49 Works

Data from: Genetic, morphological and acoustic evidence reveals lack of diversification in the colonization process in an island bird

Juan Carlos Illera, Ana M. Palmero, Paola Laiolo, Felipe Rodríguez, Ángel C. Moreno & Miguel Navascués
Songbirds with recently (i.e. early Holocene) founded populations are suitable models for studying incipient differentiation in oceanic islands. On such systems each colonization event represents a different evolutionary episode that can be studied by addressing sets of diverging phenotypic and genetic traits. We investigate the process of early differentiation in the spectacled warbler (Sylvia conspicillata) in 14 populations separated by sea barriers from three Atlantic archipelagos and from continental regions spanning from tropical to temperate...

Data from: Assessing the distribution of disease-bearing rodents in human-modified tropical landscapes

Serge Morand, Frédéric Bordes, Kim Blasdell, Shai Pilosof, Jean-François Cornu, Kittipong Chaisiri, Yannick Chaval, Jean-François Cosson, Julien Claude, Tristan Feyfant, Vincent Herbreteau, Stéphane Dupuy & Annelise Tran
1. We tested how habitat structure and fragmentation affect the spatial distribution of common murine rodents inhabiting human-dominated landscapes in southeast Asia. The spatial distribution patterns observed for each rodent species were then used to assess how changes in habitat structure may potentially affect the risk of several major rodent-borne diseases. 2. For this analysis, we used an extensive geo-referenced database containing details of rodents trapped from seven sites in Thailand, Cambodia and Lao PDR....

The interacting effect of habitat amount, habitat diversity and fragmentation on insect diversity along elevational gradients.

Enric Frago, Niry T. Dianzinga, Marie-Ludders Moutoussamt, Joëlle Sadeyen & Lala Ravaomanarivo
Aim: Elevational gradients are a useful approach to evaluate how environmental factors affect animal diversity. Decades of studies on the elevation-diversity gradient have revealed that this gradient varies greatly with taxa and geographic regions. One potential explanation for this may be the dependence of the relationship on landscape features. We explore the impact of fragmentation, habitat diversity and habitat amount on insect diversity (alpha and beta) and abundance along elevational gradients. We hypothesize that insect...

Data from: Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?

Emiliano Trucchi, Benoit Facon, Paolo Gratton, Emiliano Mori, Nils Chr. Stenseth & Sissel Jentoft
Studying the evolutionary dynamics of an alien species surviving and continuing to expand after several generations can provide fundamental information on the relevant features of clearly successful invasions. Here, we tackle this task by investigating the dynamics of the genetic diversity in invasive crested porcupine (Hystrix cristata) populations, introduced to Italy about 1500 years ago, which are still growing in size, distribution range and ecological niche. Using genome-wide RAD markers, we describe the structure of...

Data from: The effects of climate change on a mega-diverse country: predicted shifts in mammalian species richness and turnover in continental Ecuador.

Paula Iturralde-Pólit, Olivier Dangles, Santiago F. Burneo & Christine N. Meynard
Ecuador is one of 17 nations with the greatest diversity in the world, sheltering lowland and mountain regions that are considered global biodiversity hotspots. While these regions are projected to be highly impacted by climate change, it is not clear what would be the consequences for faunal diversity and conservation. To address this issue, we used an ensemble of 8 species distribution models (SDM) to determine future shifts and identify areas of high changes in...

Data from: Landscape genetics highlights the role of bank vole metapopulation dynamics in the epidemiology of Puumala hantavirus

Emmanuel Guivier, Maxime Galan, Yannick Chaval, Anne Xuéreb, Alexis Ribas Salvador, Marie-Lazzarine Poulle, Liina Voutilainen, Heikki Henttonen, Nathalie Charbonnel & Jean François Cosson
Rodent host dynamics and dispersal are thought to be critical for hantavirus epidemiology as they determine pathogen persistence and transmission within and between host populations. We used landscape genetics to investigate how the population dynamics of the bank vole Myodes glareolus, the host of Puumala hantavirus (PUUV), vary with forest fragmentation and influence PUUV epidemiology. We sampled vole populations within the Ardennes, a French PUUV endemic area. We inferred demographic features such as population size,...

