90 Works

Support for the climatic variability hypothesis depends on the type of thermal plasticity: lessons from predation rates

Ying-Jie Wang, Robby Stoks, Arnaud Sentis & Nedim Tüzün
Plastic and evolutionary changes in traits related to biotic interactions are crucial for the local persistence of populations under global warming. Yet, how acute and developmental thermal plasticity evolve and shape predation rates has been poorly studied, especially in the context of latitude-driven thermal evolution. A powerful predictive framework is given by the climatic variability hypothesis (CVH) stating that thermal plasticity and acclimation capacity evolve to be higher in high-latitude populations because these are exposed...

Supplement: Multicenter validated detection of focal cortical dysplasia using deep learning

Ravnoor S Gill, Hyo M Lee, Benoit Caldairou, Seok-Jun Hong, Carmen Barba, Francesco Deleo, Ludovico D’Incerti, Vanessa C Mendes Coelho, Matteo Lenge, Mira Semmelroch, Dewi Schrader, Fabrice Bartolomei, Maxime Guye, Andreas Schulze-Bonhage, Horst Urbach, Kyoo Ho Cho, Fernando Cendes, Renzo Guerrini, Graeme Jackson, R Edward Hogan, Neda Bernasconi & Andrea Bernasconi
Objective. To test the hypothesis that a multicenter-validated computer deep learning algorithm detects MRI-negative focal cortical dysplasia (FCD). Methods. We used clinically acquired 3D T1-weighted and 3D FLAIR MRI of 148 patients (median age, 23 years [range, 2-55]; 47% female) with histologically verified FCD at nine centers to train a deep convolutional neural network (CNN) classifier. Images were initially deemed as MRI-negative in 51% of cases, in whom intracranial EEG determined the focus. For risk...

Data from: Shifts in growth light optima among diatom species support their succession during the spring bloom in the Arctic

Dany Croteau, Thomas Lacour, Nicolas Schiffrine, Philippe-Israël Morin, Marie-Hélène Forget, Flavienne Bruyant, Joannie Ferland, Augustin Lafond, Douglas Campbell, Jean-Éric Tremblay, Marcel Babin & Johann Lavaud
Diatoms of the Arctic Ocean annually experience extreme changes of light environment linked to photoperiodic cycles and seasonal variations of the snow and sea-ice cover extent and thickness which attenuate light penetration in the water column. Arctic diatom communities exploit this complex seasonal dynamic through a well-documented species succession during spring, beginning in sea-ice and culminating in massive phytoplankton blooms underneath sea-ice and in the marginal ice zone. The pattern of diatom taxa sequentially dominating...

Data from: Variability of the atmospheric PM10 microbiome in three climatic regions of France

Abdoulaye Samaké, Jean M. F. Martins, Aurélie Bonin, Pierre Taberlet, Sébastien Conil, Olivier Favez, Alexandre Thomasson, Benjamin Chazeau, Nicolas Marchand, Jean-Luc Jaffrezo & Gaëlle Uzu
Air pollution is a major public-health concern and it is recognized that particulate matter causes damage to human health through oxidative-stress, being responsible for several million premature deaths worldwide each year. Recent findings showed that, airborne microorganisms/spores can modulate aerosol toxicity by altering the oxidative potential of PM10. Primary Biogenic Organic Aerosols (PBOA) appears to be produced by only few genera of microorganisms, emitted by surrounding vegetation in the case of a regionally-homogeneous field site....

Data from: Plotting for change: an analytic framework to aid decisions on which lineages are candidate species in phylogenomic species discovery

Arthur Georges, Peter Unmack, Mark Adams, Michael Hammer, Jerald Johnson, Bernd Gruber, André Gilles & Matthew Young
A recent study argued that coalescent-based models of species delimitation mostly delineate population structure not species, and called for the validation of candidate species using biological information additional to the genetic information, such as phenotypic or ecological data. Here we introduce a framework to interrogate genomic datasets and coalescent-based species trees for the presence of candidate species in situations where additional biological data are unavailable, unobtainable, or uninformative. For de novo genomic studies of species...

