Nicolas Salamin
(nicolas.salamin[@]unil.ch)
Beside the projects described for each member of my group, my research focus on the development of new methods to analyse organisms evolution and the application of existing methods to understand evolution in particular groups of plants. They can be grouped in three main research topics:
1. Building the Tree of Life
Building large phylogenetic trees is an NP-hard problem, and heuristic strategies have to be used to infer trees containing hundreds of terminal taxa. We are investigating the performances of current methods of reconstruction with computer simulations and empirical examples from the angiosperms. We are also developping new methods to build the Tree of Life
2. Mode and tempo of evolution
Phylogenetic trees can give insight into the mode and tempo of species evolution. We are developping methods to estimate the rate of speciation and extinction through time using a Maximum Likelihood approach coupled with Markov chain Monte Carlo techniques
3. Grass evolution
Grasses are one of the most ecologically and economically important plant family, and we are interesting in understanding what are the patterns and processes driving grass evolution. At the molecular level, we are investigating the evolution of enzyme involved in the C4 photosynthetic pathways (collaboration with Guillaume Besnard). We are also investigating the macroevolution of this family by looking at the traits affecting grass diversification and testing coevolution between grass species and herbivores (collaboration with Trevor Hodkinson at the University of Dublin, Trinity College)
Pascal-Antoine Christin
(pascal-antoine.christin[@]unil.ch)
C4 phosphoenolpyruvate carboxylase (C4 PEPC) is a key enzyme of the C4 photosynthetic pathway and allows initial fixation of atmospheric CO2. In grasses, this enzyme is encoded by the gene ppc-C4. This gene has been detected in both C3 and C4 grass sub-families. Elucidating the ppc-C4 evolution in grasses is an attractive topic allowing testing of numerous evolutionary hypothesis for the C4 adaptive trait.
In this project, we are evaluating the occurrence of positive selective events on some amino-acid residues, convergent evolution (multiple appearances) and gradual selection in C4 characteristics of the ppc-C4 enzyme during the diversification of the grass family. We use a broad sample of species representative of both the different grass sub-families and of the different photosynthetic pathways. The organization of ppc-C4 gene parts (promoter, intron 6) are analyzed in a few species and on several genotypes. Comparison between genotypes of a same species or between distantly-related species will allow us to reveal some changes and we will interpret the evolutionary significance of these re-organizations in the gene expression.
Dorothea Pio
(dorothea.pio[@]unil.ch)
Hotspots are sanctuaries of biodiversity. Yet, with global change, many species are committed to extinction and preservation plans need to be established. What do we want to preserve most? The largest number of species or the largest number of genes or characters? The main aim of this project is to investigate the relationship between species richness (number of species) and phylogenetic diversity (a measure of diversity which takes into account the genetic relatedness between species) in biodiversity hotspots. Currently conservation areas are often selected on the basis of the number of species present, and their level of rarity or endemicity. Yet, species richness may not be the best surrogate for all aspects of biodiversity, such as phylogenetic diversity, as species are not equivalent in terms of the evolutionary history they represent. Do rich communities also contain larger amounts of phylogenetic diversity or not? How are patterns of phylogenetic diversity affected by species sorting, e.g. simulating the sequential disappearance of species (extinctions)?
To answer these questions, we are using datasets on particularly diverse plant communities in the Mediterranean and South African regions, and collecting data on bat assemblages (one of the greatest contributor to mammal diversity worldwide) in Sumatra, Indonesia. A combination of spatial modeling and phylogenetic techniques are used to analyze both botanical and zoological datasets.
