Article

A molecular phylogeny of the wild onions (Allium; Alliaceae) with a focus on the western North American center of diversity

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Abstract

Nuclear ribosomal DNA (ITS and ETS) sequences from 39 native Californian (USA) Allium species and congeners were combined with 154 ITS sequences available on GenBank to develop a global Allium phylogeny with the simultaneous goals of investigating the evolutionary history (monophyly) of Allium in the Californian center of diversity and exploring patterns of adaptation to serpentine soils. Phylogenies constructed with ITS alone or ITS in combination with ETS provided sufficient resolution for investigating evolutionary relationships among species. The ITS region alone was sufficient to resolve the deeper relationships in North American species. Addition of a second marker (ETS) further supports the phylogenetic placements of the North American species and adds resolution within subgenus Amerallium, a clade containing many Californian endemics. Within the global phylogeny, the native North American species were found to be monophyletic, with the exception of Allium tricoccum and Allium schoenoprasum. All native Californian species included in the analysis fell into a monophyletic subgenus Amerallium section Lophioprason, although endemic Californian species were not monophyletic due to the inclusion of species with ranges extending beyond the California Floristic Province. The molecular phylogeny strongly supports previous morphology-based taxonomic groupings. Based on our results, serpentine adaptation appears to have occurred multiple times within section Lophioprason, while the ancestor of the Californian center of diversity may not have been serpentine-adapted.

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... With the development of molecular biological methods, many molecular studies on the classification, phylogeny and origin of Allium have been performed and many improvements have been made 1,2,11-21 , especially by using the internal transcribed spacer (ITS) region, rps16 intron and matK sequence to understand the evolutionary processes and taxonomic relationships within the genus. The research methods used in those studies are based on morphological characteristics and partial molecular data that are widely used for the classification of new species in this genus 2,8,19,20,22,23 . All of Published: xx xx xxxx open Content courtesy of Springer Nature, terms of use apply. ...
... The first clade included two species (A. prattii and A. victorialis) belonging to the second evolutionary line described in previous reports 2, 11,22 . The other species, including A. tuberosum Rottl. ...
... The other species, including A. tuberosum Rottl. ex Spreng., A. sativum, A. obliquum, and A. cepa (CMS-T, CMS-S and N), grouped into clade two, belonging to the third evolutionary line 2,11,22 . In A. cepa, CMS-T and N grouped into a sister branch and then clustered with CMS-S. ...
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The genus Allium is one of the largest monocotyledonous genera, containing over 850 species, and most of these species are found in temperate climates of the Northern Hemisphere. Furthermore, as a large number of new Allium species continue to be identified, phylogenetic classification based on morphological characteristics and a few genetic markers will gradually exhibit extremely low discriminatory power. In this study, we present the use of complete chloroplast genome sequences in genome-scale phylogenetic studies of Allium. We sequenced and assembled four Allium chloroplast genomes and retrieved five published chloroplast genomes from GenBank. All nine chloroplast genomes were used for genomic comparison and phylogenetic inference. The chloroplast genomes, ranging from 152,387 bp to 154,482 bp in length, exhibited conservation of genomic structure, and gene organization and order. Subsequently, we observed the expansion of IRs from the basal monocot Acorus americanus to Allium, identified 814 simple sequence repeats, 131 tandem repeats, 154 dispersed repeats and 109 palindromic repeats, and found six highly variable regions. The phylogenetic relationships of the Allium species inferred from the chloroplast genomes obtained high support, indicating that chloroplast genome data will be useful for further resolution of the phylogeny of the genus Allium.
... The new classification of Allium on molecular bases was made by Friesen et al. (2006). Since then the monophyletic status of Allium has been confirmed in all major studies (Nguyen et al., 2008;Li et al., 2010;Choi et al., 2012). Despite a great deal of work not all subgenera have been fully studied concerning the phylogenetic positions of all their species. ...
... Vvedenskya (Kamelin) R. M. Fritsch and subg. Porphyroprason (Ekberg) R.M. Fritsch (Friesen et al., 2006;Nguyen et al., 2008;Li et al., 2010). This monophyletic subgenus consists of ten species and some varieties (3.4 Taxonomic review and geographical distribution) and is part of the second of three evolutionary lines of Allium (Fritsch, 2001;Fritsch and Friesen, 2002;Friesen et al., 2006;Li et al., 2010). ...
... Material from A. funckiifolium and A. caputmedusae Airy Shaw was not available and is therefore not included in this analysis. According to molecular analysis from Friesen et al. (2006), Nguyen et al. (2008) and Li et al. (2010) Anguinum is sister to Caloscordum therefore we used species from this section as outgroup taxa. Specimens used for DNA sequencing and the corresponding GenBank accession numbers are presented in Table 1. ...
... Friesen then innovated the classification of Allium in publication according to molecular techniques (Friesen et al. 2006). Thereafter, Allium was affirmed monophyletically by the entire scientific reports (Choi et al. 2012;Li et al. 2010;Nguyen et al. 2008). Despite a huge body of research, perfect studies have not been conducted on the whole subgenera regarding the phylogenetic condition of their species (Friesen et al. 2006). ...
... Phylogenetic associations among Allium species on the basis of matK analyses are in line with earlier research by the use of the matK site (Abugalieva et al. 2017;Gurushidze et al. 2007;İpek et al. 2014;Li et al. 2010). A. asarence and A. cepa lied jointly in a group with no polymorphisms in some investigations (Li et al. 2010;Nguyen et al. 2008). Likewise, A. asarence and A. cepa put together in a cluster by analyzing matK in the present research. ...
... porrum) lied in close grouping with A. austroiranicum. A. Akaka was placed tightly in a group with A. breviscapum and A. sub akaka was assigned to a group close to A. alamutense and A. zagricum, which have a closer relation to a recently published report (Akhavan et al. 2015;Li et al. 2010;Nguyen et al. 2008). Similar to a latest investigation, A. pseudoampeloprasum was clustered tightly to A. atroviolaceum, A. iranicum, and A. sativum in our research ((Hirschegger et al. 2010;Veiskarami et al. 2019). ...
... Based on literature (Maire 1958, Fennane and Ibn Tattou 1998, 2008, Rankou et al. 2013, 2015, Allium valdecallosum is a very rare species, hitherto known only from Todra gorge (Morocco), where it grows in the rocky crevices of amazing vertical walls made up from Bathonian limestones and dated back to the Jurassic. However, the species has also been found at a new site in the High Atlas, in a valley near Imi-n-Tala, located south of Marrakech (Fig. 2). ...
... Scorodon Koch. However, many molecular studies (Fritsch and Friesen 2002, Friesen et al. 2006, Nguyen et al. 2008, Li et al. 2010, Hirschergger et al. 2010 have pointed out that the traditional A. sect. Scorodon s.l. is actually an assemblage of various and well differentiated phylogenetic lineages. ...
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Allium valdecallosum is a critical and poorly known species endemic to Morocco. Its diagnostic features, karyology, seed testa micro‐morphology, leaf anatomy, ecology, distribution, conservation status, and taxonomic relationships are examined. This article is protected by copyright. All rights reserved.
... This classification was supported in several later studies [9][10][11][12] and became well adopted among Allium taxonomists. In spite of these substantial efforts towards understanding of evolutionary processes and taxonomy of the genus there are still many poorly described Allium taxa available in different parts of the World and active description of wild onion species is an ongoing process [1,13,14]. ...
... The other important result was an assessment of taxonomic statuses of endemic and rare Allium species growing in Kazakhstan. The study confirms monophyletic origin of Allium genus that was established in several published reports [8,13,14]. In addition, a detailed study on comparison of Reticulatobulbosa species was performed with a major attention to morphological and molecular genetic description of species grown in Karatau State Natural Reserve. ...
Article
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Background: As part of nation-wide project to infer the genetic variation of the native flora in Kazakhstan, a study was attempted to assess phylogenetic relationships of endemic and rare Allium species. In total, 20 Allium species were collected in field trips in five different regions of Kazakhstan during 2015-2016. Most species (9) were collected in the southern part of the country along of Karatau mountains, followed by Altai mountains (5) in eastern Kazakhstan. The ITS and matK DNA regions were applied in order to assess the taxonomic relationships among species. The major goal of the study was to assess the taxonomic position of five endemic and rare species from Allium subgenus Reticulatobulbosa collected in Karatau mountains of Southern Kazakhstan. Results: The 20 collected Allium species were assessed using morphological traits and a DNA barcoding approach. The morphological analyses of four different species in subgenus Reticulatobulbosa inferred similarities of A. inconspicuum and A. barszchewskii (both from section Companulata) that were separated from A. oreoscordum and A. oreoprasoides (section Nigrimontana) by several traits, including form of bulbs and leaves, presence of bracts, shape of perianth lobes and style. The Neighbor-Joining method was applied to generate ITS and matK phylogenetic trees for two groups of populations: 1) 20 Allium species collected within the project, and 2) 50 Allium worldwide species. Conclusions: The analyses of nucleotide sequences of ITS and matK robustly confirmed the monophyletic origin of the Allium species. The variability in 20 local Allium species in ITS was 6.6 higher than in matK, therefore the topology of the ITS tree was better resolved. The taxonomy of Allium species largely coincided with a recent classification of this genus. Analyses of both ITS and matK suggest that A. oreoscordum is genetically close to A. oreoprasoides in section Nigrimontana of subgenus Reticulatobulbosa. This result was also confirmed using morphological description of individual plants of four species in subgenus Reticulatobulbosa. The study is another contribution to taxonomy clarification in Allium.
