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Fig. 7 in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Fig. 7. Hypothesized phylogeny of dendrobatids, redrawn from Vences et al. (2000: 37, fig. 1), based on neighbor-joining analysis of 16S DNA sequences aligned manually and excluding highly variable regions. Numbers are bootstrap frequencies (unlabeled nodes present in fewer than 50% of replicates).

Fig. 3 in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Fig. 3. Hypothesized phylogeny of Mannophryne, redrawn from La Marca (1995: 70, fig. 11). Synapomorphies are: A1, narrow collar, uniformly colored; B1, tadpoles with small papillae (presumably B1 on the cladogram is B0 from the text on p. 53); B2, tadpoles with large papillae (B2 is undefined in the text on p. 53; presumably it refers to B1); C1, uniformly colored dorsum; A2, wide collar without conspicuous pale markings; D1, posteroventral dark band present; A3, wide collar with pale flecks or spots; E1, bright throat coloration reduced, melanophores on anterior part of throat; A4, wide collar with large pale dots.

Fig. 2 in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Fig. 2. Hypothesized phylogeny of dendrobatids, redrawn from Myers et al. (1991: 29, fig. 20). All evidence is shown on the cladogram. In this scenario, Aromobates nocturnus is postulated to be the sister species of all other dendrobatids. All of the unquestioned synapomorphies listed for Dendrobatidae apply only to A. nocturnus and are unknown in any other dendrobatid.

Fig. 8 in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Fig. 8. Hypothesized phylogeny of dendrobatids, redrawn from Widmer et al. (2000: 561, fig. 2), based on parsimony analysis of cytochrome b sequences aligned with Clustal W (Thompson et al., 1994) (parameters not specified). Numbers are parsimony/maximum likelihood/neighbor-joining bootstrap frequencies.

Fig. 4 in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Fig. 4. Hypothesized phylogeny of dendrobatids, redrawn from Kaplan (1997: 373, fig. 3). Numbered synapomorphies are: (1) tympanum posterodorsally tilted under anterior edge of massive superficial slip of m. depressor mandibulae, (2) mercaptanlike defensive odor, (3) diurnal activity, (4) riparian–terrestrial habitat preference, (5) smaller size (,50 mm SVL), (6) m. adductor mandibulae externus superficialis absent (''s'' pattern), (7) neopalatines absent, (8) finger three of males swollen, and (9) lipophilic alkaloids present.

Fig. 19 in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Fig. 19. Examples of variation in dendrobatid maxillary teeth. A, B: lateral (A) and lingual (B) views of pictus (UMMZ 184099). Note that the teeth do not protrude beyond the edge of the maxilla. C: lateral view of riveroi (AMNH 134144). D: lateral view of subpunctatus (UMMZ 221159). E: lateral view of undulatus (AMNH 159142). F: lateral view of molinarii (UMMZ 176207). G: lateral view of dunni (UMMZ 167131). H: lateral view of nocturnus (AMNH 129940).

Fig. 11 in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Fig. 11. Hypothesized phylogeny of dendrobatids, redrawn from Santos et al. (2003: 12794, fig. 1), based on unweighted parsimony analysis of the mitochondrial transcription unit H1 (ca. 2,400 bp), aligned with ClustalX (Thompson et al., 1997) ''under various parameters … and finally adjusted by eye to produce a parsimonious alignment'' whereby ''informative sites were minimized'' (Santos et al., 2003:

Fig. 6 in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Fig. 6. Hypothesized phylogeny of dendrobatids, redrawn from Clough and Summers (2000: 342, fig. 1), based on parsimony analysis of 12S, 16S, and cytochrome b DNA sequences aligned with Clustal W (Thompson et al., 1994) (parameters not specified) and modified by eye and excluding ambiguously aligned regions. Numbers are bootstrap frequencies (unlabeled nodes present in fewer than 50% of replicates).

Fig. 12 in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Fig. 12. Hypothesized phylogeny of Dendrobates, redrawn from Symula et al. (2003: 459, fig. 3), based on maximum likelihood (under the GTR + C model) analysis of cytochrome b and cytochrome oxidase I DNA sequences aligned with ClustalX (Thompson et al., 1997) (parameters not specified). Maximum likelihood branch lengths shown above branches, parsimony bootstrap frequencies shown below branches (frequencies.75% shown).

