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Figure 1. A, Bayesian 50 in Molecular phylogeny in endemic weevils: revision of the genera of Macaronesian Cryptorhynchinae (Coleoptera: Curculionidae)

Figure 1. A, Bayesian 50% majority rule consensus for the two analysed mitochondrial genes. Numbers indicate nodal posterior probabilities. The scale shows the expected nucleotide substitutions per site. Abbreviations in parentheses denote subgenus (see text). Genus names in bold indicate new nomenclature. Circles mark colonization events (in black: invasive species). For many Macaronesian species, the respective host plants are depicted. The second page of the tree shows the taxa corresponding to the 'Atlantic clade'. B, chronogram based on relaxed phylogenetic analysis of the two mitochondrial genes, using the uncorrelated lognormal model of substitution rate variation. Numbers next to the nodes indicate mean divergence times (in Myr), with 95% confidence intervals of divergence times depicted as bars at the corresponding nodes. N.B. Although the underlying topology is that delivered by MrBayes, BEAST does not allow polytomies, which it resolves arbitrarily.

Figure 35 in Molecular phylogeny in endemic weevils: revision of the genera of Macaronesian Cryptorhynchinae (Coleoptera: Curculionidae)

Figure 35. Acalles globulipennis and Echinodera pallida: first abdominal sternite clearly longer than the three following (very narrow) segments combined (here vs. Madeiracalles albolineatus: first abdominal sternite maximally as long as the three following sternites combined (second sternite as long as or longer than sternite 3 and 4 combined).

Figures 23–24. 23 in Molecular phylogeny in endemic weevils: revision of the genera of Macaronesian Cryptorhynchinae (Coleoptera: Curculionidae)

Figures 23–24. 23, Canariacalles with rhombic eyes (in lateral view) in comparison with Aeoniacalles. 24, endophallus of Acalles xerampelinus in comparison with Canariacalles alluaudi.

Figure 2 in Molecular phylogeny of the ant tribe Myrmicini (Hymenoptera: Formicidae)

Figure 2. Majority-rule consensus tree (16 002 Bayesian trees, with a burn-in of two million generations) of 111 Myrmicinae in-group taxa and Polyergus, Formica, and Lasius (Formicinae) as out-group taxa (ALL data matrix, see Material and methods for details). On branches, full circles (•) indicate that the posterior probability = 100%; open circles (O) indicate that the posterior probability> 85%. Numbers above branches represent maximum-likelihood bootstrap support (1000 replicates). The genera of Myrmicini are indicated on the right.

Figure 1 in Molecular phylogeny of the ant tribe Myrmicini (Hymenoptera: Formicidae)

Figure 1. Majority-rule consensus tree (18 002 Bayesian trees, with a burn-in of one million generations) of 37 Myrmicini in-group taxa, and six members of Myrmicinae and two Formicinae as out-group taxa (JS data matrix, see Material and methods for details). This topology was obtained with all partition strategies (1–3, see Material and methods for details). Nodal support values were similar across analyses; the values shown were obtained from partitioning data according to gene regions (strategy 2). On branches, solid circles (•) indicate that the posterior probability = 100%; open circles (O) indicate that the posterior probability> 85%. Numbers above branches represent maximum-likelihood bootstrap support (1000 replicates). On the right, genera of Myrmicini and species groups of Myrmica and Pogonomyrmex are listed; Nearctic species groups are not known.

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Figure 3 in Molecular systematics of peppermint and cleaner shrimps: phylogeny and taxonomy of the genera Lysmata and Exhippolysmata (Crustacea: Caridea: Hippolytidae)

Figure 3. The habitus and colour pattern (dorsal view) of the shrimps Lysmata amboinensis (left) and Lysmata grabhami (right).

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Figure 2 in Molecular systematics of peppermint and cleaner shrimps: phylogeny and taxonomy of the genera Lysmata and Exhippolysmata (Crustacea: Caridea: Hippolytidae)

Figure 2. Phylogenetic tree obtained from minimum evolution (ME) analysis of the partial 16S rRNA gene for shrimps from the genus Lysmata, and other selected taxa from the Caridea. Numbers above or below the branches represent the bootstrap values obtained from maximum parsimony (MP) and ME analyses in PAUP* and MEGA 4.4 (MP/ME). The white and black squares represent the presence or absence, respectively, of a developed accessory branch in each species. The images of the shrimps (from top to bottom) represent Lysmata wurdemanni, Lysmata debelius, Lysmata hochi, and Lysmata galapagensis.

