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26 Research products, page 1 of 3

  • European Marine Science
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  • Open Access
    Project: SNSF | Investigation of the tida... (200517)

    Abstract. Ground-based remote sensing of atmospheric parameters is often limited to single station observations by vertical profiles at a certain geographic location. This is a limiting factor for investigating gravity wave dynamics as the spatial information is often missing, e.g., horizontal wavelength, propagation direction or intrinsic frequency. In this study, we present a new retrieval algorithm for multistatic meteor radar networks to obtain tomographic 3-D wind fields within a pre-defined domain area. The algorithm is part of the Agile Software for Gravity wAve Regional Dynamics (ASGARD) and called 3D-Var, and based on the optimal estimation technique and Bayesian statistics. The performance of the 3D-Var retrieval is demonstrated using two meteor radar networks: the Nordic Meteor Radar Cluster and the Chilean Observation Network De Meteor Radars (CONDOR). The optimal estimation implementation provide statistically sound solutions and diagnostics from the averaging kernels and measurement response. We present initial scientific results such as body forces of breaking gravity waves leading to two counter-rotating vortices and horizontal wavelength spectra indicating a transition between the rotational k−3 and divergent k-5/3 mode at scales of 80–120 km. In addition, we performed a keogram analysis over extended periods to reflect the latitudinal and temporal impact of a minor sudden stratospheric warming in December 2019. Finally, we demonstrate the applicability of the 3D-Var algorithm to perform large-scale retrievals to derive meteorological wind maps covering a latitude region from Svalbard, north of the European Arctic mainland, to central Norway.

  • Open Access English
    Authors: 
    Francesco Maria Sabatini; Jonathan Lenoir; Tarek Hattab; Elise A. Arnst; Milan Chytrý; Jürgen Dengler; Patrice de Ruffray; Stephan M. Hennekens; Ute Jandt; Florian Jansen; +151 more
    Countries: Switzerland, Italy, France, Norway, Finland, France, France, Norway, France, Croatia ...
    Project: EC | IMBALANCE-P (610028), SNSF | FutureWeb (184131), EC | T-FORCES (291585), EC | BACI (640176)

    Sabatini, F.M., Lenoir, J., Hattab, T., Arnst, E.A., Chytrý, M., Dengler, J., De Ruffray, P., Hennekens, S.M., Jandt, U., Jansen, F., Jiménez-Alfaro, B., Kattge, J., Levesley, A., Pillar, V.D., Purschke, O., Sandel, B., Sultana, F., Aavik, T., Aćić, S., Acosta, A.T.R., Agrillo, E., Alvarez, M., Apostolova, I., Arfin Khan, M.A.S., Arroyo, L., Attorre, F., Aubin, I., Banerjee, A., Bauters, M., Bergeron, Y., Bergmeier, E., Biurrun, I., Bjorkman, A.D., Bonari, G., Bondareva, V., Brunet, J., Čarni, A., Casella, L., Cayuela, L., Černý, T., Chepinoga, V., Csiky, J., Ćušterevska, R., De Bie, E., de Gasper, A.L., De Sanctis, M., Dimopoulos, P., Dolezal, J., Dziuba, T., El-Sheikh, M.A.E.-R.M., Enquist, B., Ewald, J., Fazayeli, F., Field, R., Finckh, M., Gachet, S., Galán-de-Mera, A., Garbolino, E., Gholizadeh, H., Giorgis, M., Golub, V., Alsos, I.G., Grytnes, J.-A., Guerin, G.R., Gutiérrez, A.G., Haider, S., Hatim, M.Z., Hérault, B., Hinojos Mendoza, G., Hölzel, N., Homeier, J., Hubau, W., Indreica, A., Janssen, J.A.M., Jedrzejek, B., Jentsch, A., Jürgens, N., Kącki, Z., Kapfer, J., Karger, D.N., Kavgacı, A., Kearsley, E., Kessler, M., Khanina, L., Killeen, T., Korolyuk, A., Kreft, H., Kühl, H.S., Kuzemko, A., Landucci, F., Lengyel, A., Lens, F., Lingner, D.V., Liu, H., Lysenko, T., Mahecha, M.D., Marcenò, C., Martynenko, V., Moeslund, J.E., Monteagudo Mendoza, A., Mucina, L., Müller, J.V., Munzinger, J., Naqinezhad, A., Noroozi, J., Nowak, A., Onyshchenko, V., Overbeck, G.E., Pärtel, M., Pauchard, A., Peet, R.K., Peñuelas, J., Pérez-Haase, A., Peterka, T., Petřík, P., Peyre, G., Phillips, O.L., Prokhorov, V., Rašomavičius, V., Revermann, R., Rivas-Torres, G., Rodwell, J.S., Ruprecht, E., Rūsiņa, S., Samimi, C., Schmidt, M., Schrodt, F., Shan, H., Shirokikh, P., Šibík, J., Šilc, U., Sklenář, P., Škvorc, Ž., Sparrow, B., Sperandii, M.G., Stančić, Z., Svenning, J.-C., Tang, Z., Tang, C.Q., Tsiripidis, I., Vanselow, K.A., Vásquez Martínez, R., Vassilev, K., Vélez-Martin, E., Venanzoni, R., Vibrans, A.C., Violle, C., Virtanen, R., von Wehrden, H., Wagner, V., Walker, D.A., Waller, D.M., Wang, H.-F., Wesche, K., Whitfeld, T.J.S., Willner, W., Wiser, S.K., Wohlgemuth, T., Yamalov, S., Zobel, M., Bruelheide, H. EU H2020 project BACI, Grant No. 640176 (...)

