Consensus Feral Sweeps and Overlaps
For the feral populations, we considered that if a selective sweep was
detected by at least two selective sweep finding methods it represented
stronger evidence of a true selective sweep. Note that this may
sometimes not be the case, as any given detection technique may be
better tuned to detecting a specific sweep type that is ‘missed’ by
other methods. Nonetheless, we chose to minimalize false positives by
focusing on consensus selective sweeps (though individual selective
sweep types are also presented in the Supplementary Tables). In the case
of the Bermudian population, 59 regions were detected in such a manner
(Supplementary Table 8), whilst in the case of the Kauai population 106
selective sweep regions were detected (Supplementary Table 9). When we
check for overlaps between these two sets of selective sweep regions,
three are detected in both population samples (Table 1), with this being
a significant enrichment over the null distribution (permutation test, p
< 0.001). Of these, one selective sweep also overlapped with
the domestication sweeps identified by Qanbari et al (Qanbari, Rubin et
al. 2019)(see Table 1). An overview figure of the locations of selective
sweeps identified by the different methods is presented in Supplementary
Figure 3.
Selective sweeps origin
identification.
To identify the origin of the three shared Hawaiian and Bermudian feral
selective sweeps (i.e. are they domesticated haplotypes that have become
fixed vs. wild Red Junglefowl haplotypes) Chromopainter software was
used (Lawson, Hellenthal et al. 2012). This takes the feral genomes and
‘paints’ on the domesticated and wild haplotypes to ascertain which are
most likely to be the donor population of a given sweep haplotype. Two
separate layer and broiler populations were used as donors, as well as
two Red Junglefowl populations (from Thailand and India, respectively).
These were then used as donors for the Bermuda and Hawaii populations,
whilst an additional run with Bermuda was also performed, also including
Hawaii as an additional donor. In the case of the Bermudian feral
selective sweeps, domesticated haplotypes were the most likely donor
populations, with broilers and layers donating similar amounts for two
of the shared selective sweeps
(chr1@17.5Mb,
chr1@32.8Mb). In the case of the
third sweep (chr2@78.3Mb), the broiler donors were the strongest donor
for the Bermudian population. A similar pattern was also seen for the
Hawaiian population, though in this case the broiler population was the
largest donor for each selective sweep (see Figure 2 A-D). The degree of
donorship from Red Junglefowl alleles was broadly similar for the two
feral populations.
By further breaking down the domesticated populations into the
individual donor sub-populations, we once again see a similar pattern,
but also that it is often only one of the two candidate donor
sub-populations that contributes the most to a particular sweep. In
particular, the layer donors are actually more prevalent when
sub-populations are used, with the brown layer donorship high for Hawaii
at chr1@17.5Mb, the white layer a
high donor for Hawaii at
chr2@78.3Mb, and the brown layer
a high donor for Bermuda at chr1@32.8Mb (see figure 2B). When focusing
on the Bermuda population, with the addition of Hawaii as a donor, we
can see a strong overlap between the two feral populations, with Hawaii
the largest donor for the sweep at
chr2@78.3 and the joint largest for
the sweep at chr1@17.5Mb (see
figure 2C, D).
Of the three shared sweeps, one also overlapped with a domestication
sweep (chr1@32.8Mb). In this case, the domesticated donor is much more
evident than either the Hawaiian or Red Junglefowl donors.
Gene annotation and
Function
The 59 selective sweeps regions detected by both methods for the
Bermudian population contain a total of 61 genes when using the Ensembl
genome annotation browser, though a large percentage are long non-coding
RNA and other gene-free regions (see Supplementary Table 8 and below). A
total of 9 fully annotated genes were identified in selective sweeps
(ADCY1, CALU, CRAMP1, DRD3, MYST/Esa1-associated, PTPRB, TAFA5,
TSNARE1, ZC3H12A ). These genes are involved in anxiety, schizophrenia,
depression and related behaviours (ADCY1, DRD3, PTRB, TAFA5,
tSNARE1 ) bone remodelling (MYST/Esa1-assctd ), eye development/
vision (PTRB ), the immune system (ZCH3H12a ) and metabolism
(CALU ). There was no enrichment for these types of gene
functions, however. Of the 61 genes, only 21 were able to be assessed in
the PANTHER over-representation analysis (using complete GO processes
setting), with the above mentioned nine genes plus a further 12
unannotated genes still included. The only enrichment was for
unclassified processes/ genes in this set (p<0.0001). Of the
61 genes, 40 were long non-coding RNAs (lncRNA). Similar results were
found with the Hawaii consensus sweep regions – in this case 171 genes
were present in these sweeps, with 131 being useable by Gene ontology
software PANTHER (Protein Analysis Through Evolutionary Relationships)
(Mi, Muruganujan et al. 2012). The only enriched GO process was once
again unclassified (p<0.0001), whilst 25 of the genes were
lncRNAs, 10 were micro, miscellaneous, or sno RNAs, 25 were unknown, and
the remainder protein coding (see Supplementary Table 9). Gene function
was very diverse in the case of the Hawaiian gene set, though of note is
the presence of SEMA3A(chr1@9.4Mb), which was one of the
three most significant improvement/ domestication-related genes detected
by Rubin et al (Rubin, Zody et al. 2010). Similarly, the genetSNARE1 was also found in a selective sweep identified by Rubin
et al. 2010.