Revised age estimates of Australopithecus-bearing deposits at Sterkfontein, South Africa

Seasons of change: Mechanisms of genome evolution in human fungal pathogens

Fungi are a diverse kingdom of organisms capable of thriving in various niches across the world including those in close association with multicellular eukaryotes. Fungal pathogens that contribute to human disease reside both within the host as commensal organisms of the microbiota and the environment. Their niche of origin dictates how infection initiates but also places specific selective pressures on the fungal pathogen that contributes to its genome organization and genetic repertoire. Recent efforts to catalogue genomic variation among major human fungal pathogens have unveiled evolutionary themes that shape the fungal genome. Mechanisms ranging from large scale changes such as aneuploidy and ploidy cycling as well as more targeted mutations like base substitutions and gene copy number variations contribute to the evolution of these species, which are often under multiple competing selective pressures with their host, environment, and other microbes. Here, we provide an overview of the major selective pressures and mechanisms acting to evolve the genome of clinically important fungal pathogens of humans.

The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa

New ages for flowstone, sediments and fossil bones from the Dinaledi Chamber are presented. We combined optically stimulated luminescence dating of sediments with U-Th and palaeomagnetic analyses of flowstones to establish that all sediments containing Homo naledi fossils can be allocated to a single stratigraphic entity (sub-unit 3b), interpreted to be deposited between 236 ka and 414 ka. This result has been confirmed independently by dating three H. naledi teeth with combined U-series and electron spin resonance (US-ESR) dating. Two dating scenarios for the fossils were tested by varying the assumed levels of ²²²Rn loss in the encasing sediments: a maximum age scenario provides an average age for the two least altered fossil teeth of 253 +82/–70 ka, whilst a minimum age scenario yields an average age of 200 +70/–61 ka. We consider the maximum age scenario to more closely reflect conditions in the cave, and therefore, the true age of the fossils. By combining the US-ESR maximum age estimate obtained from the teeth, with the U-Th age for the oldest flowstone overlying Homo naledi fossils, we have constrained the depositional age of Homo naledi to a period between 236 ka and 335 ka. These age results demonstrate that a morphologically primitive hominin, Homo naledi, survived into the later parts of the Pleistocene in Africa, and indicate a much younger age for the Homo naledi fossils than have previously been hypothesized based on their morphology.

DOI:http://dx.doi.org/10.7554/eLife.24231.001

Species of ancient humans and the extinct relatives of our ancestors are typically described from a limited number of fossils. However, this was not the case with Homo naledi. More than 1500 fossils representing at least 15 individuals of this species were unearthed from the Rising Star cave system in South Africa between 2013 and 2014. Found deep underground in the Dinaledi Chamber, the H. naledi fossils are the largest collection of a single species of an ancient human-relative discovered in Africa.

After the discovery was reported, a number of questions still remained. Not least among these questions was: how old were the fossils? The material was undated, and predictions ranged from anywhere between 2 million years old and 100,000 years old. H. naledi shared several traits with the most primitive of our ancient relatives, including its small brain. As a result, many scientists guessed that H. naledi was an old species in our family tree, and possibly one of the earliest species to evolve in the genus Homo.

Now, Dirks et al. – who include many of the researchers who were involved in the discovery of H. naledi – report that the fossils are most likely between 236,000 and 335,000 years old. These dates are based on measuring the concentration of radioactive elements, and the damage caused by these elements (which accumulates over time), in three fossilized teeth, plus surrounding rock and sediments from the cave chamber. Importantly, the most crucial tests were carried out at independent laboratories around the world, and the scientists conducted the tests without knowing the results of the other laboratories. Dirks et al. took these extra steps to make sure that the results obtained were reproducible and unbiased.

The estimated dates are much more recent than many had predicted, and mean that H. naledi was alive at the same time as the earliest members of our own species – which most likely evolved between 300,000 and 200,000 years ago. These new findings demonstrate why it can be unwise to try to predict the age of a fossil based only on its appearance, and emphasize the importance of dating specimens via independent tests. Finally in two related reports, Berger et al. suggest how a primitive-looking species like H. naledi survived more recently than many would have predicted, while Hawks et al. describe the discovery of more H. naledi fossils from a separate chamber in the same cave system.

