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Figures 37–39 in Taxonomy in the phylogenomic era: species boundaries and phylogenetic relationships among North American ants of the Crematogaster scutellaris group (Formicidae: Hymenoptera)

Figures 37–39. Crematogaster workers, showing lateral view of body (A), full-face view of head (B), and dorsal view of body (C). 37, C. parapilosa holotype (CASENT0863386); 38, C. laeviuscula (CASENT0104828); 39, C. lineolata (CASENT0922733). Images courtesy of AntWeb (www.antweb.org); photographers Zachary Griebenow (37), April Nobile (338), Wade Lee (39).

Figures 13–18 in Taxonomy in the phylogenomic era: species boundaries and phylogenetic relationships among North American ants of the Crematogaster scutellaris group (Formicidae: Hymenoptera)

Figures 13–18. Crematogaster workers, showing lateral view of body (A), full-face view of head (B) and dorsal view of body (C). 13, C. dentinodis (CASENT0102830); 14. C. vetusta holotype (CASENT0863254); 15, C. navajoa worker (CASENT0064826); 16, C. punctulata lectotype (CASENT0923318); 17, C. isolata (CASENT0922731); 18, C. sp. cf. opaca (MCZENT00589113). Images courtesy of AntWeb (www.antweb.org); photographers Jen Fogarty (13), Michele Esposito (14, 16), April Nobile (15), Wade Lee (17), Zachary Griebenow (18).

Figure 2 in Taxonomy in the phylogenomic era: species boundaries and phylogenetic relationships among North American ants of the Crematogaster scutellaris group (Formicidae: Hymenoptera)

Figure 2. Biogeography and nesting preference of the Crematogaster scutellaris group. Time-calibrated phylogeny estimated with mcmctree and codeml in PAMLv.4.9. The analysis is based on the 90% completeness matrix after application of spruceup trimming with a cut-off of 0.98 (90%-0.98-spruceup), and the best maximum likelihood tree resulting from SWSC-EN partitioning of this matrix. This matrix and tree was pruned to a reduced dataset of 34 taxa for dating analysis. Node numbers refer to Table 1, where median ages and 95% highest posterior densities (HPD) are given. Biogeographic range reconstructions with BioGeoBEARS v.1.1.2 are mapped on this chronogram as E = eastern US and north-east Mexico (orange), W = western US and north-west Mexico (dark blue), C = the Caribbean (grey), M = southern Mexico to Honduras (red), EW = combined E and W distributions (light blue), EM = combined E and M distributions (purple), EC = combined E and C distributions (dark green), WM = combined W and M distributions (peach). Respective probabilities for ancestral ranges are given in Table 1. Ancestral states for nesting preference, estimated with the R package corHMM v.2.5, are further mapped on the phylogeny; pie colours are: light green = arboreal; brown = ground-dwelling.

Figure 1 in Taxonomy in the phylogenomic era: species boundaries and phylogenetic relationships among North American ants of the Crematogaster scutellaris group (Formicidae: Hymenoptera)

Figure 1. Phylogeny of the North American Crematogaster scutellaris group. Maximum likelihood phylogenetic tree estimated from the 90% taxon completeness matrix after application of spruceup trimming with a 0.98 cut-off (90%-0.98-spruceup), using a combined best tree and ultrafast bootstrap (N = 1000) search in IQ-TREE v.1.6.12 and implementing 746 partitions. The analysis was rooted using the most distantly related outgroup taxon C. cf. rogenhoferi; the long branch leading to this taxon has been shortened for space-saving purposes. All nodes have bootstrap support = 100% unless labelled otherwise. Species images courtesy of AntWeb (www.antweb.org).

Figure 1 in Two new decapod (Crustacea: Malacostraca) complete mitochondrial genomes: bearings on the phylogenetic relationships within the Decapoda

Figure 1. Mitochondrial genome maps of Alpheus distinguendus and Panulirus ornatus. Protein-coding genes in the majority strand (J strand) are transcribed in a clockwise direction, except for those in the minority strand (N strand) indicated by underlining. The two ribosomal RNA genes are encoded by the N strand. All the darkly coloured transfer RNA (tRNA) genes encoded by the J and N strand are presented outside and inside the circular gene map, respectively. The tRNA genes are given as single-letter amino acid codes, except those encoding leucine and serine, which are labelled L1 (trnL(CUN)) and L2 (trnL (UUR)), and as S1 (trnS(AGN)) and S2 (trnS(UCN)), respectively. Numbers inside the circles represent the size of the fragments separating two adjacent genes (positive values) or the amount of shared nucleotides between two overlapping genes (negative values).

