67 Works

Data from: Temporally dynamic habitat suitability predicts genetic relatedness among caribou

Glenn Yannic, Loïc Pellissier, Maël Le Corre, Christian Dussault, Louis Bernatchez, Steeve D. Côté & S. D. Cote
Landscape heterogeneity plays a central role in shaping ecological and evolutionary processes. While species utilization of the landscape is usually viewed as constant within a year, the spatial distribution of individuals is likely to vary in time in relation to particular seasonal needs. Understanding temporal variation in landscape use and genetic connectivity has direct conservation implications. Here, we modelled the daily use of the landscape by caribou in Quebec and Labrador, Canada and tested its...

Data from: Invasive alien plants benefit more from clonal integration in heterogeneous environments than natives

Yong-Jian Wang, Heinz Müller-Schärer, Mark Van Kleunen, Ai-Ming Cai, Ping Zhang, Rong Yan, Bi-Cheng Dong & Fei-Hai Yu
What confers invasive alien plants a competitive advantage over native plants remains open to debate. Many of the world's worst invasive alien plants are clonal and able to share resources within clones (clonal integration), particularly in heterogeneous environments. Here, we tested the hypothesis that clonal integration benefits invasive clonal plants more than natives and thus confers invasives a competitive advantage. We selected five congeneric and naturally co-occurring pairs of invasive alien and native clonal plants...

Data from: Genomic and phenotypic architecture of a spruce hybrid zone (Picea sitchensis x P. glauca)

Jill A. Hamilton, Christian Lexer & Sally N. Aitken
Interspecific hybridization may enhance the capacity of populations to adapt to changing environments, and has practical implications for reforestation. We use genomewide estimates of admixture and phenotypic traits for trees in a common garden to examine the extent and direction of gene flow across a Picea hybrid zone, testing assumptions of the bounded hybrid superiority and tension zone models of hybrid zone maintenance. Seeds were collected from the ecological transition zone spanning from maritime to...

Data from: DNA metabarcoding reveals changes in the contents of carnivorous plants along an elevation gradient

Joanne E. Littlefair, Axel Zander, Clara De Sena Costa & Elizabeth L. Clare
Resource variation along abiotic gradients influences subsequent trophic interactions and these effects can be transmitted through entire food webs. Interactions along abiotic gradients can provide clues as to how organisms will face changing environmental conditions, such as future range shifts. However, it is challenging to find replicated systems to study these effects. Phytotelmata, such as those found in carnivorous plants, are isolated aquatic communities and thus form a good model for the study of replicated...

Data from: Socio-economic impact classification of alien taxa (SEICAT)

Sven Bacher, Tim M. Blackburn, Franz Essl, Piero Genovesi, Jaakko Heikkilä, Jonathan M. Jeschke, Glyn Jones, Reuben Keller, Marc Kenis, Christoph Kueffer, Angeliki F. Martinou, Wolfgang Nentwig, Jan Pergl, Petr Pyšek, Wolfgang Rabitsch, David M. Richardson, Helen E. Roy, Wolf-Christian Saul, Riccardo Scalera, Montserrat Vila, John R. U. Wilson, Sabina Kumschick & Sabrina Kumschick
Many alien taxa are known to cause socio-economic impacts by affecting the different constituents of human well-being (security; material and non-material assets; health; social, spiritual and cultural relations; freedom of choice and action). Attempts to quantify socio-economic impacts in monetary terms are unlikely to provide a useful basis for evaluating and comparing impacts of alien taxa because they are notoriously difficult to measure and important aspects of human well-being are ignored. Here, we propose a...

Data from: A structural approach for understanding multispecies coexistence

Serguei Saavedra, Rudolf P. Rohr, Jordi Bascompte, Oscar Godoy, Nathan J.B. Kraft, Jonathan M. Levine & Nathan J. B. Kraft
Although observations of species-rich communities have long served as a primary motivation for research on the coexistence of competitors, the majority of our empirical and theoretical understanding comes from two-species systems. How much of the coexistence observed in species rich communities results from indirect effects among competitors that only emerge in diverse systems remains poorly understood. Resolving this issue requires simple, scalable, and intuitive metrics for quantifying the conditions for coexistence in multispecies systems, and...

