Reconstructed Homo habilis type OH 7 suggests deep-rooted species diversity in early Homo

Hominin fossil inventory: Quantification and comparison of discrete regional and element representation among early African fossil hominins prior to the emergence of Homo erectus

For all but the past few hundred thousand years, skeletal and dental morphology is the only evidence we have of our extinct ancestors and close hominin relatives. With a few exceptions, most lists of early hominin fossils have been assembled for single sites, formations, or taxa, with little attention paid to how different regions of the skeleton contribute to taxon hypodigms. We recognize there are different ways to divide up the hominin fossil record into taxa, but here, we present an inventory of the fossil evidence for the hypodigms of 14 early African hominin taxa that predate the emergence of Homo erectus. The hypodigms are limited to specimens that have been published and unambiguously attributed to a species. We use a novel, fine-resolution coding scheme that allows us to provide detailed counts of element and subelement abundance by taxon. We then compare the element counts of the taxon hypodigms with each other and with a novel standard based on a perfectly preserved skeleton we refer to as 'hominin expected.' The resulting hypodigms generally support commonly held assumptions about the early hominin fossil record (e.g., teeth dominate the hypodigms of all taxa), but they do not support the conventional wisdom that there are differences in the regional representation of the hypodigms of taxa that are found exclusively in eastern versus southern Africa. These data and analyses are a first step in exploring the differences in the composition of early hominin hypodigms. They will allow researchers to focus their comparative research on skeletal regions that are well-represented in the early hominin fossil record, as well as serve as tools for developing and addressing hypodigm-scale hypotheses that are central to our understanding of hominin evolution.

Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans

TBC1D3 is a primate-specific gene family that has expanded in the human lineage and has been implicated in neuronal progenitor proliferation and expansion of the frontal cortex. The gene family and its expression have been challenging to investigate because it is embedded in high-identity and highly variable segmental duplications. We sequenced and assembled the gene family using long-read sequencing data from 34 humans and 11 nonhuman primate species. Our analysis shows that this particular gene family has independently duplicated in at least five primate lineages, and the duplicated loci are enriched at sites of large-scale chromosomal rearrangements on Chromosome 17. We find that all human copy-number variation maps to two distinct clusters located at Chromosome 17q12 and that humans are highly structurally variable at this locus, differing by as many as 20 copies and ∼1 Mbp in length depending on haplotypes. We also show evidence of positive selection, as well as a significant change in the predicted human TBC1D3 protein sequence. Last, we find that, despite multiple duplications, human TBC1D3 expression is limited to a subset of copies and, most notably, from a single paralog group: TBC1D3-CDKL These observations may help explain why a gene potentially important in cortical development can be so variable in the human population.

Maxillary morphology of chimpanzees: Captive versus wild environments

Morphological studies typically avoid using osteological samples that derive from captive animals because it is assumed that their morphology is not representative of wild populations. Rearing environments indeed differ between wild and captive individuals. For example, mechanical properties of the diets provided to captive animals can be drastically different from the food present in their natural habitats, which could impact cranial morphology and dental health. Here, we examine morphological differences in the maxillae of wild versus captive chimpanzees (Pan troglodytes) given the prominence of this species in comparative samples used in human evolution research and the key role of the maxilla in such studies. Size and shape were analysed using three-dimensional geometric morphometric methods based on computed tomography scans of 94 wild and 30 captive specimens. Captive individuals have on average larger and more asymmetrical maxillae than wild chimpanzees, and significant differences are present in their maxillary shapes. A large proportion of these shape differences are attributable to static allometry, but wild and captive specimens still differ significantly from each other after allometric size adjustment of the shape data. Levels of shape variation are higher in the captive group, while the degree of size variation is likely similar in our two samples. Results are discussed in the context of ontogenetic growth trajectories, changes in dietary texture, an altered social environment, and generational differences. Additionally, sample simulations show that size and shape differences between chimpanzees and bonobos (Pan paniscus) are exaggerated when part of the wild sample is replaced with captive chimpanzees. Overall, this study confirms that maxillae of captive chimpanzees should not be included in morphological or taxonomic analyses when the objective is to characterise the species.

Independent expansion, selection and hypervariability of the TBC1D3 gene family in humans

TBC1D3 is a primate-specific gene family that has expanded in the human lineage and has been implicated in neuronal progenitor proliferation and expansion of the frontal cortex. The gene family and its expression have been challenging to investigate because it is embedded in high-identity and highly variable segmental duplications. We sequenced and assembled the gene family using long-read sequencing data from 34 humans and 11 nonhuman primate species. Our analysis shows that this particular gene family has independently duplicated in at least five primate lineages, and the duplicated loci are enriched at sites of large-scale chromosomal rearrangements on chromosome 17. We find that most humans vary along two TBC1D3 clusters where human haplotypes are highly variable in copy number, differing by as many as 20 copies, and structure (structural heterozygosity 90%). We also show evidence of positive selection, as well as a significant change in the predicted human TBC1D3 protein sequence. Lastly, we find that, despite multiple duplications, human TBC1D3 expression is limited to a subset of copies and, most notably, from a single paralog group: TBC1D3-CDKL. These observations may help explain why a gene potentially important in cortical development can be so variable in the human population.

