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63 results for “maximum parsimony”
FIGURE 8 in Persepolium (Polygoneae): A new genus in Polygonaceae based on conventional Maximum Parsimony and Three-taxon statement analyses of a comprehensive morphological dataset
FIGURE 8. Leaf blade (A–B) and perianth (C–L) surface of Polygonum subsection Spinescentia (SEM): (A–F)—P. dumosum (Kotschy 242, LE): leaf blade abaxially (A–B); perianth segments outside (C–F). (G–L)—P. aridum (Sawers and Kuh-Enhker, Haussknecht s.n. LE): perianth tube outside (G); middle part of perianth segment outside (H–I); the edge of perianth segment outside (J–K); perianth segment inside (L). Scale bar = 300 μm for A; = 30 μm for B–K; = 10 μm for L. Images: O. Yurtseva.
FIGURE. 1 in Persepolium (Polygoneae): A new genus in Polygonaceae based on conventional Maximum Parsimony and Three-taxon statement analyses of a comprehensive morphological dataset
FIGURE. 1. Life history and shoots of Polygonum subsection Spinescentia: (A–C)—P. salicornioides, a dwarf undershrub with fleashy annual shoots (Kotschy 468, LE). (D–E)—P. spinosum, a dwarf shrub with lignified prickly shoots (Bornmüller 5083, LE). (F–G)—P. dumosum, a dwarf undershrub with wiry leafy annual shoots (Kotschy 242, LE). (H)—ibid (Wendelbo 790, LE). (I–J)—P. aridum, a dwarf shrub with wiry leafless annual shoots (Kuh-Enhker, Haussknecht s.n. LE). (K)—ibid (Sawers, Haussknecht s.n. LE). Images: O. Yurtseva.
FIGURE 4 in Persepolium (Polygoneae): A new genus in Polygonaceae based on conventional Maximum Parsimony and Three-taxon statement analyses of a comprehensive morphological dataset
FIGURE 4. Ocreas of Bactria and Atraphaxis: (A–C)—B. ovczinnikovii, Ukrainskaya et al. 12, MW. (D–F)—A. virgata, Gubanov 7227, MW. (G–H)—A. ariana, Gorelova s.n. LE. (I–J)—A. toktogulica, Ajdarova et al. s.n. LE. (K–M)—A. seravschanica, Boryaev & Gubanov 43, LE. Scale bar = 1 mm. Images: O. Yurtseva.
FIGURE 7 in Persepolium (Polygoneae): A new genus in Polygonaceae based on conventional Maximum Parsimony and Three-taxon statement analyses of a comprehensive morphological dataset
FIGURE 7. Perianth surface of Polygonum subsection Spinescentia (SEM): (A–I)—P. salicornioides (Kotschy 468, LE): papillate surface of perianth segments outside (A–D), perianth tube outside (E–F), and perianth segment inside (G–I). (J–L)—P. spinosum (Bornmüller 5083, LE): middle part of perianth segment outside (J), and papillate segment edge (K–L). Scale bar = 100 μm for A; = 300 μm for G; = 30 μm for B–D, H–L; =10 μm for E. Images: O.V.Yurtseva.
FIGURE 3 in Persepolium (Polygoneae): A new genus in Polygonaceae based on conventional Maximum Parsimony and Three-taxon statement analyses of a comprehensive morphological dataset
FIGURE 3. Ocreas and ocreolas of Polygonum subsection Spinescentia: (A–K)—P. dumosum, Kotschy 242, LE: (A–F)—ocreas (A– B, E–F) and lead blades (A, C–F) of vegetative part of shoot, (G-K)—ocreolas and reduced leaf blades. (L–M)—P. aridum, Sawers, Haussknecht s.n. LE: (L–M)—ocreas, (N–O)—ocreolas. (P–W)—P. salicornioides, Kotschy 468, LE: (P–S)—ocreas and a leaf blade of vegetative part of shoot, (T–W)—ocreolas. (X–Y)—P. spinosum, Bornmüller 5083, LE, leaf blades and ocreas of vegetative shoot. Scale bar = 1 mm. Images: O. Yurtseva.
