Supplemental Table S1. Samples, breeds, sizes. (Abbreviations: n, sample size; YNP, Yellowstone National Park; AKC, American
Kennel Club; Unk, unknown).
Species
Gray wolf (Canis lupus)
Origin (n)
YNP (35)
Domestic dog (Canis familiaris)
AKC (3)
AKC (4)
AKC (2)
AKC (2)
AKC (4)
Turkey, non-AKC (2)
AKC (3)
AKC (2)
AKC (1)
AKC (2)
AKC (3)
AKC (4)
AKC (1)
AKC (2)
AKC (4)
Breed (nfemales, nmales)
Breed
Abbreviation
Notes
(16, 19)
YNP
8 pairs of known genealogy
Afghan hound
(2, 1)
Akita
(2, 2)
Bassett hound
(2, 0)
Borzoi
(1, 1)
Boxer
(2, 2)
Boz
(2, 0)
Basenji
(1, 2)
Chinese crested
(Unk, unk)
English springer spaniel
(1, 0)
Siberian husky
(0, 1)
Labrador retriever
(1, 2)
Pekingese
(2, 2)
Pomeranian
(1, 0)
Portuguese water dog
(2, 0)
Pug
(2, 2)
afgh
akit
bass
1 female dropped due to low sequence
coverage
borz
box
boz
bsji
chcr
Both powderpuffs
essp
husk
1 male dropped due to large variation in
sequence coverage
lsb
peke
pom
ptwd
pug
1
AKC (4)
AKC (2)
AKC (3)
AKC (2)
AKC (1)
Samoyed
(2, 2)
Scottish terrier
(2, 0)
Sharpei
(2, 2)
Standard poodle
(1, 1)
Shetland sheep dog
(1, 0)
samo
1 female dropped due to low sequence
coverage
scot
shar
spoo
sshp
Semi-domestic dog (C. familiaris)
Australia (2)
New Guinea (4)
Dingo
(Unk, unk)
New Guinea Singing Dog
(Unk, unk)
dingo
ngsd
Village dog (C. familiaris)
Vietnam (1)
Thailand (2)
Vietnamese ridgeback
(0, 1)
Thai village dog
(1, 1)
pqu
thai
1 female dropped due to large variation in
sequence coverage
2
Supplemental Table S2. Coverage (average + SD) for 92 remaining samples prior to
filtering.
Species
Wolves
Dogs
File ID
1M
2M
3M
4M
5M
6M
7M
8M
9M
10M
11M
12M
13M
14M
15M
16M
17M
18M
19M
1F
2F
3F
4F
5F
6F
7F
8F
9F
10F
11F
12F
13F
14F
15F
16F
AFGH_1
AFGH_2
AFGH_3
AKIT_1
AKIT_2
AKIT_3
AKIT_4
BASS_1
BASS_2
BORZ_1
BORZ_2
BOX_1
BOX_2
BOX_3
Average
Coverage
37.9
32.8
38.1
33.9
31.5
29
30.2
52
30.1
32.6
34.6
33.4
29.8
53.7
33
24.9
38.8
30.5
33
29.1
31.2
27.9
29
29.5
39.2
30.4
28.8
30.7
34.8
32
32.7
34.9
31
30.8
33.2
22.1
19.6
22.4
20.3
21.1
19.2
20.6
19.5
20.1
22.5
22.5
20.7
20.8
24.3
Standard Deviation
Coverage
77
70.8
77.6
70.8
63.5
69.3
70.9
85.3
72
74.4
72.6
76.2
67.8
86.3
70.7
61.1
73
70
72.7
70.9
64.8
59.8
62.8
68.5
75.5
64.3
60.9
62.9
68.3
67.3
68
69.1
61.3
62.5
63.6
59.7
62.8
66.2
62.4
63.8
68.6
51.5
53.6
47.9
58.5
53.1
60.9
61
64.6
3
BOX_4
BSJI_1
BSJI_2
BSJI_3
CHCR_1
CHCR_2
ESSP1
HUSK_1
LAB_1
LAB_2
LAB_3
PEKE_1
PEKE_2
PEKE_3
PEKE_4
POM_1
PTWD_1
PTWD_2
PUG_1
PUG_2
PUG_3
PUG_4
SAMO_1
SAMO_2
SAMO_3
SCOT_1
SHAR_1
SHAR_2
SHAR_3
SHAR_4
SPOO_1
SPOO_2
SSHP_1
DINGO_1
DINGO_2
NGSD_1
NGSD_2
NGSD_3
NGSD_4
BOZ_1
BOZ_2
PQU_1
THAI_1
23.5
26.5
20.4
21.2
26.1
32.7
23.2
17.5
17.6
26.7
17.4
27.2
20.8
29.4
24.8
17.4
25.3
23.3
25.5
16.4
19.9
31.6
24.1
25
22.2
23.3
30.2
21.9
28.1
30.4
19.9
28.8
19
25.1
34.2
28.7
28.1
23.3
26.3
23.9
32
36.9
27
46.4
63.8
53
48.3
69.1
70.1
52.2
56.9
70.2
72.9
48.6
67.4
53.1
68.3
55.3
44.4
62.6
62.4
58.9
53
54.6
68.9
55.9
59.3
63.9
50.8
61
56
71.2
63.1
50.6
57.4
56.1
75.7
80.4
65.9
63.4
57.2
61
43
58
76.5
67.6
4
Supplemental Table S3. Annotation result of various methylation datasets from canfam3.1 Ensembl gene sets and RepeatMasker.
Proportions are provided in parentheses. Abbreviation: DMS, differentially methylated site.
