DNA reassociation kinetics and diversity indices: richness is not rich enough

Authors

  • Bart Haegeman,

  • Dimitri Vanpeteghem,

  • Jean-Jacques Godon,

  • Jérôme Hamelin


B. Haegeman (bart.haegeman@inria.fr), D. Vanpeteghem, J.-J. Godon and J. Hamelin, INRA, UR050, Laboratory of Environmental Biotechnology, Avenue des Etangs, FR-11100 Narbonne, France. BH also at: INRA-INRIA MERE research team, UMR Systems Analysis and Biometrics, 2 place Pierre Viala, FR-34060 Montpellier, France.

Abstract

DNA reassociation kinetics, also known as Cot curves, were recently used by Gans and co-workers to estimate the number of bacterial species present in soil samples. By reanalysing the mathematical model we show that rather than the number of species, Simpson and Shannon diversity indices are encoded in the experimental data. Our main tool to establish this result are the so-called Rényi diversities, closely related to Hill numbers, illustrating the power of these concepts in interpreting ecological data. We argue that the huge diversity encountered in microbial ecology can be quantified more informatively by diversity indices than by number of species.

Ancillary