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25 results for “character reconstructions”
Accuracy of phylogenetic reconstructions from continuous characters analyzed under parsimony and its parametric correlates
<p>Quantitative traits are a source of evolutionary information often difficult to handle in cladistics. Tools exist to analyze this kind of data without subjective discretization, avoiding biases in the delimitation of categorical states. Nonetheless, the ability of continuous characters to accurately infer relationships is incompletely understood, particularly under parsimony analysis. This study evaluates the accuracy of phylogenetic reconstructions from simulated matrices of continuous characters evolving under alternative evolutionary processes and analyzed by parsimony. We sampled 100 empirical trees to simulate 9,000 matrices, each containing between 25 and 50 taxa and 50 and 150 continuous characters evolving under three evolutionary processes: Brownian-Motion (BM), Ornstein-Uhlenbeck (OU) and Early-Burst (EB) with variable parametrizations. Our cladogram comparisons revealed that continuous character matrices, when discretized objectively and analyzed by parsimony in TNT, carry phylogenetic signals to infer species relationships, regardless of the evolutionary models and parameterization schemes. Interestingly, implementing Equal Weighting (EW) or Implied Weighting (IW) with varying penalization strengths against homoplasies did not affect cladogram reconstructions on the basis of continuous characters. Finally, the accuracy of continuous characters in resolving species relationships is skewed toward apical nodes of the recovered trees. Our findings provide general insights of the utility of quantitative traits in cladistics and demonstrate that their effectiveness in estimating shallower nodes is independent of the underlying evolutionary model, parameters and weighting schemes.</p>
Text-fig. 1. D&E tree of Endress and Doyle (2009), from the combined morphological and molecular analysis of Doyle and Endress (2000), with modifications based on more recent data, showing the inferred evolution of the reticulum grading character (39). Boxes under names of taxa indicate their character state; shading of branches indicates their reconstructed state based on parsimony optimization with MacClade (Maddison and Maddison 2003). Nymph = Nymphaeales, Aust = Austrobaileyales, Chlor = Chloranthaceae, Piper = Piperales, Ca = Canellales, Magnol = Magnoliales. in Early Cretaceous Monocots: A Phylogenetic Evaluation
Text-fig. 1. D&E tree of Endress and Doyle (2009), from the combined morphological and molecular analysis of Doyle and Endress (2000), with modifications based on more recent data, showing the inferred evolution of the reticulum grading character (39). Boxes under names of taxa indicate their character state; shading of branches indicates their reconstructed state based on parsimony optimization with MacClade (Maddison and Maddison 2003). Nymph = Nymphaeales, Aust = Austrobaileyales, Chlor = Chloranthaceae, Piper = Piperales, Ca = Canellales, Magnol = Magnoliales.
Fig. 3a-c in New Tools for Phylogenetic reconstruction using character state trees
Fig. 3a-c: A CST with the same structure as the one of fig. 1. The paths to the root of the states D (3a) and G (3b) are accentuated, as well as the elements of the set SDG (fig. 3c, see eq. 1).
Fig. 1 in New Tools for Phylogenetic reconstruction using character state trees
Fig. 1 (from LORENZ 1941): Resulting tree out of a species/characters-matrix of 48 mainly behavioural characters from twenty Anatid species (in fact, this graphic is matrix and tree in one).
Fig. 4a-b in New Tools for Phylogenetic reconstruction using character state trees
Fig. 4a-b: (a) Cladogram for five species (the tips T1 to T5) and the character which is coded in fig. 2b as CST. The inner nodes of the cladogram are hypothetical species. Their character state is reconstructed by the algorithm described in the text. Prominent branches denote an evolutionary step (a change of state). (b) Bifurcation of a cladogram with the character coded in fig. 3.
Fig. 2a-c in New Tools for Phylogenetic reconstruction using character state trees
Fig. 2a-c: The same character state tree with Camin – Sokal (a) and Matrioshka (b) coding, and (c) as a combination of three subcharacters (factors), each one with two states.
Fig. 1 in New Tools for Phylogenetic reconstruction using character state trees
Fig. 1: Evolution of the ovipositor and the ootheca of Dictyoptera (Insecta) as an example of a relatively complex character state tree (based on data of GRIMALDI & ENGEL 2005 and EHRMANN 2002). Each node of the tree corresponds to an observed character state.
Fig. 3 in New Tools for Phylogenetic reconstruction using character state trees
Fig. 3: Result of a Camin-Sokal parsimony phylogenetic reconstruction using the data from tab. 2a.
Fig. 2 in New Tools for Phylogenetic reconstruction using character state trees
Fig. 2: Result of a Camin-Sokal parsimony phylogenetic reconstruction using the data from tab. 1.
nRCFV: A sequence, taxon and character state-normalised metric for the pre-reconstruction evaluation of compositional heterogeneity
<p><strong><span>Motivation</span></strong></p> <p><span>Compositional heterogeneity – when the proportions of nucleotides and amino acids are not broadly similar across the dataset – is a cause of a great number of phylogenetic artefacts. Whilst a variety of methods can identify it post-hoc, few metrics exist to quantify compositional heterogeneity prior to the computationally intensive task of phylogenetic tree reconstruction. Here we assess the efficacy of one such existing, widely used, metric: Relative Composition Frequency Variability (RCFV), using both real and simulated data.</span></p> <p><strong><span>Results</span></strong></p> <p><span>Our results show that RCFV can be biased by sequence length, the number of taxa, and the number of possible character states within the dataset. However, we also find that missing data does not appear to have an appreciable value on RCFV. We discuss the theory behind this and the consequences of this for the future of the usage of the RCFV value and propose a new metric, nRCFV, which accounts for these biases. Alongside this, we present a new software that easily calculates both RCFV and nRCFV, called nRCFV_Reader.</span></p> <p><strong><span>Availability and Implementation</span></strong></p> <p><span>nRCFV has been implemented in RCFV_Reader, available at: </span><a href="https://github.com/JFFleming/RCFV_Reader"><span>https://github.com/JFFleming/RCFV_Reader</span></a><span>. Both our simulation and real data are available in this dataset.</span></p>
Data from: How many characters are needed to reconstruct a phylogeny?
