98 Works

The first African record of Isothecium algarvicum in Kroumiria (Tunisia), a relictual element of the Neogene flora?

Imen Ben Osman, Vincent Hugonnot, Serge Muller & Amina Daoud-Bouattour
Isothecium algarvicum W. E. Nicholson & Dixon, was discovered in Tunisia, which constitutes the first report of this Macaronesianoceanic species in Africa. Three distinct populations were observed in ravines in the humid Meso-Mediterranean vegetation belt of Kroumiria. The Tunisian material is fully described, with particular attention to alar and supra-alar cells, prorate cells and other morphological characteristics. The density and size of the prorate cells appear to be a robust diagnostic characteristic for the separation...

Diversification dynamics in the Neotropics through time, clades and biogeographic regions

Andrea Meseguer, Alice Michel, Pierre-Henri Fabre, Oscar Perez Escobar, Guillaume Chomicki, Ricarda Riina, Alexandre Antonelli, Pierre-Olivier Antoine, Frédéric Delsuc & Fabien Condamine
The origins and evolution of the outstanding Neotropical biodiversity are a matter of intense debate. A comprehensive understanding is hindered by the lack of deep-time comparative data across wide phylogenetic and ecological contexts. Here, we quantify the prevailing diversification trajectories and drivers of Neotropical diversification in a sample of 150 phylogenies (12,512 species) of seed plants and tetrapods and assess their variation across Neotropical regions and taxa. Analyses indicate that Neotropical diversity has mostly expanded...

Relict lineages with extreme ecology and physiology: metal hyperaccumulation on ultramafic substrates in New Caledonian Alseuosmineae (Asterales)

Karine Gotty, Gael J. Kergoat, Pierre Jouannais, Vanessa Invernón, Sylvain Merlot & Yohan Pillon
: Relict lineages are an important component of biodiversity, but it is unclear under what circumstances these groups persist. A potential example of such a group is the Alseuosmineae (Asterales) of Oceania. This clade contains the three small families – Alseuosmiaceae, Argophyllaceae and Phellinaceae. The clade has highest diversity in New Caledonia, where there are extensive ultramafic substrates, creating an extreme edaphic environment. : Using several lines of evidence we aimed to show that Alseuosmineae...

Data from: The evolutionary pathways for local adaptation in mountain hares

Iwona Giska, João Pimenta, Liliana Farelo, Pierre Boursot, Klaus Hackländer, Hannes Jenny, Neil Reid, W. Ian Montgomery, Paulo A. Prodöhl, Paulo C. Alves & José Melo-Ferreira
Understanding the evolution of local adaptations is a central aim of evolutionary biology and key for the identification of unique populations and lineages of conservation relevance. By combining RAD sequencing and whole-genome sequencing, we identify genetic signatures of local adaptation in mountain hares (Lepus timidus) from isolated and distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia. We recovered full mitochondrial DNA sequences from whole-genome sequencing data and used it to recontruct the...

Large Herbivore Nemabiomes: Patterns of Diversity and Sharing

Georgia Titcomb, Johan Pansu, Matthew Hutchinson, Kaia Tombak, Christina Hansen, Chris Baker, Tyler Kartzinel, Hillary Young & Robert Pringle
Amidst global shifts in the distribution and abundance of wildlife and livestock, we have only a rudimentary understanding of ungulate parasite communities and parasite-sharing patterns. We used qPCR and DNA metabarcoding of fecal samples to characterize gastrointestinal nematode (Strongylida) community composition and sharing among 17 sympatric species of wild and domestic large mammalian herbivore in central Kenya. We tested a suite of hypothesis-driven predictions about the role of host traits and phylogenetic relatedness in describing...

The global distribution of known and undiscovered ant biodiversity

Jamie Kass, Benoit Guénard, Kenneth Dudley, Clinton Jenkins, Fumika Azuma, Brian Fisher, Catherine Parr, Heloise Gibb, John Longino, Philip Ward, Anne Chao, David Lubertazzi, Michael Weiser, Walter Jetz, Robert Guralnick, Rumsaïs Blatrix, James Des Lauriers, David Donoso, Christos Georgiadis, Kiko Gomez, Peter Hawkes, Robert Johnson, John Lattke, Joe MacGown, William Mackay … & Evan Economo
Invertebrates constitute the majority of animal species and are critical for ecosystem functioning and services. Nonetheless, global invertebrate biodiversity patterns and their congruences with vertebrates remain largely unknown. We resolve the first high-resolution (~20-km) global diversity map for a major invertebrate clade, ants, using biodiversity informatics, range modeling, and machine learning to synthesize existing knowledge and predict the distribution of undiscovered diversity. We find that ants and different vertebrate groups have distinct features in their...

