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2,620 results for “Molecular Phylogeny”
Figure 2. Bayesian inference tree inferred from Dataset2 in First molecular phylogeny of the freshwater planarian genus Girardia (Platyhelminthes: Tricladida) unveils hidden taxonomic diversity and initiates resolution of its historical biogeography
Figure 2. Bayesian inference tree inferred from Dataset2 (COI with outgroup). Clades C to R have been collapsed for the sake of clarity. Clade A comprises unclassified samples from Mexico and Texas (USA); Clade B includes identified individuals of Girardia schubarti from Brazil and other unidentified Brazilian individuals. The outgroup (unlabelled lower clade) is composed of several representatives of genera Dugesia and Schmidtea downloaded from GenBank (Appendix). Values at nodes correspond to posterior probability. Scale bar: number of substitutions per nucleotide position.
Figure 1 in First molecular phylogeny of the freshwater planarian genus Girardia (Platyhelminthes: Tricladida) unveils hidden taxonomic diversity and initiates resolution of its historical biogeography
Figure 1. Maps showing the sampling localities for all individuals analysed in the present study, including those corresponding to GenBank sequences. A to R letters in the legend refer to the clades and singletons delimited in the phylogenetic analyses (Figs 2, 3). A, the Americas; B, Western Europe; C, Hawaii; D, Asia and Oceania. For a finer resolution, visit the interactive map at: https://www.ub.edu/planarian-maps/.
FIGURE 1 in Molecular phylogeny and morphological characterization of Paramicrothyrium bambusae sp. nov. and Tumidispora thailandica sp. nov. from leaf litter
FIGURE 1. Phylogram generated from maximum likelihood analysis is based on combined LSU and ITS sequence data. The tree is rooted with Kirschsteiniothelia lignicola (MFLUCC 10-0036). The ex-type strains are indicated in bold and the new isolates are indicated in red. Bootstrap support values ≥70% from the maximum likelihood (ML), maximum parsimony (MP) and Bayesian posterior probabilities (BYPP) values ≥0.95 are given above the nodes, respectively.
FIGURE 2 in Molecular phylogeny and morphological characterization of Paramicrothyrium bambusae sp. nov. and Tumidispora thailandica sp. nov. from leaf litter
FIGURE 2. Paramicrothyrium bambusae (MFLU 19-2729, holotype). a, b Thyriothecia on the surface of the leaf (yellow arrows). c Close-up of Thyriothecium. d, e Thyriothecia when, viewed in squash mount. f The upper wall of thyriothecium, when viewed in squash mount. g–i Conidia. j The upper view of colony. k The lower view of colony. Scale bars: d, e = 50 μm, f = 20 μm, g–i = 3 μm.
FIGURE 3 in Molecular phylogeny and morphological characterization of Paramicrothyrium bambusae sp. nov. and Tumidispora thailandica sp. nov. from leaf litter
FIGURE 3. Tumidispora thailandica (MFLU 19-2771, holotype). a, b Thyriothecia on the surface of leaf. c Close-up of Thyriothecia. d Thyriothecium when viewed in squash mount. e The upper wall of thyriothecium when viewed in squash mount. f Pseudoparaphyses. g–j Asci. k–o Ascospores (yellow arrows show appendages in upper cells). p A germinating ascospore. q The upper view of colony. r The lower view of colony. Scale bars: d = 100 μm, e = 50 μm, f–j = 20 μm, k–p = 5 μm.
Fig. 3. Phylogenetic reconstruction for 356 in Redefining the damselfly families: a comprehensive molecular phylogeny of Zygoptera (Odonata)
Fig. 3. Phylogenetic reconstruction for 356 specimens from the combined maximum likelihood analysis of 28S and 16S. Bootstrap values are shown only if below 100. Species names and classification as proposed are shown. (a) Lestoidea and Platystictoidea; (b, c) various groups; (d) Platycnemididae; (e) Coenagrionidae.
Fig. 2. Phylogenetic reconstruction for 295 in Redefining the damselfly families: a comprehensive molecular phylogeny of Zygoptera (Odonata)
Fig. 2. Phylogenetic reconstruction for 295 specimens from the combined Bayesian analysis of 28S, 16S and COI. Posterior probabilities are shown (as percentages) only if below 100%. Species names and classification as proposed are shown. (a) Lestoidea and Platystictoidea; (b, c) various groups; (d) Platycnemididae; (e) Coenagrionidae.
