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82 results for “phylogram”
Chronogram or phylogram for ancestral state estimation? Model-fit statistics indicate the branch lengths underlying a binary character's evolution: R scripts and simulated trees
<p>All R scripts used in this study, and the set of simulated phylogenetic trees used in the study.</p> <p>1. Modern methods of ancestral state estimation (ASE) incorporate branch length information, and it has been demonstrated that ASEs are more accurate when conducted on the branch lengths most correlated with a character's evolution; however, a reliable method for choosing between alternate branch length sets for discrete characters has not yet been proposed.<br><br>2. In this study, we simulate paired chronograms and phylograms, and generate binary characters that evolve in correlation with one of these. We then investigate (1) the effect of alternate branch lengths on ASE error, and (2) whether phylogenetic signal statistics and/or model-fit statistic can be used to select the branch lengths most correlated with a binary character.<br><br>3. In agreement with previous studies, we find that ASEs are more accurate when conducted on the branch lengths most correlated with the character. Phylogenetic signal statistics show limited utility for selecting the correct branch lengths, but model-fit statistics are found to be more accurate, with the correct branch lengths generally returning greater model-fit (lower AICc and BIC values). Using this method to choose between alternate branch length sets is more accurate when tree and character properties are more favorable for model optimization, and when shape differences between alternate phylogenies are greater.<br><br>4. Our results indicate that researchers conducting ASEs on discrete characters should carefully consider which branch lengths are appropriate, and, in the absence of other evidence, we suggest estimating model-fit values over alternate branch length sets and evolutionary models and choosing the branch length/model combination that returns better model fit.</p>
APPENDIX 3. — Maximum likelihood phylogram inferred from 47 taxa and 3314 in Mucoralean fungi in Thailand: novel species of Absidia from tropical forest soil
APPENDIX 3. — Maximum likelihood phylogram inferred from 47 taxa and 3314 characters based on LSU, SSU and ACT-1 matrix using GTR+G model. ML bootstrap support (≥ 70%) are indicated above the branches or near the nodes. Tree is artificially rooted using Cunninghamella homothallica (CBS 168.53), C. phaeospora (CBS 692.68), and C. bainieri (FSU319). The new species are in black bold and the type species in the dataset are indicated using T. (-) represent bootstrap support lower than 70%. (*) indicates unrecovered branching.
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732). in A study of genetic diversity among different population of Orthochirus sp. based on cytochrome C oxidase subunit I and 16srRNA sequencing
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732).
Fig. 3 in Detection of Eumonospora henryae (Apicomplexa: Sarcocystidae) from Falco columbarius (Falconiformes: Aves): Comparison of host-parasite phylogram and comments on the family Sarcocystidae Poche, 1913
Fig. 3. Phylograms of the genus Eumonospora on the left and core land birds modified from McClure et al. (2019) on the right. The boxes under Eumonospora spp. represent detected host species and the shaded boxes encompass the Afroaves. The lines connect parasites and hosts encountered, with the dotted line indicating host switching across order boundaries.
Fig. 1 in Detection of Eumonospora henryae (Apicomplexa: Sarcocystidae) from Falco columbarius (Falconiformes: Aves): Comparison of host-parasite phylogram and comments on the family Sarcocystidae Poche, 1913
Fig. 1. Optical (A, B) and differential interference contrast photomicrographs (C, D) of oocysts and sporocysts of Eumonospora sp. detected from Falco columbarius. Fig. 1A. Sporulated oocyst with stout sporozoites (SZ) inside a sporocyst (SP). Fig. 1B. A collapsed oocyst with a compact sporocyst residuum (SR) within an SP. Fig. 1C. Randomly diffused SR within an SP. Fig. 1D. Eight SZs with diffused SR. Scale bars = 10 μm.
Fig. 2 in Detection of Eumonospora henryae (Apicomplexa: Sarcocystidae) from Falco columbarius (Falconiformes: Aves): Comparison of host-parasite phylogram and comments on the family Sarcocystidae Poche, 1913
Fig. 2. Phylogenetic trees based on three concatenated datasets (A: 18S + cox1, B: 18S + 28S, and C: 28S + cox1). Phylogenetic analyses are performed via Bayesian inference (BI) and maximum likelihood (ML) methods. Nodes are labelled with probability for BI method node support (left) and bootstrap value support for the ML method (right). Similar phylograms are illustrated with both methods in all datasets. Monophyletic clade of Eumonospora spp. branches off earlier than the clade of Besnoitia spp. and the clade comprising genera Hammondia, Heydornia, Neospora, and Toxoplasma. 18S: nuclear small subunit ribosomal DNA; 28S: nuclear large subunit ribosomal DNA; cox1: mitochondrial Cytochrome C oxidase subunit 1; NA: not available.