The generality of cryptic dietary niche differences in diverse large-herbivore assemblages

Robert Pringle, Johan Pansu, Matthew Hutchinson, T. Michael Anderson, Mariska Te Beest, Colleen Begg, Keith Begg, Aurelie Bonin, Lackson Chama, Simon Chamaillé-Jammes, Eric Coissac, Joris Cromsigt, Margaret Demmel, Jason Donaldson, Jennifer Guyton, Christina Hansen, Christopher Imakando, Azwad Iqbal, Davis Kalima, Graham Kerley, Samson Kurukura, Marietjie Landman, Ryan Long, Isaack Munuo, Ciara Nutter … & Tyler Kartzinel
Ecological niche differences are necessary for stable species coexistence but are often difficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth-forms but are agnostic towards food-plant species identity. Empirical support for these models is variable, suggesting that additional mechanisms of resource partitioning may be important in sustaining large-herbivore diversity in African savannas. We used DNA metabarcoding to conduct a taxonomically...

Additional file 2 of Association between in-ICU red blood cells transfusion and 1-year mortality in ICU survivors

Alice Blet, Joel B. McNeil, Julie Josse, Bernard Cholley, Raphaël Cinotti, Gad Cotter, Agnès Dauvergne, Beth Davison, Kévin Duarte, Jacques Duranteau, Marie-Céline Fournier, Etienne Gayat, Samir Jaber, Sigismond Lasocki, Thomas Merkling, Katell Peoc’h, Imke Mayer, Malha Sadoune, Pierre-François Laterre, Romain Sonneville, Lorraine Ware, Alexandre Mebazaa & Antoine Kimmoun
Additional file 2: Supplemental Text.

Data from: The effect of copy number hemiplasy on gene family evolution

Qiuyi Li, Yao-Ban Chan, Nicolas Galtier & Celine Scornavacca
The evolution of gene families is complex, involving gene-level evolutionary events such as gene duplication, horizontal gene transfer, and gene loss (DTL), and other processes such as incomplete lineage sorting (ILS). Because of this, topological differences often exist between gene trees and species trees. A number of models have been recently developed to explain these discrepancies, the most realistic of which attempt to consider both gene-level events and ILS. When unified in a single model,...

Data from: Climatic niche lability but growth form conservatism in the African woody flora

Anaïs-Pasiphaé Gorel, Olivier J. Hardy, Gilles Dauby, Kyle G. Dexter, Ricardo A. Segovia, Kathy Steppe & Adeline Fayolle
Climatic niche evolution during the diversification of tropical plants has received little attention in Africa. To address this, we characterized the climatic niche of >4000 tropical African woody species, distinguishing two broad bioclimatic groups (forest vs. savanna) and six subgroups. We quantified niche conservatism versus lability at the genus level and for higher clades, using a molecular phylogeny of >800 genera. Although niche stasis at speciation is prevalent, numerous clades individually cover vast climatic spaces...

Additional file 2 of A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Additional file 2: Table S1. Equipment sourcing and alternatives. Table S2. Sample information. Table S3. Culturing information. Table S4. Cost estimates.

Additional file 3 of A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Additional file 3. Isolate taxonomic information, genome assembly statistics, and other metadata.

Additional file 1 of No association between habitat, autogeny and genetics in Moroccan Culex pipiens populations

Soukaina Arich, Yuki Haba, Najlaa Assaid, Megan L. Fritz, Carolyn S. McBride, Mylène Weill, Hassan Taki, M’hammed Sarih & Pierrick Labbé
Additional file 1: Table S1. CQ11 genotype data from previously published studies in Morocco. CQ11 genotype data for C. pipiens s.s. in Morocco retrieved from the literature are indicated with, for each sample, the locality of sampling, the date (year), the type of breeding site (when reported in the publication, “-” when not), the number of individuals of each CQ11 genotypes (homozygotes for the pipiens allele, for the molestus allele, and heterozygotes) and the reference....

Geographic Analysis of the Safety and Efficacy of Filgotinib in Rheumatoid Arthritis

Adis journals on behalf of:, Bernard Combe, Robin Besuyen, Antonio Gómez-Centeno, Tsukasa Matsubara, Juan José Sancho Jimenez, Zhaoyu Yin & Maya H. Buch
The above graphical abstract represents the opinions of the authors. For a full list of declarations, including funding and author disclosure statements, and copyright information, please see the full text online. (see “read the peer-reviewed publication” opposite).

Additional file 1 of Genomic characterization of peste des petits ruminants vaccine seed “45G37/35-k”, Russia

Olivier Kwiatek, Geneviève Libeau, Samia Guendouz, Chloé Corbanini, Andrey Gogin, Andrey Lunitsin, Irina Sindryakova, Denis Koblasov & Arnaud Bataille
Additional file 1. Position and frequency of the 248 nucleotide differences separating the PPR vaccine strains Nigeria/75/1 (Nig75/1) and 45G37/35-k (FRCVM). Nucleotide positions corresponding to mutations associated to the attenuation of Nigeria/75/1 are in bold [14].

Additional file 4 of A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Additional file 4. Review History.

Dataset: What makes a teddy bear comforting?

