Reticulate evolution is favoured in influenza niche switching.

Reticulate evolution is thought to accelerate the process of evolution beyond simple genetic drift and selection, helping to rapidly generate novel hybrids with combinations of adaptive traits. However, the long-standing dogma that reticulate evolutionary processes are likewise advantageous for switching ecological niches, as in microbial pathogen host switch events, has not been explicitly tested. We use data from the influenza genome sequencing project and a phylogenetic heuristic approach to show that reassortment, a reticulate evolutionary mechanism, predominates over mutational drift in transmission between different host species. Moreover, as host evolutionary distance increases, reassortment is increasingly favored. We conclude that the greater the quantitative difference between ecological niches, the greater the importance of reticulate evolutionary processes in overcoming niche barriers.\n\nSignificance StatementAre the processes that result in the exchange of genes between microbes quantitatively advantageous for those microbes when switching between ecological niches? To address this question, we consider the influenza A virus as a model microbe, with its ability to infect multiple host species (ecological niches) and undergo reassortment (exchange genes) with one another. Through our analysis of sequence data from the Influenza Research Database and the Barcode of Life Database, we find that the greater the quantitative difference between influenza hosts, the greater the proportion of reassortment events were found. More broadly, for microbes, we infer that reticulate evolutionary processes should be quantitatively favoured when switching between ecological niches.