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Figure 5 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record

Figure 5. Cartoon depicting consensus phylogenetic relationships among Anseriformes ('waterfowl') (based on Livezey, 1997) (Presbyornithidae includes the taxa Presbyornis and Teviornis; see text for details) along with a selection of wellpreserved fossil taxa: A, holotype skull of Anatalavis oxfordi in lateral view from the Lower Eocene London Clay Formation (The Natural History Museum, London, Palaeontology Department Collections, BMNH PAL 5922) (see Dyke, 2001b); B, holotype coracoid of BMNH PAL 5922 in dorsal and medial views) (scale bars = 10 mm); C, holotype carpometacarpus of Teviornis gobiensis from the Late Cretaceous Nemegt Formation of Mongolia (Palaeontological Institute of the Russian Academy of Sciences, PIN 4499–1) in dorsal and ventral views (see Kurochkin et al., 2002). Scale bar = 10 mm.

Figure 4 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record

Figure 4. Phylogenetic relationships within Palaeognathae including the well-represented fossil taxa Palaeotis and Lithornis (see text for details): A, new specimen of Lithornis from the Palaeocene-Lower Eocene Fur Formation of Denmark (Dankrae Collections of the Geologisk Museum, Copenhagen, DK 330) encased in cement stone nodule; B, skull of DK 330 acid prepared in oblique lateral view; C, palate of Lithornis in ventral view (ba, basitemporal plate; de, dentary; pa, palatine; pt, pterygoid; vo, vomer); D, the phylogenetic placement of Lithornis and Palaeotis inferred from cladistic analysis of osteological characters (see G. J. Dyke & M. van Tuinen, unpubl. data for details of analysis and matrices).

Figure 3 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record

Figure 3. Seven possible definitions for the 'radiation of birds'. The true radiation of morphology observed in today's birds may have taken place as recently as points 6 or 7. Archaic ornithurines have not been found after the K–T boundary (black arrow). Although predicted from molecular clock analyses (dotted line; see text), little convincing evidence exists for neornithine fossils preceding the K–T boundary. The variation in number of species among traditional neornithine orders indicates that the 'radiation' was not equal across every major clade. Numbers refer to the following major evolutionary bird divergences: 1, diversification of Aves; 2, origin of Neornithes; 3, diversification of Neornithes; 4, origin of Neoaves; 5, origin of most orders (including 'Neoavian comb'); 6, diversification of most orders; 7, diversification of most families.

Figure 1 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record

Figure 1. Summary cladogram to show the phylogenetic relationships at the base of Neornithes (based on Cracraft et al., 2004). Despite advances in the use of genetic data to resolve the phylogenetic relationships of birds, differences between data sets remain and have led to conflict with regard to the interrelationships of clades within Neoaves. The part of this tree to the right-hand side (relationships within Neoaves) has often been referred to as the 'neoavian comb' (Cracraft et al., 2004).

Figure 13 in Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

Figure 13. Representatives of the available family-level ingroup taxa investigated by this study, showing external shell, internal shell, and hinge features. In Veneridae: A, Callistinae, Callista chione (AMNH 302968); B, Callocardiinae, Callocardia thorae (AMNH 302989); C, Chioninae, Chione cancellata (AMNH 248270); D, Clementiinae, Clementia papyracea (AMNH 51293, 302905); E, Cyclininae, Cyclina sinensis (AMNH 32487); F, Dosiniinae, Dosinia concentrica (AMNH 190551); G, Gafrariinae, Gafrarium dispar (AMNH 303604); H, Gemminae, Gemma gemma (AMNH 155236); I, Gouldiinae, Gouldia cerina (AMNH 32949); J, Lioconchinae, Lioconcha castrensis (AMNH 303127); K, Meretricinae, Meretrix meretrix (AMNH 31674); L, Meroinae, Sunetta (= Meroe) meroe (AMNH 32476); M, Pitarinae, Pitar tumens (AMNH 303152); N, Samarangiinae, Samarangia quadrangularis (AMNH 303507); O, Sunettinae, Sunetta scripta (AMNH 303612); P, Tapetinae, Tapes literatus (AMNH 303510); Q, Venerinae, Venus verrucosa (AMNH 304017). In Veneroidea: R, Petricolidae, Petricola lapicida (AMNH 33527, 294770); S, Glauconomidae, Glauconome rugosa (NCSM 28970); T, Turtoniidae, Turtonia minuta (AMNH 177261); U, Neoleptonidae, Neolepton sulcatulum (AMNH 35004).