FIGURE 5 in Persepolium (Polygoneae): A new genus in Polygonaceae based on conventional Maximum Parsimony and Three-taxon statement analyses of a comprehensive morphological dataset
FIGURE 5. Perianths of Polygonum subsection Spinescentia: (A–C)—P. salicornioides (Kotschy 468, LE), perianth outside (A), inside (B), and segment outside (C). (D)—P. spinosum (Bornmüller 5083, LE). (E)—P. dumosum (Kotschy 242, LE); (F)—ibid, (Wendelbo 790, LE). (G–I)—P. aridum (Sawers, Haussknecht s.n. LE): mature flower (G); achene exserted from the perianth (H); young flower (I). Scale bar = 0.1 mm for C; = 0.2 mm for F, H; =0.5 mm for I; = 1 mm for the rest. Images: O. Yurtseva.
FIGURE 4. Maximum parsimony 50 in Terraria haydenii (Thelypodieae, Brassicaceae), a new mustard genus and species from the West Desert region of North America's Great Basin
FIGURE 4. Maximum parsimony 50% majority-rule consensus tree obtained using trnL–F sequence data. Branches receiving>50% support are indicated and, if present, a second value corresponds to Jackknife support. Terraria haydenii and its inverted repeat (see text) are indicated in bold.
FIGURE 3. Maximum parsimony 50 in Terraria haydenii (Thelypodieae, Brassicaceae), a new mustard genus and species from the West Desert region of North America's Great Basin
FIGURE 3. Maximum parsimony 50% majority-rule consensus tree from 207 trees obtained using rbcL sequence data. Branches receiving>50% support are indicated in bold and with a value above. If present, a second value corresponds to Jackknife analysis support. The newly discovered plant is shown in bold. Tribes are indicated to the right with larger groupings (A-F) and lineages (I-III) (see Discussion for group and lineage comparisons).
FIGURE 1. Maximum parsimony reconstructed from the combined sequences RPB2 and TEF1 in New species of Trichoderma in the Harzianum, Longibrachiatum and Viride clades
FIGURE 1. Maximum parsimony reconstructed from the combined sequences RPB2 and TEF1, with the newly described species displayed in boldface. MPBP above 50% (left) and BIPP above 90% (right) are given at the nodes.
FIGURE 1. Maximum parsimony tree constructed under a 7 in Taxonomic status of Brucepattersonius albinasus (Rodentia: Sigmodontinae)
FIGURE 1. Maximum parsimony tree constructed under a 7:1 ts:tv ratio scheme, with six haplotypes of B. griserufescens, the holotype of B. albinasus and two haplotypes from GenBank: B. iheringi and B. soricinus. Tree length = 555, CI = 0.9225, RI = 0.8673, RC = 0.8001. Numbers above the branches are bootstrap values (1000 / 500 replicates from MP / ML analyses).
FIGURE 2. Phylogram from a Maximum Parsimony analysis, representing a 50 in Molecular systematics of Malagasy poison frogs in the Mantella betsileo and M. laevigata species groups
FIGURE 2. Phylogram from a Maximum Parsimony analysis, representing a 50% majority-rule consensus tree of 65700 equally most parsimonious trees. Mantella bernhardi was defined as outgroup. Specimens with identical haplotypes were merged; numbers in brackets after names of taxa give the number of specimens with the same haplotype. Numbers at nodes are bootstrap values in percent from a Maximum Parsimony bootstrap analysis with 250 replicates. Asterisks denote posterior probabilities from a partitioned Bayesian analysis: (*)>90%; *>95%; **>99%.
FIGURE 1. Maximum parsimony phylogram inferred from partial 5.8S in Systematic analyses of Ophiocordyceps ramosissimum sp. nov., a new species from a larvae of Hepialidae in China
FIGURE 1. Maximum parsimony phylogram inferred from partial 5.8S ITS, nrSSU, EF-1α, RPB1 sequence data. Bootstrap values above the branches are from 1,000 replicates. The tree is rooted with Glomerella cingulata. Type species are marked with an asterisk.
Figure 3. Ninety-five per cent maximum parsimony networks obtained for the 12 in Mitochondrial DNA genetic variation and phylogeography of the recently described vole species Proedromys liangshanensis Liu, Sun, Zeng and Zhao, 2007 (Rodentia: Arvicolinae)
Figure 3. Ninety-five per cent maximum parsimony networks obtained for the 12 haplotypes in Proedromys liangshanensis. Circle sizes are proportional to haplotype frequencies.
