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448 results for “phylogenetic inference”
Fig. 2 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule
Fig. 2. Phylogeny based on the ITS1-5.8S-ITS2 region of 60 free-living litostomatean taxa (alignment ITSR-A). Posterior probabilities for Bayesian inference and bootstrap values for maximum likelihood were mapped onto the best ML tree. Dashes indicate posterior probabilities below 0.50 and ML bootstrap values below 50%. Sequences in bold were obtained during this study. The scale bar indicates nine substitutions per one hundred nucleotide positions. For details on taxa, evolutionary model used, and characteristics of the ITSR-A alignment, see Supplementary Table S1 and S2.
Fig. 7 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule
Fig. 7. Consensus secondary structure of ITS2 helices II and III in various higher litostomatean taxa.
Figure 2. – Maximum Likelihood phylogenetic tree inferred with the 13 in The complete mitochondrial genome of Thymallus thymallus (Linnaeus, 1758) (Actinopterygii, Salmonidae) obtained by long range PCRs and double multiplexing
Figure 2. – Maximum Likelihood phylogenetic tree inferred with the 13 protein coding genes. The values of bootstrap are represent- ed beside the nodes.
◂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. 5. Phylogenetic relationships between jellyfishes within the order Semaeostomeae inferred from nearly complete 18S in Comprehensive Analysis of the Jellyfish (Goette, 1886) (Semaeostomeae: Pelagiidae) with Description of the Complete rDNA Sequence.
Fig. 5. Phylogenetic relationships between jellyfishes within the order Semaeostomeae inferred from nearly complete 18S rDNA (A) and partial 28S rDNA sequences (B) with maximum-likelihood (ML) algorithms. ML analyses of 18S and 28S were used as the nucleotide substitution model of GTR+G. Two hydrozoans (Hydractinia echinata and Podocoryne carnea for 18S rDNA; Astrohydra japonica and Melicertissa sp. for 28S) were included as the outgroups. Additional Bayesian analysis generated similar topology of the tree compared with the ML tree. Posterior probabilities (PP) from the analyses were incorporated into the ML tree to support the strength of each branch. The first and second numbers at the nodes display bootstrap proportions (BP) (> 50%) in ML and PP (> 0.50) in Bayesian, respectively. Branch lengths are proportional to the scale given. *Represents controversial species names, because they were suspected as different species by Bayha et al. (2017).
Fig. 1 in Phylogenetic position of the freshwater fish trypanosome, Trypanosoma ophiocephali (Kinetoplastida) inferred from the complete small subunit ribosomal RNA gene sequence
Fig. 1 The neighbor-joining tree of aquatic trypanosomes constructed from complete small subunit ribosomal RNA (SSrRNA) sequences indicating the systematic position of T. ophiocephali and phylogenetic relationships among the aquatic trypanosomes whose sequences are available. T. lewisi, T. theileri, and T. avium are taken as the outgroup. Bootstrap values are shown for the maximum parsimony/neighborjoining/Bayes analyses
Fig. 10. Phylogenetic relationship among primate pinworms inferred from 18S in A pinworm's tale: The evolutionary history of Lemuricola (Protenterobius) nycticebi
Fig. 10. Phylogenetic relationship among primate pinworms inferred from 18S rDNA gene sequences. Numbers at the nodes represent ML/NJ bootstrap values, respectively.
Fig. 9. Phylogenetic relationships among primate pinworms inferred from cox1 in A pinworm's tale: The evolutionary history of Lemuricola (Protenterobius) nycticebi
Fig. 9. Phylogenetic relationships among primate pinworms inferred from cox1 gene sequences. Numbers at the nodes represent ML/NJ bootstrap values, respectively.
