scholarly journals Experimental systematics: sensitivity of cladistic methods to polarization and character ordering schemes

2015 ◽  
Vol 84 (2) ◽  
pp. 129-148 ◽  
Author(s):  
Valentin Rineau ◽  
Anaïs Grand ◽  
René Zaragüeta ◽  
Michel Laurin
Keyword(s):  
Brownian Motion ◽  
Empirical Studies ◽  
A Priori ◽  
Branch Length ◽  
Life Forms ◽  
Resolving Power ◽  
Phenotypic Traits ◽  
Character State ◽  
Phenotypic Characters ◽  
Ancestral Character State

Phenotypic characters are essential to study the evolution of extant and extinct life forms and to reconstruct the tree of life. Inside the cladistics theory, parsimony is used by a large majority of systematists working on phenotypic characters, whereas 3ta is much less widespread but has triggered important debates. Many important differences in the interpretation of the cladistic theory exist between these methods, e.g. meaning and treatment of reversals, character representation as ‘data-matrices’ in parsimony (ordered and unordered), and as rooted trees (hierarchies) in 3ta. Although 3ta has received severe criticism, mostly focused in the use of software intended to be used in parsimony, only a few empirical studies have compared these methods so far. We present the results of simulations of the evolution of phenotypic traits under a Brownian motion model to characterize differences in sensitivity between parsimony and 3ta to (1) outgroup branch length, which affects the reliability of ancestral character state estimates, (2) character state ordering scheme, and (3) ingroup branch lengths that reflect the geological age of studied taxa. Our results show that the ‘nihilistic’ attitude of leaving multistate characters unordered when criteria to order are available (e.g. , similarity, ontogeny, etc…) can decrease resolving power of the method (by 13.4% to 29.3%) and increase the occurrence of artefactual clades (by 5% to 15.6%). Increasing outgroup branch length significantly decreases resolving power and increases artefactual resolution, at least for paleontological trees. All simulations show that ordered parsimony is always superior to 3ta in tested parameter space. These results depend on the assumption in parsimony that reversals (as implied by the Brownian motion, as in most other models) can be evidence for the support of a clade a posteriori from an analysis or a priori on simulations with a known pattern. We discuss implications of these points of view compared to the assumption inherent in 3ta (i.e. , that reversals should not support a clade as other synapomorphies do) on evolutionary models.

scholarly journals Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits

2019 ◽  
Vol 68 (5) ◽  
pp. 698-716 ◽  
Author(s):  
Sergei Tarasov
Keyword(s):  
Regulatory Networks ◽  
Markov Models ◽  
Phylogenetic Inference ◽  
Phenotypic Traits ◽  
Character State ◽  
Body Parts ◽  
Ancestral Character State ◽  
State Models ◽  
Hidden States ◽  
New Framework

Abstract Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key processes—hierarchical and hidden—which are not accommodated simultaneously by the available phylogenetic methods. The hierarchical process refers to the dependencies between anatomical body parts, while the hidden process refers to the evolution of gene regulatory networks (GRNs) underlying trait development. Herein, I demonstrate that these processes can be efficiently modeled using structured Markov models (SMM) equipped with hidden states, which resolves the majority of the problems associated with discrete traits. Integration of SMM with anatomy ontologies can adequately incorporate the hierarchical dependencies, while the use of the hidden states accommodates hidden evolution of GRNs and substitution rate heterogeneity. I assess the new models using simulations and theoretical synthesis. The new approach solves the long-standing “tail color problem,” in which the trait is scored for species with tails of different colors or no tails. It also presents a previously unknown issue called the “two-scientist paradox,” in which the nature of coding the trait and the hidden processes driving the trait’s evolution are confounded; failing to account for the hidden process may result in a bias, which can be avoided by using hidden state models. All this provides a clear guideline for coding traits into characters. This article gives practical examples of using the new framework for phylogenetic inference and comparative analysis.

scholarly journals Exploring and Reconstructing Ancestral Anatomies using Ontology-Informed Approaches

2019 ◽  
Vol 3 ◽  
Author(s):  
Sergei Tarasov ◽  
Istvan Miko ◽  
Matthew Yoder ◽  
Josef Uyeda
Keyword(s):  
Phylogenetic Trees ◽  
Character State ◽  
Ancestral Reconstruction ◽  
Anatomy Ontology ◽  
Insect Order ◽  
Ancestral Character State ◽  
Body Regions ◽  
Individual Traits ◽  
History Of ◽  
Complex Characters

