Fossil hominin shoulders support an African ape-like
last common ancestor of humans and chimpanzees
Nathan M. Young
, Terence D. Capellini
, Neil T. Roach
, and Zeresenay Alemseged
Department of Orthopaedic Surgery, University of California, San Francisco, CA 94110;
Department of Human Evolutionary Biology, Harvard University,
Cambridge, MA 02138;
Broad Institute of MIT and Harvard University, Cambridge, MA 02142;
Division of Anthropology, American Museum of Natural
History, New York, NY 10024; and
Department of Anthropology, California Academy of Sciences, San Francisco, CA 94118
Edited by Richard G. Klein, Stanford University, Stanford, CA, and approved August 12, 2015 (received for review June 9, 2015)
Reconstructing the behavioral shifts that drove hominin evolution
requires knowledge of the timing, magnitude, and direction of
anatomical changes over the past ∼6–7 million years. These re-
constructions depend on assumptions regarding the morphotype
of the Homo–Pan last common ancestor (LCA). However, there is
little consensus for the LCA, with proposed models ranging from
African ape to orangutan or generalized Miocene ape-like. The
ancestral state of the shoulder is of particular interest because it
is functionally associated with important behavioral shifts in hom-
inins, such as reduced arboreality, high-speed throwing, and tool
use. However, previous morphometric analyses of both living and
fossil taxa have yielded contradictory results. Here, we generated
a 3D morphospace of ape and human scapular shape to plot evo-
lutionary trajectories, predict ancestral morphologies, and directly
test alternative evolutionary hypotheses using the hominin fossil
evidence. We show that the most parsimonious model for the
evolution of hominin shoulder shape starts with an African ape-
like ancestral state. We propose that the shoulder evolved gradu-
ally along a single morphocline, achieving modern human-like con-
figuration and function within the genus Homo. These data are
consistent with a slow, progressive loss of arboreality and in-
creased tool use throughout human evolution.
The human shoulder exhibits a unique combination of traits
for a primate, a fact that has complicated previous attempts
to reconstruct both its functional and evolutionary history. No-
tably, humans are most closely related to knuckle-walking/sus-
pensory chimpanzees and bonobos (Pan or panins) (1, 2), yet
morphometric analyses suggest that our shoulders are most
similar in shape to that of the highly arboreal, quadrumanous
orangutan (Pongo)(3–5). The hominin fossil record is similarly
complicated. Scapular remains attributed to Australopithecus
afarensis are described as similar to Gorilla (6–8) whereas the
more recent Australopithecus sediba (MH2) displays morphom-
etric affinities to both African apes (gorillas, chimpanzees, and
bonobos) and Pongo (9). This mix of character states raises the
question of whether modern human morphology reflects evolu-
tion from a more derived African ape morphology or retention of
primitive traits from an earlier ape ancestor.
A critical piece of evidence for solving this puzzle is the
morphotype of the hominin–panin last common ancestor (LCA)
(∼6–7 Mya). Although the fossil record near the hypothesized
divergence time with Pan is the most direct means of addressing
what the anatomy of the LCA shoulder was like, both hominin
and African ape fossils from this time period are rare, frag-
mentary, and poorly understood (10, 11). Despite these diffi-
culties, competing hypotheses about the LCA make explicit and
mutually exclusive predictions of the direction, magnitude, and
ordering of character transformations that we should observe in
the fossil record. Moreover, the likelihood of these alternative
hypotheses can be directly tested using the better characterized
later hominin fossil record. Specifically, given alternative ancestral
conditions, one can model the associated evolutionary trajectories
and intermediate states connecting them to the descendant pop-
ulations and test how well these predictions fit the available
Two hypotheses of the LCA postcranial morphotype have
been proposed, both requiring different selection pressures and
levels of homoplasy. In the first scenario, a number of anatomical
and locomotor traits shared among closely related African apes
are thought to be homologous (12–14) and represent the an-
cestral state of the LCA from which early hominins evolved
[an “African ape”(AA) model] (15). In particular, panins are
thought to be phenotypically conservative and thus a useful, if
imperfect, proxy for the anatomy and positional behavior of our
shared LCA (1) (Fig. 1A). In the second scenario, the mosaicism
that characterizes the known fossil ape record (e.g., refs. 16–19)
supports the argument that many living ape similarities are not
homologies (20); thus the ancestral morphotype for both apes
and humans [i.e., the “Miocene ape ancestor”(MAA)] would
reflect a more primitive, generalized postcranial morphotype and
positional behavior [an “ape convergence”(AC) model]. For
example, some have argued from differences in African ape wrist
morphology that knuckle walking behaviors evolved in parallel
(21, 22), in which case the LCA must be more primitive. Thorpe
et al. (23, 24) used similar reasoning to assert that hominins did
not evolve from a knuckle-walking LCA, but rather one that
practiced the hand-assisted, arboreal bipedality observed in liv-
ing orangutans (Fig. 1B). Lovejoy et al. (25) noted that many
features of the early hominin Ardipithecus ramidus do not re-
semble African apes and argued that this difference was evidence
Knowing the direction and pace of evolutionary change is
critical to understanding what selective forces shaped our an-
cestors. Unfortunately, the human fossil record is sparse, and
little is known about the earliest members of our lineage. This
unresolved ancestor complicates reconstructions of what be-
havioral shifts drove major speciation events. Using 3D shape
measurements of the shoulder, we tested competing evolu-
tionary models of the last common ancestor against the fossil
record. We found that a sustained shift in scapular shape oc-
curred during hominin evolution from an African ape-like an-
cestor to a modern human-like form, first present in our genus,
Homo. These data suggest a long, gradual shift out of the trees
and increased reliance on tools as our ancestors became more
Author contributions: N.M.Y., T.D.C., and N.T.R. designed research; N.M.Y., T.D.C., N.T.R.,
and Z.A. performed research; Z.A. contributed new reagents/analytic tools; N.M.Y. ana-
lyzed data; and N.M.Y., T.D.C., N.T.R., and Z.A. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
To whom correspondence should be addressed. Email: email@example.com.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.
