Éditeur(s) : HAL CCSD National Academy of Sciences
Résumé : International audience
All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.
ISSN: 0027-8424

hal-01544803
https://hal.archives-ouvertes.fr/hal-01544803
DOI : 10.1073/pnas.1206541109

Éditeur(s) : Wiley-blackwell
Résumé : The reef fauna connectivity of the West Indian Ocean (WIO) is one of the least studied globally. Here we use genetic analyses of the grouper Epinephelus merra (Bloch 1793) to determine patterns of connectivity and to identify barriers to dispersal in this WIO marine area. Phylogeographic and population-level analyses were conducted on cytochrome b sequences and microsatellites (13 loci) from 557 individuals sampled in 15 localities distributed across the West Indian Ocean. Additional samples from the Pacific Ocean were used to benchmark the WIO population structure. The high level of divergence revealed between Indian and Pacific localities (of about 4.5% in sequences) might be the signature of the major tectonic and climatic changes operating at the Plio-Pleistocene transition, congruently with numerous examples of Indo-Pacific speciation. In comparison, the E. merra sequences from the Indian Ocean constitute a monophyletic clade with a low average genetic distance (d < 0.5%). However both genetic markers indicated some structure within this ocean. The main structure revealed was the isolation of the Maldives from the WIO localities (a different group signature identified by clustering analysis, great values of differentiation). Both marker types reveal further significant structure within the WIO, mainly the isolation of the Mascarene Islands (significant AMOVA and isolation-by-distance patterns) and some patchy structure between the northernmost localities and within the Mozambique Channel. The WIO genetic structure of E. merra appeared congruent with main biogeographic boundaries and oceanographic currents.
Marine Ecology-an Evolutionary Perspective (0173-9565) (Wiley-blackwell), 2015-09 , Vol. 36 , N. 3 , P. 447-461

Droits : 2014 Blackwell Verlag GmbH
http://archimer.ifremer.fr/doc/00189/30046/28566.pdf
DOI:10.1111/maec.12153
http://archimer.ifremer.fr/doc/00189/30046/

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Motivation: Gene fusion is an important evolutionary process. It can yield valuable information to infer the interactions and functions of proteins. Fused genes have been identified as non-transitive patterns of similarity in triplets of genes. To be computationally tractable, this approach usually imposes an a priori distinction between a dataset in which fused genes are searched for, and a dataset that may have provided genetic material for fusion. This reduces the `genetic space' in which fusion can be discovered, as only a subset of triplets of genes is investigated. Moreover, this approach may have a high-false-positive rate, and it does not identify gene families descending from a common fusion event. Results: We represent similarities between sequences as a network. This leads to an efficient formulation of previous methods of fused gene identification, which we implemented in the Python program FusedTriplets. Furthermore, we propose a new characterization of families of fused genes, as clique minimal separators of the sequence similarity network. This well-studied graph topology provides a robust and fast method of detection, well suited for automatic analyses of big datasets. We implemented this method in the C++ program MosaicFinder, which additionally uses local alignments to discard false-positive candidates and indicates potential fusion points. The grouping into families will help distinguish sequencing or prediction errors from real biological fusions, and it will yield additional insight into the function and history of fused genes.
ISSN: 1367-4803

hal-01544795
https://hal.archives-ouvertes.fr/hal-01544795
DOI : 10.1093/bioinformatics/btt049

Éditeur(s) : HAL CCSD
Résumé : The modernization of agriculture is under scrutiny. It is currently debated within the growing concept and practice of agroecology that applies ecological fundaments to the design and the management of sustainable agroecosystems. In matter of ecologization of agriculture, agroecological transition may be considered as a privileged pathway. It relies on two main forms: the weak (that intends to reduce the use of chemicals by alternative practices such as their substitution by biological inputs) versus strong modernization of agriculture (based on the valorization of biodiversity providing ecosystemic services). In this article, through an analysis of the technological innovations used for the enhancement of mycorrhiza (symbiotic interactions between plants and soil microorganisms) as an illustration of the implementation of the agroecological transition in France, we wonder in what extent a strong modernization of agriculture is likely to occur.This paper shows how the conceptual framework of socio-technical regime is useful to analyze the dynamics of the agroecological transition. Our demonstration relies on an empirical material (survey of the main actors of the mycorrhiza supply chain) that permits to understand how is structured the dominant system and how it impedes the development of the alternative niche. We then give some prerequisites in terms of public action to define in what extent the niche can be supported and can compete the current system.
54. ERSA Congress "Regional development & globalization: Best practices"
Saint-Petersburg, Russia

