90 Works

Complete genomic sequences until May, 2021.

Anthony Levasseur


Philippe PAROLA

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...

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...

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,...

Data from: Elucidating the spatio-temporal dynamics of an emerging wildlife pathogen using approximate Bayesian computation

Olivier Rey, Lisa Fourtune, Ivan Paz-Vinas, Geraldine Loot, Charlotte Veyssière, Benjamin Roche & Simon Blanchet
Emerging pathogens constitute a severe threat for human health and biodiversity. Determining the status (native or non-native) of emerging pathogens, and tracing back their spatio-temporal dynamics, is crucial to understand the eco-evolutionary factors promoting their emergence, to control their spread and mitigate their impacts. However, tracing back the spatio-temporal dynamics of emerging wildlife pathogens is challenging because (i) they are often neglected until they become sufficiently abundant and pose socio-economical concerns and (ii) their geographical...

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: 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...

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: 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...

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: 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: 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...

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)...

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...

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...

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,...

Triangular Regulation of Cucurbit[8]uril 1:1 Complexes

Sébastien Combes, Khoa Truong Tran, MEHMET MENAF AYHAN, Hakim Karoui, Antal Rockenbauer, Alain Tonetto, Valérie Monnier, Laurence Charles, Roselyne Rosas, Stéphane Viel, Didier Siri, Paul Tordo, Sylvain Clair, Ruibing Wang, David Bardelang & Olivier Ouari
Triangular shapes have inspired scientists over time and are common in nature, such as the flower petals of oxalis triangularis, the triangular faces of tetrahedrite crystals, and the icosahedron faces of virus capsids. Supramolecular chemistry has enabled the construction of triangular assemblies, many of which possess functional features. Among these structures, cucurbiturils have been used to build supramolecular triangles, and we recently reported paramagnetic cucurbit[8]uril (CB[8]) triangles, but the reasons for their formation remain unclear....

Experimental 3D Velocity Field in Random Sphere Packing

Mathieu Souzy, Henri Lhuissier, Yves Méheust, Tanguy Le Borgne & Bloen Metzger



Data from: Influence of intra- and interspecific variation in predator-prey body size ratios on trophic interaction strengths

Ross N. Cuthbert, Ryan J. Wasserman, Tatenda Dalu, Horst Kaiser, Olaf L. F. Weyl, Jaimie T. A. Dick, Arnaud Sentis, Mike W. McCoy & Mhairi E. Alexander
1. Predation is a pervasive force that structures food webs and directly influences ecosystem functioning. The relative body sizes of predators and prey may be an important determinant of interaction strengths. However, studies quantifying the combined influence of intra- and interspecific variation in predator-prey body size ratios are lacking. 2. We use a comparative functional response approach to examine interaction strengths between three size classes of invasive bluegill and largemouth bass towards three scaled size...

Endometrioma ethanol sclerotherapy could increase IVF live birth rate in women with moderate-severe endometriosis

Laura Miquel, Lise Preaubert, Audrey Gnisci, Noemie Resseguier, Audrey Pivano, Jeanne Perrin & Blandine Courbiere
Objective: To examine the impact of ethanol sclerotherapy (EST) for endometrioma on in vitro fertilization (IVF) cumulative live birth rates (CLBR) in women with moderate-severe endometriosis. Methods: This retrospective cohort study included women with moderate-severe endometriosis (revised American Fertility Society stage III-IV) and endometrioma who underwent IVF with the ultra-long agonist protocol. We compared two groups: women undergoing EST for endometrioma before IVF (EST group), and women whose endometrioma was left in situ during IVF...

Individual high-quality reads (dd-RADsequencing) from: Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii

Lauric Reynes & Didier Aurelle
The development of population genomic approaches in non-model species allows for renewed studies of the impact of reproductive systems and genetic drift on population diversity. Here, we investigate the genomic signatures of partial clonality in the deep water kelp Laminaria rodriguezii, known to reproduce by both sexual and asexual means. We compared these results with the species Laminaria digitata, a closely related species that differs by different traits, in particular its reproductive mode (no clonal...

Prey and predator density-dependent interactions under different water volumes

Ross Cuthbert, Tatenda Dalu, Ryan Wasserman, Arnaud Sentis, Olaf Weyl, William Froneman, Amanda Callaghan & Jaimie Dick
Predation is a critical ecological process that directly and indirectly mediates population stabilities, as well as ecosystem structure and function. The strength of interactions between predators and prey may be mediated by multiple density-dependences concerning numbers of predators and prey. In temporary wetland ecosystems in particular, fluctuating water volumes may alter predation rates through differing search space and prey encounters rates. Using a functional response approach, we examined the influence of predator and prey densities...

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Resource Types

  • Dataset


  • 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