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Part II VIRAL AND BACTERIAL MODELS A ndrÃ©s Moya and colleagues point out advantages offered by RNA viruses for the experimental investigation of evolution (âThe Evo- lution of RNA Viruses: A Population Genetics View,â Chapter 5); notably, the phenotypic features (âphenotypic spaceâ) map fairly directly onto the âgenetic space.â In other organisms, from bacteria to humans, the expression of the genetic make up in the phenotype is mediated, to a lesser or greater degree, but always importantly, by complex interactions between genes, between cells, and with the environment. These authorsâ model is the vesicular stomatitis virus (VSV), a rhabdovirus, containing 11.2 kb of RNA encoding five proteins. The authors grow different viral clones under variable demographic and environmental conditions, and measure the evolution of fitness in these clones by competition with a control clone. Fitness generally decreases through the serial viral trans- fers from culture to culture, particularly when bottlenecks associated with transfers are small. Fitness may, however, increase when the transmission rates are high, although the response varies from clone to clone. Moya et al. conclude with an examination of the advantages and disadvantages of traditional population genetics theory for the description of viral evolu- tion vis-Ã -vis the quasi-species concept, which proposes that the target of natural selection is not a single genotype but rather a cloud of mutants distributed around a most frequent one, the âmaster sequence.â Robin M. Bush and colleagues (âEffects of Passage History and Sam- pling Bias on Phylogenetic Reconstruction of Human Influenza A Evolu- tion,â Chapter 6) had noticed in their earlier reconstruction of the phylog- 59
60 / AndrÃ©s Moya et al. eny of influenza A virus, based on the hemagglutinin gene, an excess of non-silent nucleotide substitutions in the terminal branches of the tree. They explore two likely hypotheses to account for this excess: (1) that these nucleotide replacements are host-mediated mutations that have ap- peared or substantially increased in frequency during passage of the vi- rus in the embryonated eggs in which they are culturedâthis hypothesis can account at most for 59 (7.9%) of the 745 non-silent substitutions ob- served; (2) sampling bias, induced by the preference of investigators for sequencing antigenetically dissimilar strains for the purpose of identify- ing new variants that might call for updating the vaccineâwhich seems to be the main factor accounting for the replacement excess in terminal branches. The authors point out that the matter is of consequence in vac- cine development, and that host-mediated mutations should be removed before making decisions about influenza evolution. Bruce R. Levin and Carl T. Bergstrom (âBacteria are Different: Obser- vations, Interpretations, Speculations, and Opinions about the Mecha- nisms of Adaptive Evolution in Prokaryotes,â Chapter 7) note that adaptive evolution in bacteria compared to plants and animals is different in three respects. The two most important factors are (1) the frequency of homolo- gous recombination, which is low in bacteria but high in sexual eukary- otes; and (2) the phylogenetic range of gene exchange, which is broad in bacteria but narrow (typically, intraspecific) in eukaryotes. A third factor is that the role of viruses, plasmids, and other infectiously transmitted genetic elements is nontrivial in the adaptive evolution of bacteria, while it is negligible in eukaryotes.