Éditeur(s) : Conservation International Conservation International ( Washington, D.C. )
Résumé : (Statement of Responsibility) Conservation International, United States Man and the Biosphere Program, ECOSUR, USAID ; data contributed by Paseo Pantera Consortium, University of Florida, Amigos de Sian Kaán.
(Language) Text and legend in Spanish and English.
"August 1995."
Includes text, location map, and insets showing "Biological resources", "Landscape processes", "Corridors", and "Socioeconomic resources".
Text, 3 maps with indexed tables : "Biological corridors", "Biological resources", and "Landscape processes" on verso.
Maya Forest
Maya Forest
Maya Forest
Maya Forest
Maya Forest
Maya Forest
Maya Forest
Maya Forest
Maya Forest

002285129
39667905
ALN8260
AA00004976_00001

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BackgroundFor a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today. Most proposed analogies were based on a comparison of the research objects rather than the processes that shaped their evolution. Focusing on process-based analogies, however, has the advantage of minimizing the risk of overstating similarities, while at the same time reflecting the common strategy to use processes to explain the evolution of complexity in both fields.ResultsWe compared important evolutionary processes in biology and linguistics and identified processes specific to only one of the two disciplines as well as processes which seem to be analogous, potentially reflecting core evolutionary processes. These new process-based analogies support novel methodological transfer, expanding the application range of biological methods to the field of historical linguistics. We illustrate this by showing (i) how methods dealing with incomplete lineage sorting offer an introgression-free framework to analyze highly mosaic word distributions across languages; (ii) how sequence similarity networks can be used to identify composite and borrowed words across different languages; (iii) how research on partial homology can inspire new methods and models in both fields; and (iv) how constructive neutral evolution provides an original framework for analyzing convergent evolution in languages resulting from common descent (Sapir’s drift).ConclusionsApart from new analogies between evolutionary processes, we also identified processes which are specific to either biology or linguistics. This shows that general evolution cannot be studied from within one discipline alone. In order to get a full picture of evolution, biologists and linguists need to complement their studies, trying to identify cross-disciplinary and discipline-specific evolutionary processes. The fact that we found many process-based analogies favoring transfer from biology to linguistics further shows that certain biological methods and models have a broader scope than previously recognized. This opens fruitful paths for collaboration between the two disciplines.
ISSN: 1745-6150

Droits : http://creativecommons.org/licenses/by/
hal-01378396
http://hal.upmc.fr/hal-01378396
http://hal.upmc.fr/hal-01378396/document
http://hal.upmc.fr/hal-01378396/file/unity.pdf
DOI : 10.1186/s13062-016-0145-2

Éditeur(s) : Yale University
Résumé : Sea-surface temperature images of the coastal upwelling regions off Northwest Africa show that the core of upwelling is sometimes located far from the coast. This has been documented in three regions that share a common feature, namely a wide and shallow continental shelf. This upwelling feature plays a key role in the ecology of the Canary Current System. It creates an innerfront which provides retention for biological material, e.g. fish eggs and larvae, in the highly productive nearshore environment. An analytical model has been developed based on a two dimensional extension of Ekman's solution. The linear and steady response of a homogeneous ocean forced by an upwelling-favorable wind provides a mechanism for the upwelling separation from the coast. The merging of the surface and bottom Ekman layers induces a very weak cross-shore circulation and a "kinematic barrier" for the Ekman transport divergence. In the case of an alongshore wind, the barrier is located near the isobath h ≈ 0.4D, where D is the thickness of Ekman layers. This yields an upwelling cell which is essentially concentrated in the region 0.5D < h < 1.25D, with upwelling occurring preferentially near the isobath h ≈ 0.6D. It turns out that the cross-shore width of upwelling scales with D/S, the ratio of Ekman depth to bottom topographic slope. The application of this solution to real bathymetric profiles rationalizes, not only the offshore upwelling observations in Northwest Africa, but also the influence of topography on the cross-shelf structure of a wind-driven coastal upwelling. The model also quantifies the effect of the cross-shore wind component showing how it drives the nearshore pressure gradient adjustment and how it affects the upwelling. A linear numerical experiment reproduces the theoretical steady solution, thereby allowing investigation of the transient regime. Relaxation of the hypothesis in the numerical model validates the linear assumption of the theory and then allows investigation of the sensitivity to friction parameterizations and the influence of stratification. The latter leads to an "oscillation" of the upwelling cell with seaward migration driven by outcropping and homogeneization of the water column, and, coastal incursion driven by a "boundary layers splitting" process caused by shoreward advection of the isopycnal dome and stratification of the inner shelf.
Journal of Marine Research (Yale University), 2008-09 , Vol. 66 , N. 5 , P. 589-616

Droits : 2008 Yale University
http://archimer.ifremer.fr/doc/2008/publication-6334.pdf
DOI:10.1357/002224008787536790
http://archimer.ifremer.fr/doc/00000/6334/

