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Figure 6. Four most parsimonious phylogenetic trees for 12S in New insight into the systematic position of the endemic Madagascan genus Amberiana (Hemiptera: Heteroptera: Dinidoridae) using 12S rDNA sequences

Figure 6. Four most parsimonious phylogenetic trees for 12S rDNA sequences of 28 species used in this study generated using the maximum parsimony method. Bootstrap support is indicated at nodes; the frame shows the clade consisting of Amberiana montana and Sehirus luctuosus.

Figure 5. Phylogenetic tree for 12S in New insight into the systematic position of the endemic Madagascan genus Amberiana (Hemiptera: Heteroptera: Dinidoridae) using 12S rDNA sequences

Figure 5. Phylogenetic tree for 12S rDNA sequences of 28 species used in this study generated by using the maximum likelihood method. Bootstrap support is indicated at nodes; the frame shows the clade consisting of Amberiana montana and Sehirus luctuosus.

Figure 9 in New insight into the systematic position of the endemic Madagascan genus Amberiana (Hemiptera: Heteroptera: Dinidoridae) using 12S rDNA sequences

Figure 9. Phylogenetic tree obtained from the Bayesian inference analysis of the 12S rDNA sequences of 28 species used in this study. The Bayesian posterior probabilities are indicated at each node; the frame shows the clade consisting of Amberiana montana and Sehirus luctuosus.

Figures 1−3. 1 in New insight into the systematic position of the endemic Madagascan genus Amberiana (Hemiptera: Heteroptera: Dinidoridae) using 12S rDNA sequences

Figures 1−3. 1: Amberiana montana. 2: A. major (from Lis, 1990). 3: Location of known records for the 2 Amberiana species.

Figure 4. Phylogenetic tree for 12S in New insight into the systematic position of the endemic Madagascan genus Amberiana (Hemiptera: Heteroptera: Dinidoridae) using 12S rDNA sequences

Figure 4. Phylogenetic tree for 12S rDNA sequences of 28 species used in this study generated by using the minimum evolution method. Bootstrap support is indicated at nodes; the frame shows the clade consisting of Amberiana montana and Sehirus luctuosus.

Figure 7 in New insight into the systematic position of the endemic Madagascan genus Amberiana (Hemiptera: Heteroptera: Dinidoridae) using 12S rDNA sequences

Figure 7. Strict consensus tree of 4 most parsimonious trees for 12S rDNA sequences of 28 species used in this study generated by using the maximum parsimony method. The frame shows the clade consisting of Amberiana montana and Sehirus luctuosus.

opencc-by-4.0Jun 2020View details →

Figure 2 in The Black Sea Flexopecten species-complex (Mollusca: Bivalvia: Pectinidae): Shell morphology and 16S rDNA variation

Figure 2. Frequency of occurrence depicted for 16S ribosomal DNA variants among individuals of Flexopecten glaber. A: Black Sea population, B: Mediterranean population.

Fig. 5 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation

Fig. 5. Phylogenetic tree based on analysis of mitochondrial COI sequences of the Sarcocystidae including the new Sarcocystis sp. examined in this study (black symbols). Other taxa of the Apicomplexa served as root. Evolutionary history was inferred by the Maximum Likelihood (ML) method based on the TamuraNei model, whereby 619 positions were included in the final data set. All positions with less than 95% site coverage were eliminated; that is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. Bootstrap percentages (1000 iterations) are shown next to branches. COI sequences E357-13 and E120-13 (not shown in the tree) are available at GenBank (MN732561 and MN732562, respectively).

Fig. 2 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation

Fig. 2. Ultrastructure of S. scandentiborneensis sp. nov. Note, due to ethanol-fixation some ultrastructural details are poorly resolved (e.g. membranes). A) Longitudinal section through the same sample as in Fig. 1C, showing a gross view of the sarcocyst and its villous protrusions (VP) that are sectioned in different orientations. The inset shows a cross section through various VP that reveals the arrangement of microtubules in their inner core; while in this case 16 microtubules are visible (asterisks), sections through more apical portions of the VP showed lower numbers. B) Longitudinal section through the fingerlike VPs that appear to be anchored in the ground substance (arrow) by microtubules (asterisks) that extend into each protrusion; note the electron-dense, U-shaped structure at each tip of the protrusions (arrowheads) and the apparently serrated surface of the VP (flat arrowheads). The inset shows a higher magnification of the apical part of a single VP with the typical U-shaped apex (asterisk), which appears to be connected with the host cell through an electronlucent contact zone (white arrowheads); interestingly, the protrusion appears fenestrated (also visible in the main image) possessing thorn-like structures (black arrows; the white arrow indicates a crosssectional view) that could be responsible for the serration visible at lower magnification. CZ, cystozoites; HC, host cell; VP, villous protrusion.