Anne-Sophie Tribot, Nathalie Blanc, Thierry Brassac, François Guilhaumon, Nicolas Casajus & Nicolas Mouquet
This dataset relates to a study intended to identify whether particular physical and sensory characteristics contribute to making a bear more comforting. These data were collected as part of a participatory experiment during the European Researchers' Night, on September 27, 2019, in 13 French cities simultaneously (395 participants). The file "data_teddybears" corresponds to the raw data, whose meaning and coding of each variable is detailed in the file "data_teddybears_metadata". The file "data_teddybears_finals" corresponds to sorted...

Additional file 1 of Intensified tuberculosis treatment to reduce the mortality of HIV-infected and uninfected patients with tuberculosis meningitis (INTENSE-TBM): study protocol for a phase III randomized controlled trial

Thomas Maitre, Maryline Bonnet, Alexandra Calmy, Mihaja Raberahona, Rivonirina Andry Rakotoarivelo, Niaina Rakotosamimanana, Juan Ambrosioni, José M. Miró, Pierre Debeaudrap, Conrad Muzoora, Angharad Davis, Graeme Meintjes, Sean Wasserman, Robert Wilkinson, Serge Eholié, Frédéric Ello Nogbou, Maria-Camilla Calvo-Cortes, Corine Chazallon, Vanessa Machault, Xavier Anglaret & Fabrice Bonnet
Additional file 1. Modified MARAIS Score (modified from Marais et al. [27]).

Additional file 1 of Accuracy of clinicians’ ability to predict the need for renal replacement therapy: a prospective multicenter study

Alexandre Sitbon, Michael Darmon, Guillaume Geri, Paul Jaubert, Pauline Lamouche-Wilquin, Clément Monet, Lucie Le Fèvre, Marie Baron, Marie-Line Harlay, Côme Bureau, Olivier Joannes-Boyau, Claire Dupuis, Damien Contou, Virginie Lemiale, Marie Simon, Christophe Vinsonneau, Clarisse Blayau, Frederic Jacobs & Lara Zafrani
Additional file 1: Figure S1. Physician prediction: Visual Likert Scale. Figure S2. PresagEER study timeline. Table S1. Delays between ICU admission, AKI diagnosis and RRT initiation. Table S2. RRT characteristics. Table S3. Characteristics and outcomes of AKI patients (n (%) or median (IQR)). Table S4. Multivariate analysis including variables associated with the risk of requiring RRT (without physician prediction).

Additional file 1 of Host-plant adaptation as a driver of incipient speciation in the fall armyworm (Spodoptera frugiperda)

Estelle Fiteni, Karine Durand, Sylvie Gimenez, Robert L. Meagher, Fabrice Legeai, Gael J. Kergoat, Nicolas Nègre, Emmanuelle d’Alençon & Kiwoong Nam
Additional file 1: Table S1. Summary statistics of genome assemblies showing contiguity and correctness of the assemblies (BUSCO) generated in this study and other published assemblies. Table S2. The information of each sample used in this study. Table S3. Position of targets of selective sweeps specific to the corn or grass group. Table S5. Summary statistics of genome assemblies showing contiguity and correctness of the assemblies generated using SALSA2 and 3D-DNA. Table S6. The list...

Joint modeling strategy for using electronic medical records data to build machine learning models: an example of intracerebral hemorrhage

Jianxiang Tang, Xiaoyu Wang, Hongli Wan, Chunying Lin, Zilun Shao, Yang Chang, Hexuan Wang, Yi Wu, Tao Zhang & Yu Du
Abstract Background Outliers and class imbalance in medical data could affect the accuracy of machine learning models. For physicians who want to apply predictive models, how to use the data at hand to build a model and what model to choose are very thorny problems. Therefore, it is necessary to consider outliers, imbalanced data, model selection, and parameter tuning when modeling. Methods This study used a joint modeling strategy consisting of: outlier detection and removal,...

No association between habitat, autogeny and genetics in Moroccan Culex pipiens populations

Soukaina Arich, Yuki Haba, Najlaa Assaid, Megan L. Fritz, Carolyn S. McBride, Mylène Weill, Hassan Taki, M’hammed Sarih & Pierrick Labbé
Abstract Background Mosquitoes of the Culex pipiens complex are found across the globe and are the focus of many research studies. Among the temperate species C. pipiens sensu stricto (s.s.), two forms are usually described: molestus and pipiens. These two forms are indistinguishable in terms of morphology but show behavioral and physiological differences that may have consequences for their associated epidemiology. The two forms are well defined in the northern part of the species distribution,...

Relict lineages with extreme ecology and physiology: metal hyperaccumulation on ultramafic substrates in New Caledonian Alseuosmineae (Asterales)

Karine Gotty, Gael J. Kergoat, Pierre Jouannais, Vanessa Invernon, Sylvain Merlot & Yohan Pillon
Relict lineages are an important component of biodiversity, but it is unclear under what circumstances these groups persist. A potential example of such a group is the Alseuosmineae (Asterales) of Oceania. This clade contains the three small families – Alseuosmiaceae, Argophyllaceae and Phellinaceae. The clade has highest diversity in New Caledonia, where there are extensive ultramafic substrates, creating an extreme edaphic environment. Using several lines of evidence we aimed to show that Alseuosmineae qualify as...

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