332 Works

Data from: How to evaluate community predictions without thresholding?

Daniel Scherrer, Heidi Mod & Antoine Guisan
Stacked species distribution models (S-SDM) provide a tool to make spatial predictions about communities by first modelling individual species and then stacking the modelled predictions to form assemblages. The evaluation of the predictive performance is usually based on a comparison of the observed and predicted community properties (e.g., species richness, composition). However, the most available and widely used evaluation metrics require the thresholding of single species’ predicted probabilities of occurrence to obtain binary outcomes (i.e.,...

Deer density drives habitat use of establishing wolves in the Western European Alps

Stefanie Roder, François Biollaz, Stéphane Mettaz, Fridolin Zimmermann, Ralph Manz, Marc Kery, Sergio Vignali, Luca Fumagalli, Raphaël Arlettaz & Veronika Braunisch
1. The return of top carnivores to their historical range triggers conflicts with the interests of different stakeholder groups. Anticipating such conflicts is key to appropriate conservation management, which calls for reliable spatial predictions of future carnivore occurrence. Previous models have assessed general habitat suitability for wolves, but the factors driving the settlement of dispersing individuals remain ill-understood. In particular, little attention has been paid to the role of prey availability in the recolonization process....

Rapid climate change results in long-lasting spatial homogenization of phylogenetic diversity

Bianca Saladin, Loïc Pellissier, Catherine H. Graham, Michael P. Nobis, Nicolas Salamin & Niklaus E. Zimmermann
Scientific understanding of biodiversity dynamics, resulting from past climate oscillations and projections of future changes in biodiversity, has advanced over the past decade. Little is known about how these responses, past or future, are spatially connected. Analyzing the spatial variability in biodiversity provides insight into how climate change affects the accumulation of diversity across space. Here, we evaluate the spatial variation of phylogenetic diversity of European seed plants among neighboring sites and assess the effects...

SNP datasets obtained with ddRADseq from four contact zones between Podarcis carbonelli and four other Podarcis species

Guilherme Caeiro-Dias, Alan Brelsford, Antigoni Kaliontzopoulou, Mariana Meneses-Ribeiro, Pierre-André Chrochet & Catarina Pinho
We used double digestion restriction site associated DNA (ddRAD) sequencing to discover SNPs in samples from four contact zones between Podarcis carbonelli and four other Podarcis species. We obtained a panel of SNPs for each for each contact zone and reference populations and a dataset of diagnostic SNPs between reference populations for each contact zone but excluding private alleles from references, i.e. excluding alleles that are not present in the populations of contact. The final...

Plasticity in leakiness

John Pannell
In dioecious plants, males and females frequently show ‘leaky’ sex expression, with individuals occasionally producing flowers of the opposite sex. This leaky sex expression may have enabled the colonization of oceanic islands by dioecious plant species, and it is likely to represent the sort of variation upon which selection acts to bring about evolutionary transitions from dioecy to hermaphroditism. Although leakiness is commonly reported for dioecious species, it is not known whether it has plastic...

Data from: Four myriapod relatives – but who are sisters? No end to debates on relationships among the four major myriapod subgroups

Nikolaus U. Szucsich, Daniela Bartel, Alexander Blanke, Alexander Böhm, Alexander Donath, Makiko Fukui, Simon Grove, Shanlin Liu, Oliver Macek, Ryuichiro Machida, Bernhard Misof, Yasutaka Nakagaki, Lars Podsiadlowski, Kaoru Sekiya, Shigekazu Tomizuka, Björn M. Von Reumont, Robert M. Waterhouse, Manfred Walzl, Guanliang Meng, Xin Zhou, Günther Pass & Karen Meusemann
Background: Phylogenetic relationships among the myriapod subgroups Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly resolved. The first phylogenomic study covering all subgroups resolved phylogenetic relationships congruently to morphological evidence but is in conflict with most previously published phylogenetic trees based on diverse molecular data. Outgroup choice and long-branch attraction effects were stated as possible explanations for these incongruencies. In this study, we addressed these issues by extending the myriapod and outgroup taxon sampling...

