Polymerase evolution and organism evolution.

The continuing exploration of the structure-function relationships of polymerases and the use of polymerases as phylogenetic tools complement each other, as seen in the literature for the past year. DNA-dependent RNA-polymerase gene sequences, in particular, have been used both to define functional domains in the protein encoded and recently to explore fundamental questions in evolution.     

Experimental evolution: experimental evolution and evolvability

The suggestion that there are characteristics of living organisms that have evolved because they increase the rate of evolution is controversial and difficult to study. In this review, we examine the role that experimental evolution might play in resolving this issue. We focus on three areas in which experimental evolution has been used previously to examine questions of evolvability; the evolution of mutational supply, the evolution of genetic exchange and the evolution of genetic architecture. In each case, we summarize what studies of experimental evolution have told us so far and speculate on where progress might be made in the future. We show that, while experimental evolution has helped us to begin to understand the evolutionary dynamics of traits that affect evolvability, many interesting questions remain to be answered.     

Genome evolution and the evolution of exon-shuffling--a review

Recent studies on the genomes of protists, plants, fungi and animals confirm that the increase in genome size and gene number in different eukaryotic lineages is paralleled by a general decrease in genome compactness and an increase in the number and size of introns. It may thus be predicted that exon-shuffling has become increasingly significant with the evolution of larger, less compact genomes. To test the validity of this prediction, we have analyzed the evolutionary distribution of modular proteins that have clearly evolved by intronic recombination. The results of this analysis indicate that modular multidomain proteins produced by exon-shuffling are restricted in their evolutionary distribution. Although such proteins are present in all major groups of metazoa from sponges to chordates, there is practically no evidence for the presence of related modular proteins in other groups of eukaryotes. The biological significance of this difference in the composition of the proteomes of animals, fungi, plants and protists is best appreciated when these modular proteins are classified with respect to their biological function. The majority of these proteins can be assigned to functional categories that are inextricably linked to multicellularity of animals, and are of absolute importance in permitting animals to function in an integrated fashion: constituents of the extracellular matrix, proteases involved in tissue remodelling processes, various proteins of body fluids, membrane-associated proteins mediating cell-cell and cell-matrix interactions, membrane associated receptor proteins regulating cell cell communications, etc. Although some basic types of modular proteins seem to be shared by all major groups of metazoa, there are also groups of modular proteins that appear to be restricted to certain evolutionary lineages. In summary, the results suggest that exon-shuffling acquired major significance at the time of metazoan radiation. It is interesting to note that the rise of exon-shuffling coincides with a spectacular burst of evolutionary creativity: the Big Bang of metazoan radiation. It seems probable that modular protein evolution by exon-shuffling has contributed significantly to this accelerated evolution of metazoa, since it facilitated the rapid construction of multidomain extracellular and cell surface proteins that are indispensable for multicellularity.     

Biopolymers and evolution

Biopolymers are usually studied being extracted from the whole system of a cell or of an organism. Some important features are lost during such a procedure. It is necessary to take into account the behavior of proteins and nucleic acids in metabolic networks and to investigate their evolution. The substitutions of amino-acids metabolic networks residues are biologically possible in the polypeptides and proteins if they do not influence their spatial structure and function. The correlations of the primary structure with these properties are degenerate. The protein can be treated as "an edited statistical copolymer" (Ptitsyn). In the process of "edition" an important role is played by the ions of transient metals. Nucleic acids possess similar properties. It can be shown that the deleterious mutations of proteins can be compensated by the changes of their amount, spatial and temporal characteristics of the synthesis. Not only the structure of the protein is important but also the exact answers of the questions: how much, when and where? The contemporary theory of evolution unites phylogeny and onthogeny. The directionality of evolution is determined both by natural selection and by the already existing structure of an organism. Hence many characters are not adaptive. This is valid also for the molecular level of the structure. Thus three independent groups of facts and suggestions are presented, which confirm the neutral theory of evolution (Kimura) and elucidate its physical meaning. The molecular evolution does not coincide with the biological evolution.     

Chaos and evolution

There is growing interest in applying nonlinear methods to evolutionary biology. With good reason: the living world is full of nonlinearities, responsible for steady states, regular oscillations, and chaos in biological systems. Evolutionists may find nonlinear dynamics important in studying short-term dynamics of changes in genotype frequency, and in understanding selection and its constraints. More speculatively, dynamical systems theory may be important because nonlinear fluctuations in some traits may sometimes be favored by selection, and because some long-run patterns of evolutionary change could be described using these methods.     

Extinctive evolution: Extinctive and competitive evolution combine into a unified model of evolution

Individual extinctions of abundant and widespread species of marine Protista are abrupt and precede the appearance of new species. New species evolve gradually in marginal marine environments and spread only if a suitable ecological domain is available or if such a domain is made available by the disappearance of its occupant species. Competitive evolution, with its classic processes of genetic drift, adaptation, competition, and survival of the fittest, occurs mainly in marginal environments (and possibly within broadly distributed but rare species). Extinctive evolution, on the other hand, with its processes of sudden extinctions and sudden appearances, absence of competition, absence of “missing links”, and frequent survival of the misfit or the indifferently fit is prevalent in broader environments, and more generally applicable to the paleontological record. The modern biosphere is not necessarily better adapted than its predecessors. Global mass extinction affecting different taxa across a broad spectrum of environments is caused by extraordinary environmental disturbances. A major ecosphere is vacated, which is immediately occupied by surviving misfits. These are replaced, through competitive evolution, by a rapid succession of increasingly better adapted species that can be classified into different genera and higher taxa (“macroevolution”). Equilibrium is largely re-established within a few million years. Competitive and extinctive evolution combine into a unified model of evolution.     

Paleodemography and evolution

Data on porotic hyperostosis (usually from thalassemia or sicklemia) and on morphology as related to differential survival and fertility in Early Neolithic Nea Nikomedeia (N over 90) and Middle Bronze Age Lerna (N = 234) show (a) the importance of disease, mainly falciparum malaria, in determining fertility, (b) the irregular fit between prediction from fertile family groups and observed prehistoric microevolutionary change in Greece, (c) the probable effects of nutrition and disease.