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FIGURE 5 in Molecular phylogeny of Onobrychis sect. Onobrychis (Fabaceae-Hedysareae) with insights into its taxonomy and character evolution

FIGURE 5. Character evolution of wing/standard ratio optimized on the Bayesian tree obtained from nr DNA ITS dataset. Two character states short-winged petal ≤ 0.5 vs. long-winged petal> 0.5

FIGURE 4 in Molecular phylogeny of Onobrychis sect. Onobrychis (Fabaceae-Hedysareae) with insights into its taxonomy and character evolution

FIGURE 4. Character evolution of life form optimized on the Bayesian tree obtained from nr DNA ITS dataset. Two character states perennial vs. annual

FIGURE 3 in Molecular phylogeny of Onobrychis sect. Onobrychis (Fabaceae-Hedysareae) with insights into its taxonomy and character evolution

FIGURE 3. Fifty percent majority rule consensus tree resulting from Bayesian inference of the combined nuclear and plastid dataset (nrDNA+cp). Numbers above branches are posterior probabilities (PP) and numbers below the branches are likelihood bootstrap values; values <50% are not shown.

FIGURE 1 in Molecular phylogeny of Onobrychis sect. Onobrychis (Fabaceae-Hedysareae) with insights into its taxonomy and character evolution

FIGURE 1. Fifty percent majority rule consensus tree resulting from Bayesian inference of the nrDNA ITS dataset. Numbers above branches are posterior probabilities (PP) and numbers below the branches are likelihood bootstrap values; values <50% are not shown.

FIGURE 2 in Molecular phylogeny of Onobrychis sect. Onobrychis (Fabaceae-Hedysareae) with insights into its taxonomy and character evolution

FIGURE 2. Fifty percent majority rule consensus tree resulting from Bayesian inference of the combined plastid dataset (ndhF-rlp32, rpl32-trnL (UAG) and trnG (UCC) -trnS (GCU)). Numbers above branches are posterior probabilities (PP) and numbers below the branches are likelihood bootstrap values; values <50% are not shown.

opencc-zeroJun 2023View details →

Supplementary material 2 from: Du F-C, Li Y-H, Xu K-D (2023) Morphology and molecular phylogeny of Pleurosigma pacificum sp. nov. (Pleurosigmataceae), a new tropical pelagic species from the Western Pacific Ocean. PhytoKeys 227: 99-108. https://doi.org/10.3897/phytokeys.227.103890

Maximum parsimony (MP) phylogenetic trees based on the concatenated SSU rDNA and rbcL gene sequences

FIGURE 2 in Panellus microspermus sp. nov. (Agaricales, Basidiomycota) evidenced by the morphological characters and molecular phylogeny

FIGURE 2. Basidiomata of Panellus microspermus (Holotype, Dai 24286). A Basidiomata soaked in 3% KOH for 30 minutes. B Basidiomata in situ. Scale bars: A, B = 1.0 cm. Photo by: Qiu-Yue Zhang.

FIGURE 1 in Panellus microspermus sp. nov. (Agaricales, Basidiomycota) evidenced by the morphological characters and molecular phylogeny

FIGURE 1. Phylogeny of Mycenaceae by ML analyses based on combined ITS + nLSU sequences. Branches are labeled with maximum likelihood bootstrap ≥50 % and Bayesian posterior probabilities ≥0.90, respectively. New species are indicated in bold.

FIGURE 3 in Panellus microspermus sp. nov. (Agaricales, Basidiomycota) evidenced by the morphological characters and molecular phylogeny

FIGURE 3. Microscopic structures of Panellus microspermus (Holotype, Dai 24286). a Basidiospores. b Hyphae from pileus. c A section of lamellar trama, including pleurocystidia, cheilocystidia, basidia, and basidioles. d Dichophysial hyphae and pileocystidia from pileipellis. Drawings by: Qiu-Yue Zhang.

FIGURE 6 in Molecular phylogeny and taxonomy of the genus Nanocnide (Urticaceae) with particular attention to the Ryukyu Islands endemic N. lobata

FIGURE 6. The phylogenetic tree of Nanocnide compared to the key. The labels A, B and C on the tree branches correspond to the distinguishing morphologies in the key. The up and down of the labels also correspond to the order of the key. For example, the upper branch with the label A corresponds to the first key of A.