DOI:http://dx.doi.org/10.7554/eLife.24231.002

Osteogenic tumour in Australopithecus sediba: Earliest hominin evidence for neoplastic disease

Abstract We describe the earliest evidence for neoplastic disease in the hominin lineage. This is reported from the type specimen of the extinct hominin Australopithecus sediba from Malapa, South Africa, dated to 1.98 million years ago. The affected individual was male and developmentally equivalent to a human child of 12 to 13 years of age. A penetrating lytic lesion affected the sixth thoracic vertebra. The lesion was macroscopically evaluated and internally imaged through phase-contrast X-ray synchrotron microtomography. A comprehensive differential diagnosis was undertaken based on gross- and micro-morphology of the lesion, leading to a probable diagnosis of osteoid osteoma. These neoplasms are solitary, benign, osteoid and bone-forming tumours, formed from well-vascularised connective tissue within which there is active production of osteoid and woven bone. Tumours of any kind are rare in archaeological populations, and are all but unknown in the hominin record, highlighting the importance of this discovery. The presence of this disease at Malapa predates the earliest evidence of malignant neoplasia in the hominin fossil record by perhaps 200 000 years.

Earliest hominin cancer: 1.7-million-year-old osteosarcoma from Swartkrans Cave, South Africa

Abstract The reported incidence of neoplasia in the extinct human lineage is rare, with only a few confirmed cases of Middle or Later Pleistocene dates reported. It has generally been assumed that pre-modern incidence of neoplastic disease of any kind is rare and limited to benign conditions, but new fossil evidence suggests otherwise. We here present the earliest identifiable case of malignant neoplastic disease from an early human ancestor dated to 1.8–1.6 million years old. The diagnosis has been made possible only by advances in 3D imaging methods as diagnostic aids. We present a case report based on re-analysis of a hominin metatarsal specimen (SK 7923) from the cave site of Swartkrans in the Cradle of Humankind, South Africa. The expression of malignant osteosarcoma in the Swartkrans specimen indicates that whilst the upsurge in malignancy incidence is correlated with modern lifestyles, there is no reason to suspect that primary bone tumours would have been any less frequent in ancient specimens. Such tumours are not related to lifestyle and often occur in younger individuals. As such, malignancy has a considerable antiquity in the fossil record, as evidenced by this specimen.

Papio Cranium from the Hominin-Bearing Site of Malapa: Implications for the Evolution of Modern Baboon Cranial Morphology and South African Plio-Pleistocene Biochronology

A new partial cranium (UW 88-886) of the Plio-Pleistocene baboon Papio angusticeps from Malapa is identified, described and discussed. UW 88-886 represents the only non-hominin primate yet recovered from Malapa and is important both in the context of baboon evolution as well as South African hominin site biochronology. The new specimen may represent the first appearance of modern baboon anatomy and coincides almost perfectly with molecular divergence date estimates for the origin of the modern P. hamadryas radiation. The fact that the Malapa specimen is dated between ~2.026–2.36 million years ago (Ma) also has implications for the biochronology of other South African Plio-Pleistocene sites where P. angusticeps is found.

Fossil papio cranium from !Ncumtsa (Koanaka) Hills, western Ngamiland, Botswana

Three fossils, a cranium of Papio, a cercopithecid frontal bone, and a mandible of juvenile Papio, have been recovered from cave deposits in the !Ncumtsa (Koanaka) Hills of western Ngamiland, Botswana. These specimens are significant because well-preserved crania of Papio are extremely rare in the fossil record outside of South Africa and because this is the first report of fossil primate cranial remains from Botswana. Thermoluminescence dating of surrounding cave matrix indicates an age of ≥317 ± 114 ka, within the Middle Pleistocene, although it may be older. Based on univariate and multivariate analyses, the adult !Ncumtsa specimen falls within the range of variation seen in extant forms of Papio, yet is distinct from any living species/subspecies and represents a new taxon, named here as a new subspecies of Papio hamadryas-Papio hamadryas botswanae.

