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: 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: 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: 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...

Subpopulations of sensorless bacteria drive fitness in fluctuating environments

Thomas Julou
We use quantitative time-lapse microscopy combined with microfluidics to analyse the induction dynamics of the lac operon in single bacteria cells.

Data from: Structure and dynamics of hybrid zones at multiple stages of speciation in the common vole (Microtus arvalis)

Mathias Beysard & Gerald Heckel
The genetic structure and dynamics of hybrid zones provides crucial information for the understanding of the processes and mechanisms of evolutionary divergence and speciation. In general, higher levels of evolutionary divergence between taxa are more likely to be associated with reproductive isolation and may result in suppressed or strongly restricted hybridization. In this study, we examined the structure and processes in two secondary contact zones between three deep evolutionary lineages in the common vole (Microtus...

Data from: Manipulating virulence factor availability can have complex consequences for infections

Michael Weigert, Adin Ross-Gillespie, Anne Leinweber, Gabriella Pessi, Sam P. Brown & Rolf Kuemmerli
Given the rise of bacterial resistance against antibiotics, we urgently need alternative strategies to fight infections. Some propose we should disarm rather than kill bacteria, through targeted disruption of their virulence factors. It is assumed that this approach (i) induces weak selection for resistance because it should only minimally impact bacterial fitness, and (ii) is specific, only interfering with the virulence factor in question. Given that pathogenicity emerges from complex interactions between pathogens, hosts, and...

Data from: Early arrival and climatically-linked geographic expansion of New World monkeys from tiny African ancestors

Daniele Silvestro, Marcelo F. Tejedor, Martha L. Serrano-Serrano, Oriane Loiseau, Victor Rossier, Jonathan Rolland, Alexander Zizka, Sebastian Höhna, Alexandre Antonelli & Nicolas Salamin
New World monkeys (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Here we integrate paleontological and molecular evidence to assess the evolutionary...

Data from: On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity

Nicholas Renzette, Timothy F. Kowalik & Jeffrey D. Jensen
A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, though these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV),...

Data from: Adaptive evolution during an ongoing range expansion: the invasive bank vole (Myodes glareolus) in Ireland.

Thomas A. White, Sarah E. Perkins, Gerald Heckel & Jeremy B. Searle
Range expansions are extremely common, but have only recently begun to attract attention in terms of their genetic consequences. As populations expand, demes at the wave front experience strong genetic drift, which is expected to reduce genetic diversity and potentially cause 'allele surfing', where alleles may become fixed over a wide geographic area even if their effects are deleterious. Previous simulation models show that range expansions can generate very strong selective gradients on dispersal, reproduction,...

Data from: The role of climatic tolerances and seed traits in reduced extinction rates of temperate Polygonaceae

Anna Kostikova, Nicolas Salamin & Peter B. Pearman
The latitudinal diversity gradient (LDG) is one of the most striking and consistent biodiversity patterns across taxonomic groups. We investigate the species richness gradient in the buckwheat family, Polygonaceae, which exhibits a reverse LDG and is, thus, decoupled from dominant gradients of energy and environmental stability that increase towards the tropics and confound mechanistic interpretations. We test competing age and evolutionary diversification hypotheses, which may explain the diversification of this plant family over the past...

Data from: MicroRNAs Shape Circadian Hepatic Gene Expression on a Transcriptome-Wide Scale

David Gatfield, Ngoc-Hien Du, Alaaddin Bulak Arpat & Mara De Matos
A considerable proportion of mammalian gene expression undergoes circadian oscillations. Post-transcriptional mechanisms likely make important contributions to mRNA abundance rhythms. We have investigated how microRNAs (miRNAs) contribute to core clock and clock-controlled gene expression using mice in which miRNA biogenesis can be inactivated in the liver. While the hepatic core clock was surprisingly resilient to miRNA loss, whole transcriptome sequencing uncovered widespread effects on clock output gene expression. Cyclic transcription paired with miRNA-mediated regulation was...

Data from: How a haemosporidian parasite of bats gets around: the genetic structure of a parasite, vector and host compared

Fardo Witsenburg, Laura Clément, Ludovic Dutoit, Adrià López-Baucells, Jorge Palmeirim, Dino Scaravelli, Martin Ševčík, Nicolas Salamin, Jérôme Goudet, Philippe Christe & Igor Pavlinić
Parasite population structure is often thought to be largely shaped by that of its host. In the case of a parasite with a complex life cycle, two host species, each with their own patterns of demography and migration, spread the parasite. However, the population structure of the parasite is predicted to resemble only that of the most vagile host species. In this study we tested this prediction in the context of a vector-transmitted parasite. We...

Data from: Niche width impacts vertebrate diversification

Jonathan Rolland & Nicolas Salamin
Aim: The size of the climatic niche of a species is a major factor determining its distribution and evolution. In particular, it has been proposed that niche width should be associated with the rate of species diversification. Here, we test whether species niche width affects the speciation and extinction rates of three main clades of vertebrates: amphibians, mammals and birds. Location: Global. Methods: We obtained the time-calibrated phylogenies, IUCN conservation status, species distribution maps and...

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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