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Fig. 65. Part 9 in The Amphibian Tree Of Life
Fig. 65. Part 9 of anurans from the general tree (fig. 50 [insert]): Mantellidae, Rhacophoridae, Nyctibatrachidae, Ranidae.
Fig. 58. Part 3 in The Amphibian Tree Of Life
Fig. 58. Part 3 of anurans from the general tree (fig. 50 [insert]): Hemiphractidae, Brachycephalidae, Cryptobatrachidae, Amphignathodontidae, and Hylidae.
Fig. 70 in The Amphibian Tree Of Life
Fig. 70. Generic changes suggested for bufonid taxa that we studied. This figure shows our terminals
Fig. 68 in The Amphibian Tree Of Life
Fig. 68. Maximumlikelihood tree of predominantly New World Bufonidae suggested by Pauly et al. (2004) on the basis of 2,370 bp (730 informative sites) of mitochondrial DNA (12S, tRNAVal, and 16S). Alignment was done under Clustal (Thompson et al., 1997; cost functions not disclosed) then modified manually. Gaps were considered to be missing data and the substitution model assumed for the maximumlikelihood analysis was GTR 1 G1 I.
Fig. 64. A in The Amphibian Tree Of Life
Fig. 64. A, Original tree of Jiang et al. (2005; from fig. 42) of Paini and (on right) its equivalent undirected network; B, Tree rerooted and with augmented resolution as implied by our general results,
Fig. 56. Part 2 in The Amphibian Tree Of Life
Fig. 56. Part 2 of anurans from the general tree (fig. 50 [insert]): Heleophrynidae and basal hyloids
Fig. 44 in The Amphibian Tree Of Life
Fig. 44. Maximumlikelihood tree of Holarctic Rana of Hillis and Wilcox (2005). The underlying data are ca. 2kb of mtDNA of the 12S–16S region (spanning the tRNAVal gene). Sequence alignment was done initially using Clustal W (Thompson et al., 1994), costs not disclosed, and manually adjusted, guided by assumed secondary structure, ambiguously aligned sequences discarded. It was not stated whether gaps were treated as data, but we presume not. Substitution model GTR 1 G1 PINVAR was assumed for the maximumlikelihood analysis. On the basis of previous research, the root was assumed
Fig. 41 in The Amphibian Tree Of Life
Fig. 41. Consensus of two parsimony trees of Chinese ranids from Jiang and Zhou (2005). Data were 1,005 bp of the mtDNA sequences of the 12S and 16S rRNA gene fragments (tree length 5 1485, ci 5 0.449). Sequences were aligned using ClustalX (Thompson et al., 1997), with manual modifications made subsequently. Gaps and ambiguously aligned sequences excluded from analysis. Generic names in parentheses reflect alternative usages. Generic taxonomy is updated to recognize Quasipaa (Jiang et al., 2005).
Fig. 37 in The Amphibian Tree Of Life
Fig. 37. Consensus of two equally parsimonious trees from Marmayou et al. (2000) of exemplars of Ranidae and Rhacophoridae (Ranidae: Rhacophorinae in their usage) based on 305 bp (151 informative sites) of 12S mtDNA, aligned using the program MUST (Philippe, 1993) and subsequently manually modified with reference to secondary structure models. Cost functions for alignment were not stated, nor whether gaps were treated as missing data or as evidence (ci 5 0.382, ri 5 0.429). Tree rooted on Eleutherodactylus cuneatus (5 Euhyas cuneata).
Fig. 36 in The Amphibian Tree Of Life
Fig. 36. Maximum likelihood tree of exemplars of Ranoidea, with a focus on African taxa, by Van der Meijden et al. (2005), based on mt DNA (12S and 16S rRNA) and nu DNA (RAG1, RAG2, rhodopsin), for 2,995 bp of sequence. Alignment was made using ClustalW (Thompson et al., 1994), with costs not disclosed and gaps and highly variable sites excluded from analysis. The model assumed for maximumlikelihood analysis was TrN 1 I 1 G. The tree was rooted on an hierarchical outgroups (not shown in original) composed of Latimeria, Homo, Gallus, Lyciasalamandra, Alytes (2 spp.), Agalychnis, and Litoria. The ''southern African clade'' represents Pyxicephalinae as subsequently redelimited by Dubois (2005).
Fig. 31 in The Amphibian Tree Of Life
Fig. 31. Maximumlikelihood tree of various ranoids constructed by Van der Meijden et al. (2004) on the basis of 1,566 bp of the nuclear gene RAG1. Sequence alignment was not reported. Cost functions of analysis were not provided nor which model of nucleotide evolution (as suggested by ModelTest; Posada and Crandall, 1998) was employed in the analysis. The tree was rooted on Xenopus laevis. We inserted the higher taxonomy on the right to allow easier comparison to other studies discussed in this section.
