Lindblad-Toh et al. Figure S1

1,600,000 Mixed inconsistencies Linking inconsistencies Illogical links 1,400,000 Missing read partners Negative gap Haplotype inconsistency

1,200,000

1,000,000

800,000 T e r i t o y ( b p )

600,000

400,000

200,000

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 X Chromosome Lindblad-Toh et al. Figure S2

Chr 1 Chr 21

Chr 2 Chr 22

Chr 3 Chr 23

Chr 4 Chr 24

Chr 5 Chr 25

Chr 6 Chr 26

Chr 7 Chr 27

Chr 8 Chr 28

Chr 9 Chr 29

Chr 10 Chr 30

Chr 11 Chr 31

Chr 12 Chr 32

Chr 13 Chr 33

Chr 14 Chr 34

Chr 15 Chr 35

Chr 16 Chr 36

Chr 17 Chr 37

Chr 18 Chr 38

Chr 19

1 7 13 19 Chr 20 2 8 14 20 3 9 15 21 4 10 16 22 Chr X 5 11 17 X 6 12 18 Lindblad-Toh et al. Figure S3 Dog chr 1 Dog chr 2 Dog chr 3 Dog chr 4

Dog chr 5 Dog chr 6 Dog chr 7 Dog chr 8 Dog chr 9 Dog chr 10 Dog chr 11 Dog chr 12

Dog chr 13 Dog chr 14 Dog chr 15 Dog chr 16 Dog chr 21 Dog chr 22 Dog chr 23 Dog chr 24 Dog chr 29 Dog chr 30 Dog chr 31 Dog chr 32 Dog chr 37 Dog chr 38 Dog chr X Dog chr unknown Lindblad-Toh et al. Figure S4

700 Human syntenic segments Human syntenic blocks Mouse syntenic segments 600 Mouse syntenic blocks Rat syntenic segments Rat syntenic blocks

500

400

300 N u m b e r o f l c k s g n t

200

100

500 1000 1500 2000 2500 3000 Minimum size (kb) Lindblad-Toh et al. Figure S5

All breaks 1000 kb Interchromosomal breaks

59 55 Dog Dog 38 25 Human Human 18 11 Mouse Mouse 98 93 Rodent Rodent 18 15 Rat Rat

500 kb

81 74 Dog Dog 61 42 Human Human 26 18 Mouse Mouse 108 106 Rodent Rodent 31 21 Rat Rat

300 kb

98 78 Dog Dog 93 49 Human Human 36 19 Mouse Mouse 126 123 Rodent Rodent 58 26 Rat Rat

100 kb

109 97 Dog Dog 136 66 Human Human 54 34 Mouse Mouse 131 150 Rodent Rodent 172 38 Rat Rat Lindblad-Toh et al. Figure S6

0.08 Dog Human 0.07 Mouse

0.06

0.05

0.04

0.03 F r a c t i o n f w d s

0.02

0.01

0 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7

(G+C) content (%) Lindblad-Toh et al. Figure S7

a b

0.28 0.55

0.26

0.50 0.24

0.22 0.45

0.20 ( G + C ) f r a c t i o n

D i v e r g n c a t ( A R ) 0.18 0.40

0.16

0.35 0.14

All Internal Sub- All Internal Sub- breaks telomere breaks telomere Lindblad-Toh et al. Figure S8

Lindblad-Toh et al. Figure S9

1.0

0.9

0.8

0.7

0.6 Fraction of selected windows 0.5 in clusters (estimated)

F r a c t i o n 0.4 Fraction of all windows in clusters 0.3 Fraction of selected 0.2 sequence considered

0.1 Fraction of background sequence considered 0 –5 –4 –3 –2 –1 0 1 2 3 4 5 6 7 Conservation score Lindblad-Toh et al. Figure S10

a Total human bases b Total HCNE bases c HCNE density

300,000 3500 0.009

0.008 250,000 3000 0.007 2500 200,000 0.006

2000 0.005 150,000 1500 0.004

100,000 0.003 1000 0.002 50,000 500 0.001

0 0 0 –3 –2 –1 0 1 2 3 –3 –2 –1 0 1 2 3 –3 –2 –1 0 1 2 3 Gene neighborhood Gene neighborhood Gene neighborhood Lindblad-Toh et al. Figure S11

20 20

15 15

10 10

5 5

0 0

–5 –5 M o u s e K a / ( z ) H u m a n K / s ( z ) –10 –10

–15 –15

–20 –20 –20 –15 –10 –5 0 5 10 15 20 –20 –15 –10 –5 0 5 10 15 20 Dog Ka/Ks (z) Dog Ka/Ks (z) Lindblad-Toh et al. Figure S12

a

Acceleration score (human vs. mouse) b

Acceleration score (dog vs. mouse) c

Acceleration score (human vs. dog) Lindblad-Toh et al. Figure S13

0.8 Chr 1 Chr 4 Chr 6 0.7 Chr 8 Chr 10 Chr 12 Chr 14 0.6 Chr 22 Chr 23 Chr 24 0.5 2

0.4 v e r a g A 0.3

0.2

0.1

0.0 0 100,000 200,000 300,000 400,000 500,000 600,000 700,000 800,000 900,000 1,000,000

