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 (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". 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 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. Subdivision: Subdivision of the subgenus was first proposed by Wendelbo in 1966, proposing section "Regeloprason" Wendelbo, followed in 1969 by "Melanocrommyum" Webb & Berthel., "Kaloprason" K. Koch, "Acanthoprason" Wendelbo, "Megaloprason" Wendelbo, and "Thaumasioprason" Wendelbo. Kamelin (1973) provided an alternative arrangement of sections, which was supplanted by the Gatersleben  Allium Group classification (1992) which used a broad range of variables. 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 resulting in a taxonomy based on 15 sections. These were then further subdivided into five of the sections to create 17 subsections. While "Melanocrommyum" itself appeared monophyletic, most of the sections were either para- or polyphyletic, favouring the formation of a larger number of smaller subgroups. In their study there  were a number of larger sections with 15–35 species, "Acmopetala", "Megaloprason", "Regeloprason", "Kaloprason", and "Acanthoprason". The remaining sections are either 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. This section is the most diverse one within the subgenus in which subgroups differ according to the relationships of the lengths of leaves and scapes (leaves shorter, equal or longer than scapes ) and inflorescences (fasciculate, umbellate or subglobose). The increased number of sections resulted from the splitting of some of the earlier sections, such as "Acmopetala". The two species in the resulting section "Longibidentata" are sister to all the remaining sections (core clade). This section, together with another new section, "Decipientia" form the basal clade. Although Li "et al." (2010) included three sections, their study was confined to species endemic to China. Uses: The subgenus also contains many species grown as ornamentals, such as "A. giganteum", "A. cristophii", "A. schubertii", "A. aflatunense", "A. atropurpureum", "A. nigrum" and "A. karataviense". These species are  predominantly from Southwestern and Central Asia, where they are used for both culinary and medicinal purposes. The latter usage is associated with the presence of cysteine sulphoxides and also radical scavenger activity, although many members of the subgenus possess less of these compounds and lack the distinctive taste and smell of garlic and onion, their properties appear to be associated with dithiodipyrroles and sulfur-pyridins. These substances also occur in the ornamental species, that were introduced into European and North American gardens in the early 19th century, and now are represented by an increasing number of named cultivars and hybrids . Cysteine sulphoxides are also largely responsible for the flavour and spicy taste of these species, predominantly the isomeric cysteine derivatives alliin and isoalliin. 15 sections 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. Of the seven subgenera, the large subgenus "Allium", represents the bulbous elelement. Subgenus "Butomissa". 2 sections Subgenus "Cyathophora". Asia (Tibet and the Himalayas) 3 sections Subgenus "Rhizirideum". ~ 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 Subgenus "Allium". 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 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". 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". 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". Section "Codonoprasum". Section "Codonoprason" is strongly monophyletic and has its centre of diversity in the Mediterranean  region, particularly Greece and Turkey, but extends to other areas of Europe, North Africa and the Middle East. It was originally conceived of as a separate genus, "Codonoprasum" by Reichenbach in 1828. The taxonomy of the section is complicated with inconsistent speciation. In 2005 the section was considered to consist of 58 species and 7 subspecies. 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. Historically the section has been considered to have a number of subsections. Friesen recognised 2, while  others have described 3, "e.g."; 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. Subgenus "Reticulatobulbosa". The second largest subgenus in the third evolutionary line. 5 sections. Subgenus "Polyprason". 4 sections Subgenus "Cepa". Polyphyletic. 5 sections. Etymology. The name "Allium" is ancient, and the plant was known to both the Romans and the Greeks. The name is thought to  be Celtic in origin, meaning "to burn", in reference to its taste and smell. One of the earliest uses of the name in botany, was by Joseph Pitton de Tournefort (1656- 1708).