H. naledi exhibits anatomical features shared with Australopithecus, other features shared with Homo, with several features not otherwise known in any hominin species. This anatomical mosaic is reflected in different regions of the skeleton. The morphology of the cranium, mandible, and dentition is mostly consistent with the genus Homo, but the brain size of H. naledi is within the range of Australopithecus. The lower limb is largely Homo-like, and the foot and ankle are particularly human in their configuration, but the pelvis appears to be flared markedly like that of Au. afarensis. The wrists, fingertips, and proportions of the fingers are shared mainly with Homo, but the proximal and intermediate manual phalanges are markedly curved, even to a greater degree than in any Australopithecus. The shoulders are configured largely like those of australopiths. The vertebrae are most similar to Pleistocene members of the genus Homo, whereas the ribcage is wide distally like Au. afarensis.

H. naledi has a range of body mass similar to small-bodied modern human populations, and is similar in estimated stature to both small-bodied humans and the largest known australopiths. We estimated body mass from eight femoral specimens for which subtrochanteric diameters can be measured (‘Materials and methods’), with results ranging between 39.7 kg and 55.8 kg (Table 3). No femur specimen is sufficiently complete to measure femur length accurately, but the U.W. 101-484 tibia preserves nearly its complete length, allowing a tibia length estimate of 325 mm (Figure 10). Estimates for the stature of this individual based on African human population samples range between 144.5 and 147.8 mm. Again, this stature estimate is similar to small-bodied modern human populations. It is within the range estimated for Dmanisi postcranial elements (Lordkipanidze et al., 2007), and slightly smaller than estimated for early Homo femoral specimens KNM-ER 1472 and KNM-ER 1481. Some large australopiths also had long tibiae and presumably comparably tall statures, as evidenced by the KSD-VP 1/1 skeleton from Woranso-Mille (Haile-Selassie et al., 2010).

Table 3 Dinaledi body mass estimates from femur specimens preserving subtrochanteric diameters https://doi.org/10.7554/eLife.09560.014 Specimen ID Side AP subtrochanteric breadth ML subtrochanteric breadth Mass (a) Mass (b) U.W. 101-002 R 18.5 23.6 40.0 44.7 U.W. 101-003 R 21.6 31.4 54.5 55.8 U.W. 101-018 R 18.1 23.8 39.7 44.4 U.W. 101-226 L 19.1 24.0 41.3 45.7 U.W. 101-1136 R 16.9 25.5 39.7 44.4 U.W. 101-1391 R 18.8 23.9 40.8 45.3 U.W. 101-1475 L 18.8 29.0 46.5 49.7 U.W. 101-1482 L 20.7 28.9 49.7 52.1

The endocranial volume of all H. naledi specimens is clearly small compared to most known examples of Homo. We combined information from the most complete cranial vault specimens to arrive at an estimate of endocranial volume for both larger (presumably male) and smaller (presumably female) individuals (larger composite depicted in Figure 11). The resulting estimates of approximately 560cc and 465cc, respectively, overlap entirely with the range of endocranial volumes known for australopiths. Within the genus Homo, only the smallest specimens of H. habilis, one single H. erectus specimen, and H. floresiensis overlap with these values.

Figure 11 Download asset Open asset Virtual reconstruction of the endocranium of the larger composite cranium from DH1 and DH2 overlaid with the ectocranial surfaces. (A) Lateral view. (B) Superior view. The resulting estimate of endocranial volume is 560cc. Scale bar = 10 cm. https://doi.org/10.7554/eLife.09560.016

