli), of the third class ("Stamina epigyna") of Monocots. Jean Henri Jaume Saint-Hilaire (1805), who developed the concept of Amaryllidaceae, continued Jussieu's treatment of "Allium" under Asphodeli (which he considered synonymous with Adanson's Liliaceae and Jussieu's Asphodeli). He placed "Allium" in an unnamed monotypic section of Asphodeli defined as "Fleurs en ombelle, racine bulbeuse. Calice à six parties egales" (umbellate flowers, bulbous, calyx of six equal parts).
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" (1827), 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, 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.
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." (2006) and Li "et al." (2010) 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 (1944) described 14 subgenera. Traub (1968) 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 ("Caloscordum", "Milula", "Nectaroscordum") 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 (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.
The major evolutionary lineages or lines correspond to the three major clades. Line one (the oldest) 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 (2011) 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. (type: "N. siculum"), "Caloscordum" Herb. (type: "C. neriniflorum") and "Allium" L. "sensu stricto" (type: "A. sativum") 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." (2006) and Li (2010), and subsequent additional species and revisions.
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").
Subgenus "Nectaroscordum".
Disjunct distribution, involving the western Mediterranean (type species) and southwest Asia 
Subgenus "Microscordum".
East Asia
Subgenus "Amerallium".
This large monophyletic subgenus is extremely diverse, both morphologically and ecologically and is characterised by leaves with one row of vascular bundles, absence of palisade parenchyma and a subepidermal position of laticifers, with a predominant base chromosome number x=7.
"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. 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.
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".
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.
"Amerallium" is widely distributed within North America, Europe, north Africa, Ethiopia, the Caucasus, northern Iran, southeast Tibet, and southwest China. The greatest species diversity occurs in North America with 81 species recognized in the 2002 Flora of North America (north of Mexico) and a further 13 are unique to Mexico, and a total of 26 species recognised there. 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.
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".
15 Sections
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. 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.
Subgenus "Caloscordum".
East Asia
Subgenus "Anguinum".
Two distinct distributions:
1. Eurasian-American ("A. victorialis" alliance, including "A. tricoccum") 2. East Asia ("A. prattii", "A. ovalifolium")
Subgenus "Melanocrommyum".
This Eurasian subgenus, the second largest, is complex and has had a confusing taxonomic history and is extremely diverse, morphologically. It is distributed from the Mediterranean to the Near and Middle East, to north-western China and Pakistan in the east, and southern Siberia in the north. The centre of diversity is Central Asia where it evolved, but its ancestry is located in East Asia. The 2006 classification of Fritsch and colleagues included 150 species but this has continued to grow. An extensive molecular based study in 2010 confirmed its monophyly but showed that the traditional sections were either para- or polyphyletic. On the other hand, a number of monophyletic subgroups were recognised, with about 40 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.
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.
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