234 Works

Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium

Jesse Conklin, Yvonne Verkuil, Phil Battley, Chris Hassell, Job Ten Horn, James Johnson, Pavel Tomkovich, Allan Baker, Theunis Piersma & Michaël Fontaine
Present-day ecology and population structure are the legacies of past climate and habitat perturbations, and this is particularly true for species that are widely distributed at high latitudes. The red knot, Calidris canutus, is an arctic-breeding, long-distance migratory shorebird with six recognized subspecies defined by differences in morphology, migration behavior, and annual-cycle phenology, in a global distribution thought to have arisen just since the Last Glacial Maximum (LGM). We used nextRAD sequencing of 10,881 single-nucleotide...

Data from: No evidence of foliar disease impact on crop root functional strategies and soil microbial communities: What does this mean for organic coffee?

Stephanie Gagliardi, Jacques Avelino, Roberta Fulthorpe, Elias De Melo Virginio Filho & Marney Isaac
Global climate change is increasing pest and pathogen pressures on plant communities, deteriorating optimal plant functioning. In plant communities, root functional trait expression and microbial communities are important indicators of plant functioning belowground, and, when confronted with pathogens aboveground, can simultaneously reflect plant defence strategies. Yet, while research is continuing to emerge on the response of root functional traits and microbial processes to pathogens aboveground, little work has investigated these interactions in tree-crops, or the...

North Pacific harbor porpoise SNP and microhaplotype genotypes, mitochondrial control region haplotype sequences

Phillip Morin, Brenna Forester, Karin Forney, Carla Crossman, Brittany Hancock-Hanser, Kelly Robertson, Lance Barrett-Lennard, Robin Baird, John Calambokidis, Pat Gearin, Bradley Hanson, Cassie Schumacher, Timothy Harkins, Michael Fontaine, Barbara Taylor & Kim Parsons
Harbor porpoises in the North Pacific are found in coastal waters from southern California to Japan, but population structure is poorly known outside of a few local areas. We used multiplexed amplicon sequencing of 292 loci and genotyped clusters of SNPs as microhaplotypes (N=271 samples) in addition to mtDNA sequence data (N=413 samples), to examine the genetic structure from samples collected along the Pacific coast and inland waterways from California to southern British Columbia. We...

Data from: Sequential co-infections drive parasite competition and the outcome of infection

Giacomo Zilio & Jacob Koella
1) Co-infections by multiple parasites are common in natural populations. Some of these are likely to be the result of sequential rather than simultaneous infections. The timing of the co-infections may affect their competitive interactions, thereby influencing the success of the parasites and their impact on the host. This may have important consequence for epidemiological and eco-evolutionary dynamics. 2) We examined in two ecological conditions the effect of sequential co-infection on the outcome of infection...

Data from: Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes

Marlène Chiarello, Jean-Christophe Auguet, Nicholas Graham, Thomas Claverie, Elliott Sucré, Corinne Bouvier, Fabien Rieuvilleneuve, Claudia Restrepo-Ortiz, Yvan Bettarel, Sébastien Villéger & Thierry Bouvier
Coral reefs host hundreds of thousands of animal species that are increasingly threatened by anthropogenic disturbances. These animals host microbial communities at their surface, playing crucial roles for their fitness. However the diversity of such microbiomes is mostly described in a few coral species, and still poorly defined in other invertebrates and vertebrates. Given the diversity of animal microbiomes, and the diversity of host species inhabiting coral reefs, the contribution of such microbiomes to the...

Data from: Decomposition of leaf litter mixtures across biomes: The role of litter identity, diversity and soil fauna

Shixing Zhou, Olaf Butenschoen, Sandra Barantal, I. Tanya Handa, Marika Makkonen, Veronique Vos, Rien Aerts, Matty P. Berg, Brendan McKie, Jasper Van Ruijven, Stephan Hättenschwiler & Stefan Scheu
1. At broad spatial scales, the factors regulating litter decomposition remain ambiguous, with the understanding of these factors largely based on studies investigating site-specific single litter species, whereas studies using multi litter species mixtures across sites are rare. 2. We exposed in microcosms containing single species and all possible mixtures of four leaf litter species differing widely in initial chemical and physical characteristics from a temperate forest to the climatic conditions of four different forests...

