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Datasets for phylogenetic analyses and phylogenetic trees for: Genetic barcodes for species identification and phylogenetic estimation in ghost spiders (Araneae: Anyphaenidae: Amaurobioidinae). Invertebrate Systematics, 2024
<p>We combined the COI sequence data with legacy multigene sequence data to create a new, taxon-rich phylogeny for the Amaurobioidinae. We used sequences for four loci that have been used in previous studies on the subfamily: two mitochondrial loci, COI (658bp) and ribosomal subunit 16S (16S, 410bp); and two nuclear loci, Histone H3 (H3, 327bp) and ribosomal subunit 28S (28S, 839bp). We complemented the Amaurobioidinae data with sequences from several non-amaurobioidine anyphaenids and two clubionids as outgroups. Sequence alignment was performed using the MAFFT (ver. 7.308) plugin in Geneious, allowing MAFFT to automatically select an appropriate alignment strategy based on the properties of each locus, or with the online MAFFT server (https://mafft.cbrc.jp), which consistently selected the L-INS-i algorithm. Finally, alignments of the four loci were concatenated to construct a 2234 bp multigene sequence matrix containing 692 taxa, with about 55% missing/gap data (“full” matrix henceforth). To ensure that excessive missing data did not affect the resulting topology, we also constructed a reduced matrix by removing additional COI-only specimens so that each species and morphotype was represented by just one or two specimens for which all loci were available (where possible). After realignment, this reduced matrix was 2235 bp long, included 167 taxa, and had about 22% missing/gap data (“reduced” matrix henceforth). Phylogenetic analyses under maximum likelihood, including model selection, were then conducted with IQ-TREE 2. We performed phylogenetic analyses on both concatenated matrices (the full matrix and the reduced matrix) and on each individual locus. For model selection, we provided an initial scheme that partitioned the matrix by locus, and further partitioned the protein-coding loci (COI and H3) by codon position. We used ModelFinder and searched for the best partition scheme, all in IQ-TREE. The best models (partitions) for the full dataset were: GTR+F+I+G4 (16S), GTR+F+I+I+R4 (28S), TVM+F+I+I+R2 (COI-1), TIM2+F+R4 (COI-2), GTR+F+R5 (COI-3), TVMe+G4 (H3-1-H3-2), SYM+G4 (H3-3); and for the reduced dataset: GTR+F+I+G4 (16S), GTR+F+I+G4: (28S), GTR+F+I+G4: (COI-2), GTR+F+I+G4: (COI-3), TVM+F+I+G4: (COI-1, H3-2), GTR+F+I+G4: (H3-1), GTR+F+I+G4: (H3-3). For each dataset, once the best models and partitions were defined, we executed 10 independent replicates of tree calculations followed by 1000 ultrafast bootstrap replicates, and the replicate reaching the maximum likelihood was chosen. Phylogenetic analyses under parsimony were made with TNT, under equal weights, using the “new technology” search with default values, asking for 10 independent hits to the minimal length, and submitting the resulting trees to a round of TBR branch swapping. </p>
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. 5. Maximum likelihood tree for 28S in Fig. 1 in Fig. 4 in Identification of Sexually Dimorphic Genes in Pectoral Fin as Molecular Markers for Assessing the Sex of Japanese Silver Eels ().
Fig. 5. Maximum likelihood tree for 28S (A) and COX1 (B) genes. Red branches indicate the presence of tubercles on the RV margin.
Fig. 3. Maximum likelihood tree for Culex species showing the 5 clades representing 5 subgroups. Clade I in Mosquito identification and haemosporidian parasites detection in the enclosure of the African penguins (Spheniscus demersus) at the SANBI zoological garden
Fig. 3. Maximum likelihood tree for Culex species showing the 5 clades representing 5 subgroups. Clade I is the Trifilatus Subgroup (Mattingly and Rageau, 1958) for Cx. torrentium; Clade II and III are the Pipiens Complex; Clade IV the Theileri Subgroup (Sirivanakarn, 1976) for Cx. theileri; and Clade V is the Tarsalis (Edwards, 1932) for Cx. declaratory and Apicinus Subgroups (Edwards, 1932) for Cx. mollis. Lutzia sp. used as outgroups. Sequences from this study are indicated by asterisks (*).
Figure 2. Majority rule consensus tree for the 16S in Genus Baseodiscus (Nemertea: Heteronemertea): Molecular identification of a new species in a phylogenetic context
Figure 2. Majority rule consensus tree for the 16S rRNA data resulting from the Bayesian analysis (model GTR+G+I), 1,000,000 generations. Numbers refer to posterior probabilities.
Fig. 3. Maximum likelihood tree estimated from the 215 in Morphological and Molecular Identification of Isospora sepetibensis (Chromista: Miozoa: Eimeriidae) from a New Host, Trichothraupis melanops (Passeriformes: Thraupidae: Tachyphoninae) in South America
Fig. 3. Maximum likelihood tree estimated from the 215 bp long cox1 sequences. Numbers at nodes represent bootstrap support (1,000 replicates; only values> 50% shown) for Neighbor-Joining and Maximum Likelihood, respectively. The scale-bar represents the number of nucleotide substitutions per site.
