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116 results for “Phylogenetics: methods”
FIGURE 5. A, Acutihumerus petronius n in Tanaidacea from Brazil. II. A revision of the subfamily Hemikalliapseudinae (Kalliapseudidae; Tanaidacea; Crustacea) using phylogenetic methods
FIGURE 5. A, Acutihumerus petronius n. sp. Manca I larvae. B. Paraleiopus macrochelis Silva-Brum, 1978. Manca II. Scale bars = 0.1 mm and 0.2 mm
FIGURE 6. Phylogenetic reconstruction for 33 in Revision of the genus Devadatta Kirby, 1890 in Borneo based on molecular and morphological methods, with descriptions of four new species (Odonata: Zygoptera: Devadattidae)
FIGURE 6. Phylogenetic reconstruction for 33 specimens of Devadatta and one outgroup taxon from the combined COI+16S+ITS+28S data, using Bayesian Inference analysis. Posterior probability values are shown (as percentages) if less than 100%. RMNH collection codes are shown for each specimen, with the RMNH.INS. prefix omitted for clarity.
Figure 4. Phylogenetic reconstruction for 92 in A revised classification of the genus Matrona Selys, 1853 using molecular and morphological methods (Odonata: Calopterygidae)
Figure 4. Phylogenetic reconstruction for 92 specimens from COI. Posterior probabilities (above) and bootstrap values (below) are shown. A, all the groups excluding basilaris; B, basilaris.
Figure 3. Phylogenetic reconstruction for 147 in A revised classification of the genus Matrona Selys, 1853 using molecular and morphological methods (Odonata: Calopterygidae)
Figure 3. Phylogenetic reconstruction for 147 specimens from ITS. Posterior probabilities (above) and bootstrap values (below) are shown.
Figure 6 in The radiation of Satyrini butterflies (Nymphalidae: Satyrinae): a challenge for phylogenetic methods
Figure 6. Chronogram derived from the BEAST analysis with associated posterior credibility intervals. Numbers at the branches are posterior probability values for the node to the left of the number.
Figure 2 in The radiation of Satyrini butterflies (Nymphalidae: Satyrinae): a challenge for phylogenetic methods
Figure 2. Strict consensus of 12 equally parsimonious trees (29 647 steps; consistency index, CI = 0.13; retention index, RI = 0.44) from the maximum parsimony analysis (MP). Numbers given above branches are Bremer support values and the numbers below the branches are partitioned congruence index (PCI) values for the node to the right of the number.
Figure 4 in The radiation of Satyrini butterflies (Nymphalidae: Satyrinae): a challenge for phylogenetic methods
Figure 4. 'Bipartitions tree' obtained from the Maximum Likelihood (ML) analysis in RaxML. Numbers at the branches are bootstrap values for the node to the right of the number.
Figure 5 in The radiation of Satyrini butterflies (Nymphalidae: Satyrinae): a challenge for phylogenetic methods
Figure 5. Majority-rule cladogram based on Bayesian inference (BI), modelled with a GTR + G model. Numbers at the branches are posterior probability values for the node to the right of the number.
Figure 3 in The radiation of Satyrini butterflies (Nymphalidae: Satyrinae): a challenge for phylogenetic methods
Figure 3. Reduced cladograms from (A) maximum parsimony and (B) model-based methods (Bayesian inference and maximum likelihood), showing the incongruent hypotheses of relationships for the subtribes in the Satyrini.
Figure 7 in The radiation of Satyrini butterflies (Nymphalidae: Satyrinae): a challenge for phylogenetic methods
Figure 7. Results of a dispersal–vicariance analysis (DIVA), using three as the maximum number of ancestral areas in the DIVA. The topology of relationships for the out-groups are taken from Peña & Wahlberg (2008). Many terminals that belong to the same subtribe, and are distributed in the same biogeographical area of Figure 1, appear in one leaf: other Hypocystina, Pronophilina clade 1 and Pronophilina clade 2.
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants.
FIGURE. Phylogenetic relationships among species on Poaceae shown with synoptic phylogenetic tree constructed by MP method based on ITS+28S regions of rDNA. Same color branches show phylogenetic groups. 0, I: Spermogonial and aecial host genus. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic relationships among species on Poaceae shown with synoptic phylogenetic tree constructed by MP method based on ITS+28S regions of rDNA. Same color branches show phylogenetic groups. 0, I: Spermogonial and aecial host genus.
