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.