Copyright ? 2008 by the Genetics Society of America
A Genomewide Linkage Scan for Quantitative Trait Loci Influencing the
Craniofacial Complex in Baboons (Papio hamadryas spp.)
Richard J. Sherwood,*,†,1Dana L. Duren,*,‡Lorena M. Havill,§Jeff Rogers,§,**
Laura A. Cox,§,** Bradford Towne*,††and Michael C. Mahaney§,**
*Lifespan Health Research Center, Department of Community Health, Boonshoft School of Medicine, Wright State University, Dayton,
Ohio 45420,†Department of Neuroscience, Cell Biology and Physiology, Wright State University, Dayton, Ohio 45435,‡Department of
Orthopaedic Surgery, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45409,§Department of Genetics, Southwest
Foundation for Biomedical Research, San Antonio, Texas, 78245, **Southwest National Primate Research Center, San Antonio,
Texas 78245 and††Department of Pediatrics, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45404
Manuscript received April 21, 2008
Accepted for publication July 11, 2008
Numerous studies have detected significant contributions of genes to variation in development, size, and
shape of craniofacial traits in a number of vertebrate taxa. This study examines 43 quantitative traits derived
from lateral cephalographs of 830 baboons (Papio hamadryas) from the pedigreed population housed at the
Southwest National Primate Research Center. Quantitative genetic analyses were conducted using the
SOLAR analytic platform, a maximum-likelihood variance components method that incorporates all familial
information for parameter estimation. Heritability estimates were significant and of moderate to high
magnitude for all craniofacial traits. Additionally, 14 significant quantitative trait loci (QTL) were identified
for 12 traits from the three developmental components (basicranium, splanchnocranium, and neuro-
cranium) of the craniofacial complex. These QTL were found on baboon chromosomes (and human
orthologs) PHA1 (HSA1), PHA 2 (HSA3), PHA4 (HSA6), PHA11 (HSA12), PHA13 (HSA2), PHA16
(HSA17), and PHA17 (HSA13) (PHA, P. hamadryas; HSA, Homo sapiens). This study of the genetic
architecture of the craniofacial complex in baboons provides the groundwork needed to establish the
baboon as an animal model for the study of genetic and nongenetic influences on craniofacial variation.
typic characterizations have successfully categorized these
disorders, but both approaches are confounded by the
heterogeneous nature of the presentation. For example,
single mutations may produce different phenotypic syn-
syndrome and Pfeiffer syndrome, both caused by the
same mutation in fibroblast growth factor receptor 2
(Cys278Phe) (Cohen and Kreiborg 1998; Cohen 2002).
Alternatively, a specific syndrome, such as holoprosence-
phaly, may be caused by mutations in different genes. For
or SHH have been shown to cause holoprosencephaly.
Clearly, no simple relationship exists between these
genetic errors and their resultant phenotype. Current
of normal craniofacial form are largely restricted to
zebrafish, chick, and mouse or are based on interpreta-
tions of human dysmorphic syndromes. While the
information gathered from these studies is valuable,
RANIOFACIAL anomalies are among the most
common congenital defects. Phenotypic and geno-
to humans increases as tissue engineering and gene
therapy techniques become more possible.
The primate craniofacial complex is an integrated
structure composed of several developmental and func-
tional components. During ontogeny the three primary
and the basicranium, are vulnerable to genetic and envi-
ronmental influences and often show a coordinated
tions to cranial variationhave beenconducted in human
populations and have generally shown moderately high
levelsofheritability(e.g., Lundstro ¨m1954;Nakataetal.
