Supplementary Table 1. Description of the landmarks used in skull and mandible. See Figure 1 for a
representation within the structures.
Landmark
Skull
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
39
40
41
42
43
44
45
46
47
48
Mandible
1
2
3
4
5
6
7
8
9
10
11
12
13
14
Description
Nasal bones most anterior suture
Nasal bones most posterior suture
Frontal bones most posterior suture
Parietal bones most posterior suture
Interparietal bone most posterior point on the median line
Right side, most anterior point of the suture between frontal and parietal bones
Left side, most anterior point of the suture between frontal and parietal bones
Right side, intersection between parietal, occipital and squamosal bones
Left side, intersection between parietal, occipital and squamosal bones
Right, most posterior junction of squamosal bone and the zygomatic process of the squamosal bone
Left, most posterior junction of squamosal bone and the zygomatic process of the squamosal bone
Right side, most anterior suture of the zygomatic process of the squamosal bone and jugal bone
Left side, most anterior suture of the zygomatic process of the squamosal bone and jugal bone
Right side, most anterior suture of jugal bone and the zygomatic process of the maxillary bone
Left side, most anterior suture of jugal bone and the zygomatic process of the maxillary bone
Right side, intersection of the frontal, lacrimal and the zygomatic process of the maxillary bone
Left side, intersection of the frontal, lacrimal and the zygomatic process of the maxillary bone
Right infraorbital foramen most superior point
Left infraorbital foramen most superior point
Right infraorbital foramen most inferior point
Left infraorbital foramen most inferior point
Right premaxilla-right nasal bone most anterior point of suture
Left premaxilla-left nasal bone most anterior point of suture
Most superior point of the right incisor alveolus
Most superior edge of the left incisor alveolus
Most inferior point of the right incisor alveolus
Most inferior point of the left incisor alveolus
Right premaxilla-maxilla most ventral juntion
Left premaxilla-maxilla most ventral juntion
Most anterior point of the right first molar alveolus
Most anterior point of the left first molar alveolus
Most posterior point of the right third molar alveolus
Most posterior point of the left third molar alveolus
Most inferior point of the right external acoustic meatus
Most inferior point of the left external acoustic meatus
Most superior point of the right external acoustic meatus
Most superior point of the left external acoustic meatus
Most anterior point of the right anterior palatine foramen
Most anterior point of the left anterior palatine foramen
Most posterior point of the right anterior palatine foramen
Most posterior point of the left anterior palatine foramen
Right pterygoid process, most posterior point
Left pterygoid process, most posterior point
Median-line point of the suture between occipital and basisphenoid bones
Median-line point of the suture between basisphenoid and presphenoid bones
Most posterior point of the suture between palatine bones
Foramen magnum most anterior point, Basion
Foramen magnum most posterior point, Bregma
Most superior point of the incisor alveolus
Most inferior point of the incisor alveolus
Most anterior point of the first molar alveolus
Most posterior point of the third molar alveolus
Most posterior tip of the coronoid process
Most anterior concave point of coronoid process
Most anterior point of the articular surface of the condyle
Most posterior tip of the condyle
Most anterior concave point between condyle and angular process
Most posterior tip of angular processs
Most inferior point of angular process
Ascending ramus dorsal-most ventral point
Alveolar region most inferior point
Most anterior point of the masseteric muscle insertion into the alveolar region
Supplementary Table 2. Principal components included in the mapping. The percentage of the total
variation that can be explained by all the SNPs used in the mapping is shown (pve) for PCs and for
centroid size.
PC
%var %cum
PC1*
16.6
16.6
PC2*
12.1
28.6
PC3
7.7
36.3
PC4
6.6
42.9
PC5
5.9
48.8
PC6
5.3
54.1
PC7
4.4
58.6
PC8
3.9
62.5
PC9
3.4
65.9
PC10*
2.9
68.8
PC11
2.5
71.3
PC12
2.4
73.7
PC13*
2.3
75.9
PC14*
1.9
77.8
PC15
1.7
79.5
PC16
1.5
81.1
PC17
1.3
82.4
PC18*
1.3
83.7
PC19
1.1
84.8
PC20
1
85.8
pve of total variation
Centroid Size
Skull
pve sd(pve)
0.93
0.06
0.73
0.08
0.93
0.06
0.9
0.06
0.79
0.09
0.57
0.14
0.78
0.11
0.58
0.12
0.69
0.1
0.73
0.11
0.69
0.12
0.54
0.11
0.53
0.15
0.43
0.15
0.68
0.12
0.68
0.17
0.34
0.14
0.36
0.13
0.38
0.14
0.42
0.21
64.2
72
16
pge
0.57
0.33
0.36
0.62
0.33
0.43
0.39
0.38
0.4
0.37
0.37
0.49
0.4
0.41
0.49
0.4
0.44
0.53
0.42
0.41
37.5
sd(pge)
0.3
0.29
0.28
0.26
0.29
0.28
0.29
0.28
0.28
0.27
0.28
0.3
0.28
0.29
0.28
0.27
0.29
0.3
0.29
0.27
33
25
PC
%var %cum
PC1
21.6
21.6
PC2
12.8
34.5
PC3*
8.3
42.8
PC4
7.6
50.4
PC5
6.5
56.9
PC6
5.5
62.4
PC7*
4.5
67
PC8
3.7
70.7
PC9
3.6
74.3
PC10
3
77.2
PC11*
2.8
80.1
PC12*
2.1
82.1
PC13*
2
84.1
PC14
1.8
85.9
PC15*
1.7
87.7
PC16*
1.4
89
PC17
1.4
90.4
PC18*
1.2
91.5
pve of total variation
Centroid Size
Mandible
pve sd(pve)
0.91
0.07
0.89
0.06
0.57
0.13
0.74
0.09
0.5
0.15
0.92
0.07
0.5
0.12
0.65
0.11
0.46
0.11
0.38
0.13
0.5
0.13
0.36
0.12
0.46
0.16
0.68
0.11
0.44
0.15
0.43
0.18
0.44
0.14
0.41
0.14
63.9
75
16
pge
0.44
0.21
0.39
0.34
0.35
0.24
0.37
0.33
0.43
0.4
0.37
0.34
0.48
0.33
0.44
0.4
0.4
0.46
33
sd(pge)
0.29
0.25
0.28
0.29
0.27
0.24
0.29
0.27
0.29
0.28
0.28
0.28
0.29
0.27
0.28
0.28
0.28
0.3
37
27
*indicates the PCs with significant associations. %var, percentage of total phenotypic variation
explained by each PC. %cum, cumulative variation. Pve, proportion (from 0 to 1) of the variation in
each PC explained by all the SNPs used in the mapping (“chip heritability”). Pve of total variation,
percentage of the total phenotypic variation in the mapping population explained by all the SNPs
used in the mapping, ∑𝑛1(𝑝𝑣𝑒 ∗ %𝑣𝑎𝑟), n= number of PCs. Pge, proportion (from 0 to 1) of the
variation in each PC that can be explained by SNPs of large effect. Sd, standard deviation. Pve and
pge values were calculated using the BSLMM model from GEMMA.