Reconstructing Denisovan Anatomy Using DNA Methylation Maps.

Denisovans are an extinct group of humans whose morphology remains unknown. Here, we present a method for reconstructing skeletal morphology using DNA methylation patterns. Our method is based on linking unidirectional methylation changes to loss-of-function phenotypes. We tested performance by reconstructing Neanderthal and chimpanzee skeletal morphologies and obtained >85% precision in identifying divergent traits. We then applied this method to the Denisovan and offer a putative morphological profile. We suggest that Denisovans likely shared with Neanderthals traits such as an elongated face and a wide pelvis. We also identify Denisovan-derived changes, such as an increased dental arch and lateral cranial expansion. Our predictions match the only morphologically informative Denisovan bone to date, as well as the Xuchang skull, which was suggested by some to be a Denisovan. We conclude that DNA methylation can be used to reconstruct anatomical features, including some that do not survive in the fossil record.

The DNH 7 skull of Australopithecus robustus from Drimolen (Main Quarry), South Africa.

Although the early hominin species Australopithecus robustus has been known for more than eight decades and is represented by hundreds of fossils from sites in South Africa, a complete, well-preserved skull has been elusive. DNH 7, an adult cranium and mandible from the Drimolen site, was identified, on the basis of its small size, as a presumptive female of A. robustus. Here, we provide a detailed comparative description of the specimen. In cranial, facial, and dental size, DNH 7 is confirmed to lie at the extreme small end of the A. robustus range of variation, along with a few fragmentary maxillofacial specimens from Swartkrans. In addition, relative to the classically derived craniofacial features of the Swartkrans+Kromdraai portions of the A. robustus hypodigm, primitive anatomy pervades the DNH 7 face, braincase, and cranial base. Taken together, these pieces of evidence place DNH 7 in a previously unfilled position on the robust Australopithecus morphocline, where the specimen highlights the morphological distinctions between southern and eastern African species of this group and epitomizes the anatomy expected of the group's last common ancestor.

Mechanical implications of the mandibular coronoid process morphology in Neandertals.

OBJECTIVES: Among the diagnostic features of the Neandertal mandible are the broad base of the coronoid process and its straight posterior margin. The adaptive value of these (and other) anatomical features has been linked to the Neandertal's need to cope with a large gape. The present study aims to test this hypothesis with regard to the morphology of the coronoid process. MATERIALS AND METHODS: This admittedly simple, intuitive hypothesis was tested here via a comparative finite-element study of the primitive versus modified state of the coronoid process, using two-dimensional models of the mandible. RESULTS: Our simulations demonstrate that a large gape has an unfavorable effect on the primitive state of the coronoid process: the diagonal, almost horizontal, component of the temporalis muscle resultant (relative to the long axis of the coronoid process) bends the process in the sagittal plane. Furthermore, we show that the modification of the coronoid process morphology alone reduces the process' bending in a wide gape increasing the compression to tension ratio. DISCUSSION: These results provide indirect evidence in support of the hypothesis that the modification of the coronoid process in Neandertals is necessary for enabling their mandible to cope with a large gape.

Australopithecus sediba and the emergence of Homo: Questionable evidence from the cranium of the juvenile holotype MH 1.

Malapa Hominin (MH) 1, an immature individual whose second permanent molars had recently reached occlusion at the time of death, is the holotype of Australopithecus sediba, a 2-myr-old South African taxon that has been hypothesized to link phylogenetically australopith-grade hominins to the Homo clade. Given the existence of 2.8 myr-old fossils of Homo in eastern Africa, this hypothesis implies a ghost lineage spanning at least 800 kyr. An alternative hypothesis posits a unique relationship between A. sediba and Australopithecus africanus, which predates the Malapa hominins in southern Africa and whose phylogenetic relationships remain ambiguous. The craniofacial morphology of MH 1 looms large in the framing of the two hypotheses. We evaluated these alternatives in two ways. First, we investigated whether the craniofacial morphology of MH 1 was ontogenetically stable at death. Based on data from a late-growth series of chimpanzee, gorilla, and modern human crania, we found that key aspects of MH 1's resemblance to Homo can be accounted for by its immaturity. Second, we studied MH 1 with an eye to identifying craniofacial synapomorphies shared with A. africanus. In this case, MH 1 shows unambiguous affinities in its zygomaticomaxillary and supraorbital morphology to crania from Sterkfontein Member 4, which we found to exhibit unusual derived morphology compared to Homo and other australopiths. We argue that MH 1 provides clear evidence that A. sediba was uniquely related to A. africanus and that the hypothesis of an extensive ghost lineage connecting A. sediba to the root of the Homo clade is unwarranted.