1974; Byard et al. 1984a,b, 1985a,b; Nakata 1985;
Lundstro ¨m and McWilliam 1987, 1988; Kitahara
et al. 1996; Arya et al. 2002; Duren et al. 2003; Sherwood
et al. 2003). Although relatively fewer such studies have
been conducted in nonhuman primates, the nonhuman
primate craniofacial complex also generally exhibits heri-
table components (Cheverud and Buikstra 1981a,b,
1982; McGrath et al. 1984; e.g., Cheverud et al. 1990a,b;
Cheverud 1995; Hlusko et al. 2002). Many of these
studies, however, did not include traits from all de-
velopmental components; specifically, internal features
of the basicranium were frequently absent. This study
examines fundamental features of the genetic architec-
1Corresponding author: Lifespan Health Research Center, Boonshoft
School of Medicine, Wright State University, 3171 Research Blvd.,
Kettering, OH 45420-4014. E-mail: firstname.lastname@example.org
Genetics 180: 619–628 (September 2008)
of baboons (Papio hamadryas), using modern variance
components-based statistical genetic methods.
MATERIALS AND METHODS
Data for this study were obtained from 830 animals ranging
in age from 1.7 to 28.8 years from the pedigreed baboon
Southwest National Primate Research Center (SNPRC), San
P. hamadryas anubis and P. hamadryas cynocephalus and their
hybrids. The 830 animals with cephalometric data are mem-
bers of a single, unbroken, extended pedigree containing
2426 individuals. This pedigree is six generations deep, with a
majority of the animals (and thereby the genetic information)
in generations 0 (founders) through 4.
All nonfounder animals are the results of managed breed-
ing. While most of this large pedigree is noninbred, ?500
of the youngest baboons in it are inbred progeny obtained
in a single generation of matings between selected father–
daughter, half-sibling, and avuncular relative pairs. The de-
gree of inbreeding does not approach that of small laboratory
animals such as rat and mouse, but it does increase regions of
autozygosity throughout the baboon genome, maximizing
statistical power to detect, and precision to estimate, genetic
and environmental effects on the phenotypes measured in
subsets of members of the pedigree.
generations2–5.Fullsibships range insizefrom 2(n¼372)to
12 (n ¼ 10), with the median ¼ 5. In addition to parent–
offspring and full-sib pairs, the pedigree contains 49 other
simple and complex relative pair classes from which genetic
information can be extracted in our analyses: e.g., half-siblings
(n pairs ¼ 6855), half avuncular (n ¼ 6414), half first cousins
(n ¼ 1103), half avuncular and first cousins and double half
first cousins (n ¼ 136), etc.
Animal handling: Animals were anesthetized using Ket-
amine (some animalsalsorequired 5 mg intravenous Valium)
and transported for radiography. Each animal was laid on its
side and its head positioned for alignment during imaging,
and the jaws were held shut with soft tubing. Two right lateral
cephalographs per animal were taken according to standard
veterinary radiographic procedures. Exposure times varied
on the basis of size of the animal. In general, settings of 60–70
kVp and 100–200 mA, for 0.10–0.30 sec, at a tube distance of
37in.fromsourceto plate,provided excellentimagesacross a
wide range of body sizes. Mammography film and screens
were used for all images as these provided the highest-quality
images. Head width, taken as the maximum width, was
measured at the time of radiography using a cephalometric
board. The protocol used was approved by both the In-
stitutional Animal Care and Use Committee of the SNPRC
and the Laboratory Animal Care and Use Committee of
Wright State University.
Phenotyping: Phenotyping was done using the software
package Nemoceph (CDIimaging), a commercially available
program designed for rapid and accurate collection of
cephalometric data. Although the package is designed for
use with human radiographs, it was easily adapted to collect
data from the baboon radiographs. Prior to any measure-
ments, available radiographs for each animal were first
evaluated visually to assure correct positioning of the animal.
Radiographs that demonstrated any condition that may pre-
cludeaccurate measurement(suchas excessiverotation ofthe
skull relative to the plate) were not used. The single best
radiograph of each animal was used for measurements.
Radiographs were then scanned using an Epson Expression
10000XL scanner equipped with a transparency adapter.
