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Fig. 5 in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 5. The same consensus as shown in figure 4, with stems and taxa identified for ready comparison with evolutionary changes presented in appendix 4 (change list). Stems 5, 6, 16, 20, 23, 24 represent alternative relationships not rejected by the data.

Fig. 3. Sensitivity analysis graphic. Y in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 3. Sensitivity analysis graphic. Yaxis represents the logarithm of the ratio of transversion: transition weights. The xaxis represents the logarithm of the ratio of the indel cost versus the maximal cost of a molecular change. The colors represent the zaxis, which is congruence between the molecular and morphological data partitions. Red is good, blue is bad.

Fig. 2 in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 2. Strict consensus of 192 equally parsimonious trees based on morphology alone (length = 276; CI = 0.443; RI = 0.74). Numbers on branches are Bremer values.

Fig. 6 in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 6. Phylogenetic hypotheses for the Polychrotidae of Etheridge and de Queiroz (1988), and Frost and Etheridge (1989). Circles represent hypothesized rooting points.

Fig. 1 in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 1. Single tree obtained on molecularonly data (length = 2332; CI = 0.23; RI = 0.68). Numbers on branches are Bremer values.

FIGURE 2 in A new morphological dataset reveals a novel relationship for the adzebills of New Zealand (Aptornis) and provides a foundation for total evidence neoavian phylogenetics

FIGURE 2. Majority-rule cladogram of nine most parsimonious trees (length: 2038, CI: 0.2498, RI: 0.5337, RC: 0.1333, HI: 0.7502) from analysis of our new dataset of 40 taxa and 368 osteological characters. All trees show optimization of an Aptornis defossor+Psophia obscura sister group. Synapomorphies are detailed in table 2. Extinct taxa are denoted with daggers. Majority-rule percentages are annotated above branches, followed by bootstrap support values greater than 50% in parentheses. Branch length ranges are below branches.

FIGURE 5 in A new morphological dataset reveals a novel relationship for the adzebills of New Zealand (Aptornis) and provides a foundation for total evidence neoavian phylogenetics

FIGURE 5. Synapomorphies for the pelvis of Aptornis defossor (AMNH 7300, A) and Psophia obscura (AMNH 2671, B). The pelvises are shown in ventral view. Scale bars are different for each specimen and are shown below each specimen. Labels correspond to synapomorphies, with character numbers followed by character states in parentheses. Abbreviations: cio, crista iliaca obliqua; ili, preacetabular ilium; ish, postacetabular ischium; pil, postacetabular ilium; syn, synsacrum

FIGURE 1 in A new morphological dataset reveals a novel relationship for the adzebills of New Zealand (Aptornis) and provides a foundation for total evidence neoavian phylogenetics

FIGURE 1. Strict consensus cladogram of nine most parsimonious trees (length: 2038, CI: 0.2498, RI: 0.5337, RC: 0.1333, HI: 0.7502) from analysis of our new morphological dataset of 40 taxa and 368 characters in PAUP*. Results support optimization of an Aptornis defossor + Psophia obscura sister group. Synapomorphies are detailed in table 2. Extinct taxa are denoted with daggers. Bootstrap support values greater than 50% are annotated above branches, with branch length ranges reported below branches.

FIGURE 3. A in A new morphological dataset reveals a novel relationship for the adzebills of New Zealand (Aptornis) and provides a foundation for total evidence neoavian phylogenetics

FIGURE 3. A. Resulting tree from Bayesian analysis of 32 RAG1 and RAG2 sequences. Clade credibility values greater than 90% are annotated above branches. Core Gruiformes, Ralloidea, and Gruoidea are well supported with 100% clade credibility values. The scale bar at the bottom of the tree denotes branch length. The data were run in MrBayes for 2,000,000 generations.

FIGURE 3 in A new morphological dataset reveals a novel relationship for the adzebills of New Zealand (Aptornis) and provides a foundation for total evidence neoavian phylogenetics

FIGURE 3 (continued). B. Resulting tree from Bayesian analysis of our new dataset of 40 taxa and 368 osteological characters combined with 32 sequences of RAG1 and RAG2 nuclear genes. Clade credibility values greater than 90% are annotated above branches. Extinct taxa are denoted with daggers. The scale bar at the bottom of the tree denotes branch length. The data were run in MrBayes for 1,100,000 generations.

FIG. 15 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)

FIG. 15. Main character systems scored for each included species of Rhinella. References: Filled squares, most characters of the considered character system scored (> 50%); half-filled squares, most characters not scored (<40%); empty squares, no character scored. Abbreviations: Ad. ext. morphol., Adult external morphology; Ad. musc., Adult musculature; Ad. osteol., Adult osteology; Emb. morphol., Embryonic morphology; Larv. chondrocr., Larval chondrocranium; Larv. morphol., Larval external morphology; Nat. hist., Natural history.