hal-01606449
https://hal.archives-ouvertes.fr/hal-01606449
PRODINRA : 387723

Éditeur(s) : HAL CCSD
Résumé : International audience
Symbiosis is a widespread phenomenon in the biosphere. In marine benthic environments breakdown of symbiosis is responsible for coral bleaching and dramatically affects coral reef ecosystems functioning [1]. In the water column, planktonic organisms are key component of pelagic ecosystems and a number of species form mutualistic association with microalgae forming a photosymbiosis [2]. Here we intended to investigate the genetic basis of photosymbiosis, through a transcriptomic approach on marine plankton organisms. We focused more specifically on associations occurring between radiolarian host (protist, zooplankton) and dinoflagellates symbiont (protist, phytoplankton) living inside the host cell. It has recently been highlighted that these holobionts are widespread in oligotrophic open oceans and there are also evidences of their fundamental implication in biogeochemical carbon, silica and strontium cycles [3, 4, 5, 6]. RNA-seq technologies allow obtaining an unprecedented amount of data for unicellular organisms isolated from the environment [7]. The study of such non-model holobionts datasets requires de novo assembly, which implies considerable computational resources and the potential production of chimeric sequences [8, 9].We therefore developed an original strategy aiming at accelerating and improving de novo assembly for holobiont datasets. We chose SIMKA [10] a fast kmer-based method initially developed to estimate the similarity between numerous metagenomic datasets, and which has been recently adapted to extract their common sequences. As our symbionts are identified, we used SIMKA to compare our holobionts transcriptomes to publicly available dinoflagellates transcriptomes [11] generating two datasets, one composed of reads from the symbionts and another with reads from the host (for which no reference data are currently available). Independent assemblies were then performed in parallel, accelerating the study process, and minimizing the proportion of resulting chimeric sequences. Our strategy produced a unique and comprehensive genomic dataset for Radiolaria [12, 13], and offers a pragmatic, large scale, comparison strategy to assemble and study holobionts [9]. Our new sequences obtained from holobionts study will be used for phylogenomics investigation, as reference for environmental metagenomic studies and ultimately to understand and characterize the molecular basis of symbiotic relationships in the plankton.Bibliografic references :[1] Simon K. Davy, Denis Allemand, and Virginia M. Weis. “Cell Biology of Cnidarian-Dinoflagellate Symbiosis”. In: Microbiology and Molecular Biology Reviews 76.2 (June 1, 2012), pp. 229–261. issn: 1092-2172, 1098- 5557. doi: 10.1128/MMBR.05014-11.[2] Janouškovec, J. et al. “Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics”. in: PNAS 201614842 (2016). doi:10.1073/pnas.1614842114[3] Tristan Biard et al. “In situ imaging reveals the biomass of giant protists in the global ocean”. In: Nature advance online publication (Apr. 20, 2016). issn: 0028-0836. doi: 10.1038/nature17652.[4] Lionel Guidi et al. “Plankton networks driving carbon export in the olig- otrophic ocean”. In: Nature 532.7600 (Apr. 28, 2016), pp. 465–470. issn: 0028-0836. doi: 10.1038/nature16942.[5] Diane K. Stoecker et al. “Acquired phototrophy in aquatic protists”. In: Aquatic Microbial Ecology 57.3 (Nov. 24, 2009), pp. 279–310. doi: 10.3354/ame01340.[6] Johan Decelle et al. “An original mode of symbiosis in open ocean plankton”. In: Proceedings of the National Academy of Sciences 109.44 (Oct. 30, 2012), pp. 18000–18005. issn: 0027-8424, 1091-6490. doi: 10. 1073/pnas.1212303109.[7] Sergio Balzano et al. “Transcriptome analyses to investigate symbiotic relationships between marine protists”. In: Frontiers in Microbiology 6 (Mar. 17, 2015). issn: 1664-302X. doi: 10.3389/fmicb.2015.00098.[8] Li, B. et al. “Evaluation of de novo transcriptome assemblies from RNA-Seq data”. In: Genome Biology 15, 553 (2014).[9] Sangwan, N., Xia, F. & Gilbert, J. A. “Recovering complete and draft population genomes from metagenome datasets”. In: Microbiome 4, 8 (2016).[10] Gaëtan Benoit et al. “Multiple comparative metagenomics using mul- tiset k -mer counting”. In: PeerJ Computer Science 2 (Nov. 14, 2016). doi: 10.7717/peerj-cs.94.[11] Patrick J. Keeling et al. “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing”. In: PLOS Biol 12.6 (June 2014), e1001889. issn: 1545-7885. doi: 10.1371/journal.pbio.1001889.[12] Burki, F. et al. “Evolution of Rhizaria: new insights from phylogenomic analysis of uncultured protists”. In BMC Evolutionary Biology 10, 377 (2010).
International Conference on Holobionts
Paris, France