Fig. 3 Trees obtained under the implied weighting using three concavity values k in First phylogenetic analysis of the tribe Oligaphorurini (Collembola: Onychiuridae) inferred from morphological data, with implications for generic classification
Fig. 3 Trees obtained under the implied weighting using three concavity values k = 6 (a), 9 (b), and 12 (c)
Fig. 4 Abdominal sternite IV in First phylogenetic analysis of the tribe Oligaphorurini (Collembola: Onychiuridae) inferred from morphological data, with implications for generic classification
Fig. 4 Abdominal sternite IV showing organization of furcal remnant. a, b Oligaphorura ursi Fjellberg, 1984; c Micraphorura gamae Buşmachiu and Weiner, 2013; d Oligaphorura groenlandica (Tullberg, 1876); e Dimorphaphorura inya Weiner and Kaprus, 2014; f Protaphorura eichhorni (Gisin, 1954)
Text-fig. 1. D&E tree of Endress and Doyle (2009), from the combined morphological and molecular analysis of Doyle and Endress (2000), with modifications based on more recent data, showing the inferred evolution of the reticulum grading character (39). Boxes under names of taxa indicate their character state; shading of branches indicates their reconstructed state based on parsimony optimization with MacClade (Maddison and Maddison 2003). Nymph = Nymphaeales, Aust = Austrobaileyales, Chlor = Chloranthaceae, Piper = Piperales, Ca = Canellales, Magnol = Magnoliales. in Early Cretaceous Monocots: A Phylogenetic Evaluation
Text-fig. 1. D&E tree of Endress and Doyle (2009), from the combined morphological and molecular analysis of Doyle and Endress (2000), with modifications based on more recent data, showing the inferred evolution of the reticulum grading character (39). Boxes under names of taxa indicate their character state; shading of branches indicates their reconstructed state based on parsimony optimization with MacClade (Maddison and Maddison 2003). Nymph = Nymphaeales, Aust = Austrobaileyales, Chlor = Chloranthaceae, Piper = Piperales, Ca = Canellales, Magnol = Magnoliales.
Figure 1. A in New molecular data for parasites Hammerschmidtiella indicus and Thelandros scleratus (Nematoda: Oxyurida) to infer phylogenetic position
Figure 1. A phylogenetic tree based on the 18S rDNA sequences was constructed by using the ME method. The evolutionary distance values are indicated at the nodes. The GenBank accession number for each sequence is given adjacent to the name of the corresponding species.
Figure S2 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure S2. ABGD results of COXI gene. The histogram shows distribution of genetic distances among M. arvalis samples; yellow columns show mean intralineage distances and red columns show interlineage distances. The diagram implies the lineages according to initial partitions = Group 1 (n: 21): Anatolia, China, Asian and European parts of Russia; Group 2 (n: 16): Serbia, Hungary.
Figure S1 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure S1. ABGD results of CYTB gene region. The histogram shows distribution of genetic distances among M. arvalis samples; yellow columns show mean intralineage distances and red columns show interlineage distances. The diagram implies the lineages according to initial partitions = Group 1 (n: 56): Anatolia, Georgia, Armenia, Iran, Siberia, China, Asian parts of Russia and one sample from Ukraine; Group 2 (n: 31): European parts of Russia, three samples from Ukraine, Western, Central and Eastern Europe.
Figure 7 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure 7. Bayesian tree obtained from IRBP sequences based on HKY + G parameter (Hasegawa et al., 1985). Numbers on branches show posterior probability (pb) values above 50%.
Figure 6 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure 6. Median-joining network obtained from IRBP haplotypes of Anatolian, Asian and European populations of M. arvalis. Number of mutations are shown by black lines on the branches.
Figure 5 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure 5. Bayesian tree obtained from COXI sequences based on HKY + I parameter (Hasegawa et al., 1985). Numbers on branches show posterior probability (pb) values above 50%.
Figure 4 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure 4. Median-joining network obtained from COXI haplotypes of Anatolian, Asian and European populations of M. arvalis. Number of mutations are shown by black lines on the branches.
Figure S3 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure S3. ABGD results of IRBP gene region. The histogram shows distribution of genetic distances among M. arvalis samples; yellow columns show mean intralineage distances and red columns show interlineage distances. The diagram implies the lineages according to initial partitions = Group 1 (n: 28): Anatolia, Serbia, Hungary, Iberian Peninsula; Group 2 (n: 1): one sample from Anatolia.
Figure 3 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure 3. Bayesian tree obtained from CYTB sequences based on HKY+I+G parameter (Hasegawa et al., 1985). Numbers on branches show posterior probability (pb) values above 50%.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.