Éditeur(s) : Montpellier 1
Résumé : Understanding bioaccumulation mechanisms of persistent organic pollutants (POPs) is a major issue for environmental risk assessment. In this work, polychlorinated biphenyls (PCBs), a model contaminant family, has been studied in the European hake (Merluccius merluccius), a high trophic level species from the Gulf of Lions. High concentrations of PCBs were measured in hake from this area compared to those encountered in the population of the Bay of Biscay. PCB biomagnification was highlighted along its food web from marine phytoplankton, suggesting a strong influence of diet on contamination levels. The role of other biological processes was also apprehended in order to understand the high variability of observed levels. Thus, growth, sex, and also the degree of sexual maturity appear as major factors explaining the measured concentrations in fish. A PCB bioaccumulation model in the hake, based on the Dynamic Energy Budget theory (DEB), was developed. This approach is based on a bioenergetic model, reproducing the main physiological functions of an organism (feeding, growth and reproduction), coupled with a kinetic model of contaminants. The growth and evolution of contamination levels of several PCB congeners during the life of male and female hakes is satisfactorily simulated, both in the Gulf of Lions and in the Bay of Biscay, validating the processes taken into account. This combined modelling approach appears well adapted to study the fate of contaminants in fish, and paves the way for a realistic understanding of their effects on major biological functions of fish.
La compréhension des mécanismes de bioaccumulation des contaminants organiques persistants (POP) est un enjeu majeur pour l'évaluation des risques environnementaux. Lors de ce travail, le devenir d'une famille de contaminants modèles, les polychlorobiphényles (PCB), a été étudié chez une espèce de rang trophique élevé du golfe du Lion, le merlu Européen (Merluccius merluccius). Des concentrations élevées en PCB ont été mesurées dans les merlus de ce secteur en comparaison à celles rencontrées dans la population du golfe de Gascogne. La mise en évidence d'une bioamplification des PCB le long de son réseau trophique, depuis le phytoplancton marin, suggère une influence importante de l'alimentation sur les niveaux de contamination. Le rôle d'autres processus biologiques a également été appréhendé afin de comprendre la forte variabilité des niveaux observés. Ainsi, la croissance, le sexe, mais également le degré de maturité sexuel apparaissent comme des facteurs explicatifs majeurs des concentrations en PCB mesurées dans les poissons. Un modèle de bioaccumulation des PCB chez le merlu, basé sur la théorie de Budget d'Energie Dynamique (DEB), a été développé. Il s'agit d'une approche basée sur le couplage d'un modèle bioénergétique, reproduisant les principales fonctions physiologiques de l'organisme (nutrition, croissance et reproduction), avec un modèle de cinétique des contaminants. La croissance et l'évolution des niveaux de contamination de plusieurs congénères de PCB au cours de la vie des merlus mâles et femelles est simulée de manière satisfaisante, tant dans le golfe de Gascogne que dans le golfe du Lion, validant ainsi les processus pris en compte. Cette approche combinée de modélisation apparaît tout à fait adaptée à l'étude du devenir des contaminants chez les poissons, et ouvre la voie à une compréhension réaliste de leurs effets sur les grandes fonctions biologiques de ces organismes.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2008/these-6490.pdf
http://archimer.ifremer.fr/doc/00000/6490/

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Line transect surveys are widely used in neotropical rainforests to estimate the population abundance of medium- and large-sized vertebrates. The use of indices such as Encounter Rate has been criticized because the probability of animal detection may fluctuate due to the heterogeneity of environmental conditions among sites. In addition, the morphological and behavioral characteristics (biological traits) of species affect their detectability. In this study, we compared the extent to which environmental conditions and species' biological traits bias abundance estimates in terra firme rainforests in French Guiana. The selected environmental conditions included both physical conditions and forest structure covariates, while the selected biological traits included the morphological and behavioral characteristics of species. We used the distance sampling method to model the detection probability as an explicit function of environmental conditions and biological traits and implemented a model selection process to determine the relative importance of each group of covariates. Biological traits contributed to the variability of animal detectability more than environmental conditions, which had only a marginal effect. Detectability was best for large animals with uniform or disruptive markings that live in groups in the canopy top. Detectability was worst for small, solitary, terrestrial animals with mottled markings. In the terra firme rainforests which represent ~80% of the Amazonia and Guianas regions, our findings support the use of relative indices such as the encounter rate to compare population abundance between sites in species-specific studies. Even though terra firme rainforests may appear similar between regions of Amazonia and the Guianas, comparability must be ensured, especially in forests disturbed by human activity. The detection probability can be used as an indicator of species' vulnerability to hunting and, thus, to the risk of local extinction. Only a few biological trait covariates are required to correctly estimate the detectability of the majority of medium- and large-sized vertebrates. Thus, a biological trait model could be useful in predicting the detection probabilities of rare, uncommon or localized species for which few data are available to fit the detection function.
ISSN: 1051-0761

hal-01555267
https://hal.archives-ouvertes.fr/hal-01555267
DOI : 10.1002/eap.1549
PRODINRA : 396614
PUBMED : 28419598