Ardipithecus ramidus and the evolution of the human cranial base.

The early Pliocene African hominoid Ardipithecus ramidus was diagnosed as a having a unique phylogenetic relationship with the Australopithecus + Homo clade based on nonhoning canine teeth, a foreshortened cranial base, and postcranial characters related to facultative bipedality. However, pedal and pelvic traits indicating substantial arboreality have raised arguments that this taxon may instead be an example of parallel evolution of human-like traits among apes around the time of the chimpanzee-human split. Here we investigated the basicranial morphology of Ar. ramidus for additional clues to its phylogenetic position with reference to African apes, humans, and Australopithecus. Besides a relatively anterior foramen magnum, humans differ from apes in the lateral shift of the carotid foramina, mediolateral abbreviation of the lateral tympanic, and a shortened, trapezoidal basioccipital element. These traits reflect a relative broadening of the central basicranium, a derived condition associated with changes in tympanic shape and the extent of its contact with the petrous. Ar. ramidus shares with Australopithecus each of these human-like modifications. We used the preserved morphology of ARA-VP 1/500 to estimate the missing basicranial length, drawing on consistent proportional relationships in apes and humans. Ar. ramidus is confirmed to have a relatively short basicranium, as in Australopithecus and Homo. Reorganization of the central cranial base is among the earliest morphological markers of the Ardipithecus + Australopithecus + Homo clade.

The Neandertal nature of the Atapuerca Sima de los Huesos mandibles.

The recovery of additional mandibular fossils from the Atapuerca Sima de los Huesos (SH) site provides new insights into the evolutionary significance of this sample. In particular, morphological descriptions of the new adult specimens are provided, along with standardized metric data and phylogenetically relevant morphological features for the expanded adult sample. The new and more complete specimens extend the known range of variation in the Atapuerca (SH) mandibles in some metric and morphological details. In other aspects, the addition of new specimens has made it possible to confirm previous observations based on more limited evidence. Pairwise comparisons of individual metric variables revealed the only significant difference between the Atapuerca (SH) hominins and Neandertals was a more vertical symphysis in the latter. Similarly, principal components analysis of size-adjusted variables showed a strong similarity between the Atapuerca (SH) hominins and Neandertals. Morphologically, the Atapuerca (SH) mandibles show nearly the full complement of Neandertal-derived features. Nevertheless, the Neandertals differ from the Atapuerca (SH) mandibles in showing a high frequency of the H/O mandibular foramen, a truncated, thinned and inverted gonial margin, a high placement of the mylohyoid line at the level of the M3, a more vertical symphysis and somewhat more pronounced expression of the chin structures. Size-related morphological variation in the SH hominins includes larger retromolar spaces, more posterior placement of the lateral corpus structures, and stronger markings associated with the muscles of mastication in larger specimens. However, phylogenetically relevant features in the SH sample are fairly stable and do not vary with the overall size of the mandible. Direct comparison of the enlarged mandibular sample from Atapuerca (SH) with the Mauer mandible, the type specimen of H. heidelbergensis, reveals important differences from the SH hominins, and there is no morphological counterpart of Mauer within the SH sample, suggesting the SH fossils should not be assigned to this taxon. The Atapuerca (SH) mandibles show a greater number of derived Neandertal features, particularly those related to midfacial prognathism and in the configuration of the superior ramus, than other European middle Pleistocene specimens. This suggests that more than one evolutionary lineage co-existed in the middle Pleistocene, and, broadly speaking, it appears possible to separate the European middle Pleistocene mandibular remains into two distinct groupings. One group shows a suite of derived Neandertal features and includes specimens from the sites of Atapuerca (SH), Payre, l'Aubesier and Ehringsdorf. The other group includes specimens that generally lack derived Neandertal features and includes the mandibles from the sites of Mauer, Mala Balanica, Montmaurin and (probably) Visogliano. The two published Arago mandibles differ strongly from one another, with Arago 2 probably belonging to this former group, and Neandertal affinities being more difficult to identify in Arago 13. Outside of the SH sample, derived Neandertal features in the mandible only become more common during the second half of the middle Pleistocene. Acceptance of a cladogenetic pattern of evolution during the European middle Pleistocene has the potential to reconcile the predictions of the accretion model and the two phases model for the appearance of Neandertal morphology. The precise taxonomic classification of the SH hominins must contemplate features from the dentition, cranium, mandible and postcranial skeleton, all of which are preserved at the SH site. Nevertheless, the origin of the Neandertal clade may be tied to a speciation event reflected in the appearance of a suite of derived Neandertal features in the face, dentition and mandible, all of which are present in the Atapuerca (SH) hominins. This same suite of features also provides a useful anatomical basis to include other European middle Pleistocene mandibles and crania within the Neandertal clade.

