Hierarchical Characters Research Articles

Revealing Evolutionary Patterns Behind Homogeneity: the Case of the Palaeolithic Assemblages from Notarchirico (Southern Italy)

Notarchirico is at a nodal point in time and space for understanding the settlement of Europe in terms of migration or in situ evolution. Former technological analyses have not shown significant differences between the different lithic assemblages at Notarchirico. Our approach here is to produce a phylogenetic analysis of the lithic assemblages taken as the terminal of the analysis and interpreted as cultural units. In the cladistic framework, characters are hypotheses of relationships between lithic assemblages, and homologies are hypotheses of relationships between lithic objects: cores, flakes, nodules. To effectively grasp informative lithic innovations in the assemblages, we formalise cladistic hypotheses as hierarchical characters in the framework of three-item analysis and propose a new algorithm to remove the high number of repeated terminals among trees inherent to a cladistic analysis of assemblages. Beyond the classic distinction of the presence or absence of bifaces, our analysis of the five Notarchirico layers, dated between 670 and 700 ka, highlights a well-supported cladogram grounded on complex hierarchical characters on lithic artefacts. This cladogram shows a paralogy event between the flake-free layer H, representing short-term occupancy, and the other layers representing long-term settlements. The resulting cladogram shows that relationships between lithic assemblages at Notarchirico do not follow the stratigraphy. Moreover, the Notarchirico lithic assemblages cannot be explained in an entirely local way, but seem to be part of a more complex European history.

Peptide Self-Assembled Nanostructures: From Models to Therapeutic Peptides.

Self-assembly is the most suitable approach to obtaining peptide-based materials on the nano- and mesoscopic scales. Applications span from peptide drugs for personalized therapy to light harvesting and electron conductive media for solar energy production and bioelectronics, respectively. In this study, we will discuss the self-assembly of selected model and bioactive peptides, in particular reviewing our recent work on the formation of peptide architectures of nano- and mesoscopic size in solution and on solid substrates. The hierarchical and cooperative characters of peptide self-assembly will be highlighted, focusing on the structural and dynamical properties of the peptide building blocks and on the nature of the intermolecular interactions driving the aggregation phenomena in a given environment. These results will pave the way for the understanding of the still-debated mechanism of action of an antimicrobial peptide (trichogin GA IV) and the pharmacokinetic properties of a peptide drug (semaglutide) currently in use for the therapy of type-II diabetes.

Incorporating Hierarchical Characters into Phylogenetic Analysis.

Popular optimality criteria for phylogenetic trees focus on sequences of characters that are applicable to all the taxa. As studies grow in breadth, it can be the case that some characters are applicable for a portion of the taxa and inapplicable for others. Past work has explored the limitations of treating inapplicable characters as missing data, noting that this strategy may favor trees where internal nodes are assigned impossible states, where the arrangement of taxa within subclades is unduly influenced by variation in distant parts of the tree, and/or where taxa that otherwise share most primary characters are grouped distantly. Approaches that avoid the first two problems have recently been proposed. Here, we propose an alternative approach which avoids all three problems. We focus on data matrices that use reductive coding of traits, that is, explicitly incorporate the innate hierarchy induced by inapplicability, and as such our approach extend to hierarchical characters, in general. In the spirit of maximum parsimony, the proposed criterion seeks the phylogenetic tree with the minimal changes across any tree branch, but where changes are defined in terms of dissimilarity metrics that weigh the effects of inapplicable characters. The approach can accommodate binary, multistate, ordered, unordered, and polymorphic characters. We give a polynomial-time algorithm, inspired by Fitch's algorithm, to score trees under a family of dissimilarity metrics, and prove its correctness. We show that the resulting optimality criteria is computationally hard, by reduction to the NP-hardness of the maximum parsimony optimality criteria. We demonstrate our approach using synthetic and empirical data sets and compare the results with other recently proposed methods for choosing optimal phylogenetic trees when the data includes hierarchical characters. [Character optimization, dissimilarity metrics, hierarchical characters, inapplicable data, phylogenetic tree search.].

‘Confucianization of law’ revisited

ABSTRACT The emphases of ritual, morality, and hierarchical relationships in imperial Chinese law are usually attributed to a process of “Confucianization of law” in Han dynasty. However, an interdisciplinary look at the notion of the ‘Confucianization of law’ from philosophical texts and legal materials will prove the vulnerability of such a simple conclusion. Philosophically, the Han dynasty saw first a politicization of Confucianism, which distinguished Han Confucianism from the Confucianism of previous generations. There was in fact a great contrast between Confucian ideals and Confucianization of law. Furthermore, by reading of Qin Law through the archeological material Shuihudi Qin Bamboo Texts, it can be seen that values we might label as Confucian existed already in Qin Law. These two considerations prove that simply attributing the moral and hierarchical characters of the imperial Chinese law to the single source of Confucianism does not do justice to the richness of the subject.

