Évolution contemporaine et plasticité phénotypique chez le saumon atlantique sous la lunette du transcriptome.

L’un des principaux objectifs des travaux présentés dans cette thèse était d’étudier les mécanismes moléculaires de l’évolution contemporaine chez le saumon atlantique (Salmo salar) à l’aide de la technique des bio-puces. La création de lignées de saumon d’élevage est un exemple d’évolution contemporaine dirigée par une activité humaine. La comparaison des niveaux de transcription de milliers de gènes entre saumons d’élevage, saumons sauvages et leurs hybrides nous a permis d’en identifier certains dont le niveau de transcription présentait des différences héritables entre ces groupes. Ces résultats nous renseignent sur les mécanismes génétiques de l’évolution parallèle et permettent d’évaluer l’ampleur des différences génétiques accumulées en 25 à 35 ans entre saumons d’élevage et sauvages ainsi que l’importance relative de l’additivité dans le contrôle génétique des niveaux de transcription géniques. Ils appuient l’idée que des mesures limitant les échappées de saumons d’élevage doivent être prises rapidement. Dans d’autres travaux, l’estimation du Qst ainsi que de l’héritabilité du niveau de transcription de milliers de gènes nous a permis d’appliquer une méthode nouvelle, le « balayage transcriptomique », afin d’identifier des gènes pour lesquels le contrôle génétique du niveau de transcription a potentiellement évolué en 6 générations sous l’effet de la sélection naturelle chez deux sous-populations de saumon de la rivière Ste-Marguerite. Un autre objectif de ces travaux était l’étude des mécanismes moléculaires de la plasticité phénotypique. Ainsi, la comparaison des niveaux de transcription géniques chez des juvéniles de saumons sains ou atteints de saprolegniose nous a permis d’identifier plusieurs des acteurs potentiels de la réponse immunitaire à cette infection, incluant notamment plusieurs gènes codant pour des protéines de la réponse immunitaire non-spécifique. Enfin, nous avons identifié, en comparant le niveau de transcription de 16006 gènes dans les cerveaux de saumons juvéniles dominants ou subordonnés en présence ou en l’absence de truite arc-en-ciel, certains acteurs moléculaires potentiellement impliqués dans la perte plastique de dominance sociale chez de jeunes saumons mis en présence de truites, contribuant ainsi à développer les connaissances sur les liens entre la transcription génique et la plasticité comportementale dans le contexte d’interactions compétitives entre espèces invasives et espèces indigènes.One of the main objectives of the work presented here was to study the molecular mechanisms of contemporary evolution in Atlantic salmon (Salmo salar) using microarrays. The creation of salmon breeding lines through artificial selection is an example of contemporary evolution driven by human activities. Comparing the transcription levels of thousands of genes between farmed salmon, wild salmon and their hybrids allowed us to identify genes of which the transcription level showed heritable differences between these groups. The results inform us on the genetic mechanisms of parallel evolution and allow us to evaluate the extent of the genetic differences accumulated in only 25 to 35 years of artificial selection between wild and farmed salmon as well as the prevalence of additivity in the genetic control of gene transcription. These results also support the idea that measures to markedly reduce escapes of farmed salmon and their reproduction in the wild are urgently needed. In another study, estimating gene transcription level Qst and heritability for thousands of genes allowed us to apply a new method, the «transcriptome scan», to identify genes for which the genetic control of transcription is likely to have evolved in only 6 generations under the effect of directional selection in two Atlantic salmon sub-populations from rivière Ste-Marguerite. Another goal of this thesis was to study the molecular mechanisms of phenotypic plasticity. Hence, the comparison of transcript levels from saprolegniosis-affected or healthy salmon juveniles allowed us to identify several potential actors of the immune response to this infection, including several genes coding for proteins of the acute-phase response. Finally, we compared the transcription levels of thousands of genes in the brains of socially dominant or subordinate salmon juveniles in absence or presence of rainbow trout (O. mykiss), which allowed us to identify several potential molecular actors in the plastic loss of social dominance hierarchies in salmon in presence of trout. This contributes to a better understanding of the relation between gene transcription and behavioural plasticity in the context of competitive interactions between invasive and native species

Disturbance of Social Hierarchy by an Invasive Species: A Gene Transcription Study

