49 Works

Data from: Natural selection in a post-glacial range expansion: the case of the colour cline in the European barn owl

Sylvain Antoniazza, Ricardo Kanitz, Samuel Neuenschwander, Reto Burri, Arnaud Gaigher, Alexandre Roulin & Jérôme Goudet
Gradients of variation – or clines – have always intrigued biologists. Classically, they have been interpreted as the outcomes of antagonistic interactions between selection and gene flow. Alternatively, clines may also establish neutrally with isolation-by-distance or secondary contact between previously isolated populations. The relative importance of natural selection and these two neutral processes in the establishment of clinal variation can be tested by comparing genetic differentiation at neutral genetic markers and at the studied trait....

Data from: Phylogeography of Silver Pheasant (Lophura nycthemera L.) across China: aggregate effects of refugia, introgression and riverine barriers

Lu Dong, Gerald Heckel, Wei Liang & Yanyun Zhang
The role of Pleistocene glacial cycles in forming the contemporary genetic structure of organisms has been well studied in China with a particular focus on the Tibetan Plateau. However, China has a complex topography and diversity of local climates, and how glacial cycles may have shaped the subtropical and tropical biota of the region remains mostly unaddressed. To investigate the factors that affected the phylogeography and population history of a widely distributed and nondeciduous forest...

Data from: Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization

Joana I. Meier, Vitor C. Sousa, David Alexander Marques, Oliver M. Selz, Catherine E. Wagner, Laurent Excoffier & Ole Seehausen
Modes and mechanisms of speciation are best studied in young species pairs. In older taxa, it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genus Pundamilia encompass a complex of young species and polymorphic populations. One Pundamilia species pair, P. pundamilia and P. nyererei, is particularly well suited to study speciation because sympatric population pairs occur with different levels of phenotypic differentiation and reproductive...

Data from: Species divergence and maintenance of species cohesion of three closely related Primula species in the Qinghai-Tibet Plateau

Guangpeng Ren, Rubén G. Mateo, Antoine Guisan, Elena Conti & Nicolas Salamin
Aim: Understanding the relative roles of geography and ecology in driving speciation, population divergence and maintenance of species cohesion is of great interest to molecular ecology. Closely related species that are parapatrically distributed in mountainous areas provide an ideal model to evaluate these key issues, especially when genomic data are analyzed within a spatially and ecologically explicit context. Here we used three closely related species of Primula that occur in the Himalayas, the Hengduan Mountains...

Data from: A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms

Marylaure De La Harpe, Jaqueline Hess, Oriane Loiseau, Nicolas Salamin, Christian Lexer & Margot Paris
Understanding the genetics of biological diversification across micro- and macro-evolutionary time scales is a vibrant field of research for molecular ecologists as rapid advances in sequencing technologies promise to overcome former limitations. In palms, an emblematic, economically and ecologically important plant family with high diversity in the tropics, studies of diversification at the population and species levels are still hampered by a lack of genomic markers suitable for the genotyping of large numbers of recently...

Data from: Genomics of parallel ecological speciation in Lake Victoria cichlids

Joana Isabel Meier, David Alexander Marques, Catherine Elise Wagner, Laurent Excoffier & Ole Seehausen
The genetic basis of parallel evolution of similar species is of great interest in evolutionary biology. In the adaptive radiation of Lake Victoria cichlid fishes, sister species with either blue or red-back male nuptial coloration have evolved repeatedly, often associated with shallower and deeper water, respectively. One such case are blue and red-backed Pundamilia species, for which we recently showed that a young species pair may have evolved through “hybrid parallel speciation”. Coalescent simulations suggested...

Data from: Human cooperation based on punishment reputation

Miguel Dos Santos, Daniel J. Rankin & Claus Wedekind
The threat of punishment usually promotes cooperation. However, punishing itself is costly, rare in non-human animals, and humans who punish often finish with low payoffs in economic experiments. The evolution of punishment has therefore been unclear. Recent theoretical developments suggest that punishment has evolved in the context of reputation games. We tested this idea in a simple helping game with observers and with punishment and punishment reputation (experimentally controlling for other possible reputational effects). We...

Data from: Sex chromosome turnovers and genetic drift: a simulation study

Paul A Saunders, Samuel Neuenschwander & Nicolas Perrin
The recent advances of new genomic technologies has enabled to identify and characterize sex chromosomes in an increasing number of non-model species, revealing that many plants and animals undergo frequent sex chromosome turnovers. What evolutionary forces drive these turnovers remains poorly understood, but it was recently proposed that drift might play a more important role than generally assumed. We analyzed the dynamics of different types of turnovers using individual-based simulations, and show that when mediated...

