Recent Improvement/ Domestication Signals in Feral Populations
Very little overlap existed between the selective sweeps detected in
modern domesticated populations, and those detected in the two feral
populations. Several genes have been previously identified as likely
being highly important in modern domestication, by dint of being present
in selective sweeps detected in multiple domesticated breeds (Rubin,
Zody et al. 2010). In particular, the genes TSHR , BCDO2 ,
and SEMA3A were the three genes present in the strongest domestic
sweep regions in the Rubin et al study, and in the case of TSHRand BCDO2 also contained exonic non-synonymous mutations. It is
important to note that these selective sweeps identified in (Rubin, Zody
et al. 2010) and Qanbari et al (2019) almost certainly represent modern
improvement-related domestication genes, whereby very strong recent
selection is occurring in modern broiler and layer breeds, as opposed to
early domestication-related genes that were selected during the initial
phases of chicken domestication.
In the case of TSHR , the gene is located at 40.97Mb-41.02Mb on
chromosome 5. A sweep covering 40.4-40.8Mb was detected in both feral
populations using Tajima’s D (see Supplementary Table 6), whilst a sweep
was detected using CLR in the Bermudian population at 40.17-40.19Mb, and
at 41.3Mb in the Kauai population (see Supplementary Table 4). None of
these actually overlap the TSHR gene itself, and the allele
frequency of the exonic mutation locus (present at 41020256-61bp) was
found to be variable. In the case of the Bermudian population, the SNP
present had a frequency of 3 homozygote reference individuals, 11
heterozygote individuals, and 7 homozygote variant individuals, whilst
the Hawaiian population had an allele frequency of 7 variant
homozygotes, 4 heterozygotes, and 12 homozygous alternate individuals.
When assessing the Tajima’sD result for the specific sweep region in the
Kauai population we get a Tajima’sD statistic of 1.4, with the 1%
cut-off threshold being 3.4. In the case of the Bermudian population,
two Tajima’s D statistics were calculated (for 40960000-41000000 and
41000000-41040000) with values of 2.9 and 3.5, with one being above the
1% threshold of 3.3.
Similarly, only one sweep was present within the relative vicinity ofBCDO2 (located at 6140660-6152816bp), with this sweep being
detected at 6.5Mb in the Bermudian population using CLR (see
Supplementary Table 4). In the case of the Tajima’sD statistic for this
specific sweep region, for the Bermudian population this was 1.3 (with
the cut-off being 3.3) and for the Kauai population this value was 1.1
(with the cut-off being 3.4), showing no significant fixation.
In contrast, a consensus sweep (found using both CLR and Tajimas’D) was
detected in the Kauai population at 9.4-9.44Mb on chromosome 1, that
fully overlapped the gene SEMA3A (9.34Mb-9.51Mb), and is
therefore the only one of these three improvement/ domestication genes
that has reliable support for being present in a feral population (see
Supplementary Table 8). In this case it appears that SEMA3A is
either undergoing further positive selection within feral populations,
or it retains a signal of earlier artificial selection (e.g. due to
selective neutrality and/or loss of non-domesticated alleles as the
population became feral). One further point is the gene tSNARE1,which was identified in the feralisation-related selective sweeps, is
also identified (albeit not as strongly as the above-mentioned genes) in
an earlier analysis of domestication-related G. gallus loci (Rubin et al
2010). This once again highlights the possibility that some of the
polymorphisms selected during domestication may still be advantageous
beyond captive environments, regardless of whether they serve the same
functional role(s) in feral habitats.