Mio-pliocene faunal exchanges and african biogeography: the record of fossil bovids

The development of the Ethiopian biogeographic realm since the late Miocene is here explored with the presentation and review of fossil evidence from eastern Africa. Prostrepsiceros cf. vinayaki and an unknown species of possible caprin affinity are described from the hominid-bearing Asa Koma and Kuseralee Members (∼5.7 and ∼5.2 Ma) of the Middle Awash, Ethiopia. The Middle Awash Prostrepsiceros cf. vinayaki constitutes the first record of this taxon from Africa, previously known from the Siwaliks and Arabia. The possible caprin joins a number of isolated records of caprin or caprin-like taxa recorded, but poorly understood, from the late Neogene of Africa. The identification of these two taxa from the Middle Awash prompts an overdue review of fossil bovids from the sub-Saharan African record that demonstrate Eurasian affinities, including the reduncin Kobus porrecticornis, and species of Tragoportax. The fossil bovid record provides evidence for greater biological continuity between Africa and Eurasia in the late Miocene and earliest Pliocene than is found later in time. In contrast, the early Pliocene (after 5 Ma) saw the loss of any significant proportions of Eurasian-related taxa, and the continental dominance of African-endemic taxa and lineages, a pattern that continues today.

Revisiting the "midtarsal break"

The midtarsal break was first described in this journal nearly 75 years ago to explain the ability of non-human primates to lift their heel independently of the rest of the foot. Since the initial description of the midtarsal break, the calcaneocuboid joint has been assumed to be the anatomical source of this motion. Recently, however, it has been suggested that the midtarsal break may occur at the cuboid-metatarsal joint, rather than at the calcaneocuboid joint. Data compiled from X-rays, dissections, manual manipulation of living primate feet, video of captive catarrhines, and osteological specimens concur that the midtarsal break is a complex motion caused by dorsiflexion at both joints with the cuboid-metatarsal joint contributing roughly 2/3 of total midfoot dorsiflexion, and the calcaneocuboid joint only about 1/3 of total midfoot dorsiflexion. The convexity of the proximal articular surface of the fourth and fifth metatarsals and corresponding concave cuboid facets provide skeletal correlates for the presence of midfoot dorsiflexion at the cuboid-metatarsal joint. Study of hominin metatarsals from Australopithecus afarensis, A. africanus, Homo erectus, and the metatarsals and a cuboid from the OH 8 foot show little capacity for dorsiflexion at the cuboid-metatarsal joint. These results suggest that hominins may have already evolved a stable midfoot region well adapted for the push-off phase of bipedalism by at least 3.2 million years ago. These data illuminate the evolution of the longitudinal arch and show further evidence of constraints on the arboreal capacity in early hominins.

Morphometric variation in the papionin muzzle and the biochronology of the South African Plio-Pleistocene karst cave deposits

Papionin monkeys are widespread, relatively common members of Plio-Pleistocene faunal assemblages across Africa. For these reasons, papionin taxa have been used as biochronological indicators by which to infer the ages of the South African karst cave deposits. A recent morphometric study of South African fossil papionin muzzle shape concluded that its variation attests to a substantial and greater time depth for these sites than is generally estimated. This inference is significant, because accurate dating of the South African cave sites is critical to our knowledge of hominin evolution and mammalian biogeographic history. We here report the results of a comparative analysis of extant papionin monkeys by which variability of the South African fossil papionins may be assessed. The muzzles of 106 specimens representing six extant papionin genera were digitized and interlandmark distances were calculated. Results demonstrate that the overall amount of morphological variation present within the fossil assemblage fits comfortably within the range exhibited by the extant sample. We also performed a statistical experiment to assess the limitations imposed by small sample sizes, such as typically encountered in the fossil record. Results suggest that 15 specimens are sufficient to accurately represent the population mean for a given phenotype, but small sample sizes are insufficient to permit the accurate estimation of the population standard deviation, variance, and range. The suggestion that the muzzle morphology of fossil papionins attests to a considerable and previously unrecognized temporal depth of the South African karst cave sites is unwarranted.

Possible brucellosis in an early hominin skeleton from sterkfontein, South Africa

We report on the paleopathological analysis of the partial skeleton of the late Pliocene hominin species Australopithecus africanus Stw 431 from Sterkfontein, South Africa. A previous study noted the presence of lesions on vertebral bodies diagnosed as spondylosis deformans due to trauma. Instead, we suggest that these lesions are pathological changes due to the initial phases of an infectious disease, brucellosis. The macroscopic, microscopic and radiological appearance of the lytic lesions of the lumbar vertebrae is consistent with brucellosis. The hypothesis of brucellosis (most often associated with the consumption of animal proteins) in a 2.4 to 2.8 million year old hominid has a host of important implications for human evolution. The consumption of meat has been regarded an important factor in supporting, directing or altering human evolution. Perhaps the earliest (up to 2.5 million years ago) paleontological evidence for meat eating consists of cut marks on animal remains and stone tools that could have made these marks. Now with the hypothesis of brucellosis in A. africanus, we may have evidence of occasional meat eating directly linked to a fossil hominin.