Dental morphology in Homo habilis and its implications for the evolution of early Homo

The phylogenetic position of Homo habilis is central to debates over the origin and early evolution of the genus Homo. A large portion of the species hypodigm consists of dental remains, but they have only been studied at the often worn enamel surface. We investigate the morphology of the H. habilis enamel-dentine junction (EDJ), which is preserved in cases of moderate tooth wear and known to carry a strong taxonomic signal. Geometric morphometrics is used to characterise dentine crown shape and size across the entire mandibular and maxillary tooth rows, compared with a broad comparative sample (n = 712). We find that EDJ morphology in H. habilis is for the most part remarkably primitive, supporting the hypothesis that the H. habilis hypodigm has more in common with Australopithecus than later Homo. Additionally, the chronologically younger specimen OH 16 displays a suite of derived features; its inclusion in H. habilis leads to excessive levels of variation.

Morphological and morphometric analyses of a late Middle Pleistocene hominin mandible from Hualongdong, China

Excavations in Hualongdong (HLD), East China, have yielded abundant hominin fossils dated to 300 ka. There is a nearly complete mandible that fits well with a partial cranium, and together they compose the skull labeled as HLD 6. Thus far, detailed morphological description and comparisons of the mandible have not been conducted. Here we present a comprehensive morphological, metric, and geometric morphometric assessment of this mandible and compare it with both adult and immature specimens of Pleistocene hominins and recent modern humans. Results indicate that the HLD 6 mandible exhibits a mosaic morphological pattern characterized by a robust corpus and relatively gracile symphysis and ramus. The moderately developed mental trigone and a clear anterior mandibular incurvation of the HLD 6 mandible are reminiscent of Late Pleistocene hominin and recent modern human morphology. However, the weak expression of all these features indicates that this mandible does not possess a true chin. Moreover, a suite of archaic features that resemble those of Middle Pleistocene hominins includes pronounced alveolar planum, superior transverse torus, thick corpus, a pronounced endocondyloid crest, and a well-developed medial pterygoid tubercle. The geometric morphometric analysis further confirms the mosaic pattern of the HLD 6 mandible. The combination of both archaic and modern human features identified in the HLD 6 mandible is unexpected, given its late Middle Pleistocene age and differs from approximately contemporaneous Homo members such as Xujiayao, Penghu, and Xiahe. This mosaic pattern has never been recorded in late Middle Pleistocene hominin fossil assemblages in East Asia. The HLD 6 mandible provides further support for the high morphological diversity during late Middle Pleistocene hominin evolution. With these findings, it is possible that modern human morphologies are present as early as 300 ka and earlier than the emergence of modern humans in East Asia.

The evolution and ecology of psilocybin in nature

Fungi produce diverse metabolites that can have antimicrobial, antifungal, antifeedant, or psychoactive properties. Among these metabolites are the tryptamine-derived compounds psilocybin, its precursors, and natural derivatives (collectively referred to as psiloids), which have played significant roles in human society and culture. The high allocation of nitrogen to psiloids in mushrooms, along with evidence of convergent evolution and horizontal transfer of psilocybin genes, suggest they provide a selective benefit to some fungi. However, no precise ecological roles of psilocybin have been experimentally determined. The structural and functional similarities of psiloids to serotonin, an essential neurotransmitter in animals, suggest that they may enhance the fitness of fungi through interference with serotonergic processes. However, other ecological mechanisms of psiloids have been proposed. Here, we review the literature pertinent to psilocybin ecology and propose potential adaptive advantages psiloids may confer to fungi.

