next-generation sequencing; ecological adaptation; natural selection; genomic divergence; speciation
Favre Adrien, Widmer Alex, Karrenberg Sophie (2016), Differential adaptation drives ecological speciation in campions (Silene): evidence from a multi-site transplant experiment, in New Phytologist
Zemp Niklaus, Tavares Raquel, Muyle Aline, Charlesworth Deborah, Marais Gabriel A. B., Widmer Alex (2016), Evolution of sex-biased gene expression in a dioecious plant, in Nature Plants
, 2, 1-7.
Shafer Aaron, Fior Simone, Zielinski Piotr (2015), Genomics and the challenging translation into conservation practice, in Trends in Ecology & Evolution
, 30(2), 78-87.
Seehausen Ole, Butlin Roger K., Keller Irene, Wagner Catherine E., Boughman Janette W., Hohenlohe Paul A., Peichel Catherine L., Saetre Glenn-Peter, Bank Claudia, Braennstroem Ake, Brelsford Alan, Clarkson Chris S., Eroukhmanoff Fabrice, Feder Jeffrey L., Fischer Martin C., Foote Andrew D., Franchini Paolo, Jiggins Chris D., Jones Felicity C., Lindholm Anna K., Lucek Kay, Maan Martine E., Marques David A., Martin Simon H., Matthews Blake (2014), Genomics and the origin of species, in Nature Reviews Genetics
, 15(3), 176-192.
Zemp Niklaus, Minder Aria, Widmer Alex (2014), Identification of Internal Reference Genes for Gene Expression Normalization between the Two Sexes in Dioecious White Campion, in Plos One
, 9(3), e92893.
Andrew Rose L., Bernatchez Louis, Bonin Aurelie, Buerkle C. Alex, Carstens Bryan C., Emerson Brent C., Garant Dany, Giraud Tatiana, Kane Nolan C., Rogers Sean M., Slate Jon, Smith Harry, Sork Victoria L., Stone Graham N., Vines Timothy H., Waits Lisette, Widmer Alex, Rieseberg Loren H. (2013), A road map for molecular ecology, in Molecular Ecology
, 22(10), 2605-2626.
Kaefer J., Talianova M., Bigot T., Michu E., Gueguen L., Widmer A., Zluvova J., Glemin S., Marais G. A. B. (2013), Patterns of molecular evolution in dioecious and non-dioecious Silene, in Journal of Evolutionary Biology
, 26(2), 335-346.
Muyle Aline, Zemp Niklaus, Deschamps Clothilde, Mousset Sylvain, Widmer Alex, Marais Gabriel A. B. (2012), Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia, a Plant with Young Sex Chromosomes, in Plos Biology
, 10(4), 1308-1308.
Studies of adaptation and speciation in plants are currently experiencing a major revolution. First, new sequencing technologies and conceptual advances open the doors to truly genome-wide analyses of adaptation, selection and genomic divergence in natural populations. Second, the concept of ecological speciation puts ecological adaptation into the spotlight of speciation research because it provides a direct link between ecological adaptation, divergent selection and speciation, and because it implies that speciation can occur over ecological time scales. To date, however, relevant examples of ecological speciation are scarce and empirical data on the genetic basis of the process is largely lacking.This project sets out to explore the genetic basis of ecological adaptation and its consequences for genome-wide divergence in two plant study systems, an evolutionary young and an older system. The first study system is wild carnation, Dianthus sylvestris, where natural populations occur over a large altitudinal gradient in the Alps and show strong phenotypic divergence in the absence of neutral genetic divergence. This pattern suggests that divergent natural selection underlies phenotypic divergence and has led to ecological adaptation. I propose to explore the association between ecological adaptation and incipient genomic divergence in Dianthus. The second study system includes two closely related Silene species, S. latifolia and S. dioica. These species show incomplete morphological, ecological and reproductive isolation and often hybridize upon secondary contact, yet remain distinct outside of contact zones. I propose to explore the contribution of ecological adaptation to present day reproductive isolation and genomic divergence between these two species.To assess genomic divergence between high and low altitude populations of D. sylvestris, as well as between S. latifolia and S. dioica, we will use RAD sequencing, a recently developed method that uses next-generation sequencing (NGS) to assess nucleotide variation at a genome-wide scale. Genomic regions associated with ecological adaptation will be identified using a combination of classical ecological transplant experiments and high-density QTL mapping in experimental populations. This genotyping information will be further used to study the frequency and genomic position of intrinsic reproductive barriers (incompatibilities). Together, these results will provide a novel perspective on the associations between ecological adaptation, divergent selection and speciation in plants and provide a test of the ecological speciation scenario.Developing a better understanding of the genetic basis of adaptation and its consequences for genomic divergence and speciation is not only of fundamental interest for basic science, but is also highly relevant for a society that is anxious about the consequences of climate change and the threats to biodiversity.