Data from: Predicting species occurrences with habitat network models

Damian Omar Ortiz-Rodríguez, Antoine Guisan, Rolf Holderegger & Maarten Van Strien
1. Biodiversity conservation requires modelling tools capable of predicting the presence or absence (i.e. occurrence-state) of species in habitat patches. Local habitat characteristics of a patch (lh), the cost of traversing the landscape matrix between patches (weighted connectivity; (wc), and the position of the patch in the habitat network topology (nt) all influence occurrence-state. Existing models are data demanding or consider only local habitat characteristics. We address these shortcomings and present a network-based modelling approach,...

Low adaptive potential for tolerance to ethynylestradiol, but also low toxicity, in a grayling population (Thymallus thymallus)

Lucas Marques Da Cunha, Diane Maitre & Claus Wedekind
Background: The presence of a novel pollutant can induce rapid evolution if there is additive genetic variance for the tolerance to the stressor. Continuous selection over some generations can then reduce the toxicity of the pollutant but also deplete the additive genetic variance for the tolerance and thereby slow down adaptation. One common pollutant that has been ecologically relevant for some time is 17alpha-ethynyestradiol (EE2), a synthetic compound of oral contraceptives since their market launch...

Data from: Additive genetic variation for tolerance to estrogen pollution in natural populations of Alpine whitefish (Coregonus sp., Salmonidae)

Gregory Brazzola, Nathalie Chèvre & Claus Wedekind
The evolutionary potential of natural populations to adapt to anthropogenic threats critically depends on whether there exists additive genetic variation for tolerance to the threat. A major problem for water-dwelling organisms is chemical pollution, and among the most common pollutants is 17α-ethinylestradiol (EE2), the synthetic estrogen that is used in oral contraceptives and that can affect fish at various developmental stages, including embryogenesis. We tested whether there is variation in the tolerance to EE2 within...

Data from: The REporting of studies Conducted using Observational Routinely-collected health Data (RECORD) statement: methods for arriving at consensus and developing reporting guidelines

Stuart G. Nicholls, Pauline Quach, Erik Von Elm, Astrid Guttmann, David Moher, Irene Petersen, Henrik T. Sørensen, Liam Smeeth, Sinéad M. Langan & Eric I. Benchimol
Objective: Routinely collected health data, collected for administrative and clinical purposes, without specific a priori research questions, are increasingly used for observational, comparative effectiveness, health services research, and clinical trials. The rapid evolution and availability of routinely collected data for research has brought to light specific issues not addressed by existing reporting guidelines. The aim of the present project was to determine the priorities of stakeholders in order to guide the development of the REporting...

Data from: Timeframe of speciation inferred from secondary contact zones in the European tree frog radiation (Hyla arborea group)

Christophe Dufresnes, Alan Brelsford, Jelka Crnobrnja-Isailović, Nikolay Tzankov, Petros Lymberakis & Nicolas Perrin
Background: Hybridization between incipient species is expected to become progressively limited as their genetic divergence increases and reproductive isolation proceeds. Amphibian radiations and their secondary contact zones are useful models to infer the timeframes of speciation, but empirical data from natural systems remains extremely scarce. Here we follow this approach in the European radiation of tree frogs (Hyla arborea group). We investigated a natural hybrid zone between two lineages (Hyla arborea and Hyla orientalis) of...

Data from: Systematic site selection for multispecies monitoring networks

Silvia B. Carvalho, João Gonçalves, Antoine Guisan & João Honrado
The importance of monitoring biodiversity to detect and understand changes throughout time and to inform management is increasingly recognized. Monitoring schemes should be globally unified, spatially integrated across scales, long term, and cost-efficient. We propose a framework to design optimized multispecies-targeted monitoring networks over large areas. The method builds upon previous developments on systematic conservation planning in terms of optimizing resource allocation in space, and comprises seven steps: (a) determine which questions will be addressed,...

