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FIGURE 4 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 4. The estimation of divergence time for Laudakia. (Note: Values are estimated divergence times, and the blue bars are 95% confidence intervals HPD)
FIGURE 3 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 3. Bayesian phylogenetic trees of Laudakia species on tandem sequences (CO1 and 16S). (note: the values of nodes near is BPP/BS).
FIGURE 2 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 2. Bayesian phylogenetic trees of Laudakia on the sequenced of COI. (note: the values of nodes near is BPP/BS).
FIGURE 1 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 1. Bayesian phylogenetic trees of Laudakia on the sequenced of 16S. (note: the values of nodes near is BPP/BS).
FIG. 4 in Molecular Phylogenetics of the Clingfishes (Teleostei: Gobiesocidae)- Implications for Classification
FIG. 4. Topology resulting from Bayesian analysis of the concatenated seven-gene dataset. Branches marked with an asterisk (*) have been shortened to facilitate viewing (see inset topology for original branch lengths). Numbers above branches represent posterior probabilities (PP). Red branches are those downstream of nodes with PP values 0.75. Letters (A–J) in gray circles are clades discussed in text. Rows of colored boxes to right side of image represent subfamily designations (see corresponding key) within the following three classification schemes: (1) ''traditional'' classification with ten subfamilies; (2) alternative ''reduced'' classification with two subfamilies; and (3) revised classification with ten subfamilies. See Data Accessibility for tree file.
FIG. 3 in Molecular Phylogenetics of the Clingfishes (Teleostei: Gobiesocidae)- Implications for Classification
FIG. 3. Maximum-likelihood phylogram obtained from RAxML analysis of the concatenated seven-gene dataset. Branches marked with an asterisk (*) have been shortened to facilitate viewing (see inset topology for original branch lengths). Numbers above branches represent bootstrap (BS) support values. Red branches are those downstream of nodes with BS values 75%. Letters (A–J) in gray circles are clades discussed in text. Rows of colored boxes to right side of image represent subfamily designations (see corresponding key) within the following three classification schemes: (1) ''traditional'' classification with ten subfamilies; (2) alternative ''reduced'' classification with two subfamilies; and (3) revised classification with ten subfamilies. See Data Accessibility for tree file.
FIG. 2 in Molecular Phylogenetics of the Clingfishes (Teleostei: Gobiesocidae)- Implications for Classification
FIG. 2. Previously published hypotheses of gobiesocid relationships. (A) Dendrogram of subfamilial relationships provided by Briggs (1955: 144, dendrogram 1). (B) Relationships as depicted in dendograms 2–5 from Briggs (1955: 146, 148) representing relationships within subfamilies Trachelochisminae, Lepadogastrinae, Gobiesocinae, and Diplocrepinae. (C) Topology of lepadogastrine clingfishes derived from Bayesian analysis of mitochondrial genes (12S and 16S) by Almada et al. (2008: fig. 1). (D) Topology derived from maximum-likelihood analysis of six-gene concatenated dataset by Fricke et al. (2017: fig. 1). (E) Topology derived from Bayesian analysis of six-gene concatenated dataset by Conway et al. (2017a: fig. 1). Original branch support values associated with topologies in C–E omitted. Subfamily membership indicated by colored boxes (explained in key).
FIG. 8 in Phylogenetic Relationships among Fishes in the Order Zeiformes Based on Molecular and Morphological Data
FIG. 8. Comparison of the branching patterns of molecular and combined-data trees produced with different methods. Each family recognized by Tyler et al. (2003) is a different color. Black lines indicate relationships with strong support; gray lines indicate weaker support. (A) Results from maximum likelihood analysis of molecular data. (B) Results from Bayesian inference analysis of molecular data. (C) Results from maximum likelihood analysis of combined morphological and molecular data, including three genera with morphological data only. (D) Results from Bayesian inference analysis of combined morphological and molecular data, including three genera with morphological data only.
FIG. 7 in Phylogenetic Relationships among Fishes in the Order Zeiformes Based on Molecular and Morphological Data
FIG. 7. Combined (total-evidence) molecular and morphological phylogeny of the Zeiformes based on Bayesian inference (BI) using MrBayes v.3.1.2 (Huelsenbeck and Ronquist, 2001; Ronquist and Huelsenbeck, 2003). See Figure 6 for details of outgroup relationships, and see text for detailed methods and assumptions. The combined maximum likelihood (ML) analysis using Garli v2.0 (Zwickl, 2006) produced almost identical topology and very similar relative branch lengths. Taxa with asterisks (*) are of questionable or revised identification. Taxa with two asterisks (**) are those with morphological data only. Support values at nodes are from both analyses, with BI posterior probabilities above ML bootstrap percentages. Numbers after scientific names correspond to code numbers in Table 1. Thumbnail drawings of representative species by Michael Hanson.
FIG. 1 in Phylogenetic Relationships among Fishes in the Order Zeiformes Based on Molecular and Morphological Data
FIG. 1. World map showing the collecting localities for specimens from which tissues were obtained for this study, along with the type locality for each species in the order. Specimen and type localities are most numerous in the western and southwestern Pacific, in the waters surrounding southern Africa, and on either side of the North Atlantic.
FIG. 4 in Phylogenetic Relationships among Fishes in the Order Zeiformes Based on Molecular and Morphological Data
FIG. 4. Maximum parsimony (MP) phylogeny of Zeiformes based on morphological data analyzed in PAUP v.4b10 (Swofford, 2003). The data (Table 3) are a modified version of those used by Tyler and Santini (2005) but with revised outgroups reflecting zeiform membership in the Paracanthopterygii (e.g., Grande et al., 2013), and with character deletions, additions, and edits described in the text. The characters are listed in Appendix 1. This analysis is based on 27 terminal taxa and 105 characters, and resulted in a single shortest tree of 319 steps with CI 0.567. Support values at nodes are 1000-replicate bootstrap percentages/decay (Bremer) values. Character-state optimization was in MacClade 4.08 (Maddison and Maddison, 2005) using the ACCTRAN option as used also by Tyler et al. (2003) and Tyler and Santini (2005). Thumbnail drawings of representative species are original artwork by Michael Hanson.
