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La trascendencia social de los derechos de los pacientes ha comportado en España una prolija promulgación legislativa desde el año 2000, que culmina con el desarrollo del documento conocido como testamento vital, de instrucciones previas o de voluntades anticipadas. El fundamento del testamento vital radica en el reconocimiento de la autonomía del paciente. Este respeto va más allá de la situación de competencia del paciente al permitir anticipar situaciones clínicas y sus correspondientes decisiones. El documento de voluntades anticipadas es un documento escrito que refleja un acto de responsabilidad personal, siendo de especial ayuda en enfermos crónicos que pueden evolucionar hacia situaciones de dependencia y deterioro cognitivo. Los profesionales de la salud deben conocer la legislación vigente en materia del principio de autonomía. Resulta esencial que den a conocer a sus pacientes la posibilidad de realizar este procedimiento. Es necesaria una tarea divulgativa y pedagógica ante los profesionales y la población general.

Abstract: Several indices that measure the degree of balance of a rooted phylogenetic tree have been proposed so far in the literature. In this work we define and study a new index of this kind, which we call the total cophenetic index: the sum, over all pairs of different leaves, of the depth of their lowest common ancestor. This index makes sense for arbitrary trees, can be computed in linear time and it has a larger range of values and a greater resolution power than other indices like Colless’ or Sackin’s. We compute its maximum and minimum values for arbitrary and binary trees, as well as exact formulas for its expected value for binary trees under the Yule and the uniform models of evolution. As a byproduct of this study, we obtain an exact formula for the expected value of the Sackin index under the uniform model, a result that seems to be new in the literature. [Copyright &y& Elsevier]

Abstract: Galled trees, evolutionary networks with isolated reticulation cycles, have appeared under several slightly different definitions in the literature. In this paper, we establish the actual relationships between the main four such alternative definitions: namely, the original galled trees, level-1 networks, nested networks with nesting depth 1, and evolutionary networks with arc-disjoint reticulation cycles. [Copyright &y& Elsevier]

Abstract: Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the study of reconstructibility of phylogenetic networks, Moret, Nakhleh, Warnow and collaborators introduced the so-called tripartition metric for phylogenetic networks. In this paper we show that, in fact, this tripartition metric does not satisfy the separation axiom of distances (zero distance means isomorphism, or, in a more relaxed version, zero distance means indistinguishability in some specific sense) in any of the subclasses of phylogenetic networks where it is claimed to do so. We also present a subclass of phylogenetic networks whose members can be singled out by means of their sets of tripartitions (or even clusters), and hence where the latter can be used to define a meaningful metric. [Copyright &y& Elsevier]

Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree of life. The notion of ancestral compatibility of phylogenetic trees with nested taxa was recently introduced. In this paper we analyze in detail the meaning of this compatibility from the points of view of the local structure of the trees, of the existence of embeddings into a common supertree, and of the joint properties of their cluster representations. Our analysis leads to a very simple polynomial-time algorithm for testing this compatibility, which we have implemented and is freely available for download from the BioPerl collection of Perl modules for computational biology.Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree of life. The notion of ancestral compatibility of phylogenetic trees with nested taxa was recently introduced. In this paper we analyze in detail the meaning of this compatibility from the points of view of the local structure of the trees, of the existence of embeddings into a common supertree, and of the joint properties of their cluster representations. Our analysis leads to a very simple polynomial-time algorithm for testing this compatibility, which we have implemented and is freely available for download from the BioPerl collection of Perl modules for computational biology.

Abstract.:  Magarshak et al. represented an RNA molecule as a complex vector and an RNA secondary structure Γ as a complex matrix S Γ in such a way that the molecule represented by was compatible with the secondary structure Γ if and only if . They only considered Watson-Crick base pairs and their representation cannot be extended to allow for G⋅U pairs. In this paper we study a generalization of Magarshak's representation that allows for these pairs, and in particular we provide a family of algebraic structures where that generalization can be carried out. We also show that this representation can be used to compare secondary structures, through transfer matrices which transform the representation of one secondary structure into the representation of the other.