Fig. 1 in Redefining the damselfly families: a comprehensive molecular phylogeny of Zygoptera (Odonata)
Fig. 1. Summary of Zygoptera phylogeny, based on Figs 2, 3 and the Discussion section. Only reasonably supported dichotomies are shown. The classification follows Appendix 1 (see for other genera placed near Dimeragrion, Priscagrion and Rhipidolestes) and the fate of some traditional taxa is indicated. For each recognized damselfly lineage, the known numbers of genera and species (in brackets) are shown, as is their occurrence in the Afrotropical (AT), Australasian (AU), Nearctic (NA), Neotropical (NT), Oriental (OL), Pacific (PC) and Palaearctic (PA) regions.
Figure 1 in Molecular phylogeny of the Orthurethra (Panpulmonata: Stylommatophora)
Figure 1. Bayesian phylogenetic tree of the Orthurethra based on 3370 unambiguously aligned nucleotide sites of the LSU rRNA (and 5.8S) gene. Values on nodes represent bootstrap support for maximum likelihood and neighbour-joining (1000 replicates) and posterior probabilities for Bayesian inference (based on the last 75% of trees), respectively. Bootstrap support values <50% and posterior probabilities <0.7 are not shown. The scale bar represents one substitutional change per 100 nucleotide positions. The shaded area represents the main clade.
FIGURE 3 in The molecular phylogeny and morphology revealed a new wood-rotting fungus Vararia yunnanensis (Peniophoraceae, Russulales) in Yunnan Province, China
FIGURE 3. Basidiomata of Vararia yunnanensis (CLZhao 17725). Bars: A = 0.5 cm; B = 0.5 mm. Photos by: Ying-Lian Deng.
FIGURE 4 in The molecular phylogeny and morphology revealed a new wood-rotting fungus Vararia yunnanensis (Peniophoraceae, Russulales) in Yunnan Province, China
FIGURE 4. Microscopic structures of Vararia yunnanensis (drawn from the holotype). A: Basidiospores. B: Basidia and basidioles. C: Subcylindrical cystidia. D: Tapering cystidia. E: Fusiform cystidia. F: Skeletal mycelium. G: A section of hymenium. Bars: A–G = 10 µm. Drawings by: Ying-Lian Deng.
FIGURE 1 in The molecular phylogeny and morphology revealed a new wood-rotting fungus Vararia yunnanensis (Peniophoraceae, Russulales) in Yunnan Province, China
FIGURE 1. Maximum Parsimony strict consensus tree illustrating the phylogeny of two new species of Vararia and related species in Peniophorales based on ITS+nLSU sequences. Branches are labeled with maximum likelihood bootstrap values equal to or higher than 70%, parsimony bootstrap values equal to or higher than 50% and Bayesian posterior probabilities equal to or higher than 0.95.
Figure 1. A, molecular phylogeny from MrBayes. Node labels are posterior probability support values. B in A new lineage of deep-reef gobies from the Caribbean, including two new species and one new genus (Teleostei: Gobiidae: Gobiosomatini)
Figure 1. A, molecular phylogeny from MrBayes. Node labels are posterior probability support values. B, time-calibrated tree from BEAST. Node bars are 95% highest posterior densities for age estimates. Coloured taxa are new species. Colored circles in B refer to the placement of fossil calibration points 1 through 4.
Supplementary material 1 from: Damadi E, Yazdani Moghaddam F, Ghanbarifardi M (2023) Species delimitation, molecular phylogeny and historical biogeography of the sweetlips fish (Perciformes, Haemulidae). Zoosystematics and Evolution 99(1): 135-147. https://doi.org/10.3897/zse.99.96386
Sampling information and GenBank accession numbers for the specimens included in the phylogenetic analyses
FIG. 2 in Molecular Phylogeny of the Liolaemus kriegi Complex (Iguania, Liolaemini)
FIG. 2.—Different phylogenies for the Liolaemus kriegi complex and related taxa: (a) Bayesian concatenated mitochondrial tree; (b) BEAST (v1.6.1) species tree based on nuclear genes with posterior probability values; (c) Bayesian concatenated tree that includes all genes except the mitochondrial genes of L. sp. B; and (d) BEAST species tree without L. sp. B mitochondrial genes, with posterior probability values. Where given at each node in (a) and (c), Bayesian posterior probability values (BI) are shown to the left of the slash and maximum likelihood (ML) bootstrap values are to the right (the ''-̕̕ indicates no significant support); stars on nodes represent BI = 1.0 and ML = 100%. Estimated divergence times in (d) are marked in light grey; units on the abscissa are expressed in millions of years ago.