Filtered 24,205 Unlinked 1,307
Outlier 36
FaST-LMM-EWASher’s
Annotated feature
cytosines
SMPs
SMP sites
962 cytosines
Outlier 68 DMS
Neighborhood
Intergenic
8076 (0.33)
692 (0.53)*
25 (0.69)††
685 (0.71)*
53 (0.78)
Promoter
6332 (0.26)
202 (0.15)*
2 (0.06)
131 (0.14)*
6 (0.01)**
Exon
3235 (0.13)
77 (0.06)*
1 (0.03)
60 (0.06)*
1 (0.01)††
Intron
6562 (0.27)
336 (0.26)
8 (0.22)
86 (0.09)*
8 (0.12)
RepeatMasker
DNA repeat
136 (0.01)
1 (0.00)*
0 (0.0)
6 (0.01)
0 (0.00)
LINE
978 (0.04)
27 (0.02)*
8 (0.22)**
142 (0.15)*
15 (0.22)
Low complexity
498 (0.02)
23 (0.02)
0 (0.0)
14 (0.01)†
0 (0.00)
LTR retrotransposons
363 (0.01)
15 (0.01)
0 (0.0)
34 (0.04)*
2 (0.03)
rRNA
153 (0.01)
5 (0.00)*
0 (0.0)
62 (0.06)*
1 (0.01)††
Satellite DNA
102 (0.00)
13 (0.01)*
0 (0.0)
54 (0.06)*
4 (0.06)
Simple repeats
410 (0.02)
1 (0.00)*
0 (0.0)
6 (0.01)†
0 (0.0)
SINE
2002 (0.08)
21 (0.02)*
9 (0.25)**
102 (0.11)*
13 (0.19)††
snRNA
6 (0.00)
0 (0.00)
0 (0.0)
0 (0.00)
0 (0.00)
srpRNA
1 (0.00)
0 (0.00)
0 (0.0)
0 (0.00)
0 (0.00)
tRNA
38 (0.01)
0 (0.00)*
0 (0.0)
0 (0.00)*
0 (0.00)
Unknown repeats
1 (0.00)
0 (0.00)
0 (0.0)
0 (0.00)
0 (0.00)
†
*One-tailed z-score p-value < 0.01; value is compared to the analogous filtered 24,205; One-tailed z-score p-value < 0.05; value is
compared to the analogous filtered 24,205 **One-tailed z-score p-value < 0.01; value is compared to the analogous tested dataset (e.g.
Outlier 36 SMPs compared to 1,307 SMPs; outlier 68 DMS to 962 sites); ††One-tailed z-score p-value < 0.05; value is compared to the
analogous tested dataset (e.g. Outlier 36 SMPs compared to 1,307 SMPs; outlier 68 DMS to 962 sites)
5
Supplemental Table S4. Average (±standard deviation) for methylation levels across
24,205 cytosines (nAuto=23997, nXchr=208). (Abbreviations: n, sample size; MF,
methylation frequency; GW, genome-wide; Auto, autosomes; Xchr, X chromosome).
Sample (number of individuals)
MFGW
YNP wolves (33)
0.34 ± 0.4
Purebred dogs (45)*
0.34 ± 0.4
All dogs (Purebred dog + ngsd) (51)
0.34 ± 0.4
Boz (1)
0.39 ± 0.4
Aboriginal Island dogs (ngsd, 4)
0.36 ± 0.4
Village dogs (thai, 1)
0.38 ± 0.4
*chcr (n=2) were not included due to their unknown sex.
MFAuto
0.34 ±0.4
0.34 ±0.4
0.34 ± 0.4
0.38 ± 0.4
0.36 ± 0.4
0.37 ± 0.4
MFXchr
0.75 ± 0.4
0.75 ± 0.4
0.75 ± 0.4
0.85 ± 0.3
0.84 ± 0.23
0.85 ± 0.3
6
Supplemental Table S5. Cross-validation error rates from ADMIXTURE. After outlier
removal, we used 1,307 unlinked SMPs across 33 gray wolves, 47 purebred dogs, four
New Guinea Singing Dogs, and two village dogs. The asterisk (*) indicates the lowest
error rate and thus the most likely K value to explain the data.
1291 unlinked
16 unlinked X
1307 unlinked SMPs
autosomal SMPs
chromosome SMPs
K value
CV error
K value
CV error
K value
CV error
2
0.124*
2
0.122*
2
0.290
3
0.128
3
0.124
3
0.521
4
0.126
4
0.123
4
0.548
5
0.128
5
0.127
5
0.759
6
0.133
6
0.131
6
0.520
7
0.132
7
0.134
7
0.269
8
0.141
8
0.141
8
0.221
7
Supplemental Table S6. Our total findings of outlier regions or DMS from A. SMP association scan (bolded values, p<10-19); B. sites
with significant (p<0.005) methylation (reference-corrected) differences between purebred dogs and YNP wolves. (Abbreviations:
CFA, canine chromosome; MF, methylation frequency; ∆, |MFwolf-MFpurebred|; h2, narrow sense heritability).
A.
CFA
1
Position
37861
p-value
3.54E-11
Rank
7
MFwolf,
MFpurebred
0.68, 0.41
∆
0.27
In repeat
element?
1
179308
3.73E-07
23
0.61, 0.70
0.09
Intergenic
0 (0)
2
4609977
4.21E-08
20
0.75, 0.46
0.29
Intergenic
--
3
132818
1.05E-08
14
0.31, 0.54
0.23
Intergenic
Annotation
Intergenic
Gene name
OMIM description
h2 (p-value)
0.99 (10-54)
0 (0)
PPP2R2C
Noted cognitive
disorder
3
58521165
2.01E-06
29
0.77, 0.95
0.18
Intron
3
84379587
7.52E-07
26
0.78, 0.98
0.20
Intergenic
0.99 (10-54)
6
49253
1.33E-08
15
0.64, 0.79
0.15
Intergenic
--
6
49272
4.26E-06
32
0.56, 0.32
0.24
Intergenic
--
6
172430
2.89E-08
16
0.73, 0.58
0.15
LINE
Intergenic
--
7
10985397
2.25E-19
1
0.38, 0.95
0.57
SINE
Intron
Uncharacterized
7
40156706
1.29E-06
28
0.75, 0.65
0.10
Promoter
DEGS1
9
37302938
1.65E-09
11
0.66, 0.95
0.29
SINE
Intron
SYNRG
12
71633889
3.36E-10
10
0.57, 0.77
0.20
SINE
Intergenic
0.99 (10-54)
13
38295234
1.46E-10
9
0.62, 0.95
0.33
Intergenic
0 (0)
15
48949358
7.17E-07
25
0.65, 0.72
0.07
LINE
Intron
15
61044887
2.79E-07
22
0.72, 0.91
0.19
SINE
Intergenic
--
16
21110423
5.28E-06
35
0.64, 0.90
