Computational Phylogenetics

My group is steadily increasing since my arrival in the Department of Ecology and Evolution of the University of Lausanne in 2005. I further joined the Swiss Institute of Bioinfomatics in 2008 as a group leader.

Beside the projects of each member of my group, I have been recently collaborating on the following projects:

• Grass Phylogeny Working Group II: NESCent-funded working group aiming at building an up-to-date phylogeny for the grass family. It is jointly coordinated by Erika Edwards, myself and Stephen Smith.
• Origin of C4 grasslands: NESCent-funded working group aiming at understanding why grasses have been so successful ecologically. It is jointly coordinated by Colin Osborne, Christopher Still and Caroline Strömberg.
• GrassPortal: ecological database created by Colin Osborne and colleagues at the University of Sheffield. This database is tighly linked with our own grassweb.
• Forecasting phenology: NCEAS-funded working group aiming at integrating ecology, climatology, and phylogeny to understand plant responses to climate change. It is jointly coordinated by Benjamin Cook and Elizabeth Wolkowich.
• comparative analyses on birds and owls. On-going collaboration with Alexandre Roulin within our department.

Linda's project focuses on the development of algorithms to estimate coevolving residues along protein-coding genes. The goal is to incorporate measures of coevolution within a phylogenetic framework to understand the evolutionary history of coevolution.

Funding: University of Lausanne

Funding: High-Performance and High-Productivity Computing

Papers

• Silvestro, D., Schnitlzer, J., Zizka, G. 2011. A Bayesian framework to estimate diversification rates and their variation through time and space. BMC Evolutionary Biology 11:311.

Funding: German Foundation DAAS.

Funding: Swiss National Science Foundation.

Funding: Swiss National Science Foundation.

Funding: Swiss National Science Foundation

I'm interested in understanding processes driving species radiation. My main research axis consist of studying the evolution of the ecological niche in a phylogenetic context. This research is a part of the SPEED (Spatially Explicit Evolution of Diversity) project in which it will be applied to the South-African Restionaceae (Poales) case. I've also spend some time studying other systems. In particular, the damselfishes (Pomacentridae) a coral reef fish family and one of their most charismatic clade, the clownfishes.

Selected papers

• Litsios G., Sims C.A., Wüest R.O., Pearman P.B., Zimmermann N.E., Salamin N., 2012. Mutualism with sea anemones triggered the adaptive radiation of clownfishes. BMC Evolutionary Biology 12(1) p. 212. [DOI]
• Litsios G., Pellissier L., Forest F., Lexer C., Pearman P. B., Zimmermann N. E., Salamin N., In Press. Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae). Proceedings of the Royal Society B . [DOI]
• Litsios G., Salamin N., 2012. Effects of Phylogenetic Signal on Ancestral State Reconstruction. Systematic Biology 61(3) pp. 533-538. [DOI] [Pubmed]

Funding: Swiss National Science Foundation

My research interests is on plant ecology and evolution, more specifically the evolution of plant communities in the Alps.

I am currently supervised by Nicolas Salamin and Antoine Guisan, were we are working on developing new methods to comparatively analyse the phylogenetic ecology of plant communities and how this determines their distribution in the western Swiss Alps.

Funding: Faculty of Biology and Medicine Fellowship

Funding: Faculty of Biology and Medicine Fellowship

Funding:: Chinese Academy of Sciences and Deparment of Ecology and Evolution.

Funding: Swiss National Science Foundation.

1. She first developed the MySQL query system for our upcoming database grassweb, which was further improved by Nils Arrigo.
2. She then focused on the development of a new model of codon evolution. The basic idea is to generalize current model to allow multiple substitutions per codon to occur during protein-coding gene evolution. This leads to a refined estimation of selective pressure and thus a better understanding of the evolution of functional genes.

Funding: Swiss National Science Foundation and Department of Ecology and Evolution.

2012

• Nils Arrigo: GrassWeb database (civil service July - October)
• Balazs Laurenczy: GrassWeb vizalisation (civil service April - September)
  
• Chantal Hoff: Coevolution in mammalian genes (SUR program).

2011

• Addison Martin: Evolution of AMF genes for phosphate intake (SUR program with Prof. Uta Pazkowski).

2010

• Sarah Burgy: Evolution of the ecological niche in invasive species of the Polygonaceae family.
• Jonathan El-Assad: Phylogeography of Abies alba in the Western Alps.
• Eros Gentilini: Population structure and phylogeography of Ambrosia artemisiifolia. Co-supervision with Antoine Guisan.
• Maïté Guignard: Mode of speciation in the Codonanthe/Nematanthus species complex. Co-supervision with Mathieu Perret (Botanical Gardens Geneva).
• Carrie A. Simms: Niche evolution in clownfish (SUR program).