Computational Phylogenetics
... Molecular Data, Evolutionary Modeling and Computational Tools

Overview of the group

The Computational Phylogenetics group is part of the Department of Ecology and Evolution from the University of Lausanne as well as the Swiss Institute of Bioinformatics. It also belongs to the Center for Advanced Modeling of Sciences (CADMOS).


We work on a variety of organisms and questions with a particular focus on understanding the drivers of adaptation both at the levels of the genes or genomes but also through the modeling of the evolution of the phenotypes and the ecological niche of species.

 Although our research questions are purely biological and we work on a variety of biological systems illustrated below, we make extensive use of high performance computing facilities such as vital-it of the SIB or the BlueGen/Q system of CADMOS to create and evaluate evolutionary models. The group is therefore a nice mix of theoretical people, bioinformaticians and empirical biologists, which makes discussions and lab meeting lively and interesting!


Recent publications

See the publications pages for the complete list.

L. Dib, D. Silvestro, N. Salamin. 2014. Evolutionary footprint of coevolving positions in genes. Bioinformatics, 30, 1241-1249.

G. Litsios, N. Salamin. 2014. Hybridisation and diversification in the adaptive radiation of clownfishes.BMC evolutionary biology, 14, 245.

G. Litsios, R.O. Wüest, A. Kostikova, F. Forest, C. Lexer, H.P. Linder, P.B. Pearman, N.E. Zimmermann, N. Salamin. 2014. Effects of a fire response trait on diversification in replicated radiations. Evolution, 68, 453-465.

M. Zaheri, L. Dib, N. Salamin. 2014. A generalized mechanistic codon model. Molecular Biology and Evolution, 31, 2528-2541.

A. Kostikova, G. Litsios, N. Salamin* and P.B. Pearman*. 2013. Linking life-history traits, ecology and niche breadth evolution in North American eriogonoids (Polygonaceae). American Naturalist, 182, 760-774. * = shared last authorship

C. Lexer, S. Mangili, E. Bossolini, F. Forest, K.N. Stölting, P.B. Pearman, N.E. Zimmermann, N. Salamin. 2013. 'Next generation' biogeography: towards understanding the drivers of species diversification and persistence. Journal of Biogeography, 40, 1013-1022

tP.-A. Christin, G. Besnard, E.J. Edwards and N. Salamin. 2012. Effect of genetic convergence on phylogenetic inference. Molecular Phylogenetics and Evolution, 62, 921-927.

G. Litsios, L. Pellissier, F. Forest, C. Lexer, P.B. Pearman, N.E. Zimmerman and N. Salamin. 2012. Trophic specialisation influences the rate of environmental niche evolution in damselfish. Proceedings of the Royal Society Series B, 279, 3662-3669.

G. Litsios and N. Salamin. 2012. Effects of generation time on character state reconstruction. Systematic Biology, 61, 533-538.

G. Litsios, C.A. Sims, R.O. Wüest, P.B. Pearman, N.E. Zimmerman and N. Salamin. 2012. Mutualism with sea anemones drives the adaptive radiation of clownfish. BMC Evolutionary Biology, 12, 212.

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