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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

Estimating and accounting for genotyping errors in RAD-seq experiments

Bresadola, Luisa ; Link, Vivian ; Buerkle, C. Alex ; Lexer, Christian ; Wegmann, Daniel

In: Molecular Ecology Resources, 2020, vol. 20, no. 4, p. 856–870

In non-model organisms, evolutionary questions are frequently addressed using reduced representation sequencing techniques due to their low cost, ease of use, and because they do not require genomic resources such as a reference genome. However, evidence is accumulating that such techniques may be affected by specific biases, questioning the accuracy of obtained genotypes, and as a...

Université de Fribourg

Inference of natural selection from ancient DNA

Dehasque, Marianne ; Ávila‐Arcos, María C. ; Díez‐del‐Molino, David ; Fumagalli, Matteo ; Guschanski, Katerina ; Lorenzen, Eline D. ; Malaspinas, Anna‐Sapfo ; Marques‐Bonet, Tomas ; Martin, Michael D. ; Murray, Gemma G. R. ; Papadopulos, Alexander S. T. ; Therkildsen, Nina Overgaard ; Wegmann, Daniel ; Dalén, Love ; Foote, Andrew D.

In: Evolution Letters, 2020, vol. 4, no. 2, p. 94–108

Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct...

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

Admixture mapping in interspecific Populus hybrids identifies classes of genomic architectures for phytochemical, morphological and growth traits

Bresadola, Luisa ; Caseys, Céline ; Castiglione, Stefano ; Buerkle, C. Alex ; Wegmann, Daniel ; Lexer, Christian

In: New Phytologist, 2019, vol. 223, no. 4, p. 2076–2089

The genomic architecture of functionally important traits is key to understanding the maintenance of reproductive barriers and trait differences when divergent populations or species hybridize. We conducted a genome-wide association study (GWAS) to study trait architecture in natural hybrids of two ecologically divergent Populus species. We genotyped 472 seedlings from a natural hybrid zone...

Université de Fribourg

Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication

Gros-Balthazard, Muriel ; Besnard, Guillaume ; Sarah, Gautier ; Holtz, Yan ; Leclercq, Julie ; Santoni, Sylvain ; Wegmann, Daniel ; Glémin, Sylvain ; Khadari, Bouchaib

In: The Plant Journal, 2019, p. tpj.14435

The olive (Olea europaea L. subsp. europaea) is one of the oldest and most socio‐ economically important cultivated perennial crop in the Mediterranean region. Yet, its origins are still under debate and the genetic bases of the phenotypic changes associated with its domestication are unknown. We generated RNA‐sequencing data for 68 wild and cultivated olive trees to study the genetic...

Université de Fribourg

Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria

Veeramah, Krishna R. ; Rott, Andreas ; Groß, Melanie ; Dorp, Lucy van ; López, Saioa ; Kirsanow, Karola ; Sell, Christian ; Blöcher, Jens ; Wegmann, Daniel ; Link, Vivian ; Hofmanová, Zuzana ; Peters, Joris ; Trautmann, Bernd ; Gairhos, Anja ; Haberstroh, Jochen ; Päffgen, Bernd ; Hellenthal, Garrett ; Haas-Gebhard, Brigitte ; Harbeck, Michaela ; Burger, Joachim

In: Proceedings of the National Academy of Sciences, 2018, p. 201719880

Modern European genetic structure demonstrates strong correlations with geography, while genetic analysis of prehistoric humans has indicated at least two major waves of immigration from outside the continent during periods of cultural change. However, population-level genome data that could shed light on the demographic processes occurring during the intervening periods have been absent....

Université de Fribourg

First quantitative survey delineates the distribution of chimpanzees in the Eastern Central African Republic

Aebischer, Thierry ; Siguindo, Guy ; Rochat, Estelle ; Arandjelovic, Mimi ; Heilman, Amy ; Hickisch, Raffael ; Vigilant, Linda ; Joost, Stéphane ; Wegmann, Daniel

In: Biological Conservation, 2017, vol. 213, no. Part A, p. 84–94

Vast, pristine ecosystems and their biodiversity are vanishing globally at frightening speed, but many large tracts of wilderness have not yet been systematically inventoried and important natural populations of threatened species remain poorly characterized. The forest-savanna ecotone of the Eastern Central African Republic (CAR) is one such poorly studied area. Using camera traps, transect...