FIG. 10 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)

FIG. 10. Phylogenetic relationships of Rhinella and outgroups recovered in one of the most parsimonious trees from the total evidence analysis with TNT considering gaps as a fifth state (length 25,399 steps). Values around nodes are parsimony jackknife frequencies (frequency differences value [above]/absolute [below]). An asterisk (*) indicates 100% jackknife support. Clades lacking references have <25% frequency difference values or <50% jackknife absolute frequencies. Lower left inset shows the entire cladogram with present view marked in white.

FIG. 11 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)

FIG. 11. Phylogenetic relationships of Rhinella recovered in one of the most parsimonious trees from the total evidence analysis with TNT considering gaps as a fifth state (length 25,399 steps). The clades and species groups shown are those recognized in this study. Part 1 of 4. The R . marina Clade (1): the R . arunco, R . spinulosa, and R . granulosa Groups. Black circles indicate nodes that collapse in the strict consensus. Values around nodes are parsimony jackknife frequencies (frequency differences value [above]/absolute [below]). An asterisk (*) indicates 100% jackknife support. Clades lacking references have <25% frequency difference values or <50% jackknife absolute frequencies. Lower left inset shows the entire cladogram with present view marked in white. Abbreviations: MtG, mitochondrial genome; NuG, nuclear genome.

FIG. 6 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)

FIG. 6. Hyoid plate: A, Rhinella cristinae ICN 26233 (char. 25.0), B, R . manu MHNC 4404 (char. 25.1). Arrowheads indicate the occurrence of posterior lobes of the anterolateral processes in B. Panels redrawn from Vélez-R. and Ruiz-C., 2002 (A); Chaparro et al., 2007 (B).

FIG. 2 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)

FIG. 2. Skulls (dorsal view) showing the different level of contact between nasals and frontoparietals (both bones in gray): A, Nannophryne cophotis KU 218525 (char. 8.0; species not included in this study); B, Rhinella yanachaga MUSM 24509 (char. 8.1); C, R . crucifer KU 93112 (char. 8.2); D, R . marina KU 152914 (char. 8.3). Panels A, C, D redrawn from Pramuk (2006), B redrawn from Lehr et al. (2007).

FIG. 13 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)

FIG. 13. Phylogenetic relationships of Rhinella recovered in one of the most parsimonious trees from the total evidence analysis with TNT considering gaps as a fifth state (length 25,399 steps). The clades and species groups shown are those recognized in this study. Part 3 of 4. The R . margaritifera Clade (1): R . sternosignata and the R . veraguensis and R . festae Groups. Black circles indicate nodes that collapse in the strict consensus. Values around nodes are parsimony jackknife frequencies (frequency differences value [above]/absolute [below]). An asterisk (*) indicates 100% jackknife support. Clades lacking references have <25% frequency difference values or <50% jackknife absolute frequencies. Lower left inset shows the entire cladogram with present view marked in white.

FIG. 14 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)

FIG. 14. Phylogenetic relationships of Rhinella recovered in one of the most parsimonious trees from the total evidence analysis with TNT considering gaps as a fifth state (length 25,399 steps). The clades and species groups shown are those recognized in this study. Part 4 of 4. The R . margaritifera Clade (2): the R . margaritifera Group. Black circles indicate nodes that collapse in the strict consensus. Values around nodes are parsimony jackknife frequencies (frequency differences value [above]/ absolute [below]). An asterisk (*) indicates 100% jackknife support. Clades lacking references have <25% frequency difference values or <50% jackknife absolute frequencies. Lower left inset shows the entire cladogram with present view marked in white.

FIG. 9 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)

FIG. 9. Comparison between the strict consensuses resulting from the analyses of the restricted nuclear dataset (rND) and restricted mitochondrial dataset (rMD), showing the alternative positions of Rhinella horribilis in both analyses. Circles on nodes indicate parsimony jackknife frequencies (frequency differences value [above]/absolute [below]). Nodes lacking circles have <25% frequency difference values or <50% jackknife absolute frequencies.

FIG. 1 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)

FIG. 1. Summarized relationships of Rhinella according to the main published phylogenetic hypotheses of the group. Only the topological sections corresponding to Rhinella, and putative most related outgroups (i.e., Anaxyrus and Incilius) are shown. The number of species sampled within each clade is reported in parentheses. (A) Pauly et al. (2004: fig. 2). (B) Frost et al. (2006: fig. 50). (C) Pramuk (2006: fig. 4). (D) Chaparro et al. (2007: fig. 9). (E) van Bocxlaer et al. (2010: fig. S1). (F) Pyron and Wiens (2011: fig. 2). (G) Pyron (2014: suppl. information "amph_shl.tre"). (H) Pereyra et al. (2016a: fig. 3 and appendix S12). (I) Jetz and Pyron (2018: suppl. information "amph_shl_new.tre").

FIG. 8 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)

FIG. 8. Head (lateral and dorsal views) showing the shape of the parotoid gland (in gray): A, Rhinella aff. cerradensis (char. 56.0); B, R . acutirostris (char. 56.1); C, R . arunco (char. 56.2); D, R . marina (char. 56.3).