Fig. 1 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation

Fig. 1. Light microscopy of Sarcocystis scandentiborneensis sp. nov. A and B, Haematoxylin & Eosinstained histological sections of striated musculature; C and D, Richardson's dye-stained 1.0 μm thin sections of sarcocysts. A) Tissue section of laryngeal muscle with various sarcocysts in cross section (asterisks), indicating a relatively high density of cysts in this part of musculature. B) Longitudinal section through a sarcocyst, showing a cigar-shaped appearance; however, isolated native sarcocysts, which were not available, may look different. C) Part of a longitudinal section through the tip of a sarcocyst, note the very thin ground substance (arrows) and the fine septae extending into the interior of the cyst (arrowheads); cystozoites (CZ) were loosely scattered within chambers while metrocytes were rarely seen, indicating maturity of the cyst; bars indicate the variable thickness of the cyst wall: the wall was thinner in regions where the villous protrusions were bent (right bar); note that the intense staining at the interface between host cell (HC) and parasite is part of the host cell. D) Cross-section through a sarcocyst showing cystozoites and the cyst wall (bar) including its thin ground substance (arrows).

Fig. 4 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation

Fig. 4. Mapping (to the Toxoplasma gondii reference molecule M97703) of frequencies (%) of base pair changes observed in sequence comparisons of nu clear 18S rDNA within the new Sarcocystis sp. from treeshrews (intraspecific variation: isolates E364–13 versus E357–13) and between the new species and Sarcocystis zuoi and/or S. clethrionomyelaphis (interspecific variation: E364–13 versus S. zuoi/clethrionomyelaphis). Results were combined for the two latter species to simplify the graph. Here, 87.2% of 2118 alignment positions showed moderate to high levels of consistency, while sections of ambiguous alignment did not relate to the species under investigation. Due to gaps in the alignment, not all of the observed nt changes could be mapped to a homologous position of the reference molecule (i.e., 7 out of 24 bp changes in intraspecific comparison; 33 out of 74 bp changes in interspecific comparison), in which case the position of each nt relative to the helix was inferred from neighboring nt for which such position was known. Gaps were mainly due to insertions in helices V2, V4, and V9 rendering E357-13/E364-13 longer than the sequence of T. gondii. The percentage of parsimony-informative (pi) bp changes per helix is shown for helices V1, V2, V4, V7, and V9 above each column. Also shown is the ratio of transitions versus transversions (Ti/Tv) for selected helices.

opencc-by-4.0Aug 2023View details →

Fig. 5. A data-display network constructed from uncorrected 18S rDNA p in Toxoplasma gondii and related Sarcocystidae parasites in harvested caribou from Nunavik, Canada

Fig. 5. A data-display network constructed from uncorrected 18S rDNA p-distances, using all characters, for tissue dwelling coccidians (mostly Sarcocystis spp.). Group names bear no taxonomic designation but merely assigned for discussion purposes. Bootstrap supports are displayed by the gray curves and associated values imposed on the network. Red dots indicate sequences generated in this study. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

FIGURE 5 in High rDNA polymorphisms in Astyanax lacustris (Characiformes: Characidae): new insights about the cryptic diversity in A. bimaculatus species complex with emphasis on the Paraná River basin

FIGURE 5 | Barcoding Gap. Histogram generated in the ABGD showing the intraspecific variation and interspecific divergence of haplogroups 1 (green), 2 (blue) and 3 (orange).

