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3,663 results for “Phylogenetic analysis”
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).
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)
Fig. 3 in Phylogenetic analysis of the tribe Neanurini questions tribal classification of the subfamily Neanurinae (Collembola: Neanuridae)
Fig. 3 Unambiguous morphological character optimisation obtained from an analysis of the data (Appendix 2) under implied weights (k = 17). The numbers above and below circles on the branches show character numbers and states, respectively. White and black circles represent homoplasious and non-homoplasious character state transformations, respectively
Fig. 1 Strict consensus cladogram obtained from 45 in Phylogenetic analysis of the tribe Neanurini questions tribal classification of the subfamily Neanurinae (Collembola: Neanuridae)
Fig. 1 Strict consensus cladogram obtained from 45 most parsimonious trees under equal weights. Values of Jackknife support and symmetric resampling are indicated on and below branches, respectively. Only values above 40 are indicated to facilitate the visualisation of the most internal branches. The main clades are indicated with letters (a–e) on branches
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)
Fig. 1 in Complete mitochondrial genome of Nyctalus aviator and phylogenetic analysis of the family Vespertilionidae
Fig. 1. Neighbor Joining (NJ) phylogeny of Vespertilionidae was inferred from concatenated nucleotide sequences of 13 mitogenomic protein-coding genes. Node labels indicate the bootstrap values. GenBank accession numbers for the sequences are indicated next to species designations.
Phylogenetic analysis reveals that the 'radial centric' diatom Orthoseira Thwaites (Orthoseiraceae, Bacillariophyta) is a member of a 'multipolar' diatom lineage
<p>These .zip files include input and output data for the following analyses that were used to produce this publication: gene sequence alignments (single and concatenated), PartitionFinder2, RAxML, CONSEL.</p>
Impact of algorithm choice in morphological phylogenetic analysis with inapplicable data
<p>Files to accompany Brazeau <em>et al</em>. (2019), describing the impact of using our new algorithm for handling inapplicable data.</p> <p>Details of the datasets analysed are give at <a href="https://ms609.github.io/ExploreInapplicable/r_dataset_details.html">ms609.github.io/ExploreInapplicable/r_dataset_details.html</a></p>
Fig. 3 in Molecular identification and phylogenetic analysis of Cryptosporidium, Hepatozoon and Spirometra in snakes from central China
Fig. 3. Maximum likelihood phylogenetic tree of Spirometra based on the cox1 gene. The tree was constructed with the cox1 sequences (444bp) by using the Kimura 2-parameter model with MEGA 7.0; we calculated bootstrap values with 1000 replicates. The representative sequence of Spirometra spagarnas isolated from snakes in this study are in bold print and marked by circles. Scale bar indicates nucleotide substitutions per site.
Fig. 2 in Molecular identification and phylogenetic analysis of Cryptosporidium, Hepatozoon and Spirometra in snakes from central China
Fig. 2. Maximum likelihood phylogenetic tree based on the 18S rRNA gene of Hepatozoon. The phylogenetic tree was constructed with the 18S rRNA gene sequences (670bp) by using the General time reversible model with MEGA 7.0; the bootstrap values were calculated with 1000 replicates. Representative sequences of Hepatozoon detected in this study are in bold print and marked by circles. Scale bar indicates nucleotide substitutions per site.
Fig. 1 in Molecular identification and phylogenetic analysis of Cryptosporidium, Hepatozoon and Spirometra in snakes from central China
Fig. 1. Maximum likelihood phylogenetic tree based on the SSU gene of Cryptosporidium. The phylogenetic tree SSU gene (834bp) was constructed by using the Kimura 2-parameter model with MEGA 7.0 and the bootstrap values were calculated with 1000 replicates. Representative sequences of Cryptosporidium detected in snakes in this study are in bold print and marked by circles. Scale bar indicates nucleotide substitutions per site.
Fig. 3 in Molecular characterization and phylogenetic analysis of Trypanosoma spp. detected from striped leaf-nosed bats (Hipposideros vittatus) in Zambia
Fig. 3. Species delimitation of Trypanosoma cruzi clade. Maximum likelihood phylogeny with outgroup (Trypanosoma lewisi) and with Baysian support values presented 17 linages recognized as species for the PTP analysis. Monophyletic groups in red indicated single putative species as well as terminal branches in blue.. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Molecular characterization and phylogenetic analysis of Trypanosoma spp. detected from striped leaf-nosed bats (Hipposideros vittatus) in Zambia
Fig. 1. Giemsa staining of Trypanosoma sp. from ZB17–105 in BSK-M medium Representative images of ZB17-105 in the BSK-M medium are displayed at the same magnification (x1000). (a,b) flagellates resembling promastigote forms. (c) possibly epimastigote forms under division. K: kinetoplast, N: nucleus, F: flagellum.
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 4 in CHD genes: a reliable marker for bird populations and phylogenetic analysis? Case study of the superfamily Sylvioidea (Aves: Passeriformes)
Figure 4. Maximum clade credibility trees for three data sets obtained by BI analysis in BEAST v1.8.0. MCC genealogy based on a Yule speciation process, summarized from the output of a Markov chain Monte Carlo chain run for 10 million iterations and sampled every 1000 iterations.
Figure 3 in CHD genes: a reliable marker for bird populations and phylogenetic analysis? Case study of the superfamily Sylvioidea (Aves: Passeriformes)
Figure 3. The ML tree for myoglobin gene (in blue) and for CHD-Z gene (in red); both trees are scaled in substitutions and the length of each tree and different topologies indicate that both of them are improper for phylogeny using a single gene.
Figure 1. Sex distribution for A. arundinaceus, A in CHD genes: a reliable marker for bird populations and phylogenetic analysis? Case study of the superfamily Sylvioidea (Aves: Passeriformes)
Figure 1. Sex distribution for A. arundinaceus, A. scirpaceus, and A. schoenobaenus, shown by sampling date.
Figure 1 in A comprehensive phylogenetic analysis of Grapsoidea crabs (Decapoda: Brachyura) based on mitochondrial cytochrome oxidase subunit 1 (CO1) genes
Figure 1. PCR images of eight Grapsoidea species. "1" is S. sinensis; "2" is C. sinensis; "3" is P. bidens; "4" is H. latimera; "5" is H. tientsinensis; "6" is H. wuana; "7" is H. sanguineus; "8" is V. litterata.
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732). in A study of genetic diversity among different population of Orthochirus sp. based on cytochrome C oxidase subunit I and 16srRNA sequencing
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732).
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.
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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
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