Radiographs were scanned directly into Nemoceph, which
well as theapplicationofvarious filters(e.g., falsecolor, inverse
image) that may assist in identification of cephalometric
points. All radiographs were scanned along with a 10-cm ruler
used to calibrate the images prior to measurement. Tracing of
the radiograph begins with Nemoceph prompting the user to
place markers on predefined cephalometric points (Table 1;
Figure 1). Once these points have been placed, Nemoceph
the skull, central incisors, and first molars. These outlines are
fit to the cranial contours and teeth by the user with standard
computer drawing tools (e.g., handles and anchors) to provide
an exact tracing of the craniofacial features. Once tracing is
complete, the user has the option of collecting data on the
basis of several standard craniofacial analyses, such as Rickett’s
or Steiner’s analysis (Merow and Broadbent 1990), or
defining a unique set of measures. For our purposes, we have
identified a data set that incorporates aspects of standard
orthodontic analyses in addition to measures associated with
other types of cephalometric analyses.
the radiographs, as well as three variables derived from a
principal components analysis of the neurocranial measures
described below. Forty measurements were made on the basis
of the craniometric points identified (see Table 2). Points and
measurements chosen are designed to examine variation both
within and between craniofacial components. For example,
several measures are contained within their respective com-
ponent, such as posterior base length (Ba–S), anterior base
length(S–N), and angular measures such as basicranial flexion
(N–S–Ba), which are all contained within the basicranium.
Similarly, there are measures isolated to the splanchnocra-
nium, including facial height (N–Pr) and palate length (Pr–
landmarks. Angular measures such as facial hafting (S–N–Pr)
or the mandibular plane angle also span multiple cranial
components. All linear measurements were corrected for
radiographic enlargement using an established correction
factor.ThiscorrectionfactorisbasedontheformulaXðTH ? DÞ=
TH, where X is the radiographic measurement, TH is the tube
height (a constant 37 in.), and D is the distance from the object
to the film (Sherwood et al. 2000).
Because neurocranial landmarks are difficult to reliably
discern on lateral cephalographs, a set of measurements
designed to capture themaximal amount of informationfrom
the neurocranium was defined as follows. First, a line from
sella to nasion is identified. From this reference line, addi-
tional lines are placed every 10? up to 180?. For each line, a
measurement is taken from sella to the point of intersection
with the endocranial surface. As the first five such lines do not
always intersect the endocranial surface, these measures are
not collected; there are, therefore, 13 measures available to
describe the morphology of the neurocranium.
As it could be argued that measurements defined in this
manner are not necessarily homologous between individuals
(see Gunz et al. 2008 for a discussion of analysis of semiland-
latent variables describing the overall morphology of the
neurocranium. Three components were extracted using a
varimax rotation explaining 38.3, 27.6, and 25.7% of the vari-
(Table 3) indicate that PC1 is heavily influenced by anterior
neurocranial measurements (60?–120? from S–N), PC2 is
620R. J. Sherwood et al.
influenced by intermediate measures (110?–150?), and PC3 is
influenced by posterior measures (150?–180?). Thus, in
general, individuals loading high on PC1 could be described
as anteriorly elongate, individuals loading high on PC2 could
be described as possessing taller crania, and individuals load-
ing high on PC3 could be described as posteriorly elongated.
Two trained assessors measured all radiographs. To exam-
ine interobserver reliability, a set of radiographs was traced
and measured by both observers on a regular basis. In total,
121 radiographs were assessed by both individuals. Reliability
was assessed using intraclass correlation.
Baboon genotyping and the whole-genome linkage map:
Statistical genetic analyses of these cephalometric measure-
ments took advantage of a baboon whole-genome linkage map
based on genotype data at nearly 300 microsatellite marker loci
(mean intermarker interval ¼ 8.9 cM) from .2000 pedigreed
in the human genome for nearly all marker loci in the baboon
map are known, thus facilitating the identification of likely
orthologous chromosomal regions in the two species. Con-
struction of the current baboon linkage map is described in
detail elsewhere (Rogers et al. 2000; Cox et al. 2006), and
additional information can be found at the SNPRC website
Direct comparison among homologous (orthologous) loci
reveals large regions of synteny in which the human marker
order is conserved (7 autosomes with no major rearrange-
ment, 15 with one or more rearrangements; see Rogers et al.
