96 Works

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: 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: 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: 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: 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: 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: 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: 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: 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...

Can antioxidant responses be induced by habitat fragmentation process?

Luciano Bani, Valerio Orioli, Roberto Giacchini, Paolo Parenti, Olivia Dondina, Marko Prokić, Caterina Faggio & Giulia Campli
Animal populations are increasingly forced to live in small residual natural or semi-natural areas due to habitat loss and fragmentation. Here, the viability of populations is often compromised by intrinsic threat factors typical of small and isolated populations, such as inbreeding depression, genetic drift, and environmental and demographic stochasticity. Under these circumstances, organisms may have low fitness due to inadequate physiological responses needed to face environmental challenges. However, few studies have investigated the relationship between...

Cannabidiol attenuates methamphetamine-induced conditioned place preference in male rats and viability in PC12 cells through the Sigma1R/AKT/GSK3β/CREB signaling pathway

Liu Liu, Juan Li, Chan Wang, Yue Xu, Chi-Kwan Leung, Genmeng Yang, Shucheng Lin, Shuwei Zhang, Yi Tan, Huijie Zhang, Haowei Wang, Jianxing Liu, Ming Li & Xiaofeng Zeng
Background: Methamphetamine use is associated with several negative consequences, including neurotoxicity and greater probability of exhibiting a substance use disorder. Sigma1 receptor is involved in the neurobiological basis of several drug use disorders. Cannabidiol has received attention in the treatment of drug use disorders and neurotoxicity. Objectives: To investigate the effects of cannabidiol on methamphetamine-induced conditioned place preference (CPP) and the viability of PC12 cells. Methods: Adult male rats (n = 70) underwent methamphetamine (2...

Additional file 1 of Validity and reliability of a semi-quantitative food frequency questionnaire in groups at high risk for cardiovascular diseases

Ni Yan, Nan Li, Wanlu Liu, Xiaoxia Li, Xiuying Liu, Pengju Zhang, Can Liu, Juan Li, Jiangwei Qiu, Yuhong Zhang & Yi Zhao
Additional file 1. Annex.

Additional file 1 of Validity and reliability of a semi-quantitative food frequency questionnaire in groups at high risk for cardiovascular diseases

Ni Yan, Nan Li, Wanlu Liu, Xiaoxia Li, Xiuying Liu, Pengju Zhang, Can Liu, Juan Li, Jiangwei Qiu, Yuhong Zhang & Yi Zhao
Additional file 1. Annex.

Additional file 6 of The combined impact of persistent infections and human genetic variation on C-reactive protein levels

Flavia Hodel, Olivier Naret, Clara Bonnet, Nicole Brenner, Noemi Bender, Tim Waterboer, Pedro Marques-Vidal, Peter Vollenweider & Jacques Fellay
Additional file 6: Fig. S6. Seroprevalence of tested antigens in the CoLaus|PsyCoLaus. List of the 27 antigens available from the CoLaus|PsyCoLaus study that are shared with the UK Biobank. The percentages indicate the seroprevalence of antibodies against infectious disease antigens tested using Multiplex Serology platform. The grey boxes indicate the pathogen on which the antigen protein is found, and the family to which the pathogen belongs.

Additional file 2 of Deeper genomic insights into tomato CLE genes repertoire identify new active peptides

Samy Carbonnel, Laurent Falquet & Ora Hazak
Additional file 2.

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: 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: 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: 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...

Validity and reliability of a semi-quantitative food frequency questionnaire in groups at high risk for cardiovascular diseases

Ni Yan, Nan Li, Wanlu Liu, Xiaoxia Li, Xiuying Liu, Pengju Zhang, Can Liu, Juan Li, Jiangwei Qiu, Yuhong Zhang & Yi Zhao
Abstract Background Diet is a modifiable risk factor for cardiovascular diseases (CVD), but there is still a lack of tools to assess dietary intakes of this high-risk population in Ningxia, China. Objective We aim to evaluate the validity and reliability of the semi-quantitative food frequency questionnaire (SFFQ) in the groups in Ningxia using a 24-hour dietary recall method. Method Two hundred five participants were included in the analysis. The two FFQs were 6 months apart,...

Additional file 1 of The combined impact of persistent infections and human genetic variation on C-reactive protein levels

Flavia Hodel, Olivier Naret, Clara Bonnet, Nicole Brenner, Noemi Bender, Tim Waterboer, Pedro Marques-Vidal, Peter Vollenweider & Jacques Fellay
Additional file 1: Fig. S1. Flowchart illustrating the inclusion/exclusion of individuals in the study. Orange boxes indicate the number of included antigens and pathogens.

Additional file 7 of The combined impact of persistent infections and human genetic variation on C-reactive protein levels

Flavia Hodel, Olivier Naret, Clara Bonnet, Nicole Brenner, Noemi Bender, Tim Waterboer, Pedro Marques-Vidal, Peter Vollenweider & Jacques Fellay
Additional file 7: Fig. S7. Seroprevalence of tested antigens in the UK Biobank. List of the 27 antigens available from the UK Biobank that are shared with the CoLaus|PsyCoLaus study. The percentages indicate the seroprevalence of antibodies against infectious disease antigens tested using Multiplex Serology platform. The grey boxes indicate the pathogen on which the antigen protein is found, and the family to which the pathogen belongs.

Additional file 7 of The combined impact of persistent infections and human genetic variation on C-reactive protein levels

Flavia Hodel, Olivier Naret, Clara Bonnet, Nicole Brenner, Noemi Bender, Tim Waterboer, Pedro Marques-Vidal, Peter Vollenweider & Jacques Fellay
Additional file 7: Fig. S7. Seroprevalence of tested antigens in the UK Biobank. List of the 27 antigens available from the UK Biobank that are shared with the CoLaus|PsyCoLaus study. The percentages indicate the seroprevalence of antibodies against infectious disease antigens tested using Multiplex Serology platform. The grey boxes indicate the pathogen on which the antigen protein is found, and the family to which the pathogen belongs.

Registration Year

  • 2022
    45
  • 2021
    1
  • 2020
    2
  • 2019
    1
  • 2018
    11
  • 2017
    2
  • 2016
    5
  • 2015
    9
  • 2014
    10
  • 2013
    7

Resource Types

  • Dataset
    61
  • Text
    26
  • Collection
    8
  • Image
    1

Affiliations

  • Swiss Institute of Bioinformatics
    96
  • University of Lausanne
    47
  • University of Bern
    22
  • École Polytechnique Fédérale de Lausanne
    20
  • German Cancer Research Center
    15
  • University Hospital of Lausanne
    15
  • Hainan Medical University
    11
  • Sun Yat-sen University
    11
  • Zhejiang University
    11
  • Peking University Cancer Hospital
    11