  • Open Access English
    Authors: 
    Julie Loisel; Angela V. Gallego-Sala; Matthew J. Amesbury; Gabriel Magnan; Gusti Z. Anshari; David W. Beilman; J. C. Benavides; Jerome Blewett; Philip Camill; Dan J. Charman; +60 more
    Countries: France, United Kingdom, Finland, Germany, United Kingdom, France
    Project: NSF | NNA: Collaborative Resear... (1802838), NSERC , NSF | RUI: Ecosystem responses ... (1019523), NSF | NNA: Collaborative Resear... (1802825), SNSF | Climate and Environmental... (172476)

    Peatlands are impacted by climate and land-use changes, with feedback to warming by acting as either sources or sinks of carbon. Expert elicitation combined with literature review reveals key drivers of change that alter peatland carbon dynamics, with implications for improving models. The carbon balance of peatlands is predicted to shift from a sink to a source this century. However, peatland ecosystems are still omitted from the main Earth system models that are used for future climate change projections, and they are not considered in integrated assessment models that are used in impact and mitigation studies. By using evidence synthesized from the literature and an expert elicitation, we define and quantify the leading drivers of change that have impacted peatland carbon stocks during the Holocene and predict their effect during this century and in the far future. We also identify uncertainties and knowledge gaps in the scientific community and provide insight towards better integration of peatlands into modelling frameworks. Given the importance of the contribution by peatlands to the global carbon cycle, this study shows that peatland science is a critical research area and that we still have a long way to go to fully understand the peatland-carbon-climate nexus. Peer reviewed

  • Publication . Article . Other literature type . 2020
    Open Access English
    Authors: 
    Darrell S. Kaufman; Nicholas P. McKay; Cody C. Routson; M. P. Erb; Basil A. S. Davis; Oliver Heiri; Samuel L Jaccard; Jessica E. Tierney; Christoph Dätwyler; Yarrow Axford; +83 more
    Publisher: Nature Publishing Group
    Countries: United Kingdom, Belgium, Switzerland, France, France, France, Argentina, Italy, France, Switzerland ...
    Project: SNSF | Exploring novel technolog... (180887), SNSF | CRISPR/Cas9 genome-editin... (160230)

    A comprehensive database of paleoclimate records is needed to place recent warming into the longer-term context of natural climate variability. We present a global compilation of quality-controlled, published, temperature-sensitive proxy records extending back 12,000 years through the Holocene. Data were compiled from 679 sites where time series cover at least 4000 years, are resolved at sub-millennial scale (median spacing of 400 years or finer) and have at least one age control point every 3000 years, with cut-off values slackened in data-sparse regions. The data derive from lake sediment (51%), marine sediment (31%), peat (11%), glacier ice (3%), and other natural archives. The database contains 1319 records, including 157 from the Southern Hemisphere. The multi-proxy database comprises paleotemperature time series based on ecological assemblages, as well as biophysical and geochemical indicators that reflect mean annual or seasonal temperatures, as encoded in the database. This database can be used to reconstruct the spatiotemporal evolution of Holocene temperature at global to regional scales, and is publicly available in Linked Paleo Data (LiPD) format. Measurement(s)climateTechnology Type(s)digital curationFactor Type(s)temporal interval • geographic location • proxy typeSample Characteristic - Environmentclimate systemSample Characteristic - LocationEarth (planet) Machine-accessible metadata file describing the reported data: https://www.ncdc.noaa.gov/paleo/study/27330

  • Open Access English
    Authors: 
    Anna Czarkwiani; David Dylus; Luisana Carballo; Paola Oliveri;
    Publisher: Cold Spring Harbor Laboratory
    Project: WT | Developmental and Stem Ce... (099745), SNSF | Harnessing Phylogenetic V... (150654), EC | ASSEMBLE (227799)

    ABSTRACT Regeneration as an adult developmental process is in many aspects similar to embryonic development. Although many studies point out similarities and differences, no large-scale, direct and functional comparative analyses between development and regeneration of a specific cell type or structure in one animal exist. Here, we use the brittle star Amphiura filiformis to characterise the role of the FGF signalling pathway during skeletal development in embryos and arm regeneration. In both processes, we find ligands expressed in ectodermal cells that flank underlying skeletal mesenchymal cells, which express the receptors. Perturbation of FGF signalling showed inhibited skeleton formation in both embryogenesis and regeneration, without affecting other key developmental processes. Differential transcriptome analysis finds mostly differentiation genes rather than transcription factors to be downregulated in both contexts. Moreover, comparative gene analysis allowed us to discover brittle star-specific differentiation genes. In conclusion, our results show that the FGF pathway is crucial for skeletogenesis in the brittle star, as in other deuterostomes, and provide evidence for the re-deployment of a developmental gene regulatory module during regeneration. Summary: Cellular and molecular analyses of FGF signalling perturbation during embryonic development and arm regeneration of the brittle Amphiura filiformis identify a conserved role in the formation of the skeleton in both processes.