Let Σ be an arbitrary signature and ϒ be a non-empty set of operation symbols within it. A (partial) Σ-algebra is ϒ-total when all its operations in ϒ are total: these are the partly total algebras in the title, and they include total algebras and attributed graphs. In this paper we establish a necessary and sufficient condition on a pair of homomorphisms of ϒ-total Σ-algebras for the existence of a pushout complement of them. This solves the application problem for the double-pushout transformation of these kinds of structure.

The algebraic transformation of hypergraphs, under the so-called double-pushout (DPO) approach, was invented more than two decades ago, and thoroughly developed since then. We introduce in this paper a new approach to DPO algebraic transformation of hypergraphs and, more in general, of unary partial algebras, which generalizes the aforementioned “classical” DPO approach to hypergraph transformation. While the classical approach was based on the (usual) homomorphisms of hypergraphs, our new approach is based on the total conformisms, a type of morphisms of hypergraphs imported from the theory of partial algebras, which can be described, roughly speaking, as those mappings between hypergraphs that “reflect” the structure of the target object. In this paper we give both an algebraic and an operational characterization of this new DPO transformation, first for unary partial algebras and then, as a particular case, for hypergraphs. We also study its abstract properties related to parallelism and concurrency through the determination of the HLR conditions it satisfies with respect to several natural classes of morphisms.

The cophenetic metrics d φ, p , for p  ∈ {0} ∪ [1, ∞), are a recent addition to the kit of available distances for the comparison of phylogenetic trees. Based on a fifty years old idea of Sokal and Rohlf, these metrics compare phylogenetic trees on a same set of taxa by encoding them by means of their vectors of cophenetic values of pairs of taxa and depths of single taxa, and then computing the L p norm of the difference of the corresponding vectors. In this paper we compute the expected value of the square of d φ,2 on the space of fully resolved rooted phylogenetic trees with n leaves, under the Yule and the uniform probability distributions. [ABSTRACT FROM AUTHOR]

Abstract: Hybridization networks are representations of evolutionary histories that allow for the inclusion of reticulate events like recombinations, hybridizations, or lateral gene transfers. The recent growth in the number of hybridization network reconstruction algorithms has led to an increasing interest in the definition of metrics for their comparison that can be used to assess the accuracy or robustness of these methods. In this paper we establish some basic results that make it possible the generalization to tree-child time consistent (TCTC) hybridization networks of some of the oldest known metrics for phylogenetic trees: those based on the comparison of the vectors of path lengths between leaves. More specifically, we associate to each hybridization network a suitably defined vector of ‘splitted’ path lengths between its leaves, and we prove that if two TCTC hybridization networks have the same such vectors, then they must be isomorphic. Thus, comparing these vectors by means of a metric for real-valued vectors defines a metric for TCTC hybridization networks. We also consider the case of fully resolved hybridization networks, where we prove that simpler, ‘non-splitted’ vectors can be used. [Copyright &y& Elsevier]

The Colless index for bifurcating phylogenetic trees, introduced by Colless (1982), is defined as the sum, over all internal nodes v of the tree, of the absolute value of the difference of the sizes of the clades defined by the children of v. It is one of the most popular phylogenetic balance indices, because, in addition to measuring the balance of a tree in a very simple and intuitive way, it turns out to be one of the most powerful and discriminating phylogenetic shape indices. But it has some drawbacks. On the one hand, although its minimum value is reached at the so-called maximally balanced trees, it is almost always reached also at trees that are not maximally balanced. On the other hand, its definition as a sum of absolute values of differences makes it difficult to study analytically its distribution under probabilistic models of bifurcating phylogenetic trees. In this paper we show that if we replace in its definition the absolute values of the differences of clade sizes by the squares of these differences, all these drawbacks are overcome and the resulting index is still more powerful and discriminating than the original Colless index. • We define a modification of the classical Colless index for bifurcating trees. • Our Q-Colless index classifies as most balanced exactly the maximally balanced trees. • Our Q-Colless index has a larger resolutive power than the Colless index. • We give closed formulas for its first moments under the Yule and uniform models. [ABSTRACT FROM AUTHOR]