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34 results for “maximum likelihood phylogeny”
FIGURE 1. The maximum likelihood majority rule consensus tree for the analyzed Pseudorobillarda and related taxa. RAxML bootstrap support values above 50 in Morphology and phylogeny of Pseudorobillarda eucalypti sp. nov., from Thailand
FIGURE 1. The maximum likelihood majority rule consensus tree for the analyzed Pseudorobillarda and related taxa. RAxML bootstrap support values above 50% (ML) are given at the nodes. Phylogeny tree is rooted to Schismatomma decolorans.
FIGURE 111. Maximum Likelihood tree for 12 in <strong>Revision of the genus <em>Erythromelana</em> Townsend (Diptera: Tachinidae) and analysis of its phylogeny and diversification</strong>
FIGURE 111. Maximum Likelihood tree for 12 representatives of Blondeliini and 13 Erythromelana COI sequences. Numbers above branches indicate bootstrap percentages greater than 30.
FIGURE 6. Maximum likelihood tree from a in Morphology and phylogeny of a new species, Pseudocercospora haldinae (Mycosphaerellaceae) on Haldina cordifolia from India
FIGURE 6. Maximum likelihood tree from a concatenated dataset including ribosomal gene regions nuLSU and ITS. Numbers on the branches are percent bootstrap values for MEGA5-maximum likelihood (ML), MEGA5-maximum parsimony (MP) and Bayesian posterior probabilities (PP) indicated in order ML/MP/PP. New sequence data of P. haldinae is represented in red.
Figure 3. Maximum-likelihood tree for 78 in Molecular phylogeny of the Forcipulatacea (Asteroidea: Echinodermata): systematics and biogeography
Figure 3. Maximum-likelihood tree for 78 forcipulate taxa and five velatidan taxa, based on 327 bp for the early-stage histone H3 gene plus the same rDNA sequences that were used in Figure 2. Bootstrap support values are based on 200 pseudoreplicates. Other details are as described in Figure 2.
Figure 6. Best maximum likelihood phylogeny using a in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
Figure 6. Best maximum likelihood phylogeny using a concatenated dataset of the 27 genes composing the best combination of top-ranked loci using five ranking criteria identified using measures of Tree Certainty (Salichos & Rokas, 2013). Numbers above branches (red) are bootstrap percentages based on the combined bootstrap replicates. Numbers below branches and adjacent to nodes indicate internode certainty (IC) and internode certainty all (ICA) values of the individual gene bootstrap trees compared with the best maximum likelihood tree depicted. Family/clade designations (fide Matheny et al., 2006 except 1 fide Henkel, Smith & Aime, 2010 and 2 fide Nakasone, Hibbett & Goranova, 2009) are indicated to the right of terminal labels and suborders are named with capital letters at the far right.
FIGURE 23. Maximum likelihood phylogenies for the Bubarida. A in The Sponges of the Carmel Pinnacles Marine Protected Area
FIGURE 23. Maximum likelihood phylogenies for the Bubarida. A: 28S locus, B: cox1 locus. Green clade designated the putative Bubarida; the orders and families currently housing each taxon is also shown. Genbank accession numbers are shown; bold indicates new sequences; asterisks designate type species. Node confidence is based on bootstrapping. Scale bar indicates substitutions per site. Colors indicate clades containing new taxa, as referenced in the text.
FIGURE 21. Maximum likelihood phylogenies for the Scopalinida. A in The Sponges of the Carmel Pinnacles Marine Protected Area
FIGURE 21. Maximum likelihood phylogenies for the Scopalinida. A: 28S locus, B: cox1 locus. Genbank accession numbers are shown; bold indicates new sequences. Node confidence is based on bootstrapping. Scale bar indicates substitutions per site.
FIGURE 18. Maximum likelihood phylogenies for the Halichondriidae. A in The Sponges of the Carmel Pinnacles Marine Protected Area
FIGURE 18. Maximum likelihood phylogenies for the Halichondriidae. A: 28S locus, B: cox1 locus. Genbank accession numbers are shown; bold indicates new sequences. Node confidence is based on bootstrapping. Scale bar indicates substitutions per site.