... According to the assessment of the Angiosperm Phylogeny Group, the genus Allium is placed in the family Amaryllidaceae (APGIII 2009) and is characterised by having bulbs with membranous or fibrous tunics, terminal umbel, free or almost free, 1-veined tepals, often a subgynobasic style and loculicidal capsule (Kollmann 1984). Based on molecular, morphological, anatomical and cytological data, the genus is divided into 15 subgenera and 80 sections (Tzanoudakis 1983, Berg et al. 1996, Dubouzet & Shinoda 1999, Friesen & Blattner 2000, Friesen et al. 2006, Gurushidze et al. 2008, Nguyen et al. 2008, Li et al. 2010, Choi et al. 2012). In the last decades, many Allium taxa were newly described for Turkey and the number of species known to occur is raised to approximately 220 species, half of which are endemic, evidencing that Turkey is a relevant part of the southwestern Asian centre of diversity of Allium (Kollmann 1984, Koyuncu 2012, Ekşi et al. 2015, 2016, Duman et al. 2017, Fırat et al. 2018, Ekşi & Yıldırım 2019. ...
... Allium sect. Scorodon, typified by A. moschatum Linnaeus (1753: 298), is included in the subgenus Polyprason Radić (1990: 253) (Fritsch & Friesen 2002, Friesen et al. 2006, Nguyen et al. 2008, Hirschegger et al. 2010, Li et al. 2010, Brullo et al. 2015. ...
Article
Allium shahinii, a new species of Allium sect. Scorodon, is described and illustrated from Erzincan Province, Eastern Turkey. It is a narrowly distributed geophyte growing on siliceous screes of warm exposure in mountain ranges of the nemoral and thermophilous deciduous woodland zone, showing close morphological relationships mainly with A. moschatum, A. stocksianum, A. spirophyllum, A. circumflexum but it is clearly differentiated due to perigon, outer tunic, indumentum, leaf and scape characteristics. In this study, diagnostic characters, description, taxonomic comments, photographs, distribution map, detailed illustration, the conservation status of A. shahinii and identification key are provided for A. shahinii and related taxa. According to IUCN Red List Categories and Criteria, A. shahinii is assessed here as a Critically Endangered (CR) species.
... Many nuclear genes and chloroplast genomes were recently employed in Allium studies (Friesen et al., 2006;Nguyen et al., 2008;Kim and Yoon, 2010;Li et al., 2010;Lee et al., 2017;Jin et al., 2018), which provide valuable information for the phylogenetic study of section Daghestanica. In particular, the whole chloroplast genomes that possess highly conserved gene structure and gene content, and lower substitution rate than nuclear DNA (especially in inverted repeat regions), offer promising solutions to phylogeny uncertainties (Wolfe et al., 1987;Raubeson et al., 2005;Parks et al., 2009). ...
... The results of our phylogenetic analysis strongly support that Allium is monophyletic, which is in accordance with previous studies (Friesen et al., 2006;Nguyen et al., 2008;Li et al., 2010). We also found that Agapanthus coddii was closely related to Allium (Allioideae) (Figure 7 and Supplementary Figure S3). ...
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The genus Allium (Amaryllidaceae, Allioideae) is one of the largest monocotyledonous genera and it includes many economically important crops that are cultivated for consumption or medicinal uses. Recent advances in molecular phylogenetics have revolutionized our understanding of Allium taxonomy and evolution. However, the phylogenetic relationships in some Allium sections (such as the Allium section Daghestanica) and the genetic bases of adaptative evolution, remain poorly understood. Here, we newly assembled six chloroplast genomes from Chinese endemic species in Allium section Daghestanica and by combining these genomes with another 35 allied species, we performed a series of analyses including genome structure, GC content, species pairwise Ka/Ks ratios, and the SSR component, nucleotide diversity and codon usage. Positively selected genes (PSGs) were detected in the Allium lineage using the branch-site model. Comparison analysis of Bayesian and ML phylogeny on CCG (complete chloroplast genome), SCG (single copy genes) and CDS (coding DNA sequences) produced a well-resolved phylogeny of Allioideae plastid lineages, which illustrated several novel relationships with the section Daghestanica. In addition, six species in section Daghestanica showed highly conserved structures. The GC content and the GC3s content in Allioideae species exhibited lower values than studied non-Allioideae species, along with elevated pairwise Ka/Ks ratios. The rps2 gene was lost in all examined Allioideae species, and 10 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis, seven of them are associated with photosynthesis. Our study uncovered a new species relationship in section Daghestanica and suggested that the selective pressure has played an important role in Allium adaptation and evolution, these results will facilitate our further understanding of evolution and adaptation of species in the genus Allium.
... Our sampling strategy was designed to cover those taxonomic and geographic Anguinum groups that were underrepresented in previous analyses, especially from eastern Asia, and to build on previous studies (Friesen et al. 2006;Li et al. 2010 (Fritsch and Friesen 2002;Friesen et al. 2006;Nguyen et al. 2008;Li et al. 2010). GenBank accession numbers and voucher details referred to the above-mentioned taxa are given in Appendix S1 [see Supporting Information]. ...
... The crown age of Allium was set to 34.26 Mya based on previous analysis, with a normally distributed standard deviation of 0.1. According to previous phylogenetic analyses (Fay and Chase 1996;Mes et al. 1997;Fay et al. 2000;Friesen et al. 2000Friesen et al. , 2006Nguyen et al. 2008;Li et al. 2010), Nothoscordum gracile and Tulbaghia violacea were used to root the tree. ...
Article
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A primary aim of historical biogeography is to identify the causal factors or processes that have shaped the composition and distribution of biotas over time. Another is to infer the evolution of geographic ranges of species and clades in a phylogenetic context. To this end, historical biogeography addresses important questions such as: Where were ancestors distributed? Where did lineages originate? Which processes cause geographic ranges to evolve through time? Allium subgenus Anguinum comprises approximately twelve taxa with a disjunct distribution in the high mountains from south-western Europe to eastern Asia and in northeastern North America. Although both the systematic position and the geographical limits of Anguinum have been identified, to date no molecular systematic study has been performed utilizing a comprehensive sampling of these species. With an emphasis on the Anguinum eastern Asian geographical group, the goals of the present study were: (1) to infer species-level phylogenetic relationships within Anguinum, (2) to assess molecular divergence and estimated the times of the major splits in Anguinum, and (3) to trace the biogeographic history of the subgenus. Four DNA sequences (ITS, matK, trnH-psbA, rps16) were used to reconstruct the phylogeny of Allium subgen. Anguinum. RbcL sequences were used to estimate divergences time for Allium, and sequences of ITS were used to estimate the divergence times for Anguinum and its main lineages and to provide implications for the evolutionary history of the subgenus. Phylogenetic analyses for all Allium corroborate that Anguinum is monophyletic and indicate that Anguinum is composed of two sister groups: one with a Eurasian-American distribution, and the other restricted to eastern Asia. In the eastern Asian geographical group, incongruence between gene trees and morphology-based taxonomies was recovered as was incongruence between data from plastid and nuclear sequences. This incongruence is likely due to the combined effects of a recent radiation, incomplete lineage sorting, and hybridization/introgression. Divergence time estimates suggest that the crown group of Anguinum originated during the late Miocene (ca. 7.16 Mya) and then diverged and dispersed. Biogeographic analyses using statistical dispersal-vicariance analysis (S-DIVA) and a likelihood method support an eastern Asia origin of Anguinum. It is inferred that in the late Pliocene/Early Pleistocene, with cooling climates and the uplift of the Himalayas and Hengduan Mountains, the ancestor of the eastern Asian alliance clade underwent a very recent radiation.
... Other molecular phylogenetic investigations have been concerned with the origins of economically important Allium crops (e.g., Friesen and Klaas 1998;Friesen et al. 1999;Blattner and Friesen 2006). Nguyen et al. (2008) examined the phylogeny of the western North American species and their adaptation to serpentine soils. Friesen et al.'s (2006) analysis of 195 species of Allium using the ITS region of nrDNA presented a new subgeneric classification consisting of 15 monophyletic subgenera. ...
... A scenario of rapid radiation was proposed for this clade. The first two clades contain both Old and New World species; almost all of the western North American species are classified in subgenus Amerallium (Nguyen et al. 2008), which has sparingly extended to central and eastern North America. The only other North American species are members of subg. ...
... Cyathophora were found to be non-monophyletic although 74 protein-coding genes were used (Fig. 2). Previous molecular phylogenetic studies of Allium revealed the non-monophyly of some subgenera 8,9,33 . For example, Li et al. 33 reported paraphyly of the subgenera Anguinum, Cepa, Allium, Reticulatobulbosa, and Polyprason inferred from ITS and rps16 sequences. ...
... For example, Li et al. 33 reported paraphyly of the subgenera Anguinum, Cepa, Allium, Reticulatobulbosa, and Polyprason inferred from ITS and rps16 sequences. Similarly, the monophyly of subgenera Rhizirideum, Polyprason, and Cyathophora was not corroborated by ITS and external transcribed spacer sequences 9 . Additionally, the phylogeny of Allium based on whole plastome sequences revealed the polyphyly of subgenera Cepa and Polyprason 8 . ...
