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Data from: Phylogenetic relationships of Iranian Allium sect. Allium (Amaryllidaceae, Allioideae) as inferred from nrDNA ITS, cpDNA rps16 and trnL–F sequences
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 (A. 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.
Fig. 4 in Phylogeny, classification and biogeography of Philotheca sect. Erionema (Rutaceae) based on nrDNA sequences
Fig. 4. Examples of leaf variation within the two nrDNA groups in Philotheca myoporoides subsp. myoporoides. Drawn from representative leaves of samples used in this study. NP, National Park; SF, State Forest.
Fig. 3 in Phylogeny, classification and biogeography of Philotheca sect. Erionema (Rutaceae) based on nrDNA sequences
Fig. 3. Distribution of Philotheca myoporoides subsp. myoporoides, including the distribution of samples used in this study (filled circles, with locality names given) and the nrDNA groups these belong to. Grey shading shows the distribution of specimens that are morphologically assigned to the 'southern' nrDNA group; samples from other areas are assigned here to the 'northern' group. Map is based on records in the Australasian Virtual Herbarium and our examination of specimens from MEL, NSW and CANB (primarily in terms of leaf shape, leaf size and habitat). NP, National Park; SF, State Forest.
Fig. 1 in Phylogeny, classification and biogeography of Philotheca sect. Erionema (Rutaceae) based on nrDNA sequences
Fig. 1. Distributions of taxa of Philotheca sect. Erionema. Maps are based on those of Wilson (2013) and Rozefelds (2001a, 2001b) plus our examination of herbarium material. Note that infraspecific taxa for P. buxifolia, P. brucei and P. scabra are not mapped separately.
Fig. 2 in Phylogeny, classification and biogeography of Philotheca sect. Erionema (Rutaceae) based on nrDNA sequences
Fig. 2. Majority rule consensus tree based on BI analysis of combined ITS and ETS dataset, showing mean branch lengths. Bayesian posterior probabilities are shown (either first, or above branches) along with MP bootstrap values (either second or below branches; only shown where bootstrap support is>50%). Dashed branches were not present on the MP strict consensus tree.
FIGURE 1 in Systematic position of Rivina humilis var. humilis, R. humilis var. bracteata and R. bengalensis based on nrDNA ITS and cpDNA rbcL & trnH-psbA sequence data
FIGURE 1. Best ML tree retrieved after analysing 43 taxa of family Phytolaccaceae. The best fit model of evolution GTR+G+I. The tree rooted at Hilleria latifolia (Lee et al. 2013).
FIGURE 3. A–E in Systematic position of Rivina humilis var. humilis, R. humilis var. bracteata and R. bengalensis based on nrDNA ITS and cpDNA rbcL & trnH-psbA sequence data
FIGURE 3. A–E: Rivina humilis L.var. bracteata; A) Habit (inset flowers); B) Infructescence; C) Bract; D) Fruit; E) Seed; F–J: Rivina humilis L. var. humilis; F) Habit (inset flower); G) Infructescence; H) Bract; I) Fruit; J) Seed; K–O: Rivina bengalensis S. C. Srivastava et T. K. Paul; K) Habit (inset flowers); L) Infructescence; M) Bract; N) Fruit; O) Seed.
FIGURE 1. Phylogenetic tree derived from ITS1 and ITS2 in Taxonomic identity of the Iranian diploid Triticum as evidenced by nrDNA ITS analysis
FIGURE 1. Phylogenetic tree derived from ITS1 and ITS2 sequences inferred by the Neighbor-Joining method using the Kimura 2- parameter model; all bootstrap values over 50% are shown. Sequences obtained from the NCBI are marked with the sequence accession numbers. Aegilops tauschii sequence was defined as an outgroup in the analysis. Clades 1 and 2 are associated with Triticum monococcum s. lat. and T. urartu, respectively.
FIGURE 2 in Taxonomic identity of the Iranian diploid Triticum as evidenced by nrDNA ITS analysis
FIGURE 2. Distribution map of Triticum monococcum subsp. aegilopoides (□) and Triticum urartu (■) in Iran.