Éditeur(s) : Ecole nationale supérieure agronomique de Rennes
Résumé : Describe and gain understanding on fluctuations in animal population over time and space is a central goal of population ecology. This is also crucial to ensure the sustainable management of exploited resources, particularly those with complex population dynamics such as the bluefin tuna. The goal of this work is to collect bluefin tuna catches from the ancestral Mediterranean and Atlantic trap fisheries to (i) characterise long-term fluctuations in bluefin tuna population migrating in the Mediterranean, (ii) analyse their causes et (iii) assess their implications for fisheries management. The bluefin tuna main biological and ecological characteristics are first detailed. Then, the first part presents the trap fishery, and the process of collect and validation of the historical catches. This leads to develop a data base of 54 time-series more than 20 years long, the longest ones spanning about four centuries. Mean historical catches were around 15 000 tons/year ([7 000;25 000]). Time-series are analysed in a second part. Temporal variability of trap catches may be decomposed in three components: 100-year-long periodic fluctuations, 20-year cycles and inter-annual variations. These medium- to long-term fluctuations, representing more than 50% of the variability in the time-series, were synchronous all around the western Mediterranean and adjacent North Atlantic. In contrast, short-term variability was synchronous at a local scale only. It is argued that long-term fluctuations in trap catches could be considered as a proxy for those in abundance, and a synthetic time-series is computed to depict them. Biological and ecological processes that could cause such long-term fluctuations are discussed in a third part. We tested whether long-term fluctuations in Atlantic bluefin tuna might be related to large-scale environmental changes, using long time-series of the North Atlantic Oscillation (NAO), the Length of the Day index (LOD, a proxy of the atmospheric circulation index ACI) and the temperature. Spectral analyses of trap catches, LOD and temperature displayed similar spectra with peak at low frequency, whereas those of the NAO exhibited a broad band spectrum. Regression analyses and tests of correlation did not reveal any clear relationship between trap catches on the one hand and NAO and LOD on the other hand. In contrast, long-term fluctuations in trap catches appear to be negatively and significantly related to long-term trends in temperature. Underlying processes that could explain such a relationship are discussed, with special focus on changes in migration patterns. Finally, implications of such fluctuations in term of fisheries management are discussed in a fourth part. A simulation framework, in which a simulated population dynamics model is coupled with a VPA, is built to test the pertinence of the diagnostic of stock assessment according to different scenarios on fluctuations origins and population status. In the hypothesis of fluctuations linked to variations in the recruitment, VPA appears able to reconstruct the fluctuations but the predictions may be biased if natural fluctuations are not taking into account. In the hypothesis of fluctuations linked to changes in migration pattern, VPA is not able to reconstruct the population dynamics. In a precautionary approach, quotas which follow may be unsuitable in the best case, at worst dangerous if they are defined in comparison with a reference point. The concept of cible reference points, fixe and unique over time, appears not relevant for bluefin tuna; estimate trajectory reference pertinent may prove to be more pertinent.
Décrire et comprendre les fluctuations spatio-temporelles des espèces animales constituent les enjeux majeurs de l'écologie. La question est également cruciale pour réussir la gestion durable des ressources exploitées, en particulier celle du thon rouge, grand pélagique migrateur à la dynamique complexe. L'objectif de ce travail est de collecter les captures historiques de thon rouge par les madragues méditerranéennes et proche atlantiques pour (i) caractériser les fluctuations à long terme de la population migrante en Méditerranée, (ii) étudier leur déterminisme et (iii) évaluer leurs implications en terme de gestion des pêcheries. Après avoir décrit les principales caractéristiques biologiques et écologiques du thon rouge, la première partie présente la pêcherie à la madrague, puis le processus de collecte et de validation des données historiques de captures. Ce dernier conduit à la mise en place d'une base de données de 54 séries de plus de 20 ans, dont les plus longues s'étendent sur près de 4 siècles. Les productions historiques sont estimées à environ 15 000 tonnes/an ([7 000;25 000]). Les séries historiques de captures sont analysées dans la seconde partie. Leur variabilité temporelle peut être décomposée en trois composantes : de larges cycles pseudo-séculaires, des variations périodiques d'une vingtaine d'années et des fluctuations inter-annuelles. Les fluctuations à moyen et long terme, expliquant plus de la moitié de la variance des séries, sont synchrones à l'échelle du bassin méditerranéen occidental et du proche Atlantique. La variabilité inter-annuelle, en revanche, n'est synchrone qu'à une échelle locale. On montre finalement que les fluctuations à long terme des captures peuvent être considérées comme de bons indices des tendances des abondances de la population de thons rouges migrants en Méditerranée. Une série synthétique est construite pour les décrire. Les processus biologiques et écologiques susceptibles d'être à l'origine de ces fluctuations sont discutés dans la troisième partie. L'hypothèse d'un forçage environnemental à grande échelle est testée en utilisant des indices à long terme de l'Oscillation Nord Atlantique (NAO), de la longueur du jour (LOD, un indicateur de l'indice de circulation atmosphérique ACI) et de la température. Les analyses spectrales sur les séries de captures, du LOD et des températures révèlent des spectres similaires, avec un pic sur les basses fréquences, alors que celles sur le NAO conduisent à une large bande spectrale. Les régressions et les tests de corrélations ne montrent aucune relation significative entre les captures par les madragues et le NAO et le LOD. En revanche, les fluctuations à long terme des captures apparaissent significativement et négativement corrélées avec les fluctuations à long terme des températures. Les processus sous-jacents susceptibles d'expliquer une telle relation, en particulier des changements migratoires, sont discutés. Finalement, les implications des fluctuations pour la gestion de la pêcherie sont discutées dans une quatrième partie. Un cadre de simulation, couplant un modèle de dynamique de population à une VPA, est élaboré pour tester la pertinence des diagnostics d'évaluation de stock selon différents scénarios d'origine des fluctuations et d'état de la population. Dans l'hypothèse de fluctuations liées à des variations du recrutement, la VPA apparaît capable de reconstruire les fluctuations mais les prédictions sont biaisées lorsqu'il n'est pas tenu compte des fluctuations naturelles du stock. Dans l'hypothèse de fluctuations liées à des changements migratoires, la VPA est alors incapable de reproduire la dynamique de la population. Dans une approche de précaution, les quotas qui en découlent peuvent se révéler au mieux inappropriés, au pire dangereux s'ils sont définis par rapport à un point de référence. Ce concept de point cible, fixe et unique dans le temps, apparaît inapproprié pour le thon rouge ; estimer des "trajectoires de référence" serait sans doute plus pertinent.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2003/these-65.pdf
http://archimer.ifremer.fr/doc/00000/65/

