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Figure 4 in Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics
Figure 4. Strict consensus tree resulting from the two most parsimonious trees obtained from the analysis under equal weights with continuous characters included (length = 415.88, consistency index = 0.42, retention index = 0.54). Apomorphies are plotted on branches. Black squares indicate synapomorphies; white squares indicate homoplastic state characters (parallelism and reversals) according to the character sampling. Numbers above branches indicate character number; those beneath the branch indicate the character state. *, junior synonym; genus included within Mayazomus.
Figure 9. Mayazomus estor comb. nov. Holotype homeomorphic male. A, pedipalp ectal view. Female. B in Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics
Figure 9. Mayazomus estor comb. nov. Holotype homeomorphic male. A, pedipalp ectal view. Female. B, pedipalp ectal view. Paratype heteromorphic male. Pedipalp (C, D): C, ectal view. D, mesal view. Holotype male flagellum (E–G): E, dorsal view. F, ventral view. G, lateral view. Abbreviations: Fe, femur ectal; Fv, femur ventral; AP, apical process; Dm, dorsal median; Dl, dorsal lateral; Vm, ventral median; Vl, ventral lateral. Scale bars = 0.2 mm.
Figure 10. Reference topology with mapped dermal sculpture characters showing a phylogenetic signal, continued. A, character 10. B, character 11. C, character 12. For character 12 in Sculpture and vascularization of dermal bones, and the implications for the physiology of basal tetrapods
Figure 10. Reference topology with mapped dermal sculpture characters showing a phylogenetic signal, continued. A, character 10. B, character 11. C, character 12. For character 12, the coloration is similar to that in Figure 9, whereas for character 10 (four character states) and 11 (three character states), the lightest shading refers to character state 1, and the increasingly darker shadings refer to the ascending character states. For definition of characters, see Appendix 2.
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
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Data from: A comment on the use of stochastic character maps to estimate evolutionary rate variation in a continuously valued trait
Phylogenetic comparative biology has progressed considerably in recent years. One of the most important developments has been the application of likelihood-based methods to fit alternative models for trait evolution in a phylogenetic tree with branch lengths proportional to time. An important example of this type of method is O'Meara et al.'s (2006) "noncensored" test for variation in the evolutionary rate for a continuously valued character trait through time or across the branches of a phylogenetic tree. According to this method, we first hypothesize evolutionary rate regimes on the tree (called "painting" in Butler and King, 2004); and then we fit an evolutionary model, specifically the popular Brownian model, in which the instantaneous variance of the Brownian random diffusion process has different values in different parts of the phylogeny. The authors suggest that to test a hypothesis that the state of a discrete character influenced the rate of a continuous character, one could use the approach of Neilsen (2002) to first stochastically map the discretely valued trait, and then "test to see whether the portions of the tree with one state for the discrete character have a different rate of evolution for the continuous character than portions of the tree to which the other discrete state has been mapped" (O'Meara et al., 2006, p. 931). Indeed, this has become common practice for this and other closely related methods. Here, I examine this practice. In particular, I show that evolutionary rates estimated this way (i.e., by using maximum likelihood [ML] to fit a multirate model on each stochastically mapped tree; and then averaging across trees) are systematically biased to be more similar to each other than are the underlying generating parameters. My analysis also reveals that this effect is dependent on the rate of evolution for the discrete trait. Specifically, if the rate of evolution for the discrete character is low then the difference between the true history and any stochastically mapped 1 history is generally small. This results in evolutionary rates for the continuous trait that are estimated with little bias. Conversely, if the rate of evolution for the discrete character is very high, then the true and hypothesized character histories are often extremely dissimilar, evolutionary rate estimates are biased to be more similar to each other than their underlying generating values, and we lose power to distinguish evolutionary rates on the tree.
Figure 3 from: Morales EA, Wetzel CE, Ector L (2021) New and poorly known araphid diatom species (Bacillariophyta) from regions near Lake Titicaca, South America and a discussion on the continued use of morphological characters in araphid diatom taxonomy. PhytoKeys 187: 23-70. https://doi.org/10.3897/phytokeys.187.73338
Figure 3 A–F SEM micrographs of Pseudostaurosira pulchra sp. nov. from the Bolivian Altiplano A, B outer views of valves showing axial area, striae and spines features C inner view of valve still attached to neighboring cell. Black arrow indicates absence of apical pore field. Dotted arrow points to depression into which the stria opens internally D tilted view of frustule. Notice larger valvocopula, lateral growth of spines and blister-like depositions on abvalvar edge of mantle E outer view of valve tip. Black arrow denotes absence of apical pore field. Notice round to elliptical spine base and larger areola on valve mantle. F frustule attached to neighboring valve by means of heavily silicified spines. Notice open girdle elements (white arrow) and depositions along abvalvar mantle edge. Scale bars: 2 µm (E); 4 µm (C, F); 5 µm (A, B, D).