Data from: Seasonality in communication and collective decision-making in ants

Nathalie Stroeymeyt, Caroline Jordan, Gregory Mayer, Sarah Hovsepian, Martin Giurfa & Nigel R. Franks
The ability of animals to adjust their behaviour according to seasonal changes in their ecology is crucial for their fitness. Eusocial insects display strong collective behavioural seasonality, yet the mechanisms underlying such changes are poorly understood. We show that nest preference by emigrating Temnothorax albipennis ant colonies is influenced by a season-specific modulatory pheromone that may help tune decision-making according to seasonal constraints. The modulatory pheromone triggers aversion towards low-quality nests and enhances colony cohesion...

Data from: Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth

Martial Sankar, Kaisa Nieminen, Laura Ragni, Ioannis Xenarios & Christian S. Hardtke
Among various advantages, their small size makes model organisms preferred subjects of investigation. Yet, even in model systems detailed analysis of numerous developmental processes at cellular level is severely hampered by their scale. For instance, secondary growth of Arabidopsis hypocotyls creates a radial pattern of highly specialized tissues that comprises several thousand cells starting from a few dozen. This dynamic process is difficult to follow because of its scale and because it can only be...

Data from: Male cognitive performance declines in the absence of sexual selection

Brian Hollis & Tadeusz J. Kawecki
Sexual selection is responsible for the evolution of male ornaments and armaments, but its role in the evolution of cognition—the ability to process, retain and use information—is largely unexplored. Because successful courtship is likely to involve processing information in complex, competitive sexual environments, we hypothesized that sexual selection contributes to the evolution and maintenance of cognitive abilities in males. To test this, we removed mate choice and mate competition from experimental populations of Drosophila melanogaster...

Data from: Diversifying selection and color-biased dispersal in the asp viper

Sylvain Dubey, Valérie Zwahlen, Konrad Mebert, Jean-Claude Monney, Philippe Golay, Thomas Ott, Thierry Durand, Gilles Thiery, Laura Kaiser, Silvia N. Geser & Sylvain Ursenbacher
Background: The presence of intraspecific color polymorphism can have multiple impacts on the ecology of a species; as a consequence, particular color morphs may be strongly selected for in a given habitat type. For example, the asp viper (Vipera aspis) shows a high level of color polymorphism. A blotched morph (cryptic) is common throughout its range (central and western Europe), while a melanistic morph is frequently found in montane populations, presumably for thermoregulatory reasons. Besides,...

Data from: High-density sex-specific linkage maps of a European tree frog (Hyla arborea) identify the sex chromosome without information on offspring sex

Alan Brelsford, Christophe Dufresnes & Nicolas Perrin
Identifying homology between sex chromosomes of different species is essential to understanding the evolution of sex determination. Here, we show that the identity of a homomorphic sex chromosome pair can be established using a linkage map, without information on offspring sex. By comparing sex-specific maps of the European tree frog Hyla arborea, we find that the sex chromosome (linkage group 1) shows a threefold difference in marker number between the male and female maps. In...

Data from: Evolution of reduced postcopulatory molecular interactions in Drosophila populations lacking sperm competition

Brian Hollis, David Houle & Tadeusz J. Kawecki
In many species with internal fertilization, molecules transferred in the male ejaculate trigger and interact with physiological changes in females. It is controversial to what extent these interactions between the sexes act synergistically to mediate the female switch to a reproductive state or instead reflect sexual antagonism evolved as a byproduct of sexual selection on males. To address this question, we eliminated sexual selection by enforcing monogamy in populations of Drosophila melanogaster for 65 generations...

Data from: Maternal and paternal contributions to pathogen resistance dependent on development stage in a whitefish (Salmonidae)

Emily S. Clark, Manuel Pompini, Lucas Marques Da Cunha & Claus Wedekind
1. It is often assumed that maternal and paternal contributions to offspring phenotype change over the lifetime of an individual. However, studies on parental effects typically suffer from the problems that heritabilities and maternal environmental effects are difficult to separate, and that both may depend on environmental factors and developmental stage 2. In order to experimentally disentangle maternal from paternal contributions and the likely effects of developmental stage from ecological effects, we sampled a natural...