FIG. 5 in Phylogenetic Relationships among Fishes in the Order Zeiformes Based on Molecular and Morphological Data
FIG. 5. Comparison of branching patterns of morphological trees under maximum parsimony (MP) from three studies. Each family recognized by Tyler et al. (2003) is a different color. (A) Results from Tyler et al. (2003). (B) Results from Tyler and Santini (2005). (C) Results from the morphological analysis of the present study. Black lines in C indicate relationships with strong support; gray lines indicate weaker support. Note that the new tree resembles the previous trees but with the root moved to a position near Zeidae.
FIG. 2 in Phylogenetic Relationships among Fishes in the Order Zeiformes Based on Molecular and Morphological Data
FIG. 2. Maximum likelihood (ML) phylogeny of the Zeiformes as reconstructed by Garli v2.0 (Zwickl, 2006), using sequence data for the eight molecular loci of Table 1, under the substitution models given in Table 2. Support values at nodes are bootstrap percentages. For details of the outgroup relationships see Figure 1S (see Data Accessibility). Asterisk (*) indicates sample originally cataloged as Cyttomimus affinis. Numbers after scientific names correspond to code numbers in Table 1.
FIG. 3 in Phylogenetic Relationships among Fishes in the Order Zeiformes Based on Molecular and Morphological Data
FIG. 3. Bayesian inference (BI) phylogeny of the Zeiformes as reconstructed by MrBayes v.3.1.2 (Huelsenbeck and Ronquist, 2001; Ronquist and Huelsenbeck, 2003), using sequence data for the eight molecular loci of Table 1, under the substitution models given in Table 2. Support values at nodes are posterior probabilities. For details of the outgroup relationships see Figure 2S (see Data Accessibility). Asterisk (*) indicates sample originally cataloged as Cyttomimus affinis. Numbers after scientific names correspond to code numbers in Table 1.
FIGURE 1 in Fossil calibration dates for molecular phylogenetic analysis of snakes 1: Serpentes, Alethinophidia, Boidae, Pythonidae
FIGURE 1. Time-calibrated phylogeny of Serpentes based on Pyron et al. (2013) and Reynolds et al. (2014). Numbers represent calibrated nodes in text. Fossil taxa are the calibration points for their respective nodes. Thickened bars represent well-sampled, taxonomically resolved stratigraphic distributions for the sister taxa to Pan-Serpentes and snake lineages whose first occurrences are determined by older sister taxa. Thin bars represent estimated stratigraphic distributions for taxa with poorly resolved fossil records, or no published fossil record (names in grey). "Scolecophidia" represents a paraphyletic grade with respect to Alethinophidia (see text).
Fig. 2 Phylogenetic relationships among 30 in Time-calibrated molecular phylogeny reveals a Miocene-Pliocene diversification in the Amazon miniature killifish genus Fluviphylax (Cyprinodontiformes: Cyprinodontoidei)
Fig. 2 Phylogenetic relationships among 30 species of Cyprinodontoidei, including all nominal species of Fluviphylax and three undescribed species, inferred by using partial sequences of the nuclear-encoded genes GLYT1, ENC1, RAG1, MYH6, and SREB2 and the mitochondrial gene COI, total of 5880 bp. Numbers left to the bar indicate posterior
FIGURE 1 in Fossil calibration dates for molecular phylogenetic analysis of snakes 2: Caenophidia, Colubroidea, Elapoidea, Colubridae
FIGURE 1. Phylogeny of Caenophidia from Pyron et al. (2013a) temporally calibrated on minimum ages reported here. Taxon names in grey have not been described in the fossil record. Taxon names in black have been described from fossils. See Holman (2000) and Szyndlar (2012) for records. Taxa labeled with two identifiers represent the most inclusive clades subtended by those identifiers following Pyron et al. (2013a).
Fig. 4 in Phylogenetic relationships within the flatworm genus Matuxia (Platyhelminthes, Tricladida, Continenticola) inferred from molecular data with the description of a southern lineage of the genus
Fig. 4 Matuxia tymbyra Rossi & Leal-Zanchet, sp. nov., holotype, microphotographs of transverse (a–e, g) and sagittal (f; anterior tip to the left) sections: a anterior region of body; b detail of anterior region of body; c pre-pharyngeal region; d detail of dorsal surface of pre-pharyngeal region; e detail of ventral surface of pre- pharyngeal region; f pharynx; g ovary
Fig. 5 in Phylogenetic relationships within the flatworm genus Matuxia (Platyhelminthes, Tricladida, Continenticola) inferred from molecular data with the description of a southern lineage of the genus
Fig. 5 Matuxia tymbyra Rossi & Leal-Zanchet, sp. nov.: a sagittal composite reconstruction of copulatory apparatus of the holotype; b horizontal composite reconstruction of copulatory apparatus of specimen MZU PL.00166
Fig. 2 in Phylogenetic relationships within the flatworm genus Matuxia (Platyhelminthes, Tricladida, Continenticola) inferred from molecular data with the description of a southern lineage of the genus
Fig. 2 Molecular phylogenetic relationships and species boundaries inferred from the sequences of COI and EF-1a on a Bayesian consensus tree. Node values represent posterior probabilities and likelihood
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