Data from: Evolution of longevity improves immunity in Drosophila

Daniel K. Fabian, Kathrin Garschall, Peter Klepsatel, Gonçalo Santos-Matos, Élio Sucena, Martin Kapun, Bruno Lemaitre, Robert Arking, Christian Schloetterer & Thomas Flatt
Much has been learned about the genetics of aging from studies in model organisms, but still little is known about naturally occurring alleles that contribute to variation in longevity. For example, analysis of mutants and transgenes has identified insulin signaling as a major regulator of longevity, yet whether standing variation in this pathway underlies microevolutionary changes in lifespan and correlated fitness traits remains largely unclear. Here we have analyzed the genomes of a set of...

A sparse observation model to quantify species distributions and their overlap in space and time

Liam Singer, Sadoune Ait Kaci Azzou, Thierry Aebischer, Madleina Caduff, Beat Wolf & Daniel Wegmann
Camera traps and acoustic recording devices are essential tools to quantify the distribution, abundance and behavior of mobile species. Varying detection probabilities among device locations must be accounted for when analyzing such data, which is generally done using occupancy models. We introduce a Bayesian Time-dependent Observation Model for Camera Trap data (Tomcat), suited to estimate relative event densities in space and time. Tomcat allows to learn about the environmental requirements and daily activity patterns of...

Supplementary Information for: A cautionary note on the use of genotype callers in phylogenomics

Pablo Duchen & Nicolas Salamin
Next-generation-sequencing genotype callers are commonly used in studies to call variants from newly-sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional genotype callers, such as the one from GATK, is that they are optimized for variant calling at the population level. However,...

Biodiversity effects on grape quality depend on variety and management intensity

Magdalena Steiner, James Benjamin Grace & Sven Bacher
Interactions between plants can be beneficial, detrimental or neutral. In agricultural systems competition between crop and spontaneous vegetation is a major concern. We evaluated the relative support for three non-exclusive ecological hypotheses about interactions between crop and spontaneous plants based on competition, complementarity or facilitation. The study was conducted in Swiss vineyards with different vegetation management intensities. Thirty-three vineyards planted with two different grape varieties were studied over 3 years to determine whether low-intensity vegetation...

Data from: Diversification dynamics of Cheilostome Bryozoa based on a Bayesian analysis of the fossil record

Farideh Moharrek, Paul Taylor, Daniele Silvestro, Helen Jenkins, Dennis Gordon & Andrea Waeschenbach
Cheilostomata is the most diverse and ecologically dominant order of bryozoans living today. We apply a Bayesian framework to estimate macroevolutionary rates of cheilostomes since the Late Jurassic across four datasets: I) manually curated genus ranges, II) published text-mined genus ranges, III) non-revised Paleobiology Database (PBDB) records, IV) revised and augmented PBDB records. All datasets revealed increased origination rates in the Albian, and a twin K-Pg and Danian extinction rate peak. High origination rates in...

Data from: Genome assembly of the ragweed leaf beetle, a step forward to better predict rapid evolution of a weed biocontrol agent to environmental novelties

Sarah Bouchemousse, Laurent Falquet & Heinz Müller-Schärer
Rapid evolution of weed biological control agents (BCAs) to new biotic and abiotic conditions is poorly understood and so far, only little considered both in pre-release and post-release studies, despite potential major negative or positive implications for risks of non-targeted attacks or for colonizing yet unsuitable habitats, respectively. Provision of genetic resources, such as assembled and annotated genomes, is essential to assess potential adaptive processes by identifying underlying genetic mechanisms. Here, we provide the first...

Data from: Postglacial expansion and not human persecution best explains the population structure in the endangered kea (Nestor notabilis)

Nick Dussex, D. Wegmann & B. C. Robertson
Inferring past demography is a central question in evolutionary and conservation biology. It is however sometimes challenging to infer the processes that shaped the current patterns of genetic variation in endangered species. Population sub-structuring can occur as a result of survival in several isolated refugia and subsequent recolonization processes or via genetic drift following a population decline. The kea (Nestor notabilis) is an endemic parrot widely distributed in the mountains of the South Island of...

