Éditeur(s) : HAL CCSD
Résumé : International audience
It is now well recognized that information management systems often deal with geographic information even if they often do not take advantage of it. In these systems, requirements engineering (RE) is becoming more and more important in helping stakeholders to model their requirements regarding the quality of the data.However, to date, few RE projects take geographic information and geographic constraints into account. We thus propose to study in this paper the question of managing such geographic constraints in the framework of RE. We propose an extension of the RE model and its implementation within the KAOS framework, and the use of geographic ontologies
2nd International Conference on Knowledge Management, Information and Knowledge Systems
Hammamet, Tunisia

lirmm-01230140
https://hal-lirmm.ccsd.cnrs.fr/lirmm-01230140

Éditeur(s) : HAL CCSD
Résumé : Spermatogenesis in mammals is a complex biological function including cellular processes such as proliferation, meiosis and differentiation, aiming to the production of male gametes in the testis. If the seminiferous epithelium is well described in terms of organization and cellular morphology of cells that compose it, the processes by which undifferentiated diploid germ cells enter meiosis and give haploid cells that undergo many morphological transformations, are not fully decrypted. These processes rely on the coordinated and sequential expression of genes, including specific products for each stage of germ cell development These gene products are essential at each key stage of spermatogenesis. Transcriptomics since the 1990s, and proteomics since the 2000s have contributed to the improved. understanding of these mechanisms. A long term proteomic study aiming at characterizing the proteomes of Sertoli cells and germ cells, and a recent study that characterized and quantified the transcriptome of isolated rat testicular cells at high resolution using de novo sequencing of transcripts (RNA-Seq), have been the basis of my thesis work. The latter study showed the accumulation of long non-Coding RNAs (lncRNAs) and testicular unannotated transcripts (TUTs) at meiotic and post-Meiotic stages of spermatogenesis in the rat. In this context, my thesis work aimed at validating the coding potential of many genes expressed in germ cells using RNA-Seq combined with shotgun proteomics, a so-Called PIT (Proteomics Informed by transcriptomics) approach. In this approach, the protein sequences translated from the transcripts assembled by RNA-Seq in the different testicular cell types are integrated into a custom database of protein sequences used to query mass spectrometry data obtained from proteins of meiotic and post-Meiotic cells. The PIT approach showed that 69 TUTs or lncRNA (corresponding to 44 loci) code for proteins in meiotic cells and post meiotic cells, and we confirmed experimentally the meiotic and post-Meiotic expression for two new transcripts encoding for VAMP9, a protein of the SNARE family, and a new testicular enolase T-ENOL. The post-Meiotic expression of T-ENOL protein was confirmed by immunohistochemistry using a polyclonal antibody raised against the recombinant protein. This approach also allowed us to identify new isoforms of known proteins, specific to each stage of spermatogenesis. Germ cells and Sertoli cells maintain a dialogue which is necessary to the success of spermatogenesis and spermiogenesis. Another part of my work aimed at identifying membrane proteins, in germ cells and residual bodies, that may be involved in the dialogue between Sertoli cells and germ cells, using a ICPL relative quantification proteomic approach. The ICPL analysis enabled us to establish a list of 166 proteins whose expression is differential between pachytene spermatocytes, round spermatids and residual bodies. Their differential expression suggests that these proteins may play a role in spermiogenesis. Thanks to the Gene Ontology annotations, a list of 8 proteins with a putative role in signal transduction, cell recognition or differentiation, thus potentially involved in the dialogue between Sertoli and germ cells was drawn. In addition, I provided a first proteome of rat Sertoli cells, germ cells and residual bodies obtained by shotgun proteomics.
La spermatogenèse chez les mammifères est une fonction biologique complexe incluant des processus de prolifération cellulaire, de méiose et de différenciation uniques visant à la production des gamètes mâles au sein du testicule. Si l’épithélium séminifère est bien décrit sur le plan de son organisation et de la morphologie des cellules qui le composent, les processus par lesquels les cellules germinales diploïdes indifférenciées entrent en méiose pour donner ensuite des cellules haploïdes subissant par la suite de nombreuses transformations morphologiques, ne sont pas totalement décryptés. Ils reposent sur l’expression coordonnée et séquentielle de gènes dont les produits spécifiques de chaque stade de développement des cellules germinales sont essentiels aux étapes clés de la spermatogenèse. La transcriptomique depuis les années 1990 et la protéomique depuis les années 2000 ont contribué à l’amélioration de la connaissance de ces mécanismes. Une étude protéomique visant à caractériser par des approches systématiques et différentielles les protéomes des cellules de Sertoli et de la lignée germinale, et d’autre part une étude récente, réalisée dans notre unité, qui a permis de caractériser et de quantifier le transcriptome des cellules testiculaires isolées de rat en utilisant le séquençage de novo des transcrits (RNA-Seq), ont été à la base de mes travaux de thèse. Cette dernière étude a mis en évidence l’accumulation de longs ARNs non codants (lncRNAs) et de transcrits testiculaires non annotés (TUTs) aux stades méiotique et post- méiotique de la spermatogenèse chez le rat. Dans ce contexte, mon travail a consisté à valider le potentiel codant de nombreux gènes exprimés dans les cellules germinales par une approche dite PIT (Proteomics Informed by Transcriptomics) couplant protéomique Shotgun et RNA-Seq. Dans ce type d’approche, les séquences protéiques déduites des transcrits des différents types cellulaires, assemblés par RNA-Seq, sont intégrées dans une base personnalisée de séquences protéiques utilisée pour interroger les données de spectrométrie de masse obtenues à partir de protéines de cellules méiotiques et post-Méiotiques. L’approche PIT a permis de montrer que 69 TUTs ou lncRNA (correspondant à 44 loci) codent pour des protéines dans les cellules méiotiques et post méiotiques. L’expression post-Méiotique de deux nouveaux transcrits, l’un codant pour la protéine VAMP9, une protéine de la famille SNARE, et l’autre pour une nouvelle énolase T-ENOL a pu être confirmée. L’expression post-Méiotique de T-ENOL a été confirmée par immunohistochimie à l’aide d’un anticorps polyclonal produit contre la protéine recombinante. Cette approche nous a également permis d’identifier de nouvelles isoformes de protéines connues spécifiques de chaque stade de la spermatogenèse. Les cellules germinales et les cellules de Sertoli entretiennent le dialogue nécessaire au bon déroulement de la spermatogenèse. Une autre partie de mon travail a consisté à identifier des protéines membranaires des cellules germinales et des corps résiduels, susceptibles d’intervenir dans le dialogue entre les cellules de Sertoli et les cellules germinales, par une approche protéomique de quantification relative ICPL. Cette approche a permis d’établir une liste de 166 protéines différentiellement exprimées entre les spermatocytes pachytène, les spermatides rondes et les corps résiduels, qui sont susceptibles de jouer un rôle dans la spermiogénèse. Grâce aux annotations de le Gene Ontology, j’ai pu établir une liste de 8 protéines ayant un rôle supposé dans la transduction du signal, la reconnaissance cellulaire ou bien la différenciation. Par ailleurs, j’ai pu établir par protéomique Shotgun un premier protéome des cellules de Sertoli, des cellules germinales et des corps résiduels chez le rat.
https://tel.archives-ouvertes.fr/tel-01127389

