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Section: Application Domains
Molecular based systematics and taxonomy
Defining and recognizing myriads of species in biosphere has taken phenomenal energy over the past centuries and
remains a major goal of Natural History. It is an iconic paradigm in pattern recognition (clustering has coevolved with numerical taxonomy many decades ago).
Developments in evolution and molecular biology, as well as in data analysis, have over the past decades
enabled a profound revolution, where species can be delimited and recognized by data analysis of sequences.
We aim at proposing new tools, in the framework of E-science, which make possible (
One example of this project is about the diversity of trees in Amazonian forest, in collaboration with botanists in French Guiana. Protists (unicellular Eukaryots) are by far more diverse than plants, and far less known. Molecular exploration of Eukaryotes diversity is nowadays a standard in biodiversity studies. Data are available, through metagenomics, as an avalanche and make molecular diversity enter the domain of Big Data. Hence, an effort will be invested, in collaboration with other Inria teams (GenScale, HiePACS) for porting to HPC algorithms of pattern recognition and machine learning, or distance geometry, for these tools to be available as well in metagenomics. This will be developed first on diatoms (unicellular algae) in collaboration with INRA team at Thonon and University of Uppsala), on pathogens of tomato and grapewine, within an existing network, and on bacterial communities, in collaboration with University of Pau. For the latter, the studies will extend to correlations between molecular diversity and sets of traits and functions in the ecosystem.