Open the record for dataset details and reuse information.
nRCFV: A sequence, taxon and character state-normalised metric for the pre-reconstruction evaluation of compositional heterogeneity
Open the record for dataset details and reuse information.
FIGURE 1. Ancestral character-state reconstructions for Characters 1–9 in Concentrated evolutionary novelties in the foot musculature of Odontophrynidae (Anura: Neobatrachia), with comments on adaptations for burrowing
FIGURE 1. Ancestral character-state reconstructions for Characters 1–9. Ambiguities in Macrogenioglottus alipioi and Odontophrynus carvalhoi in Characters 5–7 are due to polymorphism.
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.
Figure 2 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 2. Overview of the outer head anatomy of Epiophlebia superstes: A, ventral view with the right part displayed as a three-dimensional reconstruction in order to show the peculiar muscle arrangement of the labial prehensile mask; B, lateral view; C, frontal view; D, dorsal view. Abbreviations: acl, anteclypeus; agp, anterior genal process; antb, antennal base; cl, cleavage line; cr0lb1 + 2, cranial origin of labral muscles 0lb1 and 0lb2; cr0lb5, cranial origin of labral muscle 0lb5; cr0te3, cranial origin of tentorial muscle 0te3; e, eye; fl, flagellum; fr, frons; lbr, labrum; loc, lateral occellus; lp, labial palpus; moc, middle occellus; oc, occiput; ocr, occipital ridge; pcl, postclypeus; pe, pedicellus; prm, prementum; sc, scapus. For muscle references, see text and Table S2. Scale bar: 1 mm.
Figure 1 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 1. Methodological workflow. In three matrices (AC, NMC, and MC) the full data set of 81 characters was used. The matrices differ in coding strategies. In matrix AC the larvae were coded as independent terminal taxa. In matrix NMC the larvae were omitted, thereby reducing the number of taxa from nine to six. If larval character states differed from adult ones, the character state of the adult was coded (non-multistate approach). In matrix MC we equally incorporated the larval character states into the adult character states, but in cases where larva possess a different character state than the adult these characters were coded as multistate characters. In matrix SC (separate coding) we coded larval and adult characters as separate characters within the same species, which resulted in a higher number of characters. If characters generated by the SC approach showed no variation they were omitted from the analysis, which is why not exactly twice as many characters as in matrices AC and MC are used.
Figure 3 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 3. SEM micrographs of the outer and three-dimensional reconstructions of the inner anatomy of Epiophlebia superstes. Ventral (A) and dorsolateral (B) view of the mandible (A1, detail of the ventral region of the mandible; B1, detail of the region at the molar base). C, the labral, antennal, tentorial, and pharyngeal musculature in dorsal view. D, the mandibular muscles in dorsofrontal view (D1, same as D in dorsolateral view). E, epipharynx in posterior view (E1, detail of e). F, the labral, antennal, tentorial, and pharyngeal musculature in lateral view. Brain, 0an2, 0lb1, 0bu2, and 0hy2 omitted for clarity. Abbreviations: ata, anterior tentorial arms; br, brain; ct, corpotentorium; dta, dorsal tentorial arms; inc, incisivi; lbr, labrum; le, lateral extension of labrum; mo, mola; pe, pedicellus; phx, pharynx; sc, scapus. For muscle references see text and Table S2. Scale bar: 100 μm.
text-fig. 27. Posterior dorsal vertebrae of three theropod dinosaurs in left lateral view, showing states for several axial characters. A, Herrerasaurus ischigualastensis; penultimate dorsal vertebra; redrawn (reversed) from Novas (1993). B, Syntarsus rhodesiensis-, reconstruction of the eleventh dorsal vertebra; based on QG 1. c, unnamed compsognathine from the Lower Cretaceous of Brazil; reconstruction of the posteriormost dorsal vertebra; based on SMNK 2349 Pal. Abbreviations as in ext-figures 24 and 26, and: pg, pleurocentral groove; st, spine table. Scale bars represent 10 mm. in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 27. Posterior dorsal vertebrae of three theropod dinosaurs in left lateral view, showing states for several axial characters. A, Herrerasaurus ischigualastensis; penultimate dorsal vertebra; redrawn (reversed) from Novas (1993). B, Syntarsus rhodesiensis-, reconstruction of the eleventh dorsal vertebra; based on QG 1. c, unnamed compsognathine from the Lower Cretaceous of Brazil; reconstruction of the posteriormost dorsal vertebra; based on SMNK 2349 Pal. Abbreviations as in ext-figures 24 and 26, and: pg, pleurocentral groove; st, spine table. Scale bars represent 10 mm.
text-fig. 20. Mandible of Erlikosaurus andrewsi (a) and Oviraptor philoceratops (b) in lateral view, illustrating different states for characters 72, 75, and 77. For sources of reconstructions and identifications of the elements, see ext-figur^ 6. Scale bars represent 50 mm. in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 20. Mandible of Erlikosaurus andrewsi (a) and Oviraptor philoceratops (b) in lateral view, illustrating different states for characters 72, 75, and 77. For sources of reconstructions and identifications of the elements, see ext-figur^ 6. Scale bars represent 50 mm.
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