BACKGROUND: Ecological and evolutionary changes in native populations facing invasion by exotic species are increasingly reported. Recently, it has been shown that competition with exotic rainbow trout (Oncorhynchus mykiss) disrupts dominance hierarchies within groups of native Atlantic salmon (Salmo salar). The genetic and molecular actors underlying phenotypic plasticity are poorly understood. METHODOLOGY: Here, we aimed at identifying the genetic and molecular actors contributing to this plastic loss of dominance hierarchies as well as at identifying genes implicated in behaviours related to social dominance. By using microarrays, we compared the genome-wide gene transcription profiles in brains of dominant versus subordinate juvenile Atlantic salmon in presence or absence of a competitive rainbow trout. PRINCIPAL FINDINGS: Adding the trout competitor resulted in dominant and subordinate salmon being more similar, both behaviourally and at the level of brain gene transcription patterns. Genes for which transcription levels differed between dominant and subordinate salmon in the absence of exotic trout were mainly over-expressed in dominant salmon and included genes implicated in protein turnover, neuronal structural change and oxygen transport. CONCLUSIONS/SIGNIFICANCE: Our study provides one of the few examples demonstrating a close interplay between behavioural plasticity and gene transcription, therefore contributing to the understanding of the molecular mechanisms underlying these processes in an ecologically relevant context

Characterizing the Habitable Zones of Exoplanetary Systems with a Large Ultraviolet/Visible/Near-IR Space Observatory

Understanding the surface and atmospheric conditions of Earth-size, rocky planets in the habitable zones (HZs) of low-mass stars is currently one of the greatest astronomical endeavors. Knowledge of the planetary effective surface temperature alone is insufficient to accurately interpret biosignature gases when they are observed in the coming decades. The UV stellar spectrum drives and regulates the upper atmospheric heating and chemistry on Earth-like planets, is critical to the definition and interpretation of biosignature gases, and may even produce false-positives in our search for biologic activity. This white paper briefly describes the scientific motivation for panchromatic observations of exoplanetary systems as a whole (star and planet), argues that a future NASA UV/Vis/near-IR space observatory is well-suited to carry out this work, and describes technology development goals that can be achieved in the next decade to support the development of a UV/Vis/near-IR flagship mission in the 2020s.Comment: Submitted in response to NASA call for white papers: "Large Astrophysics Missions to Be Studied by NASA Prior to the 2020 Decadal Survey

Imaging Cool Giant Planets in Reflected Light: Science Investigations and Synergy with Habitable Planets

Planned astronomical observatories of the 2020s will be capable of obtaining reflected light photometry and spectroscopy of cool extrasolar giant planets. Here we explain that such data are valuable both for understanding the origin and evolution of giant planets as a whole and for preparing for the interpretation of similar datasets from potentially habitable extrasolar terrestrial planets in the decades to follow.Comment: Science white paper submitted to the Astro 2020 Decadal Survey on Astronomy and Astrophysics. Replace version to fix typo in co-signer name and add figure credit

HD 172555: Detection of 63 μ m [OI] emission in a debris disc

Astronomy and Astrophysics 546 (2012): L8 Reproduced with permission from Astronomy & AstrophysicsContext. HD 172555 is a young A7 star belonging to the β Pictoris moving group that harbours a debris disc. The Spitzer/IRS spectrum of the source showed mid-IR features such as silicates and glassy silica species, indicating the presence of a warm dust component with small grains, which places HD 172555 among the small group of debris discs with such properties. The IRS spectrum also shows a possible emission of SiO gas. Aims. We aim to study the dust distribution in the circumstellar disc of HD 172555 and to asses the presence of gas in the debris disc. Methods. As part of the GASPS open time key programme, we obtained Herschel/PACS photometric and spectroscopic observations of the source.We analysed PACS observations of HD 172555 and modelled the spectral energy distribution with a modified blackbody and the gas emission with a two-level population model with no collisional de-excitation. Results. We report for the first time the detection of [OI] atomic gas emission at 63.18 μm in the HD 172555 circumstellar disc. We detect excesses due to circumstellar dust toward HD 172555 in the three photometric bands of PACS (70, 100, and 160 μm).We derive a large dust particle mass of (4.8 ± 0.6) × 10−4 M⊕ and an atomic oxygen mass of 2.5 × 10−2R2 M⊕, where R in AU is the separation between the star and the inner disc. Thus, most of the detected mass of the disc is in the gaseous phaseThis research has been funded by Spanish grants AYA 2010-21161-C02-02, CDS2006-00070 and PRICIT-S2009/ESP-1496. J.-C. Augereau and J. Lebreton thank the ANR (contract ANR-2010 BLAN-0505-01, EXOZODI) and the CNES-PNP for financial support. C. Pinte, F. Menard and W.-F. Thi acknowledges funding from the EU FP7-2011 under Grant Agreement nr. 284405. G. Meeus is supported by RYC-2011-07920. G. Meeus, C. Eiroa, I. Mendigutía and B. Montesinos are partly supported by AYA-2011-26202. F.M. acknowledges support from the Millennium Science Initiative (Chilean Ministry of Economy), through grant ÒNucleus P10-022-F

Chiral and deconfinement transition from correlation functions: SU(2) vs. SU(3)

