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501 results for “Phylogenetic tree”
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.
Figure 3. Phylogenetic relationships and intra specific recombination patterns among different AlYVV molecules. The maximumlikelihood phylogenetic tree contains 27 in Alternanthera yellow vein virus (AYVV); a betasatellite independent begomovirus infecting Sonchus palustris in Pakistan
Figure 3. Phylogenetic relationships and intra specific recombination patterns among different AlYVV molecules. The maximumlikelihood phylogenetic tree contains 27 known complete genomes of AlYVV from databank and two complete genomes determined in this study (indicated in black boxes). The tree was rooted on ToLCNDV (AB613826) as an out-group. The schematic representation of recombination events detected by RDP4. Arrows and blocks at the bottom correspond respectively to open reading frames (ORFs) and intergenic regions: pre-coat protein (AV2), coat protein (CP), replication-associated proteins (Rep and REn), transcriptional protein (TrAP), and AC4 region. AlYVV from different countries were colored differently. The colors of blocks represent the different ALYVV species and strains. Numbers at nodes indicate bootstrap confidence scores (1000 replicates).
Figure 5. A phylogenetic tree was generated using the neighbor-joining method which shows the genetic relationship between C. sphaerospermum 2 in Morphological and molecular identification of Cladosporium sphaerospermum isolates collected from tomato plant residues
Figure 5. A phylogenetic tree was generated using the neighbor-joining method which shows the genetic relationship between C. sphaerospermum 2 (as indicated in red circle) and the other C. sphaerospermum isolates deposited in GenBank (NCBI)
Fig. 2 Phylogenetic tree representing relationships within Discodorididae. The latter contains about 400 species and 40 in A warning for ecologists and conservation biologists using species checklists: How the European marine fauna 'lost' all of its 16 Discodoris species (Mollusca: Gastropoda)
Fig. 2 Phylogenetic tree representing relationships within Discodorididae. The latter contains about 400 species and 40 genera, only some of which are mentioned here, with special emphasis on the genera that contain species originally described in Discodoris. Tree terminal taxa are labeled with the specific epithet followed by the generic name of the original combination in parenthesis. The current generic names are given on the right side of the braces indicating the (few) species per genus mentioned. Assignment of a generic name to a clade is based on a type species that belongs to that clade (e.g., Discodoris boholiensis is the type species of Discodoris). All genera correspond to clades, with the exception of "Montereina", a metaphyletic group at the base of Discodorididae for which no autapomorphic, diagnostic features could be found. For additional information on phylogenetic analyses, authorship of species names, etc., see Dayrat (2010a)
Data & Analysis Script for: Phylogenetic relatedness to native congeners drives insect abundance and diversity hosted by non-native trees
<p>The dataset contains all necessary data to reproduce the findings presented in Schweiger et al. 2023 - Phylogenetic relatedness to native congeners drives insect abundance and diversity hosted by non-native trees (submitted).</p> <p>The code necessary to reproduce the findings is included within this repository. The code contains comments. Please note, if you want to reproduce the findings you will have to change file path information matching your personal computer to be able to re-run the code.</p> <p>This data includes the biodiversity raw data collected for the manuscript. It <strong>does not </strong>include data used to calculate geographic, climatic or phylogenetic distances, as these data are freely available and necessary information to reproduce calculations are given within the Material & Methods section.</p> <p>All data is provided within one Excel file. Please, pay attention to the provided ReadMe sheet containing metadata information on the dataset.</p> <p>Please carefully read provided information within ReadMe, Metadata and Code description.</p>
◂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. 3. Phylogenetic trees from reported 18S in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data
Fig. 3. Phylogenetic trees from reported 18S rRNA genes of insects according to NJ. A. Based on sequences of full-length. B. Based on second conserved region.
Fig. 1. Bayesian phylogenetic tree constructed using partial cytochrome b in Unexpected absence of exo-erythrocytic merogony during high gametocytaemia in two species of Haemoproteus (Haemosporida: Haemoproteidae), including description of Haemoproteus angustus n. sp. (lineage hCWT7) and a report of previously unknown residual bodies during in vitro gametogenesis
Fig. 1. Bayesian phylogenetic tree constructed using partial cytochrome b sequences of 61 lineages of Haemoproteus, 4 lineages of Plasmodium, and Leucocytozoon sp. lSISKIN2 as outgroup. Posterior probabilities higher than 0.8 are indicated close to the respective nodes. Red font indicates the parasite lineage described in this publication. Vertical bars (A–D) show groups of closely related lineages, which complete development and produce gametocytes only in non-passerines (A, D), both non-passerines and passerines (B), and only passerines (C). Blue font indicates Haemoproteus species, which develop in non-passerine avian hosts, which are indicated by symbols (● – Psittaciformes; ∎ - Coraciiformes; ▴ - Strigiformes; ◆ - Anseriformes; ★ - Charadriiformes; ♥ - Pelecaniformes; ⋄ - Piciformes; ⊠ - Sphenisciformes; Ω - Musophagiformes; § - Trochiliformes; Ψ – Falconiformes; Σ – Columbiformes; Φ - Galliformes). Lineage names were provided (according to MalAvi database), followed by parasite species names and sequence GenBank accession numbers.