FIGURE 4. A in Molecular phylogeny and taxonomy of the genus Nanocnide (Urticaceae) with particular attention to the Ryukyu Islands endemic N. lobata

FIGURE 4. A photography of a staminate flower of N. japonica (left) and its hollow (right). The hollow is arrowed and edged by a broken line. (Japan, Chiba Pref., Katori, 28 March 2018.)

FIGURE 3. Genetic structure between N. lobata and N in Molecular phylogeny and taxonomy of the genus Nanocnide (Urticaceae) with particular attention to the Ryukyu Islands endemic N. lobata

FIGURE 3. Genetic structure between N. lobata and N. pilosa based on averaged MIG-seq data inferred using structure. The sample 1–4 and 5–9 correspond to N. lobata and N. pilosa. More precisely, the numbers correspond to the samples as follows: 1: R2. 2: R9. 3: R10. 4: R19. 5: R23. 6: KY18. 7: 33028. 8: H30528. 9: H30337.

FIGURE 2 in Molecular phylogeny and taxonomy of the genus Nanocnide (Urticaceae) with particular attention to the Ryukyu Islands endemic N. lobata

FIGURE 2. Genetic structure in Nanocnide based on averaged MIG-seq data inferred using structure. The samples 1–4, 5–9 and 10–34 correspond to N. lobata, N. pilosa and N. japonica, respectively. More precisely, the numbers correspond to the samples as follows: 1: R2. 2: R9. 3: R10. 4: R19. 5: R23. 6: KY18. 7: 33028. 8: H30528. 9: H30337. 10: Tai. 11: 602. 12: A1. 13: B2. 14: C1. 15: S2. 16: KY2. 17: KY25. 18: KY29. 19: TC2. 20: KO2. 21: KO7. 22: CH4. 23: CH10. 24: CH25. 25: CH29. 26: CH33. 27: NG2. 28: HK2. 29:HK9. 30: TH2. 31: TH16. 32: 827. 33: H30608. 34: L150039.

FIGURE 5. A in Molecular phylogeny and taxonomy of the genus Nanocnide (Urticaceae) with particular attention to the Ryukyu Islands endemic N. lobata

FIGURE 5. A seed and its mucilage of N. japonica on a tip of tweezers (Cultivated, originally collected from Japan, Tochigi Pref. Mt. Futamata on 14 April 2018.)

FIGURE 1 in Molecular phylogeny and taxonomy of the genus Nanocnide (Urticaceae) with particular attention to the Ryukyu Islands endemic N. lobata

FIGURE 1. The obtained phylogenetic trees. Left: The ML tree of ITS sequence for Nanocnide. The identical genotypes are collapsed at the right side of a triangular. Numbers near a branch stand for ML bootstrap value, MP bootstrap value, and BI posterior probability of the branch. The support in MP tree is based on the most frequent values of all the multiple MP trees. Hyphens mean the branch did not appear in the corresponding analysis. Samples with identical sequences are collapsed and listed in the same line, but a triangle on a tip of the tree shows a single sequence corresponding to the samples on listed in two lines. The sample name abbreviations for the samples from GenBank are listed in Table 3. Right: The ML tree of Nanocnide based on MIG-seq. Numbers below a branch stand for bootstrap values (1000 times) for min_samples_locus = 1 / min_samples_locus = 4. Bootstrap values less than 50 in both parameters were omitted. Abbreviation after the sample locality shows the country of the locality. (C): Mainland China, (J): Japan and (T): Taiwan.

opencc-zeroOct 2023View details →

dryad32/100

Molecular phylogeny and evolution of inflorescence types in Eperua

The Amazonian hyperdominant genus Eperua (Fabaceae) currently holds 18 described species and has two strongly different inflorescence and flower types, with corresponding different pollination syndrome. The evolution of these vastly different inflorescence types within this genus was unknown and the main topic in this study. We constructed a molecular phylogeny, based on the full nuclear ribosomal DNA and partial plastome, using Bayesian inference and maximum likelihood methods, to test whether the genus is monophyletic, whether all species are monophyletic and if the shift from bat to bee pollination (or vice versa) occurred once in this genus. All but two species are well supported by the nuclear ribosomal phylogeny. The plastome phylogeny, however, shows a strong geographic signal suggesting strong local hybridization or chloroplast capture, rendering chloroplast barcodes meaningless in this genus. With our data, we cannot fully resolve the backbone of the tree to clarify sister genera relationships and confirm monophyly of the genus Eperua. Within the genus the shift from bat to bee and bee to bat pollination has occurred several times but, in the latter, not always leading to a pendant inflorescence.

