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35 results for “plastid DNA sequences”
Data from: Phylogenetic systematics of subtribe Spiranthinae (Orchidaceae: Orchidoideae: Cranichideae) based on nuclear and plastid DNA sequences of a nearly complete generic sample
Subtribe Spiranthinae is the most species-rich lineage of terrestrial Neotropical orchids, encompassing > 500 species and 40 genera. We conducted maximum parsimony and maximum likelihood phylogenetic analyses of DNA sequence data of plastid matK-trnK and trnL-trnF and nuclear ribosomal ITS sequences for 36 genera and 182 species of Spiranthinae plus appropriate outgroups. The results strongly support monophyly of Spiranthinae (minus Discyphus, Discyphinae and Galeottiella, Galeottiellinae) and five major lineages, namely monospecific Cotylolabium (sister to the remaining Spiranthinae) and the Eurystyles, Pelexia, Spiranthes and Stenorrhynchos clades. Eighteen of the 27 genera of Spiranthinae for which more than one species was included in our analyses are monophyletic. Paraphyly of large genera, such as Cyclopogon and Sarcoglottis, resulted from segregation of particular species or groups of species exhibiting minor modifications of structures directly involved in pollination (e.g. nectary, rostellum and viscidium). Conversely, polyphyly has resulted from convergent evolution of floral attributes in distantly related species (e.g. Mesadenus). Some of the morphological characters used traditionally for generic delimitation and in non-molecular cladistic analyses of Spiranthinae are discussed against the evolutionary framework set by our molecular trees, emphasizing putative synapomorphies and problems derived from inappropriate character coding or incorrect homology assessments. Our ancestral area analysis indicates that Spiranthinae originated in eastern South America, with subsequent migrations and secondary radiations in Mesoamerica and North America, plus a derived migration from the latter region to the Old World (Spiranthes).
Data from: Pleistocene climate change and phylogeographic structure of the Gymnocarpos przewalskii (Caryophyllaceae) in the northwest China: Evidence from plastid DNA, ITS sequences, and Microsatellite
Northwestern China has a wealth of endemic species, which has been hypothesized to be affected by the complex paleoclimatic and paleogeographic history during Quaternary. In this paper, we used Gymnocarpos przewalskii as a model to address the evolutionary history and current population genetic structure of species in northwestern China. We employed two chloroplast DNA fragments (rps16 and psbB‐psbI), one nuclear DNA fragment (ITS), and simple sequence repeat (SSRs) to investigate the spatial genetic pattern of G. przewalskii. High genetic diversity (cpDNA: hS = 0.330, hT = 0.866; ITS: hS = 0.458, hT = 0.872) was identified in almost all populations, and most of the population have private haplotypes. Moreover, multimodal mismatch distributions were observed and estimates of Tajima's D and Fu's FS tests did not identify significantly departures from neutrality, indicating that recent expansion of G. przewalskii was rejected. Thus, we inferred that G. przewalskii survived generally in northwestern China during the Pleistocene. All data together support the genotypes of G. przewalskii into three groups, consistent with their respective geographical distributions in the western regions—Tarim Basin, the central regions—Hami Basin and Hexi Corridor, and the eastern regions—Alxa Desert and Wulate Prairie. Divergence among most lineages of G. przewalskii occurred in the Pleistocene, and the range of potential distributions is associated with glacial cycles. We concluded that climate oscillation during Pleistocene significantly affected the distribution of the species.
Fig. 1 in Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences
Fig. 1 Phylogenetic tree for Ranunculus species based on internal transcribed spacer (ITS) sequences. a Consensus tree inferred from the six most parsimonious trees (CI=0.72; RI=0.93). Numbers above branches show bootstrap values (3,000 replicates). b Majority-rule consensus of
FIGURES 31–36 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 31–36. Neidium vandusenense sp. nov. SEM, external view. Fig. 31. Whole valve. Fig. 32. Central valve with multiple longitudinal canals and transapical central area. Proximal raphe branches evenly hooked. Fig. 33. Apex valve face and mantle showing concave mantle wall, longitudinal canals reducing to one at the apex. Fig. 34. Valve face showing developed ridge along one side of the raphe (arrow) and scattered surface depressions along the axial area. Areolae recessed with a finger-like cribra. Fig. 35. Apex with 3 evident copulae. Copulae open bands with 2 rows of pores. Lacina extends to band base (arrow). Fig. 36. Central region showing a weak elevation of the longitudinal canal. Scale bars = 20 μm: Fig. 31; 10 μm: Figs 32, 33; 2 μm: Figs 34–36.