FIGURE 3 in High rDNA polymorphisms in Astyanax lacustris (Characiformes: Characidae): new insights about the cryptic diversity in A. bimaculatus species complex with emphasis on the Paraná River basin

FIGURE 3 | Cytotypes found in Astyanax lacustris submitted to Fluorescence in situ Hybridization (FISH) with 5S (red) and 18S rDNA (green) probes. Columns represent the chromosome pair of the karyotype and lines represent the 13 cytotypes. The first column shows the first metacentric chromosome pair of the karyotype for proportion comparison.

FIGURE 4 in High rDNA polymorphisms in Astyanax lacustris (Characiformes: Characidae): new insights about the cryptic diversity in A. bimaculatus species complex with emphasis on the Paraná River basin

FIGURE 4 | A. Bayesian Inference Phylogeny; B. Haplotype data. A. Bars on the right hand side represent the Automatic Barcode Gap Discovery (ABGD), Unweighted Pair Group Method using Arithmetic averages (UPGMA), dendrogram using the Hasegawa Kishino-Yano model with gama distribution (HKY+G) and Maximum Parsimony, respectively. B. The haplotype data show the Astyanax haplogroups 1 (in green), 2 (in blue) and 3 (in orange). Haplotypes (H) 2, 3, 4, 5, 7 and 8 (in bold with an asterisk) indicate the position of one or more individuals of this study. The black slices on the haplotypes represent slightly different individuals that do not arrange another haplotype.

FIGURE 1 in High rDNA polymorphisms in Astyanax lacustris (Characiformes: Characidae): new insights about the cryptic diversity in A. bimaculatus species complex with emphasis on the Paraná River basin

FIGURE 1 | Sampling sites of the specimens (in detail). Remaining points correspond to the sequences from BOLD System. Symbols represent the haplogroups recovered here. Haplogroup 1 represent specimens of Astyanax lacustris and one A. bimaculatus (highlighted with an asterisk*). Haplogroup 2 has only A. lacustris specimens. Haplogroup 3 indicates only one A. bimaculatus specimen. Outgroup is represented by A. scabripinnis and A. cf. fasciatus. VR = Vila Rica, SS = Sub-Sede, CA = Esquina Céu Azul, SG = São Gabriel.

FIGURE 2 in High rDNA polymorphisms in Astyanax lacustris (Characiformes: Characidae): new insights about the cryptic diversity in A. bimaculatus species complex with emphasis on the Paraná River basin

FIGURE 2 | Karyotypes of Astyanax lacustris from the Sub-Sede population representing all populations analyzed in this paper. Metaphase in Giemsa with Ag-NORs in boxes.

opencc-by-4.0Sep 2009View details →

Figure 3 in Phoronid phylogenetics (Brachiopoda; Phoronata): evidence from morphological cladistics, small and large subunit rDNA sequences, and mitochondrial cox1

Figure 3. Phoronid phylogeny. Most probable Bayesian likelihood tree (P = 0.68) from analysis of the 13tx alignment with clade credibility values from the majority rule consensus tree, which had the same topology. Where two clade credibility values are shown the first was from a run with the chiton as outgroup (not shown), and the second from a run with Phoronis ovalis as outgroup. MrBayes run commands were: charset coding_1st = 1-621\3; charset coding_2nd = 2-621\3; charset coding_3rd = 3-621\3; charset non-coding = 622-4515; partition all_4 = 4: coding_1st, coding_2nd, coding_3rd, non-coding; set partition = all_4; lset applyto=(all) nst = 6 rates = invgamma; databreaks 621 2386; unlink shape = all, pinvar = all, statefreq = all, revmat = all; prset ratepr = variable; mcmc ngen = 106 samplefreq = 100 printfreq = 5000 savebrlens = yes; plot match = all; sumt burnin = 2002. The tree shown was drawn in PAUP*4. The.con file was imported and displayed as a phylogram. Clade credibility values were added in a graphics editor.

opencc-by-4.0Sep 2009View details →

Figure 2 in Phoronid phylogenetics (Brachiopoda; Phoronata): evidence from morphological cladistics, small and large subunit rDNA sequences, and mitochondrial cox1

Figure 2. Phoronid phylogeny. Maximum likelihood phylogram based on 24tx alignment of concatenated rDNA sequences, with selected bootstrap values (%, 100 pseudoreplicates).