title: Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution.
abstract: To demonstrate that a given change in the environment has contributed to the emergence of a given genotypic and phenotypic shift during the course of evolution, one should ask to what extent such shifts would have occurred without environmental change. Of course, such tests are rarely practical but phenotypic novelties can still be correlated to genomic shifts in response to environmental changes if enough information is available. We surveyed and re-evaluated the published data in order to estimate the role of environmental changes on the course of species and genomic evolution. Only a few published examples clearly demonstrate a causal link between a given environmental change and the fixation of a genomic variant resulting in functional modification (gain, loss or alteration of function). Many others suggested a link between a given phenotypic shift and a given environmental change but failed to identify the underlying genomic determinant(s) and/or the associated functional consequence(s). The proportion of genotypic and phenotypic variation that is fixed concomitantly with environmental changes is often considered adaptive and hence, the result of positive selection, even though alternative causes, such as genetic drift, are rarely investigated. Therefore, the second aim herein is to review evidence for the mechanisms leading to fixation.
authors.affiliation: Phylogenomics Laboratory, EA 3781 Evolution Biologique Université de Provence, Case 19, Pl. V. Hugo, 13331 Marseille Cedex 03, France. Anthony.Levasseur@up.univ-mrs.fr
authors.forename: Anthony
authors.initials: A
authors.lastname: Levasseur
authors.forename: Ludovic
authors.initials: L
authors.lastname: Orlando
authors.forename: Xavier
authors.initials: X
authors.lastname: Bailly
authors.forename: Michel C
authors.initials: MC
authors.lastname: Milinkovitch
authors.forename: Etienne G J
authors.initials: EG
authors.lastname: Danchin
authors.forename: Pierre
authors.initials: P
authors.lastname: Pontarotti
mesh_terms: D000222:Adaptation, Physiological; D000818:Animals; D004777:Environment; D019143:Evolution, Molecular; D005838:Genotype; D010641:Phenotype; D012641:Selection, Genetic