58 Works

Holocene extinctions of a top predator – effects of time, habitat area and habitat subdivision

Göran Englund, Gunnar Öhlund, Fredrik Olajos, Anders Finstad, Celine Bellard & Bernard Hugueny
1. Loss of habitat and changes in the spatial configuration of habitats are major drivers of species extinctions, but the response to these drivers differs between organisms. To advance theory on how extinction risk from different types of habitat alteration relate to species-specific traits, there is a need for studies on the long-term extinction dynamic of individual species. 2. The goal of this study was to quantify how habitat area and the spatial configuration of...

Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double stranded DNA viruses

Clement Gilbert, Elisabeth Herniou, Yannis Moreau, Nicolas Lévêque, Carine Meignin, Laurent Daeffler, Brian Federici, Richard Cordaux & Vincent Loiseau
Our knowledge of the diversity and frequency of genomic structural variation segregating in populations of large double stranded (ds) DNA viruses is limited. Here we sequenced the genome of a baculovirus (AcMNPV) purified from beet armyworm (Spodoptera exigua) larvae at depths >195,000X using both short-read (Illumina) and long-read (PacBio) technologies. Using a pipeline relying on hierarchical clustering of structural variants (SVs) detected in individual short- and long-reads by six variant callers, we identified a total...

Data from: New physiological bench test reproducing noctural breathing pattern of patients with sleep disordered breathing

Petitjean Michel, Yann Rétory, Amélie Sagniez, Sébastien HARDY, François Cottin, Gabriel Roisman & Shuo Liu
Previous studies have shown that Automatic Positive Airway Pressure (APAP) devices display different behaviors when connected to a bench using theoretical respiratory cycle scripts. However, these scripts are limited and do not simulate physiological behavior during the night. Our aim was to develop a physiological bench that is able to simulate patient breathing airflow by integrating polygraph data. We developed an algorithm analyzing polygraph data and transformed this information into digital inputs required by the...

Data from: Large feet are beneficial for eiders Somateria mollissima

Anders Pape Møller & Karsten Laursen
1. Many waterbirds have fully (totipalmate) or partially webbed (palmate) feet that are used for locomotion in aquatic environments. 2. If webbed feet and wings both contribute to efficient diving, we predicted a positive association between the area of webbed feet and the size of the frontal locomotor apparatus (wing area, heart mass and breast muscle, after adjusting for any partial effects of body size). We predicted that individuals able to acquire more and better...

Data from: Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales)

Hervé Sauquet, Simon Y. W. Ho, Maria A. Gandolfo, Gregory J. Jordan, Peter Wilf, David J. Cantrill, Michael J. Bayly, Lindell Bromham, Gillian K. Brown, Raymond J. Carpenter, Daphne M. Lee, Daniel J. Murphy, J. M. Kale Sniderman & Frank Udovicic
Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen)....

Data from: Evolutionary radiations of Proteaceae are triggered by the interaction between traits and climates in open habitats

Renske E. Onstein, Gregory J. Jordan, Hervé Sauquet, Peter H. Weston, Yanis Bouchenak-Khelladi, Ian J. Wright, Raymond J. Carpenter & H. Peter Linder
Aim: Ecologically driven diversification can create spectacular diversity in both species numbers and form. However, the prediction that the match between intrinsic (e.g. functional trait) and extrinsic (e.g. climatic niche) variables may lead to evolutionary radiation has not been critically tested. Here, we test this hypothesis in the Southern Hemisphere plant family Proteaceae, which shows a spectacular diversity in open mediterranean shrublands in the Southwest Australian Floristic Region (SWAFR) and the Cape Floristic Region (CFR)....

Data from: Should the WHO growth charts be used in France?

Pauline Scherdel, Jérémie Botton, Marie-Françoise Rolland-Cachera, Juliane Léger, Fabienne Pelé, Pierre Yves Ancel, Chantal Simon, Katia Castetbon, Benoit Salanave, Hélène Thibault, Sandrine Lioret, Sandrine Péneau, Gaelle Gusto, Marie-Aline Charles & Barbara Heude
Background: Growth charts are an essential clinical tool for evaluating a child's health and development. The current French reference curves, published in 1979, have recently been challenged by the 2006 World Health Organization (WHO) growth charts. Objective: To evaluate and compare the growth of French children who were born between 1981 and 2007, with the WHO growth charts and the French reference curves currently used. Design: Anthropometric measurements from French children, who participated in 12...