Comment on "A Middle Pleistocene Homo from Nesher Ramla, Israel".

Hershkovitz et al. (Reports, 25 June 2021, p. 1424) conclude that the Nesher Ramla (NR) fossils represent a distinctive Homo paleodeme that played a role as a source population for Neanderthals. However, the highly diagnostic features of the Neanderthal mandible­clearly displayed by the NR fossils­are largely overlooked. Our analyses indicate that the NR fossils represent simply a Neanderthal.

Opposing Extremes of Zygomatic Bone Morphology: Australopithecus Boisei versus Homo Neanderthalensis.

The lateral margin of the zygomatic bone of Australopithecus boisei flares both anteriorly and laterally. As a result, the bone loses the suspensory bracing of the facial frame and is transformed into a visor-like structure that supports itself and gains its rigidity from its shape. The coronally oriented bony plates and the outline of the facial mask help the A. boisei face resist the effect of the visor-like structure, which tends to pull the bone plates of the face away from the midline. On the other hand, the nearly sagittal orientation of the zygomatic bone in Homo neanderthalensis helps the face resist torque and bending forces, which themselves stem from the positioning of the bite point on the anterior teeth. Although the zygomatic bones of these two taxa are highly specialized, they differ fundamentally from each other. Anat Rec, 300:152-159, 2017. © 2016 Wiley Periodicals, Inc.

A complete skull from Dmanisi, Georgia, and the evolutionary biology of early Homo.

The site of Dmanisi, Georgia, has yielded an impressive sample of hominid cranial and postcranial remains, documenting the presence of Homo outside Africa around 1.8 million years ago. Here we report on a new cranium from Dmanisi (D4500) that, together with its mandible (D2600), represents the world's first completely preserved adult hominid skull from the early Pleistocene. D4500/D2600 combines a small braincase (546 cubic centimeters) with a large prognathic face and exhibits close morphological affinities with the earliest known Homo fossils from Africa. The Dmanisi sample, which now comprises five crania, provides direct evidence for wide morphological variation within and among early Homo paleodemes. This implies the existence of a single evolving lineage of early Homo, with phylogeographic continuity across continents.

The cranial base of Australopithecus afarensis: new insights from the female skull.