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Figure 1 in Molecular systematics of peppermint and cleaner shrimps: phylogeny and taxonomy of the genera Lysmata and Exhippolysmata (Crustacea: Caridea: Hippolytidae)

Figure 1. Phylogenetic tree obtained from Bayesian inference (BI) analysis of the partial 16S rRNA gene for shrimps from the genus Lysmata, and other selected taxa from the Caridea. Numbers above or below the branches represent the posterior probabilities from the BI analysis and bootstrap values obtained from maximum likelihood (ML) in PAUP* (BI/ML). The white and black squares represent the presence or absence, respectively, of a developed accessory branch in each species. The images of the shrimps (from top to bottom) represent Lysmata wurdemanni, Lysmata grabhami, Lysmata intermedia, and Lysmata hochi.

Figure 3 in The new family Diapheridae, a new species of Diaphera Albers from Thailand, and the position of the Diapheridae within a molecular phylogeny of the Streptaxoidea (Pulmonata: Stylommatophora)

Figure 3. Neighbor-joining (NJ) phylogeny of the Streptaxoidea. The phylogeny includes representatives of the major stylommatophoran land snail groups and is rooted on the Opisthobranch Aplysia. The tree is based on 823 unambiguously aligned nucleotide sites with distances corrected for multiple hits using a GTR + G model (alpha = 0.197409). Bootstrap values [1000 NJ bootstraps and 1000 maximum likelihood (ML) bootstraps expressed as a percentage] and Bayesian posterior probabilities indicating support for individual branches are shown on the tree (NJ bootstraps/ML bootstraps/ Bayesian inference posterior probabilities). The scale bar corresponds to a genetic distance of 2%. The geographical distribution of streptaxid genera and their current subfamily attributions are shown. A, first fossil record of achatinoid 140 Mya. B, minimum age 80 Mya based on fossil Gibbulinella from Portugal.

Figure 2 in The new family Diapheridae, a new species of Diaphera Albers from Thailand, and the position of the Diapheridae within a molecular phylogeny of the Streptaxoidea (Pulmonata: Stylommatophora)

Figure 2. Genitalia of Diaphera prima sp. nov. (paratype CUMZ 3545). A, whole genital system. B, details of internal wall of penis. Abbreviations: ag, albumin gland; at, atrium; eg, egg; fo, free oviduct; g, gonad; hd, hermaphroditic duct; ov, oviduct; p, penis; pp, penial pilasters; pr, penial retractor muscle; sv, seminal vesicle; v, vagina; vd, vas deferens.

Figure 1. A in The new family Diapheridae, a new species of Diaphera Albers from Thailand, and the position of the Diapheridae within a molecular phylogeny of the Streptaxoidea (Pulmonata: Stylommatophora)

Figure 1. A, shell morphology of Diaphera cumingiana (Pfeiffer, 1845) (lectotype BMNH 20080230). B–G, morphology of shell and radular and living animals of Diaphera prima sp. nov. B, the shell and C, the aperture of holotype (CUMZ 3544) showing lamellae. D, juvenile specimen showing apertural lamellae (paratype CUMZ 3630). E, F, living animals (paratype CUMZ 3629): E, shell height 6.5 mm; and F, shell height 6.8 mm. G, radula morphology (paratype CUMZ 3545); arrow on top-right inset indicates the central tooth. H, I, morphology of shell of Diaphera saurini Benthem Jutting, 1962. H, the shell and I, aperture of holotype (ZMA 3.62.016) showing lamellae. Abbreviations: P, parietal lamella; Pl, palatal lamella; Bl, basal lamella; Cl, columellar lamella.