0.26
LINE
Intergenic
0 (0)
17
63715324
3.71E-08
17
0.71, 0.96
0.25
SINE
Intergenic
--
18
2402921
1.65E-09
12
0.66, 0.94
0.28
LINE
Intergenic
0.99 (10-54)
LRBA
--
0.99 (10-54)
Gene product
catalyzes desaturation
of fatty acids
0 (0)
0.99 (10-54)
Immunodeficiency
with autoimmunity
0 (0)
8
18
15238778
3.71E-08
18
0.74, 0.98
0.24
18
25317171
7.17E-14
2
0.59, 0.70
0.11
18
44990043
8.47E-08
21
0.70, 0.97
0.27
20
55919259
5.32E-06
36
0.74, 0.93
0.19
21
1420659
7.17E-14
3
0.56, 0.93
0.37
21
50277233
4.61E-06
33
0.78, 0.96
22
48102
2.80E-06
31
22
59355955
3.71E-08
24
2471
28
30
Intergenic
LINE
Intergenic
Intron
SINE
-EXT2
Excess bone
formation
-0.99 (10-54)
Intergenic
Neural adhesion
molecule in the
immunoglobulin
superfamily
Encodes the beta
subunit of folliclestimulating hormone;
associated with hypogonadotropism
Intron
CNTN5
0.18
Promoter
FSHB
0.56, 0.31
0.25
Intergenic
--
19
0.68, 0.92
0.24
Intergenic
0.99 (10-54)
4.61E-06
34
0.68, 0.78
0.10
Intergenic
0 (0)
39381398
7.17E-12
5
0.62, 0.98
0.36
Intergenic
0.99 (10-54)
38223134
4.71E-09
13
0.68, 0.99
0.31
Exon
32
10863611
2.01E-06
30
0.19, 0.03
0.16
34
52849
2.32E-13
4
0.41, 0.22
0.19
36
17278202
7.52E-07
27
0.68, 0.90
0.22
37
55537
4.04E-07
24
0.49, 0.28
0.21
SINE
0 (0)
LINE
LINE
Intron
Involved in the
hydrolysis of
nucleoside
diphosphate
derivatives
Intron
Intergenic
0.99 (10-54)
0.99 (10-54)
Intergenic
SINE
0.99 (10-54)
0.99 (10-54)
MAN2C1
NUDT9
0 (0)
RAPGEF4
Expressed
predominantly in
brain and adrenal
gland; variants have
been noted to
segregate with an
autistic phenotype
--
0 (0)
9
37
6088848
1.61E-11
6
0.53, 0.91
0.38
LINE
Intergenic
0.99 (10-54)
38
550233
6.58E-11
8
0.64, 0.96
0.32
SINE
Intergenic
--
CFA
3
Position
69553
Corrected
p-value
0.003
Rank
5
MFwolf,
MFpurebred
0.74, 0.78
∆
0.04
3
69592
0.003
4
0.74, 0.78
0.04
Intergenic
0 (0)
6
168151
0.003
3
0.33, 0.28
0.05
Intergenic
0 (0)
6
172430
0.003
2
0.73, 0.58
0.15
LINE
Intergenic
--
6
178713
0.003
8
0.33, 0.27
0.06
LINE
Intergenic
B.
In repeat
element?
Annotation
Intergenic
Gene name
h2 (p-value)
0 (0)
0 (0)
13
43138016
0.003
11
0.61, 0.53
0.08
LINE
Intron
GABRB1
15
39451104
0.003
6
0.48, 0.66
0.18
SINE
Intron
SLC17A8
15
39451120
0.003
7
0.52, 0.70
0.18
SINE
Intron
SLC17A8
16
10475592
0.003
9
0.54, 0.19
0.35
Intron
Novel
transcript
22
7972
0.004
13
0.76, 0.79
0.03
22
44061
0.004
14
0.50, 0.61
25
72494
0.00004
1
37
105637
0.003
37
105647
0.004
LINE
OMIM description
Involved in the
GABAergic
neurotransmission of
the mammalian
central nervous
system
Autosomal dominant
nonsyndromic
deafness; vesicular
glutamate transporter
Autosomal dominant
nonsyndromic
deafness; vesicular
glutamate transporter
0 (0)
0 (0)
0.99 (10-54)
0 (0)
Intergenic
0 (0)
0.11
Intergenic
0.99 (10-54)
0.51, 0.59
0.08
Intergenic
--
10
0.78, 0.80
0.02
Intergenic
0 (0)
12
0.59, 0.63
0.04
Intergenic
0 (0)
10
Supplemental Table S7. Mean methylation frequency for DMS surveyed across YNP wolf (n=33), Purebred dog (n=45), ngsd (n=4),
boz (n=1), and thai (n=1) (association scan, adjusted p<0.005). Sample size is indicated in parentheses. (Abbreviations: CFA, canine
chromosome).
Mean methylation frequency
YNP
Purebred
Type of
Rank CFA
Position
wolf
dog
ngsd
Boz
Thai
repeat
Gene name
Annotation
1
25
72494
0.506
0.590
0.643***
0.616 0.582
Intergenic
2
Intergenic
3
69553
0.738
0.775
0.832***
0.821 0.747
3
Intergenic
3
69592
0.739
0.772
0.817***
0.819 0.746
4
Intergenic
6
168151
0.325
0.281
0.310**
0.280 0.250
5
Intergenic
6
172430
0.729
0.577
0.612***
0.530 0.662
LINE
6
Intergenic
6
178713
0.328
0.272
0.315**
0.307 0.333
LINE
7
SLC17A8
15
39451104
0.481
0.662
0.436**
0.505 0.711
SINE
Intron
8
SLC17A8
15
39451120
0.521
0.699
0.468**
0.550 0.846
SINE
Intron
9
16
10475592
0.537
0.190
0.183*
0.177 0.341
Novel transcript
Intron
10
37
105637
0.782
0.800
0.811*
0.789 0.769
Intergenic
11
13
43138016
0.611
0.526
0.620**
0.668 0.586
LINE
GABRB1
Intron
12
Intergenic
22
7972
0.762
0.789
0.799*
0.813 0.807
LINE
13
Intergenic
22
44061
0.500
0.611
0.584*
0.520 0.578
14
Intergenic
37
105647
0.585
0.630
0.650*
0.630 0.588
* t-test of unequal variance between YNP wolf and ngsd, p<0.05
** t-test of unequal variance between purebred dog and ngsd, p<0.05
*** t-test of unequal variance between both comparisons, p<0.05
11
Supplemental Table S8. Gene ontology (GO) results associated with differential methylation between purebred dogs and YNP
wolves.
