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45 results for “bootstrap support”
Fig. 3. Majority with bootstrap support consensus trees for 12S in MITOCHONDRIAL 16S AND 12S rRNA SEQUENCE ANALYSIS IN FOUR SALMONID SPECIES FROM ROMANIA
Fig. 3. Majority with bootstrap support consensus trees for 12S rRNA. (a) 12S rRNA Maximum Parsimony tree; (b) 12S rRNA Neighbor Joining tree, distance model Kimura 2 Parameters, transi-
Fig. 2. Majority with bootstrap support consensus trees for 16S in MITOCHONDRIAL 16S AND 12S rRNA SEQUENCE ANALYSIS IN FOUR SALMONID SPECIES FROM ROMANIA
Fig. 2. Majority with bootstrap support consensus trees for 16S rRNA. (a) 16S rRNA Neighbor Joining tree, distance model Kimura 2 Parameters, transition/transversion ratio 2.3; (b) 16S rRNA Maximum Parsimony tree; (c) 16S rRNA Maximum Likelihood tree
◂Fig. 6 A molecular phylogeny of 56 systematically representative Peridiniaceae, including 42 accessions assignable to P. cinctum from various geographic regions. Maximum likelihood tree (– ln = 21,884.93), as inferred from a rRNA nucleotide alignment (1137 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (CZE Czech Republic, E East, GER Germany, HET Heterocapsaceae, N North, PPE Protoperidiniaceae, POL Poland, rbn ribotype n, S South, SWE Sweden, UKR Ukraine, W West) in Bumps on the back: An unusual morphology in phylogenetically distinct Peridinium aff. cinctum (= Peridinium tuberosum; Peridiniales, Dinophyceae)
◂Fig. 6 A molecular phylogeny of 56 systematically representative Peridiniaceae, including 42 accessions assignable to P. cinctum from various geographic regions. Maximum likelihood tree (– ln = 21,884.93), as inferred from a rRNA nucleotide alignment (1137 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (CZE Czech Republic, E East, GER Germany, HET Heterocapsaceae, N North, PPE Protoperidiniaceae, POL Poland, rbn ribotype n, S South, SWE Sweden, UKR Ukraine, W West)
◂Fig. 4 A molecular tree of 51 systematically representative Peridiniaceae, including all 28 accessions assignable to P. volzii. Maximum Likelihood tree (–ln = 22,017.62), as inferred from a rRNA nucleotide alignment (1,129 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (abbreviations: HET, Heterocapsaceae; PPE, Protoperidiniaceae) in Morphological and molecular variability of Peridinium volzii Lemmerm. (Peridiniaceae, Dinophyceae) and its relevance for infraspecific taxonomy
◂Fig. 4 A molecular tree of 51 systematically representative Peridiniaceae, including all 28 accessions assignable to P. volzii. Maximum Likelihood tree (–ln = 22,017.62), as inferred from a rRNA nucleotide alignment (1,129 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (abbreviations: HET, Heterocapsaceae; PPE, Protoperidiniaceae)
Рис. 1. ФиΛогенетические Αеревья хантавируса AMRV и его прироΑного носитеΛя восточноазиатской мыши Apodemus peninsulae Thomas, 1906. А. ФиΛогенетическое Αерево восточноазиатской мыши Apodemus peninsulae, построенное метоΑом «максимаΛьного правΑопоΑобия» (ML) и поΛученное на основе анаΛиза участка гена цитохрома b мтΔНК (744 п.н.). В узΛах ветвΛения указаны бутстреп-поΑΑержки, рассчитанные ΑΛя 1000 повторов. Цветными Λиниями обозначены фиΛогенетические Λинии: Αве Китайские (зеΛеный), Корейская «Korea» (синий), Амурская «Amur» (красный). ПоΛужирным шрифтом выΑеΛены собственные образцы. Названия образцов из GenBank/NCBI быΛи сокращены; B. ФиΛогенетическое Αерево из работы Α. Н. Яшиной с ΑопоΛнениями, построенное метоΑом «бΛижайшего сосеΑа» (NJ) на основе посΛеΑоватеΛьностей фрагмента М-сегмента (2737–2980 н.п.) генома хантавирусов. В узΛах ветвΛения указаны бутстреппоΑΑержки, рассчитанные ΑΛя 1000 повторов. Жирным выΑеΛены иссΛеΑованные РНК изоΛяты (Яшина 2012; Яшина и Αр. 2019) Fig. 1. Phylogenetic trees of AMRV and its natural reservoir host — the Korean field mouse Apodemus peninsulae Thomas, 1906. A. Phylogenetic tree of the Korean field mouse Apodemus peninsulae constructed by the "maximum likelihood" method (ML). The data are obtained from the analysis of the cytochrome b mtDNA gene fragments (744 bp). Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. Colored lines indicate phylogenetic lines: two Chinese (green), Korea (blue), and Amur (red). Own samples are highlighted in bold. The names of the samples from GenBank/NCBI have been shortened; B. Phylogenetic tree from L. N. Yashina's work with additions constructed by the neighbour joining method (NJ). It is based on the sequences of an M-segment fragment (2737–2980 bp) of the hantavirus genome. Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. The researched RNA isolates are highlighted in bold (Yashina 2012; Yashina et al. 2019) in Variability of the gene cyt b in the Korean field mouse Apodemus peninsulae Thomas, 1906 - a reservoir host of AMRV in the Khasansky District of Primorsky Krai
Рис. 1. ФиΛогенетические Αеревья хантавируса AMRV и его прироΑного носитеΛя восточноазиатской мыши Apodemus peninsulae Thomas, 1906. А. ФиΛогенетическое Αерево восточноазиатской мыши Apodemus peninsulae, построенное метоΑом «максимаΛьного правΑопоΑобия» (ML) и поΛученное на основе анаΛиза участка гена цитохрома b мтΔНК (744 п.н.). В узΛах ветвΛения указаны бутстреп-поΑΑержки, рассчитанные ΑΛя 1000 повторов. Цветными Λиниями обозначены фиΛогенетические Λинии: Αве Китайские (зеΛеный), Корейская «Korea» (синий), Амурская «Amur» (красный). ПоΛужирным шрифтом выΑеΛены собственные образцы. Названия образцов из GenBank/NCBI быΛи сокращены; B. ФиΛогенетическое Αерево из работы Α. Н. Яшиной с ΑопоΛнениями, построенное метоΑом «бΛижайшего сосеΑа» (NJ) на основе посΛеΑоватеΛьностей фрагмента М-сегмента (2737–2980 н.п.) генома хантавирусов. В узΛах ветвΛения указаны бутстреппоΑΑержки, рассчитанные ΑΛя 1000 повторов. Жирным выΑеΛены иссΛеΑованные РНК изоΛяты (Яшина 2012; Яшина и Αр. 2019) Fig. 1. Phylogenetic trees of AMRV and its natural reservoir host — the Korean field mouse Apodemus peninsulae Thomas, 1906. A. Phylogenetic tree of the Korean field mouse Apodemus peninsulae constructed by the "maximum likelihood" method (ML). The data are obtained from the analysis of the cytochrome b mtDNA gene fragments (744 bp). Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. Colored lines indicate phylogenetic lines: two Chinese (green), Korea (blue), and Amur (red). Own samples are highlighted in bold. The names of the samples from GenBank/NCBI have been shortened; B. Phylogenetic tree from L. N. Yashina's work with additions constructed by the neighbour joining method (NJ). It is based on the sequences of an M-segment fragment (2737–2980 bp) of the hantavirus genome. Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. The researched RNA isolates are highlighted in bold (Yashina 2012; Yashina et al. 2019)
Text-fig. 3. Phylogenetic relationship of Peignecyon felinoides n. gen. et n. sp., within some selected Amphicyonidae, and some extinct caniform carnivorans. Paramiacis exilis is the outgroup. Searches were performed by means of the Branch and Bound and a Bootstrap analysis through 1,000 replicates. One tree is obtained (length 73 steps, consistency index (CI) = 0.6301, retention index (RI) = 0.7000). The numbers below nodes are Bremer indices, and the numbers above nodes are Bootstrap support percentages (only shown ≥ 50). in A New Thaumastocyoninae (Amphicyonidae, Carnivora) From The Early Miocene Of Tuchořice, The Czech Republic
Text-fig. 3. Phylogenetic relationship of Peignecyon felinoides n. gen. et n. sp., within some selected Amphicyonidae, and some extinct caniform carnivorans. Paramiacis exilis is the outgroup. Searches were performed by means of the Branch and Bound and a Bootstrap analysis through 1,000 replicates. One tree is obtained (length 73 steps, consistency index (CI) = 0.6301, retention index (RI) = 0.7000). The numbers below nodes are Bremer indices, and the numbers above nodes are Bootstrap support percentages (only shown ≥ 50).