Data from: 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife

Maxime Galan, Maria Razzauti, Emilie Bard, Maria Bernard, Carine Brouat, Nathalie Charbonnel, Alexandre Dehne-Garcia, Anne Loiseau, Caroline Tatard, Lucie Tamisier, Muriel Vayssier-Taussat, Hélène Vignes & Jean-François Cosson
The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission...

Data from: Cytonuclear discordance among the Southeast Asian Black rats (Rattus rattus complex)

Marie Pagès, Eric Bazin, Maxime Galan, Yannick Chaval, Julien Claude, Vincent Herbreteau, Johan Michaux, Sylvain Piry, Serge Morand & Jean-François Cosson
Black rats are major invasive vertebrate pests with severe ecological, economic and health impacts. Remarkably, their evolutionary history has received little attention, and there is no firm agreement on how many species should be recognized within the black rat complex. This species complex is native to India and Southeast Asia. According to current taxonomic classification, there are three taxa living in sympatry in several parts of Thailand, Cambodia and Lao People's Democratic Republic, where this...

Data from: Genetic structure and hybridization in the species group of Ficus auriculata: can closely related sympatric Ficus species retain their genetic identity while sharing pollinators?

Zuo-Dong Wei, Noppol Kobmoo, Astrid Cruaud, Finn Kjellberg & Z.-D. Wei
Obligate mutualistic nursery pollination systems between insects and plants have led to substantial co-diversification involving at least some parallel cladogenesis, as documented in Yucca, Ficus and Phyllanthaceae. In such systems pollinators are generally species specific thus limiting hybridization and introgression among interfertile host species. Nevertheless, in the three systems, cases of one insect pollinating several plant species are reported. In most cases host plants sharing pollinators are allopatric. However in the case of the species...

Data from: Genetic differentiation of the pine processionary moth at the southern edge of its range: contrasting patterns between mitochondrial and nuclear markers

Mhamed El Mokhefi, Carole Kerdelhué, Christian Burban, Andrea Battisti, Gahdab Chakali & Mauro Simonato
The pine processionary moth (Thaumetopoea pityocampa) is an important pest of coniferous forests at the southern edge of its range in Maghreb. Based on mitochondrial markers, a strong genetic differentiation was previously found in this species between western (pityocampa clade) and eastern Maghreb populations (ENA clade), with the contact zone between the clades located in Algeria. We focused on the moth range in Algeria, using both mitochondrial (a 648 bp fragment of the tRNA-cox2) and...

Data from: Phylogenetic analyses of mitochondrial and nuclear data in haematophagous flies support the paraphyly of the genus Stomoxys (Diptera: Muscidae)

Najla Dsouli, Frédéric Delsuc, Johan Michaux, Eric De Stordeur, Arnaud Couloux, Michel Veuille & Gérard Duvallet
The genus Stomoxys Geoffroy (Diptera; Muscidae) contains species of parasitic flies that are of medical and economic importance. We conducted a phylogenetic analysis including 10 representative species of the genus including multiple exemplars, together with the closely related genera Prostomoxys Zumpt, Haematobosca Bezzi, and Haematobia Lepeletier & Serville. Phylogenetic relationships were inferred using maximum likelihood and Bayesian methods from DNA fragments from the cytochrome c oxidase subunit I (COI, 753 bp) and cytochrome b (CytB,...

Data from: Genetic structure and inferences on potential source areas for the invasive oriental fruit fly Bactrocera dorsalis (Hendel) based on mitochondrial and microsatellite markers

Wei Shi, Carole Kerdelhué & Hui Ye
Bactrocera dorsalis (Diptera: Tephritidae) is mainly distributed in tropical and subtropical Asia and in the Pacific region. Despite its economic importance, very few studies have addressed the question of the wide genetic structure and potential source area of this species. This pilot study attempts to infer the native region of this pest and its colonization pathways in Asia. Combining mitochondrial and microsatellite markers, we evaluated the level of genetic diversity, genetic structure, and the gene...

