Bioinformatics and Biomathematics of Biodiversity

The term "biodiversity", first coined in the 1980s, simply refers to the diversity of the living world. Often counted in terms of the number of species, biodiversity is not simply a matter of numbers, and the term must be taken in a very broad sense: genetic diversity within a population, diversity of interactions (between plants and herbivores, for example), diversity of functions (assimilation of nitrogen, use of water, etc.) within ecosystems, and so on. The study of biodiversity therefore covers the whole of scientific ecology, but the term, as J. Clavel notes, has certainly " gave scientific legitimacy to nature conservation in the political arena ". If we talk a lot about biodiversity, it's largely due to the awareness of its erosion under the effect of human activities and the consequences of this erosion.

Interactions of all kinds between man and biodiversity make biodiversity a hot topic: a topical issue for the general public, for example with regard to the depletion of bees and other pollinating insects; a subject of fundamental research for scientists, who are exploring the mechanisms of diversification that have taken us in almost 4 billion years from the first bacteria to giant organisms such as redwoods and whales; a subject of attention for managers and decision-makers of all kinds, for example when negotiating fishing quotas or developing transport infrastructures.

Our research contributes to shedding light on the issues mentioned above, in a continuum that ranges from the most fundamental to the most finalized, and which largely calls on ecological engineering in the broadest sense of the term. Like all other scientific fields, the study of biodiversity has become highly quantitative with the advent of computers: from automated data collection to modeling, via multiple types of statistical analysis.

The aim of this article is therefore to provide engineers with an overview of the main fields in which bioinformatics and biomathematics can be applied to the study of biodiversity. After a few examples of typical applied questions in the study of biodiversity, the presentation will follow the levels of organization of living organisms: populations (interacting individuals of the same species), communities (groups of interacting species), then ecosystems, i.e. portions of space including living beings and physical elements and subject to flows of matter and energy. We conclude with a discussion of the role of mathematics and computer science in a number of cross-disciplinary themes. The bibliography freely mixes reference texts and illustrative examples, but can serve as a starting point for more in-depth investigations.