www.pnas.org/cgi/doi/10.1073/pnas.1511220112 PNAS Early Edition
of a cautious, above-branch, arboreal LCA, more similar to early
quadrupedal Miocene apes like Proconsul than the orthograde
and suspensory crown taxa (26) (Fig. 1C).
To test these alternative evolutionary models of the Homo–Pan
LCA, we used Procrustes-based geometric morphometrics methods
to summarize the major sources of 3D variation and covariation in
the shape of one structural component of the shoulder, the scapula.
When combined with a phylogenetic hypothesis (Fig. 1D), the
resulting “phylomorphospace”provides explicit predictions about
the evolutionary trajectories connecting hypothesized ancestral and
descendant populations, associated character state transformations,
and proposed ancestral conditions (27), which we tested against the
hominin fossil record. Our results demonstrate that many seemingly
contradictory results from previous analyses are both predictable
outcomes of how scapula morphospace is occupied and consistent
with our understanding of how scapular shape is linked to function.
Moreover, they suggest explicit alternative development hypotheses
that provide a basis for future attempts to validate phylogenetic
models in human evolution.
We first performed a principal components analysis (PCA) of
scapula shape and found that the majority of hominoid variation
(∼75%) is partitioned along three axes that discriminate taxa,
have biological/functional relevance, and are meaningful above
random error (Fig. 2 A–Dand Fig. S1). The first axis (PC1) is
associated with the angle of the scapular spine and glenoid rel-
ative to the vertebral border of the blade, which is near per-
pendicular in MAA proxies and Pongo but has a more cranial
orientation in African apes and hylobatids. More perpendicular
spines tend to be longer and the blade wider, accounting for
almost all of their covariation (Fig. S2). The second axis (PC2)
distinguishes the superiorly projecting vertebral and superior
borders and relatively large supraspinous fossa in African apes
from a superior border parallel to the spine and a smaller
supraspinous in the MAA proxies, Pongo, and hylobatids. As in
previous analyses (3, 4), Homo does not significantly overlap with
any primate but instead resides in a unique position that combines
primitive “quadrupedal”characteristics like a long, robust scapular
spine that is perpendicular to the vertebral border (similar to
Nasalis,Lagothrix,andPongo, but further lateralized) with a blade
shape more typical of African apes. The third axis primarily dis-
tinguishes Gorilla and Pongo from all other taxa and is associated
with a scapular blade that is medio-laterally wider than accounted
for by PC1 alone (Fig. S3).
We next reconstructed the predicted ancestral states by
mapping the trees for each alternative phylogenetic scenario in
the comparative morphospace (Fig. 2 Eand Fand Fig. S1 Aand
B). Both the AA and AC trees locate the basal hominoid node,
reflecting the common ancestral morphotype of apes, in a region
consistent with hypothesized MAA proxies (Nasalis and Lago-
thrix) and similar to Pongo. Only close sister taxa overlap in the
first two axes of this morphospace, confirming that hominoids do
not share a common “suspensory”shoulder morphology (20, 28).
However, these trees otherwise differ in the magnitude and lo-
cation of homoplasy required.
In the AA model, a direct path from Pan to Homo predicts
changes in the apportionment of the fossae and associated blade
width as orientation of the spine became more perpendicular
relative to the vertebral border and the glenoid more inferiorly
positioned (Fig. S1Aand Movie S1). Interestingly, this vector
passes through a “Gorilla”-like morphospace and the inferred
African ape LCA along PC1. This arrangement predicts that
ancestral hominins shared the common African ape blade shape
and spine angle with Gorilla but lacked the further expansion of
the vertebral border and supraspinous found in this large African
ape. The phylomorphospace reconstruction is largely concordant
with this vector, predicting that the common ancestor of African
apes and humans was similar to Pan in blade shape, but with a
less angulated spine and wider blade as in Gorilla. This tree
therefore requires one instance of homoplasy to explain simi-
larities between Pan and gibbons in glenoid/spine angulation
whereas Gorilla exhibits an independent expansion of the
supraspinous from a generalized African ape morphotype. In this
Wrangham & Pilbeam (2001) Thorpe & Crompton (2007)
Arboreal, Quadruped (AQ)
Arboreal Biped, Cautious Climber
BLovejoy et al. (2009)
DAfrican Ape (”AA”)
Ape Convergence (”AC”)
Fig. 1. Alternative models of the hominin–panin last common ancestor (LCA). The branching pattern of living apes as inferred from genomic data is agreed
upon; however, reconstruction of ancestral nodes differs among researchers. (A) In the African ape (AA) model, hominins derive from a knuckle-walking
African ape-like LCA, typically conceived of as chimpanzee-like. (Band C) Ape convergence (AC) models hypothesize that the LCA is either a more generalized
great ape or an unknown primitive ancestral Miocene ape. AQ, arboreal quadrupedalism. (Dand E) Phylogenetic trees used to model these differences, with
evolution from a common morphotype represented by a polytomy. Hominin phylogeny based on ref. 58.
www.pnas.org/cgi/doi/10.1073/pnas.1511220112 Young et al.
scenario, both Pongo and hylobatids retain the primitive blade
shape in which the superior border more closely parallels the spine,
with the gibbons independently evolving a more cranial spine and
glenoid position with associated narrowing of the blade.