FIGURE 21. Maximum parsimony 16S rRNA phylogram for the Boophis albipunctatus group. From 485 total characters, 391 were constant and 72 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 21. Maximum parsimony 16S rRNA phylogram for the Boophis albipunctatus group. From 485 total characters, 391 were constant and 72 parsimony informative. MP searches retained 26 trees of which a strict consensus is shown. Consensus support values higher than 50, from 2000 bootstrap replicates, are shown; an asterisk indicates Bayesian posterior probabilities equal or higher than 95%. Species newly described herein are in bold.
FIGURE 7. Maximum parsimony 16S in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 7. Maximum parsimony 16S rRNA phylogram of species of the Boophis goudoti group. From 510 total characters, 340 were constant and 130 parsimony informative. MP searches retained 3681 trees of which a strict consensus is shown. Consensus support values higher than 50, from 2000 bootstrap replicates, are shown; an asterisk indicates Bayesian posterior probabilities equal or higher than 95%. Species newly described or resurrected herein are in bold.
FIGURE 1. Maximum parsimony 16S in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 1. Maximum parsimony 16S rRNA phylogram for species in the Boophis majori and B. microtympanum groups. From 480 total characters, 336 were constant and 129 parsimony informative. MP searches retained 39 trees of which a strict consensus is shown. Consensus support values higher than 50, from 2000 bootstrap replicates, are shown; an asterisk indicates Bayesian posterior probabilities equal or higher than 95%. Species newly described or resurrected herein are in bold.
FIGURE 18. Maximum parsimony 16S in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 18. Maximum parsimony 16S rRNA phylogram for species in the Boophis luteus group. From 470 total characters, 347 were constant and 111 parsimony informative. MP searches retained 60 trees of which a strict consensus is shown. Consensus support values higher than 50, from 2000 bootstrap replicates, are shown; an asterisk indicates Bayesian posterior probabilities equal or higher than 95%. The species newly described herein is in bold.
FIGURE 16. Maximum parsimony 16S in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 16. Maximum parsimony 16S rRNA phylogram for species in the Boophis albilabris group. From 535 total characters, 445 were constant and 35 parsimony informative. MP searches retained 6 trees of which a strict consensus is shown. Consensus support values higher than 50, from 2000 bootstrap replicates, are shown; an asterisk indicates Bayesian posterior probabilities equal or higher than 95%. The species newly described herein is in bold.
Data from: Maximum parsimony inference of phylogenetic networks in the presence of polyploid complexes
<p>Phylogenetic networks provide a powerful framework for modeling and analyzing reticulate evolutionary histories. While polyploidy has been shown to be prevalent not only in plants but also in other groups of eukaryotic species, most work done thus far on phylogenetic network inference assumes diploid hybridization. These inference methods have been applied, with varying degrees of success, to data sets with polyploid species, even though polyploidy violates the mathematical assumptions underlying these methods. Statistical methods were developed recently for handling specific types of polyploids and so were parsimony methods that could handle polyploidy more generally yet while excluding processes such as incomplete lineage sorting.</p> <p>In this paper, we introduce a new method for inferring most parsimonious phylogenetic networks on data that include polyploid species. Taking gene trees as input, the method seeks a phylogenetic network that minimizes deep coalescences while accounting for polyploidy. The method could also infer trees, thus potentially distinguishing between auto- and allo-polyploidy. We demonstrate the performance of the method on both simulated and biological data. The inference method as well as a method for evaluating given phylogenetic networks are implemented and publicly available in the PhyloNet software package.</p>
Fig. 4. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with ITS2 DNA sequences from 80 in A new genus and three new species of mangrove slugs from the Indo-West Pacific (Mollusca: Gastropoda: Euthyneura: Onchidiidae)
Fig. 4. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with ITS2 DNA sequences from 80 individuals (including 7 outgroups). Numbers by the branches are the bootstrap values (only numbers>50% are indicated). Numbers for each individual correspond to unique identifiers for DNA extraction. All sequences for specimens of Paromoionchis gen. nov. are new. Information on specimens can be found in the lists of material examined and in Table 1. The letter A corresponds to a clade referred to in the text. The color used for each (mitochondrial) unit is the same as that used in Figs 1–3 and 5–6.
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