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Recombination can be an important evolutionary force for RNA viruses, but the rate of recombination varies greatly between different RNA viruses. In this Analysis article, Simon-Loriere and Holmes describe the mechanisms of recombination for RNA viruses and the role of these mechanisms in viral evolution.
Horizontal gene transfer introduces into an organism genes that were not vertically transmitted from the parent organism, and therefore has the potential to interfere with phylogenetic analyses. In this Analysis article, Andam and Gogarten describe homeoalleles (alleles in bacteria and archaea that encode proteins with similar function but that have different phylogenetic origins) and their effect on phylogenetic analyses.