A molecular phylogeny of Noctuini (Lepidoptera: Noctuidae: Noctuinae)
<p>The tribe Noctuini is comprised over 520 species; many are economically important species that impact human agriculture. Despite their diversity and relevance, relationships of Noctuini have been difficult to resolve. There have been extensive morphological revisions of some of these taxa (e.g., <em>Agrotis</em>, <em>Euxoa</em>); however, there are no studies that focus exclusively on the phylogenetic relationships of the Noctuini. Currently, Noctuini is separated into two subtribes, Agrotina and Noctuina. In this study, we tested previous classification schemes with two analyses. The total evidence analysis utilized three loci for three outgroup taxa and 54 noctuine species. Using museum specimens, we collected data from cytochrome oxidase I (COI), Dopa Decarboxylase (DDC), and Elongation factor 1-α (EF1-α) to generate a dataset of 1378 base pairs (bp) for a total evidence approach. We also used previously published COI sequences for 626 species, resulting in a matrix of 690 bp, termed "the barcode analysis". We used both Maximum Likelihood and Bayesian approaches for the total evidence analysis, and ML for the barcode analysis. In both sets of results, we found equivocal support for monophyletic Agrotina and Noctuina. We found strong support for smaller, well-described genera (e.g., <em>Spaelotis</em>), but poor support for large genera such as <em>Euxoa</em>, <em>Feltia</em>, and <em>Agrotis</em>. It is likely that a combination of limited taxon/gene sampling, limited gene choice, and the rapid evolution of these species resulted in a lack of phylogenetic resolution in the total evidence topologies. Based on these results, we recommend increased taxon sampling and inclusion of loci that target these rapidly evolving lineages to achieve a better understanding of the phylogeny of Noctuini and its genera.</p>
Figure 1 in Three in one: molecular phylogeny of the genus Helodrilus (Crassiclitellata: Lumbricidae) with a description of two new genera and two new species
Figure 1. Molecular phylogenetic reconstruction of the Helodrilus s.l. species. Detail of the 50% majority-rule consensus tree obtained from the Bayesian inference phylogenetic analysis (A) and best-scoring maximum likelihood tree (B) based on the concatenated sequences of the molecular markers COI, 28S, ND1, 12S and 16S. Posterior probability values and bootstrap values close to/over 90% and over 70% (respectively) are shown beside the corresponding nodes. Species sequenced for this work are shown in bold. When several representatives of a genus were recovered as a well-supported clade they were collapsed to facilitate visual interpretation.
Figure 2 in Three in one: molecular phylogeny of the genus Helodrilus (Crassiclitellata: Lumbricidae) with a description of two new genera and two new species
Figure 2. Imetescolex moƲilensis gen. & sp. nov. Ventrolateral view of the fore body. Cl = clitellum, Gt = glandular tumescences, Mp = male pore, Tb = tubercula pubertatis.
FIGURE 7 in Molecular phylogeny of Onobrychis sect. Onobrychis (Fabaceae-Hedysareae) with insights into its taxonomy and character evolution
FIGURE 7. Character evolution of ploidy level optimized on the Bayesian tree obtained from nr DNA ITS dataset. Two characters states diploid vs. tetraploid.
FIGURE 6 in Molecular phylogeny of Onobrychis sect. Onobrychis (Fabaceae-Hedysareae) with insights into its taxonomy and character evolution
FIGURE 6. Character evolution of chromosome number optimized on the Bayesian tree obtained from nr DNA ITS dataset.Two character states x= 7 vs. x= 8
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Allen Brain Atlas
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