Article
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Allioideae includes economically important bulb crops such as garlic, onion, leeks, and some ornamental plants in Amaryllidaceae. Here, we reported the complete chloroplast genome (cpDNA) sequences of 17 species of Allioideae, five of Amaryllidoideae, and one of Agapanthoideae. These cpDNA sequences represent 80 protein-coding, 30 tRNA, and four rRNA genes, and range from 151,808 to 159,998 bp in length. Loss and pseudogenization of multiple genes (i.e., rps2, infA, and rpl22) appear to have occurred multiple times during the evolution of Alloideae. Additionally, eight mutation hotspots, including rps15-ycf1, rps16-trnQ-UUG, petG-trnW-CCA, psbA upstream, rpl32-trnL-UAG, ycf1, rpl22, matK, and ndhF, were identified in the studied Allium species. Additionally, we present the first phylogenomic analysis among the four tribes of Allioideae based on 74 cpDNA coding regions of 21 species of Allioideae, five species of Amaryllidoideae, one species of Agapanthoideae, and five species representing selected members of Asparagales. Our molecular phylogenomic results strongly support the monophyly of Allioideae, which is sister to Amaryllioideae. Within Allioideae, Tulbaghieae was sister to Gilliesieae-Leucocoryneae whereas Allieae was sister to the clade of Tulbaghieae- Gilliesieae-Leucocoryneae. Molecular dating analyses revealed the crown age of Allioideae in the Eocene (40.1 mya) followed by differentiation of Allieae in the early Miocene (21.3 mya). The split of Gilliesieae from Leucocoryneae was estimated at 16.5 mya. Biogeographic reconstruction suggests an African origin for Allioideae and subsequent spread to Eurasia during the middle Eocene. Cool and arid conditions during the late Eocene led to isolation between African and Eurasian species. African Allioideae may have diverged to South American taxa in the late Oligocene. Rather than vicariance, long-distance dispersal is the most likely explanation for intercontinental distribution of African and South American Allioideae species.
... The Allium genus is comprised of 750 species (Stearn 1992;Friesen et al. 2006), and at up-to-date around 1000 species are enumerated (Benke et al. 2021;Singh et al. 2021). Alliums are found throughout the Northern Hemisphere's Temperate and Alpine zones, with diverse hotspots in Southwest or Central Asia, Eastern Asia, and North America (Nguyen et al. 2008). The Western Himalayas of Jammu, Kashmir, Uttaranchal and Himachal Pradesh, as well as the Eastern Himalayan region of Darjeeling hill tracts of West Bengal, Sikkim, and the North-Eastern provinces, are hotspots for Allium species in India (Dutta and Bandyopadhyay 2014;Benke et al. 2021). ...
... Garlic chives (Allium tuberosum Rottler ex Sprengel) are found in the northern hemisphere's mountains and highlands, as well as in the subtropics and tropics (De Sarker et al. 1997), mountain belt of the Alps and the Caucasus to Eastern Asia (Fritsch and Friesen 2002). In India, it is one of the lesser-known vegetables that has survived and is limited to home gardens (Pandey et al. 2014) and mainly found as wild species of Allium in the Himalayas of Ladakh and Kashmir (Nguyen et al. 2008). Its wider adaptability, year-round growth and comparatively low input demand for cultivation (Rana et al. 2012), could lead to the commercialisation of this species as a leafy vegetable, that can supplement to other Alliums (Pandey et al. 2014), as a spice in culinary in the place of garlic or onion, leaves are used to flavouring the dishes and sauces, consumed as raw as salad, cooked, pickled and processed form (Hanelt et al. 1992;Negi 1992Negi , 2006Pandey et al. 2008;Han et al. 2015). ...
Article
Garlic chives (Allium tuberosum Rottler ex Sprengel) are an underutilized and neglected food crop of the Allium genus. For the future genetic development of alliums, phenotypic characterization and insights of breeding behaviour could be the aid to breed the new garlic chives varieties. Field Emission Scanning Electron Microscopy (FESEM) was used to reveal the morphological features of male gametophytes. The anther was reticulate, conspicuous, folded surface with scaly plates, and pollen was found to be sub-ovoid morphologies with long regulate and striated sexine. Spectra from FESEM-based Energy Dispersive X-ray Spectroscopy (EDS) revealed the elemental composition and distribution. The micrograph of an anther sample revealed the presence of O, C, K, P, N, Fe, Mn, Zn, and Mg minerals, as well as C, O, N, P, K, Fe, Ca, Mn, Mg, Zn, Cu, Na, and Cl minerals in the pollen grain. These insights of male gametophytes traits and characteristics, relative mineral composition and breeding behaviour could aid in the better understanding, characterization, identification and genetic improvement of A. tuberosum.
... Allium L., one of the largest genera in the family Amaryllidaceae, has about 1,100 species distributed world-wide (Li et al. 2010;Govaerts et al. 2021). The genus Allium naturally occurs in dry seasons in the northern hemisphere and South Africa (Friesen et al. 2006;Nguyen et al. 2008;Neshati and Fritsch 2009). The primary centre of evolution for the ge-nus extends across the Irano-Turanian bio-geographical region, and the Mediterranean basin and western North America are considered as the secondary centres of diversity (Friesen et al. 2006). ...
... Eduardia) and the genetic bases of adaptative evolution remain poorly understood for the Indian taxa (Pandey et al. 2021). Molecular phylogeny study of the wild Allium in different centers of diversity (Nguyen et al. 2008;Xie et al. 2019;Jang et al. 2021) has helped in unlocking many aspects of the taxon relationships. The present study uncovered a new species relationship with its closest allied species and suggested that the selective habitat pressure has played an important role in the adaptation and evolution of Allium in this habitat which will facilitate uncover more taxa in the genus. ...
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A new species, Allium negianum (Amaryllidaceae), belongs to the genus Allium subg. Rhizirideum, sect. Eduardia is described here from the Uttarakhand Himalayan region of India. This taxon grows in Malari region of Niti valley in Chamoli district and Dharma valley of Pithoragarh district, Uttarakhand, India. It is a narrowly distributed species and morphologically more closer to A. przewalskianum Regel but differentiated by its tunic color of bulb, umbel with lax flowers, peduncle length, perigone colour, size and shape and leaf anatomy. Taxonomic delineation and relationship analysis based on nuclear ribosomal Internal Transcribed Spacers (ITS) region indicated that A. negianum is distinct and related to A. przewalskianum . This study provided a comprehensive description and comparison with A. przewalskianum , an identification key and notes on the distribution of the species.
... The Allium L. genus is comprised of 750 species (Stearn, 1992Friesen et al., 2006, and at present around 1000 species are listed (Singh et al., 2021), including cultivated and wild alliums (Negi, 2006). Alliums were distributed around the Northern Hemisphere's Temperate and Alpine areas, with diverse hotspots in Southwest or Central Asia, Eastern Asia, and North America (Nguyen et al., 2008). Asia, Europe, and Northern America, which includes the Arctic are the natural ecosystems (Tatluglu, 1993). ...
... The taxonomical hierarchy is as follows for chives via kingdom: plantae (plants), subkingdom: viridiplantae (green plants), infrakingdom: streptophyta (land plants), superdivision: embryophyta (plants that produce embryos), division: tracheophyta (vascular plants), subdivision: spermatophytina (plants which form seeds), class: liliopsida (angiosperm with single cotyledon), subclass: liliidae, superorder: lilianae (monocots), order: amaryllidales (succulent herbaceous plants), family: amaryllideceae (plants bear flowers with superior ovaries in an umbel), subfamily: allioideae, tribe: allieae, genus: Allium L., subgenus: cepa, section: schoenoprasum, species: schoenoprasum L., varieties: schoenoprasum L., laurentianum Fernald, sibiricum L. Celak, or Hartman (ITIS, 2021;Tatluglu, 1993;Fritsch and Friesen, 2002;Takhtajan, 1997) Chives (Allium schoenoprasum L.) are naturally distributed in most parts of the northern hemisphere, and scattered in mountains or highlands within the subtropics and tropics (de Sarker et al., 1997), A. schoenoprasum occupy most of the Eurasian continent, but most species are distributed in the mountain belt from the Alps and Caucasus to East Asia (Fritsch and Friesen, 2002), cultivation probably began in Italy, from where it was distributed to Central and West Europe in the early middle ages (Helm, 1956). This species is found in the wild in Ladakh Himalaya and Kashmir, and has restricted commercial cultivation in India (Nguyen et al., 2008). Chives are edible spice plants widely been used in culinary as a replacement for garlic or onion, whose leaves, umbels, and flowers are used to flavouring the dishes and sauces, as well as salads and sour cream since they have an onion flavour, rich in antioxidants, vitamins and proteins (Stajner et al., 2004;Los-Kuczera, 1990). ...
Article
Chives (Allium schoenoprasum L.) are the important edible crop in the genus Allium, after onion, garlic, leek, and bunching onion. The phenotypic characterization revealed the breeding behaviour of plants for future genetic improvement of alliums, thereby the insight of the breeding system of chive could lead to the breeding of new varieties of chive. The morphological features of the male gametophytes have been revealed through Field Emission Scanning Electron Microscopy (FESEM), the surface of the male gametophyte was reticulate and shrivelled of surface, pollen found to be sub-ovoid shapes, with long regulate and striated sexine. The elemental composition and distribution were unveiled by FESEM based Energy Dispersive X-ray Spectroscopy (EDS) spectra. The micrograph of anther sample enumerated the C, O, K, P, N, Fe, Mn, Cu, and Mg minerals, and C, O, N, Fe, P, K, Zn, Mn, Cl, Ca, and Na minerals in the pollen grain. These insights could aid in the better understanding, characterization and identification of species based on the male gametophytes.
... The internal transcribed spacer (ITS) region of nrDNA has proved to be informative in the genus Allium (Dubouzet & Shinoda 1999;Friesen et al. 2000Friesen et al. , 2006Nguyen et al. 2008). ...
... 1000 replicates were chosen for bootstrap analyses in a test of phylogeny. Selection of outgroups were based on previous studies (Nguyen et al. 2008). ...
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The subgenus Butomissa (Salisb.) N. Friesen of the genus Allium L. is consisting of two sections, Butomissa and Austromontana. The subgenus is represented by four species. Present study derives results from morphology and molecular phylogenetic analyses to test the relationship between Allium ramosum and A. tuberosum of the section Butomissa. Results reveal that Allium ramosum and A. tuberosum, found to be in polytomy using molecular markers trnL-F and ITS in individual as well as combined analysis. Morphological results also reveal little to no variation. Based on the results obtained we propose that A. tuberosum may be treated as synonym of A. ramosum.