In contrast, the evolutionary vector reconstructed from either an
MAA proxy or a Pongo-like LCA to humans predicts that hominins
would be convergent on African apes in blade shape whereas the
more inferior orientation of the spine and glenoid is derived from a
similar condition in the MAA (Fig. S1Band Movie S2). The phy-
lomorphospace analysis reconstructs a different path in which the
basal hominoid node is intermediate in both blade shape and spine
angulation relative to all extant apes. In this case, the AC model
requires three independent episodes of convergence between hu-
mans, panins, and Gorilla in blade shape and two independent
events to explain convergence between Pongo and hylobatids, as
well as the previously mentioned convergence in spine angulation
predicted by the AA model for panins and hylobatids.
Consistent with the AA model, we found that, when fossil taxa
were included in the analysis (Fig. 2B), australopithecines are
intermediate between panins and Homo whereas all hominins
are arranged in a roughly temporal/phylogenetic gradient from
older and more primitive species (A. afarensis) to younger
(A. sediba) and/or more derived species (Homo ergaster,Homo
neanderthalensis)(Fig. S4). Developmental simulations under a
range of hypothetical ontogenetic vectors on average “grow”the
juvenile A. afarensis in the direction of a more African ape-like
blade shape along PC2 (Fig. 2 C–E). These data suggest that
some of the resemblance of the A. afarensis juvenile to Pongo and
MAA blade shape is attributable to the fact that, in all anthro-
poids, younger individuals tend to be wider and have less
developed fossae (29), consistent with PC2. As measured by
Procrustes distance, A. afarensis simulations are most similar in
shape to Gorilla and Nasalis (Table S1 and Fig. S5), the former
of which is consistent with previous analyses (6, 8). However, the
evolutionary vector from Pan to australopithecines and humans
passes “underneath”and not “through”the space occupied by
Gorilla in the second and third axes of the PCA and canonical
variates analysis (CVA). This simple, linear trajectory is consis-
tent with evolution from either a more Pan-like LCA or a gen-
eralized African ape, both consistent with the AA model. Both
H. ergaster and H. neanderthalensis are located in a “hyper”-human
location in morphospace, which is due to both a spine angle that
is lateralized (PC1), and the cranial orientation of the vertebral
border above the suprascapular notch (PC2). This difference
may reflect natural variability because both H. ergaster and
H. neanderthalensis are located within the 90% frequency ellipses
of the modern human sample (Fig. S2D). Alternatively, modern
humans have subsequently experienced changes in supraspinous
size and spine angulation due to selection, random drift, or a
combination of both.
By calculating evolutionary vectors through scapula shape mor-
phospace and testing these models against a better characterized
fossil record, we found that the course of hominin shoulder evolu-
tion is consistent with the AA model predictions. Specifically, fossil
Hylobates Pongo Pan Gorilla Ho. sapiens
DIK 1-1 (r)
Kebara 2 (r)
Qafzeh 9 (r)
DIK 1-1 •
DIK 1-1 •
DIK 1-1 •
DIK 1-1 •
Principal Component 1 (47.3% Variation)
Principal Component 2 (18.8% Variation)
-0.10 0.00 0.10 0.20
-0.10 0.00 0.10
Fig. 2. Comparative and evolutionary scapula shape morphospace. (Aand B) Representative hominoid scapulae and fossil hominins, shown scaled to
identical vertebral border length. (C) Developmental simulations of DIK 1-1 (A. afarensis) using growth vectors from alternate proposed LCA morphotypes.
(Top) Simulations. (Bottom) Simulations with DIK 1-1 scapula overlay (transparent blue), scaled to the same size to highlight shape differences. (D) PC1 and -2
morphospace with mean specimen warped along each axis to show associated shape changes. PC1 describes orientation of the spine relative to the blade
whereas PC2 describes differences in the borders of the supraspinous fossa. Dashed arrows show the direct evolutionary vector from hypothetical an-
cestral states (AA, African ape mean; AC, MAA mean) to modern humans. Points, individual specimens; dark ellipses, 90% confidence interval (CI) of the
mean; light ellipses, 90% CI of the sample; red points, DIK 1-1 developmental simulations. (Eand F) Phylogenetic reconstruction for the AA (tree length =
0.085, P<0.0001) and AC (tree length =0.100, P<0.0001) models illustrates alternative predictions for branching patterns and ancestral states within the
Young et al. PNAS Early Edition
hominins occupy a region of scapula morphospace that is in-
termediate between African apes and modern humans and are
arranged in a temporal gradient consistent with their inferred
phylogenetic position (Fig. S4 A–D). These data strongly support
a model in which the modern human shoulder evolved from an
African ape-like LCA via long-term, directional selection on a
single but integrated trait: a longer and more lateralized config-
uration of the spine and glenoid mapped onto a shared African
ape blade shape (Fig. 3). This result implies that previously noted
similarities of the human shoulder to quadrupedal apes and Pongo
are convergent. This interpretation is not only more parsimonious
than evolution from a generalized, quadrupedal LCA morphotype,
but is also consistent with functional explanations for the evolution
of this suite of traits in the hominin lineage and our current un-
derstanding of scapular morphogenesis and development.