We study a gauge invariant order parameter for deconfinement and the chiral condensate in SU(2) and SU(3) Yang-Mills theory in the vicinity of the deconfinement phase transition using the Landau gauge quark and gluon propagators. We determine the gluon propagator from lattice calculations and the quark propagator from its Dyson-Schwinger equation, using the gluon propagator as input. The critical temperature and a deconfinement order parameter are extracted from the gluon propagator and from the dependency of the quark propagator on the temporal boundary conditions. The chiral transition is determined using the quark condensate as order parameter. We investigate whether and how a difference in the chiral and deconfinement transition between SU(2) and SU(3) is manifest.Comment: 15 pages, 9 figures. For clarification one paragraph and two references added in the introduction and two sentences at the end of the first and last paragraph of the summary. Appeared in EPJ

The MUSCLES Treasury Survey. IV. : Scaling relations for ultraviolet, Ca II K, and energetic particle fluxes from M dwarfs

Characterizing the UV spectral energy distribution (SED) of an exoplanet host star is critically important for assessing its planet's potential habitability, particularly for M dwarfs, as they are prime targets for current and near-term exoplanet characterization efforts and atmospheric models predict that their UV radiation can produce photochemistry on habitable zone planets different from that on Earth. To derive ground-based proxies for UV emission for use when Hubble Space Telescope (HST) observations are unavailable, we have assembled a sample of 15 early to mid-M dwarfs observed by HST and compared their nonsimultaneous UV and optical spectra. We find that the equivalent width of the chromospheric Ca ii K line at 3933 Å, when corrected for spectral type, can be used to estimate the stellar surface flux in ultraviolet emission lines, including H i Lyα. In addition, we address another potential driver of habitability: energetic particle fluxes associated with flares. We present a new technique for estimating soft X-ray and >10 MeV proton flux during far-UV emission line flares (Si iv and He ii) by assuming solar-like energy partitions. We analyze several flares from the M4 dwarf GJ 876 observed with HST and Chandra as part of the MUSCLES Treasury Survey and find that habitable zone planets orbiting GJ 876 are impacted by large Carrington-like flares with peak soft X-ray fluxes ≥10−3 W m−2 and possible proton fluxes ~102–103 pfu, approximately four orders of magnitude more frequently than modern-day Earth.Publisher PDFPeer reviewe

The MUSCLES Treasury Survey. I. Motivation and overview

Ground- and space-based planet searches employing radial velocity techniques and transit photometry have detected thousands of planet-hosting stars in the Milky Way. With so many planets discovered, the next step toward identifying potentially habitable planets is atmospheric characterization. While the Sun–Earth system provides a good framework for understanding the atmospheric chemistry of Earth-like planets around solar-type stars, the observational and theoretical constraints on the atmospheres of rocky planets in the habitable zones (HZs) around low-mass stars (K and M dwarfs) are relatively few. The chemistry of these atmospheres is controlled by the shape and absolute flux of the stellar spectral energy distribution (SED), however, flux distributions of relatively inactive low-mass stars are poorly understood at present. To address this issue, we have executed a panchromatic (X-ray to mid-IR) study of the SEDs of 11 nearby planet-hosting stars, the Measurements of the Ultraviolet Spectral Characteristics of Low-mass Exoplanetary Systems (MUSCLES) Treasury Survey. The MUSCLES program consists visible observations from Hubble and ground-based observatories. Infrared and astrophysically inaccessible wavelengths (EUV and Lyα ) are reconstructed using stellar model spectra to fill in gaps in the observational data. In this overview and the companion papers describing the MUSCLES survey, we show that energetic radiation (X-ray and ultraviolet) is present from magnetically active stellar atmospheres at all times for stars as late as M6. The emission line luminosities of C iv and Mg ii are strongly correlated with band-integrated luminosities and we present empirical relations that can be used to estimate broadband FUV and XUV (≡X-ray + EUV) fluxes from individual stellar emission line measurements. We find that while the slope of the SED, FUV/NUV, increases by approximately two orders of magnitude form early K to late M dwarfs (≈0.01–1), the absolute FUV and XUV flux levels at their corresponding HZ distances are constant to within factors of a few, spanning the range 10–70 erg cm−2 s−1 in the HZ. Despite the lack of strong stellar activity indicators in their optical spectra, several of the M dwarfs in our sample show spectacular UV flare emission in their light curves. We present an example with flare/quiescent ultraviolet flux ratios of the order of 100:1 where the transition region energy output during the flare is comparable to the total quiescent luminosity of the star Eflare(UV) ∼ 0.3 L*Δt (Δt = 1 s). Finally, we interpret enhanced L(line)/LBol ratios for C iv and N v as tentative observational evidence for the interaction of planets with large planetary mass-to-orbital distance ratios (Mplan/aplan) with the transition regions of their host stars.Publisher PDFPeer reviewe