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274 results for “nuclear sequence”
Fig. 17. Phylogenetic hypothesis using nuclear gene sequences TMO-4C4 and 18S in A New Genus and Species of Pygmy Pipehorse from Taitokerau Northland, Aotearoa New Zealand, with a Redescription of Acentronura Kaup, 1853 and Idiotropiscis Whitley, 1947 (Teleostei, Syngnathidae)
Fig. 17. Phylogenetic hypothesis using nuclear gene sequences TMO-4C4 and 18S retrieved with Maximum Likelihood (ML), Maximum Parsimony (MP), and Bayesian Inference (MrBayes), representing 17 species from clade 6 from the analysis of Hamilton et al. (2017) and the new taxon. Tree rooted with the southern Australian trunk-brooder pipefish Heraldia nocturna. Nodal support at the generic level is shown in ML/MP/MrBayes order. See Data Accessibility for tree file.
Figure 5 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 5. Ancestral area reconstruction produced by means of the RASP–Bayesian binary Markov Chain Monte Carlo method and based on the occurrence of Verbesina L. (Heliantheae–Asteraceae) species. Nodes with a predicted dispersal component are circled in blue, and those with a significant vicariance component are circled in green. The green bar indicates the consensus age of the closure of the Panama Isthmus (age based on Leigh et al., 2013; O'Dea et al., 2016). BOL, Bolivia; BRA, Brazil; CAR, Caribbean; COL, Colombia; CRC, Costa Rica; ECU, Ecuador; MEX, Mexico; NIC, Nicaragua; PER, Peru; USA, United States of America; VEN, Venezuela.
Figure 4 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 4. Time-calibrated Bayesian inference tree generated using concatenated internal and external transcribed spacer data. The values at the nodes indicate mean divergence dates, and the horizontal bars indicate 95% highest posterior density ranges for the age at each node. The green bar indicates the consensus age of the closure of the Panama Isthmus (age based on Leigh et al., 2013; O'Dea et al., 2016). BOL, Bolivia; BRA, Brazil; CAR, Caribbean; COL, Colombia; CRC, Costa Rica; ECU, Ecuador; MEX, Mexico; NIC, Nicaragua; PER, Peru; USA, United States of America; VEN, Venezuela.
Figure 3 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 3. Bayesian inference tree of combined internal and external transcribed spacer data. Posterior probabilities> 0.9 are given above the branches. The red text indicates South American species. Leaf figures indicate opposite and alternate phyllotaxy. Chromosome numbers are based on Moreira & Cavalcanti (2020) and Panero & Strother (2021). BOL, Bolivia; BRA, Brazil; CAR, Caribbean; COL, Colombia; CRC, Costa Rica; ECU, Ecuador; MEX, Mexico; NA, North America; NIC, Nicaragua; PER, Peru; SA, South America; VEN, Venezuela.
Figure 2 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 2. Total distribution of Verbesina in North America, Central America, the Caribbean, and South America. (Data accessed from GBIF, https://www.gbif.org/).
Figure 1 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 1. Morphological characters in Verbesina. A, Tree of Verbesina floribunda Gardner; B, subshrubby habit of V. bipinnatifida Baker; C, capitulum of V. luetzelburgii Mattf.; D, capitulum of V. bipinnatifida; E, cypsela of V. bipinnatifida; F, cypsela of V. floribunda; G, scanning electron micrograph (SEM) of the verrucous cypsela surface of V. macrophylla (Cass.) S.F.Blake; H, inflorescence of V. macrophylla; I, pinnatipartite leaf of V. macrophylla; J, SEM of the scalariform cypsela surface of V. glabrata Hook. & Arn.; K, inflorescence of V. glabrata; L, entire leaf of V. glabrata. Vouchers: C, G.L. Moreira et al. 118 (CEN); D–E, G.L. Moreira et al. 116 (CEN); F, G.L. Moreira et al. 101 (CEN). Scale bars: C, 8 mm; D, 4 mm; E, 2 mm; F, 4 mm; G and J, 200 μm. Photographs: G. L. Moreira.