Figure 6 in Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

Figure 6. Morphological phylogeny of Veneroidea: a 50% majority-rule consensus tree (46 trees, length 162 steps, consistency index = 0.23, retention index = 0.62) based on a maximum parsimony heuristic search of the all-morphology data set (45 taxa, 31 characters). See text for a discussion of clades B (Veneridae) and 1 (Veneroidea).

Figure 9 in Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

Figure 9. Molecular phylogeny of Veneroidea: a 50% majority-rule consensus tree based on a Bayesian analysis of the combined 16S rRNA and cytochrome oxidase I (COI) data sets and a sampling of 28 001 trees (3 000 000 generations; sample frequency = 100; burn-in = 2000; heat = 0.2). Symbols and conventions as in Figure 7; bootstrap proportions (≥ 70%) are based on a parsimony analysis (250 replicates, 10 random sequence additions; equal weighting). In two cases (Corbicula fluminea and Calyptogena magnifica), sequences represent the concatenation of independent 16S and COI GenBank submissions.

Figure 5 in Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

Figure 5. Morphological phylogeny of Veneroidea. A, an example strict consensus tree. B, the best-resolved 50% majorityrule consensus tree (length 135 steps, consistency index = 0.20, retention index = 0.63) based on maximum parsimony heuristic searches of the traditional morphological data set (23 characters) and a restricted set of 45 taxa. See text for a discussion of clades A and B. Subfamily names in parentheses are not monophyletic (see text). *100%.

Figure 1 in Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

Figure 1. Mercenaria mercenaria, showing features of venerid shell morphology coded by this analysis. A, right lateral view of exterior of right valve. B, right lateral view of interior of left valve. C, dorsal view of articulated valves, anterior to the right. aams, anterior adductor muscle scar; aprms, anterior pedal retractor muscle scar; com, commarginal sculpture; esc, escutcheon; hp, hinge plate (with cardinal teeth); lig, ligament; ligp, ligamental pit; lun, lunule; mar, shell margin; pams, posterior adductor muscle scar; pl, pallial line; ps, pallial sinus; u, umbo.

Figure 4 in Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

Figure 4. Morphological phylogeny of Veneroidea. A, an example strict consensus tree. B, an example 50% majority-rule tree (length 285 steps, consistency index = 0.14, retention index = 0.72) based on maximum parsimony heuristic searches of the all-morphology data set (31 characters) and 114 taxa. See text for a discussion of supported clades. Subfamily names in parentheses are not monophyletic (see text). *100%.

Figure 8 in Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

Figure 8. Molecular phylogeny of Veneroidea: a 50% majority-rule consensus tree based on a Bayesian analysis of the cytochrome oxidase I data set and a sampling of 29 501 trees (3 000 000 generations; sample frequency = 100; burn-in = 500; heat = 0.1). Symbols and conventions as in Figure 7; bootstrap proportions (≥ 70%) are based on a parsimony analysis (250 replicates, 10 random sequence additions; Tv 2.5: Ti 1). The two sequences for Hyphantosoma caperi were obtained from the same individual. The three GenBank sequences for Cyclina sinensis were obtained from the gonadal tissue of two male specimens and one female specimen.

Figure 11 in Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

Figure 11. Molecular phylogeny of Veneroidea: a 50% majority-rule consensus tree based on a Bayesian analysis of the 16S rRNA, cytochrome oxidase I (COI), and 28S rRNA (long and short) data sets and a sampling of 29 001 trees (3 000 000 generations; sample frequency = 100; burn-in = 1000; heat = 0.2). Symbols and conventions as in Figure 7; bootstrap proportions (≥ 70%) are based on a parsimony analysis (250 replicates, 10 random sequence additions; equal weighting). The three Cyclina sinensis sequences (represented by only a short piece of COI) and a second COI sequence for Hypantosoma caperi were removed from the data set prior to undertaking these combined analyses.

Figure 12 in Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

Figure 12. Molecular phylogeny of Veneroidea: a 50% majority-rule consensus tree based on a Bayesian analysis of the 16S rRNA, cytochrome oxidase I, 28S rRNA, and histone 3 data sets for a pruned selection of 56 taxa (59 sequences) with sequences> 1200 bp in length. Branch lengths and posterior probability values based on a sampling of 29 001 trees (3 000 000 generations; sample frequency = 100; burn-in = 1000; heat = 0.5). Symbols and conventions as in Figure 7; bootstrap proportions (≥ 70%) are based on a parsimony analysis (250 replicates, 10 random sequence additions; equal weighting). In Corbicula, Mercenaria, Neotapes, and Ruditapes philippinarum, GenBank sequences represent concatenated sequences of independent GenBank submissions for some or all genes. For some other taxa (Arctica and Calyptogena), sequences represent a mixture of GenBank and newly acquired sequences for the same species.