Making meaning from fragmentary fossils: Early Homo in the Early to early Middle Pleistocene

In celebration of the 50th anniversary of the Journal of Human Evolution, we re-evaluate the fossil record for early Homo (principally Homo erectus, Homo habilis, and Homo rudolfensis) from early diversification and dispersal in the Early Pleistocene to the ultimate demise of H. erectus in the early Middle Pleistocene. The mid-1990s marked an important historical turning point in our understanding of early Homo with the redating of key H. erectus localities, the discovery of small H. erectus in Asia, and the recovery of an even earlier presence of early Homo in Africa. As such, we compare our understanding of early Homo before and after this time and discuss how the order of fossil discovery and a focus on anchor specimens has shaped, and in many ways biased, our interpretations of early Homo species and the fossils allocated to them. Fragmentary specimens may counter conventional wisdom but are often overlooked in broad narratives. We recognize at least three different cranial and two or three pelvic morphotypes of early Homo. Just one postcranial morph aligns with any certainty to a cranial species, highlighting the importance of explicitly identifying how we link specimens together and to species; we offer two ways of visualizing these connections. Chronologically and morphologically H. erectus is a member of early Homo, not a temporally more recent species necessarily evolved from either H. habilis or H. rudolfensis. Nonetheless, an ancestral-descendant notion of their evolution influences expectations around the anatomy of missing elements, especially the foot. Weak support for long-held notions of postcranial modernity in H. erectus raises the possibility of alternative drivers of dispersal. New observations suggest that the dearth of faces in later H. erectus may mask taxonomic diversity in Asia and suggest various later mid-Pleistocene populations could derive from either Asia or Africa. Future advances will rest on the development of nuanced ways to affiliate fossils, greater transparency of implicit assumptions, and attention to detailed life history information for comparative collections; all critical pursuits for future research given the great potential they have to enrich our evolutionary reconstructions for the next fifty years and beyond.

A reassessment of the distinctiveness of dryopithecine genera from the Iberian Miocene based on enamel-dentine junction geometric morphometric analyses

A vast diversity of catarrhines primates has been uncovered in the Middle to Late Miocene (12.5-9.6 Ma) of the Vallès-Penedès Basin (northeastern Spain), including several hominid species (Pierolapithecus catalaunicus, Anoiapithecus brevirostris, Dryopithecus fontani, Hispanopithecus laietanus, and Hispanopithecus crusafonti) plus some remains attributed to 'Sivapithecus' occidentalis (of uncertain taxonomic validity). However, Pierolapithecus and Anoiapithecus have also been considered junior synonyms of Dryopithecus by some authors, which entail a lower generic diversity and an inflated intrageneric variation of the latter genus. Since the distinction of these taxa partly relies on dental features, the detailed and quantitative analysis of tooth shape might help disentangling the taxonomic diversity of these Miocene hominids. Using diffeomorphic surface matching and three-dimensional geometric morphometrics, we investigate the enamel-dentine junction shape (which is a reliable taxonomic proxy) of these Miocene hominids, with the aim of investigating their degree of intra- and intergeneric variation compared with that of extant great ape genera. We conducted statistical analyses, including between-group principal component analyses, canonical variate analyses, and permutation tests, to investigate whether the individual and combined (i.e., Dryopithecus s.l.) variation of the extinct genera exceeds that of the extant great apes. Our results indicate that Pierolapithecus, Anoiapithecus, Dryopithecus, and Hispanopithecus show morphological differences of enamel-dentine junction shape relative to the extant great apes that are consistent with their attribution to different genera. Specifically, the variation displayed by the Middle Miocene taxa combined exceeds that of extant great ape genera, thus undermining the single-genus hypothesis. 'Sivapithecus' occidentalis specimens fall close to Dryopithecus but in the absence of well-preserved comparable teeth for Pierolapithecus and Anoiapithecus, their taxonomic attribution remains uncertain. Among the Hispanopithecus sample, IPS1802 from Can Llobateres stands out and might either be an outlier in terms of morphology, or represent another dryopithecine taxon.

Evolutionary history of hominin brain size and phylogenetic comparative methods

An absolutely and relatively large brain has traditionally been viewed as a distinctive characteristic of the Homo genus, with anatomically modern humans presented at the apex of a long line of progressive increases in encephalization. Many studies continue to focus attention on increasing brain size in the Homo genus, while excluding measures of absolute and relative brain size of more geologically recent, smaller brained, hominins such as Homo floresiensis, and Homo naledi and smaller brained Homo erectus specimens. This review discusses the benefits of using phylogenetic comparative methods to trace the diverse changes in hominin brain evolution and the drawbacks of not doing so.

The endocast from Dana Aoule North (DAN5/P1): A 1.5 million year-old human braincase from Gona, Afar, Ethiopia

The nearly complete cranium DAN5/P1 was found at Gona (Afar, Ethiopia), dated to 1.5-1.6 Ma, and assigned to the species Homo erectus. Its size is, nonetheless, particularly small for the known range of variation of this taxon, and the cranial capacity has been estimated as 598 cc. In this study, we analyzed a reconstruction of its endocranial cast, to investigate its paleoneurological features. The main anatomical traits of the endocast were described, and its morphology was compared with other fossil and modern human samples. The endocast shows most of the traits associated with less encephalized human taxa, like narrow frontal lobes and a simple meningeal vascular network with posterior parietal branches. The parietal region is relatively tall and rounded, although not especially large. Based on our set of measures, the general endocranial proportions are within the range of fossils included in the species Homo habilis or in the genus Australopithecus. Similarities with the genus Homo include a more posterior position of the frontal lobe relative to the cranial bones, and the general endocranial length and width when size is taken into account. This new specimen extends the known brain size variability of Homo ergaster/erectus, while suggesting that differences in gross brain proportions among early human species, or even between early humans and australopiths, were absent or subtle.

