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501 results for “Phylogenetic tree”
FIGURE 6 Bayesian phylogenetic tree inferred from LSU gene DNA sequences. Posterior probabilities greater than 50 in New Zealand species of the genus Tripyla Bastian, 1865 (Nematoda: Triplonchida: Tripylidae). I: A new species, a new record and key to long-tailed species
FIGURE 6 Bayesian phylogenetic tree inferred from LSU gene DNA sequences. Posterior probabilities greater than 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 5. Genus Protosuberites. Phylogenetic tree obtained using a in Coping with brackish water: A new species of cave-dwelling Protosuberites (Porifera: Demospongiae: Suberitidae) from the Western Mediterranean and a first contribution to the phylogenetic relationships within the genus
FIGURE 5. Genus Protosuberites. Phylogenetic tree obtained using a concatenated analysis of COI, 18S, and 28S and analyzed by both Bayesian inference (BI) and maximum likelihood (ML) methods. Numbers over branches indicate posterior probabilities and below bootstrap values. Only posterior probabilities over 0.95 and bootstrap values over 70 are indicated.
FIGURE 2. Strict consensus tree from the unweighted analysis. The same topology was obtained from 12 in Phylogenetic relationships of the comb-footed spider subfamily Spintharinae (Araneae, Araneoidea, Theridiidae), with generic diagnoses and a key to the genera
FIGURE 2. Strict consensus tree from the unweighted analysis. The same topology was obtained from 12 (PAUP, branch collapsing rule 3) and two (TNT, branch collapsing rule 1) equally most parsimonious trees (spintharine synapomorphies with character numbers above and character states below).
FIGURE 1. Bayesian phylogenetic tree inferred from SSU gene DNA sequences. Posterior probabilities great than 50 in New Zealand species of the genus Tripyla Bastian, 1865 (Nematoda: Triplonchida: Tripylidae). II: Two new, a known species and key to species
FIGURE 1. Bayesian phylogenetic tree inferred from SSU gene DNA sequences. Posterior probabilities great than 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 13. Phylogenetic tree inferred from a in Validation of the taxon Ixodes aragaoi Fonseca (Acari: Ixodidae) based on morphological and molecular data
FIGURE 13. Phylogenetic tree inferred from a partial sequence (435 characters, 113 parsimony informative) of the 16S rRNA mitochondrial gene of 12 tick species of the Ixodes ricinus complex, using I. nipponensis as outgroup. Numbers at nodes are the support values for the major branches (bootstrap) derived from 500 replicates for maximum parsimony. Number within brackets are GenBank accession numbers.
FIGURE 1. Time-calibrated phylogeny including 101 taxa built using program BEAST v1.7.5 in The phylogenetIc posItIon and taxonomIc status of the RaInbow Tree Snake Gonyophis margaritatus (Peters, 1871) (Squamata: ColubrIdae)
FIGURE 1. Time-calibrated phylogeny including 101 taxa built using program BEAST v1.7.5 (Drummond et al. 2012) with node support values representing posterior probability (left) and bootstrap support (right) from inferred Maximum Likelihood tree. Dashes for bootstrap values indicate low support or not supported by ML tree. Family Colubridae and subfamily Colubrinea are highlighted by red arrows. Taxa in genera Gonyosoma, Rhadinophis, Gonyophis, and Rhynchophis are highlighted in the red square on the tree.
FIGURE 7. Bayesian phylogenetic tree inferred from SSU rRNA gene sequences. Posterior probabilities greater than 50 in Description of Trischistoma abharensis n. sp. (Nematoda: Trischistomatidae) and first record of Tripylella intermedia (Bütschli, 1873) Brzeski & Winiszewska-Ślipinska, 1993 (Nematoda: Tripylidae) from Iran
FIGURE 7. Bayesian phylogenetic tree inferred from SSU rRNA gene sequences. Posterior probabilities greater than 50% are given on appropriate clades. Nematode species, GenBank accession numbers, and locations are listed for each taxon if known. The accession no. AY284737 was originally deposited in GenBank as Paratripyla sp., but it was used as Tripylella sp. by van Megen et. al. (2009).
FIGURE 1. Bayesian phylogenetic tree obtained with the COI, 12S, 16S in Lost and found: The Eocene family Pyramimitridae (Neogastropoda) discovered in the Recent fauna of the Indo-Pacific
FIGURE 1. Bayesian phylogenetic tree obtained with the COI, 12S, 16S, and 28S genes. Posterior probabilities are shown at nodes.
FIGURE 1. Bayesian phylogenetic tree. Only posterior probability values above 80 in DNA barcoding the phyllosoma of Scyllarides squammosus (H. Milne Edwards, 1837) (Decapoda: Achelata: Scyllaridae)
FIGURE 1. Bayesian phylogenetic tree. Only posterior probability values above 80 are shown, and branch width is proportional to posterior values.
FIGURE 5. Neighbour-joining tree obtained using K2P in New species and phylogenetic relationships of the spider genus Coptoprepes using morphological and sequence data (Araneae: Anyphaenidae)
FIGURE 5. Neighbour-joining tree obtained using K2P distances, downloaded from BOLD, showing the relationships for Coptoprepes Simon. Data presented as: Species name | Collection number | Sex | Country. Region or province | BIN number. Each color represents a different Barcode Index Number (BIN).