2000 and Cox et al. 2006 for further details). Given the degree
of similarity, throughout this article we refer to the baboon
chromosome number followed by the human number in
parentheses to facilitate comprehension of our results and
their comparison to humans. For example, ‘‘chromosome
PHA4 (HSA6)’’ designates the syntenic grouping of micro-
satellite marker loci that map to baboon chromosome 4, a
logic, ‘‘chromosome PHA3 (HSA7/21)’’ designates baboon
chromosome 3, which represents (relative to the
condition) a fusion of what are two different syntenic groups
in humans, i.e., chromosomes 7 and 21.
Cephalometric points identified on each lateral cephalograph
1. ArticulareAr The intersection of the image of the posterior border of the ramus
with the external surface of the basicranium
The anterior margin of the foramen magnum
The intersection of the nasal and frontal bones
The posterior point of the hard palate
The anterior point of the premaxilla between the upper central incisors
The pituitary fossa of the sphenoid bone
The external angle of the mandible
The most inferior point on the mandibular symphysis
The lowest, most anterior point on the mandibular symphysis
The point tangent to a perpendicular line extending from the S–N plane
The anterior point of the tip of the alveolar process of the mandible
between the lower central incisors
The center of the cross-section of the mandibular symphysis
The most anterior point of the mandibular symphysis
Teardrop-shaped area between maxilla and pterygoid process
of the sphenoid
Posterior-most point of the pterygomaxillary fissure
Inferior-most point of the orbit
Superior margin of external auditory canal
Plane defined by right and left porion and left orbitale
Line connecting nasion and pogonion
Points defined along the endocranial surface of the neurocranium
relative to the S–N plane (e.g., X100 is the point at which a line
drawn 100? from the S–N plane intersects the endocranium)
4. Posterior nasal spine
10. Posterior condylion
12. Point D
14. Pterygomaxillary fissure
15. Center of face
18. Frankfort horizontal
19. Facial plane
All points represent midline structures except where noted.
aPoints not on midline of the skull.
Figure 1.—Radiograph of female baboon. Cephalometric
points used in the analysis are identified (see Table 1 for key).
QTL of the Baboon Craniofacial Complex 621
Statistical genetic analyses: Weusedamaximum-likelihood-
based variance decomposition approach implemented in
sequential oligogenic linkage analysis routines (SOLAR)
(Almasy and Blangero 1998) to estimate heritability for
each craniofacial variable and to test for evidence of quanti-
tative trait loci (QTL) for cranial traits at 1-cM intervals
throughout the genome. This method, described in detail
of the genetic covariance between arbitrary relatives as a func-
tion of the identity-by-descent (IBD) relationships at a given
marker locus and models the covariance matrix for a pedigree
as the sum of the additive genetic covariance attributable to
the QTL, the additive genetic covariance due to the effects of
loci other than the QTL, and the variance due to unmeasured
Our linkage analyses incorporate IBD allele sharing esti-
mated from genotype data at the microsatellite markers in
the baboon linkage map. We estimated probabilities of IBD
among relatives at marker loci in the baboon linkage map,
computer package Loki (Heath 1997). We tested linkage
hypotheses at 1-cM intervals along each chromosome, using
likelihood-ratio tests, and converted the resulting likelihood-
ratio statistic to the LOD score of classic linkage analysis (Ott
We tested the hypothesis of linkage by comparing the
likelihood of a restricted model in which variance due to the
QTL equaled zero (no linkage) to that of a model in which it
did not equal zero (i.e., is estimated). The LOD score of
classical linkage analysis was obtained as the quotient of the
difference between the two ln likelihoods divided by ln 10
To control for the genomewide false positive rate, we
calculated genomewide P-values for each LOD score, using
our modification of a method suggested by Feingold et al.
(1993) that takes into account pedigree complexity and the
finite marker density of the linkage map. Accordingly, our
threshold for significant evidence of linkage (corresponding
to genomewide a ¼ 0.05) was LOD ¼ 2.75, while suggestive
evidence of linkage occurred at LOD ¼ 1.50. Respectively,
these values correspond to the expected false positive rates of
once per 20 (‘‘significant’’) and once per 10 (‘‘suggestive’’)
genomewide linkage screens (Lander and Kruglyak 1995).
