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21 results for “correlated character”
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>
Data from: Body size correlates with discrete character morphological proxies
Principal coordinates analysis (PCoA) is a statistical ordination technique commonly applied to morphology-based cladistic matrices to study macroevolutionary patterns, morphospace occupation and disparity. However, PCoA-based morphospaces are dissociated from the original data; therefore, whether such morphospaces accurately reflect body plan disparity or extrinsic factors, such as body size, remains uncertain. We collated nine character-taxon matrices of dinosaurs together with body mass estimates for all taxa and tested for relationships between body size and both the principal ordinated axis of variation (PCo1) and the entire set of PCo scores. The possible effects of body size on macroevolutionary hypotheses derived from ordinated matrices were tested by re-evaluating evidence for the accelerated accumulation of avian-type traits indicated by a strong directional shift in PCo1 scores in hypothetical ancestors of modern birds. Body mass significantly accounted for, on average, approximately 50 and 16 per cent of the phylogenetically corrected variance in PCo1 and all PCo scores, respectively. Along the avian stem lineage, approximately 30 per cent of the morphological variation is attributed to the reconstructed body masses of each ancestor. When the effects of body size are adjusted, the period of accelerated trait accumulation is replaced by a more gradual, additive process. Our results indicate that even at low proportions of variance, body size can noticeably effect macroevolutionary hypotheses generated from ordinated morphospaces. Future studies should thoroughly explore the nature of their character data in association with PCoA-based morphospaces and use a residual/covariate approach to account for potential correlations with body size.
Data from: Body size correlates with discrete character morphological proxies
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Data from: Serial homology and correlated characters in morphological phylogenetics: modeling the evolution of dental crests in placentals
Accurate modeling of the complexity of morphological evolution is crucial for morphological phylogenetics and for performing tests on a wide variety of evolutionary scenarios. In this context, morphological integration and the problem of correlated categorical characters represent a major challenge. In particular, the magnitude and implications of correlations among serially homologous structures such as teeth have been much debated but were never tested statistically within a broad phylogenetic context. Here, we present a large-scale empirical study analyzing the serial variation of cingular crests on successive molars (M1, M2 and M3) of 274 placental species in a phylogenetic context. Both likelihood analyses and analysis of phylogenetic co-distributions demonstrated highly correlated evolution in the entire sample and thus the non-independence of these serial features at a macroevolutionary scale. Likelihood analyses show that their serial variation should be better scored within a single composite character model with constrained paths for transitions enabling simultaneous changes on all three molars, which suggests a strong developmental or genetic integration. These results are congruent with current molecular and developmental knowledge related to dental morphological variation and call into question the frequent use of separate characters scored on serially homologous structures of the dentition in phylogenetic analyses. Overall, they provide long-overdue and clear empirical evidence that in-depth studies of patterns of integration constitute an essential step towards more realistic character construction and modeling. This approach is critical for more accurate morphological phylogenetics and, more generally, for testing macroevolutionary scenarios on groups of correlated characters.
Data from: Polymorphism and multiple correlated characters: do asymmetry flatfish morphs also differ in swimming performance and metabolic rate?
1. Phenotypic polymorphisms often differ in multiple correlated traits including morphology, behavior, and physiology, all of which can affect performance. How selection acts on these suites of traits can be complex and difficult to discern. Starry flounder (Platichthys stellatus) is a pleuronectid flatfish that exhibits rare polymorphism for the direction of eye migration and resulting whole-body asymmetry. P. stellatus asymmetry morphs differ subtly in several anatomical traits, foraging behavior, and stable isotope signatures, suggesting they may be ecologically segregated, yet performance and metabolic differences are unknown. 2. Here we tested the hypothesis that sinistral and dextral P. stellatus asymmetry morphs diverge in performance and routine metabolic rate (RMR) by comparing prolonged swimming endurance (time to exhaustion at a constant swimming speed), fast-start swimming velocity and acceleration, and rate of oxygen consumption. Based on subtle morphological differences in caudal tail size, we expected sinistral P. stellatus to have superior prolonged swimming endurance relative to dextral fish, but inferior fast-start performance. 4. Sinistral P. stellatus exhibited both significantly greater prolonged swimming performance and fast-start swimming performance. However, sinistral P. stellatus also exhibited greater RMR, suggesting that their general swimming performance could be enhanced by an elevated metabolic rate. 5. Divergence between P. stellatus asymmetry morphs in swimming performance and metabolic rates contributes to growing evidence of ecological segregation between them, as well as our understanding of possible ecological consequences of asymmetry direction in flatfishes. These data provide an example of the complexity of polymorphisms associated with multiple correlated traits in a rare case of asymmetry polymorphism in a marine flatfish species.