Fig. 2 in BSeptal compass^ and Bseptal formula^: a new method for phylogenetic investigations of the middle ear region in the squirrel-related clade (Rodentia: Mammalia)
Fig. 2 Septal compass: general graphical illustration of the anatomy of the right middle ear region with the relative position of the primary septa (I–III) and the secondary septa (A, B, a). One asterisk (a*) indicates the Blateral secondary septum^ of MacPhee (1981), two asterisks (**) indicate the Banterior septum^ of Wible (2009). cty cavum tympani (=tympanic cavity), fsa fossa subarcuata (=subarcuate fossa), rec recessus epitympanicus (=epitympanic recess)
Fig. 1 in BSeptal compass^ and Bseptal formula^: a new method for phylogenetic investigations of the middle ear region in the squirrel-related clade (Rodentia: Mammalia)
Fig. 1 Application of the septal compass. a Skull and right middle ear region in lateral view of Petaurista petaurista. b The right ear region of Euxerus erythropus in ventral view. The relative position of all septa is gathered by using several different orientated clipping planes. c Lateral
Data from: Phylogenetic comparative methods for evaluating the evolutionary history of function-valued traits
Phylogenetic comparative methods offer a suite of tools for studying trait evolution. However, most models inherently assume fixed trait values within species. Although some methods can incorporate error around species means, few are capable of accounting for variation driven by environmental or temporal gradients, such as trait responses to abiotic stress or ontogenetic trajectories. Such traits, often referred to as function-valued or infinite-dimensional, are typically expressed as reaction norms, dose–response curves, or time plots and are described by mathematical functions linking independent predictor variables to the trait of interest. Here, I introduce a method for extending ancestral state reconstruction to incorporate function-valued traits in a phylogenetic generalized least squares (PGLS) framework, as well as extensions of this method for testing phylogenetic signal, performing phylogenetic analysis of variance (ANOVA), and testing for correlated trait evolution using recently proposed multivariate PGLS methods. Statistical power of function-valued comparative methods is compared to univariate approaches using data simulations, and the assumptions and challenges of each are discussed in detail.
FIGURE 3. Phylogenetic tree inferred from maximum likelihood methods using 70 in Tigridiopalma longmenensis (Melastomataceae), a new species from Guangdong, China
FIGURE 3. Phylogenetic tree inferred from maximum likelihood methods using 70 protein-coding genes from the complete chloroplast genome sequences of Tigridiopalma longmenensis and other 15 species of Melastomataceae. The numbers beside the node indicate the bootstrap percentages (%) after 5000 replications of bootstrap sampling.
Figure 2. Maximum likelihood phylogenetic tree topology derived from the combined 16S in Cryptic and widespread: a recipe for taxonomic misidentification in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes sidneyi) as evident from species delimitation methods
Figure 2. Maximum likelihood phylogenetic tree topology derived from the combined 16S rRNA + COI sequence data, demonstrating the evolutionary relationships within the P. sidneyi s.l. species complex. Statistical support for nodes is provided as posterior probability values above nodes (> 0.95 PP) and bootstrap values below nodes (> 75%). An * or # denotes nodal relationships that were not supported (<0.95 PP/ <75%). Potamonautes sidneyi s.s. (clade 3) localities are marked with a dark blue triangle, while P. danielsi (clade 5) localities are marked by an orange square. The two new species, P. karooensis, (clade 2) and P. Ʋalles (clade 4), are marked by a light-blue circle and a green diamond, respectively. Specimens of P. barbarai are confined to clade 1.
Fig. 5 in To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe
Fig. 5. Phylogenetic trees of Scarabaeidae generated using UCEs; node values indicate bootstrap support. A)The tree produced with the Scarab 3kv1 probe set. B) The topology produced with the Adephaga 2.9kv1 probe set.
Fig. 1 in To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe
Fig. 1. Phylogenetic relationships based on McKenna et al. (2019) among select Coleoptera taxa relevant to or included in UCE probe design. Color (online),
Fig. 3 in To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe
Fig. 3. UCE loci recovery during in silico testing plotted against different metrics: A) average genetic distance estimated based on common gene fragments used in phylogenetics; B) average genetic distance estimated using BUSCO genes; C) N50 assembly metrics; and D) BUSCO S values.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.