Analysis
Gene Ontology
Differential
Methylation
Biological
process
Molecular
function
Category Name
(total number of
genes in
pathway)
Small molecule
metabolic
process (282)
Metabolic
process (1527)
Organic
substance
metabolic
process (1430)
Cellular
metabolic
process (1357)
Singleorganism
metabolic
process (1466)
Biological
process (2260)
Cellular process
(2012)
Primary
metabolic
process (1374)
Catalytic
activity (861)
Molecular
function (2473)
Observed
number of
genes
Expected
number of
genes
Ratio of
enrichment
(obs/expect)
Raw P value
Adjusted P
value
2
0.37
5.41
0.04
0.34
2
2.03
0.99
1.00
1.00
TUBD1,
DEGS1
TUBD1,
DEGS1
2
1.9
1.05
0.69
1.00
TUBD1,
DEGS1
2
1.8
1.11
0.65
1.00
TUBD1,
DEGS1
2
1.95
1.03
0.72
1.00
3
3
1.00
1.00
1.00
2
2.67
0.75
1.00
1.00
2
1.82
1.10
0.66
1.00
2
1.04
1.92
0.28
0.56
3
3
1.00
1.00
1.00
Observed
Genes
TUBD1,
DEGS1
TUBD1,
GABRB1,
DEGS1
TUBD1,
DEGS1
TUBD1,
DEGS1
TUBD1,
DEGS1
TUBD1,
GABRB1,
DEGS1
12
Cellular
component
Neutrality in
purebred dogs
(bootstrap
intervals)
Biological
process
Integral to
membrane
(264)
Intrinsic to
membrane
(271)
Membrane part
(419)
Membrane
(717)
2
0.34
5.88
0.04
0.13
2
0.35
5.71
0.04
0.13
2
0.54
3.70
0.09
0.20
2
0.93
2.15
0.23
0.40
Cell (2112)
Cellular
component
(2321)
2
2.73
0.73
1.00
1.00
3
3
1.00
1.00
1.00
Cell part (2112)
2
2.73
0.73
1.00
1.00
2
1.82
1.10
0.59
1.00
4
3.88
1.03
0.64
1.00
5
5.34
0.94
1.00
1.00
4
3.80
1.05
0.61
1.00
Protein
metabolic
process (684)
Singleorganism
metabolic
process (1466)
Cellular process
(2012)
Organic
substance
metabolic
process (1430)
GABRB1,
DEGS1
GABRB1,
DEGS1
GABRB1,
DEGS1
GABRB1,
DEGS1
TUBD1,
GABRB1
TUBD1,
GABRB1,
DEGS1
TUBD1,
GABRB1
CPXM2,
UBE3C
FOSL2,
CPXM2,
ADCY1,
UBE3C
FOSL2,
CPXM2,
GCOM1,
ADCY1,
UBE3C
FOSL2,
CPXM2,
ADCY1,
UBE3C
13
Biological
process (2260)
Heterocyclic
biosynthetic
process (5320)
Organic
substance
biosynthetic
process (719)
Primary
metabolic
process (1374)
Biological
regulation
(1323)
Cellular
metabolic
process (1357)
Molecular
function
Catalytic
activity (861)
Molecular
function (2473)
Protein binding
(1568)
6
6.00
1.00
1.00
1.00
FOSL2,
CPXM2,
GCOM1,
ADCY1,
GABRB1,
UBE3C
2
1.41
1.42
0.43
1.00
FOSL2,
ADCY1
2
1.91
1.05
0.62
1.00
4
3.65
1.10
0.57
1.00
2
3.50
0.57
1.00
1.00
3
3.60
0.83
1.00
1.00
4
2.09
1.91
0.12
0.46
6
6.00
1.00
1.00
1.00
2
3.80
0.53
1.00
1.00
FOSL2,
ADCY1
FOSL2,
CPXM2,
ADCY1,
UBE3C
FOSL2,
GCOM1
FOSL2,
ADCY1,
UBE3C
CPXM2,
AGPHD1,
ADCY1,
UBE3C
FOSL2,
CPXM2,
AGPHD1,
ADCY1,
GABRB1,
UBE3C
FOSL2,
UBE3C
14
Binding (2107)
Cellular
component
Organelle
(1594)
Membranebounded
organelle
(1445)
3
5.11
0.59
1.00
1.00
3
4.81
0.62
1.00
1.00
3
4.36
0.69
1.00
1.00
3
5.55
0.54
1.00
1.00
Cell part (2112)
Cell periphery
(348)
6
6.37
0.94
1.00
1.00
2
1.05
1.90
0.28
1.00
Nucleus (935)
Plasma
membrane
(331)
2
2.82
0.71
1.00
1.00
2
1.00
2.00
0.26
1.00
Cellular
component
(2321)
7
7.00
1.00
1.00
1.00
Intracellular
(1957)
4
5.90
0.68
1.00
1.00
Intracellular
part (1841)
FOSL2,
CPXM2,
UBE3C
FOSL2,
LRBA,
GCOM1
FOSL2,
LRBA,
GCOM1
FOSL2,
LRBA,
GCOM1
FOSL2,
LRBA,
GCOM1,
ADCY1,
GABRB1,
UBE3C
ADCY1,
GABRB1
FOSL2,
GCOM1
ADCY1,
GABRB1
FOSL2,
LRBA,
CPXM2,
GCOM1,
ADCY1,
GABRB1,
UBE3C
FOSL2,
LRBA,
GCOM1,
UBE3C
15
Neutrality
(permutation)
Biological
process
Membrane
(717)
Establishment
of localization
(455)
Transport (436)
Localization
(623)
Biological
regulation
(1323)
Regulation of
biological
process (1269)
Molecular
function
Biological
process (2260)
Cellular process
(2012)
Protein binding
(1568)
Molecular
function (2473)
Cellular
component
Binding (2107)
Intracellular
membranebounded
organelle
(1443)
Intracellular
part (1841)
ADCY1,
GABRB1
2
2.16
0.93
1.00
1.00
2
0.60
3.33
0.11
0.37
2
0.58
3.45
0.10
0.37
2
0.83
2.41
0.19
0.43
MYRIP,
ANXA6
MYRIP,
ANXA6
MYRIP,
ANXA6
2
1.76
1.14
0.63
0.88
DCAF6,
ANXA6
2
1.68
1.19
0.59
0.88
3
3.00
1.00
1.00
1.00
2
2.67
0.75
1.00
1.00
2
1.90
1.05
0.70
1.00
3
3.00
1.00
1.00
1.00
2
2.56
0.78
1.00
1.00
2
1.87
1.07
0.68
0.98
3
2.38
1.26
0.50
0.98
DCAF6,
ANXA6
DCAF6,
MYRIP,
ANXA6
DCAF6,
MYRIP
MYRIP,
ANXA6
DCAF6,
MYRIP,
ANXA6
MYRIP,
ANXA6
DCAF6,
MYRIP
DCAF6,
MYRIP,
ANXA6
16
Cell (2112)
Cytoplasmic
part (843)
Intracellular
(1957)
Macromolecular
complex (576)
Protein complex
(509)
Cytoplasm
(1270)
Cell part (2112)
Membranebounded (1445)
3
2.73
1.10
0.75
0.98
2
1.09
1.83
0.30
0.98
3
2.53
1.19
0.60
0.98
2
0.74
2.70
0.15
0.98
2
0.66
3.03
0.12
0.98
2
1.64
1.22
0.57
0.98
3
2.73
1.10
0.75
0.98
2
1.87
1.07
0.68
0.98
DCAF6,
MYRIP,
ANXA6
MYRIP,
ANXA6
DCAF6,
MYRIP,
ANXA6
DCAF6,
MYRIP
DCAF6,
MYRIP
MYRIP,
ANXA6
DCAF6,
MYRIP,
ANXA6
DCAF6,
MYRIP
17
Supplemental Table S9. Neutrality estimates (Dm) for polymorphic gene bodies in A) YNP wolves (ngene bodies=96) and purebred dogs
(ngene bodies=63). Number examined sites indicate number of sites in a gene body (number is the same in both YNP wolf and purebred
dog). Number segregating sites indicate the number of polymorphic sites within a gene body (YNP wolf and purebred dog are
̂ and 𝜃𝑠
̂ are two estimators of the mutation parameter used to calculate Dm (See Methods). B) Bootstrap
indicated separately). 𝜃𝜋
analyses on neutrality estimates (Dm) in purebred dogs, where the bolded values indicate that the 99.5% bootstrap confidence intervals
(BCI) do not overlap with the mean observed Dm value in purebred dogs (Dm = -0.5598).