Looking for mimicry in a snake assemblage using deep learning

Thomas De Solan, Julien Pierre Renoult, Philippe Geniez, Patrice David & Pierre-André Crochet
Batesian mimicry is a canonical example of evolution by natural selection, popularized by highly colorful species resembling unrelated models with astonishing precision. However, Batesian mimicry could also occur in inconspicuous species and rely on subtle resemblance. Although potentially widespread, such instances have been rarely investigated, such that the real frequency of Batesian mimicry has remained largely unknown. To fill this gap, we developed a new approach using deep learning to quantify visual resemblance between putative...

Data from: Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach

Jeanne Tonnabel, Isabelle Olivieri, Agnès Mignot, Tony Rebelo, Fabienne Justy, Sylvain Santoni, Stéfanie Caroli, Laure Sauné, Olivier Bouchez, Emmanuel J. P. Douzery, Emmanuel J.P. Douzery & Anthony Rebelo
Despite the recent advances in generating molecular data, reconstructing species-level phylogenies for non-models groups remains a challenge. The use of a number of independent genes is required to resolve phylogenetic relationships, especially for groups displaying low polymorphism. In such cases, low-copy nuclear exons and non-coding regions, such as 3′ untranslated regions (3′-UTRs) or introns, constitute a potentially interesting source of nuclear DNA variation. Here, we present a methodology meant to identify new nuclear orthologous markers...

Data from: Variation in host plant usage and diet breadth predict sibling preference and performance in the neotropical tortoise beetle Chelymorpha alternans (Coleoptera: Chrysomelidae: Cassidinae)

Colin R. Morrison, Clement Aubert & Donald M. Windsor
Specialized interactions between insects and the plants that they consume are one of the most ubiquitous and consequential ecological associations on the plant. Decades of investigation suggest that a narrow diet favors an individual phytophagous insect’s performance relative to a dietary generalist. However, this body of research has tended to approach questions of diet breadth and host usage from the perspective of temperate plant – insect associations. Relationships between diet breadth, host usage and variation...

Data from: Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages

Florentine Riquet, Cathy Liautard-Haag, Lucy Woodall, Carmen Bouza, Patrick Louisy, Bojan Hamer, Francisco Otero-Ferrer, Philippe Aublanc, Vickie Béduneau, Olivier Briard, Tahani El Ayari, Sandra Hochscheid, Khalid Belkhir, Sophie Arnaud-Haond, Pierre-Alexandre Gagnaire & Nicolas Bierne
Diverging semi-isolated lineages either meet in narrow clinal hybrid zones, or have a mosaic distribution associated with environmental variation. Intrinsic reproductive isolation is often emphasized in the former and local adaptation in the latter, although both can contribute to isolation. Rarely these two patterns of spatial distribution are reported in the same study system. Here we report that the long-snouted seahorse Hippocampus guttulatus is subdivided into discrete panmictic entities by both types of hybrid zones....

Data from: Partner choice creates fairness in humans

Stéphane Debove, Jean-Baptiste André, Nicolas Baumard & J.-B. Andre
Many studies demonstrate that partner choice has played an important role in the evolution of human cooperation, but little work has tested its impact on the evolution of human fairness. In experiments involving divisions of money, people become either over-generous or over-selfish when they are in competition to be chosen as cooperative partners. Hence, it is difficult to see how partner choice could result in the evolution of fair, equal divisions. Here, we show that...

Data from: Gene flow among wild and domesticated almond species: insights from chloroplast and nuclear markers

Malou Delplancke
Hybridization has played a central role in the evolutionary history of domesticated plants. Notably, several breeding programs relying on gene introgression from the wild compartment have been performed in fruit tree species within the genus Prunus but few studies investigated spontaneous gene flow among wild and domesticated Prunus species. Consequently, a comprehensive understanding of genetic relationships and levels of gene flow between domesticated and wild Prunus species is needed. Combining nuclear and chloroplastic microsatellites, we...