Droits : info:eu-repo/semantics/OpenAccess
NNT : 2014REN1S064
tel-01127389
https://tel.archives-ouvertes.fr/tel-01127389
https://tel.archives-ouvertes.fr/tel-01127389/document
https://tel.archives-ouvertes.fr/tel-01127389/file/2014REN1S064.pdf

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Cell proliferation is a hallmark of cancer and depends on complex signaling networks that are chiefly supported by protein kinase activities. Therapeutic strategies have been used to target specific kinases but new methods are required to identify combined targets and improve treatment. Here, we propose a small interfering RNA genetic screen and an integrative approach to identify kinase networks involved in the proliferation of cancer cells. The functional siRNA screen of 714 kinases in HeLa cells identified 91 kinases implicated in the regulation of cell growth, most of them never being reported in previous whole-genome siRNA screens. Based on gene ontology annotations, we have further discriminated between two classes of kinases that, when suppressed, result in alterations of the mitotic index and provoke cell-cycle arrest. Extinguished kinases that lead to a low mitotic index mostly include kinases implicated in cytosolic signaling. In contrast, extinguished kinases that result in a high mitotic index mostly include kinases implicated in cell division. By mapping hit kinases in the PhosphPOINT phosphoprotein database, we generated scale-free networks consisting of 449 and 661 protein-protein interactions for kinases from low MI and high MI groups, respectively. Further analyses of the kinase interactomes revealed specific modules such as FER- and CRKL-containing modules that connect three members of the epidermal growth factor receptor (EGFR) family, suggesting a tight control of the mitogenic EGF-dependent pathway. Based on experimental studies, we confirm the involvement of these two kinases in the regulation of tumor cell growth. Based on a combined approach of large kinome-wide siRNA screens and ontology annotations, our study identifies for the first time two kinase groups differentially implicated in the control of cell proliferation. We further demonstrate that integrative analysis of the kinase interactome provides key information which can be used to facilitate or optimize target design for new therapeutic strategies. The complete list of protein-protein interactions from the two functional kinase groups will provide a useful database for future investigations.
ISSN: 1471-2164

hal-01118475
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118475
DOI : 10.1186/1471-2164-15-1169
PUBMED : 25540073