  • Publication . Article . Other literature type . Preprint . 2019
    Open Access English
    Authors: 
    Daniel Mameri; Corina van Kammen; Ton G. G. Groothuis; Ole Seehausen; Martine E. Maan;
    Countries: Netherlands, Portugal, Switzerland
    Project: SNSF | The colours of speciation... (126340)

    Electronic supplementary material is available online at https://dx.doi.org/10.6084/m9.figshare. c.4440182 When different genotypes choose different habitats to better match their phenotypes, genetic differentiation within a population may be promoted. Mating within those habitats may subsequently contribute to reproductive isolation. In cichlid fish, visual adaptation to alternative visual environments is hypothesized to contribute to speciation. Here, we investigated whether variation in visual sensitivity causes different visual habitat preferences, using two closely related cichlid species that occur at different but overlapping water depths in Lake Victoria and that differ in visual perception (Pundamilia spp.). In addition to species differences, we explored potential effects of visual plasticity, by rearing fish in two different light conditions: broad-spectrum (mimicking shallow water) and red-shifted (mimicking deeper waters). Contrary to expectations, fish did not prefer the light environment that mimicked their typical natural habitat. Instead, we found an overall preference for the broad-spectrum environment. We also found a transient influence of the rearing condition, indicating that the assessment of microhabitat preference requires repeated testing to control for familiarity effects. Together, our results show that cichlid fish exert visual habitat preference but do not support straightforward visual habitat matching info:eu-repo/semantics/publishedVersion

  • Open Access
    Authors: 
    Javier del Campo; Thierry J. Heger; Raquel Rodríguez-Martínez; Alexandra Z. Worden; Thomas A. Richards; Ramon Massana; Patrick J. Keeling;
    Publisher: Cold Spring Harbor Laboratory
    Project: TARA | Tara Oceans (2), SNSF | Diversity and evolutionar... (145374), CIHR , EC | CAARL (331450)

    Apicomplexans are a group of microbial eukaryotes that contain some of the most well-studied parasites, including widespread intracellular pathogens of mammals such as Toxoplasma and Plasmodium (the agent of malaria), and emergent pathogens like Cryptosporidium and Babesia. Decades of research have illuminated the pathogenic mechanisms, molecular biology, and genomics of model apicomplexans, but we know surprisingly little about their diversity and distribution in natural environments. In this study we analyze the distribution of apicomplexans across a range of both host-associated and free-living environments, covering animal hosts from cnidarians to mammals, and ecosystems from soils to fresh and marine waters. Using publicly available small subunit (SSU) rRNA gene databases, high-throughput environmental sequencing (HTES) surveys such as Tara Oceans and VAMPS, as well as our own generated HTES data, we developed an apicomplexan reference database, which includes the largest apicomplexan SSU rRNA tree available to date and encompasses comprehensive sampling of this group and their closest relatives. This tree allowed us to identify and correct incongruences in the molecular identification of sequences, particularly within the hematozoans and the gregarines. Analyzing the diversity and distribution of apicomplexans in HTES studies with this curated reference database also showed a widespread, and quantitatively important, presence of apicomplexans across a variety of free-living environments. These data allow us to describe a remarkable molecular diversity of this group compared with our current knowledge, especially when compared with that identified from described apicomplexan species. This revision is most striking in marine environments, where potentially the most diverse apicomplexans apparently exist, but have not yet been formally recognized. The new database will be useful for both microbial ecology and epidemiological studies, and provide valuable reference for medical and veterinary diagnosis especially in cases of emerging, zoonotic, and cryptic infections.