A.
YNP wolf
Ensemble gene
CNKSR3
PTPRK
APBA1
EPM2A
MYH14
ENSCAFT00000045887
SHKBP1
Purebred Dog
Description
CNKSR family
member 3
protein tyrosine
phosphatase,
receptor type, K
amyloid beta (A4)
precursor proteinbinding, family A,
member 1
epilepsy,
progressive
myoclonus type 2A,
Lafora disease
(laforin)
myosin, heavy chain
14, non-muscle
Uncharacterized
protein
SH3KBP1 binding
protein 1
#examined
sites
#segregating
sites
̂𝜋
𝜃
𝜃̂𝑠
Dm
#segregating
sites
̂𝜋
𝜃
𝜃̂𝑠
Dm
1
1
0.1457
0.3859
-1.0073
-
-
-
-
2
1
0.0157
0.1484
-1.3005
-
-
-
-
4
1
0.0238
0.0690
-0.9229
-
-
-
-
2
1
0.2495
0.1484
0.9911
1
0.0221
0.1369
-1.1272
3
1
0.0211
0.0939
-1.1036
-
-
-
-
95
39
0.1073
0.1500
-0.9634
76
0.1078
0.3073
-2.1759
11
-
-
-
-
1
0.0020
0.0224
-1.1732
18
ENSCAFT00000025778
CASP4
SORL1
WBSCR17
ASPHD1
GPR139
PDXDC1
LMF1
PRM3
PAPPA2
DCAF6
SPATA45
ENSCAFT00000043311
SCYL3
Uncharacterized
protein
Canis lupus
familiaris caspase 4,
apoptosis-related
cysteine peptidase
(CASP4), mRNA.
sortilin-related
receptor, L(DLR
class) A repeats
containing
Williams-Beuren
syndrome
chromosome region
17
aspartate betahydroxylase domain
containing 1
G protein-coupled
receptor 139
pyridoxal-dependent
decarboxylase
domain containing 1
lipase maturation
factor 1
protamine 3
pappalysin 2
DDB1 and CUL4
associated factor 6
spermatogenesis
associated 45
Uncharacterized
protein
SCY1-like 3 (S.
cerevisiae)
1
1
0.4958
0.3859
0.4609
1
0.2484
0.3540
-0.446
4
1
0.0157
0.0690
-1.0885
-
-
-
-
1
-
-
-
-
1
0.0222
0.3540
-1.4011
3
1
0.0320
0.0939
-0.9383
-
-
-
-
5
2
0.1390
0.1148
0.3962
2
0.1249
0.1221
0.0434
1
-
-
-
-
1
0.0222
0.3540
-1.4011
6
1
0.0052
0.0451
-1.239
-
-
-
-
7
-
-
-
-
1
0.0031
0.0356
-1.1791
3
-
-
-
-
1
0.0146
0.0868
-1.0936
6
-
-
-
-
2
0.0072
0.0868
-1.5922
2
1
0.2313
0.1484
0.8128
1
0.0335
0.1369
-1.0148
3
1
0.2627
0.0939
2.5581
-
-
-
-
287
74
0.0627
0.0913
-1.083
125
0.0660
0.1429
-1.8177
2
1
0.0319
0.1484
-1.1412
-
-
-
-
19
ENSCAFT00000046625
DPF3
TNFAIP2
FBXL20
SYNRG
MORN5
TUBD1
CBX8
LOC490917
SCPEP1
FUBP3
ENSCAFT00000049101
TMEM131
ENSCAFT00000021381
CRELD2
Uncharacterized
protein
D4, zinc and double
PHD fingers, family
3
tumor necrosis
factor, alphainduced protein 2
F-box and leucinerich repeat protein
20
synergin, gamma
MORN repeat
containing 5
Canis lupus
familiaris tubulin,
delta 1 (TUBD1),
mRNA.