Accounting for environmental contributions to the pheno-
typic variance can improve power to detect genetic effects.
Prior to all analyses, we used likelihood-ratio tests to screen
each of the following variables for significant mean effects on
Quantitative measures collected from lateral cephalographs
Trait name Definition
Linear distance between Ar and Go
Linear distance between Ba and Ar
Linear distance between Ba and N
Linear distance between Ba and PNS
Linear distance between Ba and Pr
Linear distance between Ba and S
Angular measure between Ba–N
plane and the line from foramen
rotundum to Gn
Angular measure between
mandibular plane (Go–Me)
and N–Pog plane
Angular measure between Frankfort
horizontal and facial plane
Linear distance between Go and Me
Angular measure between Go–Gn
plane and S–N plane
Angular measure from Ar to Go to Me
Angular measure between axis of
upper and lower central incisors
Linear distance between N and PNS
Linear distance between N and Pr
Angular measure from N to S to Ba
Angular measure from N to S to PNS
Neurocranial principal component 1 score
Neurocranial principal component 2 score
Neurocranial principal component 3 score
Angular measure between occlusal
plane and S–N plane
Linear distance between PNS and Pr
Linear distance between S and PCd
Linear distance from Go to CF
Angular measure from Pr to N to Id
Angular measure from S to N to Pr
Linear distance between S and N
Linear distance between S and PNS
Linear distance between S and Pr
Linear distance between S and X60
Linear distance between S and X70
Linear distance between S and X80
Linear distance between S and X90
Linear distance between S and X100
Linear distance between S and X110
Linear distance between S and X120
Linear distance between S and X130
Linear distance between S and X140
Linear distance between S and X150
Linear distance between S and X160
Linear distance between S and X180
Angular measure from S to N to D
Angular measure from S to N to Id
Factor loading scores for principal components
decomposition of neurocranial measures
TraitFactor 1Factor 2Factor 3
Values are multiplied by 100 and rounded.
a‘‘Meaningful’’ factor loadings (loading .55).
622R. J. Sherwood et al.
the cephalographically derived variables: age, sex, age2, age 3
sex, age23 sex, and headwidth. After regressing out the mean
effects of all nominally significant (P # 0.10) covariates, we
applied an inverse Gaussian transformation to the residuals to
correct for departures from multivariate normality that might
inflate evidence for linkage (Go ¨ring et al. 2001). This trans-
formation produces standardized traits with means and
standard deviations approaching 0 and 1, respectively. All
reported linkage analyses were conducted using these nor-
malized residual data. The reported h2is residual heritability
(that part of the variance that is attributable to the additive
effects of genes after covariate effects, including those of age
and sex, are removed).
Baboons are sexually dimorphic animals, and adult
male linear measurements in this sample are ?15–25%
greater than those of females, with facial measures
tending to show greater sexual dimorphism than basi-
cranial measures; neurocranial size measures are the
least sexually dimorphic with males being ?5–7% larger
than females. Angular measures, such as basicranial
flexion or facial axis, show minimal sexual dimorphism
(?1–2% difference). Sex differences in cranial dimen-
sions begin to become evident ?4–5 years of age.
Prior to genetic analyses phenotypic data were exam-
ined for reliability, using intraclass correlation. Interob-
server reliability of measures was very high, with an
average intraclass correlation of 0.96 for all variables.