Despite its small vault size, the cranium of H. naledi is structurally similar to those of early Homo. Frontal bossing is evident, as is a marked degree of parietal bossing. There is no indication of metopic keeling, though there is slight parasagittal keeling between bregma and lambda, and some prelambdoidal flattening. The cranial vault bones are generally thin, becoming somewhat thicker in the occipital region. The supraorbital torus is well developed, though weakly arched, and is bounded posteriorly by a well-developed supratoral sulcus. The lateral corners of the supraorbital torus are rounded and relatively thin. The temporal lines are widely spaced, and there is no indication of a sagittal crest or temporal/nuchal cresting. The temporal crest is positioned on the posterior aspect of the lateral supraorbital torus, rather than on the superior aspect as in australopiths. At the posteroinferior extent of the temporal lines, they curve anteroinferiorly presenting a well-developed angular torus. The crania have a pentagonal outline in posterior view, with the greatest vault breadth located in the supramastoid region. The nuchal region exhibits sexually dimorphic development of nuchal muscle markings and the external occipital protuberance, and there is a clear indication of a tuberculum linearum in addition to the external occipital protuberance. In superior view the vault tapers from posterior to anterior, though post-orbital constriction is slight. The squamosal suture is low and gently curved, and parietal striae are well defined. The lateral margins of the orbits face laterally. A small zygomaticofacial foramen is typically present near the center of the zygomatic bone. The root of the zygomatic process of the maxilla is anteriorly positioned, at the level of the P3 or the P4. There is no indication of a zygomatic prominence, and the zygomatic arches do not flare laterally to any extent. The root of the zygomatic process of the temporal is angled downwards approximately 30° relative to FH. The root of the zygomatic process of the temporal begins to laterally expand above the level of the mandibular fossa, rather than above the level of the EAM as in australopiths. The mandibular fossa is somewhat large, and moderately deep. The articular eminence of the mandibular fossa is saddle-shaped, and oriented posteroinferiorly. Almost the entire mandibular fossa is positioned medial to the temporal squama. The entoglenoid process is elongated and faces primarily laterally. The postglenoid process is small and closely appressed to the tympanic, forming part of the posterior wall of the fossa. The petrotympanic is distinctly coronally oriented. The vaginal process is small but distinct. The crista petrosa is weakly developed and not notably sharpened. There is a strong Eustachian process. The external auditory meatus is small, oval-shaped, and obliquely oriented, and a distinct suprameatal spine is present. The mastoid region is slightly laterally inflated. The mastoid process is triangular in cross-section, with a rounded apex and a mastoid crest. The digastric groove is deep and narrow, alongside a marked juxtamastoid eminence. The canine juga are weakly developed and there is no indication that anterior pillars would have been present. A shallow, ill-defined canine fossa is indicated. The nasoalveolar clivus is flat and square-shaped. The parabolic-shaped palate is broad and anteriorly shallow, becoming deeper posteriorly.

The mandibular dentition of H. naledi is arranged in a parabolic arch. The alveolar and basal margins of the corpus diverge slightly. A single, posteriorly opening mental foramen is positioned slightly above the mid-corpus level, between the position of the P 3 and the P 4 . The mandibular corpus is relatively gracile, with a well-developed lateral prominence whose maximum extent is typically at the M 2 . A slight supreme lateral torus (of Dart) weakly delineates the extramolar sulcus from the lateral corpus. The superior lateral torus is moderately developed, running anteriorly to the mental foramen where it turns up to reach the P 3 jugum. The marginal torus is moderately developed, and defines a moderate intertoral sulcus. The posterior and anterior marginal tubercles are indicated only as slight roughenings of bone. The gracile mandibular symphysis is vertically oriented. A well-developed mental protuberance and weak lateral tubercles are delineated by a slight mandibular incisure, thereby presenting a weak mentum osseum. The post-incisive planum is steeply inclined and not-shelf-like. There is no superior transverse torus, while a weak, basally oriented inferior transverse torus is present. The anterior and posterior subalveolar fossae are continuous and deep, overhung by a well-developed alveolar prominence. The extramolar sulcus is moderately wide. The root of the ramus of the mandible originates high on the corpus at the level of the M 2 . Strong ectoangular tuberosities are indicated. A large mandibular foramen is present, with a diffusely defined mylohyoid groove.

Like the skull, the dentition of H. naledi compares most favorably to early Homo samples. Yet compared to samples of H. habilis, H. rudolfensis, and H. erectus, the teeth of H. naledi are comparatively quite small, similar in dimensions to much later samples of Homo. With both small post-canine teeth and a small endocranial volume, H. naledi joins Au. sediba and H. floresiensis in an area distinct from the general hominin relation of smaller post-canine teeth in species with larger brains (Figure 12).