The impact of estimator choice: Disagreement in clustering solutions across K estimators for Bayesian analysis of population genetic structure across a wide range of empirical datasets

Kathryn Stankiewicz, Kate Vasquez Kuntz, Jean-Baptiste Ledoux, Didier Aurelle, Joaquim Garrabou, Yuichi Nakajima, Mikael Dahl, Yuna Zayasu, Sabri Jaziri, Federica Costantini & Iliana Baums
The software program STRUCTURE is one of the most cited tools for determining population structure. To infer the optimal number of clusters from STRUCTURE output, the ΔK method is often applied. However, a recent study relying on simulated microsatellite data suggested that this method has a downward bias in its estimation of K and is sensitive to uneven sampling. If this finding holds for empirical datasets, conclusions about the scale of gene flow may have...


Philippe PAROLA

Spectres et sequences des bactéries et microbes cutanés

Nassim Hammoudi

Complete genomic sequences until May, 2021.

Anthony Levasseur


Philippe PAROLA

Data from: Age and sex-selective predation as moderators of the overall impact of predation

Sarah R. Hoy, Steve J. Petty, Alexandre Millon, D. P. Whitfield, Michael Marquiss, Martin Davison & Xavier Lambin
Currently, there is no general agreement about the extent to which predators’ impact prey population dynamics, as it is often poorly predicted by predation rates and species abundances. This could in part be caused by variation in the type of selective predation occurring. Notably, if predation is selective on categories of individuals that contribute little to future generations, it may moderate the impact of predation on prey population dynamics. However, despite its prevalence, selective predation...

Data from: The evolution of canaliculate rudists in the light of a new canaliculate polyconitid rudist from the Albian of the Central Pacific

Shin-Ichi Sano, Yasuhiro Iba, Peter W. Skelton, Jean-Pierre Masse, Yolanda M. Aguilar & Tomoki Kase
A new polyconitid rudist, Magallanesia canaliculata gen. et sp. nov., of probably late Albian age, is described from the Pulangbato area, central Cebu Island, the Philippines in the western Central Pacific and Takuyo Daini Seamount, now located in the Northwest Pacific. It is similar to Praecaprotina Yabe and Nagao, 1926, a Japanese – Central Pacific endemic genus of late Aptian – early Albian age, but differs in having canals that developed by partitioning of the...

Emergence patterns of novelty in European vegetation assemblages over the past 15 000 years

Walter Finsinger, Thomas Giesecke, Simon Brewer & Michelle Leydet
Plant communities are not stable over time and biological novelty is predicted to emerge due to climate change, the introduction of exotic species and land-use change. However, the rate at which this novelty may arise over longer time periods has so far received little attention. We reconstruct the emergence of novelty in Europe for a set of baseline conditions over the past 15 000 years to assess past rates of emergence and investigate underlying causes....

Data from: Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

Annegret Kohler, Alan Kuo, Laszlo G. Nagy, Emmanuelle Morin, Kerrie W. Barry, Francois Buscot, Bjorn Canback, Cindy Choi, Nicolas Cichocki, Alicia Clum, Jan Colpaert, Alex Copeland, Mauricio D. Costa, Jeanne Dore, Dimitrios Floudas, Gilles Gay, Mariangela Girlanda, Bernard Henrissat, Sylvie Herrmann, Jaqueline Hess, Nils Hogberg, Tomas Johansson, Hassine-Radhouane Khouja, Kurt LaButti, Urs Lahrmann … & Francis Martin
To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall–degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose....

Data from: Cryptic habitats and cryptic diversity: unexpected patterns of connectivity and phylogeographic breaks in a Mediterranean endemic marine cave mysid

Pierre-Alexandre Rastorgueff, Pierre Chevaldonné, Defne Arslan, Caroline Verna & Christophe Lejeusne
The marine cave-dwelling mysid Hemimysis margalefi is distributed over the whole Mediterranean Sea which contrasts with the poor dispersal capabilities of this brooding species. In addition, underwater marine caves are a highly fragmented habitat which further promotes strong genetic structuring, therefore providing highly informative data on the levels of marine population connectivity across biogeographic regions. This study investigates how habitat and geography have shaped the connectivity network of this poor disperser over the entire Mediterranean...