The brain of Homo habilis: Three decades of paleoneurology

In 1987, Phillip Tobias published a comprehensive anatomical analysis of the endocasts attributed to Homo habilis, discussing issues dealing with brain size, sulcal patterns, and vascular traces. He suggested that the neuroanatomy of this species evidenced a clear change toward many cerebral traits associated with our genus, mostly when concerning the morphology of the frontal and parietal cortex. After more than 30 years, the fossil record associated with this taxon has not grown that much, but we have much more information on cranial and brain biology, and we are using a larger array of digital methods to investigate the paleoneurological variation observed in the human genus. Brain volume, the size of the frontal lobe, or the gross hemispheric asymmetries are still relevant issues, but they are considered to be less central than before. More attention is instead being paid to the cortical organization, the relationships with the cranial architecture, and the influence of molecular or ecological factors. Although the field of paleoneurology can currently count on a larger range of tools and principles, there is still a general lack of anatomical information on many endocranial traits. This aspect is probably crucial for the agenda of paleoneurology. More importantly, the whole science is undergoing a delicate change, because of the growing influence of the social environment. In this sense, the disciplines working with fossils (and, in particular, with brain evolution) should take particular care to maintain a healthy professional situation, avoiding an excess of speculation and overstatement.

Paleoanthropology of cognition: an overview on Hominins brain evolution

Recent advances in neurobiology, paleontology, and paleogenetics allow us to associate changes in brain size and organization with three main "moments" of increased behavioral complexity and, more speculatively, language development. First, Australopiths display a significant increase in brain size relative to the great apes and an incipient extension of postnatal brain development. However, their cortical organization remains essentially similar to that of apes. Second, over the last 2 My, with two notable exceptions, brain size increases dramatically, partly in relation to changes in body size. Differential enlargements and reorganizations of cortical areas lay the foundation for the "language-ready" brain and cumulative culture of later Homo species. Third, in Homo sapiens, brain size remains fairly stable over the last 300,000 years but an important cerebral reorganization takes place. It affects the frontal and temporal lobes, the parietal areas and the cerebellum and resulted in a more globular shape of the brain. These changes are associated, among others, with an increased development of long-distance-horizontal-connections. A few regulatory genetic events took place in the course of this hominization process with, in particular, enhanced neuronal proliferation and global brain connectivity.

The taxonomic attribution of African hominin postcrania from the Miocene through the Pleistocene: Associations and assumptions

Postcranial bones may provide valuable information about fossil taxa relating to their locomotor habits, manipulative abilities and body sizes. Distinctive features of the postcranial skeleton are sometimes noted in species diagnoses. Although numerous isolated postcranial fossils have become accepted by many workers as belonging to a particular species, it is worthwhile revisiting the evidence for each attribution before including them in comparative samples in relation to the descriptions of new fossils, functional analyses in relation to particular taxa, or in evolutionary contexts. Although some workers eschew the taxonomic attribution of postcranial fossils as being less important (or interesting) than interpreting their functional morphology, it is impossible to consider the evolution of functional anatomy in a taxonomic and phylogenetic vacuum. There are 21 widely recognized hominin taxa that have been described from sites in Africa dated from the Late Miocene to the Middle Pleistocene; postcranial elements have been attributed to 17 of these. The bones that have been thus assigned range from many parts of a skeleton to isolated elements. However, the extent to which postcranial material can be reliably attributed to a specific taxon varies considerably from site to site and species to species, and is often the subject of considerable debate. Here, we review the postcranial remains attributed to African hominin taxa from the Late Miocene to the Middle and Late Pleistocene and place these assignations into categories of reliability. The catalog of attributions presented here may serve as a guide for making taxonomic decisions in the future.

