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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.

Fig. 7 in The Amphibian Tree Of Life

Fig. 7. Relationships of salamanders suggested by Wiens et al. (2005). Families are noted on right. Results reflect a parsimony analysis of 326 character transformations of morphology (221 parsimonyinformative), and DNA sequences from nu rRNA (212 bp from Larson, 1991; 147 parsimonyinformative) and RAG1 (1,530 bp; 624 parsimonyinformative). Sequence alignment was made using Sequencher (Gene Codes Corp.). Morphological characters identified as paedomorphic were treated as unknown for adult morphology and in some cases hypothetical terminals were relatedspecies chimaeras of composite molecular and morphological data. Molecular transformations were weighted equally in analysis. Inferred insertiondeletion events were coded as binary characters separate from the nucleotide sequence characters and indelrequired gaps within sequences were coded as missing. The tree was rooted on Gymnophiona 1 Anura.

Fig. 9 in The Amphibian Tree Of Life

Fig. 9. Tree of Plethodontidae by Mueller et al. (2004), with the traditional taxonomic assignments (Desmognathinae 1 tribes of Plethodontinae; Wake, 1966) placed on the right, with taxonomic fragments numbered for clarity. The generic taxonomy was updated to reflect name changes of former Salamandra luschani to Lyciasalamandera (Veith and Steinfartz, 2004) and Hydromantes italicus to Speleomantes. The results reflect a Bayesian analysis of entire mt DNA genomes (number of informative sites not stated, but analyzed fragments totalled 14,040 bp), with control region and ambiguously alignable region excluded. Sequences were aligned with default costs of GCG v. 10.3 (Accelrys, San Diego; cost of 8 for gap creation and extension cost of 2) and subsequently adjusted manually. It was not stated whether gaps were treated as evidence or as missing data.

Fig. 4 in The Amphibian Tree Of Life

Fig. 4. Relationships of salamanders suggested by Larson and Dimmick (1993). Families are noted on right. Typhlonectes and Xenopus were employed as outgroups. Consensus of 40 equallyparsimonious trees (length 5 460, ci 5 0.59). Data are 32 morphological and 177 molecular (nu rDNA) character transformations (from Larson, 1991). The method of DNA alignment was not specified. Gaps were excluded as evidence.

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Author information for the publication "The Earth BioGenome Project Phase II: Illuminating the Eukaryotic Tree of Life"

This Excel format file includes three sheets: 1: CREDIT information for the named authors of the publication "The Earth BioGenome Project Phase II: Illuminating the Eukaryotic Tree of Life" 2: Funding information for the named authors of the publication "The Earth BioGenome Project Phase II: Illuminating the Eukaryotic Tree of Life" 3: A listing of the individuals included in the collective authorship "The EBP Community of Scientists" in the publication "The Earth BioGenome Project Phase II: Illuminating the Eukaryotic Tree of Life"

FIGURE 4 in A modern look at the Animal Tree of Life*

FIGURE 4. Examples of deuterostome animals. (A) The enigmatic Xenoturbella bocki (photograph by G.W. Rouse). (B) The hemichordate Ptychodera bahamensis (photograph by G. Giribet). (C) Three species of crinoid echinoderms (feather stars) on a gorgonian specimen (photograph by G.W. Rouse). (D) The lancelet Branchiostoma caribaeum (photograph by G.W. Rouse).

FIGURE 3 in A modern look at the Animal Tree of Life*

FIGURE 3. Examples of basal metazoans. (A) A species of the sponge genus Diplastrella (photograph by G. Giribet). (B) The hydrozoan cnidarian Leuckartiara octona (photograph by F. Pleijel). (c) An Indopacific coral Acropora sp. (photograph by G.W. Rouse). (d) An invasive ctenophore, Mnemiopsis leidyi (photograph by F. Pleijel).

FIGURE 2 in A modern look at the Animal Tree of Life*

FIGURE 2. Conservative hypothesis of metazoan relationships summarizing findings up to 2007. Green squares indicate genomic/EST data available. Orange squares indicate ESTs generated by the authors and other participants in the NSF-funded Assembling the Protostome Tree of Life project (Dunn et al. submitted).

FIGURE 1 in A modern look at the Animal Tree of Life*

FIGURE 1. Recently discovered and unusual animals. (A) Press coverage of the discovery of the bone-eating worm Osedax (for details see Rouse and Pleijel, this volume). (B) Greenland stamp after the discovery of Micrognathozoa. (C) Detail of the cycliophoran Symbion pandora (photograph courtesy of Peter Funch). (D) An undescribed deep-sea lophenteropneust (photograph courtesy of Nick Holland [see Holland et al. 2005]).

FIGURE 5 in The Tree of Life Web Project*

FIGURE 5. First sections of some articles and notes. From top to bottom, they are: "Fabaceae Fruits" (Wojciechowski & Mahn, 2006), attached to the Fabaceae page; "Cephalopod Gills" (Young & Vecchione, 2006), attached to the cephalopod page; "Tyrannosaurid Systematics" (Holtz, 2000), attached to the Tyrannosauridae page.

FIGURE 2 in The Tree of Life Web Project*

FIGURE 2. Parts of two typical sections on a ToL branch page, the Characteristics section and the Discussion of Phylogenetic Relationships section.

FIGURE 1 in The Tree of Life Web Project*

FIGURE 1. The start of a branch page in the ToL (Laurin & Gauthier, 1996), on amniotes, showing the navigational center (the tree), links which take one to subgroups or larger groups, and the Introduction.

FIGURE 8 in The Tree of Life Web Project*

FIGURE 8. The glossary in the ToL in use. The user has moved the cursor over the highlighted word "monophyletic" and the definition is being shown.