Supplemental Figure 6. Comparative organization of the reconstructed cetartiodactyl and pecoran ancestral chromosomes with the cattle genome as a reference. Order and orientation of syntenic fragments are visualized using the Evolution Highway comparative chromosome browser. Blue and pink colors represent orientation of blocks relative to the reference, with blue indicating the same orientation, and pink indicating the opposite orientation. Pink does not always indicate an inversion because the orientation of RACFs is randomly chosen during the reconstruction. The number within each block represents a chromosome number for a reconstructed ancestor, and a lower-case letter indicates a fragment of the chromosome. Light grey blocks indicate mammalian multispecies homologous synteny blocks (msHSBs). Diamonds indicate the position of EBRs, with light and dark green showing EBRs classified as ruminant or pecoran, respectively, using FISH data. Heatmaps show the density of ruminant, cetartiodactyl, and mammalian enhancers, and ruminant gene family expansions in windows of 100 Kbp along cattle chromosomes. Cattle chr1 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 1 1 1 1 1b 1a Bases 60000 1 40000 1 1 4.0e+07 20000 1 1a 1b 1 0 1b 1 1 1 1 1 8.0e+07 1 1 1 1a 1 1c 1 1 1 1 classification 1 1 ? 1.2e+08 1 Ruminant 1 1 1a 1b 1a 1b 1b 1b 1b 1a 1 1b 1a 1b 1b 1 1b 1a Cattle chr2 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 6 2 2 2 6 2 Bases 2 20000 2 10000 6 2 6 2 0 2 2 5e+07 2 6 2 2 2 2 2 2 classification 1e+08 6 2 Pecora Ruminant 2 2 2 3a 2 2 Cattle chr3 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 3 3 3 Bases 3 15000 3 10000 3.0e+07 3 5000 3 0 3 3 3a 3 6.0e+07 3 3 3 3 3 3 3 3 classification 9.0e+07 3 Pecora 3 3 3 3 6 1.2e+08 Cattle chr4 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 8a 4 4 8a 4 8a 4 8a 4 8a 4 8a 4 8a 4 Bases 4 20000 4 15000 10000 3.0e+07 4 8a 4 5000 0 4 8a 4 8a 4 8a 4 4 8b 4 4 8b 4 8b 4 6.0e+07 8b 4 4 4 8a 8a 4 4 classification 9.0e+07 4 Ruminant 4 4 4 4 8b 4 4 4 1.2e+08 Cattle chr5 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 5 5 5 9a 5 5 Bases 80000 60000 5 40000 3.0e+07 20000 5 9a 0 5 9a 5 6 5 6.0e+07 5 5 9a 5 5 5 classification 9.0e+07 Ruminant 9b 5 5 5 9a 5 9a 6 9a 6 9a 6 1.2e+08 9a 6 Cattle chr6 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 4b 6 6 6 4a Bases 6 10000 6 3e+07 5000 6 6 0 6 6 5 6 6e+07 4a 6 6 classification 6 9e+07 Pecora 6 6 6 4c 4c 5 4c 5 4c 5 4c 5 6 4a 5 6 4c Cattle chr7 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 2a 2c 7 2b 2b Bases 2b 15000 7 10000 3e+07 5000 2a 7 0 2a 2d 2b 7 8 7 7 6e+07 7 2a 7 7 7 classification 7 ? 7 Pecora 7 Ruminant 9e+07 7 7 2a 7 7 Cattle chr8 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 25 8 25 25 8 8 8 Bases 8 15000 8 10000 3e+07 5000 8 0 8 11c 8 8 8 8 7 8 6e+07 8 8 25 8 8 8 11c classification 8 Pecora 11e Ruminant 9e+07 11d 8 8 8 11c 8 8 14 Cattle chr9 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 9 10 9 Bases 100000 9 75000 2.5e+07 50000 9 25000 9 0 9 9 9 10 9 5.0e+07 10 9 9 9 9 7.5e+07 9 classification Pecora 9 9 10 9 9 9 1.0e+08 9 Cattle chr10 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 2a 10 2a 2a 10 5 10 5 10 Bases 10 80000 10 60000 2.5e+07 40000 10 20000 5 0 10 10 5 11 10 10 5.0e+07 10 10 5 10 10 10 10 classification 10 7.5e+07 ? 5 10 Pecora 10 Ruminant 10 2a 8 10 10 5 11 10 1.0e+08 10 Cattle chr11 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 14 11 11 14 11 11 11 Bases 11 20000 15000 2.5e+07 11 10000 14 5000 11 0 11 11 14 5.0e+07 11 14 9 11 11 11 14 11 11 11 7.5e+07 classification 11 ? 14 11 Pecora 11 Ruminant 11 11 11c 11 1.0e+08 11 11b 11c 11a 9 11c Cattle chr12 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 12 Bases 13a 20000 12 15000 10000 5000 2.5e+07 12 0 12 12 13 12 5.0e+07 13a 12 12 classification 12 ? 