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Figure 5 in Systematic revision of the living species of Bullidae (Mollusca: Gastropoda: Cephalaspidea), with a molecular phylogenetic analysis

Figure 5. Involute spire and visible part of protoconch of Bulla striata (A, G), B. occidentalis (B, I–J), B. mabillei (C), B. solida (D), B. gouldiana (E), and B. punctulata (F, H). A, Siné-Saloum, Senegal (BMNH 20030781; H = 15.6 mm). B, Miami, Florida (BMNH 20030045; H = 28.8 mm). C. Tenerife Island, Canary Islands (BMNH 20020457; H = 26.9 mm). D, off Florida (HBOM 62: 281; H = 34.9 mm). E, Baja California, Mexico (CAS 067260; H = 40.6 mm). F, Guanacaste, Costa Rica (INBio 03458490; H = 13.8 mm). G, Ria Formosa, Portugal (BMNH 20050338; H = 30.1 mm). H, Puntarenas, Costa Rica (INBio 01482898; H = 19.6 mm). I–J, São Paulo, Brazil (MZUSP 30009; H = 33.6, 35.1 mm). Scale bars: A–C, E–F, J = 200 Mm; D = 500 Mm; G–I = 50 Mm.

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Figure 2 in Systematic revision of the living species of Bullidae (Mollusca: Gastropoda: Cephalaspidea), with a molecular phylogenetic analysis

Figure 2. Live animals of Atlantic and East Pacific species of Bullidae. A, Bulla striata, Ria de Alvor, Portugal; H = 29 mm (photo: M. A. E. Malaquias). B, B. occidentalis, Guanacahabibes, Cuba; H = 20 mm (photo: L. Moro). C, B. occidentalis, Sanibel Island, Florida; H = 18 mm (photo: Á. Valdés). D, B. mabillei, Tenerife, Canary Islands; H = 31 mm (photo: L. Moro). E, B. punctulata, Panama; H = 25 mm (photo: T. Gosliner). F, B. gouldiana, La Jolla, California; H = 45 mm (B. Lloyd).

Figure 5 in Phylogenetic relationships among Rhacophorinae (Rhacophoridae, Anura, Amphibia), with an emphasis on the Chinese species

Figure 5. Bayesian inference tree inferred from the combined dataset, with Buergeria defined as the outgroup. Only Bayesian posterior probabilities (BPP) of above 50% are given. Locality sites for individuals from different populations are given in parentheses.

Figure 2 in Phylogenetic relationships among Rhacophorinae (Rhacophoridae, Anura, Amphibia), with an emphasis on the Chinese species

Figure 2. Saturation plot of pairwise transitions and transversions against the uncorrected proportional sequence divergences (P distances) for the concatenated data set.

Figure 3 in Phylogenetic relationships among Rhacophorinae (Rhacophoridae, Anura, Amphibia), with an emphasis on the Chinese species

Figure 3. The consensus topology resulted from maximum parsimony (MP) analysis based on the combined data set, with Buergeria defined as the outgroup. The MP support values (1000 bootstrap replicates) of above 50% and the corresponding decay indices are given. Locality sites for individuals from different populations are given in parentheses.

Figure 1 in Phylogenetic relationships among Rhacophorinae (Rhacophoridae, Anura, Amphibia), with an emphasis on the Chinese species

Figure 1. Collection sites of samples. 1, Hainan; 2, Simao; 3, Menglun; 4, Jingdong; 5, Wenshan; 6, Jinping; 7, Jinxiu; 8, Pingbian; 9, Xichang; 10, Hongya; 11, Yongde; 12, Lvchun; 13, Hekou; 14, Nanjian; 15, Gongshan; 16, Zhaotong; 17, Banna; 18, Longling.

FIGURE 8 in A morphological, phylogenetic and phylogeographic reappraisal of the land crabs Gecarcinus quadratus De Saussure, 1853, and G. lateralis Fréminville in Guérin 1832 (Decapoda: Gecarcinidae). Are they different species?

FIGURE 8. Localities of Gecarcinus lateralis and G. quadratus analized. 1) Boca de Catán, Tamaulipas. 2) La Pesca, Tamaulipas. 3) Barra de Cazones, Veracruz. 4) Río Prieto, Veracruz. 5) Barra de Sontecomapan, Veracruz. 6) Chiltepec, Tabasco. 7) Playa Bruja, Tabasco. 8) Cayo Arcas, Campeche. 9) Arrecife Alacranes, Yucatán. 10) Banco Chinchorro, Quintana Roo. 11) Mahahual, Quintana Roo. 12) Puerto Vargas, Costa Rica. 13) Puerto Viejo, Costa Rica, 14) Bocas del Drago, Panamá. 15) Playa Higuera Blanca, Nayarit. 16) Punta Mita, Nayarit. 17) Estación de Biología Chamela, Jalisco. 18) Playa Troncones, Guerrero. 19) Playa Aragón, Oaxaca. 20) Boca del Cielo, Chiapas. 21) Playa Larga, Cuba.