Figure 2. Bayesian phylogram for cytochrome c oxidase subunit I sequences. Upper Sacramento River basin haplotypes are distributed among clades A–D in Extensive diversification of pebblesnails (Lithoglyphidae: Fluminicola) in the upper Sacramento River basin, northwestern USA
Figure 2. Bayesian phylogram for cytochrome c oxidase subunit I sequences. Upper Sacramento River basin haplotypes are distributed among clades A–D. Posterior probability values ≥ 90% are shown. Upper Sacramento River basin lineages newly discovered in this study are highlighted by the larger font. Specimen codes are from Table 1.
Figure 11. Maximum likelihood phylogram. Bootstrap values greater than 50 in Evolution of cave living in Hawaiian Schrankia (Lepidoptera: Noctuidae) with description of a remarkable new cave species
Figure 11. Maximum likelihood phylogram. Bootstrap values greater than 50% are illustrated on tree as first value; Bayesian posterior probabilities are the second value. Values <50 are not labelled. Colours represent islands (black is Hawaii Island; red is Maui, blue is Oahu; green is Kauai). Asterisks denote flightless individuals. Black circles represent dark-zone morph Schrankia howarthi; grey circles represent twilight-zone individuals. Locality information for individual moths may be found in the Appendix.
Chronogram or phylogram for ancestral state estimation? Model-fit statistics indicate the branch lengths underlying a binary character’s evolution: R scripts and simulated trees
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Bayesian consensus phylogram from the article "Systematics of Huicundomantis, a new subgenus of Pristimantis (Anura, Strabomantidae) with extraordinary cryptic diversity and eleven new species"
<p>Bayesian consensus phylogram depicting relationships within <em>Pristimantis</em> (<em>Huicundomantis</em>). Museum catalog numbers are shown before the species name. Posterior probabilities resulting from Bayesian Markov chain Monte Carlo searches appear next to the branches.</p>
FIGURE 3. Phylogram representing a in A new species of Auriculostoma (Trematoda: Allocreadiidae) from the intestine of Brycon guatemalensis (Characiformes: Bryconidae) from the Usumacinta River Basin, Mexico, based on morphology and 28 S rDNA sequences, with a key to species of the genus
FIGURE 3. Phylogram representing a hypothesis for the relationships of Auriculostoma lobata n. sp. with other allocreadiids. The tree represents the single best tree obtained from maximum likelihood analysis based on 28S rDNA sequences from allocreadiids and rooted using species of Prosthenhystera (Callodistomidae). Numbers near internal nodes indicate bootstrap support values (*= values 100%).
FIGURE 1. Maximum likelihood phylogram derived from a Bayesian backbone constraint consensus tree constructed using only taxa for which 12S, 16S, cytochrome b and cytochrome oxidase I in A new species of Dendrobates (Anura: Dendrobatidae) from the Amazonian lowlands in Perú
FIGURE 1. Maximum likelihood phylogram derived from a Bayesian backbone constraint consensus tree constructed using only taxa for which 12S, 16S, cytochrome b and cytochrome oxidase I sequence data were available. Numbers indicate posterior probabilities from the Bayesian analysis. Species of the Ventrimaculatus group are denoted with s.s. (sensu stricto), s.l. (sensu lato) and sp. aff (species affinis).
FIGURE 9. Phylogram obtained with RAxML and the combined mitochondrial sequence data. Bootstrap values above nodes. See Table 1 in Stictonectes rebeccae sp. n. from the Iberian Peninsula, with notes on its phylogenetic position (Coleoptera, Dytiscidae)
FIGURE 9. Phylogram obtained with RAxML and the combined mitochondrial sequence data. Bootstrap values above nodes. See Table 1 for localities.
