88 Works

Genomics data for the week of February 24-26, 2021

Anthony LEVASSEUR

Data from: Surviving in mountain climate refugia: new insights from the genetic diversity and structure of the relict shrub Myrtus nivellei (Myrtaceae) in the Sahara desert

Jérémy Migliore, Alex Baumel, Marianick Juin, Bruno Fady, Anne Roig, Nathalie Duong & Frédéric Médail
The identification of past glacial refugia has become a key topic for conservation under environmental change, since they contribute importantly to shaping current patterns of biodiversity. However, little attention has been paid so far to interglacial refugia despite their key role for the survival of relict species currently occurring in climate refugia. Here, we focus on the genetic consequences of range contraction on the relict populations of the evergreen shrub Myrtus nivellei, endemic in the...

Data from: Regional paleoclimates and local consequences: Integrating GIS analysis of diachronic settlement patterns and process-based agroecosystem modeling of potential agricultural productivity in Provence (France)

Daniel Contreras, Eneko Hiriart, Alberte Bondeau, Alan Kirman, Joël Guiot, Loup Bernard, Romain Suarez, Sander Van Der Leeuw & Daniel A. Contreras
Holocene climate variability in the Mediterranean Basin is often cited as a potential driver of societal change, but the mechanisms of this putative influence are generally little explored. In this paper we integrate two tools - agro-ecosystem modeling of potential agricultural yields and spatial analysis of archaeological settlement pattern data - in order to examine the human consequences of past climatic changes. Focusing on a case study in Provence (France), we adapt an agro-ecosystem model...

Data from: Warming impacts on early life stages increase the vulnerability and delay the population recovery of a long-lived habitat-forming macroalga

Pol Capdevila, Bernat Hereu, Roberto Salguero-Gómez, Graciel·La Rovira, Alba Medrano, Emma Cebrian, Joaquim Garrabou, Diego K. Kersting & Cristina Linares
1. Understanding the combined effects of global and local stressors is crucial for conservation and management, yet challenging due to the different scales at which these stressors operate. Here we examine the effects of one of the most pervasive threats to marine biodiversity, ocean warming, on the early life stages of the habitat-forming macroalga Cystoseira zosteroides, its long-term consequences for population resilience and its combined effect with physical stressors. 2. First, we performed a controlled...

Redox controls RecA protein activity via reversible oxidation of its methionine residues

Benjamin Ezraty, Camille Henry, Frederic Barras, Laurent Loiseau, Alexandra Vergnes, Didier Vertommen, Angela Mérida-Floriano, Sindhu Chitteni-Pattu, Elizabeth Anne Wood, Josep Casadesús & Michael M. Cox
Reactive oxygen species (ROS) cause damage to DNA and proteins. The RecA protein plays a central role in the bacterial response to DNA damage. Here we report that RecA itself is also targeted by ROS. In vivo consequences of RecA oxidation include defects in SOS induction, DNA repair efficiency, and P1 transduction. In vitro, oxidized RecA fails to display ATPase activity, DNA strand exchange capacity and formation of nucleofilaments. Consistently, mass spectrometry analysis of oxidized...

Conservation genetics of Armeria belgenciencis

Alex Baumel, Frédéric Médail, Marianick Juin, Thibault Paquier, Marie Clares, Perrine Laffargue, Hélène Lutard, Lara Dixon & Mathias Pires
This the data set of the paper "Population genetic structure and management perspectives for Armeria belgenciencis, a narrow endemic plant from Provence (France)" published in Plant Ecology and Evolution: ###############. The genetic structure of Armeria belgenciensis and geographically close populations of Armeria arenaria was analyzed on the basis of 328 AFLP markers using model-based and model-free clustering methods. In addition, flowering phenology was estimated to address the possibility of pre-zygotic isolation between A. belgenciensis and...

Impact of smoking cessation, coffee and bread consumption on the intestinal microbial composition among Saudis: A cross-sectional study

Steve Harakeh, Ghada Ajabnoor, Sulaiman Alfadul, Suhad Bahijri, Turki Al Amri, Dipankar Bachar, Timokratis Karamitros, Suha Farraj, Emmanouil Angelakis, Ahmed Al-Hejin, Raoult Didier, Ahmed Mirza, Esam Azhar & Abdalla Ahmed
The gut microbiota is often affected by the dietary and lifestyle habits of the host, resulting in a better efficacy that favors energy harvesting from the consumed food. Our objective was to characterize the composition of gut microbiota in adult Saudis and investigate possible association with lifestyle and dietary practices. Feces from 104 Saudi volunteers (48% males) were tested for microbiota by sequencing the V3-V4 region of bacterial 16S ribosomal RNA (rRNA). For all participants,...