These conclusions assume that reconstructed morphospaces
accurately capture potential variation and that ancestral states
can be reasonably estimated by phylogenetic reconstruction
within them. In the former, the concordance of our results with
previous analyses (e.g., ref. 29) suggests that the major contrib-
utors to primate scapula shape are contained within a few in-
tegrated variables, and therefore fossil primates are unlikely to
deviate markedly from this pattern. In the latter, there is no a
priori reason to believe that species evolve along the most direct
path between states. But in either case, these assumptions are
testable, particularly because homoplasy would be reflected by
species occupying a similar morphospace that their common an-
cestor did not. In this regard, both the AA and AC models infer that
homoplasy has occurred in the living ape shoulder but differ in
when and where convergence occurred.
The most evolutionarily labile trait in the scapula is the angle of
the spine and glenoid relative to the vertebral border, with Pan and
hylobatids at one extreme and humans at the other. In both trees,
the reconstruction of ancestral states suggests that spine angulation
is a highly evolvable trait prone to convergence. The arrangement of
hominins in a temporal sequence along this axis further corrobo-
rates that spine angle can evolve in a continuous manner in-
dependently of other scapular anatomy, consistent with what is
known of spine development (see below). In contrast, blade shape
better reflects phylogenetic relationships because humans are sim-
ilar to African apes, which together differ from the inferred prim-
itive pattern found in hylobatids, Pongo, and the MAA proxies. The
AA model reconstructs a single event to evolve African ape blade
morphology whereas the AC model predicts an intermediate an-
cestor to all apes that subsequently radiated into the living hominoid
lineages. In the case of African apes and humans, if there is no
functional association with the supraspinous shape, it is not obvious
what selective forces drove this convergence. The supraspinous
morphology of African apes, and particularly Gorilla, is thought to
be a compromise that enables stabilization of the shoulder joint
against shear forces generated during quadrupedal knuckle walking
while retaining the dorsal position that enhances climbing (30). If
this functional interpretation were correct, then any argument for
homoplasy among African apes and hominins in this trait would
imply that all three independently evolved knuckle walking.
Although the AA model is more parsimonious than the AC
model, ancestral state reconstruction of the African ape node does
not overlap either extant species. This result leaves open the
question of whether australopiths are similar to Gorilla because they
approximate the ancestral African ape morphotype or whether they
“reevolved”this generalized condition from a more Pan-like
shoulder. Although the ancestral state reconstruction supports a
generalized African ape ancestor, there are reasons to prefer a
more Pan-like condition. Notably, many morphological differences
between Pan and Gorilla are associated with body size (13, 31, 32),
and early hominin body size is comparable with the chimpanzee
(33). Body size is also strongly linked to social structure; thus, any
reconstruction invoking a Gorilla-like body size would also have
additional implications beyond the skeletal phenotype (e.g., multi-
male, multifemale in Pan troglodytes vs. a single male, multifemale
group in Gorilla) (15). Regardless, if the LCA was more Pan-like,
then early hominins reevolved a Gorilla-like spine/glenoid angle, but
if more Gorilla-like, then the more cranial angle in Pan is a later
evolutionary event convergent on some hylobatids, perhaps due to
increased arborealism relative to the ancestral African ape. Absent
fossil representatives of either Pan or Gorilla lineages, it is not
possible to discriminate these alternatives.
The correspondence of the current hominin fossil record to
both the AA evolutionary vector and the phylomorphospace, as
well as the magnitude of the phenotypic shift and the relatively
short timeframe over which it occurred, are all strong circum-
stantial evidence that these changes were predominantly driven
by sustained directional selection and not genetic drift. This in-
ference is consistent with its functional association because the
angle of the spine is directly tied to the predominant direction of
forelimb actions (e.g., overhead vs. lateralized). In particular,
selection on the relative positions of the blade and spine is as-
sociated with the cranio-caudal orientation of the glenoid (Fig.
3). This gradual shift in spine and glenoid angle affects the fiber
orientation of the pectoral and scapular muscles, altering the
position of the upper limb where force production is optimized
(34). The reduced, caudally shifted angle in Homo is consistent
with both a decreased reliance on use of the upper limb for
overhead actions, such as climbing, and the increased use of
Fig. 3. Model of shoulder shape evolution. Scapula morphospace is recon-
structed at individual time horizons (t
) for the phylogeny shown. The an-
cestral hominoid condition is reconstructed to be similar in shape and
configuration to Pongo (t
). Pongo shares with Lagothrix a penchant for
slow, cautious movements through high forest canopy, including frequent
bouts of pronograde suspensory locomotion (59–61). This similarity suggests
that derived “suspensory”postcranial characteristics of Pongo shared with
other apes are partially convergent, consistent with evidence from Sivapithecus
(16). In this model, hylobatids evolved a more cranially oriented spine and
glenoid from this morphotype, which is predicted to fall in the intermediate
). African apes evolved a unique blade shape with cranial spine (t
subsequently diversifying into Pan and Gorilla lineages (t
). Hominins retained
the ancestral African ape blade shape, but the angle of the spine relative to the
vertebral border gradually shifted (t
), consistent with realignment of the
shoulder musculature due to selection associated with more lateralized activities
and/or reduced reliance on overhead activities (e.g., climbing).