Data from: Genomic evidence for role of inversion 3RP of Drosophila melanogaster in facilitating climate change adaptation

Rahul V. Rane, Lea Rako, Siu Fai Lee, Ary A. Hoffmann & Martin Kapun
Chromosomal inversion polymorphisms are common in animals and plants, and recent models suggest that alternative arrangements spread by capturing different combinations of alleles acting additively or epistatically to favour local adaptation. It is also thought that inversions typically maintain favoured combinations for a long time by suppressing recombination between alternative chromosomal arrangements. Here, we consider patterns of linkage disequilibrium and genetic divergence in an old inversion polymorphism in Drosophila melanogaster (In(3R)Payne) known to be associated...

Data from: Resprouter fraction in Cape Restionaceae assemblages varies with climate and soil type

Rafael O. Wüest, Glenn Litsios, Félix Forest, Christian Lexer, H. Peter Linder, Nicolas Salamin, Niklaus E. Zimmermann & Peter B. Pearman
While fire-induced changes in biodiversity are well documented, less is known about how fire impacts life-history variation and diversity of functional traits that represent distinct strategies for persistence in fire-driven ecosystems. One example is the dichotomy in which ‘resprouter’ species usually survive fires to produce new growth, while ‘reseeder’ species perish and re-establish from seed. Variable relative numbers of reseeder and resprouter species in local assemblages of Restionaceae (Poales) of the Cape Floristic Region (CFR),...

Data from: Small-scale and regional spatial dynamics of an annual plant with contrasting sexual systems

Marcel E. Dorken, Robert P. Freckleton & John R. Pannell
1.Plant demography is known to depend on both spatial dynamics and life history, but how these two factors interact is poorly understood. We conducted a longitudinal study of the wind-pollinated annual plant Mercurialis annua that varies geographically in its sexual system to investigate this interaction. 2.Metapopulation demographic models predict that regular population turnover should be a more common feature of monomorphic than dimorphic populations because males and females cannot found new populations by selfing but...

Data from: Identifying homomorphic sex chromosomes from wild-caught adults with limited genomic resources

Alan Brelsford, Guillaume Lavanchy, Roberto Sermier, Anna Rausch & Nicolas Perrin
We demonstrate a genotyping-by-sequencing approach to identify homomorphic sex chromosomes and their homolog in a distantly related reference genome, based on noninvasive sampling of wild-caught individuals, in the moor frog Rana arvalis. Double-digest RADseq libraries were generated using buccal swabs from 30 males and 21 females from the same population. Search for sex-limited markers from the unfiltered data set (411 446 RAD tags) was more successful than searches from a filtered data set (33 073...

Data from: Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae)

Martha Liliana Serrano-Serrano, Anna Marcionetti, Mathieu Perret & Nicolas Salamin
Premise of the study: Despite the extensive phenotypic variation that characterizes the Gesneriaceae family, there is a lack of genomic resources to investigate the molecular basis of their diversity. We developed and compared the transcriptomes for two species of the Neotropical lineage of the Gesneriaceae. Methods and Results: Illumina sequencing and de novo assembly of floral and leaf samples were used to generate multigene sequence data for Sinningia eumorpha and S. magnifica, two species endemic...

Data from: Polydomy enhances foraging performance in ant colonies

Nathalie Stroeymeyt, Patrick Joye & Laurent Keller
Collective foraging confers benefits in terms of reduced predation risk and access to social information, but it heightens local competition when resources are limited. In social insects, resource limitation has been suggested as a possible cause for the typical decrease in per capita productivity observed with increasing colony size, a phenomenon known as Michener's paradox. Polydomy (distribution of a colony's brood and workers across multiple nests) is believed to help circumvent this paradox through its...

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  • University of Lausanne
  • Swiss Institute of Bioinformatics
  • French National Centre for Scientific Research
  • University of Neuchâtel
  • University of Bern
  • Swiss Federal Institute for Forest, Snow and Landscape Research
  • University of Zurich
  • University of Fribourg
  • Uppsala University
  • Swiss Centre of Expertise in the Social Sciences