... simmleri Beauv. and T. violacea Harv.) of the 31 species of Tulbaghia were considered (Fay & Chase 1996;Friesen et al. 2006;Nguyen et al. 2008). In such restricted molecular analyses, the potentially misleading effects of poor taxon sampling on phylogenetic analyses and their appli- cations should be kept in mind (e.g. ...
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Micromorphology and cytology of Prototulbaghia siebertii, with notes on its taxonomic significance.
... Vvedensky (1935), Xu (1980) and Stearn (1980) divided the species of Allium from Russia, China and Europe into 10, 9 and 13 sections, respectively, based on morphological characters of the rhizome, bulb, leaf and flower. Hanelt et al. (1992) divided the genus into six subgenera and 50 sections and Friesen et al. (2006) and Nguyen et al. (2008) into 15 subgenera and 56 sections using information on anatomy, cytogeography and DNA ITS sequences. ...
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The genus Allium is comprised of more than 800 species, and although previous studies have been useful in identifying the species, there is a paucity of easy-to-observe morphological characters with which to distinguish them. Thus, we determined the micromorphological characteristics of the leaf epidermis of 43 species of Allium from Central Asia using light microscopy and evaluated their taxonomic significance. Our study examined variability in epidermal cell shape and size and the stomatal apparatus. The stomatal apparatus is ellipsoid, anomocytic and amphistomatic. The shape (rectangular or rhomboid) of epidermal cells, pattern (straight or arched) of anticlinal walls, and stomatal index are stable within a species, while there are differences among species that allow for species delimitation. Based on the shape and pattern of anticlinal walls of leaf epidermal cells, the 43 sampled species could be divided into three distinct types of epidermal cells: type 1, rhomboid cell shape and straight anticlinal walls; type 2, rhomboid cell shape and arched anticlinal walls; and type 3, rectangular cell shape and straight anticlinal walls. These leaf epidermal micromorphological characters prove to be the taxonomic significance in distinguishing and delimitating species in Allium.
... Initially, the investigations involved verification of the species used in the study by genetic analysis to establish the relationship between A. sativum L13 and A. ampeloprasum. The analysed ITS region of the rDNA gene cluster has been successfully used to assess the phylogenetic relationship among the species of the genus and subgenus Allium Shinoda 1998, 1999;Mes et al. 1999;Fritsch and Friesen 2002;Ricroch et al. 2005;Friesen et al. 2006;Gurushidze et al. 2007Gurushidze et al. , 2008Ipek et al. 2008;Nguyen et al. 2008;Li et al. 2010). The phylogenetic analysis led to differentiation of A. ampeloprasum L. and A. sativum into separate clusters. ...
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Key message: Microsporogenesis in garlic. The male-sterile Allium sativum (garlic) reproduces exclusively in the vegetative mode, and anthropogenic factors seem to be the cause of the loss of sexual reproduction capability. There are many different hypotheses concerning the causes of male sterility in A. sativum; however, the mechanisms underlying this phenomenon have not been comprehensively elucidated. Numerous attempts have been undertaken to understand the causes of male sterility, but the tubulin cytoskeleton in meiotically dividing cells during microsporogenesis has never been investigated in this species. Using sterile A. sativum genotype L13 and its fertile close relative A. ampeloprasum (leek), we have analysed the distribution of the tubulin cytoskeleton during microsporogenesis. We observed that during karyokinesis and cytokinesis, in both meiotic divisions I and II, the microtubular cytoskeleton in garlic L13 formed configurations that resembled tubulin arrangement typical of monocots. However, the tubulin cytoskeleton in garlic was distinctly poorer (composed of a few MT filaments) compared with that found in meiotically dividing cells in A. ampeloprasum. These differences did not affect the course of karyogenesis, chondriokinesis, and cytokinesis, which contributed to completion of microsporogenesis, but there was no further development of the male gametophyte. At the very beginning of the successive stage of development of fertile pollen grains, i.e. gametogenesis, there were disorders involving the absence of a normal cortical cytoskeleton and dramatically progressive degeneration of the cytoplasm in garlic. Therefore, we suggest that, due to disturbances in cortical cytoskeleton formation at the very beginning of gametogenesis, the intracellular transport governed by the cytoskeleton might be perturbed, leading to microspore decay in the male-sterile garlic genotype.
... The PCR condition was identical to that described in Friesen et al. (2006). The ETS region was amplified using the primers 18S-IGS (Baldwin & Markos 1998) and ETS-all-f (Nguyen et al. 2008). The PCR condition was identical to that described in Herden et al. (2012). ...
Article
Allium palaestinum, a long-forgotten taxon of arid Israel and Jordan, is re-described here. The new description is based on Kolmann's work in 1971 and on living plants and fresh herbarium specimens. Independence of the species is confirmed not only by differing morphological and ecological features of the nearest related Allium species, but also by molecular methods. Hence, the species is no longer treated within Allium neapolitanum. Discussion on phylo-geography, distribution, conservation status and habitat is provided.
... Morphological evidence for recognizing Dipterostemon is fully supported by molecular data, which show that D. capitatum is sister to a clade composed of Brodiaea and the other species of Dichelostemma and that Dichelostemma is only monophyletic if D. capitatum is excluded (Pires et al. 2001;Pires & Sytsma 2002;Nguyen et al. 2008;Steele et al. 2012). Accordingly, a revised treatment of Dichelostemma capitatum is presented here that treats the species and its infraspecific taxa under the genus Dipterostemon. ...
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Dichelostemma capitatum (Benth.) Alph.Wood, traditionally treated as one of five geophyte species included in Dichelostemma Kunth, a genus endemic to the western USA and northern Mexico, has been the subject of nearly perpetual taxonomic confusion since the early 19th century. In this paper, I review the errors that perpetuated the misapplication of names to D. capitatum, resurrect Dipterostemon Rydb. as the alternative genus for D. capitatum, and propose new infraspecific combinations. Dichelostemma pulchellum (Salisb.) A. Heller, a name persistently misapplied to D. capitatum, is a confused name that is synonymous with D. congestum (Sm.) Kunth. Dipterostemon capitatus (Benth.) Rydb. subsp. pauciflorus (Torr.) R.E. Preston, comb. nov., and D. capitatus (Benth.) Rydb. subsp. lacuna-vernalis (L.W. Lenz) R.E. Preston, comb. nov., are proposed.
... Allium genus (Amarylidaceae) with more than 700 species of edible and medicinal species all around the world, is one of the most important plant families in Iran, its plant species have been used both as vegetable and medicinal plants for thousands of years (3). This genus is composed of different groups of perennial plants which have recently attracted great attentions because of their both pharmaceutical and alimentary benefits (4). Allium species are rich sources of phytonutrients and have been exhibited to possess many pharmacological activities including cholesterol lowering, anti-hypertensive, antispasmodic, anti-bacterial, anti-viral, antimicrobial and anti-cancer effects (5,6). ...
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Introduction: Allium paradoxum is a perennial herb in northern Iran, especially in Mazandaran province. It is locally called "Alezi" and in addition to using as raw vegetable, is also used in the preparation of regional foods. This study was aimed to investigate the main phenolic constituents of the plant. Methods: Bulbs of the plant were extracted respectively by hexane, chloroform, chloroformmethanol (9-1) and methanol in a stepwise method with increasing solvent polarity. Methanol extract was then partitioned between water and butanol. Chloroform-methanol and butanol extract constituents were isolated and purified by column chromatography and HPLC. Chemical structure of the compounds was elucidated unambiguously by spectroscopic methods, including 1D and 2D NMR and MS spectroscopy. Results: Phytochemical investigation of A. Paradoxum led to the isolation of two main phenolic compounds, a flavonoid glycoside and a tyrosol derivative. The isolated compounds were identified as kaempeferol-3-O-glucoside (1) (Astragalin) and 2-methoxy-2-(4'-hydroxyphenyl) ethanol (2-Methoxy tyrosol) (2). Conclusion: Isolation and identification of astragalin and 2-methoxy tyrosol from A. Paradoxum is reported for the first time in this study and provide a chemical basis for the explanation of pharmacological and biological activities attributed to the plant.
... The current classification schemes outline the Amaryllidaceae as a family of approximately 90 genera and 1800 species (fide Jin, 2013), divided into three subfamilies: Amarylloideae, Agapanthoideae, and Allioideae. Within the Allioideae, four monophyletic tribes have been recognized: Allieae (Nguyen et al., 2008), Tulbaghieae (Stafford and Rønsted, 2015), Gillieasieae (Escobar, 2012), and Leucocoryneae (Sassone et al., 2014a). ...
