351 Works

Data from: Homologous sex chromosomes in three deeply divergent anuran species

Alan Brelsford, Matthias Stöck, Caroline Betto-Colliard, Sylvain Dubey, Christophe Dufresnes, Hélène Jourdan-Pineau, Nicolas Rodrigues, Romain Savary, Roberto Sermier & Nicolas Perrin
Comparative genomic studies are revealing that, in sharp contrast with the strong stability found in birds and mammals, sex determination mechanisms are surprisingly labile in cold-blooded vertebrates, with frequent transitions between different pairs of sex chromosomes. It was recently suggested that, in context of this high turnover, some chromosome pairs might be more likely than others to be co-opted as sex chromosomes. Empirical support, however, is still very limited. Here we show that sex-linked markers...

Data from: Genetic diversity in frogs linked to past and future climate change on the roof of the world

Junhua Hu, Yan Huang, Jianping Jiang & Antoine Guisan
Mountains, representing storehouses of biodiversity, endemism, and threatened species, are biodiversity hotspots of great conservation importance. However, increasing evidence indicates that mountain species throughout the world are responding to climate change, past or contemporary, by shifting their geographic distributions and patterns of genetic diversity, potentially affecting their adaptive capacity and increasing risk of extinction. Using the iconic high‐elevation frog Nanorana parkeri as indicator, we showed how spatial analyses of climatic stability combined with genetic data...

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: Performance of individual vs group sampling for inferring dispersal under isolation by distance

Natacha Luximon, Eric J. Petit & Thomas Broquet
Models of isolation-by-distance formalize the effects of genetic drift and gene flow in a spatial context where gene dispersal is spatially limited. These models have been used to show that, at an appropriate spatial scale, dispersal parameters can be inferred from the regression of genetic differentiation against geographic distance between sampling locations. This approach is compelling because it is relatively simple and robust, and has rather low sampling requirements. In continuous populations, dispersal can be...

Data from: Environment and evolutionary history shape phylogenetic turnover in European tetrapods

Bianca Saladin, Wilfried Thuiller, Catherine H. Graham, Sébastien Lavergne, Luigi Maiorano, Nicolas Salamin & Niklaus E. Zimmermann
Phylogenetic turnover quantifies the evolutionary distance among species assemblages and is central to understanding the main drivers shaping biodiversity. It is affected both by geographic and environmental distance between sites. Therefore, analyzing phylogenetic turnover in environmental space requires removing the effect of geographic distance. Here, we apply a novel approach by deciphering phylogenetic turnover of European tetrapods in environmental space after removing geographic land distance effects. We demonstrate that phylogenetic turnover is strongly structured in...

Data from: Systematics of snow voles (Chionomys, Arvicolinae) revisited

Glenn Yannic, Reto Burri, Vladimir G. Malikov & Peter Vogel
To elucidate the evolutionary history of snow voles, genus Chionomys, we studied the phylogeography of Chionomys nivalis across its range and investigated its relationships with two congeneric species, C. gud and C. roberti, using independent molecular markers. Analyses were based on mitochondrial (~940 bp cyt b) and Y-chromosomal (~2020 bp from three introns) genetic variation. Our data provide conclusive evidence for a Caucasian and Middle Eastern origin for the three species and a subsequent westward...

Data from: Genetic compatibility affects division of labor in the Argentine ant Linepithema humile

Romain Libbrecht & Laurent Keller
Division of labor is central to the organization of insect societies. Within-colony comparisons between subfamilies of workers (patrilines or matrilines) revealed genetic effects on division of labor in many social insect species. Although this has been taken as evidence for additive genetic effects on division of labor, it has never been experimentally tested. To determine the relative roles of additive and non-additive genetic effects (e.g., genetic compatibility, epistasis and parent-of-origin imprinting effects) on worker behavior,...

Data from: Testing the role of the Red Queen and Court Jester as drivers of the macroevolution of Apollo butterflies

Fabien L. Condamine, Jonathan Rolland, Sebastian Höhna, Felix A. H. Sperling & Isabel Sanmartín
In macroevolution, the Red Queen (RQ) model posits that biodiversity dynamics depend mainly on species-intrinsic biotic factors such as interactions among species or life-history traits, while the Court Jester (CJ) model states that extrinsic environmental abiotic factors have a stronger role. Until recently, a lack of relevant methodological approaches has prevented the unraveling of contributions from these two types of factors to the evolutionary history of a lineage. Here we take advantage of the rapid...

Data from: How to best threshold and validate stacked species assemblages? Community optimisation might hold the answer

Daniel Scherrer, Manuela D'Amen, Rui F. Fernandes, Rubén G. Mateo & Antoine Guisan
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN TWO OTHER PUBLICATIONS. PLEASE SEE DOI: 10.1111/ddi.12548 AND https://doi.org/10.1111/geb.12357 --- The popularity of species distribution models (SDMs) and the associated stacked species distribution models (S‐SDMs), as tools for community ecologists, largely increased in recent years. However, while some consensus was reached about the best methods to threshold and evaluate individual SDMs, little agreement exists on how to best assemble individual SDMs into communities, that is, how...

Data from: Corticosterone regulates multiple colour traits in Lacerta [Zootoca] vivipara males

Luis M. San-Jose & Patrick S. Fitze
Ornamental colours usually evolve as honest signals of quality, which is supported by the fact that they frequently depend on individual condition. It has generally been suggested that some, but not all types of ornamental colours are condition dependent, indicating that different evolutionary mechanisms underlie the evolution of multiple types of ornamental colours even when these are exhibited by the same species. Stress hormones, which negatively affect condition, have been shown to affect colour traits...

Data from: The balanced-lethal system of crested newts: a ghost of sex chromosomes past?