FIGURE 4 in A morphological, phylogenetic and phylogeographic reappraisal of the land crabs Gecarcinus quadratus De Saussure, 1853, and G. lateralis Fréminville in Guérin 1832 (Decapoda: Gecarcinidae). Are they different species?

FIGURE 4. Maximum clade credibility tree based on Bayesian inference (BI) for Gecarcinus, Johngarthia and the outgroup, Cardisoma guanhumi, using the concatenated matrix of the 16S and COI genes. Probability values at the nodes refer to support values for BI and maximum likelihood (ML). In the assigned key for Mexican specimens, the last letter indicates the sex of the organism: male (M), female (H) or juvenile (JU), followed by the individual number. The organisms highlighted in red in the Atlantic Clade correspond to specimens from Costa Rica and Panama. See the locality list in table 1.

FIGURE 1 in A morphological, phylogenetic and phylogeographic reappraisal of the land crabs Gecarcinus quadratus De Saussure, 1853, and G. lateralis Fréminville in Guérin 1832 (Decapoda: Gecarcinidae). Are they different species?

FIGURE 1. Dorsal view of: A) Gecarcinus lateralis from Río Prieto, Veracruz (CNCR 33942) and B) G. quadratus from Barra de Boca del Cielo, Chiapas (CNCR 34630).

FIGURE 6 in A morphological, phylogenetic and phylogeographic reappraisal of the land crabs Gecarcinus quadratus De Saussure, 1853, and G. lateralis Fréminville in Guérin 1832 (Decapoda: Gecarcinidae). Are they different species?

FIGURE 6. Median-joining network for Gecarcinus quadratus based on the alignment of the mitochondrial gene COI. Each middle line indicates one mutational step between haplotypes. Circles represent different haplotypes and their diameters the frequency of each.

FIGURE 3 in A morphological, phylogenetic and phylogeographic reappraisal of the land crabs Gecarcinus quadratus De Saussure, 1853, and G. lateralis Fréminville in Guérin 1832 (Decapoda: Gecarcinidae). Are they different species?

FIGURE 3. Left male first gonopod (G1): Cephalic view, A) G. lateralis from Río Prieto, Veracruz (CNCR 33942); B) G. quadratus from Boca del Cielo, Chiapas (CNCR 34630). Lateral view, C) G. quadratus from Boca del Cielo, Chiapas (CNCR 34630). Ventral surface, D) G. lateralis female from Barra de Sontecomapan, Veracruz (CNCR 33943); E) G. quadratus female from Playa Higuera Blanca, Nayarit (CNCR 34012); F) G. ruricola male from Cuba (MNHN-IU-2017-8392). Frontal view, G) G. ruricola from Cuba (MNHN-IU-2017-8392) (G. ruricola photos modified from Guinot et al., 2018).

FIGURE 5 in A morphological, phylogenetic and phylogeographic reappraisal of the land crabs Gecarcinus quadratus De Saussure, 1853, and G. lateralis Fréminville in Guérin 1832 (Decapoda: Gecarcinidae). Are they different species?

FIGURE 5. Maximum likelihood tree (ML) for Gecarcinus, Johngarthia and the outgroup, Cardisoma guanhumi, using the 16S gene. Probability values at the nodes represent support values for likelihood (ML). In the assigned key for Mexican specimens, the last letter indicates whether the organism is male (M), female (H) or juvenile (JU) followed by the individual number. The organisms highlighted in red in the Atlantic Clade correspond to specimens from Costa Rica and Panama. See the locality list in table 1.

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Figure 17. Phylogenetic results. A in Phylogeny and revision of the Neotropical genus Grumichella Müller (Trichoptera: Leptoceridae), including nine new species and a key

Figure 17. Phylogenetic results. A, most parsimonious tree from equal (E1) and implied weighting analyses (I1), using k values from 13 to 100. B–D, other three most parsimonious trees from equal analyses (E2, E3 and E4, respectively). E, tree representing the strict consensus from equal weighting analyses. F, tree from implied weighting analyses (I2) using k values from 1 to 12 (* indicating the type-species, G. rostrata; dashed line indicating G. blahnik, G. cressa and G. trujilloi).