  • Publication . Article . Other literature type . 2018
    Open Access
    Authors: 
    Katherine L. Yates; Phil J. Bouchet; M. Julian Caley; Kerrie Mengersen; Christophe F. Randin; Stephen Parnell; Alan H. Fielding; Andrew J. Bamford; Stephen Ban; A. Márcia Barbosa; +40 more
    Publisher: eScholarship, University of California
    Countries: United Kingdom, France, United States, Switzerland
    Project: SNSF | SCODA - Scaling from indi... (168136), ARC | Discovery Early Career Re... (DE140100701), ARC | Discovery Early Career Re... (DE170100841)

    International audience; Predictive models are central to many scientific disciplines and vital for informing management in a rapidly changing world. However, limited understanding of the accuracy and precision of models transferred to novel conditions (their 'trans-ferability') undermines confidence in their predictions. Here, 50 experts identified priority knowledge gaps which, if filled, will most improve model transfers. These are summarized into six technical and six fundamental challenges, which underlie the combined need to intensify research on the determinants of ecological predictability, including species traits and data quality, and develop best practices for transferring models. Of high importance is the identification of a widely applicable set of transferability metrics, with appropriate tools to quantify the sources and impacts of prediction uncertainty under novel conditions. Predicting the Unknown Predictions facilitate the formulation of quantitative, testable hypotheses that can be refined and validated empirically [1]. Predictive models have thus become ubiquitous in numerous scientific disciplines, including ecology [2], where they provide means for mapping species distributions, explaining population trends, or quantifying the risks of biological invasions and disease outbreaks (e.g., [3,4]). The practical value of predictive models in supporting policy and decision making has therefore grown rapidly (Box 1) [5]. With that has come an increasing desire to predict (see Glossary) the state of ecological features (e.g., species, habitats) and our likely impacts upon them [5], prompting a shift from explanatory models to anticipatory predictions [2]. However, in many situations, severe data deficiencies preclude the development of specific models, and the collection of new data can be prohibitively costly or simply impossible [6]. It is in this context that interest in transferable models (i.e., those that can be legitimately projected beyond the spatial and temporal bounds of their underlying data [7]) has grown. Transferred models must balance the tradeoff between estimation and prediction bias and variance (homogenization versus nontransferability, sensu [8]). Ultimately, models that can Highlights Models transferred to novel conditions could provide predictions in data-poor scenarios, contributing to more informed management decisions.

  • Open Access English
    Authors: 
    Ekici, A.; Chadburn, S.; Chaudhary, N.; Hajdu, L. H.; Marmy, A.; Peng, S.; Boike, J.; Burke, E.; Friend, A. D.; Hauck, C.; +4 more
    Project: EC | PAGE21 (282700), EC | GREENCYCLESII (238366), SNSF | The evolution of mountain... (136279)

    Modeling soil thermal dynamics at high latitudes and altitudes requires representations of physical processes such as snow insulation, soil freezing and thawing and subsurface conditions like soil water/ice content and soil texture. We have compared six different land models: JSBACH, ORCHIDEE, JULES, COUP, HYBRID8 and LPJ-GUESS, at four different sites with distinct cold region landscape types, to identify the importance of physical processes in capturing observed temperature dynamics in soils. The sites include alpine, high Arctic, wet polygonal tundra and non-permafrost Arctic, thus showing how a range of models can represent distinct soil temperature regimes. For all sites, snow insulation is of major importance for estimating topsoil conditions. However, soil physics is essential for the subsoil temperature dynamics and thus the active layer thicknesses. This analysis shows that land models need more realistic surface processes, such as detailed snow dynamics and moss cover with changing thickness and wetness, along with better representations of subsoil thermal dynamics.

  • Open Access
    Authors: 
    Thierry Jauffrais; Charlotte LeKieffre; K.A. Koho; Masashi Tsuchiya; Magali Schweizer; Joan M. Bernhard; Anders Meibom; Emmanuelle Geslin;
    Publisher: Elsevier BV
    Countries: Switzerland, France
    Project: SNSF | Global nitrogen-cycling i... (149333), AKA | Microbiology: the missing... (278827), AKA | Microbiology: the missing... (283453)

    International audience; Assimilation, sequestration and maintenance of foreign chloroplasts inside an organism is termed “chloroplast sequestration” or “kleptoplasty”. This phenomenon is known in certain benthic foraminifera, in which such kleptoplasts can be found both intact and functional, but with different retention times depending on foraminiferal species. In the present study, seven species of benthic foraminifera (Haynesina germanica, Elphidium williamsoni, E. selseyense, E. oceanense, E. aff. E. crispum, Planoglabratella opercularis and Ammonia sp.) were collected from shallow-water benthic habitats and examined with the transmission electron microscope (TEM) for cellular ultrastructure to ascertain attributes of kleptoplasts. Results indicate that all these foraminiferal taxa actively obtain kleptoplasts but organized them differently within their endoplasm. In some species, the kleptoplasts were evenly distributed throughout the endoplasm (e.g., H. germanica, E. oceanense, Ammonia sp.), whereas other species consistently had plastids distributed close to the external cell membrane (e.g., Elphidium williamsoni, E. selseyense, P. opercularis). Chloroplast degradation also seemed to differ between species, as many degraded plastids were found in Ammonia sp. and E. oceanense compared to other investigated species. Digestion ability, along with different feeding and sequestration strategies may explain the differences in retention time between taxa. Additionally, the organization of the sequestered plastids within the endoplasm may also suggest behavioral strategies to expose and/or protect the sequestered plastids to/from light and/or to favor gas and/or nutrient exchange with their surrounding habitats.