hal-01575069
https://hal.inria.fr/hal-01575069

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The tree model and tree-based methods have played a major, fruitful role in evolutionary studies. However, with the increasing realization of the quantitative and qualitative importance of reticulate evolutionary processes, affecting all levels of biological organization, complementary network-based models and methods are now flourishing, inviting evolutionary biology to experience a network-thinking era. We show how relatively recent comers in this field of study, that is, sequence-similarity networks, genome networks, and gene families–genomes bipartite graphs, already allow for a significantly enhanced usage of molecular datasets in comparative studies. Analyses of these networks provide tools for tackling a multitude of complex phenomena, including the evolution of gene transfer, composite genes and genomes, evolutionary transitions, and holobionts.
ISSN: 0966-842X

Droits : http://creativecommons.org/licenses/by-nc-nd/
hal-01300043
http://hal.upmc.fr/hal-01300043
http://hal.upmc.fr/hal-01300043/document
http://hal.upmc.fr/hal-01300043/file/Network-Thinking.pdf
DOI : 10.1016/j.tim.2015.12.003

Éditeur(s) : HAL CCSD
Résumé : Evolution of organisms, genomes and genes does not strictly follow a tree-like process; symbiosis, horizontal gene transfers and gene fusions build high level composite objects with components of phylogenetically distinct origins. Such processes have been called introgressive events and are significant in evolution. They are involved in some major evolutionary transitions such as eukaryogenesis, photosynthesis acquisition in eukaryotes and the origins of major archaeal clades. Eukaryogenesis would have involved (at least) two kinds of partners: an archaeon and an alpha-proteobacterium. Photosynthetic eukaryotes arose from the integration of a cyanobacterium into a eukaryotic cell and recent findings suggested that most archaeal lineages emerged after massive acquisitions of bacterial genes. These composite lineages carry highly chimeric genomes where genes from symbiotic partners co-localize into the same genome. During my PhD thesis, I used sequence similarity networks and phylogenetic methods in order to study reticulate evolution. My research specifically focused on a previously hidden component of composite genomes: symbiogenetic genes (S genes). These chimeric genes are found in genetic mergers, and originate from the association of genes of symbiotic partners. Some association rules have been discovered. In a broad perspective, the discovery of S-genes extends the concept of genome chimerism to the within-gene level.
L'évolution des organismes, des génomes et des gènes n'est pas strictement arborescente; les symbioses, les transferts horizontaux de gènes ou encore la fusion de gènes créent des objets composites formés de parties dont les histoires évolutives sont différentes. Ces processus non arborescents sont appelés introgressifs et ont un impact non négligeable en évolution. Ils sont à l'origine de transitions évolutives majeures comme l'émergence des eucaryotes, des eucaryotes photosynthétiques ou encore de nombreux groupes d'Archaea. Dans le cas des eucaryotes, l'association et la stabilisation d'une Archaea et d'une alpha-protéobactérie a permis l'émergence d'un nouveau groupe d'organismes composites aux propriétés émergentes. L'acquisition de la photosynthèse chez les eucaryotes s'est faite via l'endosymbiose d'une cyanobactérie et, bien que débattue, l'apparition des grands groupes d'Archaea semble être concomitante avec l'acquisition de nombreux gènes d'origine bactérienne. Ces superorganismes ont la particularité d'avoir des génomes composés de gènes de différents partenaires symbiotiques. L'objectif de mon travail de thèse a constitué à étudier l'aspect introgressif de l'évolution par des méthodes de réseaux de similarité de séquence et des méthodes phylogénétiques. Je me suis particulièrement focalisé sur la détection de nouveaux gènes chimériques nommés gènes symbiogénétiques (S-gènes) car composés de parties originaires des différents partenaires symbiotiques. De tels gènes existent dans les génomes et plusieurs règles d'association ont pu être mises en évidence. Plus généralement, la présence de S-gènes étend la notion de mosaïcisme génomique au niveau infra-génique.
https://tel.archives-ouvertes.fr/tel-01536344

