Figure Legends
Figure 1. Map of China (including the South China Sea Islands, lower right corner) showing chicken populations included in this study. BEC, Baier Yellow chicken (ex-situ ); YBEC, Baier Yellow chicken (in-situ ); BYC, Beijing You chicken (ex-situ ); YBYC, Beijing You chicken (in-situ ); LSC, Langshan chicken (ex-situ ); YLSC, Langshan chicken (in-situ ). Male and female specimens are shown for the three breeds. Each subpopulation in the study consisted of 10 males and 20 females (green and brown areas in pie charts, respectively). Airplane glyphs indicate that individuals from each breed were moved from their original locations (in situin Beijing, Hangzhou, and Rudong) to Yangzhou for ex situconservation under the auspices of NCGR (National Chicken Genetic Resources) in Jiangsu.
Figure 2. Population genetic structure. (a). Neighbor-joining tree constructed using SNP data from ex-situ and in-situconserved populations of the three chicken breeds. (b). PCA analysis of subpopulations. The first three principal components are shown, and the subpopulations are color-coded according to the key to the right. (c). Inferred population genetic structure using the maximum-likelihood method under a model with ancestral components varying from K=2 to K=6.
Figure 3. Analysis of genomic diversity between in situand ex situ populations within breeds. Ho, observed heterozygosity; He, expected heterozygosity; PN, proportion of polymorphic markers; AR, allelic richness; FROH, inbreeding coefficients based on ROH; FES, inbreeding coefficient based on pedigree.
Figure 4. (a). Estimates of population nucleotide diversity (Pi-LSC10 = 0.000102248, LSC12 = 0.000105831, LSC15 = 0.000106998, YBYC = 0.000105085, BYC07 = 0.000100251, BYC10 = 9.84366e-05, BYC15 = 9.46419e-05, YBEC = 0.000107512, BEC07 = 0.000104584, BEC10 = 0.000104865, BEC15 = 9.71941e-05). (b). LD decay determined by squared correlations of allele frequencies (r2 ) against the distance between polymorphic sites.
Figure 5. Matrix showing pairwise differentiation estimates (FST ) between in situ and ex situpopulations.
Figure 6. Boxplots showing effective population sizes of thein situ and ex situ conserved populations for each breed.
Figure 7. (a). Number of runs of homozygosity (ROH) as a function of run size in kb. (b). Circos plot showing genomic location of runs of homozygosity for each of the three chicken breeds in in situ and ex situ conserved populations.
Figure 8. Circos Manhattan plots showing results forFST , Pi, and XP-EHH analyses in (a). Baier Yellow chicken, (b). Beijing You chicken, and (c). Langshan chicken.
Figure 9. Selection sweep of Beijing You chicken population. (a) Classification of sweep regions for Beijing You chicken. The X-axis represents the Di value and Y-axis represents the Pi value. The green circles satisfy criteria for sweep regions. (b) Manhattan plot for genome-wide distribution of Di and Pi values. Baier Yellow chicken and Langshan chicken served as reference groups.
Figure 10. Selection sweep of Baier Yellow chicken population. (a) Classification of sweep regions for Baier Yellow chicken. The X-axis represents the Di value and Y-axis represents the Pi value. The red circles satisfy criteria for sweep regions. (b) Manhattan plot for genome-wide distribution of Di and Pi values. Beijing You chicken and Langshan chicken served as reference groups.
Figure 11. Selection sweep of Langshan chicken chicken population. (a) Classification of sweep regions for Langshan chicken chicken. The X-axis represents the Di value and Y-axis represents the Pi value. The red circles satisfy criteria for sweep regions. (b) Manhattan plot for genome-wide distribution of Di and Pi values. Beijing You chicken and Baier Yellow chicken served as reference groups.