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely ``processually equivalent'' entities, ``processually versatile'' entities, and ``stabilized'' entities.
ISSN: 0169-3867

hal-01544796
https://hal.archives-ouvertes.fr/hal-01544796
DOI : 10.1007/s10539-012-9350-2

Éditeur(s) : HAL CCSD
Résumé : Given the technological development of embedded satellite sensors, the potential of available satellite images increases so that the question now arises of their most efficient exploitation possible. This is the purpose of the CARTAM-SAT project to fluidize the processing workflow from satellite images to users. The thesis is part of this framework.Processing operations relating to images have evolved over the years. Low-resolution images were processed by a so-called pixel approach while the high-resolution has allowed the development of a so-called object approach. The latter focuses on analysing not about the isolated pixels, but about groups of pixels representative of concrete objects on the ground. Thus, in principle, these are groups of pixels with a domain-specific remote sensing semantics.Along with satellite imagery, knowledge representation has evolved. The standards of representation have benefited from the expansion of the web to give rise to standards like OWL. This one is widely based on description logics that allow the use of automated reasoners able to infer implicit knowledge.This thesis is at the junction of these two sciences and provides an ontological approach for analysing satellite images. The aim is to formalize different types of knowledges and conceptualizations implicitly used by image processing programs and by remote sensing experts, and then reasoning automatically on an image description to obtain one semantic interpretation.This general principle may have numerous technical variations. The implementation consisted in a prototype combining a satellite image analysis library and an ontology-based reasoner. The implementation proposed in the thesis allows to explore four technical variations of the principle that lead to discussions on the complementarity of pixel and object analysis paradigms, the representation of some of the spatial relations and the role of knowledge in relation to processing.
Étant donnée l'évolution technologique des capteurs embarqués à bord des satellites, le potentiel d'images satellitaires accessible s'accroît de telle manière que se pose maintenant la question de son exploitation la plus efficace possible. C'est l'objectif du projet CARTAM-SAT que de fluidifier la chaîne de traitement depuis les satellites jusqu'aux utilisateurs des images. La thèse s'inscrit dans ce cadre. Les traitements relatifs aux images ont évolué au cours des années. Les images basse résolution étaient traitées par une approche dite pixel alors que la haute résolution a permis le développement d'une approche dite objet. Cette dernière s'attache à analyser non plus des pixels isolés, mais des groupes de pixels représentatifs d'objets concrets sur le terrain. Ainsi, en principe, ces groupes de pixels sont dotés d'une sémantique propre au domaine de la télédétection. La représentation des connaissances a évolué parallèlement aux images satellitaires. Les standards de représentation ont profité de l'expansion du web pour donner naissance à des standards comme OWL. Celui-ci repose en grande partie sur les logiques de description qui permettent l'utilisation de raisonneurs automatiques capables d'inférer une connaissance implicite.Cette thèse se place à la jonction de ces deux sciences et propose une approche ontologique d'analyse des images satellitaires. Il s'agit de formaliser différents types de connaissances et de conceptualisations implicitement utilisés par les logiciels de traitement d'image et par les experts en télédétection, puis de raisonner automatiquement sur la description d'une image pour en obtenir une interprétation sémantique.Ce principe général est susceptible de nombreuses déclinaisons techniques. La mise en œuvre a consisté en la réalisation d'un prototype alliant une bibliothèque d'analyse d'images satellitaires et un raisonneur basé sur les ontologies. L'implémentation proposée dans la thèse permet d'explorer quatre déclinaisons techniques du principe qui mènent à des discussions sur la complémentarité des paradigmes d'analyse pixel et objet, la représentation de certaines relations spatiales et la place de la connaissance par rapport aux traitements.
https://tel.archives-ouvertes.fr/tel-00998692

NNT : 2013MON20059
tel-00998692
https://tel.archives-ouvertes.fr/tel-00998692
https://tel.archives-ouvertes.fr/tel-00998692/document

