Viruses and the Evolution of Life

All biological systems, including viruses, are essentially systems that store, copy, and express information. This chapter presents some of the insights of simulated evolution and attempts to evaluate the relevance of the simulations to extant biological systems and processes that we can now observe. The study of chemical replicators, attempts to create models of catalysis from which prebiotic characteristics can be determined. The parasites of parasitic replicators would correspond to the defective viruses that are observed for most types of viruses. Defective viruses are thus exactly the parasitic replicators of a functional virus, itself a parasitic replicator. These parasites of parasites are expected to have existed even under prebiotic conditions. In addition, computer-based modeling of replicator evolution also suggests a role for the parasitic replicators as well as the parasites of parasites. The temporal component for persistent virus selection may be even more extended than for lambda. Clearly, models must first develop more formal ways to define the issues of persistence before they can provide useful insights into the successful life strategies of a persistent virus.

The evolution of the eukaryotic nucleus and the eukaryotic cell was the largest discontinuity in the evolution of all life. This chapter presents the possible role of viruses in acquisition of the nucleus, as well as other evolutionary discontinuities. As large DNA virus families have clear links to both prokaryotes and eukaryotes, they could be of central importance in the evolution of eukaryotes, although it is clear that extant viruses may also have developed and diverged after the nucleus was formed. The pore structures of the eukaryotic nucleus pose another significant dilemma for the possible prokaryotic origin of the nucleus. The author discusses the dilemma from the perspective of a putative viral origin. The viruses that are now commonly found in unicellular eukaryotes such as microalgae are of special interest in the evolution of eukaryotes because they may shed light on the relationships of large DNA viruses to the eukaryotic host and its evolution. Paramecium bursaria Chlorella virus 1 (PBCV-1) is the prototype for the phycodnavirus family, which includes chlorella viruses. In addition, photosynthetic organisms, such as cyanobacteria and Chlorella green algae, undergo photoinactivation of photosynthesis. Numerous other PBCV-1 genes also show a related pattern of similarity to eukaryotic genes and to viruses of eukaryotes and prokaryotes, but not to prokaryotic cellular genes. Overall, the viruses that infect algae appear to have most of the characteristics that would be needed to span the prokaryotic and eukaryotic kingdoms.

This chapter explores the virology and host evolution of animals which have evolved from Fungi or depended on Fungi for their evolution. It focuses on the emergence of early animals and their viruses. Furthermore, some of the characteristic virus-tissue associations known for mammals are seen for aquatic animals and their viruses. However, it often appears that there are some specific examples in which specific viruses are able to persist and inapparently infect younger forms of specific hosts. In these cases, the persistently infected hosts often function as reservoirs for viruses that cause disease in other, sometimes related species. The evolutionary reentry of some viruses (reoviruses, parvoviruses, and birnaviruses) which were present in ancestral lineages (such as Fungi) but had been absent from less distant basal metazoan predecessors (worms and basal deuterostomes) are discussed. The currently accepted view concerning the function of the adaptive immune response is that a surprisingly complex system has evolved to control parasitic invasion, especially by viruses.

As vertebrates emerged from the oceans to become land-dwelling animals, numerous basic changes in their physiology and organ structures were necessary. This chapter examines the roles that persistent viruses and especially endogenous retroviruses (ERVs) have had in the evolution of terrestrial vertebrates. The mammalian paramyxovirus lineage may trace its evolutionary origins from reptiles, through avians, to mammals, and during the course of this adaptation the reptilian and avian viruses appear to have gained the ability to establish species-specific persistent infections. Although monotreme-like mammals are evolutionarily old (predating the dinosaurs), little is known about the viruses or genomes of these early mammalian predecessors. The majority of small DNA viruses (adenoviruses, papillo-maviruses, polyomaviruses, and TT viruses) have persistent life strategies, are host specific, and are phylogenetically congruent with the evolution of their hosts. The epidemiological concept of a reservoir species has been used for many decades to help explain the recurrence of viral disease after it has apparently been eliminated from a population or habitat. With the completion of the sequencing of the human genome, one can now consider what types of genetic changes were associated with this recent stage in human evolution. The successful genomes that have colonized host cells might be expected to persist in the ecosystem and contribute this vast genetic creativity to the tree of life.