www.pnas.org/cgi/doi/10.1073/pnas.1511220112 Young et al.
lateralized behaviors, such as tool use and throwing. The slow,
sustained pace over which these changes took place suggests that,
whereas they conferred a selective advantage for lateralized actions
in the hominin lineage, they may have been balanced by a tradeoff
with other factors, such as continued use in arboreal contexts. The
early appearance of a moderate caudal shift in spine and glenoid,
dating to Australopithecus, is consistent with new evidence suggest-
ing that tool use extends well past the origins of Homo (35–37).
Interestingly, the later A. sediba has a more human-like shoulder
compared with earlier A. afarensis, suggesting that the ancestor of
A. sediba and Homo shared the more derived configuration. That
said, it is not until the emergence of later Homo that a modern
scapular configuration was largely in place (38, 39). This final
shift toward a fully lateralized spine and glenoid was likely
costly to climbing efficiency and/or arm hanging (40), while also
increasing shear stress at the shoulder and elevating the risk of
rotator cuff injury (41, 42). Given the fitness value of efficient
climbing for accessing food and avoiding predators, we speculate
that the selective forces driving this shift must also have been
Both models posit a series of changes to both the position of the
spine and the shape of the blade in multiple lineages. Later post-
natal growth has a relatively limited and similar effect on blade
shape across lineages whereas spine angle does not change with age
(29). These facts suggest that genetic regulation of the early posi-
tioning of muscles, spine, and acromion are critical to establishing
species differences rather than later growth or functional remod-
eling. Identifying the genetic and molecular mechanisms that con-
trol variation in scapular morphogenesis may provide a novel
approach to directly test among alternative evolutionary models.
For example, each model makes predictions about the timing and
history of selection on cis-regulatory elements that control de-
velopmental traits (e.g., the spine in Fig. S4A). If variation in either
regulatory or downstream sequence is the proximate target of se-
lection, then timing the signature of selection could serve as a direct
test of these hypotheses. In the AA model, one would predict there
would be evidence for concerted evolutionary sequence change
(and/or key functional base pair changes) within regulatory regions
for genes that only influence the interaction of spine and blade. In
contrast, the AC model would predict sequence evolution in regu-
latory regions for genes influencing blade and spine, and such
changes should be step-wise chronologically. In either case, changes
should date to particularly informative periods as supported by the
fossil record. Identification of the cis-regulatory architecture that
underlies the specific traits in question will be highly informative for
understanding their variation potential, testing competing evolu-
tionary scenarios, and ultimately providing the opportunity to per-
form “experimental”paleontology, by altering sequence data in
model species (43).
Materials and Methods
Data. We collected 3D landmark data from scapulae of museum specimens
from the following extant hominoid species: Homo sapiens (modern humans,
n=31), Pan troglodytes (chimpanzee, n=56), Pan paniscus (bonobo, n=
36), Gorilla gorilla (lowland gorilla, n=72), Pongo pygmaeus (Bornean
orangutan, n=48), Symphalangus syndactylus (siamang, n=41), and
Hylobates sp. (gibbon, n=35). Use of anonymized human data was ap-
proved by the University of California, San Francisco Committee on Human
Research (no. 10-01599). As proxies of the primitive Miocene ape ancestral
morphotype (MAA), we use the cercopithecoid colobine Nasalis larvatus
(proboscis monkey, n=19) and the ceboid ateline Lagothrix lagotricha
(wooly monkey, n=11), consistent with reconstructions of both Early and
Middle Miocene apes (e.g., Proconsul,Nacholapithecus) and hypothesized
functional and morphological similarity (18, 44, 45). We used adult wild-
caught males and females, one scapula per indi vidual, principally t he right.
Specimens were chosen from similar geographic localities and/or within
subspecies to minimize the effect of population heterogeneity. Missing,
broken, damaged, or pathological individuals were excluded. Three-dimensional
landmark coordinate data (x,y,z) were recorded using a Microscribe-3Dx digitizer
(Immersion Corporation) as previously described (32, 46). We obtained
3D computed-tomography (CT) data from the original specimens of DIK 1-1
(A. afarensis, right side) (13), MH2 (A. sediba, right side) (16), Kebara 2
(H. neanderthalensis, right side), and Qafzeh 9 (anatomically modern H. sapiens,
right side) and generated a 3D object in Amira 5.4 (Visage Imaging, Inc.). For
KNM WT15000 (H. ergaster, right side) and La Ferassie I (H. neanderthalensis,
right side), we used high quality casts. All 3D objects were landmarked in
Landmark Editor 3.5 (University of California, Davis). We applied a series of
landmarks to each specimen (n=13) (29, 45), excluding those not found in
all fossils (Fig. S6).
