War and peace in phylogenetics: a rejoinder on total evidence and consensus

Abstract.-For more than 10 years, systematists have been debating the superiority of character or taxonomic congruence in phylogenetic analysis. In this paper, we demonstrate that the competing approaches can converge to the same solution when a consensus method that accounts for branch lengths is selected. Thus, we propose to use both methods in combination, as a way to corroborate the results of combined and separate analyses. We could engage in this debate by opting for character congruence, taxonomic congruence, or the conditional combination approach. Rather, we prefer to suggest using combined and separate analyses jointly, as proposed by de Queiroz (1993; see also Larson, 1994). Interestingly, a distance-based procedure relying on the average consensus has been applied successfully by Lapointe et al. (1999) to combine either trees or data matrices in a coherent fashion. This hybrid procedure is defined as a global congruence approach (see Lapointe, 1998b) because it assesses neither the congruence among characters nor that among individual phylogenies; rather, it evaluates the congruence between total evidence and consensus trees. This approach can thus be used to cross-corroborate the trees obtained by combined and separate analyses. In the present paper, we apply the socalled global congruence approach to a wide variety of published datasets sampled from the systematic literature, using a uniform 88

Introducing Trait Networks to Elucidate the Fluidity of Organismal Evolution Using Palaeontological Data

International audienceExplaining the evolution of animals requires ecological, developmental, paleontological, and phylogenetic considerations because organismal traits are affected by complex evolutionary processes. Modeling a plurality of processes, operating at distinct timescales on potentially interdependent traits, can benefit from approaches that are complementary treatments to phylogenetics. Here, we developed an inclusive network approach, implemented in the command line software ComponentGrapher, and analyzed trait co-occurrence of rhinocerotoid mammals. We identified stable, unstable, and pivotal traits, as well as traits contributing to complexes, that may follow to a common developmental regulation, that point to an early implementation of the postcranial Bauplan among rhinocerotoids. Strikingly, most identified traits are highly dissociable, used repeatedly in distinct combinations and in different taxa, which usually do not form clades. Therefore, the genes encoding these traits are likely recruited into novel gene regulation networks during the course of evolution. Our evo-systemic framework, generalizable to other evolved organizations, supports a pluralistic modeling of organismal evolution, including trees and networks

Quand les bactéries font la loi : regards éthiques, épistémiques, juridiques, politiques, sociales et techniques sur l’utilisation du microbiome humain à des fins judiciaires

L’utilisation du microbiome humain à des fins judiciaires comme objet d’étude implique divers enjeux allant d’une remise en question de notre conception traditionnelle de l’identité au respect de la vie privée, en passant par le type de consentement à recueillir lors du prélèvement d’un échantillon de microbiome. La particularité de cette étude nécessite le travail conjoint d’une équipe multidisciplinaire composée de spécialistes en éthique, criminalistique, droit, microbiologie, philosophie et science politique

Hybrids and phylogenetics revisited: A statistical test of hybridization using quartets

International audienceThe occurrence of reticulations in the evolutionary history of species poses serious challenges for all modern practitioners of phylogenetic analysis. Such events, including hybridization, introgression, and lateral gene transfer, lead to evolutionary histories that cannot be adequately represented in the form of phylogenetic trees. Although numerous methods that allow for the reconstruction of phylogenetic networks have been proposed in recent years, the detection of reticulations still remains problematic. In this paper we present a Hybrid Detection Criterion (HDC) along with a statistical procedure that allows for the identification of hybrid taxa. The test assesses whether a putative hybrid is consistently intermediate between its postulated parents, with respect to the other taxa. The performance of the statistical method is evaluated using known hybrids of the genus Aphelandra (Acanthaceae) using two network methods: reticulograms and split decomposition graphs. Our results indicate that the HDC test is reliable when used jointly with split decomposition. On the other hand, the test lacks power and provides misleading results when using reticulograms. We then show how the procedure can be used as a tool to identify putative hybrids

Seeing the trees for the network: Consensus, information content, and superphylogenies

International audiencePhylogenetic inference often leads to solutions made up of multiple trees on a given set of leaves or taxa. These competing hypotheses might be the equally optimal trees obtained from the analysis of a single matrix using maximum parsimony (Hennig, 1979) or maximum likelihood (Felsenstein, 1981) or the set of most probable trees produced by Bayesian analysis (Rannala and Yang, 1996; Larget and Simon, 1999; Mau et al., 1999). They might also have been inferred independently from different data sets or even be the result of resampling methods such as the bootstrap or the jackknife (Felsenstein, 1985; Penny and Hendy, 1985, 1986). Consensus methods are commonly used to identify areas of conflict and agreement among such multiple trees; they can represent the relationships that are supported either unanimously or by a majority of trees while discarding other, less supported relationships (Bryant, 2003). Thus, a consensus method is usually defined as a function that takes as input a set, or profile, of trees on the same set of taxa and returns a single tree on the same set of taxa (Leclerc and Cucumel, 1987; Steel et al., 2000; Bryant, 2003). This function can take different forms, and many consensus methods have been proposed (see Swofford, 1991; Bryant, 2003, for reviews), amongst which the strict consensus (Sokal and Rohlf, 1981) and majority-rule consensus (Margush and McMorris, 1981) are perhaps the most widely used and understood. These various functions differ in two major respects: (1) the kind of information they preserve and (2) the way they deal with conflict among input trees. Indeed, the information contained in a tree can be considered in terms of nesting, three- or four-taxon statements, components, and branch lengths, while conflict can be left unresolved or dealt with using different criteria (Bryant, 2003). Notwithstanding these differences, most methods abide to the prevailing phylogenetic model: that of a tree embedding a hierarchy of descent. This model puts forward a fully resolved, or binary, tree as the ideal representation of evolution. In practice, consensus trees are seldom binary and they embed—i.e., are compatible with—multiple binary trees. Indeed, because it is often impossible to distinguish between hard and soft polytomies (Nelson and Platnick, 1980; Maddison, 1989) and because the latter can be resolved in a number of different ways, an unresolved tree can be refined by a set of binary trees (Rohlf, 1982; Mickevich and Platnick, 1989; Steel et al., 2000)