Fig. 2. Maximum likelihood tree estimated from the cox1 in Morphological and Molecular Identification of Isospora sepetibensis (Chromista: Miozoa: Eimeriidae) from a New Host, Trichothraupis melanops (Passeriformes: Thraupidae: Tachyphoninae) in South America
Fig. 2. Maximum likelihood tree estimated from the cox1 sequences. Numbers at nodes represent bootstrap support (1,000 replicates; only values> 50% shown) for Neighbor-Joining and Maximum Likelihood, respectively. The scale-bar represents the number of nucleotide substitutions per site.
FIGURE 3 in Phytophagous and predatory mites on olive trees in Tunisia. Catalogue, description of one new species and key for identification (Acari, Eriophyidae, Tetranychidae, Tenuipalpidae and Phytoseiidae)
FIGURE 3: Calyx of the spermatheca (a), Chelicera (b) and Macrosetae on leg IV (c) of the female of Typhlodromus (Anthoseius) mathieui n. sp.
FIGURE 1. Neighbor-joining tree derived from Cytochrome Oxidase 1 in Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with Comments on identification of adult Phaeoptyx
FIGURE 1. Neighbor-joining tree derived from Cytochrome Oxidase 1 sequences showing three genetically distinct lineages of Belizean Phaeoptyx.
FIGURE 7. Neighbor-joining tree derived from Cytochrome Oxidase 1 in Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with Comments on identification of adult Phaeoptyx
FIGURE 7. Neighbor-joining tree derived from Cytochrome Oxidase 1 sequences showing three genetically distinct lineages of Belizean Astrapogon.
FIGURE 18. Maximum Likelihood tree estimated from 1044 in Bythaelurus bachi n. sp., a new deep-water catshark (Carcharhiniformes, Scyliorhinidae) from the southwestern Indian Ocean, with a review of Bythaelurus species and a key to their identification
FIGURE 18. Maximum Likelihood tree estimated from 1044 aligned sites of the mitochondrial NADH2 gene using a General Time Reversible model and an accommodation for among site rate variation and Invariant sites (GTR+I+G model).
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.
FIGURE 2. Maximum likelihood tree estimated from the COI1 in Molecular identification of Isospora coerebae Berto, Flausino, Luz, Ferreira & Lopes, 2010 (Chromista: Miozoa: Eimeriidae) from the bananaquit Coereba flaveola (Linnaeus, 1758) (Passeriformes: Thraupidae: Coerebinae) from Brazil
FIGURE 2. Maximum likelihood tree estimated from the COI1 gene sequences of coccidian species. Numbers at the nodes show posterior probabilities under the Bayesian Inference analysis/bootstrap values derived from Maximum Likelihood analysis. Scale bar represents the number of nucleotide substitutions per site.
FIGURE 3. Maximum likelihood tree estimated from the COI2 in Molecular identification of Isospora coerebae Berto, Flausino, Luz, Ferreira & Lopes, 2010 (Chromista: Miozoa: Eimeriidae) from the bananaquit Coereba flaveola (Linnaeus, 1758) (Passeriformes: Thraupidae: Coerebinae) from Brazil
FIGURE 3. Maximum likelihood tree estimated from the COI2 gene sequences of coccidian species. Numbers at the nodes show posterior probabilities under the Bayesian Inference analysis/bootstrap values derived from Maximum Likelihood analysis. Scale bar represents the number of nucleotide substitutions per site.
FIGURE 11. Identification tree. Neighbor-Joining analysis involving 20 in Six new species of Afrotropical Allodia (Diptera: Mycetophilidae): DNA barcodes indicate recent diversification with a single origin
FIGURE 11. Identification tree. Neighbor-Joining analysis involving 20 CO1 sequences. Evolutionary distances were calculated using the p-distance model. Abbreviations: M = male, F = female. Sequences retrieved from BOLD (Ratasingham & Hebert 2007) are labelled with Process ID (see Appendix 1). See methods for details.
FIGURE 2 in Phytophagous and predatory mites on olive trees in Tunisia. Catalogue, description of one new species and key for identification (Acari, Eriophyidae, Tetranychidae, Tenuipalpidae and Phytoseiidae)
FIGURE 2: Ventral shields of the female of Typhlodromus (Anthoseius) mathieui n. sp.
FIGURE 1 in Phytophagous and predatory mites on olive trees in Tunisia. Catalogue, description of one new species and key for identification (Acari, Eriophyidae, Tetranychidae, Tenuipalpidae and Phytoseiidae)
FIGURE 1: Dorsal shield and peritreme of the female of Typhlodromus (Anthoseius) mathieui n. sp.
FIGURE 1. Neighbor-joining tree derived from mitochondrial cytochrome oxidase 1 in Identification of early life-history stages of Caribbean Apogon (Perciformes: Apogonidae) through DNA Barcoding
FIGURE 1. Neighbor-joining tree derived from mitochondrial cytochrome oxidase 1 sequences showing genetic lineages of Apogon species from Bahamas (BAH), Belize (BLZ), Curaçao (CUR), Florida (FCC, FWRI, SMS), and Saba Bank (SAB). L = larva, J = juvenile, A = adult.
Data from: Hemiptera phylogenomic resources: tree-based orthology prediction and conserved exon identification
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