Figure 3 in Two new decapod (Crustacea: Malacostraca) complete mitochondrial genomes: bearings on the phylogenetic relationships within the Decapoda

Figure 3. The secondary structures of the noncoding regions in the mt genome of Panulirus ornatus and Panulirus japonicus are labelled by A and B, respectively. The duplicate 89 bp sequences in the noncoding region of P. ornatus are compared in their secondary structures by arrows pointing to four numbers i.e. 1, 89, 428, and 516 sites in A, which correspond to Repeat sequence 1 and 2 (RS1 & RS2), in C.

Figure 2 in Two new decapod (Crustacea: Malacostraca) complete mitochondrial genomes: bearings on the phylogenetic relationships within the Decapoda

Figure 2. Comparisons amongst the putative secondary structures for functional trnR (CGA) (A) and pseudogene-like trnS (AGN) (B) from the mitochondrial (mt) genome of Alpheus distinguendus, and the functional trnS (AGN) (C) from the mt genome of Panulirus ornatus. AU/GC pairs are indicated by dashes and GU bonds are indicated by dots. The nucleotide base located in the third codon positions of pseudogene-like trnS (AGN) is G instead of the usual base U, which is indicated by an arrow.

Figure 4 in Two new decapod (Crustacea: Malacostraca) complete mitochondrial genomes: bearings on the phylogenetic relationships within the Decapoda

Figure 4. Phylogenetic analyses of the nucleotide sequence (A) and amino acid datasets (B) derived from the Decapoda using the maximum likelihood (ML) analyses and Bayesian inferences (BI), respectively. Bayesian posterior probability (BPP) and bootstrap support (BP) of each node are denoted by the asterisk indicating the well-supported values (BPP = 1.00 and simultaneously BP> 90), or otherwise are presented directly. The phylogram shown is from BI except that the a' clade was based on amino acid datasets from ML analyses. Scale bars represent 0.1 mutations per site.

Figure 2 in A new scanilepiform from the Lower Triassic of northern Gansu Province, China, and phylogenetic relationships of non-teleostean Actinopterygii

Figure 2. Holotype of Beishanichthys brevicaudalis gen. et sp. nov. (PKUP V4881). Specimen in left lateral view. See text for definition of abbreviations. Scale bar: 10 mm.

Figure 7 in A new scanilepiform from the Lower Triassic of northern Gansu Province, China, and phylogenetic relationships of non-teleostean Actinopterygii

Figure 7. Calibrated strict consensus of five most parsimonious trees, showing phylogenetic relationships and stratigraphic ranges of Scanilepiformes within the Actinopterygii. Character states supporting the clades include: A, 14 (1), 23 (1), 30 (1)*, 36 (1), 47 (1), 63 (1); B, 11 (1), 26 (1), 37 (1), 57 (1)*, 66 (1); C, 6 (1), 18 (1), 28 (1), 48 (1)*, 50 (1), 52 (1), 53 (1)*, 54 (1)*, 56 (1)*, 68 (1); D, 11 (2), 34 (1); E, 4 (2), 5 (1)*, 7 (1), 27 (1), 29 (1)*; F, 7 (2), 8 (1), 11 (3), 16 (1), 43 (1)*; G, 25 (1), 69 (1); H, 18 (0), 39 (1); I, 9 (1), 17 (1), 22 (1)*, 26 (0); J, 6 (0), 8 (0), 9 (2), 10 (1)*, 11 (4), 20 (1)*, 28 (1), 66 (0), 67 (1)*; K, 13 (1)*, 27 (0), 46 (2); L, 7 (0), 34 (0), 36 (0), 44 (1)*, 47 (0), 68 (0), 69 (0); M, 2 (1), 3 (1)*, 8 (2), 39 (0), 42 (1)*, 50 (0), 63 (2), 70 (1)*, 71 (1)*, 72 (1)*; N, 51 (1)*, 59 (1), 60 (1), 64 (1), 65 (1); O, 27 (2), 61 (1)*; P, 21 (1), 24 (1)*, 38 (1)*, 46 (1), 50 (1), 58 (1)*, 62 (1)*, 68 (0); Q, 2 (0), 19 (1)*, 25 (2), 28 (1), 31 (1)*, 35 (1), 41 (1)*, 49 (1), 64 (1); R, 1 (1)*, 27 (0), 32 (1)*, 33 (1)*, 45 (1)*. Character states with an asterisk have a consistency index of 1.0. Numerical values immediately below the nodes denote Bremer decay indices.

Figure 6 in A new scanilepiform from the Lower Triassic of northern Gansu Province, China, and phylogenetic relationships of non-teleostean Actinopterygii

Figure 6. Beishanichthys brevicaudalis gen. et sp. nov. A, PKUP V4881b, dorsal fin rays of caudal (note that scales failed to extend to caudal tip). B–G, PKUP V4882, showing: anterior dorsal fin rays (B); ridge scales (C); posterior dorsal fin rays (D); caudal fin (E); flank scales (F); and ventral scales (G). H, composite reconstruction based on PKUP V4881–4883, V4885. Scale bar: 3 mm.