FIGURES 79–82 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 79–82. Neidium lavoieanum sp. nov. SEM, internal view. Fig. 79. Half valve showing valve outline. Fig. 80. Broken longitudinal canal with areoale and internal valve face areolae. Arrow indicates renilimbia. Fig. 81. Internal central nodule with a covering over the verminae along the margin. Helictoglossae separated and aligned. Fig. 82. Apex, showing longitudinal canal extending to the apex and an erect helictoglossa next to hyaline thickened apex. Scale bars = 10 μm: Fig. 79; 5 μm: Fig. 81; 3 μm: Figs 80, 82.
FIGURES 1–5 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 1–5. Neidium iridis (Fig. 1) and Neidium beatyi sp. nov. (Figs 2 (holotype), 3–5). Scale bar = 50 μm.
FIGURES 75–78 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 75–78. Neidium lavoieanum sp. nov. SEM, external view. Fig. 75. Half valve. Fig. 76. Surface areolae with no occlusions and axial area mid-way along the valve. Fig. 77. Elevated central area with elongated areolae along the margin and recurved proximal raphe endings. Fig. 78. Apex showing lacinia and longitudinal canals extending to the apex. Scale bars = 10 μm: Fig. 75; 3 μm: Figs 76–78.
FIGURES 56–61 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 56–61. Neidium collare sp. nov. SEM, external view. Fig. 56. Whole valve. Fig. 57. Central valve with longitudinal canal and transapical central area. Proximal raphe branches deflected. Fig. 58. Valve face mantle junction with epivalve, hypovalve and copula band. Fig. 59. Valve face with developed areolae. Areolae without finger-like cribra. Fig. 60. Apex with open bands of copulae. Copulae with 2 rows of pores. Lacinia weakly developed. Fig 61. Apex showing no apparent lacinia. Longitudinal canals extend to the tip of the apex. Scale bars = 30 μm: Fig. 56; 5 μm: Figs 57, 58, 60; 3 μm: Fig. 61; 2 μm: Fig. 59.
FIGURES 37–44 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 37–44. Neidium vandusenense sp. nov.SEM, internal view.Fig. 37. Central area with offset forming interconnected helictoglossae. Surface depressions (ghost striae) present in the central area. Figs 38, 39. Apex showing upright formation of the helictoglossae at the edge of the terminal nodule. Longitudinal canals blend in with areolae. Figs 40, 41. Margin of the valve showing multiple longitudinal canals. Open chambered formation (Fig. 41 (arrow), apical and transapical). Fig. 42. Renilimbia surround hymenae covered areolae (arrow). Figs 43, 44. Open copula band with 2 rows of poroids. Scale bars = 5 μm: Figs. 37, 38, 43; 2 μm: Figs 40, 41; 1 μm: Figs 42, 44.
FIGURES 6–12 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 6–12. Neidium beatyi sp. nov. SEM, external view. Fig. 6. Whole valve. Fig. 7. Central area raphe with silica ridges along each side. Figs 8, 10. Valve margin and mantle with multiple longitudinal canals. Copulae 2 rows of poroids. Fig 9, 12. Recessed areolae chambered and interconnected with finger-like cribra. Fig. 11. Apex showing arrow-like bifurcate lacinia. Copulae (3 evident) open bands with no evident poroids. Scale bars = 20 μm: Fig. 6; 10 μm: Fig. 11; 5 μm: Figs 7–10; 2 μm: Fig 12.
FIGURES 62–68 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 62–68. Neidium collare sp. nov. SEM, internal view. Fig. 62. Whole valve. Figs 63, 67. Recessed areolae and longitudinal canals at mid-valve and close to apex. Figs 65, 66. Central area with offset forming interconnected helictoglossae. Very weak surface depressions (ghost striae) present in the central area. Remnants of renilimbia present (arrows). Fig. 64. Apex showing an erect helictoglossa at terminal nodule and single longitudinal canal extending to the apex. Fig. 68. broken valve showing the canal. Scale bars: 20 μm: Fig. 62; 5 μm: Figs 64, 65; 3 μm: Figs 63, 66, 67; 1 μm: Figs 68.
FIGURES 83 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 83. RaxML phylogenic tree construction showing boostrap (BS) confidence levels using the gene rbcL for selected taxa within the genus Neidium.
FIGURES 13–18 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 13–18. Neidium beatyi sp. nov. SEM internal view. Fig. 13. Central area with linear forming interconnected helictoglossae. Fig. 14. Apex with a curved forming helictoglossa at the edge of the terminal nodule. A single prominent longitudinal canal extends to the nodule. Figs 15, 17. Multiple longitudinal canals; at center canal similar (Fig. 15), towards apex one becomes more prominent (Fig. 17, arrow). Fig. 16. Renilimbia surround hymenae covered areolae (arrow). Fig. 18. Open chambered formation (apically and transapically) of the longitudinal canal. Scale bars = 10 μm: Fig. 14; 5 μm: Figs 13, 17; 2 μm: Fig. 15: 500 nm: Figs 16, 18.