Data from: Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps

Loic Pellissier, Hélène Niculita-Hirzel, Anne Dubuis, Marco Pagni, Nicolas Guex, Charlotte Ndiribe, Nicolas Salamin, Ioannis Xennarios, Jerome Goudet, Ian R. Sanders, Antoine Guisan & I. Xenarios
Studying patterns of species distributions along elevation gradients is frequently used to identify the primary factors that determine the distribution, diversity and assembly of species. However, despite their crucial role in ecosystem functioning, our understanding of the distribution of below-ground fungi is still limited, calling for more comprehensive studies of fungal biogeography along environmental gradients at various scales (from regional to global). Here, we investigated the richness of taxa of soil fungi and their phylogenetic...

Data from: Shifting fitness landscapes in response to altered environments

Ryan T. Hietpas, Claudia Bank, Jeffrey D. Jensen & Daniel N. A. Bolon
The role of adaptation in molecular evolution has been contentious for decades. Here, we shed light on the adaptive potential in Saccharomyces cerevisiae by presenting systematic fitness measurements for all possible point mutations in a region of Hsp90 under four environmental conditions. Under elevated salinity, we observe numerous beneficial mutations with growth advantages up to 7% relative to the wild type. All of these beneficial mutations were observed to be associated with high costs of...

Data from: Neutral and adaptive drivers of microgeographic genetic divergence within continuous populations: the case of the Neotropical tree Eperua falcata (Aubl.)

Louise Brousseau, Matthieu Foll, Caroline Scotti-Saintagne & Ivan Scotti
Background: In wild plant populations, genetic divergence within continuous stands is common, sometimes at very short geographical scales. While restrictions to gene flow combined with local inbreeding and genetic drift may cause neutral differentiation among subpopulations, microgeographical variations in environmental conditions can drive adaptive divergence through natural selection at some targeted loci. Such phenomena have recurrently been observed in plant populations occurring across sharp environmental boundaries, but the interplay between selective processes and neutral genetic...

Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes

Riddhiman Dhar, Tobias Bergmiller & Andreas Wagner
Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, sub-functionalization, and neo-functionalization. Little experimental data exists on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these...

Data from: The architecture of an empirical genotype-phenotype map

Jose Aguilar-Rodriguez, Leto Peel, Massimo Stella, Andreas Wagner & Joshua L. Payne
Recent advances in high-throughput technologies are bringing the study of empirical genotype-phenotype (GP) maps to the fore. Here, we use data from protein binding microarrays to study an empirical GP map of transcription factor (TF) binding preferences. In this map, each genotype is a DNA sequence. The phenotype of this DNA sequence is its ability to bind one or more TFs. We study this GP map using genotype networks, in which nodes represent genotypes with...

Data from: Identification of ZEB1 as a central component of the adipogenic gene regulatory network

Carine Gubelmann, Petra C. Schwalie, Sunil K. Raghav, Eva Röder, Delessa Tenagne, Elke Kiehlmann, Sebastian M. Waszak, Andrea Corsinotti, Gilles Udin, Wiebke Holcombe, Gottfried Rudowsky, Didier Trono, Christian Wolfrum & Bart Deplancke
Adipose tissue is a key determinant of whole body metabolism and energy homeostasis. Unraveling the regulatory mechanisms underlying adipogenesis is therefore highly relevant from a biomedical perspective. Our current understanding of fat cell differentiation is centered on the transcriptional cascades driven by the C/EBP protein family and the master regulator PPARγ. To elucidate further components of the adipogenic gene regulatory network, we performed a large-scale transcription factor (TF) screen overexpressing 734 TFs in mouse pre-adipocytes...

Data from: First draft genome of an iconic clownfish species (Amphiprion frenatus)

Anna Marcionetti, Victor Rossier, Joris A.M. Bertrand, Glenn Litsios, Nicolas Salamin & Joris A. M. Bertrand
Clownfishes (or anemonefishes) form an iconic group of coral reef fishes, principally known for their mutualistic interaction with sea anemones. They are characterized by particular life-history traits, such as a complex social structure and mating system involving sequential hermaphroditism, coupled with an exceptionally long lifespan. Additionally, clownfishes are considered to be one of the rare group to have experienced an adaptive radiation in the marine environment. Here, we assembled and annotated the first genome of...