Cranial base morphology differs among hominoids in ways that are usually attributed to some combination of an enlarged brain, retracted face and upright locomotion in humans. The human foramen magnum is anteriorly inclined and, with the occipital condyles, is forwardly located on a broad, short and flexed basicranium; the petrous elements are coronally rotated; the glenoid region is topographically complex; the nuchal lines are low; and the nuchal plane is horizontal. Australopithecus afarensis (3.7-3.0 Ma) is the earliest known species of the australopith grade in which the adult cranial base can be assessed comprehensively. This region of the adult skull was known from fragments in the 1970s, but renewed fieldwork beginning in the 1990s at the Hadar site, Ethiopia (3.4-3.0 Ma), recovered two nearly complete crania and major portions of a third, each associated with a mandible. These new specimens confirm that in small-brained, bipedal Australopithecus the foramen magnum and occipital condyles were anteriorly sited, as in humans, but without the foramen's forward inclination. In the large male A.L. 444-2 this is associated with a short basal axis, a bilateral expansion of the base, and an inferiorly rotated, flexed occipital squama--all derived characters shared by later australopiths and humans. However, in A.L. 822-1 (a female) a more primitive morphology is present: although the foramen and condyles reside anteriorly on a short base, the nuchal lines are very high, the nuchal plane is very steep, and the base is as relatively narrow centrally. A.L. 822-1 illuminates fragmentary specimens in the 1970s Hadar collection that hint at aspects of this primitive suite, suggesting that it is a common pattern in the A. afarensis hypodigm. We explore the implications of these specimens for sexual dimorphism and evolutionary scenarios of functional integration in the hominin cranial base.

Gorilla-like anatomy on Australopithecus afarensis mandibles suggests Au. afarensis link to robust australopiths.

Mandibular ramus morphology on a recently discovered specimen of Australopithecus afarensis closely matches that of gorillas. This finding was unexpected given that chimpanzees are the closest living relatives of humans. Because modern humans, chimpanzees, orangutans, and many other primates share a ramal morphology that differs from that of gorillas, the gorilla anatomy must represent a unique condition, and its appearance in fossil hominins must represent an independently derived morphology. This particular morphology appears also in Australopithecus robustus. The presence of the morphology in both the latter and Au. afarensis and its absence in modern humans cast doubt on the role of Au. afarensis as a modern human ancestor. The ramal anatomy of the earlier Ardipithecus ramidus is virtually that of a chimpanzee, corroborating the proposed phylogenetic scenario.

Was Australopithecus anamensis ancestral to A. afarensis? A case of anagenesis in the hominin fossil record.

We tested the hypothesis that early Pliocene Australopithecus anamensis was ancestral to A. afarensis by conducting a phylogenetic analysis of four temporally successive fossil samples assigned to these species (from earliest to latest: Kanapoi, Allia Bay, Laetoli, Hadar) using polarized character-state data from 20 morphological characters of the dentition and jaws. If the hypothesis that A. anamensis is ancestral to A. afarensis is true, then character-state changes between the temporally ordered site-samples should be congruent with hypothesized polarity transformations based on outgroup (African great ape) conditions. The most parsimonious reconstruction of character-state evolution suggests that each of the hominin OTUs shares apomorphies only with geologically younger OTUs, as predicted by the hypothesis of ancestry (tree length=31; Consistency Index=0.903). This concordance of stratigraphic and character-state data supports the idea that the A. anamensis and A. afarensis samples represent parts of an anagenetically evolving lineage, or evolutionary species. Each site-sample appears to capture a different point along this evolutionary trajectory. We discuss the implications of this conclusion for the taxonomy and adaptive evolution of these early-middle Pliocene hominins.

Does Homo neanderthalensis play a role in modern human ancestry? The mandibular evidence.

Data obtained from quantifying the upper part of the mandibular ramus (the coronoid process, the condylar process, and the notch between them) lead us to conclude that Neanderthals (both European and Middle Eastern) differ more from Homo sapiens (early specimens such as Tabun II, Skhul, and Qafzeh, as well as contemporary populations from as far apart as Alaska and Australia) than the latter differs from Homo erectus. The specialized Neanderthal mandibular ramus morphology emerges as yet another element constituting the derived complex of morphologies of the mandible and face that are unique to Neanderthals. These morphologies provide further support for the contention that Neanderthals do not play a role in modern human biological ancestry, either through "regional continuity" or through any other form of anagenetic progression.