Fig. 2. Neighbor-joining phylogenetic tree for a 219 in Prevalence of filarioid nematodes and trypanosomes in American robins and house sparrows, Chicago USA
Fig. 2. Neighbor-joining phylogenetic tree for a 219 bp region of the trypanosome 18s rRNA gene. Underlined sequences are from this study. Sequences for additional Trypanosoma spp. were downloaded from NCBI Genbank for comparison and Bodo caudatus was used as an outgroup. Numbers by branches indicate statistical bootstrap support of À50%.
Fig. 1. Neighbor-joining phylogenetic trees for a 475 in Prevalence of filarioid nematodes and trypanosomes in American robins and house sparrows, Chicago USA
Fig. 1. Neighbor-joining phylogenetic trees for a 475 bp region of the 18S rRNA gene for filarioid nematodes (A) and a 529 bp region of the filarial nematode mitochondrial cytochrome c oxidase subunit I gene (B). Sequences were obtained from bird blood clots, bird tissues, or adult nematodes recovered from birds. Underlined sequences are from this study. Additional sequences for filarial nematode species were downloaded from NCBI Genbank for comparison and Thelazia lacrimalis and Caenorhabditis elegans were used as outgroups. Numbers by branches indicate statistical bootstrap support of À50%.
Fig. 4. Maximum Likelihood phylogenetic tree generated using N in The African buffalo parasite Theileria. sp. (buffalo) can infect and immortalize cattle leukocytes and encodes divergent orthologues of Theileria parva antigen genes
Fig. 4. Maximum Likelihood phylogenetic tree generated using N-terminal sequences of T. sp. (buffalo) and T. parva PIM antigen genes. Maximum composite likelihood trees were constructed using 1000 bootstrap replicates as implemented in MEGA5; the optimal nucleotide substitution model was identified using data monkey. The tree constructed with RAxML (Stamatakis et al., 2014) using a GTR/G/I model with 100 bootstrap iterations.
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. 2 Maximum likelihood phylogenetic tree constructed using the mitochondrial cox1 gene for 103 in Genetic diversity and population genetics of large lungworms (Dictyocaulus, Nematoda) in wild deer in Hungary
ƒFig. 2 Maximum likelihood phylogenetic tree constructed using the mitochondrial cox1 gene for 103 Dictyocaulus lungworms originating from Hungary and five lungworms from GenBank indicated by their accession numbers (one dictyocaulid worm of red deer in New Zealand and four sequences of D. viviparus). Lungworms were collected from hunted deer (fallow, red and roe deer), indicated by triangle, square and circle, respectively. Geographical collecting regions are indicated for each sample
Fig. 2 Phylogenetic tree showing the relation between the Saudi Arabian haplotypes with 65 in Three species of Echinococcus granulosus sensu lato infect camels on the Arabian Peninsula
Fig. 2 Phylogenetic tree showing the relation between the Saudi Arabian haplotypes with 65 reference sequences. The Saudi Arabian haplotypes (H01-09) are in bold. The reference sequences along with their accession numbers and origin of isolate were included for each. T. solium was used as an outgroup taxon. The branch to outgroup was shortened by 0.2 substitutions per site
Fig. 3. Neighborjoining phylogenetic tree constructed from a in Report on 14 unrecorded bacterial species in Korea that belong to the phyla Bacteroidetes and Deinococcus-Thermus
Fig. 3. Neighborjoining phylogenetic tree constructed from a comparative analysis of 16S rRNA gene sequences showing the relationships between the strains isolated in this study and their relatives of the class Bacteroidetes. Numbers at nodes are levels of bootstrap support for branch points, based on 1,000 resampling; values are shown only if greater than 70%. Filled circles at nodes indicate that the corresponding nodes were also recovered using maximumlikelihood algorithm. Bar, 5% sequence divergence.
Fig. 2. Neighborjoining phylogenetic tree constructed from a in Report on 14 unrecorded bacterial species in Korea that belong to the phyla Bacteroidetes and Deinococcus-Thermus
Fig. 2. Neighborjoining phylogenetic tree constructed from a comparative analysis of 16S rRNA gene sequences showing the relationships between the strains isolated in this study and their relatives of the class DeinococcusThermus. Numbers at nodes are levels of bootstrap support for branch points, based on 1,000 resampling; values are shown only if greater than 70%. Filled circles at nodes indicate that the corresponding nodes were also recovered using maximumlikelihood algorithm. Bar, 2% sequence divergence.
Fig. 4. Neighbor-joining phylogenetic tree reconstructed from a in Isolation and characterization of four unrecorded wild yeasts from the soils of Republic of Korea in winter
Fig. 4. Neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 26S rRNA gene sequences showing the relationships of strain NH33 with closely related species. Bootstrap values (>50%) based on neighbor-joining methods are shown at the branch nodes. Bar, 0.01 substitutions per nucleotide position.
Fig. 3. Neighbor-joining phylogenetic tree reconstructed from a in Isolation and characterization of four unrecorded wild yeasts from the soils of Republic of Korea in winter
Fig. 3. Neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 26S rRNA gene sequences showing the relationships of strain NH19 with closely related species. Bootstrap values (>50%) based on neighbor-joining methods are shown at the branch nodes. Bar, 0.01 substitutions per nucleotide position.
Fig. 2. Neighbor-joining phylogenetic tree reconstructed from a in Isolation and characterization of four unrecorded wild yeasts from the soils of Republic of Korea in winter
Fig. 2. Neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 26S rRNA gene sequences showing the relationships of strains NH20 and YP416 with closely related species. Bootstrap values (>50%) based on neighbor-joining methods are shown at the branch nodes. Bar, 0.01 substitutions per nucleotide position.
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)
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