chromobox
homolog 8
Uncharacterized
protein
serine
carboxypeptidase 1
far upstream
element (FUSE)
binding protein 3
Uncharacterized
protein
transmembrane
protein 131
Uncharacterized
protein
cysteine-rich with
EGF-like domains 2
54
18
0.0763
0.0986
-0.7106
38
0.1009
0.2196
-1.7499
3
1
0.0544
0.0939
-0.599
-
-
-
-
1
1
0.0322
0.3859
-1.4832
-
-
-
-
3
1
0.0320
0.0939
-0.9383
-
-
-
-
2
1
0.3490
0.1484
1.9666
-
-
-
-
2
-
-
-
-
1
0.0109
0.1369
-1.2369
3
-
-
-
-
1
0.0932
0.0868
0.0981
2
1
0.0836
0.1484
-0.6352
-
-
-
-
32
12
0.1944
0.1170
1.991
13
0.1656
0.1418
0.5
2
2
0.9252
0.3859
2.9115
2
0.6185
0.3540
1.4489
3
1
0.1234
0.0939
0.4472
-
-
-
-
3
2
0.0432
0.2122
-1.5546
-
-
-
-
3
1
0.0658
0.0939
-0.4261
-
-
-
-
2
1
0.0157
0.1484
-1.3005
-
-
-
-
4
-
-
-
-
2
0.0109
0.1369
-1.6292
20
CNTLN
ENSCAFT00000041077
SPAG1
LIMCH1
GABRB1
TMEM165
AASDH
HYKK
ENSCAFT00000046804
OBSCN
FKBP9
CPED1
PSMB2
centlein,
centrosomal protein
Uncharacterized
protein
sperm associated
antigen 1
LIM and calponin
homology domains
1
gammaaminobutyric acid
(GABA) A receptor,
beta 1
transmembrane
protein 165
aminoadipatesemialdehyde
dehydrogenase
hydroxylysine
kinase
Uncharacterized
protein
obscurin,
cytoskeletal
calmodulin and
titin-interacting
RhoGEF
FK506 binding
protein 9, 63 kDa
cadherin-like and
PC-esterase domain
containing 1
proteasome
(prosome,
macropain) subunit,
beta type, 2
1
1
0.1890
0.3859
-0.8258
-
-
-
-
4
2
0.0237
0.1484
-1.5999
3
0.0634
0.2359
-1.5563
2
1
0.1015
0.1484
-0.459
-
-
-
-
13
1
0.0024
0.0205
-1.2275
-
-
-
-
1
1
1.3604
0.3859
4.0866
1
1.3773
0.3540
4.3213
3
2
0.0432
0.2122
-1.5546
-
-
-
-
2
-
-
-
-
1
0.0571
0.1369
-0.783
1
1
0.6107
0.3859
0.9425
1
0.5853
0.3540
0.9767
1
-
-
-
-
1
0.0222
0.3540
-1.4011
7
-
-
-
-
1
0.0223
0.0356
-0.4824
3
1
0.0320
0.0939
-0.9383
-
-
-
-
6
1
0.0541
0.0451
0.2782
-
-
-
-
1
1
0.0322
0.3859
-1.4832
-
-
-
-
21
SLC17A8
LRBA
UBE3C
ADCY1
PKD1L1
ENSCAFT00000039213
ENSCAFT00000042812
FOSL2
KCNG3
RNF103
TRIB2
CKAP5
EXT2
solute carrier family
17 (vesicular
glutamate
transporter),
member 8
LPS-responsive
vesicle trafficking,
beach and anchor
containing
ubiquitin protein
ligase E3C
adenylate cyclase 1
(brain)
polycystic kidney
disease 1 like 1
Uncharacterized
protein
Uncharacterized
protein
FOS-like antigen 2
potassium channel,
voltage gated
modifier subfamily
G, member 3
ring finger protein
103
Canis lupus
familiaris tribbles
homolog 2
(Drosophila)
(TRIB2), mRNA.
cytoskeleton
associated protein 5
exostosin
glycosyltransferase
2
6
5
1.0086
0.2948
6.3571
5
0.4409
0.2902
1.3058
7
3
0.1484
0.1206
0.4949
2
0.1028
0.0735
0.6908
4
2
0.1271
0.1613
-0.4158
1
0.1405
0.0638
1.5689
41
3
0.0160
0.0195
-0.3705
2
0.0191
0.0124
0.9224
45
1
0.0014
0.0059
-1.0565
2
0.0014
0.0113
-1.5021
1
1
0.0322
0.3859
-1.4832
1
0.0222
0.3540
-1.4011
58
14
0.1241
0.0887
1.2494
13
0.0664
0.0806
-0.5265
2
1
0.4518
0.1484
2.9739
1
0.4472
0.1369
3.0456
1
1
0.1457
0.3859
-1.0073
-
-
-
-
4
2
0.0659
0.1484
-1.0578
-
-
-
-
3
1
0.0888
0.0939
-0.0767
-
-
-
-
1
1
0.0322
0.3859
-1.4832
-
-
-
-
2
1
0.3182
0.1484
1.6645
-
-
-
-
22
NADSYN1
AMBRA1
LOC100856444
KIF5C
RNF150
TBC1D9
ARHGAP12
CELF2
LOC102154105
ARHGEF28
ZNF423
LDLRAD2
PEX14
LOC607487
IFFO2
NAD synthetase 1
autophagy/beclin-1
regulator 1
Uncharacterized
protein
kinesin family
member 5C
ring finger protein
150
TBC1 domain
family, member 9
(with GRAM
domain)
Rho GTPase
activating protein
12
CUGBP, Elav-like
family member 2
Uncharacterized
protein
Rho guanine
nucleotide exchange
factor (GEF) 28
zinc finger protein
423
low density
lipoprotein receptor
class A domain
containing 2
peroxisomal
biogenesis factor 14
Uncharacterized
protein
Canis lupus
familiaris taste
receptor, type 1,
1
1
0.2348
0.3859
-0.6337
-
-
-
-
11
1
0.0262
0.0243
0.1136
-
-
-
-
13
1
0.0122
0.0205
-0.5605
2
0.0227
0.0392
-0.7258
4
1
0.0238
0.0690
-0.9229
-
-
-
-
3
1
0.0658
0.0939
-0.4261
-
-
-
-
3
-
-
-
-
1
0.0072
0.0868
-1.2054
4
-
-
-
-
1
0.0054
0.0638
-1.1928
5
1
0.0321
0.0546
-0.577
-
-
-
-
11
1
0.0688
0.0243
2.5544
3
0.0672
0.0709
-0.1056
1
1
0.2348
0.3859
-0.6337
-
-
-
-
3
1
0.0104
0.0939
-1.2653
-
-
-
-
1
-
-
-
-
1
0.0971
0.3540
-1.0847
5
2
0.0439
0.1148
-1.1625
4
0.0775
0.2517
-1.6018
5
4
0.1297
0.2778
-1.3197
1
0.0043
0.0504
-1.1861
1
1
0.1051
0.3859
-1.1776
-
-
-
-
23
ISY1
ENSCAFT00000007458
KLHL18
KLHL26
ICAM4
CNTN5
VSTM5
C2CD3
DENND5A
MYRIP
NKTR
member 2
(TAS1R2), mRNA.
Canis lupus
familiaris ISY1
splicing factor
homolog (S.
cerevisiae) (ISY1),
mRNA.
Uncharacterized
protein
kelch-like family
member 18
kelch-like family
member 26
intercellular
adhesion molecule 4
(LandsteinerWiener blood
group)
contactin 5
V-set and
transmembrane
domain containing 5
Canis lupus
familiaris
uncoupling protein
3 (mitochondrial,
proton carrier)
(UCP3), mRNA.