One-step fabrication of in situ carbon-coated NiCo2O4@C bilayered hybrid nanostructural arrays as free-standing anode for high-performance lithium-ion batteries

Rapid developments in revolutionary electric vehicles have led to an increase in the energy-density and cycling-life requirements for Li-ion batteries (LIBs). The binary transition metal oxide NiCo2O4 is attracting considerable attention due to its much larger specific capacity than graphite. However, NiCo2O4 suffers from poor cycling performance owing to a large volume change during cycling. To address this problem, we proposed an easy strategy to fabricate in situ carbon-coated NiCo2O4 bilayered hybrid nanostructural arrays supported on Ni foam (denoted as NiCo2O4@C BHNAs–NF) as free-standing anodes for LIBs through a sucrose-assisted hydrothermal method. The in situ-synthesized uniform carbon shell can simultaneously buffer the volume change during cycling and increase the conductivity. The micro/nano-structure also possessed outstanding structural advantages, such as large surface area and hierarchical porous characters, enabling NiCo2O4@C BHNAs–NF to have excellent electrochemical performance. Its capacity can reach 1298 mAh/g at a current density of 100 mA/g, and 86% of the initial capacity can be retained after 100 cycles. All these results revealed that NiCo2O4@C BHNAs–NF was a promising candidate anode for next-generation LIBs.

A class of vertex–edge-growth small-world network models having scale-free, self-similar and hierarchical characters

The problem of uncovering the internal operating function of network models is intriguing, demanded and attractive in researches of complex networks. Notice that, in the past two decades, a great number of artificial models are built to try to answer the above mentioned task. Based on the different growth ways, these previous models can be divided into two categories, one type, possessing the preferential attachment, follows a power-law P(k)∼k−γ, 2<γ<3. The other has exponential-scaling feature, P(k)∼α−k. However, there are no models containing above two kinds of growth ways to be presented, even the study of interconnection between these two growth manners in the same model is lacking. Hence, in this paper, we construct a class of planar and self-similar graphs motivated from a new attachment way, vertex–edge-growth network-operation, more precisely, the couple of both them. We report that this model is sparse, small world and hierarchical. And then, not only is scale-free feature in our model, but also lies the degree parameter γ(≈3.242) out the typical range. Note that, we suggest that the coexistence of multiple vertex growth ways will have a prominent effect on the power-law parameter γ, and the preferential attachment plays a dominate role on the development of networks over time. At the end of this paper, we obtain an exact analytical expression for the total number of spanning trees of models and also capture spanning trees entropy which we have compared with those of their corresponding component elements.

When Homoplasy Is Not Homoplasy: Dissecting Trait Evolution by Contrasting Composite and Reductive Coding.

The conceptualization and coding of characters is a difficult issue in phylogenetic systematics, no matter which inference method is used when reconstructing phylogenetic trees or if the characters are just mapped onto a specific tree. Complex characters are groups of features that can be divided into simpler hierarchical characters (reductive coding), although the implied hierarchical relational information may change depending on the type of coding (composite vs. reductive). Up to now, there is no common agreement to either code characters as complex or simple. Phylogeneticists have discussed which coding method is best but have not incorporated the heuristic process of reciprocal illumination to evaluate the coding. Composite coding allows to test whether 1) several characters were linked resulting in a structure described as a complex character or trait or 2) independently evolving characters resulted in the configuration incorrectly interpreted as a complex character. We propose that complex characters or character states should be decomposed iteratively into simpler characters when the original homology hypothesis is not corroborated by a phylogenetic analysis, and the character or character state is retrieved as homoplastic. We tested this approach using the case of fruit types within subfamily Cinchonoideae (Rubiaceae). The iterative reductive coding of characters associated with drupes allowed us to unthread fruit evolution within Cinchonoideae. Our results show that drupes and berries are not homologous. As a consequence, a more precise ontology for the Cinchonoideae drupes is required.

Molecular classification based on apomorphic amino acids (Arthropoda, Hexapoda): Integrative taxonomy in the era of phylogenomics.

With the great development of sequencing technologies and systematic methods, our understanding of evolutionary relationships at deeper levels within the tree of life has greatly improved over the last decade. However, the current taxonomic methodology is insufficient to describe the growing levels of diversity in both a standardised and general way due to the limitations of using only morphological traits to describe clades. Herein, we propose the idea of a molecular classification based on hierarchical and discrete amino acid characters. Clades are classified based on the results of phylogenetic analyses and described using amino acids with group specificity in phylograms. Practices based on the recently published phylogenomic datasets of insects together with 15 de novo sequenced transcriptomes in this study demonstrate that such a methodology can accommodate various higher ranks of taxonomy. Such an approach has the advantage of describing organisms in a standard and discrete way within a phylogenetic framework, thereby facilitating the recognition of clades from the view of the whole lineage, as indicated by PhyloCode. By combining identification keys and phylogenies, the molecular classification based on hierarchical and discrete characters may greatly boost the progress of integrative taxonomy.