FIGURE 8. Bayesian phylogenetic tree inferred from D2D3 in First record of the root knot nematode, Meloidogyne minor in New Zealand with description, sequencing information and key to known species of Meloidogyne in New Zealand
FIGURE 8. Bayesian phylogenetic tree inferred from D2D3 gene DNA sequences of Meloidogyne minor. Posterior probabilities greater than 50% are given on appropriate clades. Nematode species, GenBank accession numbers and locations are listed for each taxon, if known.
FIGURE 1. Maximum clade credibility tree after a partitioned Bayesian analysis using 8945 in Phylogenetic analysis of the Neotropical Pristimantis leptolophus species group (Anura: Craugastoridae): molecular approach and description of a new polymorphic species
FIGURE 1. Maximum clade credibility tree after a partitioned Bayesian analysis using 8945 sites depicting the phylogenetic relationships among Pristimantis including the Pristimantis leptolophus species group. Numbers on nodes represent posterior probabilities and ultrafast bootstrap (as obtained in the ML analysis) support respectively. Asterisks represent nodal support larger than 95% in both ML and Bayesian analyses. Two dashes in ultrafast bootstrap indicate the node was not recovered in the ML analysis (see Appendix 2 for the ML tree).
FIGURE 9. Phylogenetic tree estimated from a 871 in A taxonomic revision of the Cardiocondyla nuda group (Hymenoptera: Formicidae)
FIGURE 9. Phylogenetic tree estimated from a 871bp fragment of CO I / CO using MrBayes version 3.2.2 with GTR+G+I as model for gene evolution. Bayesian posterior probabilities given as percentages at the nodes. Using two samples of the Cardiocondyla elegans species complex as outgroup, mtDNA shows a strong separation of the C. nuda species group into two major clades containing four species of the C. mauritanica species complex and three species of the C. nuda species complex. The disagreement between the species identification based on morphology and the mtDNA tree is here 3.8%.
The limits of the constant-rate birth-death prior for phylogenetic tree topology inference
<p>Birth-death models are stochastic processes describing speciation and extinction through time and across taxa, and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under constant-rate birth-death (crBD) tend to differ from empirical trees, for example with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between crBD and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which crBD differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used crBD priors with those that used other non-BD Bayesian and non-Bayesian methods, we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using crBD in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios, but also highlights that empirically observed phylogenetic imbalance is highly improbable under crBD, leading to systematic bias in data sets with limited information content.</p>
Two new species of Aphyllon from northeastern Mexico: Sequence alignments and phylogenetic trees
<p>Plants originally identified as <em>Aphyllon ludovicianum</em> that occur near Monterrey, Nuevo Leon, and Cuatro Ciénegas Bolson, Coahuila, Mexico, were found to not align with the protologue of that species, the close relative <em>A. multiflorum,</em> or any other species of <em>Aphyllon</em>. Following a detailed study of floral morphology, geographic range, host species, and phylogenetic position using dry herbarium specimens, field study and georeferenced color photographs, we propose the new binomials <em>Aphyllon spectabile </em>for the plants from Nuevo Leon and <em>Aphyllon gypsophilum</em> for the plants from Coahuila, Mexico. This increases the taxonomic diversity of <em>Aphyllon</em> to 27 species plus ten additional subspecies. <em>Gymnosperma glutinosum</em> and two species of <em>Xanthisma</em> were reported for the first time as a host species for the genus <em>Aphyllon</em>. We also provide an updated key to <em>Aphyllon</em> in Mexico. </p>
FIGURE 2. Phylogenetic results. A, Maximum likelihood tree from COI dataset rooted with Ophelia limacina. B, Maximum likelihood tree from ITS1 in Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data
FIGURE 2. Phylogenetic results. A, Maximum likelihood tree from COI dataset rooted with Ophelia limacina. B, Maximum likelihood tree from ITS1 dataset rooted according to the result for the COI dataset. Support values are shown as jackknife from parsimony analysis and bootstrap from maximum likelihood respectively separated by /. * indicates 100% values for each support measure.
FIGURE 1. Phylogenetic tree generated from a in Xenoacremonium palmarum sp. nov., a novel species associated with Phoenix dactylifera in Iran
FIGURE 1. Phylogenetic tree generated from a maximum likelihood (ML) analysis based on the combined tub2, tef1α and ITS sequences of Xenoacremonium strains. The tree was rooted using Stachybotrys chartarum CBS 129.13 as the out-group taxon. Bootstrap values obtained in maximum likelihood (ML) analysis equal or greater than 50% and Bayesian posterior probability values (BYPP) equal or greater than 0.5 are shown at the nodes, respectively.
FIGURE 5. Circular maximum parsimony phylogenetic tree with all sequenced recognised Thai Aleiodes species with a in A turbo-taxonomic study of Thai Aleiodes (Aleiodes) and Aleiodes (Arcaleiodes) (Hymenoptera: Braconidae: Rogadinae) based largely on COI barcoded specimens, with rapid descriptions of 179 new species
FIGURE 5. Circular maximum parsimony phylogenetic tree with all sequenced recognised Thai Aleiodes species with a number of named, primarily Palaearctic taxa included. Species groups that are characterizable morphologically and discussed are indicated in different colours. The tree is rooted using Heterogamus species.
FIGURE. Bayesian tree based on nuclear (ITS) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches. in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Bayesian tree based on nuclear (ITS) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches.
FIGURE. Bayesian tree based on combined plastid (matK, trnL-trnF) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Bayesian tree based on combined plastid (matK, trnL-trnF) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches
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