Éditeur(s) : HAL CCSD
Résumé : International audience
During the last decade, GIS have suffered of the lack of structured information and semantic definition of the data. The numerous origins of the data and the spatial localization of the object inferred many inconsistencies among them. Indeed, the way to collect data and the level of sampling of the boundary differ from one application to another and from one expert to another. This leads to different representations of the same reality and different models of semantically identical objects or boundaries. To allow the matching of the objects, or parts of the objects, when combining different information layers we introduced a conceptual layer which described a scene with concepts and spatial relationships based on the definition of an ontology. This layer allows detecting and solving conflicts between the common boundaries of two objects. We present in this paper the specification and the way to build and use the ontology.
Geoprocessing proceedings
Gosier, Guadeloupe

hal-00602257
https://hal.archives-ouvertes.fr/hal-00602257

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : Se analiza críticamente al lujo como «concepto» para comprenderlo dentro de la ontologización del sujeto que lo consume y lo ostenta en la actualidad. Estas dos categorías (consumo y ostentación) permiten distinguir al sujeto en dos sentidos: primero, como alguien que busca satisfacer necesidades creadas a partir de relacionar el consumo con la estetización tanto del sujeto como del mundo que lo rodea (el objeto desde un sentido estetizante); segundo, como alguien para quien el lujo es motivo justificante de relación y de des-relación con los otros. Esto a partir de analizar su forma de «hablar» ambivalente (bidireccional): el lujo dice, pero también calla; sugiere, pero no deja de imponer; abre y cierra constantemente; limita y extiende a la vez; en fin, su manera bivalente de comprender la realidad hace que sea más que una simple forma de estar en el mundo. Lo anterior nos permite explicar el por qué de la dicotomía del lujo: para algunos resulta innecesario o superfluo; para otros, en cambio, el lujo es una forma constante de afirmarse como constructo imaginario. De esto se desprende un análisis del lujo como «objeto» y como «idea de objeto»; viendo, así, la forma en que se vuelve base movible de una estetización de comportamientos ambivalentes. En otras palabras, se trata de mirar al lujo pero sin dejar de mirar al sujeto que vive «en» y «desde el lujo».
Analysed critically to the luxury as a “concept” to understand it within the ontologising of the subject that consume it and currently holds it. These two categories (consumption and ostentation) distinguish the subject in two ways: first, as someone who seeks to meet needs created from relate consumption to the aestheticisation of both the subject and the world that surrounds it (the object from a sense aestheticizing); second, as someone for whom luxury is supporting reason of relationship and des-relacion with each other. This starting to analyze his form of “speak” ambivalent (bi-directional): luxury says, but also silent; it suggests, but it doesn't impose; opens and closes constantly; limits and extends at a time; in the end, his bivalent way of understanding reality makes it more than a simple way of being in the world. This allows us to explain the reason for the dichotomy of luxury: for some it is unnecessary or superfluous; for others, on the other hand, the luxury is a constant form of asserting itself as imaginary construct. That is clear from an analysis of the luxury as «object» and «idea of object»; watching, well, how that becomes an aestheticisation of ambivalent behaviour movable base. In other words, it is the luxury look but stop looking at the subject who lives «in» and «luxury».
L’analyse critique du luxe comme « concept » pour comprendre le luxe dans l'ontologisation du sujet qui le consomme et l’occupe actuellement. Les deux catégories (consommation et ostentation) distinguent le rapport à l'objet de deux façons : tout d'abord, comme quelqu'un qui cherche à répondre aux besoins créés dans une relation de consommation et d’esthétisation à la fois du sujet en lui-même et du sujet dans son rapport au monde (l'objet d'une esthétisation de sens) ; deuxièmement, comme quelqu'un pour qui le luxe soutient la construction des relations et non-relations avec les autres. Cela commence dans l’analyser sa forme de « parle » ambivalent (bidirectionnel) : ce que le luxe dit mais aussi les silencieux ; il suggère, mais il n'impose pas ; ouvertures et fermetures ; limites et extensions ; et finalement, son mode bivalent de compréhension de la réalité qui est plus qu'une simple manière d'être au monde. Ceci nous permet d'expliquer les raisons de la dichotomie de luxe : pour certains c'est inutile ou superflu ; pour d'autres, le luxe est une forme constante d'affirmation de soi-même comme construction imaginaire. Il ressort de cette analyse le luxe en tant "objet" et "idée de l'objet"; observant l'observation comment il devient une esthétisation d’un comportement ambivalent évolutif. Autrement dit, il s’agit d’étudier le luxe, mais sans négliger le sujet qui vit dans et à travers le luxe.

