Fig. 1

Population characteristics of wild and domesticated chickens. a Neighbor-joining phylogeny among wild and domesticated chickens based on genome-wide SNP data. The wild progenitors include red jungle fowls from the Guangxi (RJF_GX), Yunnan (RJF_YN) and Hainan (RJF_HN) provinces in China. The domesticated chickens consist of Chinese native breeds, including Guangdong Xinghua (XH), Luxi Dou (LXD), Beijing You (YOU), Silkie (SILK), and commercial strains such as Recessive White Rock (RW) and White Leghorn (WL). b The principle component analysis plot based on the first two principle components. c Population stratification and individual admixture with genetic cluster (K) equivalent to 2 and 7, respectively; colors in each column represent the individual ancestry proportions. d The maximum likelihood tree among chicken populations with 5 deduced introgression events and the residual matrix of the fitted model. The introgression events are highlighted as the arrows with colors from yellow to red, which represent the various weights of introgression (left panel). The arrow direction indicates the introgression direction. The residuals of the fitted model are illustrated in the right panel, where, the color in each cell [i, j] proportionally reflects the scaled residual covariance between population i and j, i.e. the residual covariance divides the average standard error (SE) of the observed covariances across pairs of population. The color scale bar is described in the palette on the right. Small residuals represent a well-fitted model. The fraction of the variance in relatedness among populations interpreted by the fitted model is 99.96%