Figure Legends
Figure 1. (A) Admixture Plot assessing the relatedness of Bermudian chickens with a variety of different domestic breeds and Red Junglefowl. Graph shown for k=6. (B) PCA plot of the same data (PC1 vs PC2) showing the relatedness between the feral, domestic and RJF sub-populations. (C) PCA plot of the same data excluding the layer populations (PC1 vs PC2). (D) PCA plot of the same data (PC3 vs PC4)
Figure 2. Chromopainter analysis for sweeps origins. A) Chromopainter analysis showing Hawaiian (left side) and Bermudian (right side) populations at the three shared feral sweeps locations sweeps (y-axis, labelled chr1_17340927, chr1_32751411, and chr2_78310987). For the two feral populations, domestic (DOM, grey bar) and wild RJF (RJF, red bar) birds were used as donors, with the size of the red and grey bars indicating the number of chunks that were similar from each donor. Therefore, the larger the bar, the greater the donor similarity to the feral population. B) This is the same analysis as (A), however the donor populations have now been further subdivided into sub-populations (Brown Layer, White Layer, Broiler A, Broiler B, Red Junglefowl Thailand, Red Junglefowl India). (C) Chromopainter analysis of Bermudian sweeps, with this analysis also including Hawaii as a donor population, as well as domestic and RJF birds. The same y-axis notation as in (A) is used. (D) The same analysis type as in (C) however donor populations are once again subdivided as in (B).
SUPPLEMENTARY TABLE LEGENDS
Supplementary Table 1. All Extended Haplotype Homozygosity sweeps identified in Bermudian and Kauaian samples. Population, chromosome, start and end coordinates are given (in bp).
Supplementary Table 2. Selective Sweep regions identified by Extended Haplotype Homozygosity mapping in both Bermuda and Hawaii populations. The chromosome, region start and end, gene type (protein coding, lncRNA, etc), and any gene IDs are given, as well as the number of regions identified (region nr).
Supplementary Table 3. Overlaps between sweeps in domestic and feral populations. Technique used to detect the sweep, pairwise population, and genomic coordinates (in bp) are given.
Supplementary Table 4. All Composite Likelihood Ratio sweeps detected in Bermudian and Kauain samples. Population, chromosome, start and end coordinates are given (in bp).
Supplementary Table 5. Selective Sweep regions identified by Composite Likelihood Ratio mapping in both Bermuda and Hawaii populations. The chromosome, region start and end, gene type (protein coding, lncRNA, etc), and any gene IDs are given, as well as the number of regions identified (region nr).
Supplementary Table 6. Selective Sweep regions identified by Tajima’sD mapping in both Bermuda and Hawaii populations. The population, chromosome, and region start and end are given.
Supplementary Table 7. Selective Sweep regions identified by Tajima’s D in both Bermuda and Hawaii populations. The chromosome, region start and end, gene type (protein coding, lncRNA, etc), and any gene IDs are given, as well as the number of regions identified (region nr).
Supplementary Table 8. Selective Sweep regions identified by at least two sweep detection techniques in the Bermuda population. The chromosome, region start and end, gene type (protein coding, lncRNA, etc), and any gene IDs are given, as well as the number of regions identified (region nr).
Supplementary Table 9. Selective Sweep regions identified by at least two sweep detection techniques in the Hawaii (Kauai) population. The chromosome, region start and end, gene type (protein coding, lncRNA, etc), and any gene IDs are given, as well as the number of regions identified (region nr).
Supplementary Table 10. Overview of the domestic, wild and feral samples used and links to their repository website.
SUPPLEMENTARY FIGURE LEGENDS
Supplementary Figure 1. Admixture plots for K=2,3,4,5,7,8,9,10 showing number of founder populations for domestic, wild and feral chicken populations used in this study.
Supplementary Figure 2. Splitstree plot showing the relationships between feral, domestic and Red Junglefowl samples.
Supplementary Figure 3. Overview of selective sweeps detected by Tajima’s D, Composite Likelihood Ratio (CLR) and Extended Haplotype Homozygosity (EHH) mapping, as well as the domestication/ improvement selective sweeps identified by Qanbari et al. 2019. Each chromosome where a selective sweep was present is presented in its own panel, with location in Megabases (Mb) on the x-axis of each, with the results from the four different selective sweep mapping methods presented on the y-axis.