U-Pb Isotopic Age of the StW 573 Hominid from Sterkfontein, South Africa

Sterkfontein cave, South Africa, has yielded an australopith skeleton, StW 573, whose completeness has excited great interest in paleoanthropology. StW 573, or "Little Foot," was found 25 meters below the surface in the Silberberg Grotto. 238U-206Pb measurements on speleothems immediately above and below the fossil remains, corrected for initial 234U disequilibrium, yield ages of 2.17 +/- 0.17 million years ago (Ma) and 2.24(-0.07)(+0.09) Ma, respectively, indicating an age for StW 573 of close to 2.2 Ma. This age is in contrast to an age of approximately 3.3 Ma suggested by magnetochronology and ages of approximately 4 Ma based on 10Be and 26Al, but it is compatible with a faunal age range of 4 to 2 Ma.

Hominin first metatarsals (SKX 5017 and SK 1813) from Swartkrans: A morphometric analysis

Two hominin metatarsals from Swartkrans, SKX 5017 and SK 1813, have been reported by Susman and Brain [1988. New first metatarsal (SKX 5017) from Swartkrans and the gait of Paranthropus robustus. Am. J. Phys. Anthropol. 79, 451-454] and Susman and de Ruiter [2004. New hominin first metatarsal (SK 1813) from Swartkrans. J. Hum. Evol. 47, 171-181]. They found these bones to have both primitive and derived traits indicating that, while being bipedal, these hominines had a unique toe-off mechanism. We have undertaken additional multivariate morphometric analyses, comparing the fossils to the first metatarsals of modern humans and extant apes. The largest proportion of discrimination lies in the different locomotor functions: apes on the one hand and the humans and fossils on the other. While the fossils have the closest affinity to humans, they have a unique biomechanical pattern suggesting a more facultative form of bipedalism. The implications of this are, while morphometric analyses do not necessarily directly capture the described primitive and derived traits, the associated functional pattern is held within the broader morphology of the bone.

Hallucial convergence in early hominids

There is a richly documented fossil record of the evolutionary transition from ape-sized brains that are less that one-third the size of modern humans through a series of intermediate-sized brains up to the modern range. The first report on the discovery of the foot of the Stw 573 skeleton emphasized the apparent transitional nature of its great toe [Clarke, R.J., Tobias, P.V., 1995. Sterkfontein Member 2 foot bones of the oldest South African hominid. Science 269, pp. 521-524]. The hallux appeared to be intermediate in its divergence between human-like adduction and ape-like abduction. A major part of this evidence is the medial encroachment of the metatarsal I facet on the medial cuneiform. This study quantifies the variability of this feature in extant hominoids and fossil hominids. The results are consistent with the view that all currently known hominids were specialized for bipedality and lacked the ape-like ability to oppose the great toe.

Foot bones from Omo: Implications for hominid evolution

We reanalyze a hominid talus and calcaneus from Omo dating to 2.2 mya and 2.36 mya, respectively. Although both specimens occur at different localities and times, both tarsals articulate well together, suggesting a single taxon on the basis of size and function. We attribute these foot bones to early Homo on the basis of their morphology. The more modern-like tarsal morphology of these Omo foot bones makes them very similar to a talus from Koobi Fora (KNM-ER 813), a specimen attributed to Homo rudolfensis or Homo erectus. Although the Omo tarsals are a million years younger than the oldest known foot bones from Hadar, both localities demonstrate anatomical differences representing two distinct morphological patterns. Although all known hominid tarsals demonstrate clear bipedal features, the tarsal features noted below suggest that biomechanical changes did occur over time, and that certain features are associated with different hominid lineages (especially the robust australopithecines).