Shape Analysis. We performed a Procrustes superimposition to remove the
effects of scale, rotation, and alignment, and to reflect right and left scap-
ulae. We removed the effect of size heterogeneity by performing a multi-
variate regression of shape on log centroid size (LCS) within species. We used
the residuals of the group-centered means in all subsequent analyses. We first
performed a principal components analysis (PCA) to assess shape variation,
and two further analyses to take into account group information and assess
the effect of sample size differences among species: (i) a canonical variates
analysis (CVA) using species as the grouping variables and the overall pooled
covariance matrix as the measure of within-group variability, and (ii) a be-
tween-group PCA (bgPCA) using PC axes estimated from averages of each
species (47). We performed a within-configuration partial least squares (PLS)
analysis within each species and centering on the group mean to compare
covariation between variation in the spine and blade landmarks, with sig-
nificance tested by permutation (1,000 replicates). We calculated Procrustes
distances among species and tested for significance using a permutation test
for pairwise distances (10,000 iterations). From these distances, we per-
formed a cluster analysis, using the unweighted pair group with arithmetical
mean (UPGMA) method, and generated a phenetic tree using the neighbor-
joining (NJ) method (Nasalis/Lagothrix =root) in the software NTSYS-pc
(v.2.1) (48). Eigenanalysis and visualizations were performed in MorphoJ
v1.06d (49), Landmark Editor (v.3.0) (50), and the geomorph package (51)
implemented in R(v.3.2.1) (52).
Developmental Simulation. To compare DIK 1-1 to the adult morphospace, we
performed a developmental simulation using allometric estimates under
different assumptions of growth (Pan,Gorilla,Pongo, and Nasalis) (32). To do
this analysis, we performed a Procrustes superimposition including the four
extant species and DIK 1-1 so that all individuals and ontogenetic vectors
were in the identical shape space. We next performed a multivariate re-
gression of shape on log centroid size for each species age series alone and
calculated the associated species-specific ontogenetic vector (Fig. S7). We
next estimated adult shape by adding the product of each ontogenetic
vector times LCS (=0.75, the difference in LCS between juvenile and adult)
to the DIK 1-1 Procrustes coordinates (53). Simulations were visualized by
transforming the DIK1-1 specimen to the target adult landmark configura-
tion in Landmark Editor (v.3.5) (Fig. 2C).
Phylogenetic Morphospace. We implemented squared-change parsimony (54)
to (i) map alternative phylogenetic trees (Fig. 1 Band C) onto the continuous
shape space defined by PCA, bgPCA, and CVA, (ii) reconstruct alternative
ancestral morphotypes (i.e., nodes), and (iii ) infer evolutionary trajectories
(30, 55, 56). Squared-change parsimony is a generalization of maximum
likelihood-based methods where all branch lengths are “1.”We justify this
simplification by the fact that, with the exception of H. neanderthalensis,
branch lengths are unknown for hominin fossil taxa. All trees reflect the
currently accepted branching pattern as inferred from genomic datasets and
calibrated from the fossil record (2) (Fig. 1 Dand Eand Table S2), but the AC
trees differ in that a shared ancestral morphotype is represented by a si-
multaneous origin modeled as a hard polytomy (branch length of “0”) (Fig.
1E). In both cases, the MAA state corresponds to Nasalis and Lagothrix,
which are also used to root the tree. Trees were generated in Mesquite
v.3.01 (57). For each tree, we calculated the total branch length and tested
the hypothesis of no phylogenetic signal using a permutation design (10,000
replicates) as implemented in MorphoJ v.1.06c (49).
ACKNOWLEDGMENTS. The Peabody Museum, Museum of Comparative
Zoology, American Museum of Natural History, National Museum of Natural
History, Field Museum of Natural History, Cleveland Museum of Natural
History, University of Zürich-Irchel, Zooligische Staatssammlung, Musée Royale
de l’Afrique Centrale, Powell-Cotton Museum, Kyoto University Primate Re-
search Institute, and Japan Monkey Center provided access to specimens.
T. Nalley assisted with segmentation of DIK1-1. K. Carlson provided computed
tomography (CT) data for MH2. S. Mellilo kindly provided a subset of the adult
human landmark data. B. Feeley provided additional human imaging data
Young et al. PNAS Early Edition
(CHR no. 10-01599). J. Camacho assisted in the CT scanning of La Ferassie I. I.
Hershkovitz provided CT data for Kebara 2 and Qafzeh 9. Funding was pro-
vided through grants from the National Science Foundation (Grant BCS-
1518596 to T.D.C., N.M.Y., and N.T.R.) and the generosity of Margaret and
William Hearst (Z.A.). N.M.Y. acknowledges funding from National Institutes
of Health Grants R01DE019638 and R01DE021708 and the ongoing support
of the University of California, San Francisco OrthopaedicTrauma Institute,
T. Miclau, R. Marcucio, and the Laboratory for Skeletal Regeneration.
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www.pnas.org/cgi/doi/10.1073/pnas.1511220112 Young et al.