Figure 5 from: Morales EA, Wetzel CE, Ector L (2021) New and poorly known araphid diatom species (Bacillariophyta) from regions near Lake Titicaca, South America and a discussion on the continued use of morphological characters in araphid diatom taxonomy. PhytoKeys 187: 23-70. https://doi.org/10.3897/phytokeys.187.73338
Figure 5 A–F SEM images of Pseudostaurosira heteropolaris sp. nov. from the Bolivian Altiplano A, B Valve views showing striation pattern and features of the axial area, virgae, vimines, and spine location C side view of complete frustule and neighboring cell showing girdle bands (white arrows denote open copulae). White arrows point to open girdle elements D close up of C showing details of spines with bifurcations with pinnatifid projections, characteristics of the striae on valve mantle and the features of the blisters E broken frustule with girdle bands. Pattern of volae within areolae is also shown F frustule in side, tilted view. Notice open copulae (white arrow) and reduced apical pore field with cavernous poroids (black arrow). Scale bars: 1 µm (D); 3 µm (A–C, E); 4 µm (F).
Figure 2 from: Morales EA, Wetzel CE, Ector L (2021) New and poorly known araphid diatom species (Bacillariophyta) from regions near Lake Titicaca, South America and a discussion on the continued use of morphological characters in araphid diatom taxonomy. PhytoKeys 187: 23-70. https://doi.org/10.3897/phytokeys.187.73338
Figure 2 A–F SEM images of little known "araphid" diatoms from the Bolivian Altiplano A, BNanofrustulum cataractarumA specimen from the Desaguadero River, showing quasifract girdle elements with prominent ligulae (white arrows) B specimen from the Sajama River showing common internal depression into which the areolae open (dotted arrows) and the blister-like depositions of silica at the abvalvar edge of the mantle C, DN. rarissimum from the Desaguadero River C small, spineless valve D internal view showing apical and foot pole pore fields (black arrows) and internal depressions containing all areolae within a stria (dotted arrow) E, FPseudostaurosira sajamaensis from the Desaguadero River E top view showing gradual transition of valve face to mantle and the reduced apical pore fields (black arrow) F side view of two half cells still attached by heavily silicified spines. Notice open girdle elements (white arrows). Scale bars: 1 µm (B); 3 µm (C, E); 4 µm (A, D); 5 µm (F).
Figure 1 from: Morales EA, Wetzel CE, Ector L (2021) New and poorly known araphid diatom species (Bacillariophyta) from regions near Lake Titicaca, South America and a discussion on the continued use of morphological characters in araphid diatom taxonomy. PhytoKeys 187: 23-70. https://doi.org/10.3897/phytokeys.187.73338
Figure 1 A–M' LM images of little known and new "araphid" diatoms from the Bolivian Altiplano A–ENanofrustulum cataractarumF–LN. rarissimumM–SPseudostaurosira sajamaensisT–ZP. pulchra sp. nov. (Fig. 1U is the holotype) A'–G' P. aedes sp. nov. (Fig. 1A' is the holotype). H'–M' P. heteropolaris sp. nov. (Fig. 1I' is the holotype). Scale bar: 10 µm.
Figure 8 from: Morales EA, Wetzel CE, Ector L (2021) New and poorly known araphid diatom species (Bacillariophyta) from regions near Lake Titicaca, South America and a discussion on the continued use of morphological characters in araphid diatom taxonomy. PhytoKeys 187: 23-70. https://doi.org/10.3897/phytokeys.187.73338
Figure 8 A–F SEM images of Pseudostaurosira frankenae sp. nov. A, B titled frustules showing external features; notice open girdle elements in B (white arrows) C, D internal view of valves showing internal elliptic depositions on striae (dashed arrows) and depression of the apical pore field (black arrows) E close-up of frustule apex (B) showing the externally occluded apical pore field, showing only a single row of poroids (black arrow) F close-up of frustule tip (A) showing open girdle bands (white arrow). Scale bars: 2 µm (E, F); 3 µm (C); 5 µm (A, B, D).
Figure 10 from: Morales EA, Wetzel CE, Ector L (2021) New and poorly known araphid diatom species (Bacillariophyta) from regions near Lake Titicaca, South America and a discussion on the continued use of morphological characters in araphid diatom taxonomy. PhytoKeys 187: 23-70. https://doi.org/10.3897/phytokeys.187.73338
Figure 10 A–F SEM images of Pseudostaurosira oblonga sp. nov. A, B external views showing apical pore fields covered with small flaps (black arrow in A) and other characteristics C, E internal valve features stressing on apical pore fields and striae in a depression (black arrows in C and dashed arrow in C and E respectively) D, F titled views of valves showing girdle bands (white arrow in F) and apical pore field (black arrow in F). Scale bars: 4 µm (B, C, E, F); 5 µm (A, D).