Data from: Parallel evolution of behaviour during independent host-shifts following maize introduction into Asia and Europe

Vincent Calcagno, Clémentine Mitoyen, Philippe Audiot, Sergine Ponsard, Giu-Zhen Gao, Zhao-Zhi Lu, Zhen-Ying Wang, Kang-Lai He, Denis Bourguet & Gui-Zhen Gao
Maize was introduced into opposite sides of Eurasia 500 years ago, in Western Europe and in Asia. This caused two host-shifts in the phytophagous genus Ostrinia, O. nubilalis (the European corn borer; ECB) and O. furnacalis (the Asian corn borer; ACB) are now major pests of maize worldwide. They originated independently from Dicot-feeding ancestors, similar to O. scapulalis (the Adzuki bean borer; ABB). Unlike other host-plants, maize is yearly harvested, and harvesting practices impose severe...

Data from: Are generalist Aphidiinae (Hym. Braconidae) mostly cryptic species complexes?

Stéphane A. P. Derocles, Manuel Plantegenest, Jean-Yves Rasplus, Alexia Marie, Darren M. Evans, David H. Lunt & Anne Le Ralec
Aphidiinae are mostly composed of specialist parasitoids and the few species described as generalist are suspected to be composed of cryptic specialists, almost indistinguishable based on morphological characteristics. The use of molecular markers has proven to be a useful tool for revealing cryptic species complexes and here we use seven mitochondrial and nuclear gene fragments to study possible genetic differentiation among seven Aphidiinae generalists. Maximum likelihood (ML) trees and Bayesian Poisson tree processes (bPTP) models...

Data from: Demographic history and genomic diversity and divergence in blue tit populations across heterogeneous environments

Charles Perrier, Quentin Rougemont & Anne Charmantier
Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio-temporal variation in population demography and variation in recombination rate and diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous versus evergreen forests and insular versus mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous...

Population density does not affect seasonal regulations of reproductive physiology in male water vole.

Kévin Poissenot, Chantal Moussu, Morgane Brachet, Didier Chesneau, Philippe Chemineau, Martine Migaud, Nathalie Charbonnel & Matthieu Keller
Most small rodent species display cyclic fluctuations in their population density. The mechanisms behind these cyclical variations are not yet clearly understood. Density-dependent effects on reproductive function could affect these population variations. The fossorial water vole ecotype, Arvicola terrestris, undergoes a multi-year cycle dynamic with outbreak peaks. Here, we monitored different water vole populations over three years, in spring and autumn, to evaluate whether population density be related to male reproductive physiology. Our results show...

Data from: Microsatellite evolutionary rate and pattern in Schistocerca gregaria inferred from direct observation of germline mutations

Marie-Pierre Chapuis, Christophe Plantamp, Réjane Streiff, Laurence Blondin, Cyril Piou & M.-P. Chapuis
Unravelling variation among taxonomic orders regarding the rate of evolution in microsatellites is crucial for evolutionary biology and population genetics research. The mean mutation rate of microsatellites tends to be lower in arthropods than in vertebrates, but data are scarce and mostly concern accumulation of mutations in model species. Based on parent-offspring segregations and a hierarchical Bayesian model, the mean rate of mutation in the orthopteran insect Schistocerca gregaria was estimated at 2.1e-4 per generation...

Data from: Barriers to gene flow in the marine environment: insights from two common intertidal limpet species of the Atlantic and Mediterranean

Alexandra Sá Pinto, Madalena Simas Branco, Paulo Barros Alexandrino, Michaël C. Fontaine & Stuart J. E. Baird
Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit...

Data from: Genotype-specific interactions between parasitic arthropods

Marion Orsucci, Maria Navajas & Simon Fellous
Despite the ubiquity of coinfection, we know little of the effects of intra-specific genetic variability on coinfection by distinct parasite species. Here we test the hypothesis that parasite multiplication depends on the combination of parasite genotypes that coinfect the host (that is Genotype.parasite × Genotype.parasite interaction). To that aim, we infected tomato leaves with the ecto-parasitic mites Tetranychus urticae and Tetranychus evansi. We tested all possible combinations between four T. urticae and two T. evansi...