FIGURE 6. Correlation between characters 4–5 and 1–6 in Quantitative analysis of interspecific and ontogenetic variation in Osteoglossum species (Teleostei: Osteoglossiformes: Osteoglossidae)
FIGURE 6. Correlation between characters 4–5 and 1–6, including all size classes of Osteoglossum species. Numbers represent species and classes, where, 1= postembryos and juveniles of O. ferreirai; 2= adults of O. ferreirai; 3= postembryos and juveniles of O. bicirrhosum; 4= adults of O. bicirrhosum.
FIGURE 4. Correlation between characters 13–14 and 1–2 in Quantitative analysis of interspecific and ontogenetic variation in Osteoglossum species (Teleostei: Osteoglossiformes: Osteoglossidae)
FIGURE 4. Correlation between characters 13–14 and 1–2, including all size classes of Osteoglossum species. Numbers represent species and classes, where, 1= postembryos and juveniles of O. ferreirai; 2= adults of O. ferreirai; 3= postembryos and juveniles of O. bicirrhosum; 4= adults of O. bicirrhosum.
FIGURES 6–9 in Character correlation and its use for identification
FIGURES 6–9. Dichotomous cladogram, ordered correlations, and output. 6, dichotomous cladogram that results in zero correlation between characters 0 and 1; 7, one correlation graph showing the maximal possible correlation between two additive characters; 8, correlation with incomplete ordering; 9, output to determine which state-combinations are compatible only with state 1 of the third character (combinations that predict only 2:1 in bold).
FIGURES 2–5. Pectinate cladogram and unordered correlations. 2 in Character correlation and its use for identification
FIGURES 2–5. Pectinate cladogram and unordered correlations. 2, pectinate tree, optimized for characters 0 and 1; 3, correlation of characters 0 (x) and 1 (y) on pectinate tree ("·": observed state combination; 0: zero extra steps needed; 1: one extra step needed); 4, pectinate tree with optimization for characters 2 and 3, showing ambiguity; 5, correlation of characters 2 (x) and 3 (y) on pectinate tree.
text-fig. 58. Diagrams showing how character distribution in a cladogram indicates gaps in the fossil record, a, arrangement of three taxa in a cladogram; synapomorphies a-f support the monophyly of the clade (B-C). B, if gradual acquisition of characters is assumed, several taxa must be missing in the phylogeny between taxon A and clade (B-C). The number of taxa missing is positively (though not necessarily linearly) correlated with the number of synapomorphies that diagnose any given node. in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 58. Diagrams showing how character distribution in a cladogram indicates gaps in the fossil record, a, arrangement of three taxa in a cladogram; synapomorphies a-f support the monophyly of the clade (B-C). B, if gradual acquisition of characters is assumed, several taxa must be missing in the phylogeny between taxon A and clade (B-C). The number of taxa missing is positively (though not necessarily linearly) correlated with the number of synapomorphies that diagnose any given node.
Data for: Correlated evolution of categorical characters under a simple model
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Data from: Polymorphism and multiple correlated characters: do asymmetry flatfish morphs also differ in swimming performance and metabolic rate?