Data from: De novo assembly and comparative analysis of the Ceratodon purpureus transcriptome

Péter Szövényi, Pierre-François Perroud, Aikaterini Symeonidi, Sean Stevenson, Ralph S. Quatrano, Stefan A. Rensing, Andrew C. Cuming & Stuart F. McDaniel
The bryophytes are a morphologically and ecologically diverse group of plants that have recently emerged as major model systems for a variety of biological processes. In particular, the genome sequence of the moss, Physcomitrella patens, has significantly enhanced our understanding of the evolution of developmental processes in land plants. However, to fully explore the diversity within bryophytes, we need additional genomic resources. Here we describe analyses of the transcriptomes of a male and a female...

Data from: The consequences of not accounting for background selection in demographic inference

Gregory B. Ewing & Jeffrey D. Jensen
Recently, there has been increased awareness of the role of background selection (BGS) in both data analysis and modelling advances. However, BGS is still difficult to take into account because of tractability issues with simulations and difficulty with nonequilibrium demographic models. Often, simple rescaling adjustments of effective population size are used. However, there has been neither a proper characterization of how BGS could bias or shift inference when not properly taken into account, nor a...

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: Genomic landscape of early ecological speciation initiated by selection on nuptial colour

David Alexander Marques, Kay Lucek, Marcel Philipp Haesler, Anna Fiona Feller, Joana Isabel Meier, Catherine Wagner, Laurent Excoffier, Ole Seehausen & Catherine E. Wagner
Ecological speciation is the evolution of reproductive isolation as a consequence of direct divergent natural selection or ecologically mediated divergent sexual selection. While the genomic signature of the former has been extensively studied in recent years, only few examples exist for genomic differentiation where environment-dependent sexual selection has played an important role. Here, we describe a very young (~90 years old) population of threespine sticklebacks exhibiting phenotypic and genomic differentiation between two habitats within the...

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: Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences

Fanny Pouyet, Simon Aeschbacher, Alexandre Thiéry & Laurent Excoffier
Disentangling the effect on genomic diversity of natural selection from that of demography is notoriously difficult, but necessary to properly reconstruct the history of species. Here, we use high-quality human genomic data to show that purifying selection at linked sites (i.e. background selection, BGS) and GC-biased gene conversion (gBGC) together affect as much as 95% of the variants of our genome. We find that the magnitude and relative importance of BGS and gBGC are largely...

Data from: Phylogeography and support vector machine classification of colour variation in panther chameleons

Djordje Grbic, Suzanne V. Saenko, Toky M. Randriamoria, Adrien Debry, Achille P. Raselimanana & Michel C. Milinkovitch
Lizards and snakes exhibit colour variation of adaptive value for thermoregulation, camouflage, predator avoidance, sexual selection and speciation. Furcifer pardalis, the panther chameleon, is one of the most spectacular reptilian endemic species in Madagascar, with pronounced sexual dimorphism and exceptionally large intraspecific variation in male coloration. We perform here an integrative analysis of molecular phylogeography and colour variation after collecting high-resolution colour photographs and blood samples from 324 F. pardalis individuals in locations spanning the...

Data from: Extensive variation at MHC DRB in the New Zealand sea lion (Phocarctos hookeri) provides evidence for balancing selection

Amy J. Osborne, Monika Zavodna, B. L. Chilvers, Bruce C. Robertson, Sandra S. Negro, Martin A. Kennedy & Neil J. Gemmell
Marine mammals are often reported to possess reduced variation of major histocompatibility complex (MHC) genes compared with their terrestrial counterparts. We evaluated diversity at two MHC class II B genes, DQB and DRB, in the New Zealand sea lion (Phocarctos hookeri, NZSL) a species that has suffered high mortality owing to bacterial epizootics, using Sanger sequencing and haplotype reconstruction, together with next-generation sequencing. Despite this species’ prolonged history of small population size and highly restricted...

Data from: High mutation rates limit evolutionary adaptation in Escherichia coli

Kathleen Sprouffske, José Aguilar-Rodríguez, Paul Sniegowski & Andreas Wagner
Mutation is fundamental to evolution, because it generates the genetic variation on which selection can act. In nature, genetic changes often increase the mutation rate in systems that range from viruses and bacteria to human tumors. Such an increase promotes the accumulation of frequent deleterious or neutral alleles, but it can also increase the chances that a population acquires rare beneficial alleles. Here, we study how up to 100-fold increases in Escherichia coli’s genomic mutation...

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...

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  • Swiss Institute of Bioinformatics
  • University of Lausanne
  • University of Bern
  • University of Zurich
  • Swiss Federal Institute of Aquatic Science and Technology
  • École Polytechnique Fédérale de Lausanne
  • University of Fribourg
  • Swiss Federal Institute for Forest, Snow and Landscape Research
  • Swiss Federal Institute of Technology in Zurich
  • University of the Basque Country