Data from: How much would it cost to monitor farmland biodiversity in Europe?

Ilse R. Geijzendorffer, Stefano Targetti, Manuel K. Schneider, Dick J. Brus, Philippe Jeanneret, Robert H. G. Jongman, Martin Knotters, Davide Viaggi, Siyka Angelova, Michaela Arndorfer, Debra Bailey, Katalin Balzacs, András Báldim, Marion M. B. Bogers, Robert G.H. Bunce, Jean-Philippe Choisis, Peter Dennis, Sebastian Eiter, Wendy Fjellstad, Jürgen F. Friedel, Tiziano Gomiero, Arjan Griffioen, Max Kainz, Anikó Kovács-Hostyánszki, Gisela Lüscher … & András Báldi
To evaluate progress on political biodiversity objectives, biodiversity monitoring provides information on whether intended results are being achieved. Despite scientific proof that monitoring and evaluation increase the (cost) efficiency of policy measures, cost estimates for monitoring schemes are seldom available, hampering their inclusion in policy programme budgets. Empirical data collected from 12 case studies across Europe were used in a power analysis to estimate the number of farms that would need to be sampled per...

Data from: Rapid divergence of genome architectures following the origin of an ectomycorrhizal symbiosis in the genus Amanita

Jaqueline Hess, Inger Skrede, Maryam Chaib De Mares, Matthieu Hainaut, Bernard Henrissat & Anne Pringle
Fungi are evolutionary shape shifters and adapt quickly to new environments. Ectomycorrhizal (EM) symbioses are mutualistic associations between fungi and plants and have evolved repeatedly and independently across the fungal tree of life, suggesting lineages frequently reconfigure genome content to take advantage of open ecological niches. To date analyses of genomic mechanisms facilitating EM symbioses have involved comparisons of distantly related species, but here, we use the genomes of three EM and two asymbiotic (AS)...

Data from: High-speed motility originates from cooperatively pushing and pulling flagella bundles in bilophotrichous bacteria

Klaas Bente, Sarah Mohammadinejad, Mohammad A. Charsooghi, Felix Bachmann, Agnese Codutti, Christopher T. Lefèvre, Stefan Klumpp & Damien Faivre
Bacteria propel and change direction by rotating long, helical filaments, called flagella. The number of flagella, their arrangement on the cell body and their sense of rotation hypothetically determine the locomotion characteristics of a species. The movement of the most rapid microorganisms has in particular remained unexplored because of additional experimental limitations. We show that magnetotactic cocci with two flagella bundles on one pole swim faster than 500 μm·s-1 along a double helical path, making...

Energetic mismatch induced by warming decreases leaf litter decomposition by aquatic detritivores

Tom Réveillon, Thibaut Rota, Eric Chauvet, Antoine Lecerf & Arnaud Sentis
1. The balance of energetic losses and gains is of paramount importance for understanding and predicting the persistence of populations and ecosystem processes in a rapidly changing world. Previous studies suggested that metabolic rate often increases faster with warming than resource ingestion rate, leading to an energetic mismatch at high temperature. However, little is known about the ecological consequences of this energetic mismatch for population demography and ecosystem functions. 2. Here, we combined laboratory experiments...

Water availability rather than temperature control soil fauna community structure and prey-predator interactions

Adriane Aupic-Samain, Virginie Baldy, Ninon Delcourt, Paul Henning Krogh, Thierry Gauquelin, Catherine Fernandez & Mathieu Santonja
The ongoing climate change may strongly impact soil biodiversity with cascading effects on the processes they drive. Thus, it is of prime interest to improve our knowledge about responses by soil organisms such as collembolans to expected shifts in environmental conditions by considering communities comprising both detritivores and predators. The aim of the present study was to evaluate how simulated climate change and predation under laboratory conditions alter a collembolan community. To infer the impact...

