Effective population size in the past estimated from linkage disequilibrium data. Inset graph shows effective population size for the European humans over the same period; from (13). Breeds as in Fig. 1.

(A) Population structure assessed by InStruct. Bar plot, generated by DISTRUCT, depicts classifications with the highest probability under the model that assumes independent allele frequencies and inbreeding coefficients among assumed clusters. Each individual is represented by a vertical bar, often partitioned into colored segments with the length of each segment representing the proportion of the individual’s genome from K = 2, 3, or 9 ancestral populations. Breeds are separated by black lines. NDA, N’Dama; SHK, Sheko; NEL, Nelore; BRM, Brahman; GIR, Gir; SGT, Santa Gertrudis; BMA, Beefmaster; ANG, Angus; RGU, Red Angus; HFD, Hereford; NRC, Norwegian Red; HOL, Holstein; LMS, Limousin; CHL, Charolais; BSW, Brown Swiss; JER, Jersey; GNS, Guernsey; PMT, Piedmontese; RMG, Romagnola. (B) Principal components PC1 and PC2 from all SNPs. Taurine breeds remain separated from indicine breeds, and admixed breeds are intermediate.

Nucleotide diversity across five ENCODE regions resequenced in 47 animals from ANG, Angus; BRM, Brahman; and HOL, Holstein. (A) Watterson’s estimate (θ) of the population mutation rate per base pair (pooled across regions). (B) Average pairwise nucleotide distance (π) within breeds. (C and E) Non-parametric bootstrap estimates of diversity ratios among the three populations on the basis of θ. (D and F) Nonparametric bootstrap estimates of diversity ratios among the three populations on the basis of π.