92 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: 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: 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: 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: 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: 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: 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...

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,...

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...

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: Tracking population genetic signatures of local extinction with herbarium specimens

Christoph Rosche, Annnett Baasch, Karen Runge, Philipp Brade, Sabrina Träger, Christian Parisod & Isabell Hensen
Background and Aims Habitat degradation and landscape fragmentation dramatically lower population sizes of rare plant species. Decreasing population sizes may, in turn, negatively affect genetic diversity and reproductive fitness which can ultimately lead to local extinction of populations. Although such extinction vortex dynamics have been postulated in theory and modelling for decades, empirical evidence from local extinctions of plant populations is scarce. In particular, comparisons between current vs. historical genetic diversity and differentiation are lacking...

Additional file 1 of Deeper genomic insights into tomato CLE genes repertoire identify new active peptides

Samy Carbonnel, Laurent Falquet & Ora Hazak
Additional file 1.

Swiss Glacier Mass Balance (release 2022)

Direct measurements of glacier mass balance - the sum of snow accumulation and snow/ice melt - are carried out on selected glaciers in Switzerland. Based on point observations, typically acquired in April/May and September, glacier-wide quantities of seasonal mass balance (winter/summer/annual) are evaluated, expressed as a an area-averaged value of water eqivalent. The dataset contains all available observations up to present and is delivered as four separate .csv files with results both for the exact...

Data from: Unexpected ancestry of Populus seedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species

Dorothea Lindtke, Zachariah Gompert, Christian Lexer & C. Alex Buerkle
In the context of potential interspecific gene flow, the integrity of species will be maintained by reproductive barriers that reduce genetic exchange, including traits associated with prezygotic isolation or poor performance of hybrids. Hybrid zones can be used to study the importance of different reproductive barriers, particularly when both parental species and hybrids occur in close spatial proximity. We investigated the importance of barriers to gene flow that act early versus late in the life...

Data from: Plant neighbours rather than soil biota determine impact of an alien plant invader

Yan Sun, Heinz Müller-Schärer & Urs Schaffner
1. Various factors have been shown contributing to the ecosystem impact of invasive alien plants, but their relative importance remains unclear. We focused on the effects of neighbouring plant community and soil biota as these biotic factors have been repeatedly put forward to explain invasion success (e.g. as components of the novel weapons and of the biotic release hypothesis). 2. To assess their relative importance in explaining the high impact of Centaurea stoebe during the...

Data from: Components of reproductive isolation between Orchis mascula and O. pauciflora

Giovanni Scopece, Antonio Croce, Christian Lexer & Salvatore Cozzolino
Studies of the strength and nature of reproductive isolation (RI) between species can greatly contribute to our understanding of speciation. Although the role of RI in speciation is well recognized, there is a dearth of information on the contributions of different barriers between related plant species. Here, we estimated multiple components of RI between two Mediterranean orchid sister species (Orchis mascula and Orchis pauciflora), disentangling the strength and absolute contributions of seven different isolating mechanisms....

Data from: Patterns of genetic diversity and differentiation in resistance gene clusters of two hybridizing European Populus species

Celine Caseys, Kai N. Stölting, Thelma Barbara, Santiago C. Gonzalez-Martinez & Christian Lexer
Resistance genes (R-genes) are essential for long-lived organisms such as forest trees, which are exposed to diverse herbivores and pathogens. In short-lived model species, R-genes have been shown to be involved in species isolation. Here, we studied more than 400 trees from two natural hybrid zones of the European Populus species Populus alba and Populus tremula for microsatellite markers located in three R-gene clusters, including one cluster situated in the incipient sex chromosome region. The...

Data from: Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood)

Adriana Suarez-Gonzalez, Charles Hefer, Camille Christie, Oliver Corea, Christian Lexer, Quentin C. B. Cronk, Carl J. Douglas, Charles A. Hefer & Camille Christe
Natural hybrid zones in forest trees provide systems to study the transfer of adaptive genetic variation by introgression. Previous landscape genomic studies in Populus trichocarpa, a keystone tree species, indicated genomic footprints of admixture with its sister species P. balsamifera and identified candidate genes for local adaptation. Here, we explored patterns of introgression and signals of local adaptation in P. trichocarpa and P. balsamifera, employing genome resequencing data from three chromosomes in pure species and...