Genetic influences on dentognathic morphology in the Jirel population of Nepal

Patterns of genetic variation and covariation impact the evolution of the craniofacial complex and contribute to clinically significant malocclusions in modern human populations. Previous quantitative genetic studies have estimated the heritabilities and genetic correlations of skeletal and dental traits in humans and nonhuman primates, but none have estimated these quantitative genetic parameters across the dentognathic complex. A large and powerful pedigree from the Jirel population of Nepal was leveraged to estimate heritabilities and genetic correlations in 62 maxillary and mandibular arch dimensions, incisor and canine lengths, and post-canine tooth crown areas (N ≥ 739). Quantitative genetic parameter estimation was performed using maximum likelihood-based variance decomposition. Residual heritability estimates were significant for all traits, ranging from 0.269 to 0.898. Genetic correlations were positive for all trait pairs. Principal components analyses of the phenotypic and genetic correlation matrices indicate an overall size effect across all measurements on the first principal component. Additional principal components demonstrate positive relationships between post-canine tooth crown areas and arch lengths and negative relationships between post-canine tooth crown areas and arch widths, and between arch lengths and arch widths. Based on these findings, morphological variation in the human dentognathic complex may be constrained by genetic relationships between dental dimensions and arch lengths, with weaker genetic correlations between these traits and arch widths allowing for variation in arch shape. The patterns identified are expected to have impacted the evolution of the dentognathic complex and its genetic architecture as well as the prevalence of dental crowding in modern human populations.

Morphological variation of the maxilla in modern humans and African apes

Differences in morphology among modern humans and African apes are frequently used when assessing whether hominin fossils should be attributed to a single species or represent evidence for taxic diversity. A good understanding of the degree and structure of the intergeneric, interspecific, and intraspecific variation, including aspects such as sexual dimorphism and age, are key in this context. Here we explore the variation and differences shown by the maxilla of extant hominines, as maxillary morphology is central in the diagnosis of several hominin taxa. Our sample includes adults of all currently recognized hominine species and subspecies, with a balanced species sex ratio. In addition, we compared the adults with a small sample of late juveniles. The morphology of the maxillae was captured using three-dimensional landmarks, and the size and shape were analyzed using geometric morphometric methods. Key observations are that 1) the maxillae of all extant hominine species and subspecies show statistically significant differences, but complete separation in shape is only seen at the genus level; 2) the degree of variation is not consistent between genera, with subspecies of Gorilla being more different from each other than are species of Pan; 3) the pattern of sexual shape dimorphism is different in Pan, Gorilla, and Homo, often showing opposite trends; and 4) differentiation between maxillary shapes is increased after adjustment for static intraspecific allometry. These results provide a taxonomically up-to-date comparative morphological framework to help interpret the hominin fossil record, and we discuss the practical implications in that context.

Comparative morphology and physiology of the vocal production apparatus and the brain in the extant primates

Objective data mainly from the comparative anatomy of various organs related to human speech and language is considered to unearth clues about the mechanisms behind language development. The two organs of the larynx and hyoid bone are considered to have evolved towards suitable positions and forms in preparation for the occurrence of the large repertoire of vocalization necessary for human speech. However, some researchers have asserted that there is no significant difference of these organs between humans and non-human primates. Speech production is dependent on the voluntary control of the respiratory, laryngeal, and vocal tract musculature. Such control is fully present in humans but only partially so in non-human primates, which appear to be able to voluntarily control only supralaryngeal articulators. Both humans and non-human primates have direct cortical innervation of motor neurons controlling the supralaryngeal vocal tract but only human appear to have direct cortical innervation of motor neurons controlling the larynx. In this review, we investigate the comparative morphology and function of the wide range of components involved in vocal production, including the larynx, the hyoid bone, the tongue, and the vocal brain. We would like to emphasize the importance of the tongue in the primary development of human speech and language. It is now time to reconsider the possibility of the tongue playing a definitive role in the emergence of human speech.

Anthroengineering: an independent interdisciplinary field

In recent decades, funding agencies, institutes and professional bodies have recognized the profound benefits of transdisciplinarity in tackling targeted research questions. However, once questions are answered, the previously abundant support often dissolves. As such, the long-term benefits of these transdisciplinary approaches are never fully achieved. Over the last several decades, the integration of anthropology and engineering through inter- and multidisciplinary work has led to advances in fields such as design, human evolution and medical technologies. The lack of formal recognition, however, of this transdisciplinary approach as a unique entity rather than a useful tool or a subfield makes it difficult for researchers to establish laboratories, secure permanent jobs, fund long-term research programmes and train students in this approach. To facilitate the growth and development and witness the long-term benefits of this approach, we propose the integration of anthropology and engineering be recognized as a new, independent field known as anthroengineering. We present a working definition for anthroengineering and examples of how anthroengineering has been used. We discuss the necessity of recognizing anthroengineering as a unique field and explore potential novel applications. Finally, we discuss the future of anthroengineering, highlighting avenues for moving the field forward.