Advanced search in Research products
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The following results are related to European Marine Science. Are you interested to view more results? Visit OpenAIRE - Explore.
26 Research products, page 1 of 3
  • Open Access
    Project: SNSF | Investigation of the tida... (200517)

    Abstract. Ground-based remote sensing of atmospheric parameters is often limited to single station observations by vertical profiles at a certain geographic location. This is a limiting factor for investigating gravity wave dynamics as the spatial information is often missing, e.g., horizontal wavelength, propagation direction or intrinsic frequency. In this study, we present a new retrieval algorithm for multistatic meteor radar networks to obtain tomographic 3-D wind fields within a pre-defined domain area. The algorithm is part of the Agile Software for Gravity wAve Regional Dynamics (ASGARD) and called 3D-Var, and based on the optimal estimation technique and Bayesian statistics. The performance of the 3D-Var retrieval is demonstrated using two meteor radar networks: the Nordic Meteor Radar Cluster and the Chilean Observation Network De Meteor Radars (CONDOR). The optimal estimation implementation provide statistically sound solutions and diagnostics from the averaging kernels and measurement response. We present initial scientific results such as body forces of breaking gravity waves leading to two counter-rotating vortices and horizontal wavelength spectra indicating a transition between the rotational k−3 and divergent k-5/3 mode at scales of 80–120 km. In addition, we performed a keogram analysis over extended periods to reflect the latitudinal and temporal impact of a minor sudden stratospheric warming in December 2019. Finally, we demonstrate the applicability of the 3D-Var algorithm to perform large-scale retrievals to derive meteorological wind maps covering a latitude region from Svalbard, north of the European Arctic mainland, to central Norway.

  • Open Access English
    Authors: 
    Francesco Maria Sabatini; Jonathan Lenoir; Tarek Hattab; Elise A. Arnst; Milan Chytrý; Jürgen Dengler; Patrice de Ruffray; Stephan M. Hennekens; Ute Jandt; Florian Jansen; +151 more
    Countries: Switzerland, Italy, France, Norway, Finland, France, France, Norway, France, Croatia ...
    Project: EC | IMBALANCE-P (610028), SNSF | FutureWeb (184131), EC | T-FORCES (291585), EC | BACI (640176)

    Sabatini, F.M., Lenoir, J., Hattab, T., Arnst, E.A., Chytrý, M., Dengler, J., De Ruffray, P., Hennekens, S.M., Jandt, U., Jansen, F., Jiménez-Alfaro, B., Kattge, J., Levesley, A., Pillar, V.D., Purschke, O., Sandel, B., Sultana, F., Aavik, T., Aćić, S., Acosta, A.T.R., Agrillo, E., Alvarez, M., Apostolova, I., Arfin Khan, M.A.S., Arroyo, L., Attorre, F., Aubin, I., Banerjee, A., Bauters, M., Bergeron, Y., Bergmeier, E., Biurrun, I., Bjorkman, A.D., Bonari, G., Bondareva, V., Brunet, J., Čarni, A., Casella, L., Cayuela, L., Černý, T., Chepinoga, V., Csiky, J., Ćušterevska, R., De Bie, E., de Gasper, A.L., De Sanctis, M., Dimopoulos, P., Dolezal, J., Dziuba, T., El-Sheikh, M.A.E.-R.M., Enquist, B., Ewald, J., Fazayeli, F., Field, R., Finckh, M., Gachet, S., Galán-de-Mera, A., Garbolino, E., Gholizadeh, H., Giorgis, M., Golub, V., Alsos, I.G., Grytnes, J.-A., Guerin, G.R., Gutiérrez, A.G., Haider, S., Hatim, M.Z., Hérault, B., Hinojos Mendoza, G., Hölzel, N., Homeier, J., Hubau, W., Indreica, A., Janssen, J.A.M., Jedrzejek, B., Jentsch, A., Jürgens, N., Kącki, Z., Kapfer, J., Karger, D.N., Kavgacı, A., Kearsley, E., Kessler, M., Khanina, L., Killeen, T., Korolyuk, A., Kreft, H., Kühl, H.S., Kuzemko, A., Landucci, F., Lengyel, A., Lens, F., Lingner, D.V., Liu, H., Lysenko, T., Mahecha, M.D., Marcenò, C., Martynenko, V., Moeslund, J.E., Monteagudo Mendoza, A., Mucina, L., Müller, J.V., Munzinger, J., Naqinezhad, A., Noroozi, J., Nowak, A., Onyshchenko, V., Overbeck, G.E., Pärtel, M., Pauchard, A., Peet, R.K., Peñuelas, J., Pérez-Haase, A., Peterka, T., Petřík, P., Peyre, G., Phillips, O.L., Prokhorov, V., Rašomavičius, V., Revermann, R., Rivas-Torres, G., Rodwell, J.S., Ruprecht, E., Rūsiņa, S., Samimi, C., Schmidt, M., Schrodt, F., Shan, H., Shirokikh, P., Šibík, J., Šilc, U., Sklenář, P., Škvorc, Ž., Sparrow, B., Sperandii, M.G., Stančić, Z., Svenning, J.-C., Tang, Z., Tang, C.Q., Tsiripidis, I., Vanselow, K.A., Vásquez Martínez, R., Vassilev, K., Vélez-Martin, E., Venanzoni, R., Vibrans, A.C., Violle, C., Virtanen, R., von Wehrden, H., Wagner, V., Walker, D.A., Waller, D.M., Wang, H.-F., Wesche, K., Whitfeld, T.J.S., Willner, W., Wiser, S.K., Wohlgemuth, T., Yamalov, S., Zobel, M., Bruelheide, H. EU H2020 project BACI, Grant No. 640176 (...)