Data from: Seasonal variability of groundwater level effects on the growth of Carex cinerascens in lake wetlands

Wenjuan Feng, Pierre Mariotte, Xu Ligang, Alexandre Buttler, Luca Bragazza, Jiahu Jiang & Mathieu Santonja
Groundwater level is crucial for wetland plant growth and reproduction, but the extent of its effect on plant growth can vary along with changed precipitation and temperature at different seasons. In this context, we investigated the effect of two groundwater levels (10 cm vs. 20 cm depth) on growth and reproductive parameters of Carex cinerascens, a dominant plant species in the Poyang Lake wetland, during three seasons (spring, summer and autumn) and during two consecutive...

Data from: Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral (Corallium rubrum)

Marine Pratlong, Anne Haguenauer, Sandrine Chenesseau, Kelly Brener, Guillaume Mitta, Eve Toulza, M. Bonabaud, S. Rialle, Didier Aurelle & Pierre Pontarotti
Sexual reproduction is widespread among eukaryotes, and the sex-determining processes vary greatly among species. While genetic sex determination (GSD) has been intensively described in bilaterian species, no example has yet been recorded among non-bilaterians. However, the quasi-ubiquitous repartition of GSD among multicellular species suggests that similar evolutionary forces can promote this system, and that these forces could occur also in non-bilaterians. Studying sex determination across the range of Metazoan diversity is indeed important to understand...

Data from: TAF4, a subunit of transcription factor II D, directs promoter occupancy of nuclear receptor HNF4A during post-natal hepatocyte differentiation

Daniil Alpern, Diana Langer, Benoit Ballester, Stephanie Le Gras, Christophe Romier, Gabrielle Mengus & Irwin Davidson
The functions of the TAF subunits of mammalian TFIID in physiological processes remain poorly characterised. Here we describe a novel function of TAFs in directing genomic occupancy of a transcriptional activator. Using liver-specific inactivation in mice, we show that the TAF4 subunit of TFIID is required for post-natal hepatocyte maturation. TAF4 promotes pre-initiation complex (PIC) formation at post-natal expressed liver function genes and down-regulates a subset of embryonic expressed genes by increased RNA polymerase II...

Data from: Introducing resprouters to enhance Mediterranean forest resilience: importance of functional traits to select species according to a gradient of pine density

Jordane Gavinet, Bernard Prévosto & Catherine Fernandez
Resprouter species are important for Mediterranean ecosystem resilience, but they are scarce in landscapes dominated by pioneer pines. Sound knowledge of resprouter seedling functional responses and establishment success across different pine habitats would help guide forest restoration efforts. Four broadleaved resprouter species, that is two shrubs – Arbutus unedo and Pistacia terebinthus – and two trees – Fraxinus ornus and Sorbus domestica – were planted under an experimentally created gradient of pine cover from totally...

Data from: Improving access and continuity of care for homeless people: how could general practitioners effectively contribute? results from a mixed study.

Maeva Jego, Dominique Grassineau, Hubert Balique, Anderson Loundou, Roland Sambuc, Alexandre Daguzan, Gaetan Gentile & Stéphanie Gentile
Objectives: To analyze the views of general practitioners (GPs) about how they can provide care to homeless people (HP) and to explore which measures could influence their views. Design: Mixed-methods design (qualitative –> quantitative (cross-sectional observational)  qualitative). Qualitative data were collected through semi-structured interviews; quantitative data were collected through questionnaires with closed questions. Quantitative data were analyzed with descriptive statistical analyses on SPPS; a content analysis was applied on qualitative data. Setting: primary care;...

Data from: Improving PCR detection of prey in molecular diet studies: importance of group-specific primer set selection and extraction protocol performances

Diane Zarzoso-Lacoste, Emmanuel Corse & Eric Vidal
While morphological identification of prey remains in feces of predators is the method most commonly used to study trophic interactions, many studies indicate that this method does not detect all consumed prey. Polymerase Chain Reaction based methods are increasingly used to detect prey DNA in the predator food bolus and have proved themselves efficient, with high accuracy. When studying complex diet samples, the extraction of total DNA is a critical step, as PCR inhibitors may...

Threatened salmon rely on a rare life history strategy in a warming landscape

Flora Cordoleani, Corey Phillis, Anna Sturrock, Alyssa FitzGerald, George Whitman, Anthony Malkassian, Peter Weber & Rachel Johnson
Rare phenotypes and behaviours within a population are often overlooked, yet they may serve a heightened role for species imperilled by rapid warming. In threatened spring-run Chinook salmon spawning at the southern edge of the species range, we show late-migrating juveniles are critical to cohort success in years characterized by droughts and ocean heatwaves. Late migrants rely on cool river temperatures over summer, increasingly rare due to the combined effects of warming and impassable dams....