Fig. 48 in The Amphibian Tree Of Life
Fig. 48. Consensus of weighted parsimony trees of Rhacophoridae suggested by J.A. Wilkinson et al. (2002), with their subfamily taxonomy on right. (This is Mantellidae and Rhacophoridae of other authors.) The tree was based on 2kb (of 12S and 16S mt rRNA as well as tRNAVal). Alignment was manual, guided by models of secondary structure with ambiguously aligned segments discarded. In analysis, transversions were weighted twice transitions. Whether reatment of gaps were treated as evidence of relationship or as missing data was not stated. Chirixalus eiffingeri was placed in Kurixalus by Ye, Fei, and Dubois (In Fei, 1999), and Chirixalus idiootocus was transferred into an explicitly polyphyletic/paraphyletic Aquixalus by Delorme et al. (2005). The tree was rooted on Nidirana adenopleura and Aquarana catesbeiana.
Fig. 27 in The Amphibian Tree Of Life
Fig. 27. Implied consensus of two most parsimonious trees of African toads studied by Cunningham and Cherry (2004), showing 22N 20N transition point and reversal to 22N in the Bufo pardalis group, and alternative placements of Bufo maculatus. The underlying data are sequences from mtDNA (12S, 16S, ND2, and the tRNA genes flanking ND2) and nuDNA (ACTC and rhodopsin). Alignment of 12S and 16S were made initially with ClustalX (Thompson et al., 1997), costs not disclosed, and adjusted manually, guided by models of secondary structure. Alignment of coding, tRNA and intron sequences involved so few length variables that these were done manually. Gaps and missing data were treated as unknowns. Outgroups not show in tree: Dendropsophus labialis (Hylidae); Euhyas cuneata (Leptodactylidae: Eleutherodactylinae), Limnodynastes dorsalis (Limnodynastidae); Heleophryne natalensis (12S only; Heleophrynidae); H. purcelli (16S only; Heleophrynidae); Nesomantis thomasetti (Sooglossidae); Rana temporaria (Ranidae).
Fig. 40 in The Amphibian Tree Of Life
Fig. 40. Maximumlikelihood tree of ranoids of Delorme et al. (2004), based on sequences from 12S and 16S rRNA for a total of 1198 bp. Alignment was made using the program SeAl (Rambaut, 1995; cost functions not provided) and by comparison with models of secondary structure. Gaps were treated as missing data. The maximumlikelihood nucleotide substitution model accepted was TrN 1 I 1 G.
Fig. 20 in The Amphibian Tree Of Life
Fig. 20. Consensus of 12 equally parsimonious trees of selected members of Megophryidae of Delorme and Dubois (2001), rooted on Scaphiopus and Pelodytes. Underlying data were 54 transformation of morphology, rooted on Pelodytes and Scaphiopus (ci 5 0.581; ri 5 0.713). Although the tree and a list of the underlying character transformation were provided, no association was made between the character transformations and taxa or particular branches on the tree, rendering the analysis practically unrepeatable. Nominal subfamilies are noted on the right.
Fig. 17 in The Amphibian Tree Of Life
Fig. 17. Tree of amphibians provided by San Mauro et al. (2005). This tree reflects a maximumlikelihood analysis of 1,368 bp of the nuclear proteincoding gene RAG1, assuming the GTR 1 G 1 I substitution model (as suggested by ModelTest v. 3.6; Posada and Crandall, 1998). Sequence alignment was made manually with only one gap excluded from analysis.
Fig. 14 in The Amphibian Tree Of Life
Fig. 14. Narrative tree of relevant anuran taxa by Ford and Cannatella (1993). A branch subtending Hylidae 1 Pseudidae in the original figure is collapsed per errata distributed with reprint. An asterisk was used by these authors to denote a metataxon, and quotation marks to denote nonmonophyly.
Fig. 10 in The Amphibian Tree Of Life
Fig. 10. Parsimony tree of Plethodontidae by Macey (2005), a reanalysis of entire mt DNA genome sequence data provided by Mueller et al. (2004). On right are the traditional taxonomy and Macey's revised subfamilial taxonomy, which is substantially identical to that suggested by Chippindale et al. (2004; fig. 11). The generic taxonomy is updated to reflect name changes of former Salamandra luschani (Veith and Steinfartz, 2004) and Hydromantes italicus.
Fig. 12 in The Amphibian Tree Of Life
Fig. 12. Salamandrid relationships suggested by Titus and Larson (1995) based on a parsimony analysis of 44 morphological character transformations and 431 informative sites of ca. 1.8 kb of the 12S and 16S mt rRNA and tRNAVal fragments of mtDNA. Sequence alignment was done using MALIGN (W.C. Wheeler and Gladstein, 1992) with equal weighting of transversions and transitions and a gap penalty cost of 6. Sequence data and morphology in parsimony analysis had equal costs and gaps were treated as evidence. The tree was rooted on Eurycea 1 Phaeognathus; tree length 5 2,081. Generic names are updated to reflect the naming of Lyciasalamandra (Veith and Steinfartz, 2004) and the partition of Triturus into Mesotriton, Lissotriton (not studied by Titus and Larson, 1995), and Triturus (GarcíaParís et al., 2004b).
Fig. 11 in The Amphibian Tree Of Life
Fig. 11. Tree of Plethodontidae suggested by Chippindale et al. (2004) based on parsimony analysis of 104 transformation series of morphology and 1,493 informative sites of nu DNA (RAG1) and mt DNA (cytochrome c and ND4a). On the right (left to right) are the old taxonomy of plethodontids and the taxonomy recommended by Chippindale et al. (2004). Sequences were aligned manually with only singlecodon indels; gaps were considered missing data in the analysis.
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