7.5e+07 13b 12 12 13a 12 Cattle chr13 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 19 17b 13 13 24b 17a Bases 13 15000 24a 2e+07 10000 5000 24a 13 0 24a 4e+07 19 24b 13 19 13 17a 13 19 19 13 6e+07 classification 13 ? Ruminant 19 8e+07 Cattle chr14 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 14 15 14 14 15 Bases 20000 15 14 15000 2e+07 10000 14 5000 0 14 15 14 14 4e+07 14 14 14 14 6e+07 classification Pecora 15 14 14 14 8e+07 14 15 Cattle chr15 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 7a 15 7a 15 Bases 15 30000 2e+07 20000 15 10000 0 7b 15 15 15 4e+07 7a 15 7c 7a 15 6e+07 15 classification 15 Pecora 7a 15 15 8e+07 7b Cattle chr16 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 16 3a 16 16 Bases 15000 10000 2e+07 3b 16 5000 0 16 16 16 3a 4e+07 16 3a 16 16 3b 16 3a 16 3a 16 classification 6e+07 16 Pecora 16 3a 16 16 16 8e+07 3b Cattle chr17 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 17 17 Bases 5000 17 4000 3000 4a 2000 2e+07 1000 17 0 17 17 17 18 4e+07 4b 17 17 17 17 17 classification Ruminant 23a 17 6e+07 17 23b 23b Cattle chr18 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 18b 18 18a Bases 80000 18 60000 40000 20000 0 2e+07 18c 18 18a 18a 22 18 18 4e+07 18 classification ? Pecora 18b Ruminant 18 6e+07 18d 18d Cattle chr19 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 19 Bases 19 50000 40000 30000 19 20000 10000 0 2e+07 19 16 19 21 19 4e+07 19 19 classification 19 ? 19 16 19 6e+07 19 Cattle chr20 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 2a 20 20 20 Bases 20000 20 15000 10000 5000 2e+07 20 0 20 20 19 20 4e+07 2a 20 20 classification 20 ? 20 20 6e+07 20 20 Cattle chr21 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 5 20 21 21 5 Bases 21 75000 50000 21 25000 2e+07 0 5 5 5 5 20 5 21 4e+07 21 5 21 classification ? Pecora 5 Ruminant 5 6e+07 22 21 27 5 Cattle chr22 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 8a 22 24 1a 22 Bases 15000 1a 24 10000 1a 24 1a 5000 0 2e+07 22 22 22 1a 24 4e+07 22 classification ? 22 Ruminant 22 1a 1a 6e+07 1a Cattle chr23 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 20 23 Bases 1e+07 23 30000 20000 10000 0 20 23 2e+07 26 3e+07 23 23 classification 20 ? 4e+07 23 23 5e+07 Cattle chr24 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 17b 24 24 Bases 20000 15000 10000 24 5000 0 2e+07 24 24 17a 24 23 24 24 4e+07 24 24 classification Ruminant 24 17b 24 6e+07 Cattle chr25 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 25 Bases 12500 25 10000 1e+07 7500 5000 2500 0 25 2e+07 21 28 25 3e+07 classification 25 ? 4e+07 Cattle chr26 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 26 Bases 1e+07 50000 12b 12a 40000 30000 26 20000 10000 0 26 2e+07 12b 12a 3e+07 26 12b 12a classification ? 4e+07 26 26 26 5e+07 12b 12a 12b 12a Cattle chr27 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 27 Bases 20000 1e+07 15000 27 10000 5000 0 27 27 2e+07 22 27 27 27 3e+07 classification ? 4e+07 1a Cattle chr28 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 0e+00 12a 12b 12a 12a 28 Bases 12a 1e+07 28 10000 5000 0 28 2e+07 28 12a 28 3e+07 12b 28 classification Ruminant 28 4e+07 Cattle chr29 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 29 Bases 1e+07 7a 80000 60000 29 40000 20000 0 29 2e+07 7a 29 25 3e+07 7b 29 7b 29 classification 7b ? 4e+07 Ruminant 29 7a 29 5e+07 Cattle chrX DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions Xb Xh Xh Xb X Xb X Xb X X Bases Xe X Xe Xf X 20000 X Xe Xf 10000 Xh X 0 Xd Xe X 5e+07 Xd Xg Xd X Xd Xg X Xf Xd Xf Xd X Xb Xb Xi X Xb Xi Xg Xc Xb Xg Xc X X Xc X X Xa X 1e+08 Xc Xa X X Xa X classification ? X Xa X X Xa Xc Xa Xc Xa Xc Xa Xa Xc Xa Xc.