The average intraobserver difference for linear metrics
was 1.12 mm, and the average difference for angular
measures was 2.9? (complete details are provided in
supplemental material). Basic quantitative genetic anal-
yses detected significant (P , 0.001) additive genetic
components to the variance (i.e., heritability, h2) for all
43 craniofacial traits measured in this study: Heritability
estimates ranged from 0.13 (for Ba-Ar) to 0.71 (for
gonial angle) with average h2¼ 0.43.
that we could detect the effects of genes on their
variation, we performed whole-genome linkage screens
to localize QTL accounting for these genetic effects.
teen significant QTL (LOD . 2.75) were identified for
12 craniofacial traits (Figure 2) and these results are
presented in Table 4 and Figures 3 and 4. One QTL was
found on each of chromosomes PHA1 (HSA1), PHA13
(HSA2), PHA17 (HSA13), and PHA16 (HSA17), three
QTL were found on chromosome PHA2 (HSA3), five
QTL were found on chromosome PHA4 (HSA6), and
two QTL were found on chromosome PHA11 (HSA12).
of developmental components, the basicranium (those
structures supporting the brain), the splanchnocra-
nium (the face and mandible), and the neurocranium
(the bones surrounding the brain). Because these
components share similar developmental history and
function, we investigated the significant QTL for each
component for common patterns. As some traits in-
cluded aspects of multiple components, we investigated
The basicranial measurements for which significant
the basicranium. In the initial whole-genome screen for
this trait we detected significant evidence for two QTL:
PHA1 (HSA1) with LOD ¼ 2.89. However, when we
performed a second, sequential, whole-genome linkage
screen conditional on the PHA4 Ba–Ar QTL, the
evidence for a second QTL was neither significant nor
interval orthologous to HSA6q21.2, was estimated to
account for between 85 and 100% of the detected
additive genetic effects on variation in Ba–Ar; and these
effects were responsible for ?11.3% of the residual
Figure 2.—Angular (A) and linear (B) measures collected
from lateral cephalographs. Measurements shown are those
for which were detected one or more QTL accounting for
a significant proportion of their variance.
QTL of the Baboon Craniofacial Complex623
phenotypic variance in the trait. Another measure for
which we detected a significant QTL, Ba–PNS, describes
the position of the hard palate relative to the basicra-
nium. With LOD ¼ 3.70, we localized this QTL to a
region of the short (p) arm of PHA11 orthologous to
the residual phenotypic variance, in the measure. The
third measure, N–S–Ba (sometimes referred to as the
saddle angle), describes basicranial flexion. Basicranial
flexion is frequently discussed when comparing non-
human primates, with a relatively unflexed cranial base,
to modern humans who possess a strongly flexed cranial
Figure 3.—Genomewide linkage results
for basicranial and neurocranial traits.
Quantitative trait loci for craniofacial traits in pedigreed baboons
Baboon (PHA) Human region orthologous to 1-LOD support interval
Chromosome cMcCytogenetic location Width (ntb) No. of known genesd
Posterior condylion 825 0.12 0.156 3.34 0.011
NeuroPC3 830 0.36 0.119 3.12 0.020
S–N–Pr822 0.34 0.122 3.17 0.018
Go–Gn–S815 0.33 0.116 2.94 0.031
S–PNS 811 0.37 0.102 2.93 0.021
Facial taper 811 0.47 0.147 3.32 0.012
Ba–Ar 819 0.0
S–X110 830 0.40 0.166 3.01 0.026
S–X100 830 0.41 0.170 3.01 0.026
N–S–Ba 822 0.24 0.096 3.45 0.009
Ba–PNS808 0.28 0.131 3.70 0.005
Facial taper811 0.53 0.094 2.89 0.035
N–Pr 822 0.25 0.193 2.88 0.036
0.113 3.96 0.003
ntb, nucleotide bases.
aMaximum-likelihood heritability estimates from linkage models: h2
residual phenotypic variance due to the effect of the QTL, and h2is the residual heritability, i.e., the proportion of the phenotypic
variance in the trait due to the effects of genes other than the QTL.
bGenomewide P-value associated with the LOD score calculated using a modification of a method suggested by Feingold et al.
(1993) that takes into account pedigree complexity and the finite marker density of the baboon whole-linkage map used in these
cLocation in centimorgans from the pter-most marker locus in the baboon genetic linkage map for that chromosome.
dWithin regions of human syntenic groups likely to be orthologous to the region of the baboon genome containing the 1-LOD
support interval for the QTL.
qis the QTL-specific heritability, i.e., the proportion of the
624 R. J. Sherwood et al.
to roughly the same chromosomal region in which we
also detected the QTL for Ba–PNS—i.e., the p arm of
PHA11 (HSA12). Approximately 29% of the additive
genetic variance and 10% of the residual phenotypic
variance in this trait could be attributed to this QTL.