Fig. 3. Maximum likelihood tree constructed from 38 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and relatives using a in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences
Fig. 3. Maximum likelihood tree constructed from 38 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and relatives using a transition/transversion rate ratio of 1.6. Branch lengths are proportional to the number of expected nucleotide substitutions per site.
Fig. 2 in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences
Fig. 2. Neighbor-joining tree inferred form the analysis of 39 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and its relatives using a transition/transversion rate ratio of 1.6. Branch lengths are proportional to distance estimated from the two parameter method of Kimura. Numbers at nodes indicate bootstrap values for 100 replicate analyses. On this tree, bootstrap values <20% are not indicated.
Fig. 1 in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences
Fig. 1. Strict consensus of 11 parsimony trees derived from equally-weighted parsimony analysis of combined nuclear DNA ITS1 and ITS2 sequences from Daucus and its relatives using all unambiguously-aligned positions (CIs with and without uninformative characters= 0.6613 and 0.5817; RI=0.8387). From the left to the right, names of taxa, sections, and clades are given. Numbers above the nodes indicate the number of times a monophyletic group occurred in 100 bootstrap replicates; AutoDecay values are given below.
Fig. 1 in Taxonomic review of the umbelliferous taxa Heracleum moellendorffii complex in Korea based on molecular phylogenies of nuclear ribosomal ITS sequences
Fig. 1. Cladograms inferred from the analysis of 29 nuclear ribosomal DNA ITS1 and ITS2 sequences from the genus Heracleum and an outgroup. (A) The strict consensus of two minimal length 138-step trees derived from equally weighted maximum parsimony analysis of combined nuclear rDNA ITS and 5.8S sequences (CI's with and without uninformative characters=0.91 and 0.89, respectively; RI=0.95). Numbers above nodes indicate the number of times a monophyletic group occurred in 100 bootstrap replicates; decay values are presented below. (B) The Maximum likelihood tree using a transition/tranversion rate ratio of 1.5. Branch lengths are proportional to the number of expected nucleotide substitutions per site. Boxes A, B, and C indicate clades H. maximum-moellendorffii, H. subbipinnatum, and H. sphondylium, respectively.
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%.
Figure 1. Figure 1 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure 1. Figure 1. Location map of AUMAC samples and GenBank Sequences (modified from Yiğit et al. 20161). Black line is the border of arvalis and obscurus forms; dotted lines show possible hybridization zone of the two forms. Western Europe (1: Orkney Island, 2: Spain, 3: France, 4: Belgium), Central Europe (5: Germany, 6: Switzerland, 7: Czech Republic), Eastern Europe (8: Austria, 9: Slovenia, 10: Bosnia, 11: Montenegro, 12: Serbia, 13: Hungary, 14: Poland, 15: Ukraine, 16: European Russia/Vladimir, 17: European Russia/ Arkhangelsk Oblast) groups are 'arvalis' form. Anatolia and its surroundings (18: Anatolia/Ardahan, Kars and Erzurum provinces, 19: Iran, 20: Armenia) and Asia (21: Russia/Orenburg Oblast, 22: Russia/ Chelyabinsk Oblast, 23: China/Xinjiang, 24: Siberia) belong to 'obscurus' form.
Fig. 3 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data
Fig. 3. — Strict consensus of 10,000 most parsimonious trees resulting from the analysis of 58 ITS sequences; tree length = 725 steps; consistency index = 0.518; retention index = 0.734. Clades denoted by brackets are those referred to in text. Values along branches are bootstrap percentages. Placement of Polyscias elegans (discussed in text) is denoted by an asterisk. Labels for the Tieghemopanax group and other clades in "Polyscias sensu lato" follow PLUNKETT et al. (2001).
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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
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International Brain Laboratory public data
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OpenNeuro
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