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Dataset and R Code for Species-level Avian Influenza Phylogenetic Generalized Least Squares Regression

Dataset for Species-level Avian Influenza Phylogenetic Generalized Least Squares (PGLS) Regression: Variables include taxonomic information for each species, # of IAV-positive individuals, # of IAV-tested individuals, the prevalence of IAV, the proportion of diet made up of different food types, the proportion of foraging time spent in different strata (below water, water surface, ground, understory, etc), sampling-related variables (mean latitude, mean date, the proportion of hatch year individuals), migration and territoriality category, climatologic variables, mean clutch size, and mating system. R Code for PGLS and Avian Influenza Prevalence ContMap.

Fig. 4 in Phylogenetic and morphological analysis of Gloydius himalayanus (Serpentes, Viperidae, Crotalinae), with the description of a new species

Fig. 4 (continued). Median-joining haplotype networks of all nuclear genes, with clades identified in mitochondrial and multi-locus phylogenetic trees indicated by boxes labelled as a) RAG1; b) cmos; c) PRLR; d) UBN1; e) NT3. The haplotype network branch diversity (HBd) for each clade is indicated in a box in each gene network.

Fig. 4 in Phylogenetic and morphological analysis of Gloydius himalayanus (Serpentes, Viperidae, Crotalinae), with the description of a new species

Fig. 4 (continued on next page). Median-joining haplotype networks of all nuclear genes, with clades identified in mitochondrial and multi-locus phylogenetic trees indicated by boxes labelled as a) RAG1; b) cmos; c) PRLR; d) UBN1; e) NT3. The haplotype network branch diversity (HBd) for each clade is indicated in a box in each gene network.

Fig. 7. a–d in Phylogenetic and morphological analysis of Gloydius himalayanus (Serpentes, Viperidae, Crotalinae), with the description of a new species

Fig. 7. a–d. Gloydius chambensis sp. nov., holotype, ♂ (Specimen Number 18.13; Churah Valley, HARC R359). a. Whole body b–d. Close-up of the head in dorsal (b), lateral (c) and ventral (d) views. d. The first and 10th ventrals have been marked with black marker to assist with counting scales. e. A whole body view of specimen 17.v20 from Bhanjraru, Chamba. Photos provided by J.B. Owens and V. Santra.

Fig. 1 in Phylogenetic and morphological analysis of Gloydius himalayanus (Serpentes, Viperidae, Crotalinae), with the description of a new species

Fig. 1. Locations of all specimens used in the study for morphological and phylogenetic analysis. The position of two significant mountain ranges of the Lesser Himalayas, Pir Panjal and Dhauladhar, are indicated by dashed lines. An inset showing the current known distribution of Gloydius himalayanus (Günther, 1864) is also shown, with limits determined by the known altitudinal range (900–5000 m). The maps were constructed using Digital Elevation Models on QGIS ver. 3.22.1. The boundaries used on this map do not imply the expression of any opinion whatsoever on the part of the authors concerning the legal status of any country, territory, or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. Dotted and dashed lines on maps represent approximate border lines for which there may not be full agreement.

Fig. 3 in Phylogenetic and morphological analysis of Gloydius himalayanus (Serpentes, Viperidae, Crotalinae), with the description of a new species

Fig. 3. Multispecies coalescent tree from *Beast. The tips indicate the assigned taxa, and branch labels are posterior probabilities. Clades A–F are as in Fig. 2. The tip labelled "Gloydius_himalayanus_HP1" corresponds to the Chamba specimens and HP2 to the samples from eastern Himachal Pradesh.

Fig. 6 in Phylogenetic and morphological analysis of Gloydius himalayanus (Serpentes, Viperidae, Crotalinae), with the description of a new species

Fig. 6. Canonical Variate analysis of Gloydius himalayanus (Günther, 1864) morphological data. Different analyses represent different combinations of characters and specimens as described in the text, a trade-off required by the presence of missing data. a. More characters, fewer specimens (n = 24): the main discriminating characters on CV1 are Supoc (with lower counts at more positive values), 14to12SC, 12to10SC and 8to6SC (occurring more posteriorly at more positive values) and on CV2 are Latgular, Strtemp, Supoc (with higher counts at more positive values). b. Intermediate number of characters and specimens (n = 27): the main discriminating characters on CV1 is Supoc (with higher counts at more positive values), and on CV2 are Latgular, Stripe, Supoc (with higher counts at more positive values) and Stripe and Sublab (with higher counts at more negative values). c. More specimens, fewer characters (n = 31): the main discriminating characters on CV1 is Supoc (with higher counts at more positive values), and on CV2 are Latgular and Strtemp (with higher counts at more positive values). This analysis requires a priori groups to be defined; however, Dalhousie/Kalatop specimens were plotted onto axes extracted using all other groups. In these analyses, CV1 and CV2 summarise 82, 85, and 95% of the variation present, respectively, with CV1 representing ca 60% in all cases.