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Concept: Archaic Homo sapiens


We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237-581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

Concepts: Human, Evolution, Africa, Species, Chromosome, Human evolution, Archaic Homo sapiens, XY sex-determination system


The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537-542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the “Out of Africa” model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains.

Concepts: DNA, Human, Human genome, Mitochondrial DNA, Science, Sequence, Human evolution, Archaic Homo sapiens


We report here a neurocranial abnormality previously undescribed in Pleistocene human fossils, an enlarged parietal foramen (EPF) in the early Late Pleistocene Xujiayao 11 parietal bones from the Xujiayao (Houjiayao) site, northern China. Xujiayao 11 is a pair of partial posteromedial parietal bones from an adult. It exhibits thick cranial vault bones, arachnoid granulations, a deviated posterior sagittal suture, and a unilateral (right) parietal lacuna with a posteriorly-directed and enlarged endocranial vascular sulcus. Differential diagnosis indicates that the perforation is a congenital defect, an enlarged parietal foramen, commonly associated with cerebral venous and cranial vault anomalies. It was not lethal given the individual’s age-at-death, but it may have been associated with secondary neurological deficiencies. The fossil constitutes the oldest evidence in human evolution of this very rare condition (a single enlarged parietal foramen). In combination with developmental and degenerative abnormalities in other Pleistocene human remains, it suggests demographic and survival patterns among Pleistocene Homo that led to an elevated frequency of conditions unknown or rare among recent humans.

Concepts: Human, Evolution, Skull, Neanderthal, Human evolution, Pleistocene, Archaic Homo sapiens, Bregma


Uncertainties surround the timing of modern human emergence and occupation in East and Southeast Asia. Although genetic and archeological data indicate a rapid migration out of Africa and into Southeast Asia by at least 60 ka, mainland Southeast Asia is notable for its absence of fossil evidence for early modern human occupation. Here we report on a modern human cranium from Tam Pa Ling, Laos, which was recovered from a secure stratigraphic context. Radiocarbon and luminescence dating of the surrounding sediments provide a minimum age of 51-46 ka, and direct U-dating of the bone indicates a maximum age of ~63 ka. The cranium has a derived modern human morphology in features of the frontal, occipital, maxillae, and dentition. It is also differentiated from western Eurasian archaic humans in aspects of its temporal, occipital, and dental morphology. In the context of an increasingly documented archaic-modern morphological mosaic among the earliest modern humans in western Eurasia, Tam Pa Ling establishes a definitively modern population in Southeast Asia at ~50 ka cal BP. As such, it provides the earliest skeletal evidence for fully modern humans in mainland Southeast Asia.

Concepts: Human, Southeast Asia, Europe, Asia, Human evolution, Archaic Homo sapiens, Humans, Anatomically modern humans


A key event in human evolution is the expansion of modern humans of African origin across Eurasia between 60 and 40 thousand years (kyr) before present (bp), replacing all other forms of hominins. Owing to the scarcity of human fossils from this period, these ancestors of all present-day non-African modern populations remain largely enigmatic. Here we describe a partial calvaria, recently discovered at Manot Cave (Western Galilee, Israel) and dated to 54.7 ± 5.5 kyr bp (arithmetic mean ± 2 standard deviations) by uranium-thorium dating, that sheds light on this crucial event. The overall shape and discrete morphological features of the Manot 1 calvaria demonstrate that this partial skull is unequivocally modern. It is similar in shape to recent African skulls as well as to European skulls from the Upper Palaeolithic period, but different from most other early anatomically modern humans in the Levant. This suggests that the Manot people could be closely related to the first modern humans who later successfully colonized Europe. Thus, the anatomical features used to support the ‘assimilation model’ in Europe might not have been inherited from European Neanderthals, but rather from earlier Levantine populations. Moreover, at present, Manot 1 is the only modern human specimen to provide evidence that during the Middle to Upper Palaeolithic interface, both modern humans and Neanderthals contemporaneously inhabited the southern Levant, close in time to the likely interbreeding event with Neanderthals.

Concepts: Human, Hominidae, Chimpanzee, Neanderthal, Human evolution, Pleistocene, Prehistory, Archaic Homo sapiens


Genetic evidence for anatomically modern humans (AMH) out of Africa before 75 thousand years ago (ka) and in island southeast Asia (ISEA) before 60 ka (93-61 ka) predates accepted archaeological records of occupation in the region. Claims that AMH arrived in ISEA before 60 ka (ref. 4) have been supported only by equivocal or non-skeletal evidence. AMH evidence from this period is rare and lacks robust chronologies owing to a lack of direct dating applications, poor preservation and/or excavation strategies and questionable taxonomic identifications. Lida Ajer is a Sumatran Pleistocene cave with a rich rainforest fauna associated with fossil human teeth. The importance of the site is unclear owing to unsupported taxonomic identification of these fossils and uncertainties regarding the age of the deposit, therefore it is rarely considered in models of human dispersal. Here we reinvestigate Lida Ajer to identify the teeth confidently and establish a robust chronology using an integrated dating approach. Using enamel-dentine junction morphology, enamel thickness and comparative morphology, we show that the teeth are unequivocally AMH. Luminescence and uranium-series techniques applied to bone-bearing sediments and speleothems, and coupled uranium-series and electron spin resonance dating of mammalian teeth, place modern humans in Sumatra between 73 and 63 ka. This age is consistent with biostratigraphic estimations, palaeoclimate and sea-level reconstructions, and genetic evidence for a pre-60 ka arrival of AMH into ISEA. Lida Ajer represents, to our knowledge, the earliest evidence of rainforest occupation by AMH, and underscores the importance of reassessing the timing and environmental context of the dispersal of modern humans out of Africa.

