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Figure 2 in On the evolution and diversification of an Andean clade of reptiles: combining morphology and DNA sequences of the palluma group (Liolaemidae: Phymaturus)

Figure 2. The total-evidence consensus tree. Red nodes, numbered 1–6, are those found in previous studies (see Fig. 1): node 1, vociferator clade (vociferator group of Morando et al., 2013); node 2, bibronii clade (present study); node 3, verdugo lineage (clade F of Lobo et al., 2012a; verdugo group of Morando et al., 2013); node 4, mallimaccii subclade (clade G of Lobo et al., 2012a; mallimacci group of Morando et al., 2013); node 5, antofagastensis lineage (clade H of Lobo et al., 2012a); node 6, punae lineage (clade I of Lobo et al., 2012a); node 7, roigorum subclade (roigorum group of Morando et al., 2013), but including the verdugo lineage (node 3). Values below branches are jackknife percentages. Phymaturus illustrating the tree, from top to the bottom: males of Phymaturus damasense, Phymaturus roigorum, Phymaturus verdugo, and Phymaturus williamsi. For more details, see the main text.

Figure 6. A in On the evolution and diversification of an Andean clade of reptiles: combining morphology and DNA sequences of the palluma group (Liolaemidae: Phymaturus)

Figure 6. A, transparent mesenterium of Phymaturus palluma (MCN 2651; character 213). Scale bar: 10 mm. B, same mesenterium, but completely melanic in Phymaturus patagonicus (MCN 3561). Scale bar: 10 mm. C, external surface of rectum of Phymaturus verdugo (MCN 1961; character 214). Scale bar: 5 mm. D, Longitudinal folds of the internal mucosa of rectum in Phymaturus payuniae (MCN 2879; character 215). Scale bar: 5 mm.

Figure 1. A, C in On the evolution and diversification of an Andean clade of reptiles: combining morphology and DNA sequences of the palluma group (Liolaemidae: Phymaturus)

Figure 1. A, C, recent Phymaturus palluma group topologies published using different sources of data. A, morphological hypothesis of Lobo et al. (2012a); B, molecular ('all genes') topology of Morando et al. (2013). Numbers indicates congruent nodes (relationships) between both studies. Even though these two studies share only half of the terminal taxa, respectively, and different optimality criteria for phylogenetic analyses were used (parsimony versus Bayesian), almost half of the resulting nodes are congruent. B, D, Pruning these two topologies (deleting terminal taxa not shared by both analyses), the same topology is recovered for both studies, with the exception of the position of Phymaturus roigorum.

Figure 4 in On the evolution and diversification of an Andean clade of reptiles: combining morphology and DNA sequences of the palluma group (Liolaemidae: Phymaturus)

Figure 4. Ontogeny of melanism in throat, chest, sides, and dorsum of head in Phymaturus dorsimaculatus. A, ventral, lateral, and dorsal views of juvenile male (65.1 mm snout–vent length, SVL; MCN 1578); B, juvenile male (80.3 mm SVL; MCN 1570); C, adult male (89.8 mm SVL; MCN 1572). D–G, colour pictures of different species of males of Phymaturus: D, colour picture of a live Phymaturus dorsimaculatus male (photo by F. Lobo); E, Phymaturus verdugo (photo by F. Lobo); F, Phymaturus punae (photo by J.C. Acosta); G, Phymaturus bibronii (photo by A. Laspiur).

Figure 5 in On the evolution and diversification of an Andean clade of reptiles: combining morphology and DNA sequences of the palluma group (Liolaemidae: Phymaturus)

Figure 5. Evolution of head melanism, optimized on one of the eight most parsimonious trees found from totalevidence analysis for the palluma group (all topologies imply the same scheme of changes for this particular character); blue, melanic head pigmentation absent, reticulated pattern conspicuous or in some cases any pattern at all; green, melanic throats and sides of heads, dorsum of head reticulated; purple, complete melanic heads (throats, sides, and dorsum of heads).

Figure 9. A in On the evolution and diversification of an Andean clade of reptiles: combining morphology and DNA sequences of the palluma group (Liolaemidae: Phymaturus)

Figure 9. A, temporal scales of Phymaturus dorsimaculatus (MCN 1569) showing two organ scales (character 233); scale bar, 2 mm. B, cloacal region of Phymaturus verdugo (MCN 1960; Character 236); scale bar, 5 mm. C, female of Phymaturus verdugo (MCN 1958; snout–vent length, SVL = 99.8 mm; character 237). D, Phymaturus querque male (MCN 3863; SVL = 104.9 mm; character 249). E, Phymaturus paihuanense female (SSUC–Re 0422; photo by A. Laspiur; character 252). F, hemipenis of Phymaturus roigorum (MCN 1963; character 253); scale bar, 5 mm.

Figure 8. A in On the evolution and diversification of an Andean clade of reptiles: combining morphology and DNA sequences of the palluma group (Liolaemidae: Phymaturus)

Figure 8. A, tibial dorsal scalation of Phymaturus patagonicus (MCN 3561). B, central area of the same view of P. patagonicus (same specimen) tibia, showing scales in detail (character 220). Almost every dorsal tibial scale carries a spine and a scale organ on the distal tip of the scale (arrow; character 222). C, tibial dorsal scalation of Phymaturus palluma (MCN 3131). D, central area of the same view of P. palluma (same specimen). Scale organs hidden under the scale spines. E, tibial dorsal scalation of Phymaturus denotatus (MCN 3160). F, central area of the same view of P. denotatus (same specimen). The arrow indicates granular scales spread out among tibial scales (character 223). Scale bars: A, C, E, 5 mm; B, D, F, 2 mm.

