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53 results for “character coding”
Figure 1 in Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda
Figure 1. Midgut morphology of 'typical prosobranch'; adapted from Smith (1967). Abbreviations: dgd, digestive gland duct; e, oesophagus; gc, gastric chamber; gs, gastric shield; ig, intestinal groove; sa, sorting area; ss, style sac; t1, major typhlosole; t2, minor typhlosole.
Figure 9 in Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda
Figure 9. Histology of anterior oesophagus; ventro-lateral folds. (A) Macleaniella moskalevi. Scale bar = 0.5 mm. (B) Theodoxus fluviatilis. Scale bar = 0.5 mm. (C) Neocyclotus dysoni ambiguum. Scale bar = 0.5 mm. (D) Lampanella minima. Scale bar = 1 mm. (E) Strombus mutabilis. Scale bar = 0.5 mm. (F) Crepidula plana. Scale bar = 1 mm. (G) Bithynia tentaculata. Scale bar = 1 mm. (H) Littorina littorea. Scale bar = 0.5 mm. Abbreviations: bp, buccal pouch; bg, buccal ganglion; ca, radular cartilage; ceg, cerebral ganglion; df, dorsal fold; e, oesophagus; r, radula; sgl, salivary gland; vf, ventral fold; vlf, ventro-lateral fold.
Figure 10 in Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda
Figure 10. Histology of anterior oesophagus; ventral folding absent. (A) Neverita duplicata. Scale bar = 0.5 mm. (B) Nitidiscala tinctum. Scale bar = 0.5 mm. (C) Panarona clavatula. Scale bar = 0.5 mm. (D) Prunum apicinum. Scale bar = 0.5 mm. (E) Conus jaspideus. Scale bar = 0.5 mm. (F) Ilyanassa obsoletus. Scale bar = 0.5 mm. (G) Urosalpinx cinerea. Scale bar = 1 mm. Abbreviations: asg, accessory salivary gland; ca, radular cartilage; ceg, cerebral ganglion; df, dorsal fold; dl, duct of gland of Leiblein; e, oesophagus; int, intestine; j, jaw; ps, proboscis sheath; r, radula; sgd, salivary gland duct; sgl, salivary gland; vc, ventral channel.
Figure 18 in Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda
Figure 18. Midgut morphology. White arrows indicate direction of ciliary currents. (A) Prunum apicinum, dorsal view. (B) Conus jaspideus, dorsal view. Scale bar = 100 Mm. Abbreviations: dgd, digestive gland duct; e, oesophagus; gp, glandular pad; t1, major typhlosole.
Figure 32 in Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda
Figure 32. Evolution of the style sac. Black hashmarks indicate forward changes, grey hashmarks indicate forward homoplasies (DELTRAN). Inset shows optimization of 'style sac present/absent.' Hashmark indicates 'loss of style sac' in Macleaniella moskalevi.
Figure 23 in Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda
Figure 23. Kidney morphology; derived caenogastropods with two differentiated lobes of lamellae. (A) Neverita duplicata, dorsal view. Kidney opened between lobes of differentiated lamellae. (B) Cypraea robertsi, dorsal view. Intestine removed to reveal internal details. (C) Panarona clavatula, dorsal view, posterior chamber on left, anterior chamber on right. Kidney roof opened between lobes of primary and secondary lamellae. Note meronephridial condition (no interdigitation of lamellae) and that dorsal branch of afferent renal vessel supplies both primary and secondary tubules. (D) Prunum apicinum, dorsal view. Note small region of secondary tubules within kidney roof supplied by dorsal branch of afferent renal vessel. (E) Ilyanassa obsoletus, dorsal view. Note pycnonephridial condition (interdigitation of lamellae). Scale bar = 1 mm. Abbreviations: al, anterior kidney lobe; arv, afferent renal vessel; au, auricle; darv, dorsal branch of afferent renal vessel; int, intestine; ng, nephridial gland; np, nephropore; per, pericardium; pl, posterior kidney lobe; rpc, reno-pericardial canal; ve, ventricle.
