236 Works

Retrospective analysis of SARS-CoV-2 omicron invasion over delta in French regions in 2021–22: a status-based multi-variant model

Thomas Haschka, Elisabeta Vergu, Benjamin Roche, Chiara Poletto & Lulla Opatowski
Abstract Background SARS-CoV-2 is a rapidly spreading disease affecting human life and the economy on a global scale. The disease has caused so far more then 5.5 million deaths. The omicron outbreak that emerged in Botswana in the south of Africa spread around the globe at further increased rates, and caused unprecedented SARS-CoV-2 infection incidences in several countries. At the start of December 2021 the first omicron cases were reported in France. Methods In this...

Additional file 2 of Parallel evolution of amphioxus and vertebrate small-scale gene duplications

Marina Brasó-Vives, Ferdinand Marlétaz, Amina Echchiki, Federica Mantica, Rafael D. Acemel, José L. Gómez-Skarmeta, Diego A. Hartasánchez, Lorlane Le Targa, Pierre Pontarotti, Juan J. Tena, Ignacio Maeso, Hector Escriva, Manuel Irimia & Marc Robinson-Rechavi
Additional file 2: Figure S1. BraLan3 genome assembly and annotation quality comparison. Drer, Ggal, Mmus, Hsap, Bflo and Bbel correspond to the latest available genome assemblies for zebrafish, chicken, mouse, human, Florida amphioxus (B. floridae) and an Asian amphioxus (B. belcheri), respectively (see Methods). Blan2 corresponds to the latest genome reference for the European amphioxus previous to this publication [8] and Blan3 corresponds to BraLan3, the genome reference for the European amphioxus presented in this...

Additional file 3 of Parallel evolution of amphioxus and vertebrate small-scale gene duplications

Marina Brasó-Vives, Ferdinand Marlétaz, Amina Echchiki, Federica Mantica, Rafael D. Acemel, José L. Gómez-Skarmeta, Diego A. Hartasánchez, Lorlane Le Targa, Pierre Pontarotti, Juan J. Tena, Ignacio Maeso, Hector Escriva, Manuel Irimia & Marc Robinson-Rechavi
Additional file 3. Supplementary Note 1.

Additional file 4 of Parallel evolution of amphioxus and vertebrate small-scale gene duplications

Marina Brasó-Vives, Ferdinand Marlétaz, Amina Echchiki, Federica Mantica, Rafael D. Acemel, José L. Gómez-Skarmeta, Diego A. Hartasánchez, Lorlane Le Targa, Pierre Pontarotti, Juan J. Tena, Ignacio Maeso, Hector Escriva, Manuel Irimia & Marc Robinson-Rechavi
Additional file 4. Review history.

A CO2-free cloud mask from IASI radiances for climate applications (from IASI/Metop-C)

simon whitburn
The IASI Cloud Detection product (IASI CLD) is a cloud mask available at the IASI pixel level (L2) that was developed for climate applications purposes. The algorithm is detailed in Whitburn et al. (2022, Atmospheric Measurement Techniques). It combines (1) a high sensitivity to cloud detection, (2) a very good consistency over time and between the three IASI instruments and (3) simplicity in its parametrization. The method is based on the use of a supervised...

Dataset for METAPOPGEN 2.0: a multi-locus genetic simulator to model populations of large size

Marco Andrello, Christelle Noirot, Florence Débarre & Stéphanie Manel
Multi-locus genetic processes in subdivided populations can be complex and difficult to interpret using theoretical population genetics models. Genetic simulators offer a valid alternative to study multi-locus genetic processes in arbitrarily complex scenarios. However, the use of forward-in-time simulators in realistic scenarios involving high numbers of individuals distributed in multiple local populations is limited by computation time and memory requirements. These limitations increase with the number of simulated individuals. We developed a genetic simulator, MetaPopGen...