  • Open Access English
    Authors: 
    Julie Loisel; Angela V. Gallego-Sala; Matthew J. Amesbury; Gabriel Magnan; Gusti Z. Anshari; David W. Beilman; J. C. Benavides; Jerome Blewett; Philip Camill; Dan J. Charman; +60 more
    Countries: France, United Kingdom, Finland, Germany, United Kingdom, France
    Project: NSF | NNA: Collaborative Resear... (1802838), NSERC , NSF | RUI: Ecosystem responses ... (1019523), NSF | NNA: Collaborative Resear... (1802825), SNSF | Climate and Environmental... (172476)

    Peatlands are impacted by climate and land-use changes, with feedback to warming by acting as either sources or sinks of carbon. Expert elicitation combined with literature review reveals key drivers of change that alter peatland carbon dynamics, with implications for improving models. The carbon balance of peatlands is predicted to shift from a sink to a source this century. However, peatland ecosystems are still omitted from the main Earth system models that are used for future climate change projections, and they are not considered in integrated assessment models that are used in impact and mitigation studies. By using evidence synthesized from the literature and an expert elicitation, we define and quantify the leading drivers of change that have impacted peatland carbon stocks during the Holocene and predict their effect during this century and in the far future. We also identify uncertainties and knowledge gaps in the scientific community and provide insight towards better integration of peatlands into modelling frameworks. Given the importance of the contribution by peatlands to the global carbon cycle, this study shows that peatland science is a critical research area and that we still have a long way to go to fully understand the peatland-carbon-climate nexus. Peer reviewed

  • Publication . Article . Other literature type . 2020
    Open Access English
    Authors: 
    Darrell S. Kaufman; Nicholas P. McKay; Cody C. Routson; M. P. Erb; Basil A. S. Davis; Oliver Heiri; Samuel L Jaccard; Jessica E. Tierney; Christoph Dätwyler; Yarrow Axford; +83 more
    Publisher: Nature Publishing Group
    Countries: United Kingdom, Belgium, Switzerland, France, France, France, Argentina, Italy, France, Switzerland ...
    Project: SNSF | Exploring novel technolog... (180887), SNSF | CRISPR/Cas9 genome-editin... (160230)

    A comprehensive database of paleoclimate records is needed to place recent warming into the longer-term context of natural climate variability. We present a global compilation of quality-controlled, published, temperature-sensitive proxy records extending back 12,000 years through the Holocene. Data were compiled from 679 sites where time series cover at least 4000 years, are resolved at sub-millennial scale (median spacing of 400 years or finer) and have at least one age control point every 3000 years, with cut-off values slackened in data-sparse regions. The data derive from lake sediment (51%), marine sediment (31%), peat (11%), glacier ice (3%), and other natural archives. The database contains 1319 records, including 157 from the Southern Hemisphere. The multi-proxy database comprises paleotemperature time series based on ecological assemblages, as well as biophysical and geochemical indicators that reflect mean annual or seasonal temperatures, as encoded in the database. This database can be used to reconstruct the spatiotemporal evolution of Holocene temperature at global to regional scales, and is publicly available in Linked Paleo Data (LiPD) format. Measurement(s)climateTechnology Type(s)digital curationFactor Type(s)temporal interval • geographic location • proxy typeSample Characteristic - Environmentclimate systemSample Characteristic - LocationEarth (planet) Machine-accessible metadata file describing the reported data: https://www.ncdc.noaa.gov/paleo/study/27330

  • Open Access English
    Authors: 
    Anna Czarkwiani; David Dylus; Luisana Carballo; Paola Oliveri;
    Publisher: Cold Spring Harbor Laboratory
    Project: WT | Developmental and Stem Ce... (099745), SNSF | Harnessing Phylogenetic V... (150654), EC | ASSEMBLE (227799)

    ABSTRACT Regeneration as an adult developmental process is in many aspects similar to embryonic development. Although many studies point out similarities and differences, no large-scale, direct and functional comparative analyses between development and regeneration of a specific cell type or structure in one animal exist. Here, we use the brittle star Amphiura filiformis to characterise the role of the FGF signalling pathway during skeletal development in embryos and arm regeneration. In both processes, we find ligands expressed in ectodermal cells that flank underlying skeletal mesenchymal cells, which express the receptors. Perturbation of FGF signalling showed inhibited skeleton formation in both embryogenesis and regeneration, without affecting other key developmental processes. Differential transcriptome analysis finds mostly differentiation genes rather than transcription factors to be downregulated in both contexts. Moreover, comparative gene analysis allowed us to discover brittle star-specific differentiation genes. In conclusion, our results show that the FGF pathway is crucial for skeletogenesis in the brittle star, as in other deuterostomes, and provide evidence for the re-deployment of a developmental gene regulatory module during regeneration. Summary: Cellular and molecular analyses of FGF signalling perturbation during embryonic development and arm regeneration of the brittle Amphiura filiformis identify a conserved role in the formation of the skeleton in both processes.