Figure 3 in Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

Figure 3. Morphological phylogeny of Veneroidea: an example 50% majority-rule consensus tree (length 234 steps, consistency index = 0.13, retention index = 0.74) based on a maximum parsimony heuristic search of the traditional morphological data set (23 characters) and 114 taxa. See text for a discussion of clades A, B, and C. Subfamily names in parentheses are not monophyletic (see text). *100%.

Figure 7 in Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

Figure 7. Molecular phylogeny of Veneroidea: a 50% majority-rule consensus tree based on a Bayesian analysis of the 16S rRNA data set and a sampling of 29 401 trees (3 000 000 generations; sample frequency = 100; burn-in = 600; heat = 0.2). Branch lengths are presented in (A) and support indices in (B). Posterior probability values (≥ 90%) are shown above the line; bootstrap proportions (≥ 70%) based on a parsimony analysis (250 replicates, 10 random sequence additions; Tv 2.8: Ti 1) are shown below the line. Sequences obtained from GenBank are indicated by GB following the species name. Multiple sequences are included for five taxa: Ruditapes philippinarum (one from a maternally derived and one from a paternally derived mitochondrial lineage); Circe rivularis (sequences from two specimens from different locations); and Mercenaria mercenaria, Venus verrucosa, and Chamelea gallina (one GB sequence, one newly derived sequence). Taxa designated as outgroups are shown in bold. The hollow circle indicates the node supporting a monophyletic Veneroidea = Veneridae (including Turtonia and the Petricolidae). Labelled nodes (filled circles) refer to specific clades discussed in the text.

Figure 10 in Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

Figure 10. Molecular phylogeny of Veneroidea: a 50% majority-rule consensus tree based on a Bayesian analysis of the long 28S rRNA data set and a sampling of 29 001 trees (3 000 000 generations; sample frequency = 100; burn-in = 1000; heat = 0.2). Symbols and conventions as in Figure 7; bootstrap proportions (≥ 70%) are based on a parsimony analysis (250 replicates, 10 random sequence additions; Tv 2: Ti 1).

Figure 10. Hinge architecture. A in Reconstructing the Anomalodesmata (Mollusca: Bivalvia): morphology and molecules

Figure 10. Hinge architecture. A, Pandora patula; B, Laternula constricta; C, Myochama anomioides; D, Cleidothaerus albidus; E, Lyonsiella formosa; F, Poromya buttoni; G, Euciroa galatheae; H, Cuspidaria undata. A–D, F, G redrawn from Prezant (1998), E redrawn from Allen & Turner (1974), H redrawn from Poutiers (1984).

Figure 9 in Reconstructing the Anomalodesmata (Mollusca: Bivalvia): morphology and molecules

Figure 9. Scanning electron micrograph of (A) spicule on the outer surface of the juvenile shell of Brechites vaginiferus (Clavagellidae). Scale bar = 2 µm. B, arenophilic threads with associated debris on the external surface of the shell of Lyonsia sp. Scale bar = 50 µm.

Figure 8 in Reconstructing the Anomalodesmata (Mollusca: Bivalvia): morphology and molecules

Figure 8. Scanning electron micrographs of different anomalodesmatan shell microstructures. A, sheet nacre (Cleidothaerus albidus). Scale bar = 5 µm; B, coarse homogeneous (Entodesma saxicola). Scale bar = 20 µm; C, fine homogeneous (Cuspidaria cuspidata). Scale bar = 2 µm.

Figure 7 in Reconstructing the Anomalodesmata (Mollusca: Bivalvia): morphology and molecules

Figure 7. Key characters mapped on Maximum Likelihood tree topology constrained for monophyletic septibranchs in Figure 6. Filled diamonds indicate nonhomoplastic character state transitions, open diamonds indicate convergent changes or reversals [homoplastic changes]. Characters: 1, homogeneous shell microstructures, 0 – absent, 1 – fine crystals (<1 µm in diameter), 2 – coarse crystals (> 5 µm); 2, spicules, 0 – absent, 1 – present on juvenile shell only, 2 – present on adult shell; 3, chondrophores, 0 – absent, 1 – present; 4, lithodesma, 0 – absent, 1 – present in anterior position, 2 – present in more ventral position, 3 – only present in juvenile; 5, fourth pallial aperture, 0 – absent, 1 – present; 6, arenophilic glands, 0 – absent, 1 – present; 7, septum, 0 – absent, 1 – thin, 2 – muscular; 8, stomach type of Purchon (1987a), 0 – type IV, 1 – type II, 2 – type V.