Ancestral character state reconstruction has been long used to gain insight into the evolution of individual traits in organisms. However, organismal anatomies (= entire phenotypes) are not merely ensembles of individual traits, rather they are complex systems where traits interact with each other due to anatomical dependencies (when one trait depends on the presence of another trait) and developmental constraints. Comparative phylogenetics has been largely lacking a method for reconstructing the evolution of entire organismal anatomies or organismal body regions. Herein, we present a new approach named PARAMO (Phylogenetic Ancestral Reconstruction of Anatomy by Mapping Ontologies, Tarasov and Uyeda 2019) that takes into account anatomical dependencies and uses stochastic maps (i.e., phylogenetic trees with an instance of mapped evolutionary history of characters, Huelsenbeck et al. 2003) along with anatomy ontologies to reconstruct organismal anatomies. Our approach treats the entire phenotype or its component body regions as single complex characters and allows exploring and comparing phenotypic evolution at different levels of anatomical hierarchy. These complex characters are constructed by ontology-informed amalgamation of elementary characters (i.e., those coded in character matrix) using stochastic maps. In our approach, characters are linked with the terms from an anatomy ontology, which allows viewing them not just as an ensemble of character state tokens but as entities that have their own biological meaning provided by the ontology. This ontology-informed framework provides new opportunities for tracking phenotypic radiations and anatomical evolution of organisms, which we explore using a large dataset for the insect order Hymenoptera (sawflies, wasps, ants and bees).

Moral epistemology

2018 ◽  
Author(s):  
Ralph Wedgwood
Keyword(s):  
Reflective Equilibrium ◽  
Empirical Studies ◽  
A Priori ◽  
Moral Epistemology ◽  
Moral Judgments ◽  
Moral Thinking ◽  
Moral Intuitions ◽  
Moral Beliefs ◽  
Factual Proposition ◽  
The Way

Epistemology is the study of knowledge and justified belief. So moral epistemology is the study of what would be involved in knowing, or being justified in believing, moral propositions. Some discussions of moral epistemology interpret the category of ‘moral propositions’ broadly, to encompass all propositions that can be expressed with terms like ‘good’ or ‘bad’ or ‘ought’. Other discussions have focused on a narrower category of moral propositions – such as propositions about what rights people have, or about what we owe to each other. According to so-called noncognitivists, one cannot strictly speaking know (or be justified in believing) a moral proposition in the same sense in which one can know (or be justified in believing) an ordinary factual proposition. Other philosophers defend a cognitivist position, according to which it is possible to know or be justified in believing moral propositions in the very same sense as factual propositions. If one does know any moral propositions, they must presumably be true; and the way in which one knows those moral truths must provide access to them. This has led to a debate about whether one could ever know moral truths if a realist conception of these truths – according to which moral truths are not in any interesting sense of our making – were correct. Many philosophers agree that one way of obtaining justified moral beliefs involves seeking ‘reflective equilibrium’ – that is, roughly, considering theories, and adjusting one’s judgments to make them as systematic and coherent as possible. According to some philosophers, however, seeking reflective equilibrium is not enough: justified moral beliefs need to be supported by moral ‘intuitions’. Some hold that such moral intuitions are a priori, akin to our intuitions of the self-evident truths of mathematics. Others hold that these intuitions are closely related to emotions or sentiments; some theorists claim that empirical studies of moral psychology strongly support this ‘sentimentalist’ interpretation. Finally, moral thinking seems different from other areas of thought in two respects. First, there is particularly widespread disagreement about moral questions; and one rarely responds to such moral disagreement by retreating to a state of uncertainty as one does on other questions. Secondly, one rarely defers to other people’s moral judgments in the way in which one defers to experts about ordinary factual questions. These two puzzling features of moral thinking seem to demand explanation – which is a further problem that moral epistemology has to solve.

scholarly journals Backward Stochastic Differential Equations Driven by G-Brownian Motion with Double Reflections

2020 ◽  
Author(s):  
Hanwu Li ◽  
Yongsheng Song
Keyword(s):  
Brownian Motion ◽  
Differential Equations ◽  
Stochastic Differential Equations ◽  
A Priori Estimates ◽  
A Priori ◽  
Backward Stochastic Differential Equations ◽  
Penalization Method ◽  
Priori Estimates ◽  
Uniqueness And Existence

Abstract In this paper, we study the reflected backward stochastic differential equations driven by G-Brownian motion with two reflecting obstacles, which means that the solution lies between two prescribed processes. A new kind of approximate Skorohod condition is proposed to derive the uniqueness and existence of the solutions. The uniqueness can be proved by a priori estimates and the existence is obtained via a penalization method.

