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FIGURES 1–6 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURES 1–6. Representative light microscope brightfield images of specimens of Pinnunavis edkuensis, sp. nov., which initiated this study. The specimens range from 121 to 63 µm. Figure 5 is an image of the holotype specimen. The 10 µm scale bar in the lower left corner of Fig. 1 applies to all Figs 1–6.

FIGURE 18 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 18(a)–(c). Drawings of Navicula yarrensis from Grunow's Bildersammlung: (a) specimen G1061.58 from sample 1061, "Yarra", p. 58, (b) specimen G1061.59 from sample 1061, "fossil Ausgraben [?], valve views (left) and paired girdle views (right), p. 59, and (c) specimen G1489.59 from sample 1489, "South Yarra", p. 59. The specimen codes were added by the authors, not Grunow, and have the form of "G' for Grunow, sample number, and Bildersammlung page number, e.g. G1061.58. The breadth-length relationships of these specimens in the context of all others in this study are in Fig. 20. Images courtesy of the Naturhistorisches Museum-Wien.

FIGURE 29 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 29. Linear regression of axial-area relative warp 1 scores and valve length in Pinnunavis edkuensis, P. edkuensis and P. zalatii ("aegyptiaca"). Signs of RW1 scores are reversed compared to Fig. 27.

FIGURE 23 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 23. Relative warp analysis of Pinnunavis edkuensis and subsets of P. zalatii, P. yarrensis and the Port Elizabeth samples using mantle shape descriptors showing an overlay of color-coded valve length (µm) contours for selected taxa and the lectotype illustration. A single contouring was applied to P. zalatii. This chart in other respects is the same as Fig. 22. Relative warp 1 and 2 scores increase to the right and toward the top, respectively.

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Data from: Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: A case study with the lizard Anolis roosevelti

In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, molecular genetic data have become very easy and inexpensive to obtain for many species. However, some lineages are poorly represented in or absent from tissue collections, or are unavailable for molecular analysis for other reasons such as restrictive biological sample export laws. Other species went extinct recently and are only available in formalin museum preparations or perhaps even as sub-fossils. In this brief communication we present a new method for placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny of extant taxa using continuous character data. This method is based on a relatively simple modification of an established Maximum Likelihood (ML) method for phylogeny inference from continuous traits. We show that the method works well on simulated trees and data. We then apply it to the case of placing the Culebra Island Giant Anole (Anolis roosevelti) into a phylogeny of Caribbean anoles. Anolis roosevelti is a 'crown-giant' ecomorph anole hypothesized to have once been found throughout the Spanish, U.S., and British Virgin Islands, but that has not been encountered or collected since the 1930s. Although this species is widely thought to be closely related to the Puerto Rican giant anole, A. cuvieri, our ML method actually places A. roosevelti in a different part of the tree and closely related to a clade of morphologically similar species. We are unable, however, to reject a phylogenetic position for A. roosevelti that places it as sister taxon to A. cuvieri; although close relationship with the remainder of Puerto Rican anole species is strongly rejected by our method.

FIGURE 5 in Measuring relative flower size in Anthurium (Araceae) as a continuous quantitative character

FIGURE 5. Comparison of relative flower size (RFS) between spadix zones within three populations of Anthurium erskinei and A. talmonii. Boxplots show untransformed RFS values. Populations: ersk_Lencois: A. erskinei, Lençóis; talm_Lencois: A. talmonii, Lençóis; talm_Mucuge: A. talmonii, Mucugê. Computed in R (R Core Team. 2013).

FIGURE 2. Anthurium talmonii. A in Measuring relative flower size in Anthurium (Araceae) as a continuous quantitative character

FIGURE 2. Anthurium talmonii. A. Natural population in habitat on rock outcrops. B. Spadix in close-up showing the flowers. C. Inflorescence rotated to a horizontal position, showing the spadix and the three spadix zones sampled for flower and spadix diameter measurements. Ba: Base zone. d: spadix diameter. M: Middle zone. U: Upper zone. w: flower transverse width. Scale bars: 1.0 cm (B and C); 10.0 cm (A).

FIGURE 1. Anthurium erskinei. A in Measuring relative flower size in Anthurium (Araceae) as a continuous quantitative character

FIGURE 1. Anthurium erskinei. A. Natural population in habitat on rock outcrops. B. Spadix in close-up showing the flowers. C. Inflorescence rotated to a horizontal position, showing the spadix, spathe and the three spadix zones sampled for flower and spadix diameter measurements. Ba: Base zone. d: spadix diameter. M: Middle zone. U: Upper zone. w: flower transverse width. Scale bars: 1.0 cm (B and C); 10.0 cm (A).

FIGURE 4 in Measuring relative flower size in Anthurium (Araceae) as a continuous quantitative character

FIGURE 4. Comparison of relative flower size (RFS) in three populations (one of Anthurium erskinei and two of A. talmonii). Boxplots show RFS values plotted as natural logarithms to achieve homogeneity of variances. Populations: ersk_Lencois: A. erskinei, Lençóis; talm_Lencois: A. talmonii, Lençóis; talm_Mucuge: A. talmonii, Mucugê. Computed in R (R Core Team 2013).