Data from: Genetic load, inbreeding depression and hybrid vigor covary with population size: an empirical evaluation of theoretical predictions

Jennifer N. Lohr & Christoph R. Haag
Reduced population size is thought to have strong consequences for evolutionary processes as it enhances the strength of genetic drift. In its interaction with selection, this is predicted to increase the genetic load, reduce inbreeding depression, and increase hybrid vigour, and in turn affect phenotypic evolution. Several of these predictions have been tested, but comprehensive studies controlling for confounding factors are scarce. Here we show that populations of Daphnia magna, which vary strongly in genetic...

Data from: The adaptive significance of chromosomal inversion polymorphisms in Drosophila melanogaster

Martin Kapun & Thomas Flatt
Chromosomal inversions, structural mutations that reverse a segment of a chromosome, cause suppression of recombination in the heterozygous state. Several studies have shown that inversion polymorphisms can form clines or fluctuate predictably in frequency over seasonal time spans. These observations prompted the hypothesis that chromosomal rearrangements might be subject to spatially and/or temporally varying selection. Here we review what has been learned about the adaptive significance of inversion polymorphisms in the vinegar fly Drosophila melanogaster,...

Data from: Increased temperature disrupts the biodiversity-ecosystem functioning relationship

Elodie C. Parain, Rudolf P. Rohr, Sarah M. Gray & Louis-Félix Bersier
Gaining knowledge of how ecosystems provide essential services to humans is of primary importance, especially with the current threat of climate change. Yet, little is known about how increased temperature will impact the biodiversity-ecosystem functioning (BEF) relationship. We tackled this subject theoretically and experimentally. We developed a BEF theory based on mechanistic population dynamic models, which allows the inclusion of the effect of temperature. Using experimentally established relationships between attack rate and temperature, the model...

Data from: Comparative analysis of the shape and size of the middle ear cavity of turtles reveals no correlation with habitat ecology

Christian Foth, Serjoscha W. Evers, Walter G. Joyce, Virginie S. Volpato & Roger B. J. Benson
The middle ear of turtles differs from other reptiles in being separated into two distinct compartments. Several ideas have been proposed as to why the middle ear is compartmentalized in turtles, most suggesting a relationship with underwater hearing. Extant turtle species span fully marine to strictly terrestrial habitats, and ecomorphological hypotheses of turtle hearing predict that this should correlate with variation in the structure of the middle ear due to differences in the fluid properties...

Data from: Structural complexity and large-sized trees explain shifting species richness and carbon relationship across vegetation types

Sylvanus Mensah, Valere Salako & Thomas Seifert
1. It is prominently claimed that enhancing forest diversity would play a dual role of nature conservation and climate regulation. While the idea is intuitively appealing, studies show that species richness effects on aboveground carbon (AGC) are not always positive, but instead unpredictable especially across scales and complex terrestrial systems having large-diameter and tall-stature trees. Previous studies have further considered structural complexity and larger trees as determinants of AGC. Yet it remains unclear what drives...

Ancient mitogenomics clarifies radiation of extinct Mascarene giant tortoises (Cylindraspis spp.)

Christian Kehlmaier, Eva Graciá, Patrick D. Campbell, Margaretha D. Hofmeyr, Silke Schweiger, Albert Martínez-Silvestre, Walter Joyce & Uwe Fritz
The five extinct giant tortoises of the genus Cylindraspis belong to the most iconic species of the enigmatic fauna of the Mascarene Islands that went largely extinct after the discovery of the islands. To resolve the phylogeny and biogeography of Cylindraspis, we analysed a data set of 45 mitogenomes that includes all lineages of extant tortoises and eight near-complete sequences of all Mascarene species extracted from historic and subfossil material. Cylindraspis is an ancient lineage...

Data from: Cyclin dependent kinase 5 (CDK5) regulates the circadian clock

Andrea Brenna, Iwona Olejniczak, Rohit Chavan, Jürgen Ripperger, Sonja Langmesser, Elisabetta Cameroni, Zehan Hu, Claudio De Virgilio, Jörn Dengjel & Urs Albrecht
Circadian oscillations emerge from transcriptional and post-translational feedback loops. An important step in generating rhythmicity is the translocation of clock components into the nucleus, which is regulated in many cases by kinases. In mammals, the kinase promoting the nuclear import of the key clock component Period 2 (PER2) is unknown. We observed that the cyclin-dependent kinase 5 (CDK5) regulates the mammalian clock involving phosphorylation of PER2. Knock-down of Cdk5 in the suprachiasmatic nuclei (SCN), the...

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