Fig 1.
Geographic provenance of samples and overall genetic profile illustrating intensification of domestic contribution into wild red junglefowl.
(A) Distribution map of all five red junglefowl (Gallus gallus) subspecies following McGowan et al. (2020) [83]. Circles refer to collection localities for the samples used in this study. The numbers next to the black circles are the sample size for each modern red junglefowl population (sample size was 1 for all red circles). The distribution of subspecies spadiceus, the putative ancestor of modern chickens, is encircled by a stippled line, and divided into its northern and southern range as defined in this work. (B) D-statistics testing for excess allele sharing between domestic chickens and red junglefowl of the ancestral subspecies spadiceus using the phylogeny (((spadiceus-historic, spadiceus-modern), chicken), Bambusicola thoracicus) from various parts of the range of spadiceus (from top to bottom): the ‘entire range’ of spadiceus (n = 85), ‘northern range’ (see map in panel a) (n = 61), northern Thailand and Myanmar only (n = 56), ‘southern range’ (see map in panel a) (n = 75), and Singapore plus adjacent Malay Peninsula (n = 60). All D-values are significantly non-zero (|Z|>3), indicating a strong signal of domestic introgression into modern samples. (C) Principal component analysis (PCA) of historic samples of red junglefowl and modern domestic chickens (n = 61) based on 7,492,873 SNPs. Javan subspecies bankiva removed from plot because it emerged in widely-divergent position (S2 Fig). (D) PCA of subspecies spadiceus and domestic chickens (n = 62) based on 2,709,190 SNPs. Individuals labelled with an asterisk (*) pertain to four modern Singaporean junglefowl inferred to have little domestic ancestry (see Fig 2). The percentage of total variation explained by each principal component is shown in brackets. See methods for explanation on each dataset’s sample size. The map was obtained from the R package rnaturalearth using Natural Earth medium scale data (1:50m) from https://www.naturalearthdata.com/downloads/.
Fig 2.
Ancestry inference of 15 representative modern red junglefowl from four localities across the range of Gallus gallus spadiceus.
(A) Multi-Dimensional Scaling plot from Struct-f4 (K = 4) assuming no admixture based on 2,603,726 SNPs. Modern red junglefowl samples are highlighted with a black frame; historic red junglefowl samples are to the right of the modern ones (teal), and domestic chicken samples to the left (green). The color legend indicates which population each sample is assigned to regardless of actual identity (RJF = red junglefowl). (B) Individual ancestry profiles from Struct-f4 (K = 4) based on 2,603,726 SNPs. Colors refer to genomic contributions as inferred in 2A. ‘Out’ refers to the outgroups used in the analysis. (C) Local ancestry inference based on 143,526 SNPs using Efficient inference of local ancestry (EILA). Only the top 15 chromosomes (Chr 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 16, 20) with the most SNPs called are illustrated. Blue coloration refers to domestic ancestry and red coloration refers to wild ancestry. The percentage of genome-wide SNPs with domestic ancestry is given on the bottom right.
Fig 3.
Positive selection on genomic islands of differentiation between chickens and wild red junglefowl.
(A) DXY (pairwise divergence) between historic wild individuals of each red junglefowl subspecies versus modern chickens in 50kb sliding windows with a step size of 10kb across the chicken reference genome. Alternating hues of blue denote different chromosomes and the horizontal black dotted lines denote the 99th percentile of DXY of autosomes (bottom) and the Z chromosome (top). Arrows indicate genic regions located within genomic islands of high differentiation between chickens and junglefowl which are under selection in domestic chickens; their colors refer to the main function of genes following (B). (B) Branches under positive selection that were inclusive of domestic chickens calculated using aBSREL (red: uncorrected p-value ≤ 0.05) for genes that are highly divergent between chickens and wild junglefowl. Seven outgroups across the avian phylogeny were used in this analysis (signatures of selection in outgroups not depicted, see S6 Fig).
Table 1.
Function of genes located on genomic islands of high differentiation between chickens and junglefowl which are under selection in chickens.
Only CERKL was found to be under selection in both chickens and wild spadiceus; the remainder were found to be under selection uniquely in chickens. Values are rounded to 3 significant figures (s.f.).