Figure 14 in Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda
Figure 14. Midgut morphology. White arrows indicate direction of ciliary currents. (A) Petaloconchus varians, dorsal view. (B) Crepidula plana, dorsal view. Scale bar = 1 mm. Abbreviations: c, caecum; cf, ciliated fold; ctr, ciliary tract; dgd, digestive gland duct; e, oesophagus; gp, glandular pad; gs, gastric shield; if, intestinal flap; sa, sorting area; ss, style sac; t1, major typhlosole; t2, minor typhlosole.
Figure 5 in Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda
Figure 5. Histology of subradular organ. (A) Neocyclotus dysoni ambiguum. Transverse section. Note bi-layered jaw. Scale bar = 0.5 mm. (B) Marisa cornuarietis. Sagittal section. Note bi-layered jaw. Scale bar = 0.5 mm. (C) Lampanella minima. Transverse section. Note jaw with exposed rods. Scale bar = 1 mm. (D) Strombus mutabilis. Transverse section. Scale bar = 0.5 mm. (E) Crepidula plana. Transverse section. Scale bar = 1 mm. (F) Littorina littorea. Sagittal section. Scale bar = 1 mm. (G) Neverita duplicata. Transverse section. Scale bar = 0.5 mm. (H) Panarona clavatula. Transverse section. Scale bar = 1 mm. Abbreviations: c., radular cartilage; j, jaw; mo, mouth; r, radula; srm, subradular membrane; sro, subradular organ.
Figure 17 in Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda
Figure 17. Midgut morphology. White arrows indicate direction of ciliary currents. (A) Nitidiscala tinctum, dorsal view. (B) Panarona clavatula, dorsal view. Note paired folds on midgut floor between oesophageal aperture and large digestive gland duct. Scale bar = 100 Mm. Abbreviations: dgd, digestive gland duct; e, oesophagus; gp, glandular pad; ig, intestinal groove; int, intestine; t1, major typhlosole; t2, minor typhlosole.
Figure 22 in Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda
Figure 22. Kidney morphology; basal caenogastropods with undifferentiated lamellae. (A) Neocyclotus dysoni ambiguum, lateral view. Dotted line indicates removed lateral lobe overhanging pericardium. Scale bar = 1 mm. (B) Bithynia tentaculata, dorsal view. Scale bar =.5 mm. (C) Petaloconchus varians, ventral view. Horizontal line indicates base of mantle cavity. Excretory tubules within pallial portion revealed by ventral incision. Scale bar = 0.5 mm. (D) Strombus mutabilis. Dorsal view. Scale bar = 1 mm. Abbreviations: arv, afferent renal vessel; au, auricle; ng, nephridial gland; np, nephropore; per, pericardium; rpc, reno-pericardial canal; ve, ventricle.
Figure 24 in Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda
Figure 24. Circum-oesophageal nerve ring morphology. (A) Neocyclotus dysoni ambiguum. Scale bar = 0.5 mm. (B) Lampanella minima. Scale bar = 0.5 mm. (C) Crepidula plana. Scale bar = 0.5 mm. (D) Cypraea robertsi. Upper diagram depicts cerebral, pleural, supra-esophageal, and sub-oesophageal ganglia; lower diagram depicts pedal ganglia and pedal cords. Scale bar = 1 mm. (E) Nitidiscala tinctum. Scale bar = 0.25 mm. (F) Prunum apicinum. Scale bar = 0.5 mm. (G) Ilyanassa obsoletus. Scale bar = 0.5 mm. Abbreviations: bg, buccal ganglion; ceg, cerebral ganglion; d, dialyneury; e, oesophagus; pc, pedal cord; pdg, pedal ganglion; plg, pleural ganglion; ppg, propodial ganglion; sb, sub-oesophageal ganglion; sc, statocone; sp, supra-oesophageal ganglion; z, zygoneury.
