Fig. 2

Population genetics and LD decay. a NJ tree generated using polymorphisms detected in the 29 individual chickens. The scale bar represents the evolutionary distances measured by p-distance. Each of the 9 breeds has been assigned a distinct color. b Three-way PCA plots based on the 29 chickens. Symbol colors indicate breed (key on right). c Genetic structure of samples from 29 individuals for K groups using the ADMIXTURE program. K is the number of presumed ancestral groups, which was varied in the analysis from 2 to 10. The optimal K value was obtained with the least CV error value. d Decay of LD for XGF, YVC, RJF, TBC and XBC chickens measured by R²