  • Publication . Article . Other literature type . Preprint . 2019
    Open Access English
    Authors: 
    Daniel Mameri; Corina van Kammen; Ton G. G. Groothuis; Ole Seehausen; Martine E. Maan;
    Countries: Netherlands, Portugal, Switzerland
    Project: SNSF | The colours of speciation... (126340)

    Electronic supplementary material is available online at https://dx.doi.org/10.6084/m9.figshare. c.4440182 When different genotypes choose different habitats to better match their phenotypes, genetic differentiation within a population may be promoted. Mating within those habitats may subsequently contribute to reproductive isolation. In cichlid fish, visual adaptation to alternative visual environments is hypothesized to contribute to speciation. Here, we investigated whether variation in visual sensitivity causes different visual habitat preferences, using two closely related cichlid species that occur at different but overlapping water depths in Lake Victoria and that differ in visual perception (Pundamilia spp.). In addition to species differences, we explored potential effects of visual plasticity, by rearing fish in two different light conditions: broad-spectrum (mimicking shallow water) and red-shifted (mimicking deeper waters). Contrary to expectations, fish did not prefer the light environment that mimicked their typical natural habitat. Instead, we found an overall preference for the broad-spectrum environment. We also found a transient influence of the rearing condition, indicating that the assessment of microhabitat preference requires repeated testing to control for familiarity effects. Together, our results show that cichlid fish exert visual habitat preference but do not support straightforward visual habitat matching info:eu-repo/semantics/publishedVersion

  • Open Access
    Authors: 
    Javier del Campo; Thierry J. Heger; Raquel Rodríguez-Martínez; Alexandra Z. Worden; Thomas A. Richards; Ramon Massana; Patrick J. Keeling;
    Publisher: Cold Spring Harbor Laboratory
    Project: TARA | Tara Oceans (2), SNSF | Diversity and evolutionar... (145374), CIHR , EC | CAARL (331450)

    Apicomplexans are a group of microbial eukaryotes that contain some of the most well-studied parasites, including widespread intracellular pathogens of mammals such as Toxoplasma and Plasmodium (the agent of malaria), and emergent pathogens like Cryptosporidium and Babesia. Decades of research have illuminated the pathogenic mechanisms, molecular biology, and genomics of model apicomplexans, but we know surprisingly little about their diversity and distribution in natural environments. In this study we analyze the distribution of apicomplexans across a range of both host-associated and free-living environments, covering animal hosts from cnidarians to mammals, and ecosystems from soils to fresh and marine waters. Using publicly available small subunit (SSU) rRNA gene databases, high-throughput environmental sequencing (HTES) surveys such as Tara Oceans and VAMPS, as well as our own generated HTES data, we developed an apicomplexan reference database, which includes the largest apicomplexan SSU rRNA tree available to date and encompasses comprehensive sampling of this group and their closest relatives. This tree allowed us to identify and correct incongruences in the molecular identification of sequences, particularly within the hematozoans and the gregarines. Analyzing the diversity and distribution of apicomplexans in HTES studies with this curated reference database also showed a widespread, and quantitatively important, presence of apicomplexans across a variety of free-living environments. These data allow us to describe a remarkable molecular diversity of this group compared with our current knowledge, especially when compared with that identified from described apicomplexan species. This revision is most striking in marine environments, where potentially the most diverse apicomplexans apparently exist, but have not yet been formally recognized. The new database will be useful for both microbial ecology and epidemiological studies, and provide valuable reference for medical and veterinary diagnosis especially in cases of emerging, zoonotic, and cryptic infections.