Figure 4 from: Morales EA, Wetzel CE, Ector L (2021) New and poorly known araphid diatom species (Bacillariophyta) from regions near Lake Titicaca, South America and a discussion on the continued use of morphological characters in araphid diatom taxonomy. PhytoKeys 187: 23-70. https://doi.org/10.3897/phytokeys.187.73338
Figure 4 A–F SEM images of Pseudostaurosira aedes sp. nov. from the Bolivian Altiplano A top, tilted view of valve showing axial area, slightly raised virga, valve face areolae covered with bilobed or disk-like flaps, and slightly larger valve mantle areola covered with two or more flaps B, D, E, F girdle views showing features of the valve mantle, open girdle elements with larger valvocopula (white arrows in D and E). Notice serrate spines with well-developed stipules in F which have varying patterns C inner view showing reduced apical pore field (black arrow) and single depression into which the areolae open internally (dotted arrow). Scale bars: 4 µm (D); 5 µm (A–C, E, F).
Figure 7 from: Morales EA, Wetzel CE, Ector L (2021) New and poorly known araphid diatom species (Bacillariophyta) from regions near Lake Titicaca, South America and a discussion on the continued use of morphological characters in araphid diatom taxonomy. PhytoKeys 187: 23-70. https://doi.org/10.3897/phytokeys.187.73338
Figure 7 A–F SEM images of Pseudostaurosira vulpina sp. nov. A, B valve views showing striation pattern, features of the axial area, spine position and presence of depressed apical pore fields (black arrows) C, D close-ups with details of apical pore fields areolae and spines E tilted view of a frustule showing open girdle bands with overlapping extremes (white arrows) F internal view showing apical pore fields and the internal disk-like areolar depositions. Scale bars: 2 µm (C, D); 5 µm (A, B, E, F).
Figure 9 from: Morales EA, Wetzel CE, Ector L (2021) New and poorly known araphid diatom species (Bacillariophyta) from regions near Lake Titicaca, South America and a discussion on the continued use of morphological characters in araphid diatom taxonomy. PhytoKeys 187: 23-70. https://doi.org/10.3897/phytokeys.187.73338
Figure 9 A–F SEM images of Pseudostaurosira occulta sp. nov. A, B external views of valves showing apical pore fields (black arrow in A) and other features C internal view of valve showing depressions containing the striae (dashed arrow) D internal close-up showing apical pore field depression (black arrow) and striae depression (dashed line) E close-up on valve apex showing flaps on apical pore field (black arrow) and open girdle element (white arrow) F close-up on cell-cell connection showing apical pore field covered with flaps (black arrow) and open girdle element (white arrow). Scale bars: 2 µm (D, E); 3 µm (F); 5 µm (A–C).
Figure 6 from: Morales EA, Wetzel CE, Ector L (2021) New and poorly known araphid diatom species (Bacillariophyta) from regions near Lake Titicaca, South America and a discussion on the continued use of morphological characters in araphid diatom taxonomy. PhytoKeys 187: 23-70. https://doi.org/10.3897/phytokeys.187.73338
Figure 6 A–V LM images of little known and new "araphid" diatoms from the Bolivian Altiplano A–DPseudostaurosira vulpina stat. nov. E–IP. frankenae sp. nov. (Fig. 6E is the holotype) J–OP. occulta sp. nov. (Fig. 6K corresponds to the holotype) P–VP. oblonga sp. nov. (Fig. 6R corresponds to the holotype). Scale bar: 10 µm.
FIGURE 5 in Continuous character variation within the Glossopleura-Anoria-Sonoraspis plexus: Dolichometopid trilobites from the Cadiz Formation (Cambrian: Miaolingian, Wuliuan), California
FIGURE 5. Distributions of EL/GL ratios for Glossopleura and Anoria specimens measured for this study. Individual generic and total-sample distributions are normal by Kolmogorov-Smirnov tests.
FIGURE 7 in Continuous character variation within the Glossopleura-Anoria-Sonoraspis plexus: Dolichometopid trilobites from the Cadiz Formation (Cambrian: Miaolingian, Wuliuan), California
FIGURE 7. Principal components analysis of dolichometopid cranial measurements at genus level. Glossopleura = blue polygons. Sonoraspis = red polygons. Anoria = black polygons. A) PC1 vs PC2. B) PC1 vs PC3. C) PC2 vs PC3. Genera coded by color as noted above. Species denoted by symbols as listed alphabetically here: Glossopleura boccar (open blue squares), G. campbelli (open blue diamonds), G. lodensis (blue stars), G. mckeei (solid blue dots), G. mohavensis (blue dashes), G. producta (open blue triangles), G. similaris (vertical blue bars), G. stephenensis (open blue ovals), G. utahensis (inverted open blue triangles), G. walcotti (filled blue triangles), G. yatesi (filled inverted triangles); Sonoraspis californica (filled red circles), S. gomezi (filled red squares); Anoria baton (black X), A. bessus (open black circles), A. tontoensis (filled black squares).
Data from: A comment on the use of stochastic character maps to estimate evolutionary rate variation in a continuously valued trait
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Heart Chamber Evolution Reveals Roles of Gene/Genome Duplications on Continuous Character Evolution in Vertebrates
GEO Series GSE73522. Ciona intestinalis; Petromyzon marinus; Danio rerio. 3 samples. Type: Expression profiling by high throughput sequencing.
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