Éditeur(s) : HAL CCSD
Résumé : il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : ACTIVITY_REPORT
Understanding genomic evolution in wild populations is of particular importance because evolution is a central process in our understanding of populations’ history and their future response to global changes. In addition to fundamental knowledge, the study of populations’ evolution has wide applications such as conservation/restoration genetics or epidemiology. Indeed, genetic diversity is the ‘fuel’ for populations’ evolution and adaptation to new conditions, and estimating the extent and the geographic structure of genetic diversity, as well as identifying the evolutionary forces behind (demography, gene flow, and adaptation) are thus major challenges in the current context of global changes. [br/]A particular attention is currently devoted to the process of genetic divergence in wild populations, with emphases on gene flow, local adaptation, and their interactions. Indeed, adaptation in wild populations is supported in many species by many kinds of experiments based on both quantitative phenotypic traits and molecular data. However, the processes governing populations’ evolution are poorly understood in the tropical rainforest of Amazonia, and the relative influence of neutral and adaptive processes are continuously discussed. [br/]I am a young scientist interested in the process of genomic divergence in wild (tree) populations. I aimed at understanding how evolution structures the genetic diversity and governs molecular divergence in wild populations, with particular emphases on gene flow and local adaptation. During five years as a young scientist, I worked on answering the following questions, focusing on two tree species occupying vulnerable areas: mainly [i]Eperua falcata[/i] in Amazonia and, to a lesser extent, [i]Abies alba[/i] in the Mediterranean area.[br/][u]Scientific questions:[/u][br/]- Which evolutionary drivers are responsible of the structure of genetic diversity in wild populations occupying wide areas? This question was addressed at different geographical scales: from large (regional) to very local (microgeographic) scales. [br/]- What is the relative influence of neutral (gene flow, inbreeding) and adaptive drivers in the process of genetic divergence?[br/]- Is microgeographic adaptation possible in spite of extensive gene flow between populations occupying the extreme boundaries of an ecological gradient? [br/]- What is the extent of natural selection in the (whole) genome of wild populations? [br/][br/]My research work is at the interface between three promising disciplines: Evolutionary genomics (i.e. the study of populations evolution and the evolutionary drivers behind), Bioinformatics (i.e. the treatment of next-generation data), and Bayesian modelling (i.e. the empirical calibration of complex mechanistic model). I intend to take advantage of the recent advances in sequencing and informatic technologies to bring up to date the field of ecological genetics and evolutionary biology, by developing modern research strategies to study the process of genomic divergence in wild populations.
https://hal.archives-ouvertes.fr/hal-01204218