Phylogenomics, plastome structure and species identification in Mahonia (Berberidaceae)

Ruchang Tong, Chaoxia Gui, Yu Zhang, Na Su, Xiaoqi Hou, Meng Liu, Zhaoping Yang, Bing Kang, Zhaoyang Chang, Florian Jabbour & Liang Zhao
Abstract Background Elucidating the phylogenetic relationships within species-rich genera is essential but challenging, especially when lineages are assumed to have been going through radiation events. Mahonia Nutt. (Berberidaceae) is a genus with cosmopolitan distribution, comprising approximately 100 species, two of which are known as Caulis Mahoniae (M. bealei and M. fortunei) with crucial pharmacological significance in Chinese herbal medicine. Mahonia is a taxonomically challenging genus, and intrageneric phylogenetic relationships still need to be explored using...

Multiple retrograde tracing methods compatible with 3DISCO clearing

Shuai Han, Dongdong Li, Yuhui Kou, Zhongguo Fu & Xiaofeng Yin
Exploring the spatial relationship of various neuron pools in the spinal cord is crucial and difficult due to its complexity. The single-labelling tracing and sectioning were employed in previous studies exploring the distribution of spinal motor neuron pools, which could only delineate one single motor neuron pool in one specimen and could not achieve intact-tissue observation. Here, with combination of neuroanatomy tracing techniques and the optical clearing technique, we developed a multiple retrograde tracing method...

Data from: Feather bacterial load shapes the trade-off between preening and immunity in pigeons

Sarah Leclaire, Gábor Árpád Czirják, Abdessalem Hammouda & Julien Gasparini
Background: Complex communities of bacteria inhabit the feathers of all birds. Under normal conditions, individuals maintain a healthy state by defending themselves against these potential invaders by preening. The immune system is only triggered when bacteria gain access into the body. Preening is, however, costly and may trade-off with investment in the immune system. To shed light on how birds balance the trade-off between immunity and preen secretions when facing high or low feather bacterial...

Data from: Diet is the primary determinant of bacterial community structure in the guts of higher termites

Aram Mikaelyan, Carsten Dietrich, Tim Köhler, Michael Poulsen, David Sillam-Dussès & Andreas Brune
The gut microbiota of termites plays critical roles in the symbiotic digestion of lignocellulose. While phylogenetically ‘lower termites’ are characterized by a unique association with cellulolytic flagellates, higher termites (family Termitidae) harbour exclusively prokaryotic communities in their dilated hindguts. Unlike the more primitive termite families, which primarily feed on wood, they have adapted to a variety of lignocellulosic food sources in different stages of humification, ranging from sound wood to soil organic matter. In this...

Data from: Evidence for parasite-mediated selection during short-lasting toxic algal blooms

François Blanquart, Myriam Valero, Catharina Alves-De-Souza, Aliou Dia, Frédéric Lepelletier, Estelle Bigeard, Christian Jeanthon, Christophe Destombe & Laure Guillou
Parasites play a role in the control of transient algal blooms, but it is not known whether parasite-mediated selection results in coevolution of the host and the parasites over this short time span. We investigated the presence of coevolution between the toxic dinoflagellate Alexandrium minutum and two naturally occurring endoparasites during blooms lasting a month in two river estuaries, using cross-inoculation experiments across time and space. Higher parasite abundance was associated with a large daily...

Data from: New material of Palaeoamasia kansui (Embrithopoda, Mammalia) from the Eocene of Turkey and a phylogenetic analysis of Embrithopoda at the species level

Ozan Erdal, Pierre-Olivier Antoine & Sevket Sen
Since the discovery of the megaherbivore Arsinoitherium zitteli Beadnell (early Oligocene of Egypt), the extinct order Embrithopoda has remained an enigmatic group, with disputed affinities among ungulates. In this study, new specimens of Palaeoamasia kansui from the early Palaeogene of Turkey are described and a synthetic dental terminology is proposed for embrithopods. Based on 130 cranial–mandibular and dental characters, the first phylogenetic analysis of embrithopods is carried out in aim to enhance the position of...

Data from: Experimental exposure to trace metals affects plumage bacterial community in the feral pigeon

Marion Chatelain, Adrien Frantz, Julien Gasparini & Sarah Leclaire
Bacteria are fundamental associates of animals, and recent studies have highlighted their major role in host behaviour, immunity or reproductive investment. Thus, any environmental factor modifying bacterial community may affect host fitness. In birds, trace metals emitted by anthropogenic activities accumulate onto the plumage where they may alter bacterial community and ultimately affect bird fitness. Although trace metals are current major environmental issues in urban habitats, their effects on feather bacterial community have never been...