Figure 6 in Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea

Figure 6. The maximum-likelihood (ML) tree inferred from the small subunit ribosomal RNA (SSU rRNA) gene sequences of 63 spirotrichous taxa, showing the position of Bergeriella ovata gen. et sp. nov. (boxed), and the phylogenetic relationships among the taxa possessing midventral cirral rows (i.e. urostylids s.l.; branches are depicted by thick lines, and species names are highlighted in bold text). Nodal support for branches in the ML, Bayesian inference (BI), and neighbour-joining (NJ) trees are marked in order. Bootstrap values lower than 50% and Bayesian posterior probabilities lower than 0.70 are replaced with hyphens. Clades with different topologies in the NJ tree relative to the ML and BI trees are indicated with asterisks. All branches are drawn to scale. The scale bar corresponds to five substitutions per 100 nucleotide positions. Phacodinium and Protocruzia were taken as out-group taxa.

Figure 3 in Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea

Figure 3. Ventral (A, C, E, G) and dorsal (B, D, F, H) views of Bergeriella ovata gen. et sp. nov. in morphogenesis (A–D) and regeneration (E–H), after impregnation with protargol. A, an early divider, showing the oral primordium (arrow) and fronto-ventral-transverse (FVT) anlagen (arrowhead) of the proter. The double arrowheads mark the anlagen for the nonmigratory row, which comes from the posteriormost FVT streak. B, the same specimen as shown in (A), showing the enlarged macronuclear nodules and the formation of the dorsal kinety anlagen (arrows). C, an individual at a late stage of division, with all cirri developed; note the structures that will respectively form the enlarged postoral ventral cirri (arrowheads) and the delicate left ventral cirri (arrows). The double arrowheads indicate the anlagen for the nonmigratory row. D, the differentiating marginal row (arrows) and dorsal kineties; note that the macronuclear nodules are separating. E, F, an early reorganizer, showing the oral primordium (arrow in E), FVT streak (arrowhead), nonmigratory row (double arrowheads) and dorsal kinety anlagen; the arrows in (F) indicate the anlagen for the right and left marginal rows, which are derived within the parental structure. G, H, a middle-stage reorganizer, with a further proliferation of kinetosomes, showing the first frontal cirrus (arrow in G) generated from the undulating membrane anlagen, the basal bodies developed from FVT streaks (arrowhead), the anlagen for the nonmigratory row (double arrowheads), and the anlagen for the right and left marginal rows (arrows in H). Abbreviations: DK, dorsal kineties; DKA, dorsal kinety anlagen. Scale bars: 40 Mm.

Figure 2 in Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea

Figure 2. Photomicrographs of Bergeriella ovata gen. et sp. nov. from life. A, ventral view of a specimen. B, C, ventral view of slender and fat forms; the arrow indicates the wide and bright oral field. D, lateral view. E, F, lateral (E) and dorsal (F) views, showing the distribution of the granules; the arrows mark the granule rows near the base of each marginal cirrus, the arrowheads point to the granule rows along with midventral rows, and the double arrowheads mark the granule bands in the gap between the somatic kineties. G, H, showing the cortical granules (arrows), the fibres associated with cirri (arrowheads), and a dorsal cilium (double arrowheads). I, focusing on the oral field; note the paroral membrane (arrowhead) and the endoral membrane (arrow). J, the cortical granules (arrow) near the base of marginal cirri. K, lateral view of the posterior portion; arrows point to the enlarged postoral ventral cirri. L, globular lipid droplets in the cytoplasm. Scale bars: 50 Mm.

Figure 1 in Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea

Figure 1. Bergeriella ovata gen. et sp. nov. drawn from life (A–C, E–F) and after impregnation with protargol (D, G–J). A, ventral view of a specimen. B, different body shapes. C, section of the ventral infraciliature, showing the fibres associated with the postoral ventral cirri (double arrowheads) and the obliquely arranged left ventral cirri (arrow). D, distribution of cortical granules (arrow) near the marginal cirri. E, F, distribution of the cortical granules on the ventral (E) and dorsal (F) sides; the arrow indicates the granules along the nonmigratory row, and the arrowheads point to the granular rows along the dorsal kineties. G, left lateral side view of the infraciliature. H–I, ventral (H) and dorsal (I) views of the infraciliature; note the enlarged postoral ventral cirri (dashed lines), the frontal cirri (dashed lines), and the three dorsal kineties (arrows). J, ventral view of an early divider; the arrow indicates the oral primordium of the proter, the arrowheads mark the old endoral membranes in dedifferentiation, and the double arrowhead points to the oral primordium of the opisthe. Abbreviations: AZM, adoral zone of membranelles; BC, buccal cirri; DK, dorsal kineties; EM, endoral membrane; FC, frontal cirri; LMR, left marginal row; LVR, left ventral rows; MVR, midventral rows; NMR, nonmigratory row; PM, paroral membrane; PVR, postoral ventral rows; RMR, right marginal row. Scale bars: 40 Mm (A–C, F–J); 15 Mm (E).