PhD available: Evolutionary Niche dyNamics of Invasive Species (ENNIS)
The ENNIS project seeks to understand the relationship between the evolutionary history of a clade, the niche variation and accompanying variation in the distribution of species, and the tendency for plant species to become invasive and/or naturalized. The project will focus on clades that have naturalized and invasive species in Switzerland and central Europe. We will use an interdisciplinary approach that includes activities in niche modeling, sequencing DNA regions, phylogenetic reconstruction and modeling trait evolution. The research includes characterization of the niches and distribution of clade members using multivariate statistics and niche-based species distribution modeling, bioinformatics approaches to the use of biodiversity (e.g. GBIF), sequence (Genbank), and phylogenetic (Treebase) databases, as well as public and other databases on the distribution of invasive and naturalized species. A substantial portion of the research will involve production of DNA sequence data to complete phylogenetic trees of species in one or more clades that contain invasive and naturalized species in central Europe. Collection of material for sequencing, and additional data on species global distributions, will involve visiting national herbaria, botanical gardens, individual researchers, and fieldwork throughout the sum distribution of the species in the focal clades. Phylogenetic reconstruction of evolutionary relationships and modeling of evolutionary processes of ecological diversification will be approached through the use of experimental software, as well as the development of original algorithms.
The Ph.D. Position
The position includes funding for three years. You will be matriculated in the Ecology and Evolution doctoral program of the University of Lausanne (UNIL) and will be a member of both the Department of Ecology and Evolution (DEE) at that institution and at the Federal Research Institute WSL, located in Birmensdorf near Zürich. You will spend substantial periods in residence at both institutions during the three-year period under the supervision of. Drs. Peter B. Pearman (WSL) and Nicolas Salamin (UNIL). Extensive international travel, especially during the first years of the project, may be required for success in the project. You will gain knowledge and experience in both modeling of species climate niches using GIS and programming in C language and within the R package. You will learn techniques required for tissue collection, DNA extraction and sequencing. You will further become proficient at phylogenetic reconstruction and in modeling the evolution of niche characteristics during clade diversification.
Starting salary: approx. SFr 42,500/yr + benefits
Requirements:
As a candidate for the Ph.D. position, you must hold a Masters of Science or equivalent by the time you begin on the project and enroll at the UNIL. You must have sufficient capability in English to read and learn to write scientific papers, and to communicate orally both informally with colleagues and formally in giving presentations at scientific conferences. You should have a university background in evolutionary biology and ecology, an excellent academic record, and proven quantitative skills acquired through coursework. You must be highly motivated, demonstrate good initiative, and able to work independently in the office, lab, and field while maintaining focus and perspective on the shared goals and objectives of the ENNIS project. You should also possess excellent organizational skills so as to work with large amounts of data and, with the supervision of the PI’s, develop a schedule of intermediate objectives, plan/carry-out the logistics of data collection, and conduct lab work and modeling.
Ideally…
You should ideally have interpersonal skills that are sufficient for communicating with data providers from diverse countries and the collaborators upon whom s/he will be dependent for full success. Ideally, you should also have experience in multiple programming languages (C, Fortran, R, Matlab, etc.) and have a working understanding of GIS. Ideally, candidates will provide evidence of ability to produce scientific papers and deliver oral presentations.
To your advantage…
It will be extremely advantageous that you have a license to drive manual-shift cars and small trucks, and possess or be eligible for a credit card. It will also be advantageous for you to be able to speak, in addition to English, another European language such as German or French. You should be physically capable of collecting plant material in the field, potentially in developing countries and away from roads and paved paths. Cross-cultural experience and sensitivity to cultural differences may prove helpful.
Starting date:
You would hopefully be ready to begin by June 1st, 2009
To Apply:
Please send a letter explaining your interest and career goals, your official university transcripts (not copies) showing all university degrees (e.g. Bachelors, Masters) and coursework, your complete CV (we actually prefer no personal photo, but please include the names, post and email addresses, and work telephone number of 3 referees who are familiar with your academic performance and intellectual capabilities), and 1 copy of each publication (if you have any) to:
Peter B. Pearman
Land Use Dynamics
Federal Research Institute WSL
Zürcherstrasse 111
CH-8903 Birmensdorf
Applications will be accepted until February 15, 2009 or until an acceptable applicant is found.
For additional information on the project and institutes, please see the following web sites:
After reviewing the information available at the web sites, please direct further questions to:
Peter B. Pearman (pearman [@] wsl.ch)
Or
Nicolas Salamin (Nicolas.Salamin [@] unil.ch)