DENN/MADD
domain containing
5A
myosin VIIA and
Rab interacting
protein
natural killer cell
3
-
-
-
-
1
0.0072
0.0868
-1.2054
1
1
0.0672
0.3859
-1.3363
1
0.0458
0.3540
-1.3015
1
-
-
-
-
1
0.0708
0.3540
-1.196
2
1
0.1015
0.1484
-0.459
1
0.2487
0.1369
1.0967
1
1
0.0672
0.3859
-1.3363
1
0.1248
0.3540
-0.9678
1
1
1.3604
0.3859
4.0866
-
-
-
-
3
2
0.0428
0.2122
-1.5579
2
0.0146
0.1955
-1.6793
2
1
0.1943
0.1484
0.4499
1
0.0941
0.1369
-0.4203
1
1
0.3859
0.3859
-0.0002
-
-
-
-
5
1
0.1027
0.0546
1.24
1
0.0177
0.0504
-0.8429
2
-
-
-
-
1
0.0109
0.1369
-1.2369
24
triggering receptor
UBE2E1
ATP1B3
RBL1
TOP1
SLMO2
TCFL5
FOXO1
ENSCAFT00000012239
MLPH
GPR133
ENSCAFT00000047590
SCN8A
ANO6
CPXM2
FBXL17
Uncharacterized
protein
ATPase, Na+/K+
transporting, beta 3
polypeptide
retinoblastoma-like
1
Uncharacterized
protein
slowmo homolog 2
(Drosophila)
transcription factorlike 5 (basic helixloop-helix)
forkhead box O1
Uncharacterized
protein
Canis lupus
familiaris
melanophilin
(MLPH), mRNA.
G protein-coupled
receptor 133
Uncharacterized
protein
sodium channel,
voltage gated, type
VIII alpha subunit
anoctamin 6
carboxypeptidase X
(M14 family),
member 2
Uncharacterized
protein
8
-
-
-
-
1
0.0027
0.0311
-1.177
5
1
0.0126
0.0546
-1.0805
-
-
-
-
5
2
0.0187
0.1101
-1.5378
4
0.1195
0.2746
-1.3384
3
1
0.0211
0.0939
-1.1036
-
-
-
-
1
1
0.2830
0.3859
-0.4316
-
-
-
-
8
1
0.0240
0.0336
-0.3967
-
-
-
-
1
1
0.0322
0.3859
-1.4832
-
-
-
-
1
1
0.7863
0.3859
1.6792
1
0.4662
0.3540
0.4741
1
-
-
-
-
1
0.0222
0.3540
-1.4011
10
1
0.0031
0.0267
-1.2303
1
0.0088
0.0247
-0.8294
2
-
-
-
-
2
0.1524
0.3540
-1.1044
2
1
0.1756
0.1484
0.2668
-
-
-
-
3
-
-
-
-
1
0.0072
0.0868
-1.2054
5
1
0.0653
0.0546
0.2774
1
0.0948
0.0504
1.1405
6
-
-
-
-
1
0.0036
0.0418
-1.1819
25
SPATA9
RASA1
PPP2R2C
RPS23
POLR2M
ITGA11
MAN2C1
PRDM15
ENSCAFT00000048553
NUDT9
CAMK2D
OSBPL11
PHC3
RAPGEF4-201
RAPGEF4-202
spermatogenesis
associated 9
RAS p21 protein
activator (GTPase
activating protein) 1
protein phosphatase
2, regulatory
subunit B, gamma
ribosomal protein
S23
polymerase (RNA)
II (DNA directed)
polypeptide M
integrin, alpha 11
mannosidase, alpha,
class 2C, member 1
PR domain
containing 15
Uncharacterized
protein
nudix (nucleoside
diphosphate linked
moiety X)-type
motif 9
calcium/calmodulindependent protein
kinase II delta
oxysterol binding
protein-like 11
polyhomeotic
homolog 3
(Drosophila)
Rap guanine
nucleotide exchange
factor (GEF) 4
Rap guanine
3
1
0.0320
0.0939
-0.9383
-
-
-
-
8
3
0.0238
0.1069
-1.6744
-
-
-
-
2
1
0.2313
0.1484
0.8128
-
-
-
-
5
-
-
-
-
2
0.0221
0.1061
-1.3853
5
4
0.6710
0.2824
3.4214
5
0.6235
0.3566
1.8903
1
-
-
-
-
1
0.0222
0.3540
-1.4011
1
1
0.9573
0.3859
2.396
-
-
-
-
2
1
0.0319
0.1484
-1.1412
-
-
-
-
6
1
0.0432
0.0451
-0.0604
1
0.0147
0.0418
-0.8381
1
1
0.6107
0.3859
0.9425
-
-
-
-
3
1
0.1004
0.0939
0.0986
-
-
-
-
3
2
0.1858
0.2122
-0.2432
1
0.0611
0.0868
-0.3895
1
1
0.2830
0.3859
-0.4316
-
-
-
-
1
1
0.0672
0.3859
-1.3363
-
-
-
-
3
1
0.1569
0.0939
0.9553
-
-
-
-
26
NHEJ1
BROX
ANXA6
nucleotide exchange
factor (GEF) 4
nonhomologous
end-joining factor 1
BRO1 domain and
CAAX motif
containing
annexin A6
1
1
0.0672
0.3859
-1.3363
-
-
-
-
7
1
0.0044
0.0385
-1.2358
-
-
-
-
4
1
0.0078
0.0690
-1.2512
1
0.0688
0.0638
0.1042
B.
