11 Works

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: 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: 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: 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: 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: 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: 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: Fundamental and realized feeding niche breadths of sexual and asexual stick insects

Chloé Larose, Darren J. Parker & Tanja Schwander
The factors contributing to the maintenance of sex over asexuality in natural populations remain unclear. Ecological divergences between sexual and asexual lineages could help to maintain reproductive polymorphisms, at least transiently, but the consequences of asexuality for the evolution of ecological niches are unknown. Here, we investigated how niche breadths change in transitions from sexual reproduction to asexuality. We used host plant ranges as a proxy to compare the realized feeding niche breadths of five...

Data from: Phylodynamic model adequacy using posterior predictive simulations

Sebastian Duchene, Remco Bouckaert, David A Duchene, Tanja Stadler & Alexei J Drummond
Rapidly evolving pathogens, such as viruses and bacteria, accumulate genetic change at a similar timescale over which their epidemiological processes occur, such that it is possible to make inferences about their infectious spread using phylogenetic time-trees. For this purpose it is necessary to choose a phylodynamic model. However, the resulting inferences are contingent on whether the model adequately describes key features of the data. Model adequacy methods allow formal rejection of a model if it...

Registration Year

  • 2018

Resource Types

  • Dataset


  • Swiss Institute of Bioinformatics
  • University of Lausanne
  • University of Zurich
  • University of Bern
  • University of Pennsylvania
  • Swiss Federal Institute of Aquatic Science and Technology
  • Santa Fe Institute
  • University of Melbourne
  • Lanzhou University
  • University of Southampton