|Principal Component Analysis (PCA)||ADMIXTURE Analysis||Runs of Homozygosity (ROH)|
Principal Component Analysis (PCA)
Genetic affiliation and population structure are shown by PCA plots for three datasets. Each plot indicates one sample. The dataset of “Species of Gallus include all 1,986 samples. After removing Ceylon Jungle Fowl, Green Jungle Fowl, and Grey Jungle Fowl samples, the dataset of “Gallus gallus” refers to a total of 1,961 samples belonging to domestic chicken and Red Jungle Fowl. After removing G. g. bankiva, G. g. jabouillei, and some G. g. gallus individuals as outliers to other Red Jungle Fowl, the dataset of “Geographic region” contains 1,915 samples from domestic chicken and Red Jungle Fowl.
The inference of populations and individual ancestries is revealed by ADMIXTURE clustering for all 1986 samples. Length of each colored bar represents the proportion of proposed ancestry in the sample. Choosing “Region”, ”Category”, and/or “Purpose” to show different target population(s). The number of proposed ancestries is determined by “which K”.
Runs of Homozygosity (ROH)
Runs of homozygosity (ROH) indicates long tracts of homozygous genotypes inherited from identical haplotypes of a common ancestor. Larger populations have fewer, shorter ROH, whereas isolated or bottlenecked populations have more, somewhat longer ROH. Admixture brings the fewest ROH, whereas inbreeding causes long ROH. The level of ROH is measured by number and length. Choosing “which ROH” to show ROH patterns under “region” or “species” level. The length of ROH can be defined in “ROH range”.