Figure 8 in Molecular phylogeny and taxonomy of three anaerobic plagiopyleans (Alveolata: Ciliophora), retrieved from two geographically distant localities in Asia and North America

Figure 8. Maximum likelihood (ML) tree inferred from the small subunit rRNA gene sequences, revealing the positions of the 21 newly obtained sequences (red font). Numbers near branches indicate ML bootstrap values and BI posterior probabilities. Black circles represent full support (ML/BI, 100/1.00) in both analyses. Disagreements in topology between ML and BI are marked with asterisks. The scale bar corresponds to 2 changes per 100 nucleotide positions. Abbreviation: sp = species.

Figure 4 in Molecular phylogeny and taxonomy of three anaerobic plagiopyleans (Alveolata: Ciliophora), retrieved from two geographically distant localities in Asia and North America

Figure 4. Drawings of Plagiopyla rariseta from life (A–C, E) and aħer protargol staining (D, F–I). A, ventral view of a representative individual, arrowheads show caudal cilia. B, C, resting (B) and extruded (C) extrusomes. D, dorsal view, showing position of striated band, cytoproct (red arrow), dense ciliary row (black arrow) and contractile vacuole pores (arrowheads). E, different body shapes. F, details of oral region, showing oral opening and buccal cavity. G, details of dikinetids on right front side of striated band. H, I, ventral (H) and dorsal (I) views of the holotype to show somatic and oral kineties, arrow indicates striated band, arrowhead shows dense ciliary row, red kinetosomes indicate dikinetids on right front side of striated band. Abbreviations: CV, contractile vacuole; Ex, extrusomes; SB, striated band. Scale bars: 30 μm (A, E, H, I), 25μm (C).

Figure 5 in Molecular phylogeny and taxonomy of three anaerobic plagiopyleans (Alveolata: Ciliophora), retrieved from two geographically distant localities in Asia and North America

Figure 5. Photomicrographs of Plagiopyla rariseta from life (A–C, H–O) and aħer protargol staining (D–G). A, B, ventral views of different individuals, showing different body shape. C, extruded extrusomes (arrowheads). D, details of oral opening and buccal cavity tube (arrowhead). E, macronucleus and slightly enveloped micronucleus (arrowhead). F, G, ventral (F) and dorsal (G) views of the holotype to show somatic and oral kineties, arrowhead shows dense ciliary row. H, I, oral region, showing buccal cavity (arrowheads) under different focal planes. J, ventral view of a slightly compressed cell. K, posterior region of cell, arrowhead indicates contractile vacuole, arrow marks cortical ridges. L, curved extrusomes (arrowheads) under the cortex. M, posterior end of cell, showing caudal cilia (arrowhead). N, contractile vacuole pores (arrowheads). O, dorsal view, arrowhead shows striated band. Scale bars: 30 μm.

Figure 2 in Molecular phylogeny and taxonomy of three anaerobic plagiopyleans (Alveolata: Ciliophora), retrieved from two geographically distant localities in Asia and North America

Figure 2. Drawings of Trimyema foissneri from life (A–D) and aħer protargol staining (E–I). A, leħ lateral view of a representative individual, arrow shows acontractile vacuole, red arrowhead shows food vacuole, yellow arrowheads show somatic cilia. B, different body shape in different viewing angles. C, leħ lateral view, showing buccal cavity (arrow) and position of macronucleus. D, disposition of the ciliary girdles. E, oral ciliature, red dots showing kinetidal composition at the anterior part of OK1. F, lateral view of oral ciliature, showing the shorter oral kinety 3 (in red). G, macronucleus and micronucleus (arrowheads), the position of the laưer being variable (1, 2). H, I, ventral (H) and dorsal (I) views of the holotype to show somatic and oral kineties, arrows show argentophilic lines connecting longitudinal somatic ciliary rows, arrowheads show epaulet. Abbreviations: CC, caudal cilia; Ma, macronucleus; OK, oral kinety; SK, somatic kineties; VLF, ventrolateral fragment. Scale bars: 15 μm (A, C); 10 μm (H, I).