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.