Data from: HDAC1/2-dependent P0 expression maintains paranodal and nodal integrity independently of myelin stability through interactions with neurofascins

Valérie Brügger, Stefanie Engler, Jorge A. Pereira, Sophie Ruff, Michael Horn, Hans Welzl, Emmanuelle Münger, Adrien Vaquié, Páris N. M. Sidiropoulos, Boris Egger, Peter Yotovski, Luis Filgueira, Christian Somandin, Tessa C. Lühmann, Maurizio D’Antonio, Teppei Yamaguchi, Patrick Matthias, Ueli Suter & Claire Jacob
The pathogenesis of peripheral neuropathies in adults is linked to maintenance mechanisms that are not well understood. Here, we elucidate a novel critical maintenance mechanism for Schwann cell (SC)–axon interaction. Using mouse genetics, ablation of the transcriptional regulators histone deacetylases 1 and 2 (HDAC1/2) in adult SCs severely affected paranodal and nodal integrity and led to demyelination/remyelination. Expression levels of the HDAC1/2 target gene myelin protein zero (P0) were reduced by half, accompanied by altered...

Data from: Reorganization of interaction networks modulates the persistence of species in late successional stages

Serguei Saavedra, Simone Cenci, Ek Del-Val, Karina Boege & Rudolf P. Rohr
1.Ecological interaction networks constantly reorganize as interspecific interactions change across successional stages and environmental gradients. This reorganization can also be associated with the extent to which species change their preference for types of niches available in their local sites. Despite the pervasiveness of these interaction changes, previous studies have revealed that network reorganizations have a minimal or insignificant effect on global descriptors of network architecture, such as: connectance, modularity, and nestedness. However, little is known...

Data from: Neurons in primate visual cortex alternate between responses to multiple stimuli in their receptive field

Kang Li, Vladislav Kozyrev, Søren Kyllingsbæk, Stefan Treue, Susanne Ditlevsen & Claus Bundesen
A fundamental question concerning representation of the visual world in our brain is how a cortical cell responds when presented with more than a single stimulus. We find supportive evidence that most cells presented with a pair of stimuli respond predominantly to one stimulus at a time, rather than a weighted average response. Traditionally, the firing rate is assumed to be a weighted average of the firing rates to the individual stimuli (response-averaging model) (Bundesen...

Data from: Thin-film structural coloration from simple fused scales in moths

Cédric Kilchoer, Ullrich Steiner & Bodo D. Wilts
The metallic coloration of insects often originates from diverse nanostructures ranging from simple thin films to complex three-dimensional photonic crystals. In Lepidoptera, structural coloration is widely present and seems to be abundant in extant species. However, even some basal moths exhibit metallic coloration. Here, we have investigated the origin of the vivid metallic colours of the wing scales of the basal moth Micropterix aureatella by spectrophotometry and scanning electron microscopy. The metallic gold-, bronze- and...

Data from: Selection against recombinant hybrids maintains reproductive isolation in hybridizing Populus species despite F1 fertility and recurrent gene flow

Camille Christie, Kai N. Stölting, Luisa Bresadola, Barbara Fussi, Berthold Heinze, Daniel Wegmann, Christian Lexer & Camille Christe
Natural hybrid zones have proven to be precious tools for understanding the origin and maintenance of reproductive isolation (RI) and therefore species. Most available genomic studies of hybrid zones using whole- or partial-genome resequencing approaches have focused on comparisons of the parental source populations involved in genome admixture, rather than exploring fine-scale patterns of chromosomal ancestry across the full admixture gradient present between hybridizing species. We have studied three well-known European ‘replicate’ hybrid zones of...