Data from: Fire evolution in the radioactive forests of Ukraine and Belarus: future risks for the population and the environment

Nikolaos Evangeliou, Yves Balkanski, Anne Cozic, Wei Min Hao, Florent Mouillot, Kirsten Thonicke, Ronan Paugam, Sergey Zibtsev, Timothy A. Mousseau, Rong Wang, Benjamin Poulter, Alex Petkov, Chao Yue, Patricia Cadule, Brigitte Koffi, Johannes W. Kaiser & Anders Pape Møller
This paper analyzes the current and future status of forests in Ukraine and Belarus that were contaminated after the nuclear disaster in 1986. Using several models, together with remote sensing data and observations, we studied how climate change in these forests may affect fire regimes. We investigated the possibility of 137Cs displacement over Europe by studying previous fire events, and examined three fire scenarios that depended on different emission altitudes of 137Cs, assuming that 10%...

Data from: Local dynamics of a fast evolving sex-ratio system in Drosophila simulans

Héloïse Bastide, Pierre R. Gérard, David Ogereau, Michel Cazemajor & Catherine Montchamp-Moreau
By distorting Mendelian transmission to their own advantage, X-linked meiotic drive elements can rapidly spread in natural populations, generating a sex-ratio bias. One expected consequence is the triggering of a coevolutionary arms race between the sex chromosome that carries the distorter and suppressors counteracting its effect. Such an arms race has been theoretically and experimentally established, and can have many evolutionary consequences. However, its dynamics in contemporary populations is still poorly documented. Here, we investigate...

Data from: Why do mixotrophic plants stay green? A comparison between green and achlorophyllous orchid individuals in situ

Melanie Roy, Cedric Gonneau, Alain Rocheteau, Daniel Berveiller, Jean-Claude Thomas, Claire Damesin, Marc André Selosse, D. Berveiller, C. Damesin, M. Roy, C. Gonneau, A. Rocheteau & M.-A. Selosse
Some forest plants adapt to shade by mixotrophy, i.e., they obtain carbon both from photosynthesis and from their root mycorrhizal fungi. Fully achlorophyllous species using exclusively fungal carbon (the so-called mycoheterotrophic plants) have repeatedly evolved from such mixotrophic ancestors. However, adaptations for this evolutionary transition, and the reasons why it has happened a limited number of times, remain unknown. We investigated this using achlorophyllous variants (i.e., albinos) spontaneously occurring in Cephalanthera damasonium, a mixotrophic orchid....

Data from: Ecological co-associations influence species’ responses to past climatic change: an example from a Sonoran Desert bark beetle

Ryan C. Garrick, John D. Nason, Rodney J. Dyer & Juan F. Fernández-Manjarrés
Ecologically interacting species may have phylogeographic histories that are shaped both by features of their abiotic landscape, and by biotic constraints imposed by their co-association. The Baja California peninsula provides an excellent opportunity to examine the influence of abiotic vs. biotic factors on patterns of diversity in plant-insect species. This is because past climatic and geological changes impacted the genetic structure of plants quite differently to that of co-distributed free-living animals (e.g., herpetofauna and small...

Data from: Multiple components of environmental change drive populations of breeding waders in seminatural grasslands

Karsten Laursen, Javier Balbontín, Ole Thorup, Henrik Haaning Nielsen, Tommy Asferg & Anders Pape Møller
Environments are rapidly changing due to climate change, land-use, intensive agriculture and the impact of hunting on predator populations. Here we analysed long-term data recorded during 1928-2014 on the size of breeding populations of waders at two large nature reserves in Denmark, Vejlerne and Tipperne, to determine the effects of components of environmental change on breeding populations of waders. Waders are closely associated with coastal marshes and meadows, and such habitats have been reduced extensively...

Data from: Escape from predators and genetic variance in birds

Yiting Jiang & Anders Pape Møller
Predation is a common cause of death in numerous organisms, and a host of anti-predator defenses have evolved. Such defenses often have a genetic background as shown by significant heritability and micro-evolutionary responses towards weaker defenses in the absence of predators. Flight initiation distance (FID) is the distance at which an individual animal takes flight when approached by a human, and hence it reflects the life history compromise between risk of predation and the benefits...