Article
At present the subfamily Allioideae is included within the Amaryllidaceae, which is an economic important bulb crop subfamily that includes onion, garlic, and ornamental species worldwide. The Allioideae includes four tribes geographically disjunct namely: Allieae, widespread in the northern hemisphere, tribe Tulbaghieae distributed in South Africa, and tribes Leucocoryneae and Gilliesieae are endemic to South America. Although we agree with the current tribal circumscription of the Leucocoryneae including Beauverdia, Ipheion, Latace, Leucocoryne, Nothoscordum, and Tristagma, there are still taxonomic and phylogenetic uncertainties regarding the monophyly, phylogenetic relationships, and divergence time of several lineages in a biogeographic context. In this study, a comprehensive molecular phylogeny of the tribe Leucocoryneae was inferred based on nuclear ribosomal ITS and plastid (ndhF and matK) sequences. We used Bayesian inference and maximum parsimony analyses to predict ancestor-descendant relationships. Our results confirmed the monophyly of the four tribes of subfamily Allioideae. Similarly, within the Leucocoryneae, Ipheion, Leucocoryne, and Nothosocordum Sect. Inodorum were also monophyletic; Tristagma and Nothoscordum would be monophyletic if including Ipheion and Beauverdia, respectively. Network analyses were implemented to reveal putative scenarios of reticulate evolution. Both, current and ancestral hybridization events have presumably occurred among species of Nothoscordum Sect. Nothoscordum and Beauverdia favored by spatial overlapping of populations, flowering synchrony and a puzzling pattern of cytogenetic attributes. The estimation of divergence time indicates that the tribe Leucocoryneae originated in the Late Oligocene in southern South America with possible ancestors in Africa. Most crown lineages within the tribe diversified in conjunction with biogeographical events during the Late Miocene to Pliocene. We posit that new suitable environments available after the Andean uplift and during the Age of the Southern Plains provided the favorable geographic setting for the major lineages of Leucocoryneae in southern Pampas, extra-Andean Patagonia, Andean mountains, and in Chile. Hybridization, polyploidization, and Robertsonian translocations of chromosomes have been the driving forces and major sources of speciation in the evolution of tribe Leucocoryneae.
... The classification of the genus Allium (Amaryllidaceae) has been intricate since the pioneer work of Don (1827) and subsequent treatments (Regel 1875;Vvedensky 1935;Feinbrun 1943;Omelczuk 1962), but recent classifications (Friesen & al. 2006;Nguyen & al. 2008;Li & al. 2010) divided the genus into three unnamed clades which are referred to as lineages, and which together form 15 different subgenera. These clades were raised to generic level (Allium, Caloscordum and Nectaroscordum) by Banfi & al. (2011) although this treatment is still questionable. ...
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A revision of species in Allium subsect. Allium occurring on the Maltese Islands was done on field and herbarium data. A. ampeloprasum L., the presumed endemic A. melitense (Borg.) Ciferri & Giacomini and A. commutatum Guss. are the three species mentioned in the Maltese floras within this group. The results clearly encompassed four different taxonomic units, corresponding to A. polyanthum Schult. & Schult. f. which has never been recorded for the Maltese Islands, two populations of A. commutatum and two forms (one sterile, one fertile) of their putative hybrid A. commutatum × A. polyanthum growing on few coastal areas. A. ampeloprasum is excluded from the Maltese islands while A. melitense is synonymised with A. polyanthum. All past records of A. commutatum (apart from a giant form) are referred to A. polyanthum. Moreover, A. . commutatum × A. polyanthum is reported from Sicily for the first time.
... Allium is probably the largest and most diverse monocotyledonous genera, comprised of over 920 species that are mainly distributed in seasonally dry regions of the Northern Hemisphere (Friesen et al. 2006;Fritsch et al. 2010;Herden et al. 2016;Li et al. 2010), with its main center of diversity located in southwest and central Asia (Choi and Oh 2011;Nguyen et al. 2008;Sarker et al. 1997). This genus consists of perennial herbs characterized by tunicate bulbs, narrowbased leaves, and head-like inflorescences with superior ovaries. ...
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Allium ochotense and Allium microdictyon are commonly known as ‘Mountain garlic’ and are popular, economically important species in many countries such as Korea, China, and Mongolia. Their leaves are used as culinary side dishes and in traditional medicines. In Korea, these two species are at risk of extinction due to damage to their natural habitat and thus, conservation and breeding programs are needed. However, their identification relies mostly on morphological data, which is limited and until recently, led to classifying these two species under A. victorialis. In the present study, a simple and reliable method of molecular identification was developed to distinguish A. ochotense from A. microdictyon that targets four barcoding regions: the internal transcribed spacer (ITS), the maturase K gene (matK), the chloroplast psbA-trnH intergenic region, and the ribulose-bisphosphate carboxylase large subunit gene (rbcL). Single nucleotide polymorphisms (SNPs) were found in ITS and matK regions, and species-specific primers were designed based solely on the SNP at position 680 of the ITS region that could differentiate A. ochotense from A. microdictyon. Using these primers in amplification refractory mutation system (ARMS)-PCR, A. ochotense, and A. microdictyon could be simultaneously and efficiently distinguished. This study is the first to report a simple, rapid, and efficient method for discriminating A. ochotense and A. microdictyon, indicating the utility of species-specific markers in the development of conservation and breeding programs.
... Despite several reports on the classification of Allium species, like many other species belonging to this genus, the phylogenetic position of Mooseer is still a matter of controversy (Mes et al. 1997;Shinoda 1998, 1999;Fritsch and Friesen 2002;Friesen et al. 2006;Li et al. 2010). The internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) loci, including the 5.8s nrDNA and the two spacers ITS1 and ITS2, has proven to be a valuable source of phylogenetic information at the generic and sub-generic levels (Baldwin et al. 1995;Blattner 2004) and has been successfully used for taxonomic classification in the Allium genus (Dubouzet and Shinoda 1999;Friesen et al. 2006;Gurushidze et al. 2007Gurushidze et al. , 2008Nguyen et al. 2008). Dubouzet et al. (1997) proposed the first molecular phylogeny of the subgenus Rhizirideum G. Don ex Koch based on ITS markers. ...
Article
We evaluated the genetic diversity of Iranian Mooseer (Allium stipitatum Regel. syn. A. hirtifolium Boiss.) using morphological traits and AFLP markers and determined the phylogenetic relationships and the position of Iranian Mooseer among domesticated and wild edible alliums using internal transcribed spacer (ITS) sequence data. Four EcoRI and MseI AFLP primer combinations rendered produced 376 markers, 204 being polymorphic (53.28% polymorphism). AFLP data separated clearly the Kazeroun accession, originating from the warmer Southern region of Iran, from the other 20 accessions. According to the morphological evaluation data, Khansar, Kouhrang and Daran accessions showed the highest means for bulb weight. Cluster analysis based on morphological traits divided the Mooseer germplasms into three main groups. The ITS results indicated that Iranian Mooseer clustered with other A. stipitatum accessions, but with small differences. They were phylogenetically close to Iranian wild edible alliums and clearly differentiated from other domesticated alliums. Separation of three Iranian Mooseers from A. stipitatum samples originated from other countries in two distinct groups according to their ITS sequence shows that probably these two groups have divergent evolutionary paths.
... Based on literature (Stearn 1978, Tzanoudakis 1983, Tzanoudakis and Vosa 1988, Brullo et al. 2001, A. meteoricum was included in the sect. Scorodon Koch, but as highlighted by Brullo et al. (2018), this traditional section is actually an assemblage of various and well-differentiated phylogenetic lineages (see Fritsch and Friesen 2002, Friesen et al. 2006, Nguyen et al. 2008, Hirschegger et al. 2010, Li et al. 2010). ...
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A new species, Allium albanicum, is described and illustrated from Albania (Balkan Peninsula). It grows on serpentines or limestone in open rocky stands with a scattered distribution, mainly in mountain locations. Previously, the populations of this geophyte were attributed to A. meteoricum Heldr. & Hausskn. ex Halácsy, described from a few localities of North and Central Greece. These two species indeed show close relationships, chiefly regarding some features of the spathe valves, inflorescence and floral parts. They also share the same diploid chromosome number 2n =16 and similar karyotype, while seed testa micro-sculptures and leaf anatomy reveal remarkable differences. There are also several morphological features that allow them to be differentiated at specific level. The inclusion of both species into a newly described section Pseudoscorodon of the subgen. Allium is proposed. An analytic key to the species, included in the new section, is also provided.
... Although the embryology of Brodiaea and Dichelostemma is quite similar, the inner integument of the ovule of D. capitatum consists of two cell layers, similar to that of Muilla and Triteleia Douglas ex Lindl., but different from the multilayered inner integument that represents a synapomorphy of Brodiaea and the other Dichelostemma species (Berg 1978(Berg , 1996(Berg , 2003. The morphological evidence for recognizing Dipterostemon is fully supported by the molecular data, which show that Dichelostemma is only monophyletic if D. capitatum is excluded (Pires et al. 2001;Pires & Sytsma 2002;Nguyen et al. 2008;Steele et al. 2012). ...
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Dichelostemma lacuna-vernalis L.W. Lenz was proposed in 1974 for populations of a diminutive Dichelostemma associated with vernal pool terrain. The author of Dichelostemma in the 1993 edition of The Jepson Manual did not accept the new species, reporting that the morphological and ecological characteristics of D. lacuna-vernalis were within the ranges for D. capitatum (Benth.) Alph.Wood. The purpose of this paper was to test the validity of D. lacuna-vernalis using a morphometric analysis of eighteen morphological characters in populations of D. capitatum and D. lacuna-vernalis sampled in the field and by comparing plants of both taxa grown under common garden conditions. The data were subjected to cluster analysis, principal components analysis, and discriminant analysis. The results of the analysis confirm the morphological distinctness of D. lacuna-vernalis and support its recognition as a separate taxon. Based on current taxonomic concepts in the Brodiaeoideae, this taxon is best recognized at subspecies rank, as D. capitatum subsp. lacuna-vernalis (L. W. Lenz) D.W. Taylor. Populations of D. capitatum subsp. lacuna-vernalis are distinguished by their short scapes (ca. 15 cm), inflorescences with one or two flowers, short (≤4 mm) perianth tubes, and outer perianth lobes that are ovate, decurrent at the base, and wider than the inner perianth lobes.
... The internal transcribed spacer (ITS) region of nrDNA is a valuable resource of phylogenetic information at the generic and subgeneric levels (Baldwin 1992, Baldwin et al. 1995, Blattner 2004, Hörandl et al. 2005, and has also proved to be informative for Allium (Dubouzet & Shinoda 1999, Friesen et al. 2000, 2006, Gurushidze et al. 2007, Nguyen et al. 2008, Li et al. 2010. As a result of the molecular studies carried out with the use of the data obtained from ITS gene regions, A. rothii and A. chrysantherum are sister taxa in a weakly supported (PP55/BS-) clade of A. sect. ...
