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 appeared or substantially increased in frequency during passage of the virus in the embryonated eggs in which they are cultured—this hypothesis can account at most for 59 (7.9%) of the 745 non-silent substitutions observed; (2) sampling bias, induced by the preference of investigators for sequencing antigenetically dissimilar strains for the purpose of identifying new variants that might call for updating the vaccine—which 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 vaccine development, and that host-mediated mutations should be removed before making decisions about influenza evolution.
Bruce R. Levin and Carl T. Bergstrom (“Bacteria are Different: Observations, Interpretations, Speculations, and Opinions about the Mechanisms of Adaptive Evolution in Prokaryotes, ” 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 homologous recombination, which is low in bacteria but high in sexual eukaryotes; 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.