NNT : 2016PA066534
tel-01536344
https://tel.archives-ouvertes.fr/tel-01536344
https://tel.archives-ouvertes.fr/tel-01536344/document
https://tel.archives-ouvertes.fr/tel-01536344/file/2016PA066534.pdf

Éditeur(s) : HAL CCSD Springer Verlag (Germany)
Résumé : In this paper we study merosity in the genus Urospatha within the framework of a resolved phylogeny of the Araceae. We analyse how a transition from dimerous or tetramerous merosity to pentamerous or hexamerous merosity can occur developmentally in the Lasioideae. In Urospatha, initiation of floral primordia along the inflorescence is acropetal, while development of flowers is basipetal. This indicates the presence of two distinct phases in the development of the Urospatha inflorescence. The first phase corresponds to initiation of flowers and establishment of the phyllotactic pattern, and the second phase to differentiation of floral organs. Urospatha is characterized by the presence of trimerous, tetramerous, pentamerous and rarely hexamerous flowers. In all types of flowers, the stamens are closely associated and opposite to the tepals. Pentamerous flowers are formed by addition of a sector comprising a stamen and tepal. Likewise, in the case of hexamerous flowers, two sectors are added. In the Lasioideae, the increase in the number of tepals and stamens is linked with two developmental processes that have appeared independently in the subfamily: (1) addition of one or two stamen-petal sectors (Anaphyllopsis and Urospatha), and (2) independent increase in the number of tepals and stamens on whorls, more or less organized and inserted in alternate position (Dracontium). Tetramerous whorls as they occur in basal Lasioideae would be homologous to two dimerous whorls from an evolutionary point of view.
ISSN: 0378-2697

hal-01019867
https://hal.archives-ouvertes.fr/hal-01019867
DOI : 10.1007/s00606-011-0475-6

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We compile field data collected along the eastern part of the North Pyrenean Zone (NPZ) to point to a tectonic evolution under peculiar thermal conditions applying to the basin sediments in relation with the opening of the Cretaceous Pyrenean rift. Based on this compilation, we show that when thinning of the continental crust increased , isotherms moved closer to the surface with the result that the brittle-ductile transition propagated upward and reached sediments deposited at the early stage of the basin opening. During the continental breakup, the pre-rift Mesozoic cover was efficiently decoupled from the Paleozoic basement along the Triassic evaporite level and underwent drastic ductile thinning and boudinage. We suggest that the upper Albian and upper Creta-ceous flysches acted as a blanket allowing temperature increase in the mobile pre-rift cover. Finally, we show that continuous spreading of the basin floor triggered the exhumation of the metamorphic, ductily sheared pre-rift cover, thus contributing to the progressive thinning of the sedimentary pile. In a second step, we investigate the detailed geological records of such a hot regime evolution along a reference-section of the eastern NPZ. We propose a balanced restoration from the Mouthoumet basement massif (north) to the Boucheville Albian basin (south). This section shows a north to south increase in the HT Pyrenean imprint from almost no metamorphic recrystallization to more than 600 °C in the pre-and syn-rift sediments. From this reconstruction, we propose a scenario of tectonic thinning involving the exhumation of the pre-rift cover by the activation of various detachment surfaces at different levels in the sedimentary pile. In a third step, examination of the architecture of current distal passive margin domains provides confident comparison between the Pyrenean case and modern analogs. Finally, we propose a general evolutionary model for the pre-rift sequence of the Northeastern Pyrenean rifted margin.
ISSN: 0040-1951

Droits : http://creativecommons.org/licenses/by-nc-nd/
insu-01355131
https://hal-insu.archives-ouvertes.fr/insu-01355131
https://hal-insu.archives-ouvertes.fr/insu-01355131/document
https://hal-insu.archives-ouvertes.fr/insu-01355131/file/TECTO10807-Incorporated%20changes-rev2.pdf
DOI : 10.1016/j.tecto.2016.07.022