Detection of selection by calculating nucleotide diversity ratio (pi) pi wild/pi cultivated

Question

[Hann]

Hello everyone,

I've read a couple of plants genomics papers they use nucleotide diversity (π) ratio as ( π wild population/π cultivated population) with a sliding window to detect selection.

I know that diversity is affected by selection and of course many other processes, and that populations with lower nucleotide diversity are most likely under selection

I was reading a lot to understand why exactly ((( π wild/π cultivated ))) didn't really find an explanation of what's the reason for using wild population.

Thanks, :)

[microfuge]

Diversity is is also strongly affected by bottleneck caused due to domestication. Typically a small founder individuals/population is selected for domestication and gene flow and from population is reduced in the domesticated ones. Domestication causes inbreeding and in plants typically so called lines are maintained. The diversity reduction by such processes tends to be genomewide but selection will cause diversity loss around the selected variant as it increases in frequency rapidly taking the linked variants along. The diversity loss due to domestication and selection in the same region will tend to be stronger. So the ratio of both pi values along the windows gives a sense of diversity loss in that window/region and the outliers might indicate selection as the diversity loss is even stronger than the background. As always there are multiple factors in play which includes recombination.

Answer 1

[Hann]

Perfect! Thank you very much for the explanation =)