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Rineau, V.

Publications and source records attributed to Rineau, V..

3 recordsLinked to original sources

Cladistic hypotheses as degree of equivalence relational structures: implications for three-itemstatements

Three-item statements, as minimal informative rooted binary phylogenetic trees on three items, are the minimal units of cladistic information. Their importance for phylogenetic reconstruction, consensus and supertree methods relies on both (i) the fact that any cladistic tree can always be decomposed into a set of three-item statements, and (ii) the possibility, at least under some conditions, to build a new cladistic tree by combining all or part of the three-item statements deduced from several prior cladistic trees. In order to formalise such procedures, several k-adic rules of inference, i.e., rules that allow us to deduce at least one new three-item statement from exactly k other ones, have been identified. However, no axiomatic background has been proposed, and it remains unknown if a particular k-adic rule of inference can be reduced to more basic rules. In order to solve this problem, we propose here to define three-item statements in terms of degree of equivalence relations. Given both the axiomatic definition of the latter and their strong connection to hierarchical classifications, we establish a list of the most basic properties for three-item statements. With such an approach, we show that it is possible to combine five three-item statements from basic rules although they are not combinable only from dyadic rules. Such a result suggests that all higher k-adic rules are well reducible to a finite set of simpler rules.

evolutionary biology

Rethinking Pleijel's (1995) characters under a hierarchical point of view

In 1995, Pleijel raised an issue on the coding of complex (multistate) characters: to find a unique coding approach satisfying both informational and semantical criteria. Following Pleijels work, this study aims to propose a new answer to this problematic. We proposed here to use hierarchical characters instead of classical partitional ones as hierarchy allows to deal effectively with the different uncertainties met by phylogeneticists since the beginning of phylogenetic data matrices: missing data, inapplicable data and polymorphism. We translated all previous proposed approaches into hierarchical ones and add three new approaches, only coded using hierarchy. Using phylogenetic and show with different metric how one of these new approaches displaces the other ones. The results from this study then supports the idea than phylogenetic characters should be coded using only hierarchies, as they offer a better management of uncertainties and propose new approaches more informative.

evolutionary biology

Information Content of Trees: Three-taxon Statements Inference Rules and Dependency

AO_SCPLOWBSTRACTC_SCPLOWThe three-taxon statement is the fundamental unit of rooted trees in Cladistics, stating that for three terminal taxa, two are more related to each other than to a third. Because of their fundamental role in phylogenetics, three-taxon statements are present in methodological research of various disciplines in evolutionary biology, as in consensus methods, supertree methods, species-tree methods, distance metrics, and even phylogenetic reconstruction. However, three-taxon statements methods are subject to important flaws related to information redundancy. We aim to study the behavior of three-taxon statements and the interactions among them in order to enhance their performance in evolutionary studies. We show here how specific interactions between three-taxon statements are responsible of the emergence of redundancy and dependency within trees, and how they can be used for the improvement of weighting procedures. Our proposal is subsequently empirically tested in the supertree framework using simulations. We show that three-taxon statements using fractional weights perform drastically better than classical methods such as MRP or methods using unweighted statements. Our study shows that appropriate fractional weighting of three taxon statements is of critical importance for removing redundancy in any method using three-taxon statements, as in consensus, supertrees, distance metrics, and phylogenetic or biogeographic analyses.

evolutionary biology