Figure 3 in Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda
Figure 3. Male reproductive morphology. (A) Lampanella minima. Note connective tissue between renal vas deferens and pericardium and accessory lobe of prostatic tissue on mantle cavity floor alongside proximal prostate. (B) Petaloconchus varians. (C) Crepidula plana. Note terminal papilla. (D) Strombus mutabilis. Note seminal groove continuous along ventral aspect of penis. (E) Cypraea robertsi. Note seminal groove continuous along ventral aspect of penis. (F) Prunum apicinum. Penial duct not shown. Arrow indicates slit-like communication between proximal prostate and mantle cavity. (G) Ilyanassa obsoletus. Arrow indicates fused, tube-like communication between proximal prostate and mantle cavity. Scale bar = 1 mm. Abbreviations: ped, penial duct; pe, penis; per, pericardium; pr, prostate; pvd, pallial vas deferens; sg, seminal groove.
Figure 8 in Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda
Figure 8. Histology of anterior oesophagus; ventral fold. (A) Macleaniella moskalevi. Scale bar = 0.5 mm. (B) Theodoxus fluviatilis. Scale bar = 0.5 mm. (C) Neocyclotus dysoni ambiguum. Scale bar = 0.5 mm. (D) Lampanella minima. Scale bar = 1 mm. (E) Strombus mutabilis. Scale bar = 0.5 mm. (F) Littorina littorea. Scale bar = 0.5 mm. (G) Cypraea robertsi. Note that ventral fold is offset to the right. Scale bar = 0.5 mm. Abbreviations: bp, buccal pouch; bg, buccal ganglion; c., radular cartilage; ceg, cerebral ganglion; df, dorsal fold; e.g. oesophageal gland; r, radula; sgd, salivary gland duct; sgl, salivary gland; vf, ventral fold; vlf, ventro-lateral fold.
Figure 28 in Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda
Figure 28. Evolution of the reproductive system. Black hashmarks indicate forward changes, grey hashmarks indicate forward homoplasies (DELTRAN).
Data and code for "Revealing the free energy landscape of halide perovskites: Metastability and transition characters in CsPbBr3 and MAPbI3"
<p>This record contains a neuroevolution potential (NEP) model (<code>nep-MAPI-SCAN.txt</code> ) for MAPbI3 used in the linked publication. The model can be used in conjunction with the <a href="https://gpumd.org">GPUMD package</a>. The <a href="https://calorine.materialsmodeling.org">calorine package</a> provides a Python interface to GPUMD.<br> Several primitive structures in extended xyz format can be found in the <code>*.xyz</code> files. These structures have been relaxed using the NEP model included here. The <code>demo-for-using-structures-and-model.py</code> script illustrates how to access the structures and model.</p>
Data from: The fundamental role of character coding in Bayesian morphological phylogenetics
<p>Phylogenetic trees establish a historical context for the study of organismal form and function. Most phylogenetic trees are estimated using a model of evolution. For molecular data, modeling evolution is often based on biochemical observations about changes between character states. For example, there are four nucleotides, and we can make assumptions about the probability of transitions between them. By contrast, for morphological characters, we may not know a priori how many character states there are per character, as both extant sampling and the fossil record may be highly incomplete, which leads to an observer bias. For a given character, the state space may be larger than what has been observed in the sample of taxa collected by the researcher. In this case, how many evolutionary rates are needed to even describe transitions between morphological character states may not be clear, potentially leading to model misspecification. To explore the impact of this model misspecification, we simulated character data with varying numbers of character states per character. We then used the data to estimate phylogenetic trees using models of evolution with the correct number of character states and an incorrect number of character states. The results of this study indicate that this observer bias may lead to phylogenetic error, particularly in the branch lengths of trees. If the state space is wrongly assumed to be too large, then we underestimate the branch lengths, and the opposite occurs when the state space is wrongly assumed to be too small.</p>
Data from: The fundamental role of character coding in Bayesian morphological phylogenetics
Open the record for dataset details and reuse information.