Data from: Spatial heterogeneity in landscape structure influences dispersal and genetic structure: empirical evidence from a grasshopper in an agricultural landscape

Bertrand Gauffre, Sophie Mallez, Marie-Pierre Chapuis, Leblois Raphael, Isabelle Litrico, Sabrina Delaunay, Isabelle Badenhausser & Raphael Leblois
Dispersal may be strongly influenced by landscape and habitat characteristics that could either enhance or restrict movements of organisms. Therefore, spatial heterogeneity in landscape structure could influence gene flow and the spatial structure of populations. In the past decades, agricultural intensification has led to the reduction in grassland surfaces, their fragmentation and intensification. As these changes are not homogeneously distributed in landscapes, they have resulted in spatial heterogeneity with generally less intensified hedged farmland areas...

Data from: Mixing of porpoise ecotypes in southwestern UK waters revealed by genetic profiling

Michael C. Fontaine, Oliver Thatcher, Nicolas Ray, Sylvain Piry, Andrew Brownlow, Nicholas J. Davison, Paul Jepson, Rob Deaville & Simon J. Goodman
Contact zones between ecotypes are windows for understanding how species may react to climate changes. Here, we analysed the fine-scale genetic and morphological variation in harbour porpoises (Phocoena phocoena) around the UK by genotyping 591 stranded animals at nine microsatellite loci. The data were integrated with a prior study to map at high resolution the contact zone between two previously identified ecotypes meeting in the northern Bay of Biscay. Clustering and spatial analyses revealed that...

Data from: Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range

Thomas M. Vignaud, Johann Mourier, Jeffrey A. Maynard, Raphael Leblois, Julia L. Y. Spaet, Eric Clua, Valentina Neglia, Serge Planes & Julia L.Y. Spaet
For free-swimming marine species like sharks, only population genetics and demographic history analyses can be used to assess population health/status as baseline population numbers are usually unknown. We investigated the population genetics of blacktip reef sharks, Carcharhinus melanopterus; one of the most abundant reef-associated sharks and the apex predator of many shallow water reefs of the Indian and Pacific Oceans. Our sampling includes 4 widely separated locations in the Indo-Pacific and 11 islands in French...

Data from: Avian malaria: a new lease of life for an old experimental model to study the evolutionary ecology of Plasmodium

Romain Pigeault, Julien Vézilier, Stéphane Cornet, Flore Zélé, Antoine Nicot, Philippe Perret, Sylvain Gandon & Ana Rivero
Avian malaria has historically played an important role as a model in the study of human malaria, being a stimulus for the development of medical parasitology. Avian malaria has recently come back to the research scene as a unique animal model to understand the ecology and evolution of the disease, both in the field and in the laboratory. Avian malaria is highly prevalent in birds and mosquitoes around the world and is amenable to laboratory...

Data from: Short-term variations in gene flow related to cyclic density fluctuations in the common vole

Bertrand Gauffre, Karine Berthier, Pablo Inchausti, Yannick Chaval, Jean-François Cosson & Vincent Bretagnolle
In highly fluctuating populations with complex social systems genetic patterns are likely to vary in space and time due to demographic and behavioural processes. Cyclic rodents are extreme examples of demographically instable populations that often exhibit strong social organisation. In such populations, kin structure and spacing behaviour may vary with density fluctuations and impact both the composition and spatial structure of genetic diversity. In this study, we analysed the multiannual genetic structure of a cyclic...

Trade-off between deep learning for species identification and inference about predator-prey co-occurrence

Olivier Gimenez, Maëlis Kervellec, Jean-Baptiste Fanjul, Anna Chaine, Lucile Marescot, Yoann Bollet & Christophe Duchamp
Deep learning is used in computer vision problems with important applications in several scientific fields. In ecology for example, there is a growing interest in deep learning for automatizing repetitive analyses on large amounts of images, such as animal species identification. However, there are challenging issues toward the wide adoption of deep learning by the community of ecologists. First, there is a programming barrier as most algorithms are written in Python while most ecologists are...

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  • Centre de Biologie et de Gestion des Populations
  • French National Centre for Scientific Research
  • French National Institute for Agricultural Research
  • University of Montpellier
  • Centre de Coopération Internationale en Recherche Agronomique pour le Développement
  • Centre d'Ecologie Fonctionnelle et Evolutive
  • Mahidol University
  • University of Barcelona
  • University of Hull
  • Yunnan University