FIGURE 6. Phylogram from a in A complex of Transversotrematidae (Platyhelminthes: Digenea) associated with mullid fishes of the Indo-West Pacific Region, including the descriptions of four new species of Transversotrema
FIGURE 6. Phylogram from a MP analysis of sequences from the partial 28S region (D1–D3) of all known marine transversotrematid groups from the Indo-West Pacific region. This is tree one of 27 most parsimonious trees (length = 630). The consistency index is (0.723849), the retention index is (0.796296) and the composite index is 0.629453 (0.576399) for all sites and parsimony-informative sites). The percentage of replicate trees in which the associated taxa are clustered together in the bootstrap test (1000) replicates are shown next to the branches. The Complete Deletion option resulted in a total of 809 positions in the final dataset, of which 244 were parsimony informative Note that the sequences for T. haasi, C. formosa, P. steeri and B. fusiformis were obtained from GenBank. All sequences from the T. licinum complex are from fish collected from Heron Island.
FIGURE 2. Maximum likelihood phylogram generated from a in Mitochondrial DNA reveals a new species of parachuting frog (Rhacophoridae: Rhacophorus) from Sumatra
FIGURE 2. Maximum likelihood phylogram generated from a fragment of 16S mitochondrial DNA. Unless otherwise noted, support values appear above branches and correspond to posterior probabilities (BAYES), maximum likelihood bootstrapping (ML), parsimony bootstrapping (MP), and minimum evolution bootstrapping (ME), respectively. Nodes not receiving topological support are indicated with "NS".
FIGURE 14. Unrooted Neighbour-joining phylogram the 28S in A new species of Cymodoce Leach, 1814 (Crustacea: Isopoda: Sphaeromatidae) based on morphological and molecular data, with a key to the Northern Indian Ocean species
FIGURE 14. Unrooted Neighbour-joining phylogram the 28S rDNA: D8 expansion fragment of Cymodoce delavrii, C. tribullis and C. waegelei based on p-distances.
FIGURE 6. Maximum Likelihood inference phylogram from Analysis 1 recovering a in Flightless Notaris (Coleoptera: Curculionidae: Brachycerinae: Erirhinini) in Southwest China: monophyly, mtDNA phylogeography and evolution of habitat associations
FIGURE 6. Maximum Likelihood inference phylogram from Analysis 1 recovering a clade of Notaris + Tournotaris. Terminal labels consist of a taxonomic name (to a genus and/or species), followed by BOLD Sample ID, then by GenBank accession, then by Barcode Index Numbers (BINs, Ratnasingham & Hebert 2013), then by Museum abbreviation. Digits at internodes are bootstrap values from Analysis 1 followed, after a slash, by those from Analysis 2. Habitus images (not to scale) are denoted by abbreviated genus and species letters on the same level with the terminal.
FIGURE 2. Cytochrome b maximum likelihood phylogram for the genus Carollia. Support statistics from a maximum likelihood bootstrap analysis and a in On the phylogenetic position of Carollia manu Pacheco et al., 2004 (Chiroptera: Phyllostomidae: Carolliinae)
FIGURE 2. Cytochrome b maximum likelihood phylogram for the genus Carollia. Support statistics from a maximum likelihood bootstrap analysis and a Bayesian analysis are indicated at each resolved node. For the maximum likelihood analysis (ML), white indicates bootstrap frequencies ≤ 50%, grey indicates bootstrap frequencies between 50% and 75%, and black indicates bootstrap frequencies ≥ 75%. For the Bayesian analysis (BPP), white indicates posterior probabilities <0.95, whereas black indicates posterior probabilities ≥ 0.95.
FIGURE 1. Phylogram constructed for Cytospora using a in Cytospora berberidicola sp. nov. (Diaporthales, Cytosporaceae) in China
FIGURE 1. Phylogram constructed for Cytospora using a combined dataset of actin (ACT), internal transcribed spacer (ITS), RNA polymerase II second largest subunit (RPB2), translation elongation factor 1-alpha (TEF1) and beta-tubulin (TUB2) genes, based on the best-parsimonious tree. Maximum likelihood bootstrap support values above 70% are shown. The thickened branches indicate posterior probabilities greater than 0.95 obtained from BI. Scale bar = 0.2. Diaporthe vaccinii CBS 160.32 was used as the outgroup. Ex-type strains are in bold. Strains from the current study are in bold and blue.
FIGURE 1. The best scoring phylogram generated from a in Colletotrichum dracaenigenum, a new species on Dracaena fragrans
FIGURE 1. The best scoring phylogram generated from a final MP dataset based on combined ITS, GAPDH, CHS-1, ACT and TUB2 sequence data. Bootstrap support values for maximum parsimony (MP, left) and maximum likelihood (ML, middle) are greater than 60% and Bayesian posterior probabilities (PP, right) equal to or greater than 0.95 are indicated at the nodes. The new taxon is bolded in red.
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