Feral Chicken Ancestry
An Admixture analysis was used to compare the two feral populations with two Red Junglefowl populations (one collected from the wild, the other from a zoo population), two broiler populations, and two layer populations (all from Qanbari et al. 2019). This analysis found that these populations showed the most support for six founder populations (CV-error n=6, 0.79268, next lowest scores were n=5 Cve=0.79773, n=7 Cve=0.79791, n=8 Cve=0.79800, n=4 Cve=0.80401). The feral chickens clustered with one another, as did the Red Junglefowl populations (though some White Layer introgression appeared in the Indian Red Junglefowl population). The two broiler populations appeared to have different origins, as did the White and Brown layer populations (see Figure 1). Focusing solely on the two feral populations, the Bermudian population had more introgression from Brown layers and Broilers from population A, whilst the Kauai feral population had more introgression from the White layer population. All other Admixture plots are shown in Supplementary Figure 1.
A PCA plot of the data displays a similar pattern to the Admixture results (see Figure 1B). Initially, the two Layer populations were both related and showed pronounced divergence to the other analyzed breeds (most likely due to being the most intensively selected of all the modern domesticated breeds). When these two populations were removed to better visualize the remaining population structure (see Figure 1C), feral, broiler and Red Junglefowl all clustered by themselves with their respective population pairs. A similar pattern was observed when comparing Principal Component 3 with Principal Component 4 (Figure 1D).
As a further analysis, we expressed the shared chunk count matrix from Chromopainter as a dissimilarity matrix by subtracting each element from the maximum shared chunk count using the Splitstree v4 package (Huson and Bryant 2005). This allowed us to again visualize the relationships between the feral, wild and domestic populations (see Supplementary Figure 2). Once again, the two feral populations clustered adjacent to one another, whilst the other domestic and wild sub-populations were all distinct from one another.