Data from: The diversity of population responses to environmental change

Fernando Colchero, Owen R. Jones, Dalia A. Conde, Dave Hodgson, Felix Zajitschek, Benedikt R. Schmidt, Aurelio F. Malo, Susan C. Alberts, Peter H. Becker, Sandra Bouwhuis, Anne M. Bronikowski, Kristel M. De Vleeschouwer, Richard J. Delahay, Stefan Dummermuth, Eduardo Fernández-Duque, John Frisenvænge, Martin Hesselsøe, Sam Larson, Jean-Francois Lemaitre, Jennifer McDonald, David A.W. Miller, Colin O'Donnell, Craig Packer, Becky E. Raboy, Christopher J. Reading … & Chris J. Reading
The current extinction and climate change crises pressure us to predict population dynamics with ever-greater accuracy. Although predictions rest on the well-advanced theory of age-structured populations, two key issues remain poorly-explored. Specifically, how the age-dependency in demographic rates and the year-to-year interactions between survival and fecundity affect stochastic population growth rates. We use inference, simulations, and mathematical derivations to explore how environmental perturbations determine population growth rates for populations with different age-specific demographic rates and...

Data from: Including community composition in biodiversity-productivity models

Nadine Sandau, Rudolf P. Rohr, Russell E. Naisbit, Yvonne Fabian, Odile T. Bruggisser, Patrik Kehrli, Alexandre Aebi & Louis-Félix Bersier
1. Studies on biodiversity and ecosystem functioning (BEF) have elicited debate over the interpretation of the positive relationship between species richness and plant productivity. Manipulating richness cannot be achieved without affecting composition; it is thus essential to consider the latter in statistical models. 2. We firstly review existing approaches that use species richness as an explanatory variable and propose modifications to improve their performance. We use an original dataset to illustrate the analyses. The classical...

Distal and proximal hypoxia response elements cooperate to regulate organ-specific erythropoietin gene expression

Roland Wenger, Ilaria M.C. Orlando, Véronique N. Lafleur, Federica Storti, Patrick Spielmann, Lisa Crowther, Sara Santambrogio, Johannes Schödel, David Hoogewijs & David R. Mole
While it is well-established that distal hypoxia response elements (HREs) regulate hypoxia-inducible factor (HIF) target genes such as erythropoietin (Epo), an interplay between multiple distal and proximal (promoter) HREs has not been described so far. Hepatic Epo expression is regulated by a HRE located downstream of the EPO gene, but this 3' HRE is dispensable for renal EPO gene expression. We previously identified a 5' HRE and could show that both HREs direct exogenous reporter...

Data from: Genes mirror geography in Daphnia magna

Peter D. Fields, Céline Reisser, Marinela Dukić, Christoph R. Haag & Dieter Ebert
Identifying the presence and magnitude of population genetic structure remains a major consideration in evolutionary biology as doing so allows one to understand the demographic history of a species as well as make predictions of how the evolutionary process will proceed. Next-generation sequencing methods allow us to reconsider previous ideas and conclusions concerning the distribution of genetic variation, and what this distribution implies about a given species evolutionary history. A previous phylogeographic study of the...

Data from: Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae)

Christian Lexer, Rafael O. Wüest, Sofia Mangili, Myriam Heuertz, Kai N. Stolting, Peter B. Pearman, Felix Forest, Nicolas Salamin, Niklaus E. Zimmermann & Eligio Bossolini
Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species-rich radiations inhabiting the world’s biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analyzed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species-rich and ecologically important plant family of the Cape...

What’s in a band? The function of the colour and banding pattern of the Banded Swallowtail

Eunice Tan, Bodo Wilts, Brent Tan & Antonia Monteiro
Butterflies have evolved a diversity of colour patterns, but the ecological functions for most of these patterns are still poorly understood. The Banded Swallowtail butterfly, Papilio demolion demolion, is a mostly black butterfly with a greenish-blue band that traverses the wings. The function of this wing pattern remains unknown. Here, we examined the morphology of black and green-blue coloured scales, and how the colour and banding pattern affects predation risk in the wild. The protective...

Data from: Ecological and genetic factors influencing the transition between host-use strategies in sympatric Heliconius butterflies

Richard M. Merrill, Russell E. Naisbit, James Mallet & Chris D. Jiggins
Shifts in host-plant use by phytophagous insects have played a central role in their diversification. Evolving host-use strategies will reflect a trade-off between selection pressures. The ecological niche of herbivorous insects is partitioned along several dimensions, and if populations remain in contact, recombination will break down associations between relevant loci. As such, genetic architecture can profoundly affect the coordinated divergence of traits and subsequently the ability to exploit novel habitats. The closely related species Heliconius...

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