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.7315
http://journals.openedition.org/etudescaribeennes/7315

Éditeur(s) : HAL CCSD
Résumé : International audience
Semantic web standards, tools, ontologies and related technologies have considerably matured in the recent years. Nowadays, accessing a wide catalogue of biological, social, environmental, and ecological data sources helps stakeholders working on biodiversity to answer their complex questions. Will the real time access to web resources effectively support the definition of strategies to conserve and manage biodiversity? How might semantic web technologies help us to handle the complex and heterogeneous big data related to biodiversity? The workshop aims to identify the key challenges faced by the bioinformatics community, discuss potential solutions and identify the opportunities emerging from the trans-disciplinary interactions between Plant Science and Informatics experts. Therefore, we expect the bioinformatics experts to explain how they apply semantic web standards and tools to their scientific topic, from biology, agriculture, agro-ecology, genomics, environmental studies, to social sciences, citizen sciences. Research papers presenting various aspects of semantic web technologies applied to biodiversity data, ranging from position papers to implemented systems descriptions and their evaluation, will be selected. We are particularly interested in the use of the semantic technologies to design and develop systems that supports research on agricultural and wild biodiversity conservation and management for food security. Examples may include strategies for resilience to climate change pressures, sustainability of productive ecosystems, ecosystems services monitoring or territories management, rather than systems supporting only research on climate patterns or soil erosion.
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757

lirmm-00831757
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757/document

Éditeur(s) : HAL CCSD
Résumé : International audience
GEOBIA 2012
Rio de Janeiro, France

hal-01107866
https://hal.archives-ouvertes.fr/hal-01107866

Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
ISSN: 0305-1048

hal-01146849
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146849
DOI : 10.1093/nar/gkv350
PUBMED : 25897122

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Saccharomyces cerevisiae is an established model organism for the molecular analysis of fundamental biological processes. The genomes of numerous strains have been sequenced, and the transcriptome and proteome ofmajor phases during the haploid and diploid yeast life cycle have been determined. However, much less is known about dynamic changes of the proteome when cells switch from mitotic growth to meiotic development. We report a quantitative protein profiling analysis of yeast cell division and differentiation based on mass spectrometry. Information about protein levels was integrated with strand-specific tiling array expression data. We identified a total of 2366 proteins in at least one condition, including 175 proteins showing a statistically significant > 5-fold change across the sample set, and 136 proteins detectable in sporulating but not respiring cells. We correlate protein expression patterns with biological processes and molecular function by Gene Ontology term enrichment, chemoprofiling, transcription interference and the formation of double stranded RNAs by overlapping sense/antisense transcripts. Our work provides initial quantitative insight into protein expression in diploid respiring and differentiating yeast cells. Critically, it associates developmentally regulated induction of antisense long noncoding RNAs and double stranded RNAs with fluctuating protein concentrations during growth and development.
ISSN: 1874-3919

hal-01485858
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01485858
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01485858/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01485858/file/Becker%20et%20al.%20-%20The%20protein%20expression%20landscape%20of%20mitosis%20and%20me.pdf
DOI : 10.1016/j.jprot.2016.12.016

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual and stem from our assumptions of how a gene evolves, others are practical, and depend on the algorithmic decisions implemented in existing software. Therefore, to make progress in the study of homology, both ontological and epistemological questions must be considered. In particular, defining homologous genes cannot be solely addressed under the classic assumptions of strong tree thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent and divergence and the problems of homology detection are primarily methodological. Gene homology could also be considered under a different perspective where genes evolve as ``public goods,'' subjected to various introgressive processes. In this latter case, defining homologous genes becomes a matter of designing models suited to the actual complexity of the data and how such complexity arises, rather than trying to fit genetic data to some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information. Here we show how important aspects of the problems raised by homology detection methods can be overcome when even more fundamental roots of these problems are addressed by analyzing public goods thinking evolutionary processes through which genes have frequently originated. This kind of thinking acknowledges distinct types of homologs, characterized by distinct patterns, in phylogenetic and nonphylogenetic unrooted or multirooted networks. In addition, we define `` family resemblances'' to include genes that are related through intermediate relatives, thereby placing notions of homology in the broader context of evolutionary relationships. We conclude by presenting some payoffs of adopting such a pluralistic account of homology and family relationship, which expands the scope of evolutionary analyses beyond the traditional, yet relatively narrow focus allowed by a strong tree-thinking view on gene evolution.
ISSN: 0737-4038

hal-01544794
https://hal.archives-ouvertes.fr/hal-01544794
DOI : 10.1093/molbev/mst228