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Allium dönmezii is described as a new species from east Anatolia, Turkey. The molecular marker ITS (Internal Transcribed Spacer of nuclear ribosomal DNA) confirms that the new species belongs to A. sect. Melanocrommyum. The diagnostic characters of the new species are morphologically compared with the related A. woronowii, A. serpentinicum, and A. moderense, as well as with A. rothii and A. chrysantherum. In addition, the ITS regions of A. purpureoviride and A. chrysantherum were sequenced and uploaded on GenBank for the first time.
... For Githopsis and Hemizonia that were not present in the megaphylogeny, we determined their positions in the tree according to the Open Tree of Life and branch lengths according to family-level megaphylogeny. For all congeners, we obtained their relative positions and branch lengths from megaphylogeny, the Open Tree of Life or published genus-specific trees (47)(48)(49)(50)(51)(52)(53). In the cases where branch length was not available for a species (Astragalus rattanii, Calochortus amabilis, Castilleja attenuate, Castilleja rubicundula, Mimulus layneae, and Trifolium obtusiflorum), we used the phylogenetic information of the closest relative within the same genus as a surrogate from the aforementioned sources. ...
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Mechanisms that favor rare species are key to the maintenance of diversity. One of the most critical tasks for biodiversity conservation is understanding how plant-pollinator mutualisms contribute to the persistence of rare species, yet this remains poorly understood. Using a process-based model that integrates plant-pollinator and interspecific pollen transfer networks with floral functional traits, we show that niche partitioning in pollinator use and asymmetric facilitation confer fitness advantage of rare species in a biodiversity hotspot. While co-flowering species filtered pollinators via floral traits, rare species showed greater pollinator specialization leading to higher pollination-mediated male and female fitness than abundant species. When plants shared pollinator resources, asymmetric facilitation via pollen transport dynamics benefited the rare species at the cost of the abundant ones, serving as an alternative diversity-promoting mechanism. Our results emphasize the importance of community-wide plant-pollinator interactions that affect reproduction for biodiversity maintenance.
... The genus Allium of kingdom plantae in family alliaceae, subfamily allioideae, tribe allieae (Chase et al. 2016). The Central Asia and Mediterranean region are known as main center of origin, western north America as small center of biodiversity (Nguyen et al. 2008;Li et al. 2010;Wheeler et al. 2013) of genera Allium and its natural habitat found at Northern hemisphere (Fritsch and Friesen 2002). Anciently alliums have been used as herbs, spices, condiments, medicine, and ornaments (Li et al. 2010). ...
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Alliumsareessential cropsindaily diet for their flavor and medicinal value, which are highly cross pollinated crops, prone to inbreeding, or continuous selfing, and biennial crop cycles import complexity in the alliums improvement. However, interspecific hybridization aided for the introgression of genes responsible for resistance to pests, diseases and abiotic factors, which can minimize or eliminate the use of plant protection agents. Furthermore, the transfer of novel metabolites and odor molecules into edible Allium species thus could be beneficial to human health. It increases the genetic diversity by gaining new gene reservoirs, and useful in the genetic improvement of alliums. In this scenario, the wild relatives of alliums could be used to introduce resistant genes, as the genus Allium has an untapped gene pool. . among alliums for cross compatibility and desirable trait introgression in this review. As a result, it gives an insight to the breeder to use specific species to increase their genetic base. However, understanding species compatibility is a need for commencing a hybridization program and an important aspect in introgression breeding. We reviewed the attempts at interspecific hybridization
... Effective molecular approaches should cover the variability of the genome as a whole and correlate with the phenotypic variability of the species [12]. The study of the genetic biodiversity of the genus Allium is carried out using the analysis of individual genes from the chloroplast and nuclear genome [65,66]. The application of these approaches is effective for species identification. ...
Article
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Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology.
... Most taxa produce remarkable amounts of cysteine sulphoxides causing the well-known characteristic odor and taste (Friesen et al. 2006). Allium is distributed naturally in the northern hemisphere and in South Africa, mostly in regions with dry seasons (De Sarker et al. 1997;Friesen et al. 2006;Nguyen et al. 2008;Neshati and Fritsch 2009). The classification of Allium by Friesen et al. (2006) based on molecular phylogenetic analyses includes 15 subgenera and 56 sections. ...
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Allium section Rhizirideum is reviewed for South Korea and neighboring northeastern China based on critical observation of wild populations and herbarium materials. Species delimitations are re-evaluated on the basis of morphological and somatic chromosome numbers, resulting in the recognition of five species. Allium dumebuchum from Ulleungdo Island, South Korea, is described as a new species. This species is most similar to A. senescens due to its habits, but is clearly distinguished particularly by its rhomboid scapes in cross-secion, light purple perianth color, entire and narrowly triangular inner filaments, and flowering season from late September. One previously recognized species is placed into synonymy: A. pseudosenescens (under A. senescens ). Photographs and a key to species of Allium section Rhizirideum in South Korea and northeastern China are provided in addition to information on nomenclatural types, synonymies, chromosome numbers, distribution, and specimens examined.
... Genus Allium has been classified into subgenera and sections based on morphological characteristics such as shape of the rhizome/bulb; shape and size of perianth, filament, pistil, capsule, seed; anatomy of root, leaf, scape, ovary; and chromosome number (Hanelt et al., 1992;Friesen et al., 2006;Neshati and Fritsch, 2009;Nguyen et al., 2008;Choi and Oh, 2011). Based on morphology of rhizome/bulb characters and molecular study Allium has been grouped phylogenetically into three main evolutionary lines (Friesen et al., 2006;Li et al., 2010). ...
... Allium Linneaus (1753: 294) is one of the largest monocot genera with about 1,000 species (Govaerts et al. 2020) naturally distributed throughout the northern hemisphere (Stearn 1978, 1992, Fritsch & Friesen 2002. The main centres of biodiversity are located in Southwestern and Central Asia and in the Mediterranean region, a smaller centre is found in western North America (Friesen et al. 2006, Nguyen et al. 2008, Li et al. 2010, Wheeler et al. 2013. The genus is characterized by bulbs (often in rhizomes) enclosed in membranous, fibrous or reticulate tunics, free or basally connate tepals and often a subgynobasic style (Friesen et al. 2006). ...
Article
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Allium toksanbaicum from South East Kazakhstan is described as a new species. Molecular markers reveal a close relationship to A. obliquum and some other central Asian species of the section Oreiprason. We investigated the phylogenetic relationship of the new species based on sequences of two chloroplast spacers (rpl32-trnL and trnQ-rps16) and the nuclear ribosomal DNA internal transcribed spacer (ITS) region. The new species is diploid with a chromosome number of 2n = 2x = 16. A detailed morphological description, illustrations and karyotype features of the new species are given. With its falcate leaves, the new species is very similar to A. carolinianum from the section Falcatifolia, but in the shape of the inflorescence and flowers it is very different from it. From A. obliquum it differs for the purple colour of flowers and filaments, as well as the presence of teeth at the base of inner stamens.
... Other authors have focused on the origins and evolution of the main species of Allium [4,11,12], the phylogeny of the Cepa (Mill.) section [13] and the phylogenetic configuration of Western North American species [14]. ...
Article
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The genus Allium covers more than 800 species, signaling among the largest among monocotyledons. The genus contains many economically important species, including garlic, leeks, onions, chives and Chinese chives. Due to the high conservation of chloroplast genomes compared to nuclear genomes and mitochondrial genome, sequence of chloroplasts in Amaryllidaceae have been consistently used for species identification and various in silico programs and strategies have been used to identify, characterize and compare plastid genome regions. Plastome from 15 species of the Amaryllidaceae family revealed similarity in both sequences and in the organization of their gene regions. The base pairs (bp) number ranged from 145,819 (A. paradoxum) to 159,125 (A. ursinum). In respect the GC content, the species presented a variation between 36.7% (A. schoenoprasum and A. sativum) and 37.5% (A. coddii) and the gene space ranged from 84.760 (A. paradoxum) to 94.766 (A. sativum). The genes that encode proteins showed values between 78 (A. paradoxum) to 89 (A. cepa). Phylogenetic trees acquired through alignment of complete plastomas and the plastidial matK gene revealed similarity to the proposed classification for the family. For the genus Allium, there was the formation of three clades with perfect correspondence of the clusters to the three evolutionary lines of the genus.
... Many economically important species are included, such as garlic, leek, onion and shallot. Two centres for Allium species diversity were suggested in previous studies (Fritsch and Friesen, 2002;Nguyen et al., 2008), one is from the Mediterranean Basin to central Asia and Pakistan, and the other is in North America. It is widely accepted that the Allium species can be classified into 15 subgenera and 72 sections (Friesen et al., 2006). ...