Data from: Cladistic assignment of specimens to species of the cystoporate bryozoan genera Strotopora Ulrich and Cliotrypa Ulrich and Bassler using gap-coded characters
Gap-coding permits the use of continuous metric characters in cladistic analyses. Character means are converted to integer equivalents by placing character state divisions in the locations of phenetic breaks between specimen clusters, under the assumption that these breaks represent the locations of bottlenecks in character distributions. Similarities and differences between specimens from closely related species of cystoporate bryozoans were evaluated for the first time by converting continuous morphometric measurements into gap-coded binary and multistate characters and analyzing them cladistically, rather than just phenetically, across multiple species of Strotopora, Cliotrypa ramosa and Fistulipora compressa. Our results demonstrate that cladistic analysis of gap-coded morphological characters can be effective in resolving phylogenetic relationships at low taxonomic levels (within and among genera) while objectively highlighting both the morphological features that specimens (taxa) share and those characteristics that differentiate them. Differences in cystiphragm abundances and sizes, especially in the proximal portions of colonies, discriminate between species of Strotopora. Colony size and growth form, abundances and lengths of hemiphragms, and sizes of cystopores discriminate between Strotopora and the closely related genus Cliotrypa. Cladistic patterns indicate that Strotopora foveolata Ulrich is a valid species with Strotopora dermata as its junior subjective synonym. Fistulipora compressa is reassigned to the genus Strotopora whereas a decision on the taxonomic status of Cliotrypa ramosa requires a broader cladistic analysis of fistuliporine genera.
Figure 5 in Coding characters from different life stages for phylogenetic reconstruction: a case study on dragonfly adults and larvae, including a description of the larval head anatomy of Epiophlebia superstes (Odonata: Epiophlebiidae)
Figure 5. The single most-parsimonious trees from the TNT analyses: A, matrix AC (artificial coding; tree length, L = 113; consistency index, CI = 79; retention index, RI = 77); B, matrix NMC, applying non-multistate coding and preferring the adult character state over the larval state in the case of character state conflict (L = 89; CI = 88; RI = 83); C, matrix MC, applying a multistate coding strategy in cases of conflict between larval and adult morphology (L = 57; CI = 91; RI = 85); D, matrix SC, coding larval and adult characters seperately within the same taxon (L = 159; CI = 88; RI = 82). Non-homoplasious character changes are indicat- ed with black squares; homoplasious characters are indicated with white squares. Trait numbers are indicated above squares, state changes below. The 'M' below the character state changes in (C) indicates a multistate character optimized as an autapomorphy. For trait references, see Table S1 and Table S6; for detailed trees, see Figure S7.
Figure 4 in Coding characters from different life stages for phylogenetic reconstruction: a case study on dragonfly adults and larvae, including a description of the larval head anatomy of Epiophlebia superstes (Odonata: Epiophlebiidae)
Figure 4. SEM micrographs and three-dimensional reconstructions of the maxillae, labium, and hypopharynx of Epiophlebia superstes. A, ventral view of the maxilla, scale bar: 1 mm. B, ventral view of the maxilla, with musculature shown. C, dorsal view of the maxilla. D, dorsal view of the maxilla, with musculature shown. E, labium in dorsal view. Scale bar: 1 mm. E1, detail of the apical area of the labium. Scale bar: 500 μm. E2, detail of E1. Scale bar: 5 μm. F, musculature of the labium and hypopharynx in dorsolateral view. G, musculature of the labium and hypopharynx in lateral view. Abbreviations: ca, cardo; dse, dentisetae; eh, end hook; hyp, hypopharnyx; inc, incisivi; lac, lacinia; lp, labial palpus; mh, moveable hook; ml, median lobe; mp, maxillar palpus; pm, postmentum; prm, prementum; set, setae; st, stipes; trod, T-shaped cuticular rod. For muscle references see text and Table S2.
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