title: Some considerations for analyzing biodiversity using integrative metagenomics and gene networks.
abstract: BACKGROUND
  Improving knowledge of biodiversity will benefit conservation biology, enhance bioremediation studies, and could lead to new medical treatments. However there is no standard approach to estimate and to compare the diversity of different environments, or to study its past, and possibly, future evolution.
  
  
  OBJECTIVE
  We argue that there are two conditions for significant progress in the identification and quantification of biodiversity. First, integrative metagenomic studies - aiming at the simultaneous examination (or even better at the integration) of observations about the elements, functions and evolutionary processes captured by the massive sequencing of multiple markers - should be preferred over DNA barcoding projects and over metagenomic projects based on a single marker. Second, such metagenomic data should be studied with novel inclusive network-based approaches, designed to draw inferences both on the many units and on the many processes present in the environments.
  
  
  METHODS
  We reached these conclusions through a comparison of the theoretical foundations of two molecular approaches seeking to assess biodiversity: metagenomics (mostly used on prokaryotes and protists) and DNA barcoding (mostly used on multicellular eukaryotes), and by pragmatic considerations of the issues caused by the 'species problem' in biodiversity studies.
  
  
  CONCLUSIONS
  Evolutionary gene networks reduce the risk of producing biodiversity estimates with limited explanatory power, biased either by unequal rates of LGT, or difficult to interpret due to (practical) problems caused by type I and type II grey zones. Moreover, these networks would easily accommodate additional (meta)transcriptomic and (meta)proteomic data.
authors.affiliation: UMR CNRS 7138 Systématique, Adaptation, Evolution, Université Pierre et Marie Curie, Paris, France.
authors.forename: Lucie
authors.initials: L
authors.lastname: Bittner
authors.forename: Sébastien
authors.initials: S
authors.lastname: Halary
authors.forename: Claude
authors.initials: C
authors.lastname: Payri
authors.forename: Corinne
authors.initials: C
authors.lastname: Cruaud
authors.forename: Bruno
authors.initials: B
authors.lastname: de Reviers
authors.forename: Philippe
authors.initials: P
authors.lastname: Lopez
authors.forename: Eric
authors.initials: E
authors.lastname: Bapteste
mesh_terms: D000818:Animals; D044822:Biodiversity; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D008962:Models, Theoretical