Quantifying maxillary development in chimpanzees and humans: An analysis of prognathism and orthognathism at the morphological and microscopic scales

Facial orientation (projection and degree of prognathism) and form in hominins is highly variable, likely related to evolutionary modifications of the microscopic process of bone modeling (the simultaneous cellular activities of bone formation and resorption) during ontogeny. However, in anteriorly projected faces such as those of early hominins, little is known about the link between bone modeling and facial developmental patterns. Similarly, these aspects have been infrequently investigated in extant great apes. In this study, quantitative methods were applied to a cross-sectional ontogenetic sample of 33 chimpanzees (Pan troglodytes verus) and 59 modern humans (Homo sapiens) to compare the development of maxillary prognathism to orthognathism at both microscopic and macroscopic (or morphological) scales using surface histology and geometric morphometric techniques. Chimpanzees express on average lower amounts of bone resorption than humans on the maxillary periosteum throughout ontogeny; however, the premaxilla is consistently resorbed from early stages on. The presence of bone resorption in the chimpanzee premaxilla, such as that seen in some early hominins, suggests a more ape-like pattern of maxillary bone modeling in these specimens. However, this shows that similarities in bone modeling patterns can lead to variations in shape, suggesting that other aspects of facial growth (such as modifications of rates and timings of development, as well as sutural growth) also played a crucial role in facial evolution.

Relative tooth size, Bayesian inference, and Homo naledi

OBJECTIVES

Size-corrected tooth crown measurements were used to estimate phenetic affinities among Homo naledi (~335-236 ka) and 11 other Plio-Pleistocene and recent species. To assess further their efficacy, and identify dental evolutionary trends, the data were then quantitatively coded for phylogenetic analyses. Results from both methods contribute additional characterization of H. naledi relative to other hominins.

MATERIALS AND METHODS

After division by their geometric mean, scaled mesiodistal and buccolingual dimensions were used in tooth size apportionment analysis to compare H. naledi with Australopithecus africanus, A. afarensis, Paranthropus robustus, P. boisei, H. habilis, H. ergaster, H. erectus, H. heidelbergensis, H. neanderthalensis, H. sapiens, and Pan troglodytes. These data produce equivalently scaled samples unaffected by interspecific size differences. The data were then gap-weighted for Bayesian inference.

RESULTS

Congruence in interspecific relationships is evident between methods, and with many inferred from earlier systematic studies. However, the present results place H. naledi as a sister taxon to H. habilis, based on a symplesiomorphic pattern of relative tooth size. In the preferred Bayesian phylogram, H. naledi is nested within a clade comprising all Homo species, but it shares some characteristics with australopiths and, particularly, early Homo.

DISCUSSION

Phylogenetic analyses of relative tooth size yield information about evolutionary dental trends not previously reported in H. naledi and the other hominins. Moreover, with an appropriate model these data recovered plausible evolutionary relationships. Together, the findings support recent study suggesting H. naledi originated long before the geological date of the Dinaledi Chamber, from which the specimens under study were recovered.

The primitive brain of early Homo

The brains of modern humans differ from those of great apes in size, shape, and cortical organization, notably in frontal lobe areas involved in complex cognitive tasks, such as social cognition, tool use, and language. When these differences arose during human evolution is a question of ongoing debate. Here, we show that the brains of early Homo from Africa and Western Asia (Dmanisi) retained a primitive, great ape-like organization of the frontal lobe. By contrast, African Homo younger than 1.5 million years ago, as well as all Southeast Asian Homo erectus, exhibited a more derived, humanlike brain organization. Frontal lobe reorganization, once considered a hallmark of earliest Homo in Africa, thus evolved comparatively late, and long after Homo first dispersed from Africa.

Morphological integration of the canine region within the hominine alveolar arch

The early hominin record is characterized by numerous shifts in dental proportions (e.g., canine reduction and megadontia) linked to changes in diet and social behavior. Recent studies suggest that hominins exhibit a reduction in the magnitude of covariation between the anterior and posterior dental components compared with other extant great apes. They point toward, but do not directly test, the relative independence of canine morphology within the hominin alveolar arch. This study focuses specifically on the how the canine region covaries with other regions of the dental arch because the canine region has drastically reduced in size and changed in shape across human evolution. We examine extant primate species most commonly used as a comparative framework for fossil hominin morphology: Gorilla gorilla (n = 27), Pan troglodytes (n = 27), and Homo sapiens (n = 30). We used geometric morphometric methods to test for size and shape covariation between the canine region with other dental regions. We also examined the influence of sexual dimorphism and allometry on intraspecific and interspecific patterns of covariation. The analysis of size and shape covariation between the mandibular canine and other individual tooth regions elucidated complex, species-specific, and sex-specific morphological relationships in the mandibular alveolar arch. There was little evidence to support different patterns of morphological integration between humans on the one hand and nonhuman apes on the other. Canine region morphology was relatively independent from other dental regions across species based on shape and did not significantly covary more with either the incisor or postcanine region in any species. The size correlations between the canine and other dental regions were moderate to high. The species-specific results of this study question the ability to make a priori assumptions about morphological integration in the extant hominin mandibular alveolar arch and its application to the fossil record.

