Université de Fribourg

Detecting selection from linked sites using an f-model

Galimberti, Marco ; Leuenberger, Christoph ; Wolf, Beat ; Szilágyi, Sándor Miklós ; Foll, Matthieu ; Wegmann, Daniel

In: Genetics, 2020, vol. 216, no. 4, p. 1205–1215

Allele frequencies vary across populations and loci, even in the presence of migration. While most differences may be due to genetic drift, divergent selection will further increase differentiation at some loci. Identifying those is key in studying local adaptation, but remains statistically challenging. A particularly elegant way to describe allele frequency differences among populations...

Université de Fribourg

Low prevalence of lactase persistence in bronze age europe indicates ongoing strong selection over the last 3,000 years

Burger, Joachim ; Link, Vivian ; Blöcher, Jens ; Schulz, Anna ; Sell, Christian ; Pochon, Zoé ; Diekmann, Yoan ; Žegarac, Aleksandra ; Hofmanová, Zuzana ; Winkelbach, Laura ; Reyna-Blanco, Carlos S. ; Bieker, Vanessa ; Orschiedt, Jörg ; Brinker, Ute ; Scheu, Amelie ; Leuenberger, Christoph ; Bertino, Thomas S. ; Bollongino, Ruth ; Lidke, Gundula ; Stefanović, Sofija ; Jantzen, Detlef ; Kaiser, Elke ; Terberger, Thomas ; Thomas, Mark G. ; Veeramah, Krishna R. ; Wegmann, Daniel

In: Current Biology, 2020, p. -

Lactase persistence (LP), the continued expression of lactase into adulthood, is the most strongly selected single gene trait over the last 10,000 years in multiple human populations. It has been posited that the primary allele causing LP among Eurasians, rs4988235-A [1], only rose to appreciable frequencies during the Bronze and Iron Ages [2, 3], long after humans started consuming milk from...

Université de Fribourg

Apex predators decline after an influx of pastoralists in former Central African Republic hunting zones

Aebischer, Thierry ; Ibrahim, Tidjani ; Hickisch, Raffael ; Furrer, Roman D. ; Leuenberger, Christoph ; Wegmann, Daniel

In: Biological Conservation, 2020, vol. 241, p. 108326

Pastoralism is spreading in Central Africa, where many protected areas are under consideration to be opened for grazing, in particular hunting zones. Here we document the loss of biodiversity followed by an influx of transhumant pastoralism into previously uninhabited and virtually pristine habitat in the Central African Republic. Our track count and camera trap surveys of 2012, 2016 and...

Université de Fribourg

Inference of evolutionary jumps in large phylogenies using Lévy processes

Duchen, Pablo ; Leuenberger, Christoph ; Szilágyi, Sándor M. ; Harmon, Luke ; Eastman, Jonathan ; Schweizer, Manuel ; Wegmann, Daniel

In: Systematic Biology, 2017, p. -

Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance...

Consortium of Swiss Academic Libraries

Analysis of Ratios in Multivariate Morphometry

Baur, Hannes ; Leuenberger, Christoph

In: Systematic Biology, 2011, vol. 60, no. 6, p. 813-825

Université de Fribourg

The optimal rate for resolving a near-polytomy in a phylogeny

Steel, Mike ; Leuenberger, Christoph

In: Journal of Theoretical Biology, 2017, vol. 420, p. 174–179

The reconstruction of phylogenetic trees from discrete character data typically relies on models that assume the characters evolve under a continuous-time Markov process operating at some overall rate λ. When λ is too high or too low, it becomes difficult to distinguish a short interior edge from a polytomy (the tree that results from collapsing the edge). In this note, we investigate the rate...

Université de Fribourg

Inferring heterozygosity from ancient and low coverage genomes

Kousathanas, Athanasios ; Leuenberger, Christoph ; Link, Vivian ; Sell, Christian ; Burger, Joachim ; Wegmann, Daniel

In: Genetics, 2017, vol. 205, no. 1, p. 317–332

While genetic diversity can be quantified accurately from high coverage sequencing data, it is often desirable to obtain such estimates from data with low coverage, either to save costs or because of low DNA quality, as is observed for ancient samples. Here, we introduce a method to accurately infer heterozygosity probabilistically from sequences with average coverage Embedded Image of a...

Université de Fribourg

Likelihood-free inference in high-dimensional models

Kousathanas, Athanasios ; Leuenberger, Christoph ; Helfer, Jonas ; Quinodoz, Mathieu ; Foll, Matthieu ; Wegmann, Daniel

In: Genetics, 2016, vol. 203, no. 2, p. 893–904

Methods that bypass analytical evaluations of the likelihood function have become an indispensable tool for statistical inference in many fields of science. These so-called likelihood-free methods rely on accepting and rejecting simulations based on summary statistics, which limits them to low-dimensional models for which the value of the likelihood is large enough to result in manageable...