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Background and aims: The genus Allium L., one of the largest monocotyledonous genera and one that includes many economically important crops with nutritional and medicinal value, has been the focus of classification or phylogeny studies for centuries. Recent studies suggested that the genus can be divided into 15 subgenera and 72 sections, which were further classified into three evolutionary lineages. However, the phylogenetic relationships reconstructed by one or two loci showed weaker support, especially for the third evolutionary lineage, which might not show the species relationships very clearly and could hinder further adaptive and evolutionary study. Methods: In this study, a total of 39 complete chloroplast genomes of Allium (covering 12 Allium subgenera) were collected, and combining these with 125 species of plastomes from 19 other families of monocots, we reconstructed the phylogeny of the genus Allium, estimated the origin and divergence time of the three evolutionary lineages and investigated the adaptive evolution in this genus and related families. Results: Our phylogenetic analysis confirmed the monophyly and three evolutionary lineages of Allium, while new species relationships were detected within the third evolutionary lineage. The divergence time of the three evolutionary lineages was estimated to be in the early Eocene to the middle Miocene, and numerous positive selected genes (PSGs) and PSGs with high average Ka/Ks values were found in Allium species. Conclusions: Our results detected a well-supported phylogenetic relationship of Allium. The PSGs and PSGs with high Ka/Ks values, as well as diversified morphologies, complicated chromosome characteristics and unique reproductive modes may play important roles in the adaptation and evolution of Allium species. This is the first study that conducted phylogenetic and evolutionary analyses on the genus Allium combined with the plastome and morphological and cytological data. We hope that this study can contribute to further analysis of Allium for other researchers.
... Its remarkable taxonomic diversity is accompanied by occurrence of polyploidy (4x, 5x, 6x, 8x and 10x) and a high disploidy as shown by several base chromosome numbers x = 7, 8, 9, and 11 (Peruzzi et al. 2017). It constitutes an interesting group of species which has led to numerous molecular studies in order to elucidate infrageneric relationships and sectional classifications (Nguyen et al. 2008;Fritsch et al. 2010;Gurushidze et al. 2010;Wheeler et al. 2013;Herden et al. 2016;Li et al. 2010Li et al. , 2016Sinitsyna et al. 2016). The origin of Allium crops and ornamental taxa were also investigated (Friesen et al. 1999;Gurushidze et al. 2007;Hirschegger et al. 2010;Veiskarami et al. 2019). ...
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The economically important Allium ampeloprasum L. represents a polyploid complex, comprising hexa- and octoploid Great Headed Garlic horticultural cultivars (6x–8x GHG) and several traditional varieties of the tetraploid (4x) leeks (Leek, Bulbous leek, Kurrat and Pearl onion). Its wild representatives were indicated as rare in the Mediterranean region. This study aims to explore the diversity and origin of polyploidy in this complex, including its wild relatives A. baeticum Bossier and A. guttatum Steven with particular focus on the poorly investigated North-African region. Natural populations were sampled in Algeria in various bioclimatic conditions, then subjected to karyological and molecular phylogenetic analyses based on nuclear rDNA ITS region and chloroplast trnL–trnF and trnD–trnT intergenic spacers. Comparative analyses included available Genbank accession sequences representing old-world relatives. Chromosome count surveys revealed an unexpected higher occurrence of diploid (2n = 16) than tetraploid (2n = 32) cytotypes. The phylogenetic analyses first allowed positioning the Algerian material within the A. ampeloprasum complex. Interestingly, all the Algerian diploid and tetraploid populations from A. ampeloprasum and A. baeticum form a distinct monophyletic group. The results provide novel and robust evidence demonstrating that the North African diploid A. ampeloprasum genetic pool widely contributed as a source of progenitors not only for the A. ampeloprasum and A. baeticum Algerian tetraploids, but also in the formation of the GHG and Leek cultivated allopolyploids. Therefore, the North African populations emerge as an important reservoir of new wild genetic resources of great interest for tracing the origin of crop domestication and for breeding programs of cultivated varieties.
... Allium ampeloprasum L. includes commonly cultivated vegetables such as leek, great-headed garlic, pearl onion, kurrat, and Persian leek which share the same name, as well as wild representatives (wild leek or broadleaf wild leek), although there is still controversy regarding the taxonomy of this species [57][58][59]. The use of native species is very common in the Mediterranean basin, either as food or as ingredients in folk medicine, while ethnopharmacological studies confirm the popularity of the species as an antihypertension remedy [60,61]. ...
Article
Background There is increasing interest from the pharmaceutical and food industry in natural antioxidant and bioactive compounds derived from plants as substitutes for synthetic compounds. The genus Allium is one of the largest genera, with more than 900 species, including important cultivated and wild species, having beneficial health effects. Objective The present review aims to unravel the chemical composition of wild Allium species and their health-related effects, focusing on the main antioxidant compounds. For this purpose, a thorough study of the literature was carried out to compile reports related to health effects and the principal bioactive compounds. Considering the vast number of species, this review is divided in subsections where the most studied species are presented, namely Allium ampeloprasum, A. flavum, A. hookeri, A. jesdianum, A. neapolitanum, A. roseum, A. stipitatum, A. tricoccum, and A. ursinum, with an additional composite section for less studied species. Conclusion The genus Allium includes several wild species, many of which are commonly used in traditional and folklore medicine while others are lesser known or are of regional interest. These species can be used as sources of natural bioactive compounds with remarkable health benefits. Several studies have reported these effects and confirmed the mechanisms of action in several cases, although more research is needed in this field. Moreover, considering that most of the studies refer to results obtained from species collected in the wild under uncontrolled conditions, further research is needed to elucidate the effects of growing conditions on bioactive compounds and to promote the exploitation of this invaluable genetic material.
... Most taxa produce remarkable amounts of cysteine sulphoxides causing the well-known characteristic odor and taste (Friesen et al., 2006). Allium is distributed naturally in the northern hemisphere and in South Africa, mostly in regions with dry seasons (de Sarker et al., 1997;Friesen et al., 2006;Nguyen et al., 2008;Neshati and Fritsch, 2009). The classification of Allium by Friesen et al. (2006) based on molecular phylogenetic analyses includes 15 subgenera and 56 sections. ...
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Allium ulleungense (subg. Anguinum, Amaryllidaceae), from Ulleungdo Island, Korea, is described as a new species. It is clearly distinguished from its close relatives, A. microdictyon and A. ochotense, by its broader leaves and larger whitish perianth and by its diploid chromosome number, which is 2n = 2x = 16. The lengths of the chromosomes range from 11.3 to 15.75 μm. Molecular phylogenetic analyses using nuclear and chloroplast markers also clearly indicate that A. ulleungense is genetically distinct from other species of the subg. Anguinum.
... Most of the first evolutionary line species belong to the subgenus Amerallium, being the largest subgenus of Allium in this lineage. The classification and phylogeny of this taxon is the main focus of molecular studies (Wheeler et al., 2013;Samoylov et al., 1995;Samoylov et al., 1999;Nguyen et al., 2008). The morphology and ecology of American and the Old-World species of the subg. ...
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... The main centres of biodiversity are located in arid and sub-arid regions of Southwestern and Central Asia, and in the Mediterranean region. The significantly smaller centre is in western North America [5,[7][8][9]). The genus is characterized by bulbs (often formed on rhizomes) enclosed in membranous, fibrous, or reticulate tunics, free or basally connate sepals, and usually a subgynobasic style [7]. ...
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Polymorph Allium pallasii s.l. from monotypic A. sect. Pallasia was studied using a wide spectrum of methods and divided into two clearly morphologically, geographically, cytologically and genetically isolated species: A. pallasii s. str.—North-East Kazakhstan, Western Siberia, and the Altai Mountains; A. caricifolium—Kyrgyzstan, Northwest China, South-East Kazakhstan until Zaysan Lake in the east. Despite serious genetic differences, both species are sisters and are related to species of the A. sect. Codonoprasum (Subg. Allium). Allium caricifolium differs from A. pallasii s. str. by taller stems, dense inflorescence, and with filaments longer than perianth. The possible phylogenetic reasons for the separation of these species are discussed. A nomenclature analysis of synonyms was carried out.
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Allium is a particularly species rich (more than 800 species) and economically important genus, with numerous taxonomic problems at all levels of classification. In this study, we try to uncover the phylogenetic relationships in the common leek Allium ampeloprasum based on selected samples of this species and its putative relatives in sect. Allium from Iran. The silica‐dried leaf samples of 56 accessions representing 23 species of Allium were sequenced for this study, 53 sequences of nrDNA ITS, 35 sequences of plastid rps16 and 52 sequences of trnL‐F were generated and several accessions were extracted from GenBank in order to cover all recognized main lineages in the genus. Maximum Parsimony and Bayesian Inference generated similar trees, but the placement of A. ampeloprasum and its relatives differs slightly in the nuclear versus plastid datasets. In the nrITS tree A. ampeloprasum is retrieved in a highly supported clade with A. iranicum, while in the combined plastid tree A. ampeloprasum formed a highly supported clade with A. vineale. This supports the hypothesis of a possible hybrid origin of A. ampeloprasum. Allium iranicum formed a clade in the plastid tree, but was resolved as paraphyletic in the nrITS tree, probably due to presence of multiple non‐concerted copies of nrITS. Close relationships are suggested between following species: A. aznavense and A. wendelboi with A. talyschense, A. erubescens and A. rotundum with A. scorodoprasum, and A. abbasii with A. phanerantherum. This article is protected by copyright. All rights reserved.
Chapter
The phylogenetic relationships within the angiosperms have been and continue to be a field of active research in plant systematics. Much progress has been made with the use of phylogenetic methodologies and algorithms and the elucidation of morphological, anatomical, embryological, palynological, karyological, chemical, and molecular evolution. The more recent use of entire plastome and cistron genomes and multiple nuclear genes has been particularly useful in assessing higher level angiosperm relationships. Whole genomes have been obtained for a number of plants, data that may be commonplace in the near future. But, research continues, especially with respect to certain recalcitrant groups. For a more precise understanding of relationships within a particular group, there is no substitute for consulting the most recent, primary scientific literature.
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Allium yamadagensis is described here as a new species. This taxon belongs to the genus Allium section Allium and grows in Malatya Province (eastern Anatolia, Turkey). It is a narrowly distributed species and morphologically most similar to A. sintenisii, A. erzincanicum, A. ekimianum and A. asperiflorum but it is clearly differentiated due to scabrid pedicel surfaces, presence of bracteoles at pedicel bases, inner filament lengths, colour, length and surface of tepals. A comprehensive description, distribution map, identification key, and detailed illustrations are provided for A. yamadagensis.