Christine Grossen, Samuel Neuenschwander & Nicolas Perrin
Balanced lethal systems are more than biological curiosities: As theory predicts, they should quickly be eliminated through the joint forces of recombination and selection. That such systems might become fixed in natural populations poses a challenge to evolutionary theory. Here we address the case of a balanced lethal system fixed in crested newts and related species, which makes 50% of offspring die early in development. All adults are heteromorphic for chromosome pair 1. The two...

Data from: Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference

Aaron B. A. Shafer, Claire R. Peart, Sergio Tusso, Inbar Maayan, Alan Brelsford, Christopher W. Wheat & Jochen B. W. Wolf
Restriction site-associated DNA sequencing (RAD-seq) provides high-resolution population genomic data at low cost, and has become an important component in ecological and evolutionary studies. As with all high-throughput technologies, analytic strategies require critical validation to ensure accurate and unbiased interpretation. To test for the impact of bioinformatic data processing on downstream population genetic inferences, we analysed mammalian RAD-seq data (>100 individuals) with 312 combinations of methodology (de novo vs. mapping to references of increasing divergence)...

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: Neutral and selection-driven decay of sexual traits in asexual stick insects

Tanja Schwander, Bernard J. Crespi, Regine Gries & Gerhard Gries
Environmental shifts and lifestyle changes may result in formerly adaptive traits becoming non-functional or maladaptive. The subsequent decay of such traits highlights the importance of natural selection for adaptations, yet its causes have rarely been investigated. To study the fate of formerly adaptive traits after lifestyle changes, we evaluated sexual traits in five independently derived asexual lineages, including traits that are specific to males and therefore not exposed to selection. At least four of the...

Data from: Origin and genome evolution of polyploid green toads in Central Asia: evidence from microsatellite markers

Caroline Betto-Colliard, Roberto Sermier, Spartak Litvinchuk, Nicolas Perrin & Matthias Stöck
Polyploidization, which is expected to trigger major genomic reorganizations, occurs much less commonly in animals than in plants, possibly because of constraints imposed by sex-determination systems. We investigated the origins and consequences of allopolyploidization in Palearctic green toads (Bufo viridis subgroup) from Central Asia, with three ploidy levels and different modes of genome transmission (sexual versus clonal), to (i) establish a topology for the reticulate phylogeny in a species-rich radiation involving several closely related lineages...

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: Hummingbird pollination and the diversification of angiosperms: an old and successful association in Gesneriaceae

Martha Liliana Serrano-Serrano, Jonathan Rolland, John Clark, Nicolas Salamin & Mathieu Perret
The effects of specific functional groups of pollinators in the diversification of angiosperms are still to be elucidated. We investigated whether the pollination shifts or the specific association with hummingbirds affected the diversification of a highly diverse angiosperm lineage in the Neotropics. We reconstructed a phylogeny of 583 species from the Gesneriaceae family and detected diversification shifts through time, inferred the timing and amount of transitions among pollinator functional groups, and tested the association between...

Data from: Climatic niche evolution is faster in sympatric than allopatric lineages of the butterfly genus Pyrgus

Camille Pitteloud, Nils Arrigo, Tomasz Suchan, Alicia Mastretta-Yanes, Roger Vila, Vlad Dinca, Juan Hernández-Roldán, Ernst Brockmann, Yannick Chittaro, Irena Kleckova, Luca Fumagalli, Sven Buerki, Loïc Pellissier & Nadir Alvarez
Understanding how speciation relates to ecological divergence has long fascinated biologists. It is assumed that ecological divergence is essential to sympatric speciation, as a mechanism to avoid competition and eventually lead to reproductive isolation, while divergence in allopatry is not necessarily associated with niche differentiation. The impact of the spatial context of divergence on the evolutionary rates of abiotic dimensions of the ecological niche has rarely been explored for an entire clade. Here, we compare...

Data from: Reflections of the social environment in chimpanzee memory: applying rational analysis beyond humans

Jeffrey R. Stevens, Julian N. Marewski, Lael J. Schooler & Ian C. Gilby
In cognitive science, the rational analysis framework allows modelling of how physical and social environments impose information-processing demands onto cognitive systems. In humans, for example, past social contact among individuals predicts their future contact with linear and power functions. These features of the human environment constrain the optimal way to remember information and probably shape how memory records are retained and retrieved. We offer a primer on how biologists can apply rational analysis to study...

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...

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...

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....

Scale-dependence of ecological assembly rules: insights from empirical datasets and joint species distribution modelling

Heidi Mod, Mathieu Chevalier, Miska Luoto & Antoine Guisan
1. A comprehensive understanding of the scale-dependency of environmental filtering and biotic interactions influencing the local assembly of species is paramount to derive realistic forecasts of the future of biodiversity and efficiently manage ecological communities. A classical assumption is that environmental filters are more prevalent at larger scales with diminishing effects towards the finest scales where biotic interactions become more decisive. Recently, a refinement was proposed stipulating that the scale-dependency of biotic interactions should relate...

Cephalic biomechanics underpins the evolutionary success of trilobites

Jorge Esteve, Jordi Marcé-Nogué, Francesc Pérez-Peris & Emily Rayfield
Arthropods (i.e. insects, spiders, crustaceans, myriapods and others), are the most successful Phanerozoic animals. The group are characterised by the possession of a segmented body, jointed limbs and a hard cuticle that is episodically moulted. One highly successful, but now extinct, group of arthropods are the trilobites. Trilobites underwent episodic moulting (ecdysis), and most trilobites possess facial sutures, lines of weakness in the cephalon, via which the exuviae is shed and the animal emerges. However,...

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...

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Resource Types

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