Evolutionary processes and evolutionary noise at the molecular level

Summary On account, notably, of a competition between different component functions for individual sites in polypeptide chains, each protein molecule represents a functional compromise, with some functions optimized, but the overall state of the molecule –suboptimal–. The proposal is made that the selection coefficient relating to a protein molecule under given conditions can in principle be broken down into partial selection coefficients relevant to the different functions that the molecule carries out. At generalfunction sites, each fixation improves some function, while others deteriorate, at first nonsignificantly, and the overall adaptive state of the molecule fluctuates around its maximum. A selective mechanism is described whereby kaleidoscopic changes in primary structure at variable sites are indefinitely promoted, independently of any environmental changes and with the molecule remaining close to a state of maximal overall adaptation. The paradoxical aspect of this proposal is analyzed. The implication of specific functions in substitutions at general-function sites is noted. Further, it is shown that a certain category of changes in the internal environment of the organism can be integrated into the constantenvironment model for selection. Genetic sufficiency is considered a notion more adequate than genetic optimality for describing biological fitness and for providing a basis for the present model. On this basis selection occurs without genetic load. Multipolymorphism is one of the consequences. Several lines of evidence, in particular observations on polymorphism in deep sea organisms, seem to support the model. It is pointed out that it provides a theoretical foundation for a molecular evolutionary clock. The theoretical constancy of the clock depends on the constancy of functional density. The question of the evolution of functional density is examined. Comparisons of observed substitution frequencies with values expected on a random basis are rejected as a measure of the contribution to evolution of nondetermination. They are considered to reflect a hierarchy in the resistance of the molecules to different amino acid residues as substituents. A limited component of –true– randomness, again accompanied by selection, is on the other hand provided by the model. Most amino acid substitutions are considered evolutionary noise, even though noise compatible with selection. It is proposed that evolutionarily significant substitutions may be identified by monitoring changes in functional density and weighted functional density.Directeur de Recherche at Centre National de la Recherche Scientifique, Paris.     

Polychaete/amphipod ratios: An approach to validating simple benthic indicators

Among the macro-invertebrates used for the assessment of soft-bottom communities, most polychaetes are classified as tolerant/opportunistic to pollution while amphipods are considered as sensitive. These taxa have been used in several ecological indices, such as the simple abundance ratio between Polychaeta and Amphipoda or the Benthic Opportunist Annelids Amphipods (BO2A) index, to assess the Ecological Quality Status -EcoQs- of soft-bottom communities. In terms of Taxonomic Sufficiency (TS), the polychaete/amphipod ratio (i.e. at the level of the class/order) has been proved to be effective in identifying major changes in benthic communities following disturbances. However, an underlying issue is to assess the acceptable TS limit value needed to state accurately the quality of the benthic environment. We tested three indices using 18 series of observations carried out in five north-eastern Atlantic and Mediterranean zones impacted by oil spills, oil and gas production, brine and urban sewage, harbours and aquaculture farms within impacted and control areas. Similar results to BO2A were obtained when limiting the TS at the level of Polychaete opportunistic families, which required a lower degree of taxonomic expertise, and classifying all amphipods as sensitive taxa. In such a way that the EcoQs given by the BPOFA (Benthic Polychaete Opportunistic Families Amphipods) was very similar to those given by the BO2A (Benthic Opportunistic Annelids Amphipods).