Figure 2. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 2. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 4. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI and 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 4. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI and 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 3. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 3. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 1. - Bayesian phylogeny of Euptychia based on one mitochondrial (COI) and one nuclear (EF1-a) gene. Posterior probabilities are listed above and bootstrap values below branches. A dash denotes bootstrap support lower than 50%. (Euptychiaattenboroughi is not included in the analysis – see text for details.)
Figure 1. - Bayesian phylogeny of Euptychia based on one mitochondrial (COI) and one nuclear (EF1-a) gene. Posterior probabilities are listed above and bootstrap values below branches. A dash denotes bootstrap support lower than 50%. (Euptychiaattenboroughi is not included in the analysis – see text for details.)
Figure 10. - Maximum-likelihood phylogeny of Epicephala species based on sequences of the COI, ArgK and EF1α genes. Numbers above nodes are maximum-likelihood bootstrap support values based on 1,000 replications. The Japanese Epicephala species are marked in blue. Symbols right to species names donate ovipositor morphology: inverted U-shape, rounded apically; inverted V-shape, acute apically.
Figure 10. - Maximum-likelihood phylogeny of Epicephala species based on sequences of the COI, ArgK and EF1α genes. Numbers above nodes are maximum-likelihood bootstrap support values based on 1,000 replications. The Japanese Epicephala species are marked in blue. Symbols right to species names donate ovipositor morphology: inverted U-shape, rounded apically; inverted V-shape, acute apically.
Data from: Robustness of Felsenstein's versus transfer bootstrap supports with respect to taxon sampling
<p><span>The bootstrap method is based on resampling sequence alignments and re-estimating trees. Felsenstein's bootstrap proportions (FBP) is the most common approach to assess the reliability and robustness of sequence-based phylogenies. However, when increasing taxon sampling (i.e., the number of sequences) to hundreds or thousands of taxa, FBP tends to return low supports for deep branches. The Transfer Bootstrap Expectation (TBE) has been recently suggested as an alternative to FBP. TBE is measured using a continuous transfer index in [0,1] for each bootstrap tree, instead of the binary {0,1} index used in FBP to measure the presence/absence of the branch of interest. TBE has been shown to yield higher and more informative supports, while inducing a very low number of falsely supported branches.</span> <span>Nonetheless, it has been argued that TBE must be used with care due to sampling issues, especially in datasets with high number of closely related taxa. In this study, we conduct multiple experiments by varying taxon sampling and comparing FBP and TBE support values on different phylogenetic depth, using empirical datasets. Our results show that the main critique of TBE stands in extreme cases with shallow branches and highly unbalanced sampling among clades, but that TBE is still robust in most cases, while FBP is inescapably negatively impacted by high taxon sampling. We suggest guidelines and good practices in TBE (and FBP) computing and interpretation.</span></p>
Data from: Robustness of Felsenstein’s versus transfer bootstrap supports with respect to taxon sampling
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The asymptotic behavior of bootstrap support values in molecular phylogenetics