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...

DATA FROM REAL-TIME PCR ASSAY FOR THE DETECTION OF DERMATOPHYTES

Stéphane Ranque

Data from: The more the better – polyandry and genetic similarity are positively linked to reproductive success in a natural population of terrestrial salamanders (Salamandra salamandra)

Barbara A. Caspers, E. Tobias Krause, Ralf Hendrix, Michael Kopp, Oliver Rupp, Katrin Rosentreter & Sebastian Steinfartz
Although classically thought to be rare, female polyandry is wide-spread and may entail significant fitness benefits. If females store sperm over extended periods of time, the consequences of polyandry will depend on the pattern of sperm storage, and some of the potential benefits of polyandry can only be realized if sperm from different males is mixed. Our study aimed to determine patterns and consequences of polyandry in an amphibian species, the fire salamander, under fully...

Data from: Distribution patterns of microbial communities in ultramafic landscape: a metagenetic approach highlights the strong relationships between diversity and environmental traits

Laurent Bordez, Philippe Jourand, Marc Ducousso, Fabian Carriconde, Yvon Cavaloc, Sébastien Santini, Jean M. Claverie, Laurent Wantiez, Antoine Leveau & Hamid Amir
Microbial species richness and assemblages across ultramafic ecosystems were investigated to assess the relationship between their distributional patterns and environmental traits. The structure of microorganism communities in the Koniambo massif, New Caledonia, was investigated using a metagenetic approach correlated with edaphic and floristic factors. Vegetation cover and soil properties significantly shaped the large phylogenetic distribution of operational taxonomic unit within microbial populations, with a mean per habitat of 3.477 (±317) for bacteria and 712 (±43)...

Data from: One-locus-several-primers: a strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

Emmanuel Corse, Christelle Tougard, Gaït Archambaud-Suard, Jean-François Agnèse, Françoise D. Messu Mandeng, Charles F. Bilong Bilong, David Duneau, Lucie Zinger, Rémi Chappaz, Charles C. Y. Xu, Emese Meglécz & Vincent Dubut
In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. Our results underline the lack of predictability of both...

Data from: Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay

Lucie Bittner, Angélique Gobet, Stéphane Audic, Sarah Romac, Elianne S. Egge, Sébastien Santini, Hiroyuki Ogata, Ian Probert, Bente Edvardsen & Colomban De Vargas
Haptophytes are a key phylum of marine protists, including ~300 described morphospecies and 80 morphogenera. We used 454 pyrosequencing on large subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from size-fractioned plankton samples collected in the Bay of Naples. One group-specific primer set targeting the LSU rDNA D1/D2 region was designed to amplify Haptophyte sequences from nucleic acid extracts (total DNA or RNA) of two size fractions (0.8–3 or 3–20 μm) and two...

Data from: How can ten fingers shape a pot? Evidence for equivalent function in culturally distinct motor skills

Enora Gandon, Reinoud J. Bootsma, John A. Endler, Leore Grosman & Alex Mesoudi
Behavioural variability is likely to emerge when a particular task is performed in different cultural settings, assuming that part of human motor behaviour is influenced by culture. In analysing motor behaviour it is useful to distinguish how the action is performed from the result achieved. Does cultural environment lead to specific cultural motor skills? Are there differences between cultures both in the skills themselves and in the corresponding outcomes? Here we analyse the skill of...

Data from: Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species

Emese Meglécz, Gabriel Nève, Ed Biffin & Michael G. Gardner
Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within...

Data from: A multispecies approach reveals hot-spots and cold-spots of diversity and connectivity in invertebrate species with contrasting dispersal modes

Abigail E. Cahill, Aurelien De Jode, Sophie Dubois, Zoheir Bouzaza, Didier Aurelle, Emilie Boissin, Olivier Chabrol, Romain David, Emilie Egea, Jean-Baptiste Ledoux, Bastien Merigot, Alexandra Anh-Thu Weber & Anne Chenuil
Genetic diversity is crucial for species’ maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed...

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: Functional traits, not productivity, predict openness to seedling recruitment in alpine plant communities under climatic warming

Eric Meineri, Kari Klanderud, John Guittar, Deborah Goldberg & Vigdis Vandvik
Understanding the degree to which plant communities are open to seedling recruitment is key to predicting how they will be impacted by climate change. We experimentally assessed whether communities assembled under colder climates were inherently more open to recruitment than warmer-climate communities, after controlling for differences in the current climate under which the communities were growing. We then tested whether variation in openness to recruitment could be explained by community biomass or by the plant...

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