PT  - JOURNAL ARTICLE
AU  - Kristen K. Irwin
AU  - Stefan Laurent
AU  - Sebastian Matuszewski
AU  - Séverine Vuilleumier
AU  - Louise Ormond
AU  - Hyunjin Shim
AU  - Claudia Bank
AU  - Jeffrey D. Jensen
TI  - On the importance of skewed offspring distributions and background selection in viral population genetics
AID  - 10.1101/048975
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 048975
4099  - http://biorxiv.org/content/early/2016/04/15/048975.short
4100  - http://biorxiv.org/content/early/2016/04/15/048975.full
AB  - Many features of viral populations make them excellent candidates for population genetic study, including a very high rate of mutation, high levels of nucleotide diversity, exceptionally large census population sizes, and frequent positive selection. However, these attributes also mean that special care must be taken in population genetic inference. For example, highly skewed offspring distributions, frequent and severe population bottleneck events associated with infection and compartmentalization, and strong purifying selection all affect the distribution of genetic variation but are often not taken in to account. Here, we draw particular attention to multiple-merger coalescent events and background selection, discuss potential mis-inference associated with these processes, and highlight potential avenues for better incorporating them in to future population genetic analyses.