hal-01204218
https://hal.archives-ouvertes.fr/hal-01204218
PRODINRA : 286326

Éditeur(s) : Pergamon-elsevier Science Ltd
Résumé : Environmental variables affect many processes of fish biology and their fluctuations are thought to be one of the main factors in variability of fish stocks. Recent work has shown that the variability of the environment in the frequency domain (i.e., the environmental noise) can interact with endogenous processes (e.g., density dependence) and affect fluctuations of animal populations. In this study, we investigate whether fluctuations of large pelagics' time series are affected by environmental noise and whether life-history traits of species modulate this response. By analysing several environmental variables and a large dataset of tuna and billfish catch per unit effort (CPUE) time series from the Atlantic, we show that in environments dominated by long-term fluctuations (i.e., red noise) CPUE time series were less variable and displayed smoother fluctuations. Furthermore, larger, slower-growing and later-maturing species were found to be more sensitive to changes of environmental noise than species with a shorter turnover rate. Our results suggest that environmental noise interacts with fish biology; understanding how it is integrated into biological processes might provide important insights to understand the responses of fish stocks dynamics to exploitation and environmental changes. (C) 2010 Elsevier Ltd. All rights reserved.
Progress In Oceanography (0079-6611) (Pergamon-elsevier Science Ltd), 2010-07 , Vol. 86 , N. 1-2 , P. 267-275

Droits : 2010 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00011/12230/9083.pdf
DOI:10.1016/j.pocean.2010.04.025
http://archimer.ifremer.fr/doc/00011/12230/

Éditeur(s) : Oxford Univ Press
Résumé : Biological reference points are important tools for fisheries management. Reference points are not static, butmay change when a population's environment or the population itself changes. Fisheries-induced evolution is one mechanism that can alter population characteristics, leading to "shifting" reference points by modifying the underlying biological processes or by changing the perception of a fishery system. The former causes changes in "true" reference points, whereas the latter is caused by changes in the yardsticks used to quantify a system's status. Unaccounted shifts of either kind imply that reference points gradually lose their intended meaning. This can lead to increased precaution, which is safe, but potentially costly. Shifts can also occur in more perilous directions, such that actual risks are greater than anticipated. Our qualitative analysis suggests that all commonly used reference points are susceptible to shifting through fisheries-induced evolution, including the limit and "precautionary" reference points for spawning-stock biomass, B-lim and B-pa, and the target reference point for fishing mortality, F-0.1. Our findings call for increased awareness of fisheries-induced changes and highlight the value of always basing reference points on adequately updated information, to capture all changes in the biological processes that drive fish population dynamics.
Ices Journal Of Marine Science (1054-3139) (Oxford Univ Press), 2013-07 , Vol. 70 , N. 4 , P. 707-721

Droits : 2013 International Council for the Exploration of the Sea. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
http://archimer.ifremer.fr/doc/00151/26228/24302.pdf
DOI:10.1093/icesjms/fst077
http://archimer.ifremer.fr/doc/00151/26228/