FIGURE 7. Phylogenetic maximum likelihood reconstruction using partial 28S in A new species of Cycloporus from the Adriatic Sea, with an updated phylogeny of the families Euryleptidae and Stylostomidae (Polycladida, Platyhelminthes)
FIGURE 7. Phylogenetic maximum likelihood reconstruction using partial 28S sequences (accession numbers in brackets) of polyclads, rooted with Macrostomum lignano; branches other than Euryleptidae and Stylostomidae collapsed. Bootstrap nodal support of 200 non-parametric bootstrap replicates. Full tree in Suppl. Mat. 2. Cycloporus pinkipus sp. n. marked in pink. Additional representatives of Cycloporus written in red. Representatives of Eurylepta written in light green. Branches of Euryleptidae in light green. Branches of Stylostomidae in light blue. Branches of Pseudocerotidae in purple. Scale bar indicates the number of substitutions per site.
indicate branches. above MrBayes numbers by inferred The . supports Ixodes of probability subgenera 22 posterior the of Inference 16 from Bayesian ticks of indicate genomes mitochondrial branches below 40 numbers of The sequences. RAxML nucleotide by the inferred from support inferred bootstrap Phylogenies Likelihood . 2 FIGURE Maximum in A new subgenus, Australixodes n. subgen. (Acari: Ixodidae), for the kiwi tick, Ixodes anatis Chilton, 1904, and validation of the subgenus Coxixodes Schulze, 1941 with a phylogeny of 16 of the 22 subgenera of Ixodes Latreille, 1795 from entire mitochondrial genome sequences
indicate branches. above MrBayes numbers by inferred The . supports Ixodes of probability subgenera 22 posterior the of Inference 16 from Bayesian ticks of indicate genomes mitochondrial branches below 40 numbers of The sequences. RAxML nucleotide by the inferred from support inferred bootstrap Phylogenies Likelihood . 2 FIGURE Maximum
FIGURE 2. Maximum likelihood phylogeny inferred from cox1 in Exploring gene sequences and phylogenetic relationships of four terrestrial planarian species (Platyhelminthes; Tricladida; Geoplanidae) in Europe
FIGURE 2. Maximum likelihood phylogeny inferred from cox1 sequences (dataset 1). Tree scale corresponds to the number of substitutions per site. Numbers at nodes correspond to the ultrafast bootstrap support values (showing only values from 70% to 100%). Countries of origin labelled as 3-digit alpha code: AUS (Australia), BRA (Brazil), ESP (Spain), FRA (France), GBR (UK), NZL (New Zealand), PAN (Panama). Results from species in this study are highlighted in red (Australopacifica atrata), blue (Artioposthia exulans), and green (Marionfyfea adventor).
Fig. 3. Maximum likelihood phylogeny for 72 unique haplotypes obtained from O. hatcheri, O in Populations of Odontesthes (Teleostei: Atheriniformes) in the Andean region of Southern South America: body shape and hybrid individuals
Fig. 3. Maximum likelihood phylogeny for 72 unique haplotypes obtained from O. hatcheri, O. bonariensis, and O. smitti. Haplotype labels indicate their sampling locality (as explained in Fig. 1 and Table 1) and the number of individuals (in parentheses). Several common haplotypes were recovered from several individuals from the same or different localities (most significantly haplotype 5). Monophyly of haplotypes from each species is supported by 100% bootstrap values, and two groups of O. hatcheri haplotypes (from EPU and CDP, indicated by heavier lines) also received strong bootstrap support. All other nodes were weakly supported by bootstrap analyses. *: presumptive hybrids individuals identified on meristic and morphological characters (Table 2).
Figure 2. Maximum-likelihood tree for 95 in Molecular phylogeny of the Forcipulatacea (Asteroidea: Echinodermata): systematics and biogeography
Figure 2. Maximum-likelihood tree for 95 forcipulate taxa and nine velatidan taxa, rooted on 111 taxa belonging to the Valvatida, Paxillosida, and Notomyotida (these taxa have been omitted for clarity), and based on 261 bp of sequence data for the 12S rDNA gene and 437 bp for the 16S rDNA gene. Bootstrap support values are based on 250 pseudoreplicates and are shown as percentages when ± 50%. Named clades correspond either to traditional taxonomic groups or to geographically restricted lineages.
Figure 3. Maximum likelihood phylogeny showing the relationships among Indo-Burmese Cyrtodactylus species using mitochondrial NADH dehydrogenase subunit 2 in Morphological and molecular phylogenetic data reveal another new species of bent-toed gecko (Cyrtodactylus Gray: Squamata: Gekkonidae) from Mizoram, India
Figure 3. Maximum likelihood phylogeny showing the relationships among Indo-Burmese Cyrtodactylus species using mitochondrial NADH dehydrogenase subunit 2 gene. Numbers at each node are bootstrap support values. Preceding each species name is the NCBI accession number.
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