  • Publication . Article . Other literature type . 2018
    Open Access
    Authors: 
    Katherine L. Yates; Phil J. Bouchet; M. Julian Caley; Kerrie Mengersen; Christophe F. Randin; Stephen Parnell; Alan H. Fielding; Andrew J. Bamford; Stephen Ban; A. Márcia Barbosa; +40 more
    Publisher: eScholarship, University of California
    Countries: United Kingdom, France, United States, Switzerland
    Project: SNSF | SCODA - Scaling from indi... (168136), ARC | Discovery Early Career Re... (DE140100701), ARC | Discovery Early Career Re... (DE170100841)

    International audience; Predictive models are central to many scientific disciplines and vital for informing management in a rapidly changing world. However, limited understanding of the accuracy and precision of models transferred to novel conditions (their 'trans-ferability') undermines confidence in their predictions. Here, 50 experts identified priority knowledge gaps which, if filled, will most improve model transfers. These are summarized into six technical and six fundamental challenges, which underlie the combined need to intensify research on the determinants of ecological predictability, including species traits and data quality, and develop best practices for transferring models. Of high importance is the identification of a widely applicable set of transferability metrics, with appropriate tools to quantify the sources and impacts of prediction uncertainty under novel conditions. Predicting the Unknown Predictions facilitate the formulation of quantitative, testable hypotheses that can be refined and validated empirically [1]. Predictive models have thus become ubiquitous in numerous scientific disciplines, including ecology [2], where they provide means for mapping species distributions, explaining population trends, or quantifying the risks of biological invasions and disease outbreaks (e.g., [3,4]). The practical value of predictive models in supporting policy and decision making has therefore grown rapidly (Box 1) [5]. With that has come an increasing desire to predict (see Glossary) the state of ecological features (e.g., species, habitats) and our likely impacts upon them [5], prompting a shift from explanatory models to anticipatory predictions [2]. However, in many situations, severe data deficiencies preclude the development of specific models, and the collection of new data can be prohibitively costly or simply impossible [6]. It is in this context that interest in transferable models (i.e., those that can be legitimately projected beyond the spatial and temporal bounds of their underlying data [7]) has grown. Transferred models must balance the tradeoff between estimation and prediction bias and variance (homogenization versus nontransferability, sensu [8]). Ultimately, models that can Highlights Models transferred to novel conditions could provide predictions in data-poor scenarios, contributing to more informed management decisions.

  • Open Access English
    Authors: 
    Ekici, A.; Chadburn, S.; Chaudhary, N.; Hajdu, L. H.; Marmy, A.; Peng, S.; Boike, J.; Burke, E.; Friend, A. D.; Hauck, C.; +4 more
    Project: EC | PAGE21 (282700), EC | GREENCYCLESII (238366), SNSF | The evolution of mountain... (136279)

    Modeling soil thermal dynamics at high latitudes and altitudes requires representations of physical processes such as snow insulation, soil freezing and thawing and subsurface conditions like soil water/ice content and soil texture. We have compared six different land models: JSBACH, ORCHIDEE, JULES, COUP, HYBRID8 and LPJ-GUESS, at four different sites with distinct cold region landscape types, to identify the importance of physical processes in capturing observed temperature dynamics in soils. The sites include alpine, high Arctic, wet polygonal tundra and non-permafrost Arctic, thus showing how a range of models can represent distinct soil temperature regimes. For all sites, snow insulation is of major importance for estimating topsoil conditions. However, soil physics is essential for the subsoil temperature dynamics and thus the active layer thicknesses. This analysis shows that land models need more realistic surface processes, such as detailed snow dynamics and moss cover with changing thickness and wetness, along with better representations of subsoil thermal dynamics.

  • Open Access
    Authors: 
    Thierry Jauffrais; Charlotte LeKieffre; K.A. Koho; Masashi Tsuchiya; Magali Schweizer; Joan M. Bernhard; Anders Meibom; Emmanuelle Geslin;
    Publisher: Elsevier BV
    Countries: Switzerland, France
    Project: SNSF | Global nitrogen-cycling i... (149333), AKA | Microbiology: the missing... (278827), AKA | Microbiology: the missing... (283453)

    International audience; Assimilation, sequestration and maintenance of foreign chloroplasts inside an organism is termed “chloroplast sequestration” or “kleptoplasty”. This phenomenon is known in certain benthic foraminifera, in which such kleptoplasts can be found both intact and functional, but with different retention times depending on foraminiferal species. In the present study, seven species of benthic foraminifera (Haynesina germanica, Elphidium williamsoni, E. selseyense, E. oceanense, E. aff. E. crispum, Planoglabratella opercularis and Ammonia sp.) were collected from shallow-water benthic habitats and examined with the transmission electron microscope (TEM) for cellular ultrastructure to ascertain attributes of kleptoplasts. Results indicate that all these foraminiferal taxa actively obtain kleptoplasts but organized them differently within their endoplasm. In some species, the kleptoplasts were evenly distributed throughout the endoplasm (e.g., H. germanica, E. oceanense, Ammonia sp.), whereas other species consistently had plastids distributed close to the external cell membrane (e.g., Elphidium williamsoni, E. selseyense, P. opercularis). Chloroplast degradation also seemed to differ between species, as many degraded plastids were found in Ammonia sp. and E. oceanense compared to other investigated species. Digestion ability, along with different feeding and sequestration strategies may explain the differences in retention time between taxa. Additionally, the organization of the sequestered plastids within the endoplasm may also suggest behavioral strategies to expose and/or protect the sequestered plastids to/from light and/or to favor gas and/or nutrient exchange with their surrounding habitats.