Young et al. 10.1073/pnas.1511220112
Canonical Axis 1 (47% Variation)
Canonical Axis 2 (23% Variation)
-6 3 0 3 6 9
bgPC 1 (46.8% Shape Variation)
bgPC 2 (20.1% Shape Variation)
-0.20 -0.10 0.00 0.10 0.20 0.30
-0.20 -0.10 0.00 0.10 0.20
-0.10 0.00 0.10 0.20 0.30
-0.10 0.00 0.10 0.20 0.30
Principal Component 1 (45.4% Variation)
Principal Component 2 (19.1% Variation)
Principal Component 1 (45.4% Variation)
Principal Component 2 (19.1% Variation)
Fig. S1. Extended shape analyses. (Aand B) Principal components analysis (PCA) using only the extant species. Phylogenetic reconstructions are shown as branching patterns, with ancestral nodes at branch joints. Dashed lines show the most direct
evolutionary path between hypothesized ancestral and descendant states. AA, African ape model; AC, ape convergence model. (C) Canonical variates analysis (CVA) showing the first two axes. Distribution of species and associated shape vectors are
similar to those identified in the PCA (Fig. 2) but show greater separation due to the methodology. (D) Phylogenetic reconstructions within the CVA morphospace using a method of squared-change parsimony on the CV1 and -2 axes while using
alternative tree hypotheses (Fig. 1 Dand E). Results show that a simple morphocline separates Pan and Homo in CV1 for the AA model, and a two-step process in CV1 and -2 for the AC model. (E) Results of the between-group principal components
analysis (bgPCA) are largely identical to the PCA and CVA although there is reduced discrimination of African apes, suggesting that Pan and Gorilla may be even more similar when sample size effects are taken into account. (F) The phylogenetic
reconstruction within the bgPCA morphospace is also concordant with other ordination results. Color coding is the same as in Fig. 2D. Red dots represent different developmental simulations of DIK 1-1 (A. afarensis).
Young et al. www.pnas.org/cgi/content/short/1511220112 1of7
% Total Squared Covariance
Fig. S2. Partial least squares (PLS) results. (A) Distribution of covariation between blade and spine shows that the majority of shape variation is associated with
the first axis. (B) Plot of PLS1 axes for blade and spine variation shows a highly significant association of shape variation covariation (R
(C) Associated PLS shape vector direction and magnitudes for positive (+0.10) and negative (−0.15) shown on the mean configuration (red, blade landmarks;
blue, spine landmarks).
Young et al. www.pnas.org/cgi/content/short/1511220112 2of7
-0.20 -0.10 0.00 0.10 0.20 0.30
0.20 0.10 0.00 - 0.10 - 0.20
Principal Component 1 (47.3% Shape Variation)
Principal Component 3 (9.3% Shape Variation)
AA Model AC Model
PC1 (47.3% Variation)
PC2 (18.8% Variation)
PC3 (9.3% Variation)
Fig. S3. Extended PCA results. (A) Visualization of PC3 shape changes from positive (Top) to negative (Bottom). Gorilla and Pongo differ from all other taxa in having moderately wider scapula beyond those identified in PC1. (B) Three-dimensional scatterplot of PC1, PC2, and PC3.
Dashed lines show approximate direct evolutionary vectors connecting hypothesized ancestral and descendant species for the AA and AC models. (C) Two-dimensional scatterplot of PC1 vs. PC3 with examples of Gorilla and Pongo shown. (D) Reconstructed phylogenetic trees from
the PC1 and PC3 morphospace from Fig. 2. Note that the PC3 axis is reversed in Aand Brelative to the trees shown in Cand D.
Young et al. www.pnas.org/cgi/content/short/1511220112 3of7
y = -188.29x + 9.4688
R = 0.74475
-0.15 -0.10 -0.05 0.00 0.05 0.10
Millions of Years Ago (mya)
y = -93.821x + 21.273
R = 0.35565
0.00 0.05 0.10 0.15 0.20 0.25 0.30
Millions of Years Ago (mya)
y = 17.992x + 2.0509
R = 0.00916
-0.02 0.00 0.02 0.04 0.06 0.08 0.10 0.12
Millions of Years Ago (mya)
y = -24.886x + 5.6978
R = 0.86158
-0.20 -0.10 0.00 0.10 0.20 0.30
Millions of Years Ago (mya)
PC1 : Spine Angle PC2 : Blade Shape
Fig. S4. PC scores versus time. (A–D) Regressions of PC1 shape scores on both estimated divergence time (ancestral nodes) and geologic age (fossils) illustrate
alternative predictions for the timing and strength of selection in the hominin lineage on spine and glenoid orientation.
UPGMA Neighbor JoiningAB
0.00 0.05 0.10 0.16 0.21
0.05 0.10 0.15 0.20 0.26
Fig. S5. Procrustes distance trees. (A) Tree generated using the unweighted pair group method with arithmetic mean (UPGMA) method. (B) Tree generated
using the neighbor joining (NJ) method. In both cases, A. afarensis is associated with Gorilla whereas either H. ergaster or H. neanderthalensis is associated with
H. sapiens. Procrustes distances and significance values are found in Table S1.
Young et al. www.pnas.org/cgi/content/short/1511220112 4of7
1: Suprascapular notch
2: Superior point on vertebral border
3: Intersection of spine with vertebral border
4: Inferior point on vertebral border
5: Superior lateral point of teres major fossa
6: Lateral most extent of spine
7: Glenoid neck
8: Root of spine
9: Inferior extent of glenoid
10: Dorsal side of glenoid
11: Ventral extent of glenoid
12: Superior extent of glenoid
13: Shallowest extent of glenoid
Fig. S6. Scapula landmarks. Descriptions and locations of the 3D landmarks used in this study are shown on a representative P. troglodytes scapula (Left)
shown in dorsal and medial view.