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
Résumé : The presence of biological matter (biofilms) in deep geological sites for storage of, for instance, toxic elements or groundwater in aquifers was clearly proved. That biomass triggers physical and chemical processes which greatly modify the durability and the sustainability of the sites. These processes, mainly from oxidative/reductive reactions, are poorly understood. This is mainly due to the fact that former studies were done at the macroscopic level far away from the micrometric scale where relevant processes induced by bacteria take place. Investigations at microscopic level are needed. Thus, we developed an experimental set-up based on the combined use of optical microscopy (transmission), atomic force microscopy (AFM) and electrical and electro-chemical AFM microscopy (EC_AFM) in order to get simultaneous information on topographic and electro-chemical processes. The first highly sensitive step was to use AFM with biological samples in liquid environment: wepresent here a study about AFM imaging of living, moving or self-immobilized bacteria, in their genuine physiological liquid medium and in true in vivo conditions. No external immobilization protocol, neither chemical nor mechanical was needed. For the first time, the native gliding movements of Gram negative Nostoc cyanobacteria upon the surface were studied by AFM. AFM height and mechanical stiffness data were simultaneously acquired. From these, mechanical parameters, inner turgor pressure and Young modulus, were derived for different bacterial species (Anabaenopsis circularis, Rhodococcus wratislaviensis). Our study revealed that AFM imaging is thus possible on moving living species. These results open a large window on new studies of both dynamical phenomena of practical and fundamental interests such as the formation of biofilms and dynamic properties of bacteria in real physiological conditions. The second delicate step was to combine AFM and optical measurements with electrical ones. We mounted a new experimental set-up coupling real-time (i) monitoring of optical properties as the optical density (OD) evolution related to bulk bacterial growth in liquid or as the counting of number of bacteria adhering on the surface of the sample as well and (ii) electrical and electrochemical measurements. Furthermore, these results will shortly be applied to the optimized monitoring of the in-situ activity of bacteria consuming oil pollutants, following this way, in real-time, the bioremediation of an oilcontaminated soil (ANR ECOTECH_BIOPHY program).
La présence de matière biologique (biofilms) dans les sites de stockage géologique profond, d'éléments toxiques ou encore de l'eau potable des aquifères est maintenant clairement démontrée. Cette biomasse est à l'origine de processus physiques et chimiques qui modifient considérablement la durabilité et la pérennité des sites concernés. Ces processus, principalement de type oxydo-réductif, sont encore mal compris. Ceci est principalement dû aux méthodes d'investigation, principalement macroscopiques, loin de l'échelle micrométrique caractéristique des bactéries. Seules des études, basées sur des méthodes d'investigation locale, peuvent apporter les informations requises. Ainsi, nous avons développé un dispositif expérimental basé sur l'utilisation combinée de la microscopie optique (en transmission), la microscopie à force atomique (AFM) et la microscopie AFM en mode électrique et électrochimique (EC_AFM) afin d'obtenir des informations simultanées sur la topographie de l'échantillon et sur les processus électrochimiques à l'échelle des bactéries. La première étape sensible consistait à utiliser l'AFM sur des échantillons biologiques en milieu liquide: nous présentons ici les résultats de l'imagerie AFM en milieu liquide de plusieurs types de bactéries dans leurs conditions physiologiques naturelles (conditions in vivo). Aucun protocole d'immobilisation, ni chimique ni mécanique, n'a été nécessaire; et pour la première fois, les mouvements de reptation de cyanobactéries Nostoc ont été étudiés par l'AFM. Les études AFM ont permis d'acquérir des données topographiques mais aussi mécaniques : nous avons pu ainsi mesurer le module d'Young, la pression de turgescence de différentes souches bactériennes (Anabaenopsis circularis, Rhodococcus wratislaviensis). Cette étude complète, a révélé que l'imagerie AFM est donc possible sur des espèces vivantes en mouvement. Ces résultats ouvrent une grande fenêtre sur de nouvelles études d'intérêts tels que la formation de biofilms et les propriétés dynamiques de bactéries dans des conditions physiologiques réelles. La deuxième étape délicate était de combiner l'AFM aux mesures optiques et électriques. Nous avons développé un nouveau dispositif expérimental permettant (i) le suivi de l'évolution de la croissance bactérienne par la mesure des propriétés optiques comme la densité optique DO (pour le développement bactérien en volume - milieu planctonique) , ou l'analyse de l'image du substrat par comptage du nombre de bactéries sur la surface de l'échantillon (biofilm), et (ii) les mesures électriques et électrochimiques. L'ensemble de ces résultats sera prochainement appliqué au développement de nouveaux outils de surveillance d'une biodépollution de terrain contaminé par les hydrocarbures, par le suivi in situ et en temps réel de l'activité de bactéries dépolluantes (ECOTECH_BIOPHY ANR).
https://tel.archives-ouvertes.fr/tel-01044714

tel-01044714
https://tel.archives-ouvertes.fr/tel-01044714
https://tel.archives-ouvertes.fr/tel-01044714/document
https://tel.archives-ouvertes.fr/tel-01044714/file/theseDhahri2013.pdf

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) : Gauthier-Villars
Résumé : In contrast to plants, predation on animals is usually lethal. Analysis of the effect of predation on animal populations and on predator-prey dynamics typically assumes this is the case. However, sublethal predation occurs in echinoderms, primarily on the arms of crinoids, asteroids, and ophiuroids. Sublethal predation is important in these echinoderms as it meets one of Harris' (1989) major criteria, affecting basic biological processes such as acquisition of food and allocation of nutrients to growth and reproduction. Sublethal predation would have an effect on their ecological role. It is essential to consider sublethal predation in the analysis of the life-histories of these species.
Oceanologica Acta (0399-1784) (Gauthier-Villars), 1996 , Vol. 19 , N. 3-4 , P. 431-440

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00094/20499/18168.pdf
http://archimer.ifremer.fr/doc/00094/20499/

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : The diversity and functional identity of organisms are known to be relevant to the maintenance of ecosystem processes but can be variable in different environments. Particularly, it is uncertain whether ecosystem processes are driven by complementary effects or by dominant groups of species. We investigated how community structure (i.e., the diversity and relative abundance of biological entities) explains the community-level contribution of Neotropical ant communities to different ecosystem processes in different environments. Ants were attracted with food resources representing six ant-mediated ecosystem processes in four environments: ground and vegetation strata in cropland and forest habitats. The exploitation frequencies of the baits were used to calculate the taxonomic and trophic structures of ant communities and their contribution to ecosystem processes considered individually or in combination (i.e., multifunctionality). We then investigated whether community structure variables could predict ecosystem processes and whether such relationships were affected by the environment. We found that forests presented a greater biodiversity and trophic complementarity and lower dominance than croplands, but this did not affect ecosystem processes. In contrast, trophic complementarity was greater on the ground than on vegetation and was followed by greater resource exploitation levels. Although ant participation in ecosystem processes can be predicted by means of trophic-based indices, we found that variations in community structure and performance in ecosystem processes were best explained by environment. We conclude that determining the extent to which the dominance and complementarity of communities affect ecosystem processes in different environments requires a better understanding of resource availability to different species.
ISSN: 0029-8549

hal-01606497
https://hal.archives-ouvertes.fr/hal-01606497
DOI : 10.1007/s00442-016-3741-z
PRODINRA : 407457

