On the importance of skewed offspring distributions and background selection in viral population genetics

21 22 Many features of viral populations make them excellent candidates for 23 population genetic study, including a very high rate of mutation, high levels of 24 nucleotide diversity, exceptionally large census population sizes, and frequent 25 positive selection. However, these attributes also mean that special care must 26 be taken in population genetic inference. For example, highly skewed 27 offspring distributions, frequent and severe population bottleneck events 28 associated with infection and compartmentalization, and strong purifying 29 selection all affect the distribution of genetic variation but are often not taken 30 in to account. Here, we draw particular attention to multiple-merger coalescent 31 events and background selection, discuss potential mis-inference associated 32 with these processes, and highlight potential avenues for better incorporating 33 them in to future population genetic analyses. 34