Drimolen cranium DNH 155 documents microevolution in an early hominin species

Paranthropus robustus is a small-brained extinct hominin from South Africa characterized by derived, robust craniodental morphology. The most complete known skull of this species is DNH 7 from Drimolen Main Quarry, which differs from P. robustus specimens recovered elsewhere in ways attributed to sexual dimorphism. Here, we describe a new fossil specimen from Drimolen Main Quarry, dated from approximately 2.04-1.95 million years ago, that challenges this view. DNH 155 is a well-preserved adult male cranium that shares with DNH 7 a suite of primitive and derived features unlike those seen in adult P. robustus specimens from other chronologically younger deposits. This refutes existing hypotheses linking sexual dimorphism, ontogeny and social behaviour within this taxon, and clarifies hypotheses concerning hominin phylogeny. We document small-scale morphological changes in P. robustus associated with ecological change within a short time frame and restricted geography. This represents the most highly resolved evidence yet of microevolutionary change within an early hominin species.

Hominin dental remains from the Pliocene localities at Lomekwi, Kenya (1982-2009)

Increasing evidence for both taxonomic diversity and early stone manufacture during the Pliocene highlights the importance of the hominin fossil record from this epoch in eastern Africa. Here, we describe dental remains from Lomekwi (West Turkana, Kenya), which date from between 3.2 and 3.5 Ma. The sample was collected between 1982 and 2009 and includes five gnathic specimens and a total of 67 teeth (mostly isolated permanent postcanine teeth). Standard linear dimensions indicate that, although the Lomekwi teeth are relatively small, there is broad overlap in size with contemporary Australopithecus afarensis and Australopithecus deyiremeda specimens at most tooth positions. However, some dental characters differentiate this sample from these species, including a relatively large P₄ and M₃ compared with the M₁, a high incidence of well-developed protostylids, and specific accessory molar cuspules. Owing to a lack of well-preserved tooth crowns (and the complete absence of mandibular teeth) in the holotype and paratype of Kenyanthropus platyops, and limited comparable gnathic morphology in the new specimens, it cannot be determined whether these Lomekwi specimens should be attributed to this species. Attribution of these specimens is further complicated by a lack of certainty about position along the tooth row of many of the molar specimens. More comprehensive shape analyses of the external and internal morphology of these specimens, and additional fossil finds, would facilitate the taxonomic attribution of specimens in this taxonomically diverse period of human evolution.

Contemporaneity of Australopithecus, Paranthropus, and early Homo erectus in South Africa

Understanding the extinction of Australopithecus and origins of Paranthropus and Homo in South Africa has been hampered by the perceived complex geological context of hominin fossils, poor chronological resolution, and a lack of well-preserved early Homo specimens. We describe, date, and contextualize the discovery of two hominin crania from Drimolen Main Quarry in South Africa. At ~2.04 million to 1.95 million years old, DNH 152 represents the earliest definitive occurrence of Paranthropus robustus, and DNH 134 represents the earliest occurrence of a cranium with clear affinities to Homo erectus These crania also show that Homo, Paranthropus, and Australopithecus were contemporaneous at ~2 million years ago. This high taxonomic diversity is also reflected in non-hominin species and provides evidence of endemic evolution and dispersal during a period of climatic variability.

All who wander are not lost

New hominin cranial fossils highlight the early exploits of Homo erectus

Australopithecus afarensis endocasts suggest ape-like brain organization and prolonged brain growth

Human brains are three times larger, are organized differently, and mature for a longer period of time than those of our closest living relatives, the chimpanzees. Together, these characteristics are important for human cognition and social behavior, but their evolutionary origins remain unclear. To study brain growth and organization in the hominin species Australopithecus afarensis more than 3 million years ago, we scanned eight fossil crania using conventional and synchrotron computed tomography. We inferred key features of brain organization from endocranial imprints and explored the pattern of brain growth by combining new endocranial volume estimates with narrow age at death estimates for two infants. Contrary to previous claims, sulcal imprints reveal an ape-like brain organization and no features derived toward humans. A comparison of infant to adult endocranial volumes indicates protracted brain growth in A. afarensis, likely critical for the evolution of a long period of childhood learning in hominins.

