9 Works

Dataset for quantification of CFUs using AI

Adrian Egli & Michael Moucka
In recent years, smartphones and software have developed to help to automate imaging processes and thereby support digitalization in clinical microbiology laboratories. Due to the time-consuming nature of manual bacterial colony counting, diverse apps for smartphones have been developed to quantify the number of colony-forming units (CFUs) on agar plate images. Currently, at least four different apps with a colony counter function exist. Our study aimed to compare the accuracy of the apps compared to...

Why and how we should join the shift from significance testing to estimation

Daniel Berner & Valentin Amrhein
A paradigm shift away from null hypothesis significance testing seems in progress. Based on simulations, we illustrate some of the underlying motivations. First, p-values vary strongly from study to study, hence dichotomous inference using significance thresholds is usually unjustified. Second, ‘statistically significant’ results have overestimated effect sizes, a bias declining with increasing statistical power. Third, ‘statistically non-significant’ results have underestimated effect sizes, and this bias gets stronger with higher statistical power. Fourth, the tested statistical...

Molecular evolution and depth-related adaptations of rhodopsin in the adaptive radiation of cichlid fishes in Lake Tanganyika

Virginie Ricci, Fabrizia Ronco, Zuzana Musilova & Walter Salzburger
The visual sensory system is essential for animals to perceive their environment and is thus under strong selection. In aquatic environments, light intensity and spectrum differ primarily along a depth gradient. Rhodopsin (RH1) is the only opsin responsible for dim-light vision in vertebrates and has been shown to evolve in response to the respective light conditions, including along a water depth gradient in fishes. In this study, we examined the diversity and sequence evolution of...

Number of growth days and not length of the growth period determines radial stem growth of temperate trees

Sophia Etzold, Frank Sterck, Arun Bose, Sabine Braun, Nina Buchmann, Werner Eugster, Arthur Gessler, Ansgar Kahmen, Richard Peters, Lorenz Walthert, Yann Vitasse, Kasia Zieminska, Haeni Matthias, Micah Wilhelm, Volodymyr Trotsiuk & Zweifel Roman
Radial stem growth dynamics at seasonal resolution are essential to understand how forests respond to climate change. We studied daily radial growth of 160 individuals of seven temperate tree species at 47 sites across Switzerland over eight years. Growth of all species peaked in the early part of the growth season and commenced shortly before the summer solstice, but with species-specific seasonal patterns. Day length set a window of opportunity for radial growth. Within this...

Functional traits and their plasticity shift from tolerant to avoidant under extreme drought

Rosa Elisabeth Kramp, Pierre Liancourt, Maximiliane Herberich, Lara Saul, Sophie Weides, Katja Tielbörger & Maria Májeková
Under climate change, extreme droughts will limit water availability for plants. However, the species-specific responses make it difficult to draw general conclusions. We hypothesized that changes in species’ abundance in response to extreme drought can be best explained by a set of water economic traits under ambient conditions in combination with the ability to adjust these traits towards higher drought resistance. We conducted a four-year field experiment in temperate grasslands using rainout shelters with 30%...

Blast output from: Lost in dead wood? Environmental DNA sequencing from dead wood shows little signs of saproxylic beetles

Nathalie Winiger, Sebastian Seibold, Kay Lucek, Jörg Müller & Gernot Segelbacher
eDNA metabarcoding has become a standard method for assessing wood-inhabiting fungi and bacteria, yet determination of dead-wood-inhabiting beetles still relies on time-consuming collection of beetle specimens. We thus tested whether beetle species can be identified by eDNA sequencing of wood in a mesocosm experiment that manipulated species assemblages. Dead wood samples were taken at exit holes of beetles and DNA was extracted and analyzed using two comparative methods: (i) metabarcoding with standard arthropod primers (421...

The EDA receptor (EDAR) is a candidate gene for lateral plate number variation in stickleback fish

Telma G. Laurentino, Nicolas Boileau, Fabrizia Ronco & Daniel Berner
Variation in lateral plating in stickleback fish represents a classical example of rapid and parallel adaptation in morphology. The underlying genetic architecture involves polymorphism at the ectodysplasin-A (EDA) gene. However, lateral plate number is influenced by additional loci that remain poorly characterized. Here we search for such loci by performing genome-wide differentiation mapping based on pooled whole-genome sequence data from a European stickleback population variable in the extent of lateral plating, while tightly controlling for...

The implications of incongruence between gene tree and species tree topologies for divergence time estimation

Tom Carruthers, Miao Sun, William Baker, Stephen Smith, Jurriaan De Vos & Wolf Eiserhardt
Phylogenetic analyses are increasingly being performed with datasets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene...

A model of digestive tooth corrosion in lizards: experimental tests and taphonomic implications

Krister T. Smith, Orr Comay, Lutz Maul, Fabio Wegmüller, Jean-Marie Le Tensorer & Tamar Dayan
Abstract Corrosion patterns induced by gastric fluids on the skeleton of prey animals may depend on the nature of the corrosive agents (acid, enzymes) as well as on the composition of the hard parts and the soft tissues that surround them. We propose a framework for predicting and interpreting corrosion patterns on lizard teeth, our model system, drawing on the different digestive pathways of avian and non-avian vertebrate predators. We propose that high-acid, low-enzyme systems...

Registration Year

  • 2022
    9

Resource Types

  • Dataset
    9

Affiliations

  • University of Basel
    9
  • University of Würzburg
    1
  • University of Michigan–Ann Arbor
    1
  • Senckenberg Nature Research Society
    1
  • Royal Botanic Gardens, Kew
    1
  • Aarhus University
    1
  • University of California, Berkeley
    1
  • University of Freiburg
    1
  • Charles University
    1
  • Technical University of Munich
    1