Figure 5 in Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea

Figure 5. Photomicrographs of regeneration in Bergeriella ovata gen. et sp. nov. after impregnation with protargol. A, B, ventral views of middle reorganizers, showing the oral primordium (arrow in A), fronto-ventral-transverse (FVT) anlagen (arrowheads), and the anlagen for the nonmigratory row (double arrowhead); the arrow in (B) points to the undulating membrane anlagen. C, a middle-stage reorganizer; the arrow marks the first frontal cirrus generated from the undulating membrane anlagen, and the arrowheads indicate the anlagen for the nonmigratory row. D, dorsal view of the same specimen, showing the anlagen for the left marginal row (arrow) and the dorsal kinety anlagen (arrowheads).

Figure 4 in Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea

Figure 4. Photomicrographs of Bergeriella ovata gen. et sp. nov. after impregnation with protargol. A, infraciliature of the ventral posterior portion, showing the nonmigratory row (arrow), the postoral (arrowheads), and the left ventral cirri (double arrowheads). B, infraciliature of an anterior portion, showing the frontal cirri (arrows), buccal cirri (arrowhead), and the undulating membranes (double arrowheads). C, left lateral view, showing the left ventral rows, and the left marginal row (arrow). D, dorsal kineties, in which kinetosomes become more densely spaced from left to right (arrows). E, dorsal view, showing the anterior portion of the nonmigratory row (arrowhead) and the right marginal row (arrow). F, nuclear apparatus, some with replication bands can be seen. G, H, ventral and dorsal views of an early stage divider, showing the undulating membrane anlagen (arrow in G), FVT anlagen (arrowheads), and the anlagen for the nonmigratory row, which come from the posteriormost FVT streak (double arrowheads) of the opisthe. The arrows in (H) indicate the dorsal kineties anlagen. I, early divider showing the appearance of the oral primordium (arrow) and the enlarged macronuclear nodules of the proter. J, separating ellipsoid macronuclear nodules. K, L, ventral views of a late-stage divider (same specimen), showing the developed cirri of the proter (K) and the opisthe (L); the arrows indicate the migrating postoral and left ventral cirri, and the arrowheads indicate the anlagen for the nonmigratory row. M, dorsal view of the same specimen shown in (K) and (L), showing the anlagen of the marginal rows (arrows) and the new dorsal kineties.

Fig. 4 in Molecular phylogeny of the Eremias persica complex of the Iranian plateau (Reptilia: Lacertidae), based on mtDNA sequences

Fig. 4. The maximum-likelihood (ML) chronogram for the evolution of the Eremias persica complex of the Iranian plateau. The time scale was calibrated based on palaeogeographical evidence (see the text for details). The time bar represents the approximate time of past branching events in millions of years before the present. The numbers indicate the ML bootstrap values (200 replicates).

Fig. 2 in Molecular phylogeny of the Eremias persica complex of the Iranian plateau (Reptilia: Lacertidae), based on mtDNA sequences

Fig. 2. Patterns of nucleotide substitution. Pairwise proportions of transitions (s) and transversion (v) versus JC69 distance, derived from the combined data set. The graph indicates there is low saturation in the data set.

Fig. 3 in Molecular phylogeny of the Eremias persica complex of the Iranian plateau (Reptilia: Lacertidae), based on mtDNA sequences

Fig. 3. Bayesian inference phylogram (GTR + I + G model) based on 1533 base pairs of the cytochrome b and 12S sequence data set. The numbers next to the nodes are clade credibility values, from the Bayesian analysis, followed by maximum-parsimony bootstrap values (1000 replicates), and those next to the curved brackets indicate the localities in Figure 1.