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Université de Fribourg

Genomic footprints of repeated evolution of CAM photosynthesis in a Neotropical species radiation

De La Harpe, Marylaure ; Paris, Margot ; Hess, Jaqueline ; Barfuss, Michael Harald Johannes ; Serrano‐Serrano, Martha Liliana ; Ghatak, Arindam ; Chaturvedi, Palak ; Weckwerth, Wolfram ; Till, Walter ; Salamin, Nicolas ; Wai, Ching Man ; Ming, Ray ; Lexer, Christian

In: Plant, Cell & Environment, 2020/n/a//-

The adaptive radiation of Bromeliaceae (pineapple family) is one of the most diverse among Neotropical flowering plants. Diversification in this group was facilitated by shifts in several adaptive traits or “key innovations” including the transition from C3 to CAM photosynthesis associated with xeric (heat/drought) adaptation. We used phylogenomic approaches, complemented by differential...

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

Systematics of Vriesea (Bromeliaceae): phylogenetic relationships based on nuclear gene and partial plastome sequences

Machado, Talita Mota ; Loiseau, Oriane ; Paris, Margot ; Weigand, Anna ; Versieux, Leonardo M ; Stehmann, João Renato ; Lexer, Christian ; Salamin, Nicolas

In: Botanical Journal of the Linnean Society, 2020, vol. 192, no. 4, p. 656–674

Vriesea is the second largest genus in Tillandsioideae, the most diverse subfamily of Bromeliaceae. Although recent studies focusing on Tillandsioideae have improved the systematics of Vriesea, no consensus has been reached regarding the circumscription of the genus. Here, we present a phylogenetic analysis of core Tillandsioideae using the nuclear gene phyC and plastid data obtained from...

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

Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae

Loiseau, Oriane ; Olivares, Ingrid ; Paris, Margot ; Harpe, Marylaure de La ; Weigand, Anna ; Koubínová, Darina ; Rolland, Jonathan ; Bacon, Christine D. ; Balslev, Henrik ; Borchsenius, Finn ; Cano, Angela ; Couvreur, Thomas L. P. ; Delnatte, César ; Fardin, Frédérique ; Gayot, Marc ; Mejía, Fabian ; Mota-Machado, Talita ; Perret, Mathieu ; Roncal, Julissa ; Sanin, Maria José ; Stauffer, Fred ; Lexer, Christian ; Kessler, Michael ; Salamin, Nicolas

In: Frontiers in Plant Science, 2019, vol. 10, p. -

The tribe Geonomateae is a widely distributed group of 103 species of Neotropical palms which contains six ecologically important understory or subcanopy genera. Although it has been the focus of many studies, our understanding of the evolutionary history of this group, and in particular of the taxonomically complex genus Geonoma, is far from complete due to a lack of molecular data....

Université de Fribourg

A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms

de La Harpe, Marylaure ; Hess, Jaqueline ; Loiseau, Oriane ; Salamin, Nicolas ; Lexer, Christian ; Paris, Margot

In: Molecular Ecology Resources, 2019, p. -

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...

Université de Fribourg

Molecular ecology studies of species radiations: current research gaps, opportunities and challenges

la Harpe, Marylaure de ; Paris, Margot ; Karger, Dirk N. ; Rolland, Jonathan ; Kessler, Michael ; Salamin, Nicolas ; Lexer, Christian

In: Molecular Ecology, 2017, p. -

Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to...

Université de Fribourg

Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow

Christe, Camille ; Stölting, Kai N. ; Paris, Margot ; Fraїsse, Christelle ; Bierne, Nicolas ; Lexer, Christian

In: Molecular Ecology, 2017, vol. 26, no. 1, p. 59–76

Speciation often involves repeated episodes of genetic contact between divergent populations before reproductive isolation (RI) is complete. Whole-genome sequencing (WGS) holds great promise for unravelling the genomic bases of speciation. We have studied two ecologically divergent, hybridizing species of the ‘model tree’ genus Populus (poplars, aspens, cottonwoods), Populus alba and P....

Université de Fribourg

Causes and consequences of large clonal assemblies in a poplar hybrid zone

Macaya-Sanz, David ; Heuertz, Myriam ; Lindtke, Dorothea ; Vendramin, Giovanni G. ; Lexer, Christian ; González-Martínez, andSantiago C.

In: Molecular Ecology, 2016, vol. 25, no. 21, p. 5330–5344

Asexual reproduction is a common and fundamental mode of reproduction in plants. Although persistence in adverse conditions underlies most known cases of clonal dominance, proximal genetic drivers remain unclear, in particular for populations dominated by a few large clones. In this study, we studied a clonal population of the riparian tree Populus alba in the Douro river basin (northwestern...

Université de Fribourg

Gene flow and diversification in a species complex of Alcantarea inselberg bromeliads

Lexer, Christian ; Marthaler, Fabienne ; Humbert, Sarah ; Barbará, Thelma ; Harpe, Marylaure de la ; Bossolini, Eligio ; Paris, Margot ; Martinelli, Gustavo ; Versieux, Leonardo M.

In: Botanical Journal of the Linnean Society, 2016, vol. 181, no. 3, p. 505–520

Inselberg-adapted species of bromeliads (Bromeliaceae) have been suggested as model systems for understanding the evolutionary genetics of species complexes and radiations in terrestrial, island-like environments. Bromeliads are particularly suitable for addressing the potential roles of interspecific gene exchange during plant speciation and radiation. We have studied populations of five...