Concepts: Human, Science, Mammal, Primate, Human evolution, Archaic Homo sapiens, Humans, Homo sapiens idaltu


Uniquely, with respect to Middle Pleistocene hominins, anatomically modern humans do not possess marked browridges, and have a more vertical forehead with mobile eyebrows that play a key role in social signalling and communication. The presence and variability of browridges in archaic Homo species and their absence in ourselves have led to debate concerning their morphogenesis and function, with two main hypotheses being put forward: that browridge morphology is the result of the spatial relationship between the orbits and the brain case; and that browridge morphology is significantly impacted by biting mechanics. Here, we virtually manipulate the browridge morphology of an archaic hominin (Kabwe 1), showing that it is much larger than the minimum required to fulfil spatial demands and that browridge size has little impact on mechanical performance during biting. As browridge morphology in this fossil is not driven by spatial and mechanical requirements alone, the role of the supraorbital region in social communication is a potentially significant factor. We propose that conversion of the large browridges of our immediate ancestors to a more vertical frontal bone in modern humans allowed highly mobile eyebrows to display subtle affiliative emotions.

Concepts: Human, Evolution, Skull, Human evolution, Archaic Homo sapiens, Hominini, Humans, Anatomically modern humans


Some present-day humans derive up to ∼5% [1] of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals [2]. We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry [3]. In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10(-7) to 3.2 × 10(-7) for Denisovan and 2.2 × 10(-3) to 2.9 × 10(-3) for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.

Concepts: Gene, Human, Human genome, Chromosome, Neanderthal, Human evolution, Archaic Homo sapiens, Humans


Comparing modern humans and Neanderthals, we have previously shown that recent modern humans (RMH) and Neanderthals differ in anterior root lengths, and that this difference cannot be explained by group differences in overall mandibular size. Here, we first document the evolutionary changes of root size and shape of the anterior upper and lower dentition in a broad chronological and geographical framework. We then use the size and shape differences between RMH and Neanderthals to classify several isolated teeth from Kebara cave and Steinheim, and to interpret the anterior tooth roots of the Tabun C2 mandible. Our samples comprise permanent mandibular and maxillary incisors and canines from early Homo, Neanderthals, as well as extant and fossil modern humans (N = 359). In addition to root length, we measured cervical root diameter and area, total root volume, root pulp volume and root surface area from μCT scans. We quantified root shape variation using geometric morphometrics. Our results show that Neanderthals have not only significantly larger anterior roots than RMH overall, but also different root shapes for each tooth type. In the context of the ‘teeth-as-tools’ hypothesis, this could be an adaptation to better sustain high or frequent loads on the front teeth. We demonstrate that the two isolated incisors stored with the Steinheim skull are very likely recent. Tabun C2 shows an anterior dentition similar in size and shape to Neanderthals while its molar roots are non-Neanderthal. Two of the five isolated teeth from Kebara are classified as Neanderthals. Interestingly, early modern humans overlap with Neanderthals and RMH in root size and shape. Anterior roots of the Lower and Middle Pleistocene specimens are at least as large as Neanderthals, suggesting that Neanderthals retained a primitive pattern, which should prompt caution in the assessment of the earliest forms of modern humans.

Concepts: Human, Primate, Teeth, Neanderthal, Human evolution, Canine tooth, Pleistocene, Archaic Homo sapiens


The biomechanical characterization of lower limb long bones in the chrono-ecogeographically diverse species Homo erectus is a fundamental step for assessing evolutionary changes in locomotor mode and body shape that occurred within the genus Homo. However, the samples available for the Early and earlier Middle Pleistocene are small and widely scattered in time and space, thus limiting our understanding of the nature and polarity of morphological trends. Compared to the African fossil record, loading histories based on detailed biomechanical assessment of diaphyseal strength in Indonesian H. erectus lower limb long bones have not been assessed. By using a microtomographic record (μCT), we performed a quantitative analysis of the biomechanical properties and structural organization of Kresna 11, a late Early Pleistocene adult H. erectus femoral shaft from the Sangiran Dome, Central Java. Relative to the modern human condition, Kresna 11 shows the predominant mediolateral cortical thickening (hypertrophy) and the distal displacement of the minimum diaphyseal breadth characteristic of early Homo femora, associated nonetheless with relatively modest cortical thickness within the mid-proximal portion. Synthetic functional imaging of the shaft through the planar representation of its inner structure has revealed distal thickening of the medial cortex, a feature previously unreported in H. erectus. The increase in relative mediolateral bending strength observed in Kresna 11 supports the hypothesis that, rather than simply reflecting differences in patterns of locomotor loading, biomechanical properties of the femoral shaft in archaic Homo are strongly influenced by body shape, i.e., variations in pelvic breadth and femoral neck length.

Concepts: Human, Evolution, Cerebral cortex, Fossil, Human evolution, Archaic Homo sapiens, Homo erectus, Homo ergaster