Figure 10. A in On the evolution and diversification of an Andean clade of reptiles: combining morphology and DNA sequences of the palluma group (Liolaemidae: Phymaturus)

Figure 10. A, orbitosphenoid bone in Phymaturus aguanegra (MCN 968; character 240); the arrow indicates the cartilaginous margin of the fenestra epioptica. B, Phymaturus zapalensis (MCN 1486). C, ectopterygoid of Phymaturus spurcus (MCN 1249; character 241). D, same bone in Phymaturus laurenti (MCN 326). Abbreviations: ecp, ectopteygoid; fep, fenestra epioptica; fm, fenestra metoptica; fop, fenestra optica; fpr, fenestra prootica; j, jugal; pt, pterygoid. Scale bars: 1 mm.

Figure 3 in On the evolution and diversification of an Andean clade of reptiles: combining morphology and DNA sequences of the palluma group (Liolaemidae: Phymaturus)

Figure 3. Independent topologies found by separate molecular and morphological analyses (the numbers below branches in A, B, and C, represent jackknife values). A, strict parsimony analysis of morphological data. B, implied weights analysis (k = 3) of morphological data. C, all-genes analysis with strict parsimony. D, Bayesian analysis of all genes concatenated. Numbers below branches represent posterior probabilities (>0.70). Green nodes are those congruent with the total-evidence analysis.

Figure 7 in On the evolution and diversification of an Andean clade of reptiles: combining morphology and DNA sequences of the palluma group (Liolaemidae: Phymaturus)

Figure 7. Epiaxial musculature fascia (characters 216–219): A, no pigmentation of fascia dorsal among axial muscles of Phymaturus roigorum (MCN 2102); B, lateral pigmentation between axial muscles forming longitudinal lines, neural spines delineated in black in Phymaturus aguanegra (MCN 3288). C, lateral and dorsal fascia of axial muscles pigmented in Phymaturus spurcus (FML 1244). D, same condition, but less melanic, observed in Phymaturus tenebrosus (MCN 1263). Neural spines highlighted in white. Scale bars: 10 mm. Abbreviations: ld, longissimus dorsi muscle; ts, transversospinalis muscle.

Figure 6 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Figure 6. Hypothetical radiation schemes for Uromastyx and possibly relevant geological events. Approximate distribution range for each taxon (Wilms, 2001) is shown with its abbreviated name: Hard (Uromastyx hardwickii), Aca (U. acanthinura), Mali (U. d. maliensis), Gey (U. geyri), Dis (U. d. dispar), Oce (U. ocellata), Mac (U. macfadyeni), Aeg (U. a. aegyptia), Mic (U. a. microlepis), Orn (U. ornata) and Ben (U. benti).

Figure 5 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Figure 5. Neighbour-joining tree constructed based on maximum likelihood distances from 1503 alignable nucleotide sites (the HKY model and transition/transversion ratio of 3.48). The tree was rooted with Chamaeleo africanus as an outgroup. Bootstrap probabilities are shown for neighbour joining, maximum likelihood and maximum parsimony analyses (from left to right). Underlined values mean that the branch was not reconstructed in the best tree topology by the corresponding analyses. Note that two distinct sequence haplotypes are included for Uromastyx acanthinura and U. ocellata. See Material and methods for more details on the analytical conditions. The nucleotide sequences taken from the database are: Chamaeleo africanus (accession No., AF448743), Chlamydosaurus kingii (AF128469), Physignathus lesueurii (AF128463), Acanthosoura capra (AF128498), Salea horsfieldii (AF128490), Trapelus savignii (AF128512), Leiolepis guentherpetersi (AF128461), Leiolepis belliana (U82689), Laudakia caucasia (AF028681) and Laudakia lehmanni (AF028677).

Figure 4 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Figure 4. Secondary structures of the inserted sequences found between tRNAGln and tRNAIle genes. The 128 bp insert for Uromastyx ornata can assume alternative secondary structures either with an extremely stable and long stem region (A) or with a clover-leaf structure for the second tRNAGln gene (or pseudogene) and a stable stem-and-loop structure (B). The 59 bp inserted for U. ocellata may also assume a somewhat less stable stem-and-loop structure (C). Heavy-strand sequences are shown and numbers refer to the corresponding positions in their light-strand sequences shown in Fig. 3A. Bars in stems represent Watson–Crick base pairs and dots stand for wobble G–U pairs for RNA.

Figure 2 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Figure 2. Evolution of mitochondrial gene organization in Uromastyx. A, typical vertebrate organization plesiomorphic to lizards. B, typical organization for acrodont lizards including Leiolepis and likely the direct common ancestor of Leiolepis and Uromastyx. C, typical Uromastyx organization in which the putative origin of light-strand replication (black box) disappeared from the WANCY tRNA gene cluster. D, organization for U. ornata and likely for the direct common ancestor of U. ornata and U. ocellata, which has an insertion containing a stem-and-loop structure (hatched box) and the second tRNAGln gene or pseudogene (Q*). E, organization for U. ocellata in which Q* disappeared. See Figs 3 and 4 for sequences and secondary structures of the inserted region in U. ornata and U. ocellata.

Figure 3 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Figure 3. Nucleotide sequences of the inserted region between the tRNA Gln and tRNAIle genes. A, alignment between the 128 bp insertion in Uromastyx ornata and the 59 bp insertion in U. ocellata (65% identity). B, alignment between the original tRNAGln gene and its second copy within the inserted region for U. ornata (49% identity). Light-strand and heavystrand sequences are shown for A and B, respectively. Dots indicate identity with the first sequence and dashes denote a gap.

Figure 1 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Figure 1. Position of primers used for amplification and/or sequencing. See Table 1 for the primer sequences; numbers of primers correspond to those in Table 1.