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— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
Article
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data, In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Article
Chloroplast DNA (cpDNA) variability has been examined in 16 Allium species of the subgenera Amerallium and Bromatorrhiza according to the recently accepted classification in order to test conflicting ideas of their taxonomic relationships. Combinations of ten restriction enzymes and nine heterologous cpDNA probes were used to identify more than 1000 restriction fragments, 197 of these were informative. A phenetic analysis was carried out, and the resulting UPGMA and Neighbour joining dendrograms allow us to divide the 16 species into two groups. The first one includes species of several American sections of subg. Ameraltium, the second group combines all Old World species of subg. Amerallium and subg. Bromatorrhiza. The Bromatorrhiza accessions are interspersed among the typical Ameralliums and are separated from one another, thus confirming the artificial character of this group, which had to be dissolved and incorporated into subg. Amerallium. Two species of the former subg. Bromatorrhiza cluster with the South-European sects. Briseis and Narkissoprason, whereas the two other species with a basic chromosome number x = 8 are rather isolated within subg. Amerallium. These E Himalayan–SW Chinese plants take an intermediate position between the two large x = 7 and x = 8 subgroups of Allium, suggesting a key role for them as a basic group in the diversification process of the genus.
Article
Allium is a large variable genus containing ≅ 700 species, among them the economically important crops bulb onion, garlic and leek and many other crop species of minor or local importance. As the methods became available and more refined, systematic studies using biochemical and molecular markers were published to complement and offset the growing amount of data based on morphological, anatomical and other traditional approaches. Using isozymes and later restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNAs (RAPDs), phylogenetic problems were addressed at all systematic levels of the genus and the interrelationships among crop species and their close relatives. The analysis of hybrid plants is another important application of molecular markers. Markers allow verification of the hybrid's cytoplasm, the composition of the nuclear genome, and investigation of introgression in backcrossing experiments.
Article
The utility of the chloroplast DNA (cpDNA) restriction mapping of 18 Allium species of the subgenera Amerallium, Melanocrommyum, Allium and Bromatorrhiza have been cladistically analysed, according to the recently proposed paraphyletic origin of the subgenera Bromatorrhiza and Amerallium. The size of the restriction fragment and the precise fragment order of A. zebdanense cpDNA were determined for 10 enzymes. The parsimony analysis confirms strongly the subdivision of the genus Allium in two main groups with different basic chromosome numbers (x = 7 and x = 8), which had been earlier proposed on the basis of morphological, karyological, anatomical and other molecular markers. Subgenus Amerallium (x = 7) itself is distinctly differentiated into two main subgroups, representing the Eurasian and the American taxa. The subgeneric status of Bromatorrhiza has to be cancelled, its members must be subordinated as sections to subgenus Amerallium (sect. Bromatorrhiza) and to one of the Eurasian subgenera with x = 8 (probably to the subgenus Allium or Rhizirideum).
Article
 Phylogenetic analysis of ITS DNA sequences of various Old and New World Alliums suggests the reinclusion of Nectaroscordum and affirms the reestablishment of Caloscordum as subgenera of genus Allium. The results sanction the elimination of the Old World Allium species from subg. Amerallium Traub and endorse Wendelbo’s definition of subg. Molium (excluding sect. Porphyrason).
Article
 Sequence analysis of the ITS region of nuclear ribosomal DNA from subgeneric representatives of Allium L. produced phylogenetic trees which concurred with previous conclusions based on classical taxonomy. Phylogenetic analysis revealed a closer relationship between Nectaroscordum siculum and Allium cernuum (representing Amerallium) than between A. cernuum and the rest of the Allium species employed in this study. The phylogeny of subg. Melanocrommyum based on ITS sequences largely agreed with inferences made by previous researchers based on morphology or a restriction analysis of chloroplast DNA. However, the phylogenetic positions of Allium protensum and Allium macleanii based on ITS sequences did not correspond to their morphological similarity with Allium schubertii and Allium giganteum, respectively.
Article
Subgrade serpentine substrates are exceptionally difficult to revegetate due to multiple limitations including low N, P, and K, low Ca:Mg molar ratios, high levels of heavy metals including Ni, Cr, and Co, low organic matter, low CEC, and low water holding capacity. To examine the influence of plant origin on the success of the revegetation of serpentine substrates, granite and serpentine accessions of Achillea millefolium were grown on subgrade serpentine substrate amended with yard waste compost, slow-release NPK fertilizer, and/or CaSO4 · 2H2O (gypsum). The goals of this study were to: (1) identify the substrate amendment combination that maximized establishment of A. millefolium on serpentine substrate, (2) compare seedling establishment, survival, and growth of the serpentine and granite A. millefolium accessions in order to determine if a serpentine edaphic ecotype of A. millefolium exists and if this ecotype is superior to the granite accession for the establishment of vegetation on serpentine substrate and (3) if a serpentine edaphic ecotype of A. millefolium does exist, what physiological features with respect to mineral nutrition convey a higher tolerance of serpentine for this ecotype than the nonserpentine ecotype. Seedling establishment, survival, and growth were greatest for A. millefolium when the subgrade serpentine substrate was amended with 30% (v/v) compost and 220mgkg substrate−1 each of N, P, and K. The serpentine A. millefolium accession displayed a greater tolerance of the subgrade serpentine substrate, serpentine topsoil, and the amended subgrade serpentine substrate than the granite accession. Higher capacity of the serpentine A. millefolium accession for selective Ca translocation from roots to the shoot resulted in a significantly higher shoot Ca:Mg molar ratio than the granite accession and appeared to be the most important physiological feature conveying greater tolerance of the serpentine accession for serpentine substrates.
Article
The utility of chloroplast DNA variation for checking a recently proposed infrageneric classification of the genusAllium was tested. cpDNA restriction patterns of 49 species representing the main subgenera, sections, and subsections of the existing classification were compared. 363 different fragments generated by 4 restriction enzymes were identified and analysed by UPGMA clustering. The resulting phenogram largely confirms the subgeneric classification based on an integration of morphological and other methods.
Article
Many species of the paleotropical pioneer tree genus Macaranga Thou. (Euphorbiaceae) live in association with ants. Various types of mutualistic interactions exist, ranging from the attraction of unspecific ant visitors to obligate myrmecophytism. In the latter, nesting space and food bodies are exchanged for protection by highly specific ant partners (mainly species of the myrmicine genus Crematogaster). As a first step toward elucidating the coevolution of ant–plant interactions in the Macaranga–Crematogaster system, we have initiated a molecular investigation of the plant partners' phylogeny. Nuclear ribosomal DNA internal transcribed spacer (ITS) sequences were analyzed for 73 accessions from 47 Macaranga species, representing 17 sections or informally described species groups. Three accessions from the putative sister taxon Mallotus Lour, were included as outgroups. Cladograms of the ITS data revealed Macaranga to be nested within Mallotus. ITS sequences are highly similar within section Pachystemon s.str., suggesting a relatively recent and rapid radiation of obligate myrmecophytes within this section. Forty-three accessions, mainly of ant-inhabited species, were additionally investigated by random amplified polymorphic DNA (RAPD) and microsatellite-primed PCR (MP-PCR) techniques. Phenetic analysis of RAPD and MP-PCR banding profiles generally confirmed the ITS results. Best resolutions for individual clades were obtained when ITS and RAPD/MP-PCR data were combined into a single matrix and analyzed phenetically. The combined analysis suggests multiple (four) rather than a single evolutionary origin of myrmecophytism, at least one reversal from obligate myrmecophytism to nonmyrmecophytism, and one loss of mutualistic specifity.
Article
The 3' region of the external transcribed spacer (ETS) of 18S-26S nuclear ribosomal DNA was sequenced in 19 representatives of Calycadenia/Osmadenia and two outgroup species (Compositae) to assess its utility for phylogeny reconstruction compared to rDNA internal transcribed spacer (ITS) data. Universal primers based on plant, fungal, and animal sequences were designed to amplify the intergenic spacer (IGS) and an angiosperm primer was constructed to sequence the 3' end of the ETS in members of tribe Heliantheae. Based on these sequences, an internal ETS primer useful across Heliantheae sensu lato was designed to amplify and sequence directly the 3' ETS region in the study taxa, which were the subjects of an earlier phylogenetic investigation based on ITS sequences. Size variation in the amplified ETS region varied across taxa of Heliantheae sensu lato from approximately 350 to 700 bp, in part attributable to an approximately 200-bp tandem duplication in a common ancestor of Calycadenia/Osmadenia. Phylogenetic analysis of the 200-bp subrepeats and examination of apomorphic changes in the duplicated region demonstrate that the subrepeats in Calycadenia/Osmadenia have evolved divergently. Phylogenetic analyses of the entire amplified ETS region yielded a highly resolved strict consensus tree that is nearly identical in topology to the ITS tree, with strong bootstrap and decay support on most branches. Parsimony analyses of combined ETS and ITS data yielded a strict consensus tree that is better resolved and generally better supported than trees based on either data set analyzed separately. We calculated an approximately 1.3- to 2.4-fold higher rate of sequence evolution by nucleotide substitution in the ETS region studied than in ITS-1 + ITS-2. A similar disparity in the proportion of variable (1.3 ETS:1 ITS) and potentially informative (1.5 ETS:1 ITS) sites was observed for the ingroup. Levels of homoplasy are similar in the ETS and ITS data. We conclude that the ETS holds great promise for augmenting ITS data for phylogenetic studies of young lineages.
Article
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Infrageneric grouping of Allium—the Gatersle-ben approach
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How many species of Allium are known? Kew Magazine 9
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