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Genetics and molecular biology have been instrumental for a better understanding of heritable defects causing human infertility over the past decades. More recently, the field of reproductive biology has harnessed genome biological approaches to gain insight into molecular processes underlying normal and pathological gametogenesis and gamete function. We are currently witnessing yet another quantum leap in our ability to monitor the flow of information from the genome via the transcriptome to the proteome: tiling arrays that cover both strands of a given target genome and RNA-Seq, a method based on ultra-high throughput DNA sequencing, enable us to study noncoding and protein-coding transcripts with unprecedented precision and depth at a reasonable cost. These technologies have spawned a thriving discipline within the bioinformatics field that employs information technology for managing and interpreting biological high-throughput data. This review outlines database projects and online analysis tools useful for life scientists in general and discusses in detail selected projects that have specifically been developed for researchers and clinicians in the field of reproductive biology. This article is part of a Special Issue entitled: Molecular Genetics of Human Reproductive Failure.
ISSN: 0006-3002

hal-00877444
https://hal.archives-ouvertes.fr/hal-00877444
DOI : 10.1016/j.bbadis.2012.05.018
PUBMED : 22687534

Éditeur(s) : Université de Bretagne Occidentale
Résumé : Study of mineral suspended particulate matter (SPM) is essential to understand ecosystem dynamics. SPM influences light penetration which is closely related to primary production and carries pollutants and nutrients within the water masses. This work aims to study near-surface mineral SPM dynamics in the English Channel using two complementary methods: remote-sensing by satellites and numerical modelling. Firstly, MODIS and MERIS satellite images processed by the IFREMER semi-analytical algorithm and describing non-algal SPM, are analysed to build three statistical models which are able to estimate near-surface SPM using simple variables, e.g., tidal coefficient, significant wave height and mean chlorophyll-a concentration. Secondly, the three-dimensional hydrosedimentary model ROMS (Regional Ocean Modeling System) is applied in the English Channel. It considers tidal forcing along open boundaries, wind stress at the sea-surface, wave-current interactions in the bottom boundary layer and realistic heterogeneous bottom sediments. Results of the more sophisticated statistical model is also used to impose SPM concentrations at open boundaries. Sensitivity tests on SPM boundary conditions show the importance of prescribing realistic sediment concentrations to improve the model predictions. Biological influences on mineral SPM are also tested using settling velocity and critical shear stress for erosion which vary with seasons. Both statistical and numerical models highlight and locate respective influences of tide, waves and biology on mineral SPM. Numerical predictions indicate that near-surface SPM is mainly composed of silts (>70%). Near-surface suspended silts come largely from seabed resuspension alongshore in the Eastern Channel and from the open boundaries of our limited-area coastal model at the West of Cotentin Peninsula and offshore. Near-surface SPM variations are investigated at semi-diurnal, neap-spring tidal cycle time scales and during a wave event. Finally, dynamics of sediments in the turbidity maximum zone around the Isle of Wight is examined depending on hydrodynamical conditions in order to distinguish the role played by advection and local erosion/settling processes in this area. Keywords: Suspended particulate matter, satellite, remote-sensing, modelling, English Channel, sediments, turbidity, tide, wave
L'étude des matières en suspension (MES) minérales est essentielle pour comprendre le fonctionnement des écosystèmes en Manche : les MES influencent la pénétration de la lumière dans la colonne d'eau, paramètre clé pour la production biologique, et sont susceptibles de transporter des polluants et nutriments. Lors de ce travail, la dynamique des MES minérales de surface en Manche est étudiée à l'aide de deux méthodes complémentaires : l'observation par satellite et la modélisation numérique tridimensionnelle. Dans un premier temps, les images satellite MODIS et MERIS, traitées par l'algorithme semi-analytique développé par l'IFREMER et représentant les MES non-algales de surface, sont analysées afin d'élaborer trois modèles statistiques permettant d'estimer la MES de surface en fonction de variables basiques telles que le coefficient de marée, la hauteur significative des vagues et la concentration moyenne en chlorophylle-a. Dans un deuxième temps, le modèle hydrosédimentaire multiclasse tridimensionnel ROMS (Regional Ocean Modeling System) est implémenté en Manche. Il prend en considération le forçage par la marée aux frontières ouvertes, la contrainte exercée par le vent à la surface de la mer, l'interaction houle-courant en couche limite de fond et l’hétérogénéité spatiale réaliste du lit sédimentaire. Les résultats du modèle statistique le plus sophistiqué sont également utilisés pour forcer la concentration en MES aux frontières ouvertes du domaine de calcul. Des tests de sensibilité sur les conditions limites montrent l'importance de considérer de manière réaliste les sédiments entrant en Manche par les frontières ouvertes lors de la modélisation numérique. L'influence de la biologie sur les MES minérales est testée en utilisant une formulation de la vitesse de chute et de la contrainte critique d'érosion variant saisonnièrement. Grâce à ces deux outils associés, les influences respectives de la marée, de la houle et de la biologie sur les MES minérales sont mises en avant et localisées en Manche. Le modèle numérique prédit que les MES de surface sont composées principalement de silts (>70%). Les silts en suspension en surface proviennent majoritairement du lit sédimentaire près des côtes en Manche orientale et des frontières ouvertes du domaine de calcul à l'ouest de la presqu'île du Cotentin et au large en Manche centrale et orientale. Les variations des MES de surface sont ensuite étudiées aux échelles des cycles de marée semi-diurnes, vive-eau/morte-eau et autour d'un épisode de houles. Enfin, l'évolution de la concentration de sédiments dans la zone de forte turbidité autour de l'île de Wight peut être analysée suivant les conditions hydrodynamiques afin d'évaluer les rôles respectifs des processus locaux d'érosion/dépot et d'advection dans la génération de ces turbidités remarquables. Mots-clés : Matière en suspension, télédétection, satellite, modélisation, Manche, sédiments, turbidité, marée, houle