De Verwerving Van Morfologische Regels in Schrift (III)

1999 ◽  
Vol 61 ◽  
pp. 97-110
Author(s):  
Marjolein van Dort-Slijper ◽  
Gert Rijlaarsdam ◽  
Eva Breedveld
Keyword(s):  
Negative Transfer ◽  
Empirical Studies ◽  
A Priori ◽  
Recognition Task ◽  
Past Tense ◽  
Production Task ◽  
The Past ◽  
Verb Inflection ◽  
Group 6 ◽  
Special Case

In order to provide textbook authors with empirical data on the acquisition in Dutch of written morphology in nouns, verbs and adjectives, several empirical studies have been undertaken. In this article, the third study reports on the performance of the morpheme -e in a special case of adjectives in Dutch: the adjectives derived from participles. The study tries to determine the possible interference between the morphological rules for verb inflection (past tense) and adjective declension in reading and writing. Five classes of adjectives were distinguished according to order of relative difficulty established a priori. Subjects (n=157, grade 6, 7 and 8 from two schools) individually completed a compre-hension and a production task in which factors were systematically varied. Also a recognition test on the spelling of the past tense of verbs was administered. The results showed an effect of categories of verbal adjectives in the production task, but only for groups 7 and 8; group 6 was not sensitive to the differences between the categories. In the recognition task, no effect of type of adjective (verbal or normal) was found for groups 7 and 8; but for group 6, performance on verbal adjectives was lower for the three most difficult categories of adjectives. In the production task, all three groups performed lower on verbal adjectives than normal adjectives in the two most difficult categories of adjectives. It turned out that groups which acquired spelling rules for the past tense of verbs to a higher level, made more errors in the spelling of verbal adjectives, especially in the two categories of adjectives which related the strongest to the spelling of verbs. It was concluded that indications were found that negative transfer or interference is present. Authors recommend changing the order of phases in which spelling rules are trained: from 'adjective declension-verb inflection (past tense)-verbal adjective declension' to 'adjective declension (including verbal adjective declension)-verb declension (past tense).

scholarly journals Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)

IMA Fungus ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Claudio G. Ametrano ◽  
Felix Grewe ◽  
Pedro W. Crous ◽  
Stephen B. Goodwin ◽  
Chen Liang ◽  
...  
Keyword(s):  
Character State ◽  
Ancestral Character State ◽  
Wide Range ◽  
Tree Inference ◽  
Ancestral Character State Reconstruction ◽  
Inference Methods ◽  
Genome Scale ◽  
The Impact ◽  
Rock Inhabiting Fungi ◽  
Scale Data

Abstract Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.

Convergence to the tiniest detail: vocal sac structure in torrent-dwelling frogs

2019 ◽  
Author(s):  
Agustín J Elias-Costa ◽  
Julián Faivovich
Keyword(s):  
Background Noise ◽  
Evolutionary History ◽  
Visual Display ◽  
Character State ◽  
Visual Displays ◽  
State Reconstruction ◽  
Ancestral Character State ◽  
History Of ◽  
Ancestral Character State Reconstruction ◽  
Detection And Recognition

Abstract Cascades and fast-flowing streams impose severe restrictions on acoustic communication, with loud broadband background noise hampering signal detection and recognition. In this context, diverse behavioural features, such as ultrasound production and visual displays, have arisen in the evolutionary history of torrent-dwelling amphibians. The importance of the vocal sac in multimodal communication is being increasingly recognized, and recently a new vocal sac visual display has been discovered: unilateral inflation of paired vocal sacs. In the diurnal stream-breeding Hylodidae from the Atlantic forest, where it was first described, this behaviour is likely to be enabled by a unique anatomical configuration of the vocal sacs. To assess whether other taxa share this exceptional structure, we surveyed torrent-dwelling species with paired vocal sacs across the anuran tree of life and examined the vocal sac anatomy of exemplar species across 18 families. We found striking anatomical convergence among hylodids and species of the distantly related basal ranid genera Staurois, Huia, Meristogenys and Amolops. Ancestral character state reconstruction identified three new synapomorphies for Ranidae. Furthermore, we surveyed the vocal sac configuration of other anuran species that perform visual displays and report observations on what appears to be unilateral inflation of paired vocal sacs, in Staurois guttatus – an extremely rare behaviour in anurans.

Is Crew Resource Management Training Effective in Healthcare Settings?

2013 ◽  
Vol 2 (1) ◽  
pp. 105-107 ◽  
Author(s):  
Paul O’Connor ◽  
Angela O’Dea ◽  
Ivan Keogh
Keyword(s):  
Resource Management ◽  
Evaluation Studies ◽  
Meta Analysis ◽  
Empirical Studies ◽  
A Priori ◽  
Crew Resource Management ◽  
Management Training ◽  
Medium Effect ◽  
Healthcare Settings ◽  
Crew Resource Management Training

The healthcare industry has seen a recent proliferation in the adoption of team training, such as crew resource management (CRM). Empirical studies of the effectiveness of CRM-type training in healthcare were subjected to meta-analysis. Fourteen CRM evaluation studies were found to fulfill the a priori criteria for inclusion in the meta-analysis. The metrics of CRM training effectiveness analyzed were: reactions, attitudes, knowledge, behaviors, and organization. CRM trained participants responded positively to CRM, the training had large effects on the participants’ knowledge and behaviors, and a medium effect on their attitudes. The training was also found to have a medium effect on the number of errors/adverse events and a small effect on the time to complete clinical tasks. Although there are methodological limitations that mean the results from this study should be treated with a little caution, the findings are nevertheless encouraging.

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