Data from: Invasion history and demographic processes associated with rapid morphological changes in the Red-whiskered bulbul established on tropical islands

Ariane Le Gros, Philippe Clergeau, Dario Zuccon, Raphaël Cornette, Blake Mathys & Sarah Samadi
The Red-whiskered bulbul is a very successful invasive bird species. Morphological differences have been reported among individuals inhabiting the humid and dry coasts of Reunion Island, in a 30-year-old population. This suggests a capacity for rapid local adaptation which could explain the general invasive success of this species. However, the origin and invasion history of this population is unknown. It is therefore not possible to establish with certainty the cause of these morphological differences. Here,...

Data from: Factors essential for L,D-transpeptidase-mediated peptidoglycan cross-linking and β-lactam resistance in Escherichia coli

Christiane Bouchier, Jean-Emmanuel Hugonnet, Michel Arthur, Dominique Mengin-Lecreulx, Yves Brun, Michael Van Nieuwenhze, Louis B Rice, Alejandro Monton, Tanneke Den Blaauwen, Etienne Carbonnelle, Carole Veckerlé & Kuyek Tu
The target of β-lactam antibiotics is the D,D-transpeptidase activity of penicillin-binding proteins (PBPs) for synthesis of 4→3 cross-links in the peptidoglycan of bacterial cell walls. Unusual 3→3 cross-links formed by L,D-transpeptidases were first detected in Escherichia coli more than four decades ago, however no phenotype has previously been associated with their synthesis. Here we show that production of the L,D-transpeptidase YcbB in combination with elevated synthesis of the (p)ppGpp alarmone by RelA lead to full...

Data from: Trait evolution and historical biogeography shape assemblages of annual killifish

Andrew Helmstetter, Alexander Papadopulos, Javier Igea & Tom Van Dooren
Aim: Different species assemblages of annual killifish possess replicated body size distributions yet have unique sets of species in each area of endemism. Here, we use models of trait evolution and historical biogeography to discover how size variation originated and has been restructured. Location: South America. Taxon: Austrolebias (Cyprinodontiformes). Methods: We sampled 63 individuals from 26 Austrolebias species. Using phylogenetic trees (BEAST2), data on environmental variables at sampling locations and size data we compare different...

From individuals to populations: How intraspecific competition shapes thermal reaction norms

Thomas Tully, François Mallard, Vincent Le Bourlot, Christie Le Coeur, Monique Avnaim, Romain Peronnet & David Claessen
1. Most ectotherms follow the temperature-size rule (TSR): in cold environments individuals grow slowly but reach a large asymptotic length. Intraspecific competition can induce plastic changes of growth rate and asymptotic length and competition may itself be modulated by temperature. 2. Our aim is to disentangle the joint effects of temperature and intraspecific competition on growth rate and asymptotic length. 3. We used two distinct clonal lineages of the Collembola Folsomia candida, to describe thermal...

Data from: Determinants of tree cover in tropical floodplains

Joshua H. Daskin, Filipe Aires & A. Carla Staver
In uplands, water availability and fire limit tree cover, differentiating between tropical forest, savanna, and grassland biomes. In contrast, we know less about tropical floodplain tree cover determinants, although these habitats similarly include near-treeless grasslands, moderately treed savannas, and forests. Using GIS and remotely sensed data from 13 large tropical and sub-tropical floodplain ecosystems on five continents, we show that floodplain tree cover increases with climatic water balance (= rainfall - potential evapotranspiration) and decreases...

Data from: The evolution of dual meat and milk cattle husbandry in Linearbandkeramik societies

Rosalind E. Gillis, Lenka Kovačiková, Stéphanie Brehard, Emilie Guthmann, Ivana Vostrovská, Hana Nohálová, Rose-Marie Arbogast, László Domboróczki, Joachim Pechtl, Alexandra Anders, Arkadiusz Marciniak, Anne Tresset & Jean-Denis Vigne
Cattle dominate archaeozoological assemblages from the north-central Europe between the sixth and fifth millennium BC and are frequently considered as exclusively used for their meat. Dairy products may have played a greater role than previously believed. Selective pressure on the lactase persistence mutation has been modelled to have begun between 6000 and 4000 years ago in central Europe. The discovery of milk lipids in late sixth millennium ceramic sieves in Poland may reflect an isolated...