<p>The phylogenetic bootstrap is the most commonly used method for assessing statistical confidence in estimated phylogenies by non-Bayesian methods such as maximum parsimony and maximum likelihood (ML). It is observed that bootstrap support tends to be high in large genomic datasets whether or not the inferred trees and clades are correct. Here we study the asymptotic behavior of bootstrap support for the ML tree in large datasets when the competing phylogenetic trees are equally right or equally wrong. We consider phylogenetic reconstruction as a problem of statistical model selection when the compared models are nonnested and misspecified. The bootstrap is found to have qualitatively different dynamics from Bayesian inference, and does not exhibit the polarized behavior of posterior model probabilities, consistent with the empirical observation that the bootstrap is more conservative than Bayesian probabilities. Nevertheless bootstrap support similarly shows fluctuations among large datasets, with no convergence to a point value, when the compared models are equally right or equally wrong. Thus in large datasets strong support for wrong trees or models is likely to occur. Our analysis provides a partial explanation for the high bootstrap support values for incorrect clades observed in empirical data analysis.</p>
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. The Bayesian tree of the Adaintum pedatum complex based on chloroplast markers and corresponding rhizome type. Support values (Bayesian inference posterior probability (BIPP) (upper) ≥ 0.5, and maximum likelihood bootstrap support (MLBS) (nether) ≥ 50%) are shown above the main branches, the thickened branches indicate MLBS=100 and BIPP=1. Yellow bar means erect rhizome; blue bar means creeping rhizome; gray bar means decumbent or short-creeping rhizome. in Adiantum japonicum, a new species of the Adiantum pedatum complex (Pteridaceae) from Japan
FIGURE. The Bayesian tree of the Adaintum pedatum complex based on chloroplast markers and corresponding rhizome type. Support values (Bayesian inference posterior probability (BIPP) (upper) ≥ 0.5, and maximum likelihood bootstrap support (MLBS) (nether) ≥ 50%) are shown above the main branches, the thickened branches indicate MLBS=100 and BIPP=1. Yellow bar means erect rhizome; blue bar means creeping rhizome; gray bar means decumbent or short-creeping rhizome.
FIGURE. Phylogenetic tree based on RAxML analyses of a combined LSU, ITS and SSU dataset. Bootstrap support values for ML and MP equal to or greater than 75% and PP value greater than 0.95 are in thickened. Ex-type isolates are in bold, and new taxa are indicated in red. The tree is rooted with Atractospora aquatica (S-1297) and A. aquatica (MFLU 18–2322). in Conlarium sichuanense sp. nov., on Ficus virens from Sichuan Province, China
FIGURE. Phylogenetic tree based on RAxML analyses of a combined LSU, ITS and SSU dataset. Bootstrap support values for ML and MP equal to or greater than 75% and PP value greater than 0.95 are in thickened. Ex-type isolates are in bold, and new taxa are indicated in red. The tree is rooted with Atractospora aquatica (S-1297) and A. aquatica (MFLU 18–2322).
FIGURE. Maximum likelihood phylogram of Multiclavula spp. based on ITS sequences. Rooted to Clavulina cristata. Bar = estimated changes/nucleotide. Support values above or below branches: Bayesian posterior probability/maximum likelihood bootstrap. in New and interesting species of Agaricomycetes from Panama
FIGURE. Maximum likelihood phylogram of Multiclavula spp. based on ITS sequences. Rooted to Clavulina cristata. Bar = estimated changes/nucleotide. Support values above or below branches: Bayesian posterior probability/maximum likelihood bootstrap.
FIGURE. Maximum likelihood phylogram of Humidicutis spp. based on ITS sequences. Rooted to Humidicutis marginata. Bar = estimated changes/nucleotide. Support values above or below branches: Bayesian posterior probability/maximum likelihood bootstrap. in New and interesting species of Agaricomycetes from Panama
FIGURE. Maximum likelihood phylogram of Humidicutis spp. based on ITS sequences. Rooted to Humidicutis marginata. Bar = estimated changes/nucleotide. Support values above or below branches: Bayesian posterior probability/maximum likelihood bootstrap.
FIGURE. Bayesian MCMC phylogram of Gliophorus spp. based on ITS sequences. Rooted to Hygrophorus pudorinus. Bar = estimated changes/nucleotide. Support values above or below branches: Bayesian posterior probability/maximum likelihood bootstrap. in New and interesting species of Agaricomycetes from Panama
FIGURE. Bayesian MCMC phylogram of Gliophorus spp. based on ITS sequences. Rooted to Hygrophorus pudorinus. Bar = estimated changes/nucleotide. Support values above or below branches: Bayesian posterior probability/maximum likelihood bootstrap.
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