FIGURE 1 in Species delimitation of Stemona (Stemonaceae) based on sequences of five plastid DNA regions
FIGURE 1. Sampling sites of the 23 Stemona populations from China and two populations from Indonesia.
FIGURE 2 in Species delimitation of Stemona (Stemonaceae) based on sequences of five plastid DNA regions
FIGURE 2. Bayesian tree produced by analysis of five non-coding plastid DNA regions. Clade support is for maximum parsimony bootstrap percentages, maximum likelihood bootstrap percentages and Bayesian posterior probabilities in this order. Different topologies between the BI, MP, and ML trees are marked by asterisks.
FIGURE 3 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data
FIGURE 3. Bayesian maximum clade reliability trees based on combined nuclear At103 and chloroplast rps16, trnL-F datasets for Dracaena, Sansevieria, and selected outgroups. The values above the branch represent the maximum parsimony bootstrap percentage (BS), and the ones below are the Bayesian posterior probability (PP). Bold branches indicate strong support, interpreted as ≥ 70 BS and ≥ 95 PP. Long branches were shortened by half their length (indicated by \\).
FIGURE 2 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data
FIGURE 2. Bayesian maximum clade credibility trees based on nuclear At103 (A) and chloroplast rps16, trnL-F (B) datasets for Dracaena and Sansevieria. Outgroups were trimmed from the Figure. The values above the branch represent the maximum parsimony bootstrap percentage (BS), and the ones below are the Bayesian posterior probability (PP). Bold branches indicate strong support, interpreted as ≥ 70 BS and ≥ 95 PP.
FIGURE 1 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data
FIGURE 1. Representative morphological diversity in the dracaenoid genera, Dracaena and Sansevieria. A, Dracaena draco subsp. draco, Spain, Canary Islands, Tenerife, Icod de los Vinos; B, D. konaensis, origin: USA, Hawai'i, Big Island, Kona coast, in cultivation at Kew (Acc. No. 2008-239); C, D. arborea, Gabon, Woleu-Ntem Rd, Mitzic to Njole; D, D. laxissima, São Tomé and Príncipe, São Nicolau; E, D. goldieana, origin: Gabon, in cultivation at Kew (Acc. No. 1990-2300); F, D. aubryana, Gabon, Woleu-Ntem Rd Mitzic to Njole; G, Sansevieria frequens, Kenya, Laikipia District, Ngare Ndare Farm (type locality); H, S. aethiopica, Namibia, 74 km from Windhoek, on road to Walvis Bay; I, S. fischeri, Kenya, Munda, 18.9 km NE of Mwatate on Taveta road; J, S. pinguicula, Kenya, by Kowi airstrip, north bank of Tiva Lugga; K, S. ascendens, Kenya, Coast Province, Kwale District, around base of Taru Hill (type locality); L, S. kirkii var. pulchra, in cultivation (private collection, Miami, FL). Photographs by A, L. Mucina; B, I. Willey; C, E–F, T.H.J. Damen; D, J.J.F.E. de Wilde; G-K, L. E. Newton; L, S. Zona.
FIGURE 4 in Phylogenetic relationships of Discyphus scopulariae (Orchidaceae, Cranichideae) inferred from plastid and nuclear DNA sequences: evidence supporting recognition of a new subtribe, Discyphinae
FIGURE 4. Phylogenetic relationships in Spiranthinae inferred from nuclear (ITS) and plastid (rbcL, matK-trnK, trnL-trnF) DNA sequences by maximum likelihood (ML). The main tree is the ML tree; numbers under branches are bootstrap proportions from the ML bootstrap analysis. The inset on the upper left hand is the ML tree with branches drawn proportional to branch lengths. The major clades referred to in the text are marked as follows: a, Stenoptera clade; b, Prescottia clade; c, "core" Cranichidinae; d, Spiranthinae (excluding Discyphus). The position of Discyphus is indicated by an asterisk (*).
FIGURE 3 in Phylogenetic relationships of Discyphus scopulariae (Orchidaceae, Cranichideae) inferred from plastid and nuclear DNA sequences: evidence supporting recognition of a new subtribe, Discyphinae
FIGURE 3. Phylogenetic relationships in Spiranthinae inferred from nuclear (ITS) and plastid (rbcL, matK-trnK, trnL-trnF) DNA sequences by maximum parsimony (MP). The main tree is the strict consensus of 24 most parsimonious trees (MPTs) recovered by the analysis; numbers under branches are bootstrap proportions (from the MP bootstrap analysis). The inset on the upper left hand is one of the 24 MPTs with branches drawn proportional to branch length. The major clades referred to in the text are marked as follows: a, Stenoptera clade; b, Prescottia clade; c, "core" Cranichidinae; d, Spiranthinae (excluding Discyphus). The position of Discyphus is indicated by an asterisk (*).
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OpenNeuro
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