Our analyses yielded significant evidence for four
QTL affecting three splanchnocranial features. We
localized one of these, a QTL accounting for 44% of
facial length, N–Pr, to a region of PHA16 that corre-
sponds to HSA17p12. For S–PNS, a linear measure of
facial positioning relative to the basicranium, we local-
area of PHA4p that is orthologous to HSA6p21.2. This
QTL accounted for ?22 and 10.2%, respectively, of the
trait. Our analyses of an angular measure of overall
facial positioning, facial taper, returned significant
evidence for two QTL: One, accounting for 15% of
the additive genetic variance and 9.4% of the residual
phenotypic variance in the trait, was localized to PHA17
(HSA13q13.3); and the other, accounting for 24 and
14.7% of these respective variance components, map-
ped to PHA4q (HSA6q12).
We localized three significant QTL for neurocranial
traits. Two of these, influencing variation in the highly
correlated S-100 and S-110 variables, mapped to the
same location: i.e., 140 cM from the pter-most marker
p, or short, arm of the chromosome) on PHA4, a region
that is orthologous to HSA6q27. The estimated effect of
these QTL on these two correlated measures was
genetic variance and 17% of the residual phenotypic
variance, in these measures. The third QTL was detected
when we analyzed a synthetic variable, PC3, obtained
from a principal components analysis of all neurocranial
metrics. The QTL for PC3, which (as noted earlier)
is localized to PHA2 (HSA3q13.13) and accounts for
?25% of the additive genetic effects on variation in this
Pr), mandible (Go–Gn–S), and the mandibularcondyle
(posterior condylion). The QTL for the former two
traits, S–N–Prand Go–Gn–S, map to identical locations,
110 cM from the pter-most marker locus on PHA2, a
region corresponding to HSA3q11.2, and explain
roughly the same proportion of the genetic and pheno-
typic variation in the two traits (i.e., 25 and 12%, respec-
tively). The QTL influencing variation in posterior
condylion maps to a region of PHA13 that is ortholo-
gous to HSA2p21. Although accounting for only 15.6%
of the residual phenotypic variation, the gene(s) at this
locus accounted for .50% of the detected genetic
effects on this trait.
This study is the first to identify QTL influencing
variation in craniofacial traits in a nonhuman primate.
In addition to substantively augmenting our statistical
power to detect and localize genes influencing variation
in quantitative traits, the size, configuration, and com-
position of this pedigreed sample can facilitate the
detection of the effects of other factors on these
craniofacial traits. As noted, the age range for the .
800 baboons in this single, complex pedigree spanned
27 years and included young and adult animals. Our
study does not address the question of age-specific
Figure 4.—Genomewide linkage results
for splanchnocranium and mixed-compo-
QTL of the Baboon Craniofacial Complex625
genetic contributions to craniofacial variation (i.e., ge-
that can do so, while making use of all the genetic and
phenotypic information in this large and complex pedi-
gree, are available (Almasy et al. 2001; Diego et al. 2003;
Havill and Mahaney 2003) and a comprehensive anal-
ysis of age-specific genetic effects is in progress.
Candidate genes: To investigate potential positional
candidate genes under the QTL regions identified in
our analyses, the current literature was searched for
known genes affecting craniofacial structures in orthol-
ogous regions of the human genome. Several reports
were found, indicating that mutations in some areas of
interest we identified are associated with dysmorphic
craniofacial patterns. For instance, the SIX3 gene found
on HSA2p21, and linked to the posterior condylion
measure in baboons, has been identified as a causative
factor in holoprosencephaly, a disorder with severe
craniofacial dysmorphology including cyclopia and a
midline proboscis situated above the eye (Wallis et al.