FIGURE 1 in Molecular phylogenetics of Pterocyclus (Apiaceae) based on nrDNA ITS sequences: revised circumscription with a restored species
FIGURE 1. Consensus tree obtained from maximum likelihood analysis of sixty-three nrDNA ITS sequences. Numbers above and below nodes are bootstrap support and posterior probability presented as percentages, respectively. The newly sampled accessions are shown in bold.
FIGURE 2. A in Molecular phylogenetics of Pterocyclus (Apiaceae) based on nrDNA ITS sequences: revised circumscription with a restored species
FIGURE 2. A) Lectotype of Pterocyclus wolffianus Fedde ex H. Wolff from E (E00000149); B) Lectotype of Pterocyclus forrestii (Diels) Pimenov & Kljuykov from E (E00000166); C) Isolectotype of Pterocyclus angelicoides (DC.) Klotzsch from K (K000685357); D) Isotype of Pterocyclus rotundatus (DC.) Pimenov & Kljuykov from K (K000685356).
FIGURE 4 in Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters
FIGURE 4. Mericarp morphology of Meeboldia yunnanensis, S. microloba, S. thibetica, Tongoloa zhongdianensis and Hymenidium apiolens (a–c, d–f, g–i, j–l and m–o). Fruit views are dorsal side, commissural side and transverse section for each row from left to right. Scale bars are 1 mm. Terminologies followed Kljuykov et al. (2004). cv = commissural vittae; lr = lateral rib; mar = marginal rib; mer = median rib; vv = vallecular vittae.
FIGURE 1 in Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters
FIGURE 1. Phylogenetic tree of Acronema clade (A) and Sinodielsia clade (B) derived from Bayesian inference analysis using the ITS dataset. The numbers above and below the nodes are BI-PP and ML-BS presented as percentages, respectively (> 50%). Those nodes not occurring in the ML tree are indicated by pound symbols (#). The names of the clades follow the study of Downie et al. (2010).
FIGURE 6 in Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters
FIGURE 6. Habit and morphology of Sinodielsia microloba. a. Habit. b. Compound umbels. c. Flowers. d. Cauline leaf. e. Bracts. f. Bracteoles. g. Basal leaves. h. Root. i. Fruits.
FIGURE 3 in Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters
FIGURE 3. Specimen and fruits of Meeboldia achilleifolia. a. Specimen of M. achilleifolia (From herbarium BM, barcode BM000622295, Wallich 568 (Natural History Museum 2014)). b. Attachment on the specimen with note "Meeboldia 3402 Type of Meeboldia". c. Morphology of fruits in the attachment. d. Fruits drawing of M. achilleifolia from previous research (Pu & Peng 2005).
FIGURE 5 in Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters
FIGURE 5. Diagnostic morphological characters of Meeboldia yunnanensis from Kunming, Yunnan. a. Habit. b–c. Compound umbels. d. Basal leaf. e. Root. f. Fruits.
FIGURE 2 in Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters
FIGURE 2. Phylogenetic tree of Meeboldia, Sinodielsia and their relatives derived from Bayesian inference analysis using concatenated rpl16 and rps16 introns dataset. The numbers above and below the nodes are BI-PP and ML-BS presented as percentages, respectively (> 50%). Those nodes not occurring in the ML tree are indicated by pound symbols (#). The names of the clades follow the study of Downie et al. (2010).
FIGURE 7 in Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters
FIGURE 7. Terminal leaflets of basal leaves, from 3 populations of Meeboldia yunnanensis and 1 population of Sinodielsia delavayi. Scale bars are 10 mm. P1. Population of M. yunnanensis from Kunming. P2. Population of S. delavayi from Baisha River, Eryuan. P3. Population of M. yunnanensis from Haba village, Zhongdian. P4. Population of M. yunnanensis from Tiger Leaping Gorge, Zhongdian.
Data from: Phylogenetic relationships of Iranian Allium sect. Allium (Amaryllidaceae, Allioideae) as inferred from nrDNA ITS, cpDNA rps16 and trnL–F sequences
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nrDNA internal and external transcribed spacer sequences for investigating the systematics of Dieteria
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