Figure 12 Download asset Open asset Brain size and tooth size in hominins. The buccolingual breadth of the first maxillary molar is shown here in comparison to endocranial volume for many hominin species. H. naledi occupies a position with relatively small molar size (comparable to later Homo) and relatively small endocranial volume (comparable to australopiths). The range of variation within the Dinaledi sample is also fairly small, in particular in comparison to the extensive range of variation within the H. erectus sensu lato. Vertical lines represent the range of endocranial volume estimates known for each taxon; each vertical line meets the horizontal line representing M1 BL diameter at the mean for each taxon. Ranges are illustrated here instead of data points because the ranges of endocranial volume in several species are established by specimens that do not preserve first maxillary molars. https://doi.org/10.7554/eLife.09560.017

In comparison to H. habilis, H. rudolfensis, and H. erectus, the teeth of H. naledi are not only small, but also markedly simple in crown morphology. Maxillary and mandibular molars lack extensive crenulation, secondary fissures and supernumerary cusps. The M1 has an equal-sized metacone and paracone, and has a slight expression of Carabelli's trait represented by a small cusp or shallow pit. I1 exhibits slight occlusal curvature with trace marginal ridges and variably small tuberculum dentale. I2 exhibits greater occlusal curvature and tuberculum dentale expression but neither upper incisor has double shovelling or interruption groove. The mandibular canines of H. naledi have a small occlusal area, and have a distal marginal cuspule as a topographically distinct expression of the cingular margin. The P 3 is double-rooted, fully bicuspid with metaconid and protoconid of approximately equal height and occlusal area separated by a distinct longitudinal groove, has a distally extensive talonid, and an occlusal outline approximately symmetrical with respect to the mesiodistal axis. P 4 likewise has a distally extensive talonid and approximately symmetrical occlusal outline (Figure 5). M 1 and M 2 lack cusp 6 and cusp 7, except for very slight expression in a small fraction of specimens, and have a very faint subvertical depression rather than a distinct or extensive protostylid. Like australopiths and some early Homo specimens, H. naledi has an increasing molar size gradient in the mandibular dentition (M1 < M2 < M3).

The lower limb of H. naledi is defined not only by a unique combination of primitive and derived traits, but also by the presence of unique features in the femur and tibia. Like all other bipedal hominins, H. naledi possesses a valgus knee and varus ankle. The femoral neck is long, anteverted, and anteroposteriorly compressed. Muscle insertions for the M. gluteus maximus are strong and the femur has a well-marked linea aspera with pilaster variably present. The patella is relatively anteroposteriorly thick. The tibia is mediolaterally compressed with a rounded anterior border, a large proximal attachment for the M. tibialis posterior, and a thin medial malleolus. The fibula is gracile with laterally oriented lateral malleolus, a relatively circular neck and a convex surface for the proximal attachment of the M. peroneus longus. Unique features in the lower limb of H. naledi include a depression in the superior aspect of the femoral neck that results in two mediolaterally oriented pillars inferoposteriorly and superoanteriorly, and a strong distal attachment of the pes anserinus on the tibia.

The foot and ankle of H. naledi are largely humanlike (Figure 9). The tibia stands orthogonally upon the talus, which is moderately wedged, with a mediolaterally flat trochlea having medial and lateral margins at even height, a form distinct from the strong keeling seen in OH 8 (H. habilis) and several tali from Koobi Fora. The talar head and neck exhibit strong, humanlike torsion; the horizontal angle is higher than in most humans, similar to that found in australopiths. The calcaneus is only moderately robust, but possesses the plantar declination of the retrotrochlear eminence and plantarly positioned lateral plantar process found in both modern humans and Au. afarensis. The peroneal trochlea is small, unlike that found in australopiths and similar only to that in H. sapiens and Neanderthals. The talonavicular, subtalar joints and calcaneocuboid joints are humanlike in possessing minimal ranges of motion and evidence for a locking, rigid midfoot. The intermediate and lateral cuneiforms are proximodistally elongated. The hallucal tarsometatarsal joint is flat and proximodistally aligned indicating that H. naledi possessed an adducted, non-grasping hallux. The head of the first metatarsal is mediolaterally expanded dorsally, indicative of a humanlike windlass mechanism. The foot possesses humanlike metatarsal lengths, head proportions, and torsion.