1999). Sato et al. (2007) identified a patient with a
deletion spanning HSA3q11.2, linked to the trait Go–
Gn–S in our study, that presented with the rare
condition of congenital arhinia (complete absence of
the nose). Additionally, deletions in the HSA17p12
region, linked to N–Pr in this study, have been impli-
cated in cleft palate associated with Smith–Magenis
syndrome (Andrieux et al. 2007). Additional disorders
such as cleidocranial dysplasia (HSA6p21.2), Opitz trig-
onocephaly (OTCS; HSA3q13.13), and cat eye syndrome
(CECR1; HSA22q11.1) are caused by mutations in regions
linked to craniofacial features in our study. Chromosomal
regions identified in these linkage analyses, therefore, are
identified as containing genes with some effect on cranial
Genetics of the craniofacial complex: Recent advan-
ces in developmental biology have led to the discovery
of a number of genes and gene products important in
the development of the skeleton and, specifically, the
skull. However, as is the case with many systems, our
primary understanding of the specific genes related to
craniofacial morphology comes from animal models
phylogenetically distant from humans, such as zebra-
etal.1997; Leamyetal.1999, 2000; Workmanetal.2002;
Helms and Schneider 2003; Albertson and Yelick
2004; Eames and Helms 2004), or from genetic disor-
ders associated with human craniofacial anomalies
(Slavkin 1983; Olsen 1998; Slavkin 2001; Cohen
2002). Many of these anomalies affect multiple tissue
types and are often not restricted to cranial structures
(Richtsmeier 1987; Cohen and Kreiborg 1991,
1994a,b). Additionally, these disorders are frequently
characterized by high degrees of genetic and pheno-
typic heterogeneity. While the advances made by study-
ing dysmorphic syndromes are significant, they do not
provide an adequate characterization of the genetic
background to normal craniofacial development and
morphology. This study presents our initial analyses to
identify QTL influencing craniofacial traits in a non-
human primate species.
This study demonstrates that all craniofacial compo-
nents are characterized by significant heritability of
moderate to high magnitude, suggesting that cranial
components are relatively similarly influenced by envi-
in the significant QTL identified for the craniofacial
traits from common components or for traits from dif-
ferent components. This lack of patterning with regard
to QTL for craniofacial features suggests a level of inde-
pendence of the craniofacial components and traits.
Issues regarding the integration and modularity of mor-
phological characters are particularly important with
regard to the craniofacial complex (e.g., Cheverud and
Buikstra 1981b; Cheverud 1982, 1995, 1996, 2001;
Wagner and Altenberg 1996; Cheverud et al. 1997;
Mezey et al. 2000), and future research will further
In conclusion, this study demonstrates that quantita-
tive traits comprising the craniofacial complex in
baboons are under significant genetic influence. Sev-
genes responsible for variation in these traits. Future
work will interrogate these chromosomal regions to
thebaboonandextend ouranalyses toincludehumans.
The authors are indebted to the Southwest National Primate
Research Center (SNPRC), specifically Suzette Tardif and Karen Rice,
for facilitating this research. We express our sincere gratitude to the
staff of the SNPRC responsible for radiography of the animals—
Shannon Theriot, M. J. Bell, Terry Naegelin, and Wade Hodgson. We
are also grateful to Kimberly Lever, Rebecca Junker, and Joe Wagner
for phenotyping and database assistance. This work was supported in
part by the National Institute of Dental and Craniofacial Research
(National Institutes of Health, NIH) grants DE016692 and DE016408
to R. J. Sherwood, by NIH grant P51 RR13986 to the SNPRC, and by
NIH grant P01HL28972. Development and implementation of the
SOLAR statistical genetics analysis package is supported by grant
MH059490 from the National Institute of Mental Health. This
investigation was conducted in facilities constructed with support
from Research Facilities Improvement Program grants C06 RR15456,
C06 RR017515, and C06 RR013556 from the National Center for
Research Resources, NIH. The supercomputing facilities used in this
work at the AT&T Genomics Computing Center were supported by a
gift from the SBC Foundation.
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