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Figure 2. D in Neotypification of Drawida hattamimizu Hatai, 1930 (Annelida, Oligochaeta, Megadrili, Moniligastridae) as a model linking mtDNA (COI) sequences to an earthworm type, with a response to the 'Can of Worms' theory of cryptic species

Figure 2. D. hattamimizu unscaled habitus (from Watanabe, 2005, fig. 1 after Hatai's 1931 original).

COI sequences dataset of Dicronocephalus species in this study.

Explanation note: This COI data includes 50 individual sequences of the examined Dicronocephalus species and subspecies in this study

opencc-by-4.0Aug 2021View details →

FI GU R E 3 Maximum likelihood phylogenetic tree of the Hyalospheniformes with a focus on Apodera, Alocodera, and Padaungiella based on COI gene sequences. Bootstrap values (bs) and Bayesian posterior probabilities (p.p.) are indicated respectively between branches. COI sequences from genera other than Apodera were retrieved from GenBank in Superficially described and ignored for 92 years, rediscovered and emended: Apodera angatakere (Amoebozoa: Arcellinida: Hyalospheniformes) is a new flagship testate amoeba taxon from Aotearoa (New Zealand)

FI GU R E 3 Maximum likelihood phylogenetic tree of the Hyalospheniformes with a focus on Apodera, Alocodera, and Padaungiella based on COI gene sequences. Bootstrap values (bs) and Bayesian posterior probabilities (p.p.) are indicated respectively between branches. COI sequences from genera other than Apodera were retrieved from GenBank

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Fig. 3 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species

Fig. 3. Phylogenetic position of Macrobiotus sp., Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.

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Fig. 1 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species

Fig. 1. Phylogenetic position of D. lindholmi and L. a. exigua, Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.

Fig. 5 in Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence

Fig. 5. Distribution and frequency of Prosthenorchis elegans haplotypes (A–F) and haplogroups (I–II) by locality and individual. URRAS: Unidad de Rescate y Rehabilitacíon de Animales Silvestres, Universidad Nacional de Colombia; AMVA: Area Metropolitana del Valle de Aburŕa; WCS: Wildlife Conservation Society-Colombia.

Fig. 4 in Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence

Fig. 4. Phylogenetic tree obtained using Bayesian Inference (BI) and Maximum Likelihood (ML); node supports are provided for BI\ML. Outgroup taxa: Oncicola sp, AF417000; O. luehe = Oncicola luehe, JN710452; M. ingens = Macracanthorhynchus ingens, AF416997; M. hirudinaceus = Macracanthorhynchus hirudinaceus, FR856886; O. tortuous = Oligacanthorhynchus tortuous, AF416999.

Fig. 3 in Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence

Fig. 3. Haplotype network of Prosthenorchis elegans. Network shows relationships among P.elegans haplotypes (A–F) recovered from Saguinus leucopus and Cebus albifrons based on 633 bp of COI. All branches are of unit length (one mutational step). Labeled open circles represent observed haplotypes; areas of circles are proportional to the number observed for each haplotype. Filled circles indicate inferred haplotypes not found among sampled individuals. Double lines indicate variable sites (49, 274 and 293) resulting in changes in amino acid. Haplogroups are identified.

Fig. 2 in Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence

Fig. 2. External morphology of Prosthenorchis elegans via scanning electron microscopy (SEM). A. View of entire body of parasite. B. Proboscis armed with hooks.

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.

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Fig. 2. Statistical parsimony cladogram network representing relationships among the 45 haplotypes for a 615 in Genetic diversity of Halyomorpha halys (Hemiptera, Pentatomidae) in Korea and comparison with COI sequence datasets from East Asia, Europe, and North America

Fig. 2. Statistical parsimony cladogram network representing relationships among the 45 haplotypes for a 615 bp fragment of the COI gene of Halyomorpha halys. Each circle is labeled with haplotype number, and the size of each circle is proportional to the frequency of each haplotype [H3 (n = 353); H1 (n = 285); H22 (n = 43); H8 (n = 34); H33 (n = 23); H2 (n = 16); H32 (n = 8); H7, H9–H13, and H43 (n = 3); H6, H14, H34, H39, and H40 (n = 2); H4–H5, H12, H15–H21, H23, H30–H31, H35–H38, H41, H42, and H44–H51 (n = 1)]. Differing colors indicate countries in which samples were collected.

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Aligned and trimmed 16S and COI DNA sequences of Oceaniidae (Hydrozoa)

Aligned and trimmed 16S and COI sequences of Oceaniidae (Hydrozoa) used for the study "The polyps of Oceania armata identified by DNA barcoding (Cnidaria, Hydrozoa)" Format is Fasta, files are text files

Figure 2. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.

Figure 2. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.

Figure 4. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI and 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.

Figure 4. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI and 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.

Figure 10. - Maximum-likelihood phylogeny of Epicephala species based on sequences of the COI, ArgK and EF1α genes. Numbers above nodes are maximum-likelihood bootstrap support values based on 1,000 replications. The Japanese Epicephala species are marked in blue. Symbols right to species names donate ovipositor morphology: inverted U-shape, rounded apically; inverted V-shape, acute apically.

Figure 10. - Maximum-likelihood phylogeny of Epicephala species based on sequences of the COI, ArgK and EF1α genes. Numbers above nodes are maximum-likelihood bootstrap support values based on 1,000 replications. The Japanese Epicephala species are marked in blue. Symbols right to species names donate ovipositor morphology: inverted U-shape, rounded apically; inverted V-shape, acute apically.

Fig. 1 in Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence

Fig. 1. Photo showing the characteristic external morphology of Prosthenorchis elegans.