FIGURE 6 in Measuring relative flower size in Anthurium (Araceae) as a continuous quantitative character

FIGURE 6. Comparison of relative flower size (RFS) in three populations of Anthurum erskinei and A. talmonii. Left Column: original RFS values. Right Column: bootstrapped mean RFS values (means of 10,000 samples of 25 RFS values, with replacement). Populations:- ersk_Lencois: A. erskinei, Lençóis; talm_Lencois: A. talmonii, Lençóis; talm_Mucuge: A. talmonii, Mucugê. Computed in R (R Core Team 2013).

FIGURE 3 in Measuring relative flower size in Anthurium (Araceae) as a continuous quantitative character

FIGURE 3. Phenological phases in Anthurium talmonii (A–F) and A. erskinei (G–L) respectively, with the enlarged detail. Pre-anthesis (A, G); Female anthesis (B, H); Male anthesis (C, I); Post-anthesis (D, J); Pre-fruiting (E, K), Fruiting (F, L). Scale bars: 1.0 cm. Photos by T.A. Pontes©, except F (macro): L. Pataro©.

Figure 10 in Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics

Figure 10. Mayazomus estor comb. nov. holotype male. Chelicera (A–C): A, mesal view. B, fixed finger. C, moveable finger. Paratype female. Spermathecae: D, dorsal view. Scale bars = 0.05 mm.

Figure 8 in Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics

Figure 8. Mayazomus estor comb. nov. Paratype male. Habitus: A, dorsal view. Paratype female. Habitus: B, dorsal view. Scale bar = 1 mm.

Figure 11 in Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics

Figure 11. Homoplasy statistics: retention indexes (crosses) and consistency indexes (circles) for informative discrete and continuous characters (see Material and methods) from analysis with equal weights.

Figure 5. Preferred single tree resulting from the analysis under implied weights with concavity constant k in Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics

Figure 5. Preferred single tree resulting from the analysis under implied weights with concavity constant k = 100. Clade support is indicated above (Bremer support values) and below [symmetric resampling values; only significant values (over 50%) are presented] branches. Sensitivity plots ('Navajo rugs') indicate the recovery of the nodes in the analysis under implied weights with different values of k (black squares indicate monophyly; white squares indicate nonmonophyly).

Figure 7 in Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics

Figure 7. Strict consensus tree of five most parsimonious trees obtained by excluding continuous characters from the analysis with equal weights. The tree shows the poor resolution of the relationships inside Mayazomus and the inclusion of Hansenochrus as the sister group of Rowlandius, demonstrating the importance of continuous characters for phylogenetic studies in Mayazomus.

Figure 6. Preferred single tree resulting from analyses under implied weights with concavity constant k in Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics

Figure 6. Preferred single tree resulting from analyses under implied weights with concavity constant k = 100, 60, and 30, and equivalent to one of the most parsimonious trees recovered in the analysis with equal weights and continuous characters. Images on the tree represent the morphological congruence of the clades with the structures pictured (pedipalps and spermathecae). The genus Mayazomus is clearly separated from Rowlandius by the presence of robust pedipalps and trochanters with apical process; the clade (Mayazomus yaax + Mayazomus estor) is supported by the rounded distal margin of the pedipalp femur; the clade (Mayazomus loobil + Mayazomus infernalis) is supported by the presence of a patella curved in a 'U'-shape; and spermathecae with lobes slender and subequal in length; the clade (Mayazomus aluxe + Mayazomus kaamuul) is supported by setae Fv1 and Fv2 located distally and projected, with spermathecal lateral lobes reduced and wider than medial lobes.

Figure 3 in Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics

Figure 3. Relative position of cheliceral group three (G3) setae. A, seta 4 basally; B, seta 2 and 4 basally; C, seta 3 distally.

Figure 1 in Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics

Figure 1. Mayazomus infernalis. Measurements used to generate the morphometric ratios used as continuous characters in the phylogenetic analyses. A, propeltidium; B, male flagellum; C, male pedipalp. Abbreviations: Lpro, length of propeltidium; Ltro, length of trochanter; Lfe, length of femur; Lpat, length of patella; Ltib, length of tibia; Htro, height of trochanter; Hfe, height of femur; Hpat, height of patella; Htib, height of tibia; WB, width at the base of the bulb; WDl1, width at the level of seta Dl1; WDl3, width at the base of seta Dl3; B, bulb of flagellum; P, pedicel of flagellum; Lf, length of flagellum.

Figure 2 in Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics

Figure 2. Position and nomenclature of pedipalp setae. Mayazomus infernalis, A, femur; B, patella–tibia. Stenochrus pecki, C, femur; D, patella–tibia. Hubbardia pentapeltis, E, femur; F, patella–tibia. Abbreviations: Fe, Femur ectal; Fv, Femur ventral; Fd, Femur dorsal; Fvr, Femur ventral row; Fm, Femur median; Pe, Patella ectal; Pm, Patella mesal; Ter, Tibial ectal row; Tmr, Tibial medial row; Tir, Tibial internal row.