Distance (bp) Lindblad-Toh et al. Figure S14

0.8 Observed data Model (F = 12%) 0.7 Model (F = 30%) Model (F = 50%)

0.6

0.5 2

0.4 v e r a g A 0.3

0.2

0.1

0.0 0 100,000 200,000 300,000 400,000 500,000 600,000 700,000 800,000 900,000

Distance (bp) Lindblad-Toh et al. Figure S15 Lindblad-Toh et al. Figure S16 Lindblad-Toh et al. Figure S17 b a Average number of haplotypes (>3%) Average number of haplotypes (>3%) 10 12 0 2 4 6 8 0 1 2 3 4 5 6 7 8 Acros bred set Acros bred set Al withn bred dogs Al withn bred dogs Akita Bulmastif Basenji f Bulmastif springe English spaniel f springe English spaniel wolfhund Irish Glen of teri Imal wolfhund Irish Pug Pug Rotweilr Rotweilr Lindbla-T Figure S18 oh etal. Lindblad-Toh et al. Figure S19 Lindblad-Toh et al. Figure S20 Lindblad-Toh et al. Figure S21

Glen of English Labrador Irish Golden Imaal springer Rottweiler Pug retriever wolfhound retriever terrier spaniel Bullmastiff Basenji Akita Akita 0.29 0.19 0.35 0.27 0.40 0.20 0.42 0.52 0.50 0.73 Basenji 0.70 0.59 0.69 0.64 0.85 0.52 0.64 0.74 0.95 Bullmastiff 0.32 0.22 0.32 0.28 0.67 0.19 0.45 0.92 English springer spaniel 0.54 0.42 0.44 0.40 0.63 0.35 0.75 Glen of Imaal terrier 0.65 0.66 0.71 0.83 0.45 0.69 Golden retriever 0.66 0.56 0.54 0.54 0.80 Irish wolfhound 0.71 0.70 0.78 0.86 Labrador retriever 0.68 0.62 0.79 Pug 0.79 0.78 Rottweiler 0.77 Lindblad-Toh et al. Figure S22

a b c 1.0 1.0 1.0

0.9 0.9 0.9

0.8 0.8 0.8

0.7 0.7 0.7 30,000 0.6 0.6 0.6 15,000 7,500 0.5 0.5 0.5

0.4 0.4 0.4

0.3 0.3 0.3 C u m l a t i v e f r c o n ( % ) C u m l a t i v e f r c o n ( % ) C u m l a t i v e f r c o n ( % )

0.2 0.2 0.2

0.1 0.1 0.1

0 0 0

0 10 20 30 40 50 0 10 20 30 40 50 0 5 10 15 20 Log likelihood ratio Log likelihood ratio Log likelihood ratio Lindblad-Toh et al. Figure S23

97 Arctic fox 100 Kit fox Corsac fox 66 62 Ruppell's fox Red fox 100 Blanford's fox 76 Fennec fox Cape fox 52 Raccoon dog Bat-eared fox Short-eared dog Crab-eating fox 100 60 Culpeo 77 Sechuran fox 65 Darwin's fox 97 Chilla Pampas fox Hoary fox 82 Maned wolf 100 Bush dog 73 Side-striped jackal 100 Black-backed jackal Golden jackal 100 61 74 Dog 55 Gray Wolf 85 Coyote Ethiopian wolf Dhole African wild dog 100 Gray fox Island fox 100 Black bear Giant panda 100 Elephant seal Walrus Lindblad-Toh et al. Figure S24

100 Arctic fox 52 Kit fox

99 79 Ruppell's fox Red fox 76 Corsac fox 100 Cape fox 71 Blanford's fox 67 Fennec fox 55 Raccoon dog Bat-eared fox Short-eared dog 91 Crab-eating fox 50 Culpeo 68 57 Darwin's fox Chilla 99 94 Pampas fox Sechuran fox Hoary fox 100 96 Maned wolf 100 Bush dog 100 Side-striped jackal Black-backed jackal Golden jackal Dog 68 78 98 Gray Wolf Coyote Ethiopian wolf Dhole African wild dog 100 Gray fox Island fox 100 Black bear Giant panda 100 Elephant seal Walrus Lindblad-Toh et al. Figure S25

100 Arctic fox A 100 16 Kit fox D 13 Corsac fox 52 C 67 1 Ruppell's fox E 81 B 2 4 Red fox 100 Cape fox 47 G (4) 96 Blanford's fox H F 1 7 Fennec fox 75 I 4 Raccoon dog Bat-eared fox Short-eared dog Crab-eating fox 100 P 11 Culpeo J 80 81 2 Sechuran fox AB O L 6 3 2 Chilla 100 M K R 2 Pampas fox 11 93 N Darwin's fox 4 Hoary fox

95 Maned wolf Q 100 5 Bush dog AA 36 100 Side-striped jackal S 14 Black-backed jackal 727 Side-striped jackal 100 V 93 Dog 75 1 T Z 1 78 6 99 Gray wolf W 3 U 9 Coyote 92 (2) 6 X Ethiopian wolf 78 3 Y Dhole African wild dog 100 Gray fox AC 90 Island fox (9) Black bear Giant panda Elephant seal Walrus