News
Extinction risk of wildcats in the Jura mountains.
See more
"Avis d'Experts" Interviews
We are interested in understanding how the biodiversity that is surrounding us has originated and is maintained. We approach this wide subject by conducting several well-defined research lines that examine the role played by extrinsic factors such as allopatric divergence, past climatic or environmental changes or the introduction of invasive species by humans. We also analyze how intrinsic factors may drive new diversity like adaptation to new environments, the emergence of selectively advantageous traits, or the ability to have an accelerated substitution rate. In parallel, we develop new bioinformatics or laboratory methods to facilitate our investigations. We use a wide panel of techniques, approaches and methods that range from field experiments to genome sequencing, assembly and annotation.
Our Softwares
Current projects
Diversity, Adaptive Evolution and Key Innovations in Neotropical Fishes
Drivers of fish diversification in the Neotropics
Why do tropical regions of the world harbor the vast majority of Earth’s biodiversity? This is the basic question underlying our research project on ichthyological biodiversity in Tropical South America. Our researches aim at understanding how evolutionary and ecological processes have shaped the current fish diversity in the Neotropics.
To gain some insights into this very challenging topic, several lines of reseach are pursued in collaboration with colleagues from Brazilian and Argentinean institutions, and from the Museum of Natural History of Geneva.
At the intra-specific level, we investigate the processes that shape population structures by applying approaches from ecological and population landscape genetics.
We study continental fish radiation by inferring the diversification history of the endemic and species-rich catfish genus Hypostomus across South America. By combining calibrated phylogenies, morphological and ecological ancestral traits reconstructions and historical biogeography, we aim at unraveling the processes underlying rapid diversification at the species level.
The roled played by paleoclimatic changes on Neotropical fish diversification is a central question that we tackle by inferring and analyzing the evolutionary history of selected freshwater fish taxa that we collected in several isolated tributaries as well as in the main course of rivers. Our working hypothesis is that during the driest periods of the Plio-Pleistocene, the water flow of rivers may have been reduced up to the point of disconnecting some tributaries from the rest of the basin, whereas a reconnection was achieved during the next humid period. This past fragmentation-reconnection dynamic may explain part of the fish diversity observed today.
Adaptive Evolution
We also conduct comparative transcriptomics studies to examine the role played by adaptive evolution in traits that may explain species survival and diversification in the Neotropical region, such as resistance to hypoxia and to warm water temperatures.
An exoskeleton covered with teeth
Most vertebrates have teeth in their mouth to process their food. However, in a very curious groups of Neotropical catfishes, the Loricariidae, teeth can be found not only in the mouth, but also all over their bodies. These extra-oral teeth (denticles) are arranged on their body surface, including their fin rays, and are an integral part of an intricate exoskeletal system that also includes dermal bony plates. We hypothesize that this protective and spiny exoskeleton is a key determinant of the tremendous species diversity characterizing this group. We use developmental and genetic approaches to find the genes and gene expression regulators that allowed the formation of these skeletal and dental structures in such an unlikely place as the trunk.
Fundings :
- Swiss National Science Foundations (SNF)
- Institute of Genetics and Genomics of Geneva (iGE3)
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil
- Brazilian-Swiss joint Research Programme (BSJRP) grant, SNSF - EPFL
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
- Swiss bilateral science & technology cooperation program, Argentina, SNSF - EPFL
Interspecific hybridization: its impact on ecology, evolution and conservation
Natural hybridization has played an important role in the evolution of many plant and animal taxa. However, when hybridization is caused by anthropogenic factors, it may lead to serious consequences for parental species persistance. This is particularly true in rare or threatened species, because if the population size is too small, their genotype may be gradually replaced by that of hybrids. This research project aims at modeling interspecific hybridization in order to evaluate its impact on the demography, ecology, and evolution of the parental species. We highlight the potential effects of exotic invasive species and habitat modifications, in particular due to global climate change. Our models offer a tool to estimate under which conditions the increasing rate of hybridization can represent a threat to species persistance and to provide guidance when choosing alternative conservation strategies.
Funding :
- Center for Advanced Modeling Science (CADMOS), Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3)
Methodology in Molecular Phylogenetics
The swift advance of gene sequencing technologies has produced a flood of data that we can use to infer evolutionary relationships among organisms. However, the staggering pace at which these data are produced surpasses the pace at which methods for their analysis are developed. This often leaves us using tools that are not fit for analyzing all of our data. In this project, we are interested in developing algorithms of data filtering that tailor these large-scale datasets to better fit the limitations of the methods we have available today. In this way, the information that is extracted from these data is clear, and the effect of noise and of misinterpreted signals is reduced.
Funding :
- Swiss National Science Foundations (SNF)
- Institute of Genetics and Genomics of Geneva (iGE3)
How can population size and structure influence genome evolution?
In this project we address the issue of how genome evolution is affected by micro-evolutionary factors such as population structure and effective population size. We use empirical observations and data taken from the literature to draw hypotheses. We then examine our hypotheses using population simulation approaches.
A fast method to identify genes under positive selection: DWin and PSGfinder
Genes evolving under positive Darwinian selection are expected to be involved in the evolution of adaptive traits. With the rapid increase of genomic data, it becomes possible to build the catalogue of positively selected genes (PSG) in a species, but current methods for identifying PSGs are too conservative and rather slow. This project is aimed at developing a fast and accurate method (DWin) to screen a collection of protein-coding genes belonging to a pair or a triplet of related species in search of PSGs. Our method is implemented in the software PSGfinder, which is being tested on well-characterized sets of genes that have experienced episodes of positive selection along the evolution of cetaceans. The PSGfinder software was the training work of a former master student, Joël Tuberosa, and it was partly tested in Weber et al. (2017).
The current reference for the PSGfinder software is: Tuberosa J., Juan I. Montoya-Burgos J. I. 2017. PSGfinder: fast identification of genes under divergent positive selection using the dynamic windows method. bioRxiv 193722; doi: https://doi.org/10.1101/193722.
Assembling the genome of a Loricariidae
With about 900 valid species, the Loricariidae is the most diversified freshwater fish family endemic to the Neotropics. Taking advantage of next-generation DNA sequencing technologies and our laboratory’s expertise in bioinformatics, we are now sequencing and assembling the genome of one representative, Ancistrus dolichopterus. This annotated new genome will serve to investigate the intrinsic determinants of the tremendous species diversity found in this family.