Data from: Connecting genomic patterns of local adaptation and niche suitability in teosintes

Jonas Aguirre-Liguori, Maud Tenaillon, Alejandra Vázquez-Lobo, Brandon Gaut, Juan Jaramillo-Correa, Salvador Montes-Hernandez, Valeria Souza, Luis Eguiarte, J. A. Aguirre-Liguori, J. P. Jaramillo-Correa, V. Souza, L. E. Eguiarte & M. I. Tenaillon
The central-abundance hypothesis predicts that local adaptation is a function of the distance to the center of a species’ geographic range. To test this hypothesis, we gathered genomic diversity data from 49 populations, 646 individuals and 33,464 SNPs of two wild relatives of maize, the teosintes Zea mays ssp. parviglumis and Zea. mays. ssp. mexicana. We examined the association between the distance to their climatic and geographic centroids and the enrichment of SNPs bearing signals...

Data from: Genetic diversity of oilseed rape fields and feral populations in the context of coexistence with GM crops

Diane Bailleul, Sébastien Ollier & Jane Lecomte
Despite growing concern about transgenes escaping from fields, few studies have analysed the genetic diversity of crops in an agroecosystem over several years. Accurate information about the dynamics and relationship of the genetic diversity of crops in an agroecosystem is essential for risk assessment and policies concerning the containment of genetically modified crops and their coexistence with crops grown by conventional practices. Here, we analysed the genetic diversity of oilseed rape plants from fields and...

Data from: Induction of sexual reproduction and genetic diversity in the cheese fungus Penicillium roqueforti

Jeanne Ropars, Manuela López-Villavicencio, Joëlle Dupont, Alodie Snirc, Guillaume Gillot, Monika Coton, Jean-Luc Jany, Emmanuel Coton & Tatiana Giraud
The emblematic fungus Penicillium roqueforti is used throughout the world as a starter culture in the production of blue-veined cheeses. Like other industrial filamentous fungi, P. roqueforti was thought to lack a sexual cycle. However, an ability to induce recombination is of great economic and fundamental importance, as it would make it possible to transform and improve industrial strains, promoting the creation of novel phenotypes and eliminating the deleterious mutations that accumulate during clonal propagation....

Data from: Co-occurrence and hybridization of anther-smut pathogens specialized on Dianthus hosts

Elsa Petit, Casey Silver, Amandine Cornille, Pierre Gladieux, Lisa Rosenthal, Emily Bruns, Sarah Yee, Janis Antonovics, Tatiana Giraud & Michael Hood
Host specialization has important consequences for the diversification and ecological interactions of obligate pathogens. The anther-smut disease of natural plant populations, caused by Microbotryum fungi, has been characterized by specialized host-pathogen interactions, which contribute in part to the isolation among these numerous fungal species. This study investigated the molecular variation of Microbotryum pathogens within the geographic and host-specific distributions on wild Dianthus species in southern European Alps. In contrast to prior studies on this pathogen...

Data from: Virtual patients and sensitivity analysis of the Guyton model of blood pressure regulation: towards individualized models of whole-body physiology

Robert Moss, Thibault Grosse, Ivanny Marchant, Nathalie Lassau, François Gueyffier & S. Randall Thomas
Mathematical models that integrate multi-scale physiological data can offer insight into physiological and pathophysiological function, and may eventually assist in individualized predictive medicine. We present a methodology for performing systematic analyses of multi-parameter interactions in such complex, multi-scale models. Human physiology models are often based on or inspired by Arthur Guyton’s whole-body circulatory regulation model. Despite the significance of this model, it has not been the subject of a systematic and comprehensive sensitivity study. Therefore,...

Data from: Comparing van Oosterhout and Chybicki-Burczyk methods of estimating null allele frequencies for inbred populations

Pascal Campagne, Peter E. Smouse, Georges Varouchas, Jean-Francois Silvain, Bruno Le Rü, P. Campagne, J.-F. Silvain, B. Leru, G. Varouchas & P. E. Smouse
In spite of the usefulness of codominant markers in population genetics, the existence of null alleles raises challenging estimation issues in natural populations that are characterized by positive inbreeding coefficients (F > 0). Disregarding the possibility of F > 0 in a population will generally lead to overestimates of null allele frequencies. Conversely, estimates of inbreeding coefficients (F) may be strongly biased upwards (excess homozygotes), in the presence of nontrivial frequencies of null alleles. An...