Ensembl gene list
EPM2A
ENSCAFT00000045887
SHKBP1
CRELD2
5_8S_RRNA
GABRB1
AASDH
HYKK
PRNA
OBSCN
SLC17A8
LRBA
UBE3C
ADCY1
PKD1L1
ENSCAFT00000039213
Purebred dog
Observed Dm
-1.1272
-2.1759
-1.1732
-1.6292
-1.5563
4.3213
-0.7830
0.9767
-1.4011
-0.4824
1.3058
0.6908
1.5689
0.9224
-1.5021
-1.4011
99.5% BCI
[-1.1272,0.0000]
[-2.6895,-0.5478]
[-1.1732,0.0000]
[-1.6292,0.0000]
[-1.9072,-0.2942]
[3.5176,4.3692]
[-1.2369,0.0002]
[-0.4460,2.5042]
[-1.4011,0.0000]
[-1.1791,0.462]
[-0.6894,3.5817]
[0.3558,2.6460]
[0.4630,2.3832]
[0.4162,2.5009]
[-1.5482,0.0000]
[-1.4011,0.0000]
# sites
examined
2
95
11
4
4
1
2
1
1
7
6
7
4
41
45
1
# sites
segregating
1
76
1
2
3
1
1
1
1
1
5
2
1
2
2
1
Purebred
dog
̂
𝜃𝜋
Purebred
dog
̂
𝜃𝑠
0.0221
0.1078
0.0020
0.0109
0.0634
1.3773
0.0571
0.5853
0.0222
0.0223
0.4409
0.1028
0.1405
0.0191
0.0014
0.0222
0.1369
0.3073
0.0224
0.1369
0.2359
0.3540
0.1369
0.3540
0.3540
0.0356
0.2902
0.0735
0.0638
0.0124
0.0113
0.3540
Significant
in DmDiff
yes
yes
yes
27
ENSCAFT00000042812
FOSL2
ENSCAFT00000049369
TBC1D9
ARHGAP12
ENSCAFT00000012091
LDLRAD2
PEX14
ENSCAFT00000035834
ENSCAFT00000006963
H1FOO
KLHL18
KLHL26
ICAM4
VSTM5
ENSCAFT00000008943
MYRIP
NKTR
ENSCAFT00000009308
RBL1
NEK1
MLPH
GPR133
ENSCAFT00000047590
ANO6
CPXM2
-0.5265
3.0456
-0.7258
-1.2054
-1.1928
-0.1056
-1.0847
-1.6018
-1.1861
-1.2054
-1.3015
-1.1960
1.0967
-0.9678
-1.6793
-0.4203
-0.8429
-1.2369
-1.1770
-1.3384
0.4741
-1.4011
-0.8294
-1.1044
-1.2054
1.1405
[-1.3035,1.4598]
[2.9061,3.0582]
[-1.2675,1.1186]
[-1.2054,0.0000]
[-1.1928,0.0000]
[-0.3346,2.6286]
[-1.4011,0.0000]
[-2.0275,0.2643]
[-1.1861,0.0000]
[-1.2054,0.0000]
[-1.4011,0.0000]
[-1.4011,0.0000]
[-0.0445,2.2056]
[-1.4011,0.0000]
[-1.6793,0.0000]
[-1.1272,0.5937]
[-1.1861,0.0000]
[-1.2369,0.0000]
[-1.1770,0.0000]
[-1.8598,1.3629]
[-0.8453,2.0062]
[-1.4011,0.0000]
[-1.1742,0.0000]
[-1.7538,0.0084]
[-1.2054,0.0000]
[0.1074,2.0755]
58
2
13
3
4
11
1
5
5
3
1
1
2
1
3
2
5
2
8
5
1
1
10
2
3
5
13
1
2
1
1
3
1
4
1
1
1
1
1
1
2
1
1
1
1
4
1
1
1
2
1
1
0.0664
0.4472
0.0227
0.0072
0.0054
0.0672
0.0971
0.0775
0.0043
0.0072
0.0458
0.0708
0.2487
0.1248
0.0146
0.0941
0.0177
0.0109
0.0027
0.1195
0.4662
0.0222
0.0088
0.1524
0.0072
0.0948
0.0806
0.1369
0.0392
0.0868
0.0638
0.0709
0.3540
0.2517
0.0504
0.0868
0.3540
0.3540
0.1369
0.3540
0.1955
0.1369
0.0504
0.1369
0.0311
0.2746
0.3540
0.3540
0.0247
0.3540
0.0868
0.0504
yes
yes
yes
28
ENSCAFT00000011918
RPS23
POLR2M
ITGA11
ENSCAFT00000048553
OSBPL11
ANXA6
ACAP1
SORL1
ASPHD1
GPR139
LMF1
PRM3
PAPPA2
DCAF6
ENSCAFT00000043311
ENSCAFT00000046625
MORN5
TUBD1
ENSCAFT00000045469
SCPEP1
-1.1819
-1.3853
1.8903
-1.4011
-0.8381
-0.3895
0.1042
-0.4460
-1.4011
0.0434
-1.4011
-1.1791
-1.0936
-1.5922
-1.0148
-1.8177
-1.7499
-1.2369
0.0981
0.5000
1.4489
[-1.1819,0.0000]
[-1.6057,0.0000]
[1.0183,4.3890]
[-1.4011,0.0000]
[-1.1819,0.0000]
[-1.0936,0.5847]
[-0.8504,1.1507]
[-1.3015,0.8071]
[-1.4011,0.0000]
[-0.8234,1.1767]
[-1.4011,0.0000]
[-1.1791,0.0000]
[-1.2054,0.0000]
[-1.5922,0.0000]
[-1.2369,0.0000]
[-2.3549,-0.2846]
[-2.3744,0.1261]
[-1.2369,0.0000]
[-0.7477,1.1700]
[-0.6038,2.7782]
[0.2443,2.7496]
6
5
5
1
6
3
4
1
1
5
1
7
3
6
2
287
54
2
3
32
2
1
2
5
1
1
1
1
1
1
2
1
1
1
2
1
125
38
1
1
13
2
0.0036
0.0221
0.6235
0.0222
0.0147
0.0611
0.0688
0.2484
0.0222
0.1249
0.0222
0.0031
0.0146
0.0072
0.0335
0.0660
0.1009
0.0109
0.0932
0.1656
0.6185
0.0418
0.1061
0.3566
0.3540
0.0418
0.0868
0.0638
0.3540
0.3540
0.1221
0.3540
0.0356
0.0868
0.0868
0.1369
0.1429
0.2196
0.1369
0.0868
0.1418
0.3540
yes
yes
yes
29
Supplemental Figure S1. Examples of how PCA was used to identify/exclude outlier
samples. A) PCA of 93 samples, of which three are identified as outliers; B) PCA of 90
samples, of which an additional three outliers are identified for exclusion; C) PCA of 87
of which an additional outlier is identified for exclusion; D) the final dataset after
removing seven outliers.
30
Supplemental Figure S2. Population assignments from ADMIXTURE for K=2-4 of
1,307 unlinked SMPs, excluding outlier samples. Epigenetic clusters are labeled
(Abbreviations: ngsd, New Guinea Singing Dog; village, Boz and Thai village dogs). The
best fit level of partitioning is found at K=2 (see Supplemental Table S4).
31
Supplemental Figure S3. Quantile-quantile plots of the negative log10 p-values from
association analysis. Dashed lines show the 95% confidence intervals. Large deviations
from the diagonal (red lines) are indicative of inflation.
32
Supplemental Figure S4. Heritability across the wolf genome for A) narrow sense; B)
broad sense heritability (n=23997 methylation marks). Inner circle corresponds to zero
values and outer circle corresponds to values near one.
33
Supplemental Figure S5. Manhattan plots for methylation marks with non-zero variance
components from A) Analysis 1 (n=4504); B) Analysis 2 (n=1432). Horizontal dashed
lines represent the genome-wide significance threshold correcting for multiple testing,
5.68= -log10(2.08 x 10^-6).
34