Data from: Evolutionary rescue in populations of Pseudomonas fluorescens across an antibiotic gradient

Johan Ramsayer, Oliver Kaltz & Michael E. Hochberg
Environmental change represents a major threat to species persistence. When change is rapid, a population's only means of persisting may be to evolve resistance. Understanding such ‘evolutionary rescues’ is important for conservation in the face of global change, but also in the agricultural and medical sciences, where the objective is rather population control or eradication. Theory predicts that evolutionary rescue is fostered by large populations and genetic variation, but this has yet to be tested....

Data from: Additional molecular support for the new chordate phylogeny

Frédéric Delsuc, Georgia Tsagkogeorga, Nicolas Lartillot & Hervé Philippe
Recent phylogenomic analyses have suggested tunicates instead of cephalochordates as the closest living relatives of vertebrates. In direct contradiction with the long accepted view of Euchordates, this new phylogenetic hypothesis for chordate evolution has been the object of some skepticism. We assembled an expanded phylogenomic dataset focused on deuterostomes. Maximum-likelihood using standard models and Bayesian phylogenetic analyses using the CAT site-heterogeneous mixture model of amino-acid replacement both provided unequivocal support for the sister-group relationship between...

Data from: QTL mapping of volatile compound production in Saccharomyces cerevisiae during alcoholic fermentation

Matthias Eder, Isabelle Sanchez, Claire Brice, Carole Camarasa, Jean-Luc Legras & Sylvie Dequin
Background: The volatile metabolites produced by Saccharomyces cerevisiae during alcoholic fermentation, which are mainly esters, higher alcohols and organic acids, play a vital role in the quality and perception of fermented beverages, such as wine. Although the metabolic pathways and genes behind yeast fermentative aroma formation are well described, little is known about the genetic mechanisms underlying variations between strains in the production of these aroma compounds. To increase our knowledge about the links between...

Data from: Nesting sites of giant honey bees modulated by landscape patterns

Charlotte Pavageau, Cédric Gaucherel, Claude Garcia & Jaboury Ghazoul
1. The composition of agro-ecological landscapes is thought to have important implications for the production of major crops through its effects on pollinator abundance and behaviour. 2. We explored the roles of land cover and land cover heterogeneity on bee nest distribution for Apis dorsata, a key species for coffee pollination, in a complex agroforest landscape. We emphasized scaling and non-uniform effects by combining two different approaches of spatial analysis, the point-pattern analysis and surface-pattern...

Data from: Measuring and interpreting sexual selection metrics - evaluation and guidelines

Nils Anthes, Ines K. Häderer, Nico K. Michiels & Tim Janicke
(1) Routine assessments of overall sexual selection, including comparisons of its direction and intensity between sexes or species, rely on summary metrics that capture the essence of sexual selection. Nearly all currently employed metrics require population-wide estimates of individual mating success and reproductive success. The resulting sexual selection metrics, however, can heavily and systematically vary with the chosen approaches in terms of sampling, measurement, and analysis. (2) Our review illustrates this variation using the Bateman...

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: Do North Atlantic Eels show parallel patterns of spatially varying selection?

Malene G. Ulrik, José Martín Pujolar, Anne-Laure Ferchaud, Magnus W. Jacobsen, Thomas D. Als, Pierre Alexandre Gagnaire, Jane Frydenberg, Peder K. Bøcher, Bjarni Jónsson, Louis Bernatchez & Michael M. Hansen
Background: The two North Atlantic eel species, the European and the American eel, represent an ideal system in which to study parallel selection patterns due to their sister species status and the presence of ongoing gene flow. A panel of 80 coding-gene SNPs previously analyzed in American eel was used to genotype European eel individuals (glass eels) from 8 sampling locations across the species distribution. We tested for single-generation signatures of spatially varying selection in...

Data from: Are pollinators the agents of selection on flower colour and size in irises?