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Data from: Serial homology and correlated characters in morphological phylogenetics: modeling the evolution of dental crests in placentals
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Data from: Data set incongruence and correlated character evolution: an example of functional convergence in the hind-limbs of stifftail diving ducks
The unwitting inclusion of convergent characters in phylogenetic estimates poses a serious problem for efforts to recover phylogeny. Convergence is not inscrutable, however, particularly when one group of characters tracks phylogeny and another set tracks adaptive history. In such cases, convergent characters may be correlated with one or a few functional anatomical units and readily identifiable using comparative methods. Stifftail ducks (Oxyurinae) offer one such opportunity to study correlated character evolution and function in the context of phylogenetic reconstruction. Morphological analyses place stifftail ducks as part of a large clade of diving ducks that includes the sea ducks (Mergini), Hymenolaimus, Merganetta, and Tachyeres, and possibly the pochards (Aythyini). Molecular analyses, on the other hand, place stifftails far from other diving ducks and suggest, moreover, that stifftails are polyphyletic. Mitochondrial cytochrome b gene sequences of eight stifftail species traditionally supposed to form a clade were compared with each other and with sequences from 50 other anseriform and galliform species. Stifftail ducks are not the sister group of sea ducks, but lie outside the typical ducks (Anatinae). Of the four traditional stifftail genera, monophyly of Oxyura and its sister group relationship with Nomonyx are strongly supported. Heteronetta probably is the sister group of that clade, but support is weak. Biziura is not a true stifftail. Within Oxyura, Old World species (O. australis, O. leucocephala, O. maccoa) appear to form a clade, with New World species (O. jamaicensis, O. vittata) branching basally. Incongruence between molecules and morphology is interpreted to be the result of adaptive specialization and functional convergence in the hind limbs of Biziura and true stifftails. When morphological characters are divided into classes, only hind-limb characters are significantly in conflict with the molecular tree. Null models of synonomous and nonsynonomous substitution based on patterns of codon-degeneracy and chemical dissimilarity, likewise, indicate that the nucleotide and amino acid changes postulated by the molecular tree are more plausible than those postulated by the morphological tree. These findings teach general lessons about the utility of highly adaptive characters (in particular those related to foraging ecology) and underscore the problems that convergence can pose for attempts to recover phylogeny. They also demonstrate how the concept of natural data partitions and simple models of evolution (e.g., parsimony, likelihood, neutrality) can be used to test the accuracy of independent phylogenetic estimates and provide arguments in favor of one tree topology over another.
Data from: Bayesian estimation of species divergence times using correlated quantitative characters
Discrete morphological data have been widely used to study species evolution, but the use of quantitative (or continuous) morphological characters is less common. Here, we implement a Bayesian method to estimate species divergence times using quantitative characters. Quantitative character evolution is modelled using Brownian diffusion with character correlation and character variation within populations. Through simulations, we demonstrate that ignoring the population variation (or population "noise") and the correlation among characters leads to biased estimates of divergence times and rate, especially if the correlation and population noise are high. We apply our new method to the analysis of quantitative characters (cranium landmarks) and molecular data from carnivoran mammals. Our results show that time estimates are affected by whether the correlations and population noise are accounted for or ignored in the analysis. The estimates are also affected by the type of data analysed, with analyses of morphological characters only, molecular data only, or a combination of both; showing noticeable differences among the time estimates. Rate variation of morphological characters among the carnivoran species appears to be very high, with Bayesian model selection indicating that the independent-rates model fits the morphological data better than the autocorrelated-rates model. We suggest that using morphological continuous characters, together with molecular data, can bring a new perspective to the study of species evolution. Our new model is implemented in the MCMCtree computer program for Bayesian inference of divergence times.
Clinical Characters and Outcome of Acute Myeloid Leukemia Patients on Correlation to CD200 and CD56 Expression
ClinicalTrials.gov study NCT05512104. IPD Sharing: UNDECIDED. Countries: 0. Publications: 1.
Data from: Data set incongruence and correlated character evolution: an example of functional convergence in the hind-limbs of stifftail diving ducks
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Data from: Analysis of Character Correlations Among Wood Decay Mechanisms, Mating Systems, and Substrate Ranges in Homobasidiomycetes
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Data from: Bayesian estimation of species divergence times using correlated quantitative characters
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FIGURES 10–13 in Character correlation and its use for identification
FIGURES 10–13. Cladograms of Nasserzadeh et al. (2017) and correlations of continuous characters. 10, single cladogram from equal weights for the Sternolophus dataset (length = 146.130); 11, correlation graph based on cladogram with equal weights (x-axis: char. 0; y-axis: char. 7); 12, single cladogram from implied weighting; 13, correlation of characters 0 and 7 based on implied-weighting cladogram.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.