En los últimos años, algunos autores han venido sosteniendo que la validez de la representación arborescente del patrón filético generado por la evolución está siendo menoscabada por el reconocimiento del impacto evolutivo que tendrían la transferencia genética horizontal, la simbiogénesis, la especiación por hibridación y la introgresión. Esa concepción o representación cladogenética de la evolución sólo nos dejaría ver un aspecto parcial de las relaciones de filiación que conectan a los diferentes linajes de seres vivos; ocultando otro aspecto cuya representación (...) más adecuada sería un reticulado de relaciones entre taxones. Con todo, aún sin poner en tela de juicio la frecuencia y la relevancia explicativa de dichos fenómenos, en este trabajo se intentará mostrar que su admisión y reconocimiento no tiene por qué ir en detrimento de esa concepción cladogenética de la evolución cuya relativización se está pregonando. Por el contrario, la comprensión y la representación de tales fenómenos supone dicha concepción. Palabras clave: Filogénesis, Especiación por hibridación, Introgresión, Simbiogénesis, TGH. (shrink)

All disciplines must define their basic units and core processes. In evolutionary biology, the core process is natural selection and the basic unit of selection and adaptation is the individual. To operationalize the theory of natural selection we must count individuals, as they are the bearers of fitness. While canonical individuals have often been taken to be multicellular organisms, the hierarchy of life shows that new kinds of individuals have evolved. A variety of criteria have been used to define biological (...) individuality. Some criteria rely on the presence/absence of a particular property while others advocate an approach that reflects the process of natural selection. The plethora of approaches to classifying individuality has resulted in confusion regarding how to study individuality in a given taxon. (shrink)

Nous proposons dans cet article une caractérisation, à notre connaissance, nouvelle, d’une distorsion cognitive : la requalification dans le même pôle. Une telle caractérisation prend place au sein du modèle général des distorsions cognitives (Franceschi, 2007). Nous commençons par définir un modèle étendu des distorsions cognitives, intégrant les éléments du cadre conceptuel des matrices de concepts (Franceschi, 2002), afin de permettre une définition élargie du système de taxons. Nous nous attachons ensuite à définir la requalification dans le même pôle et (...) à la distinguer d’une distorsion cognitive voisine : la requalification dans l’autre pôle. (shrink)

-/- Species lists play an important role in biology and practical domains like conservation, legislation, biosecurity and trade regulation. However, their effective use by non-specialist scientific and societal users is sometimes hindered by disagreements between competing lists. While it is well-known that such disagreements exist, it remains unclear how prevalent they are, what their nature is, and what causes them. In this study, we argue that these questions should be investigated using methods based on taxon concept rather than methods (...) based on Linnaean names, and use such a concept-based method to quantify disagreement about bird classification and investigate its relation to research effort. We found that there was disagreement about 38% of all groups of birds recognized as a species, more than three times as much as indicated by previous measures. Disagreement about the delimitation of bird groups was the most common kind of conflict, outnumbering disagreement about nomenclature and disagreement about rank. While high levels of conflict about rank were associated with lower levels of research effort, this was not the case for conflict about the delimitation of bird groups. This suggests that taxonomic disagreement cannot be resolved simply by increasing research effort. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental (...) stages across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a (...) post-translational modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)