Fig. 5 in Morphological and molecular phylogenetic characterization of Sarcocystis kani sp. nov. and other novel, closely related Sarcocystis spp. infecting small mammals and colubrid snakes in Asia

Fig. 5. Maximum Likelihood (ML) phylogenetic reconstruction of the mitochondrial Cytochrome C oxidase Subunit I (cox1) gene tree of the Sarcocystis spp. under investigation. Where possible, sequences of the same species were used as shown in the 18S rRNA gene tree, including the outgroup. The newly sequenced Sarcocystis spp. are marked with black symbols. A total of 25 nucleotide sequences and 603 sites of the barcode area (all codon positions included) was analyzed with 1000 bootstrap replicates. Branch support from three replicate analyses is shown. The evolutionary history was inferred by using ML based on the HKY model. The tree with the highest log likelihood (– 6438.6551) is shown. A discrete Gamma distribution was used to model evolutionary rate differences among sites (four categories [+G, parameter = 0.9037]). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 17.4959% sites). All positions with less than 98% site coverage were eliminated. Branch lengths are measured in the number of substitutions per site. Note the long branch lengths of ruminant Sarcocytis spp. in comparison to other members of the Sarcocystidae as well as eimeriid coccidia from phylogenetically diverse hosts.

Fig. 2 in Morphological and molecular phylogenetic characterization of Sarcocystis kani sp. nov. and other novel, closely related Sarcocystis spp. infecting small mammals and colubrid snakes in Asia

Fig. 2. Ultrastructure of Sarcocystis sp.1 from the mangrove snake in abdominal musculature of a Sprague-Dawley rat; a) One μm-thin section through a resin-embedded, toluidine-stained sarcocyst showing densely-packed cystozoites (CZ) that were contained in septate compartments; the arrow indicates the cyst wall with small protrusions, which are clearly visible because host cell (HC) tissue is removed at this position; b) gross view of the cyst wall and cystozoites in a longitudinal section; the black arrow indicates a thin septum that separated the compartments filled with cystozoites; protrusions (PT) were broad, short, and irregularshaped, often with a reticulate base that rested on a thin layer of ground substance (GS); c) cross-section of sarcocyst, showing the primary cyst wall at higher magnification to consist of electron-dense, knob-like structures with intermittent invaginations; it appeared as if the primary wall was fenestrated (asterisk) allowing exchange of fine granular material (arrowheads) between the interior and exterior of the cyst; the exterior space between the protrusions was entirely filled with granular substance. d) metrocytes exclusively divided by endodyogeny as only cells with two developing zoites (asterisks) were observed; the white arrow points at deposits of highly electron-dense matter that could form larger clusters in the GS of the septae.

Fig. 1 in Morphological and molecular phylogenetic characterization of Sarcocystis kani sp. nov. and other novel, closely related Sarcocystis spp. infecting small mammals and colubrid snakes in Asia

Fig. 1. Light microscopic observations on the development of Sarcocystis sp.1 in striated musculature of Sprague-Dawley rats; a) typical sporocysts, here in fecal smear from Boiga dendrophila, that were used for infection of rats; sporocysts contained a granular residual body (asterisk) and four sporozoites (SP), which are all visible in the upper sporocyst; b) full-length micrograph of a typical (native) sarcocyst of Sarcocystis sp.1 in striated belly musculature, the arrows indicating folds of the cysts' body; c) high magnification of the cyst wall of a native sarcocyst, the arrows pointing at the apparently smooth wall; this is the same cyst as depicted in Fig. 2a; the inset shows freshly released, live cystozoites under phase-contrast light microscopy.

Fig. 4 in Morphological and molecular phylogenetic characterization of Sarcocystis kani sp. nov. and other novel, closely related Sarcocystis spp. infecting small mammals and colubrid snakes in Asia

Fig. 4. Predicted secondary structure of helix 38 in domain V7 of the 18S rRNA of Sarcocystis sp.1, Sarcocystis sp.2, S. attenuati, S. scandentiborneensis, and S. zuoi in comparison to S. clethrionomyelaphis (shaded inset). The 7-nt long motif 5′-AAUUCGU-3' (relative to all Apicomplexan taxa examined; nt in italic letters in shaded oval) mapped to a hairpin loop position of helix 38 and was characteristic for all species of the S. zuoi – complex; the motif was one nt (Cytosine) shorter in helix 38 of S. clethrionomyelaphis. Sequences were aligned to a secondary structure model of the Eukarya using SSU-ALIGN. The numbering of nucleotides (bars) and helices is based on the 1881 nt-long structural template. Position 1430 corresponds to position 1357 of the predicted secondary structure of Toxoplasma gondii (RH strain) as published by Gagnon et al. (1996).

Fig. 3 in Morphological and molecular phylogenetic characterization of Sarcocystis kani sp. nov. and other novel, closely related Sarcocystis spp. infecting small mammals and colubrid snakes in Asia

Fig. 3. Bayesian Inference (BI) of the 18S rRNA phylogeny of Sarcocystis spp. infecting colubrid snakes and small mammals in Asia; the S. zuoi – complex of species is highlighted by the shaded box. This complex excludes S. clethrionomyelaphis, which branches off basally. All new sequences, including a new isolate of S. zamani from Sumatra, are highlighted by black symbols. The known definitive and/or intermediate hosts associated with the selected sequences of the S. zuoi-group are indicated. Eimeriid species from phylogenetically diverse hosts served as outgroups. Bayesian posterior probabilities of three independent analyses (and alignments) are indicated behind each node, showing only one value if results of replicates were identical.