Data from: Habitat formation prevails over predation in influencing fouling communities

Jean-Charles Leclerc & Frédérique Viard
Coastal human-made structures, such as marinas and harbours, are expanding worldwide. Species assemblages described from these artificial habitats are novel relative to natural reefs, particularly in terms of the abundance of non-indigenous species (NIS). Although these fouling assemblages are clearly distinctive, the ecosystem functioning and species interactions taking place there are little understood. For instance, large predators may influence the fouling community development either directly (feeding on sessile fauna) or indirectly (feeding on small predators...

Data from: Breaking the cipher: ant eavesdropping on the variational trail pheromone of its termite prey

Xiao-Lan Wen, Ping Wen, Cecilia A. L. Dahlsjӧ, David Sillam-Dussès & Jan Šobotník
Predators may eavesdrop on their prey using innate signals of varying nature. In regards to social prey, most of the prey signals are derived from social communication and may therefore be highly complex. The most efficient predators select signals that provide the highest benefits. Here, we showed the use of eusocial prey signals by the termite-raiding ant Odontoponera transversa. O. transversa selected the trail pheromone of termites as kairomone in several species of fungus-growing termites...

Data from: Neutron imaging investigation of fossil woods: non-destructive characterization of microstructure and detection of in situ changes as occurring in museum cabinets

Giliane P. Odin, Véronique Rouchon, Frédéric Ott, Nathalie Malikova, Pierre Levitz, Laurent J. Michot & Natalie Malikova
This paper discusses the applicability of neutron imaging techniques for probing the internal microstructure of several fossil woods upon wetting and drying, two phenomena occurring in museum cabinets and endangering the fossil woods. Investigations were carried out using lignites (fossil woods) from two French localities (Rivecourt, Parisian Basin, Oise – Paleogene; Angeac, Aquitanian Basin, Charente – Cretaceous), which present different macroscopic behavior upon drying. Thanks to the high sensitivity of neutrons to hydrogen content, it...

Data from: Balancing yield with resilience and conservation objectives in harvested predator-prey communities

Eric Tromeur & Nicolas Loeuille
The global overexploitation of fish stocks is endangering many marine food webs. Scientists and managers now call for an ecosystem-based fisheries management, able to take into account the complexity of marine ecosystems and the multiple ecosystem services they provide. By contrast, many fishery management plans only focus on maximizing the productivity of harvested stocks. Such practices are suggested to affect other ecosystem services, altering the integrity and resilience of natural communities. Here we show that...

Data from: Resveratrol supplementation reduces oxidative stress and modulates the immune response in free-living animals during a viral infection

Manrico Sebastiano, Marcel Eens, Simone Messina, Hamada Ablelgawad, Kévin Pineau, Gerrit T.S. Beemster, Olivier Chastel, David Costantini, Hamada AbdElgawad & Gerrit T. S. Beemster
1. Diet quality may have an important effect on the regulation of oxidative status and the immune system during an infectious disease. However, the relationship among intake of specific dietary molecules, an individual’s oxidative status and the occurrence and progress of a viral disease remains almost unexplored in free-living organisms. 2. Here, we study a wild, long-lived animal, the Magnificent frigatebird Fregata magnificens to investigate: i) the differences in a number of physiological traits (biomarkers...

Data from: Unraveling the seasonal epidemiology of pneumococcus

Matthieu Domenech De Cellès, Hélène Arduin, Daniel Lévy-Bruhl, Scarlett Georges, Cécile Souty, Didier Guillemot, Laurence Watier & Lulla Opatowski
Infections caused by Streptococcus pneumoniae—including invasive pneumococcal diseases (IPDs)—remain a significant public health concern worldwide. The marked winter seasonality of IPDs is a striking, but still enigmatic aspect of pneumococcal epidemiology in nontropical climates. Here we confronted age-structured dynamic models of carriage transmission and disease with detailed IPD incidence data to test a range of hypotheses about the components and the mechanisms of pneumococcal seasonality. We find that seasonal variations in climate, influenza-like illnesses, and...

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