Little Foot and big thoughts—a re-evaluation of the Stw573 foot from Sterkfontein, South Africa

The part of the fossil assemblage Stw573 consisting of some medial foot bones was initially reported by Clarke & Tobias (Science 269 (2002) 521). They found it to have both ape- and human-like qualities, being human-like proximally and ape-like distally. We have undertaken a re-examination of this pedal assemblage using a multivariate analysis; while we also found ape- and human-like qualities, they are in direct conflict with the original findings of Clarke and Tobias. We report an essentially ape-like morphology proximally and a human-like morphology distally; the talus and navicular were found to be ape-like and the medial cuneiform human-like. We also undertook a morphometric analysis of the medial cuneiform from the fossil assemblage OH8, as this was not included in the original OH8 study of Kidd et al (J Hum Evol 31 (1996) 269); this cuneiform was found to have a human-like morphology. Thus, the medial column findings from the two assemblages are very similar. This finding, coupled with the re-evaluation of the stratigraphy at Sterkfontein (Am J Phys Anthrop 119 (2002) 192), suggests that the two may have been contemporaneous. We also note that three broad patterns of modification have been identified, equating to proximal-distal lateral-medial (cranio-caudal) and dorsal plantar (posterior-anterior). It has not escaped our notice that these patterns are each controlled by specific genes or growth factors; we thus see a morphometric expression of our developmental past.

The context of Stw 573, an early hominid skull and skeleton from Sterkfontein Member 2: taphonomy and paleoenvironment

The reconstructed taphonomic and paleoenvironmental contexts of a ca. 4 million-year-old partial hominid skeleton (Stw 573) from Sterkfontein Member 2 are described through presentation of the results of our analyses of the mammalian faunal assemblage associated stratigraphically with the hominid. The assemblage is dominated by cercopithecoids (Parapapio and Papio) and felids (Panthera pardus, P. leo, Felis caracal, and Felidae indet.), based on number of identified specimens, minimum number of elements and, minimum number of individuals. In addition, the assemblage is characterized by a number of partial skeletons and/or antimeric sets of bones across all taxonomic groups. There is scant indication of carnivore chewing in the assemblage. These observations, in addition to other taphonomic data, suggest that the remains of many animals recovered in Member 2 are from individuals that entered the cave on their own-whether accidentally by falling through avens connecting the cave to the ground surface above or by intentional entry-and were then unable to escape, rather than primarily through systematic collection by a biotic, bone-accumulating agent. The taphonomic conclusion that animals with climbing proclivities (i.e., primates and carnivores) are preferentially preserved over other taxa, ultimately because of those proclivities, urges caution in assessing the fidelity of the assemblage for reconstruction of the Member 2 paleoenvironment. With that caveat, we infer that the Member 2 paleoenvironment was typified by rolling, rock-littered and brush- and scrub-covered hills, indicated by the abundant F. caracal and cercopithecoid fossils recovered and the identified presence of the extinct Caprinae Makapania broomi. In addition, the valley bottom may have retained standing water year-round, perhaps supporting some tree cover--a setting suitable for the well-represented ambush predator P. pardus and suggested by the presence of Alcelaphini. Finally, the reconstructed taphonomic and paleoenvironmental settings of Sterkfontein Member 2 are compared to penecontemporaneous sites in South and East Africa.

The carbon isotope ecology and diet of Australopithecus africanus at Sterkfontein, South Africa

The stable carbon isotope ratio of fossil tooth enamel carbonate is determined by the photosynthetic systems of plants at the base of the animal's foodweb. In subtropical Africa, grasses and many sedges have C(4)photosynthesis and transmit their characteristically enriched 13C/(12)C ratios (more positive delta13C values) along the foodchain to consumers. We report here a carbon isotope study of ten specimens of Australopithecus africanus from Member 4, Sterkfontein (ca. 2.5 to 2.0Ma), compared with other fossil mammals from the same deposit. This is the most extensive isotopic study of an early hominin species that has been achieved so far. The results show that this hominin was intensively engaged with the savanna foodweb and that the dietary variation between individuals was more pronounced than for any other early hominin or non-human primate species on record. Suggestions that more than one species have been incuded in this taxon are not supported by the isotopic evidence. We conclude that Australopithecus africanus was highly opportunistic and adaptable in its feeding habits.

Lower Pliocene hominid remains from Sterkfontein

Cosmogenic aluminum-26 and beryllium-10 burial dates of low-lying fossiliferous breccia in the caves at Sterkfontein, South Africa, show that associated hominid fossils accumulated in the Lower Pliocene. These dates indicate that the skeleton StW 573 and newly discovered specimens from Jacovec Cavern have much the same age: approximately 4 million years. These specimens are thus of an age similar to Australopithecus anamensis from East Africa.