Daniel Souto-Vilarósa, Ana Vuleta, Sanja Manitašević Jovanović, Sanja Budečević, Hui Wang, Yuval Sapir & Eric Imbert
Plant-pollinator interactions are believed to play a major role in the evolution of floral traits. Flower colour and flower size are important for attracting pollinators, directly influencing reproduction, and thus expected to be under pollinator-mediated selection. Pollinator-mediated selection is also proposed to play a role in maintaining flower colour polymorphism within populations. However, pigment concentrations, and thus flower colour, are also under selective pressures independent of pollinators. We quantified phenotypic pollinator-mediated selection on flower colour...

Data from: Hot spots become cold spots: coevolution in variable temperature environments

Alison B. Duncan, Eike Dusi, Franck Jacob, Johan Ramsayer, Michael E. Hochberg & Oliver Kaltz
Antagonistic coevolution between hosts and parasites is a key process in the genesis and maintenance of biological diversity. Whereas coevolutionary dynamics show distinct patterns under favourable environmental conditions, the effects of more realistic, variable conditions are largely unknown. We investigated the impact of a fluctuating environment on antagonistic coevolution in experimental microcosms of Pseudomonas fluorescens SBW25 and lytic phage SBWΦ2. High-frequency temperature fluctuations caused no deviations from typical coevolutionary arms-race dynamics. However, coevolution was stalled...

Data from: Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

France Denoeud, Simon Henriet, Sutada Mungpakdee, Jean-Marc Aury, Corinne Da Silva, Henner Brinkmann, Jana Mikhaleva, Lisbeth C. Olsen, Claire Jubin, Cristian Cañestro, Jean-Marie Bouquet, Gemma Danks, Julie Poulain, Coen Campsteijn, Marcin Adamski, Ismael Cross, Fekadu Yadetie, Matthieu Muffato, Alexandra Louis, Stephen Butcher, Georgia Tsagkogeorga, Anke Konrad, Sarabdeep Singh, Marit F. Jensen, Evelyne Huynh Cong … & Daniel Chourrout
Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on...

Data from: Environmental effects on the detection of adaptation

Sara Magalhães, Elodie Blanchet, Martijn Egas & Isabelle Olivieri
Detecting adaptation involves comparing the performance of populations evolving in different environments. This detection may be confounded by effects due to the environment experienced by organisms prior to the test. We tested whether such confounding effects occur, using spider-mite selection lines on two novel hosts and one ancestral host, after 15 generations of selection. Mites were either sampled directly from the selection lines, or subjected to a common juvenile or to a common maternal environment,...

Data from: Disentangling the pathways of land use impacts on the functional structure of fish assemblages in Amazon streams

Rafael P. Leitão, Jansen Zuanon, David Mouillot, Cecília G. Leal, Robert M. Hughes, Philip R. Kaufmann, Sébastien Villéger, Paulo S. Pompeu, Daniele Kasper, Felipe R. De Paula, Silvio F. B. Ferraz & Toby A. Gardner
Agricultural land use is a primary driver of environmental impacts on streams. However, the causal processes that shape these impacts operate through multiple pathways and at several spatial scales. This complexity undermines the development of more effective management approaches, and illustrates the need for more in-depth studies to assess the mechanisms that determine changes in stream biodiversity. Here we present results of the most comprehensive multi-scale assessment of the biological condition of streams in the...

Data from: Vertically transmitted symbiont reduces host fitness along temperature gradient

Eike Dusi, Sascha Krenek, Martina Schrallhammer, René Sachse, Gisep Rauch, Oliver Kaltz, Thomas Berendonk & T. U. Berendonk
Parasites with exclusive vertical transmission from host parent to offspring are an evolutionary puzzle. With parasite fitness entirely linked to host reproduction, any fitness cost for infected hosts risks their selective elimination. Environmental conditions likely influence parasite impact, and thereby the success of purely vertical transmission strategies. We tested for temperature-dependent virulence of Caedibacter taeniospiralis, a vertically transmitted bacterial symbiont of the protozoan Paramecium tetraurelia. We compared growth of infected and cured host populations at...

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