Warm range margin of boreal bryophytes and lichens not directly limited by temperatures

Caroline Greiser, Johan Ehrlén, Miska Luoto, Eric Meineri, Sonia Merinero, Benny Willman & Kristoffer Hylander
1. Species at their warm range margin are potentially threatened by higher temperatures, but may persist in microrefugia. Whether such microsites occur due to more suitable microclimate or due to lower biotic pressure from e.g. competitive species, is still not fully resolved. 2. We examined whether boreal bryophytes and lichens show signs of direct climate limitation, i.e. whether they perform better in cold and/or humid microclimates at their warm range margin. We transplanted a moss,...

Innate immunity promotes sleep through epidermal antimicrobial peptides

Marina Patricia Sinner, Florentin Masurat, Jonathan Ewbank, Nathalie Pujol & Henrik Bringmann
Wounding and infection trigger a protective innate immune response that includes the production of antimicrobial peptides in the affected tissue as well as increased sleep. Little is known, however, how peripheral wounds or innate immunity signal to the nervous system to increase sleep. We found that during C. elegans larval molting, an epidermal tolloid/BMP-1-like protein called NAS-38 promotes sleep. NAS-38 is negatively regulated by its thrombospondin domain and acts through its astacin protease domain to...

Data from: A strong east–west Mediterranean divergence supports a new phylogeographic history of the carob tree (Ceratonia siliqua, Leguminosae) and multiple domestications from native populations

Juan Viruel, Nicolas Le Galliot, Samuel Pironon, Jean Pierre Suc, Gonzalo Nieto Feliner, Fatma Lakhal-Mirleau, Marianick Juin, Marjorie Selva, Magda Bou Dagher-Kharrat, Lahcen Ouahmane, Stefano La Malfa, Katia Diadema, Hervé Sanguin, Frédéric Médail & Alex Baumel
Aim: Phylogeography of fruit trees is challenging due to the recurrent exchanges between domesticated and wild populations. Here we tested the eastern refugium hypothesis (ERH) for the carob tree, Ceratonia siliqua, which supports its natural and domestication origins in the Eastern Mediterranean and a feral origin in the West. Location: Mediterranean basin Taxon: Ceratonia siliqua L., Leguminosae Methods: Divergence time of the divergence between the carob tree and its sister species (C. oreothauma) was estimated...

Data from: Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing

Carole P. Elliott, Neal J. Enright, Richard J. N. Allcock, Michael G. Gardner, Emese Meglécz, Janet Anthony & Siegfried L. Krauss
The development and screening of microsatellite markers have been accelerated by next-generation sequencing (NGS) technology and in particular GS-FLX pyro-sequencing (454). More recent platforms such as the PGM semiconductor sequencer (Ion Torrent) offer potential benefits such as dramatic reductions in cost, but to date have not been well utilized. Here, we critically compare the advantages and disadvantages of microsatellite development using PGM semiconductor sequencing and GS-FLX pyro-sequencing for two gymnosperm (a conifer and a cycad)...

Data from: Contribution of spatial heterogeneity in effective population sizes to the variance in pairwise measures of genetic differentiation

Jérôme G. Prunier, Vincent Dubut, Lounes Chikhi & Simon Blanchet
1. Pairwise measures of neutral genetic differentiation are supposed to contain information about past and on-going dispersal events and are thus often used as dependent variables in correlative analyses to elucidate how neutral genetic variation is affected by landscape connectivity. However, spatial heterogeneity in the intensity of genetic drift, stemming from variations in population sizes, may inflate variance in measures of genetic differentiation and lead to erroneous or incomplete interpretations in terms of connectivity. Here,...

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  • Aix-Marseille University
  • French National Centre for Scientific Research
  • Méditerranée Infection Foundation
  • Marseille Public University Hospital System
  • University of Oslo
  • University of Rennes 1
  • University of Toulouse
  • McGill University
  • Centre national de la recherche scientifique
  • University of Adelaide