Missing data in craniometrics: a simulation study

International audienceCraniometric measurements represent a useful tool for studying the differentiation of mammal populations. However, the fragility of skulls often leads to incomplete data matrices. Damaged specimens or incomplete sets of measurements are usually discarded prior to statistical analysis. We assessed the performance of two strategies that avoid elimination of observations: (1) pairwise deletion of missing cells, and (2) estimation of missing data using available measurements. The effect of these distinct approaches on the computation of inter-individual distances and population differentiation analyses were evaluated using craniometric measurements obtained from insular populations of deer mice Peromyscus maniculatus (Wagner, 1845). In our simulations, Euclidean distances were greatly altered by pairwise deletion, whereas Gower's distance coefficient corrected for missing data provided accurate results. Among the different estimation methods compared in this paper, the regression-based approximations weighted by coefficients of determination (r(2)) outperformed the competing approaches. We further show that incomplete sets of craniometric measurements can be used to compute distance matrices, provided that an appropriate coefficient is selected. However, the application of estimation procedures provides a flexible approach that allows researchers to analyse incomplete data sets

Phylogeographic Structure of the White-Footed Mouse and the Deer Mouse, Two Lyme Disease Reservoir Hosts in Québec.

Modification of a species range is one of many consequences of climate change and is driving the emergence of Lyme disease in eastern Canada. The primary reservoir host of the bacteria responsible for Lyme disease, Borrelia burgdorferi, is the white-footed mouse (Peromyscus leucopus), whose range is rapidly shifting north into southern Québec. The deer mouse, P. maniculatus, is occurring over most Québec province and is a less competent host for B. burgdorferi. Here, we compared the phylogeographic structure of both Peromyscus species in Québec. Using a combination of multiple mitochondrial DNA markers and phylogeographic methods, we detected an ongoing and rapid expansion of P. leucopus, while P. maniculatus appears more stable. Haplotype and populations networks indicated that populations of P. maniculatus exhibit more genetic structure than P. leucopus across the study area. Furthermore, significant and consistent genetic divergences between populations of the two species on both sides of the St. Lawrence River suggest that distinct lineages of P. leucopus and P. maniculatus with different ancestral origins colonized Southern Québec following the Last Glacial Maximum. The phylogeographic structure of pathogens is expected to mirror the structure observed in their reservoir hosts. As different strains of Borrelia burgdorferi may be associated with different levels of pathogenicity and immune responses of their hosts, our results are helpful at better understanding the pattern of spread of Lyme disease in a zone of emergence, and associated risk for human populations

CompositeSearch: A Generalized Network Approach for Composite Gene Families Detection

International audienceGenes evolve by point mutations, but also by shuffling, fusion, and fission of genetic fragments. Therefore, similarity between two sequences can be due to common ancestry producing homology, and/or partial sharing of component fragments. Disentangling these processes is especially challenging in large molecular data sets, because of computational time. In this article, we present CompositeSearch, a memory-efficient, fast, and scalable method to detect composite gene families in large data sets (typically in the range of several million sequences). CompositeSearch generalizes the use of similarity networks to detect composite and component gene families with a greater recall, accuracy, and precision than recent programs (FusedTriplets and MosaicFinder). Moreover, CompositeSearch provides user-friendly quality descriptions regarding the distribution and primary sequence conservation of these gene families allowing critical biological analyses of these data

El tenis en la escuela

Se pretende acercar a la escuela el deporte del tenis a través de una propuesta en la que el profesor de educación física disponga de las herramientas necesarias para articular la actividad sin grandes conocimientos técnicos. El objetivo es pretender la mejora del repertorio motor del alumno a través de una serie de prácticas que entrañen la resolución de propuestas que comprometan los procesos de toma de decisiones, análisis de situaciones, colaboración, oposición,etc., olvidándonos de aspectos técnicos sobre la ejecución de los gestos específicos del deporte que se va a desarrollar. La estructura del texto pasa por una justificación del porqué el tenis como un contenido más del currículo escolar, pasando luego a exponer elementos propios del deporte, desde los aspectos históricos hasta los estructurales o el reglamento, aportando un conocimiento básico sobre esta modalidad deportiva. A continuación se plantean las etapas del tenis en el marco escolar (golpes básicos del tenis, estilos de enseñanza aplicados al tenis,etc.) para finalizar proponiendo el desarrollo de dos unidades didácticas para la etapa de Primaria a modo de ejemplo.CataluñaBiblioteca de Educación del Ministerio de Educación, Cultura y Deporte; Calle San Agustín 5 -3 Planta; 28014 Madrid; Tel. +34917748000; [email protected]

Primers used for amplifying the five mtDNA regions used in this study.

<p>Primers used for amplifying the five mtDNA regions used in this study.</p