Droits : 2013 UBO
http://archimer.ifremer.fr/doc/00157/26783/24884.pdf
http://archimer.ifremer.fr/doc/00157/26783/

Éditeur(s) : HAL CCSD
Résumé : International audience
The pollination of Philodendron solimoesense (subgenus Meconostigma) was studied in four populations of French Guiana. Flowering is asynchronous within each population during July, and the flowering cycle is a 2-d process. Numerous insects visit Philodendron inflorescences, but the main pollinator seems to be Cyclocephala colasi (Scarabaeidae, Dynastinae). The pollination process displays aspects typical of beetle pollination: the production of heat and of a strong odor, the presence of a food reward (stigmatic secretion and sterile male flowers), and the presence of a copulation chamber. Flower heat production is important (ca. 117C above the ambient air) and may help to volatilize the fragrance. Attraction and choice-test experiments showed that C. colasi is not likely to depend on chemical information (such as pheromone) to localize conspecifics but may rely instead on stimuli produced by the inflorescences in order to meet mating partners
International Journal of Plant Sciences

hal-01202475
https://hal.archives-ouvertes.fr/hal-01202475

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : Understanding the genetic mechanisms of speciation and basis of species differences is among the most important challenges in evolutionary biology. Two questions of particular interest are what roles divergent selection and chromosomal differentiation play in these processes. A number of recently proposed theories argue that chromosomal rearrangements can facilitate the development and maintenance of reproductive isolation and species differences by suppressing recombination within rearranged regions. Reduced recombination permits the accumulation of alleles contributing to isolation and adaptive differentiation and protects existing differences from the homogenizing effects of introgression between incipient species. Here, we examine patterns of genetic diversity and divergence in rearranged versus collinear regions in two widespread, extensively hybridizing sunflower species, Helianthus annuus and Helianthus petiolaris, using sequence data from 77 loci distributed throughout the genomes of the two species. We find weak evidence for increased genetic divergence near chromosomal break points but not within rearranged regions overall. We find no evidence for increased rates of adaptive divergence on rearranged chromosomes; in fact, collinear chromosomes show a far greater excess of fixed amino acid differences between the two species. A comparison with a third sunflower species indicates that much of the nonsynonymous divergence between H. annuus and H. petiolaris probably occurred during or soon after their formation. Our results suggest a limited role for chromosomal rearrangements in genetic divergence, but they do document substantial adaptive divergence and provide further evidence of how species integrity and genetic identity can be maintained at many loci in the face of extensive hybridization and gene flow.
ISSN: 0737-4038

hal-01032153
https://hal.archives-ouvertes.fr/hal-01032153
DOI : 10.1093/molbev/msp043

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high-throughput sequencing. From outer Oslofjorden, S Norway, nano- and picoplanktonic samples were collected monthly for 2years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta-specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA-sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September-October (autumn) and lowest in April-May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP-3-5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in-depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters. See also the Perspective by Massana
ISSN: 0962-1083

hal-01545321
https://hal.archives-ouvertes.fr/hal-01545321
DOI : 10.1111/mec.13160

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