Figure 1 in A new scanilepiform from the Lower Triassic of northern Gansu Province, China, and phylogenetic relationships of non-teleostean Actinopterygii

Figure 1. Map showing the type locality of Beishanichthys brevicaudalis gen. et sp. nov. in northern Gansu Province, China.

Figure 5 in A new scanilepiform from the Lower Triassic of northern Gansu Province, China, and phylogenetic relationships of non-teleostean Actinopterygii

Figure 5. Beishanichthys brevicaudalis gen. et sp. nov. (PKUP V4882, part and counterpart). Specimens in right and left lateral views, respectively. Scale bar: 10 mm.

Figure 4 in A new scanilepiform from the Lower Triassic of northern Gansu Province, China, and phylogenetic relationships of non-teleostean Actinopterygii

Figure 4. Beishanichthys brevicaudalis gen. et sp. nov. A, C, PKUP V4883. B, holotype (PKUP V4881, counterpart slab). Specimens in right lateral view. See text for definition of abbreviations. Scale bar: 5 mm.

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Figure 2. Phylogenetic relationships amongst 21 in Revision of Chaetodipus arenarius (Rodentia: Heteromyidae)

Figure 2. Phylogenetic relationships amongst 21 specimens of the concatenated cytochrome b and cytochrome c oxidase subunit III gene sequences of the Chaetodipus arenarius complex. The main topology was the same as the one used for the Bayesian inference analyses (A), maximum likelihood (B), maximum parsimony, consensus of four trees (C) and bootstrap of the neighbor-joining (D). The three groups are monophyletic. Clade I contains specimens of C. arenarius and has three subclades (indicated in D) with strong geographical relationships. (Ia) includes specimens northward to the Vizcaino Desert; (Ib) contains specimens southward to the Vizcaino Desert and Magdalena Island; and (Ic) contains specimens from the Loreto area bordering the Gulf of California. Clade II contains specimens of Chaetodipus dalquesti and Clade III contains specimens of Chaetodipus siccus. The acronym for each species is at the tip of each branch (A, C. arenarius; D, C. dalquesti; S, C. siccus), the locality numbers are as shown in Figure 1 and the haplotype (H) numbers listed in Table 1 are shown in parentheses. The values at the nodes are branch support for each of the analyses.

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Figure 14. Phylogenetic analysis. A, B in The cranial anatomy, ontogeny, and relationships of Karpinskiosaurus secundus (Amalitzky) (Seymouriamorpha, Karpinskiosauridae) from the Upper Permian of European Russia

Figure 14. Phylogenetic analysis. A, B, two equally parsimonious trees recovered by PAUP* 4.0b10 from a heuristic search of 35 taxa and 155 characters. C, bootstrap percentages on a 50% majority-rule consensus tree.

FIG. 2. G in Karyotype comparison of five African Vespertilionini species with comments on phylogenetic relationships and proposal of a new subtribe

FIG. 2. G-banded karyotype of a female N. guineensis, 2n = 26. Bold numbers for chromosomal arms indicate homology validated with painting probes from Myotis (MMY) or tree shrew (TBE30)

FIG. 6. C in Karyotype comparison of five African Vespertilionini species with comments on phylogenetic relationships and proposal of a new subtribe

FIG. 6. C-banded metaphase spreads of (A) P. brunnea, (B) N. happoldorum, and (C) N. schlieffenii. X and Y chromosomes and heterochromatic segments of interest are indicated, numbers refer to MMY homologies. In (B), arrows point to those heterochromatic segments which showed differences between the homologs and arrowheads point to C-positive segments on pairs NHA11 and NHA13. For further explanation see main text

FIG. 5 in Karyotype comparison of five African Vespertilionini species with comments on phylogenetic relationships and proposal of a new subtribe

FIG. 5. Rearranged bi-armed pair 3/4 of P. brunnea depicted from left to right after G-banding, C-banding, FISH with E. macaco painting probe EMA8 and T. belangeri probe TBE6. The extant centromere is indicated by a dash, the ancestral centromere position by an asterisk. In the basic karyotype, EMA8 homologous sequences were located in the proximal region of the MMY3 homologous chromosomal arms, whereas here they are found in the long arm of P. brunnea chromosome 3/4 (TBE6, homologous to parts of MMY4, was used to delimit the proximal and distal regions of the MMY4 homologous segment in P. brunnea chromosome 3/4)

FIG. 1. G in Karyotype comparison of five African Vespertilionini species with comments on phylogenetic relationships and proposal of a new subtribe

FIG. 1. G-banded karyotype of a male L. kirinyaga, 2n = 32. Chromosomal arms are numbered according to the scheme of Bickham (1979) for Myotis species. The nucleolus organizer region (NOR) is indicated by an arrowhead