Fig. 6 in Morphological and molecular phylogenetic characterization of Sarcocystis kani sp. nov. and other novel, closely related Sarcocystis spp. infecting small mammals and colubrid snakes in Asia

Fig. 6. Mapping of (A) potential heme ligand binding sites and (B) amino acid variability among different lineages of tissue cyst-forming coccidia in the barcode area of the mitochondrial COX1 protein. A) Map of putative heme ligand binding sites (arrowheads) in a protein sequence alignment of selected taxa used in the phylogenetic tree of cox1. Identical/conservative aa positions are highlighted by light background, variable positions and gaps are shown against black background. Helix 1 (H1) is shown partial, starting at position 14 of the global barcode alignment (Pentinsaari et al., 2016); aa sequences of helices 2 (H2) and 6 (H6) are shown in full length, while putative heme binding sites of loop 3–4 (L3-4) were in its anterior part only. Domain boundaries and putative ligand binding sites were derived from COX1 of template organisms Saccharomyces cerevisiae and Bos taurus by sequence alignment against Toxoplasma gondii applying three-dimensional homology modelling of protein structure. The complete alignment of the six helices of the barcode area is shown in Supplementary Fig. S2. Note that aa numbering of the barcode area of the Apicomplexan sequence is different to the global alignment, because the former showed one additional aa and domain boundaries were slightly altered. The nucleotide sequence KC209732 of S. tenella (GenBank) is also registered in the barcode reference database BOLD (accession number JRPAA5858-15; http://boldsystems.org); the aa barcode position 14 (Glycine) shown here corresponds to position 16 of the aa translation of GenBank record KC209732. B) 'Heat map' of aa changes (darker shades of green = more changes, number of changes indicated) in the barcode area among chemically/structurally different aa groups in different lineages of tissue cyst-forming coccidia relative to the COX1 protein sequence of T. gondii. Because helix 1 was truncated, records of aa changes in this area are incomplete.

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Figure 1 in The complete mitochondrial genome of Parnassius actius (Lepidoptera: Papilionidae: Parnassinae) with the related phylogenetic analysis

Figure 1. Circular map of the mitochondrial genome of P. actius. The abbreviations for the genes are as follows: COI, COII and COIII refer to the cytochrome oxidase subunits; Cytb refers to cytochrome B; ATP6 and ATP8 refer to subunits 6 and 8 of ATPase; ND1–6 grefers to components of NADH dehydrogenase. The tRNAs are indicated by the IUPAC-IUB single letter amion acid codes, while L1, L2, S1, S2 denote tRNALeu(CUN), tRNALeu(UUR), tRNASer(AGN) and tRNASer(UCN), respectively. Gene names that are not underlined indicate the direction of transcription from left to right, and with underline indicates right to left. The P. actius mitogenome was sequenced by using 7 short fragments (SF1–SF7) and 7 long fragments (LF1–LF7) as templates, shown as single lines within a circle.

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Figure 7 in The complete mitochondrial genome of Parnassius actius (Lepidoptera: Papilionidae: Parnassinae) with the related phylogenetic analysis

Figure 7. Bayesian Inference and maximum likelihood phylograms of the 45 Parnassius species in this study (Numbers on each node correspond to the posterior probability values of the BI analysis (left) and the ML bootstrap percentage values for 1000 replicates (right), posterior probability values below 0.5 or bootstrap percentage values below 50% was not shown on the diagram).

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Fig. 5 in Phylogenetic relationships of the bumblebees Bombus moderatus, B. albocinctus, B. burjaeticus, B. florilegus and B. cryptarum based on mitochondrial DNA markers: a complex of closely related taxa with circumpolar distribution (Hymenoptera: Apidae: Bombus))

Fig. 5: Tree topology calculated as Maximum-Likelihood tree using Bayesian MCMC analysis with the general time reversal model of base substitution and gamma distribution for degraded DNA of museum specimens, only parsimony informative triplets included.

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Fig. 4 in Phylogenetic relationships of the bumblebees Bombus moderatus, B. albocinctus, B. burjaeticus, B. florilegus and B. cryptarum based on mitochondrial DNA markers: a complex of closely related taxa with circumpolar distribution (Hymenoptera: Apidae: Bombus))

Fig. 4: Observed diagnostic character changes with position numbers mapped onto the Maximum- Likelihood tree. Black box = unambiguous diagnostic charactercharacter change, grey box = ambiguous diagnostic charactercharacter change, and white box = character change.