The phalanges are moderately curved, slightly more so than in H. sapiens. The only primitive anatomies found in the foot of H. naledi are the talar head and neck declination and sustentaculum tali angles, suggestive of a lower arched foot with a more plantarly positioned and horizontally inclined medial column than typically found in modern humans (Harcourt-Smith et al., 2015).

The axial skeleton presents a combination of derived (mainly aspects of the vertebrae) and seemingly primitive (mainly the ribs) traits. The preserved adult T10 and T11 vertebrae are proportioned similarly to Pleistocene Homo, with transverse process morphology most similar to Neandertals. The neural canals of these vertebrae are large in comparison to the diminutive overall size of the vertebrae, proportionally recalling Dmanisi H. erectus, Neandertals, and modern humans. The 11th rib is straight (uncurved), similar to Au. afarensis, and the shape of the upper rib cage appears narrow, as assessed from first and second rib fragments, suggesting that the thorax was pyramidal in shape. The 12th rib presents a robust shaft cross-section most similar to Neandertals. This combination is not found in other hominins and might reflect allometric scaling at a small trunk size.

The Dinaledi iliac blade is flared and shortened anteroposteriorly, resembling Au. afarensis or Au. africanus. The ischium is short with a narrow tuberoacetabular sulcus, and the ischiopubic and iliopubic rami are thick, resembling Au. sediba and H. erectus. This combination of iliac and ischiopubic features has not been found in other fossil hominins (Figure 13).

Figure 13 Download asset Open asset Selected pelvic specimens of H. naledi. U.W. 101-1100 ilium in (A) lateral view showing a weak iliac pillar relatively near the anterior edge of the ilium, with no cristal tubercle development; (B) anterior view, angled to demonstrate the degree of flare, which is clear in comparison to the subarcuate surface. U.W. 101-723 immature sacrum in (C) anterior view; and (D) superior view. U.W. 101-1112 ischium in (E) lateral view; and (F) anterior view, demonstrating relatively short tuberacetabular diameter. Scale bar = 2 cm. https://doi.org/10.7554/eLife.09560.018

The shoulder of H. naledi is configured with the scapula situated high and lateral on the thorax, short clavicles, and little or no torsion of the humerus. The humerus is notably slender for its length, with prominent greater and lesser tubercles bounding a deep bicipital groove, with a small, non-projecting humeral deltoid tuberosity and brachioradialis crest. Distally, the humerus has a wide lateral distodorsal pillar and narrow medial distodorsal pillar, and a medially-displaced olecranon fossa with septal aperture. The Dinaledi radius and ulna diaphyses exhibit little curvature. The radius has a globular radial tuberosity, prominent pronator quadratus crest, and reduced styloid process.

The hand shares many derived features of modern humans and Neandertals in the thumb, wrist, and palm, but has relatively long and markedly curved fingers (Kivell et al., 2015). The thumb is long relative to the length of the other digits, and includes a robust metacarpal with well-developed intrinsic (M. opponens pollicis and M. first dorsal interosseous) muscle attachments (Figure 6). The pollical distal phalanx is large and robust with a well-developed ridge along the distal border of a deep proximal palmar fossa for the attachment of flexor pollicis longus tendon. Ungual spines also project proximopalmarly from a radioulnarly expanded apical tuft with a distinct area for the ungual fossa. The wrist includes a boot-shaped trapezoid with an expanded non-articular palmar surface, an enlarged and palmarly-expanded trapezoid-capitate joint, and a trapezium-scaphoid joint that extends further onto the scaphoid tubercle. Overall, carpal shapes and articular configurations are very similar to those of modern humans and Neandertals, and unlike those of great apes and other extinct hominins. However, the H. naledi wrist lacks a third metacarpal styloid process, has a more radioulnarly oriented capitate-Mc2 joint, and has a relatively small trapezium-Mc1 joint compared to humans and Neandertals. Moreover, the phalanges are long (relative to the palm) and more curved than most australopiths.