3.6 3.9 4.2 4.5 4.8 5.1 5.4 5.7 6.0
Log Centroid Size
Au. afarensis (N=1)
Go. gorilla (N=167)
Pa. troglodytes (N=146)
Po. pygmaeus (N=53)
Na. larvatus (N=56)
Fig. S7. Growth vectors used for developmental simulation. Multivariate regression of group shape on log centroid size for the taxa shown. Individual growth
vectors were generated by performing the same multivariate regression analysis using the Procrustes coordinates from the group superimposition but per-
formed on each species alone. The Procrustes coordinates of A. afarensis (DIK 1-1) were simulated at an adult size corresponding to an increase of log centroid
size of 0.75, consistent with achieving an adult outcome (dashed ellipses) in each of the taxa used.
Young et al. www.pnas.org/cgi/content/short/1511220112 5of7
Table S1. Procrustes distances between species pairs below the diagonal and Pvalues (10,000 permutations) above
Species A. afa A. sed G. gor H. erg H. nea H. sap Hy. sp. L. lag N. lar P. pan P. tro P. pyg S. syn
A. afarensis —0.141 *** 0.039 0.037 *** *** 0.000 *** *** *** *** ***
A. sediba 0.132 —0.014 n/a 0.333 0.164 0.023 0.019 0.050 0.016 0.017 0.018 0.003
G. gorilla 0.128 0.206 —0.012 0.000 *** *** *** *** *** *** *** ***
H. ergaster 0.199 0.153 0.275 —n/a 0.176 0.014 0.080 0.026 0.011 0.010 0.021 0.008
H. neander. 0.215 0.175 0.286 0.089 —0.025 0.001 0.002 0.001 0.001 0.001 0.001 0.000
H. sapiens 0.159 0.130 0.229 0.132 0.111 —*** *** *** *** *** *** ***
Hy. sp. 0.200 0.265 0.190 0.374 0.382 0.311 —*** *** *** *** *** ***
L. lagotricha 0.155 0.197 0.213 0.263 0.268 0.204 0.197 —*** *** *** *** ***
N. larvatus 0.121 0.134 0.181 0.206 0.216 0.162 0.216 0.113 —*** *** *** ***
P. paniscus 0.170 0.223 0.133 0.330 0.346 0.284 0.130 0.233 0.198 —*** *** ***
P. troglodytes 0.152 0.208 0.118 0.314 0.326 0.260 0.124 0.214 0.188 0.046 —*** ***
P. pygmaeus 0.163 0.195 0.188 0.260 0.246 0.179 0.208 0.150 0.136 0.221 0.200 —***
S. syndactylus 0.207 0.267 0.186 0.379 0.388 0.321 0.059 0.232 0.239 0.112 0.106 0.228 —
A. afarensis (A. afa), Australopithecus afarensis;A. sediba (A. sed), Australopithecus sediba;G. gorilla (G. gor), Gorilla gorilla;
H. ergaster (H. erg), Homo ergaster;H. neander.(H. nea), Homo neanderthalensis;H. sapiens (H. sap), Homo sapiens;Hy.sp.,Hylobates
sp.; L. lagotricha (L. lag), Lagothrix lagotricha;N. larvatus (N. lar), Nasalis larvatus;P. paniscus (P. pan), Pan paniscus;P. troglodytes (P. tro),
Pan troglodytes;P. Pygmaeus (P. pyg), Pongo pygmaeus;S. Syndactylus (S. syn), Symphalangus syndactylus.***P≤0.001.
Table S2. Average PC1 scores, geologic ages, and estimated
PC1 Age, Mya
Mean SD Estimate Low High
H. sapiens 0.195 0.027 0.000 ——
AMHs 0.189 —0.106 0.097 0.116
H. neander. 0.251 0.019 0.063 0.058 0.068
H. ergaster 0.228 —1.550 1.500 1.600
A. sediba 0.117 —1.977 1.974 1.980
A. afarensis 0.063 0.013 3.330 3.310 3.350
Panins −0.067 0.030 6.600 6.000 7.000
African apes −0.036 0.044 8.600 7.700 9.200
P. pygmaeus 0.091 0.037 18.300 16.300 20.800
MAA 0.086 0.031 30.500 26.900 36.400
Dashes indicate the diagonal, for which there is no value. AMHs, anatom-
ically modern H. sapiens.
Young et al. www.pnas.org/cgi/content/short/1511220112 6of7
Movie S1. Pan–Homo evolutionary transformation. Example of a thin-plate spline (TPS) deformation between representative P. troglodytes and H. sapiens
scapulae in which landmark configurations have been scaled to the same size and aligned to the vertebral border. Shape differences are primarily associated
with the orientation of the spine and glenoid angle, which become more inferiorly oriented. Note that blade shape remains largely unchanged.
Movie S2. Pongo–Homo evolutionary transformation. Thin-plate spline (TPS) deformation between representative P. pygmaeus and H. sapiens scapulae in
which landmark configurations have been scaled to the same size and aligned to the vertebral border. Shape transformations into the human state consist of
both a more inferior orientation of the spine and glenoid angle, and changes to the shape of the supraspinous fossa, particularly the cranial orientation of the
Young et al. www.pnas.org/cgi/content/short/1511220112 7of7