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.