Data from: Cuckoos host range is associated positively with distribution range and negatively with evolutionary uniqueness

Federico Morelli, Yanina Benedetti, Anders P. Moller, Wei Liang & Luis M. Carrascal
1. The evolutionary distinctiveness (ED) score is a measure of phylogenetic isolation that quantifies the evolutionary uniqueness of a species. 2. Here, we compared the ED score of parasitic and non-parasitic cuckoo species worldwide, to understand whether parental care or parasitism represent the largest amount of phylogenetic uniqueness. Next, we focused only on 46 cuckoo species characterized by brood parasitism with a known number of host species, we explored the associations among ED score, number...

Data from: Tillage and herbicide reduction mitigate the gap between conventional and organic farming effects on foraging activity of insectivorous bats

Kévin Barré, Isabelle Le Viol, Romain Julliard, François Chiron & Christian Kerbiriou
The increased use of pesticides and tillage intensification is known to negatively affect biodiversity. Changes in these agricultural practices such as herbicide and tillage reduction have variable effects among taxa, especially at the top of the trophic network including insectivorous bats. Very few studies compared the effects of agricultural practices on such taxa, and overall, only as a comparison of conventional versus organic farming without accurately accounting for underlying practices, especially in conventional where many...

Data from: The role of visual cues in mother–pup reunions in a colonially breeding mammal

Kaja Wierucka, Benjamin J. Pitcher, Robert Harcourt & Isabelle Charrier
Parental care is an important factor influencing offspring survival and adult reproductive success in many vertebrates. Parent-offspring recognition ensures care is only directed to filial young, avoiding the costs of misallocated resource transfer. It is essential in colonial mammal species, such as otariids (fur seals and sea lions), in which repeated mother-offspring separations increase the risk of misdirecting maternal effort. Identification of otariid pups by mothers is known to be multimodal, yet the role of...

Data from: A nonrandom subset of olfactory genes is associated with host preference in the fruit fly Drosophila orena

Aaron A. Comeault, Antonio Serrato-Capuchina, David A. Turissini, Patrick J. McLaughlin, Jean R. David & Daniel R. Matute
Specialization onto different host plants has been hypothesized to be a major driver of diversification in insects, and traits controlling olfaction have been shown to play a fundamental role in host preferences. A diverse set of olfactory genes control olfactory traits in insects, and it remains unclear whether specialization onto different hosts is likely to involve a nonrandom subset of these genes. Here, we test the role of olfactory genes in a novel case of...

Data from: A quantitative framework for investigating risk of deadly collisions between marine wildlife and boats

Julien Martin, Quentin Sabatier, Timothy A. Gowan, Christophe Giraud, Eliezer Gurarie, C. Scott Calleson, Joel G. Ortega-Ortiz, Charles J. Deutsch, Athena Rycyk, Stacie M. Koslovsky & Charles Scott Calleson
Speed regulations of watercraft in protected areas are designed to reduce lethal collisions with wildlife but can have economic consequences. We present a quantitative framework for investigating the risk of deadly collisions between boats and wildlife. We apply encounter rate theory to demonstrate how marine mammal-boat encounter rate can be used to predict the expected number of deaths associated with management scenarios. We illustrate our approach with management scenarios for two endangered species: the Florida...

Data from: Wintering areas predict age-related breeding phenology in a migratory passerine bird

Cosme López-Calderón, Keith A. Hobson, Alfonso Marzal, Javier Balbontín, Marivel Reviriego, Sergio Magallanes, Luz García-Longoria, Florentino De Lope & Anders P. Møller
Understanding connections between breeding, stopover and wintering grounds for long-distance migratory birds can provide important insight into factors influencing demography and the strength of carry-over effects among various periods of the annual cycle. Using previously described, multi-isotope (δ13C, δ15N, δ2H) feather isoscapes for Africa, we identified the most probable wintering areas for house martins (Delichon urbica) breeding at Badajoz in southwestern Spain. We identified two most-probable wintering areas differing in latitude in West Africa. We...

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  • University of Paris-Sud
  • French National Centre for Scientific Research
  • French National Institute for Agricultural Research
  • Agro ParisTech
  • University of Extremadura
  • Aarhus University
  • University of Zurich
  • Sorbonne University
  • Paris Diderot University
  • University of Adelaide
  • Centre d'Ecologie Fonctionnelle et Evolutive
  • University of North Carolina at Chapel Hill
  • Australian National University
  • University of Melbourne
  • University of Otago