Co-occurrence of Acheulian and Oldowan artifacts with Homo erectus cranial fossils from Gona, Afar, Ethiopia

Although stone tools generally co-occur with early members of the genus Homo, they are rarely found in direct association with hominins. We report that both Acheulian and Oldowan artifacts and Homo erectus crania were found in close association at 1.26 million years (Ma) ago at Busidima North (BSN12), and ca. 1.6 to 1.5 Ma ago at Dana Aoule North (DAN5) archaeological sites at Gona, Afar, Ethiopia. The BSN12 partial cranium is robust and large, while the DAN5 cranium is smaller and more gracile, suggesting that H. erectus was probably a sexually dimorphic species. The evidence from Gona shows behavioral diversity and flexibility with a lengthy and concurrent use of both stone technologies by H. erectus, confounding a simple "single species/single technology" view of early Homo.

DHEAS and Human Development: An Evolutionary Perspective

Adrenarche, the post-natal rise of DHEA and DHEAS, is unique to humans and the African Apes. Recent findings have linked DHEA in humans to the development of the left dorsolateral prefrontal cortex (LDPFC) between the ages of 4-8 years and the right temporoparietal junction (rTPJ) from 7 to 12 years of age. Given the association of the LDLPFC with the 5-to-8 transition and the rTPJ with mentalizing during middle childhood DHEA may have played an important role in the evolution of the human brain. I argue that increasing protein in the diet over the course of human evolution not only increased levels of DHEAS, but linked meat consumption with brain development during the important 5- to-8 transition. Consumption of animal protein has been associated with IGF-1, implicated in the development of the adrenal zona reticularis (ZR), the site of DHEAS production. In humans and chimps, the zona reticularis emerges at 3-4 years, along with the onset of DHEA/S production. For chimps this coincides with weaning and peak synaptogenesis. Among humans, weaning is completed around 2 ½ years, while synaptogenesis peaks around 5 years. Thus, in chimpanzees, early cortical maturation is tied to the mother; in humans it may be associated with post-weaning provisioning by others. I call for further research on adrenarche among the African apes as a critical comparison to humans. I also suggest research in subsistence populations to establish the role of nutrition and energetics in the timing of adrenarche and the onset of middle childhood.

Genes with human-specific features are primarily involved with brain, immune and metabolic evolution

Background

Humans have adapted to widespread changes during the past 2 million years in both environmental and lifestyle factors. This is evident in overall body alterations such as average height and brain size. Although we can appreciate the uniqueness of our species in many aspects, molecular variations that drive such changes are far from being fully known and explained. Comparative genomics is able to determine variations in genomic sequence that may provide functional information to better understand species-specific adaptations. A large number of human-specific genomic variations have been reported but no currently available dataset comprises all of these, a problem which contributes to hinder progress in the field.

Results

Here we critically update high confidence human-specific genomic variants that mostly associate with protein-coding regions and find 856 related genes. Events that create such human-specificity are mainly gene duplications, the emergence of novel gene regions and sequence and structural alterations. Functional analysis of these human-specific genes identifies adaptations to brain, immune and metabolic systems to be highly involved. We further show that many of these genes may be functionally associated with neural activity and generating the expanded human cortex in dynamic spatial and temporal contexts.

Conclusions

This comprehensive study contributes to the current knowledge by considerably updating the number of human-specific genes following a critical bibliographic survey. Human-specific genes were functionally assessed for the first time to such extent, thus providing unique information. Our results are consistent with environmental changes, such as immune challenges and alterations in diet, as well as neural sophistication, as significant contributors to recent human evolution.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2886-2) contains supplementary material, which is available to authorized users.

Dental evolutionary rates and its implications for the Neanderthal-modern human divergence

The origin of Neanderthal and modern human lineages is a matter of intense debate. DNA analyses have generally indicated that both lineages diverged during the middle period of the Middle Pleistocene, an inferred time that has strongly influenced interpretations of the hominin fossil record. This divergence time, however, is not compatible with the anatomical and genetic Neanderthal affinities observed in Middle Pleistocene hominins from Sima de los Huesos (Spain), which are dated to 430 thousand years (ka) ago. Drawing on quantitative analyses of dental evolutionary rates and Bayesian analyses of hominin phylogenetic relationships, I show that any divergence time between Neanderthals and modern humans younger than 800 ka ago would have entailed unexpectedly rapid dental evolution in early Neanderthals from Sima de los Huesos. These results support a pre-800 ka last common ancestor for Neanderthals and modern humans unless hitherto unexplained mechanisms sped up dental evolution in early Neanderthals.

Complete permanent mandibular dentition of early Homo from the upper Burgi Member of the Koobi Fora Formation, Ileret, Kenya

The KNM-ER 64060 dentition derives from a horizon that most likely dates to between 2.02 and 2.03 Ma. A proximate series of postcranial bones (designated KNM-ER 64061) derives from the same siltstone unit and may be associated with the dentition, but their separation on the surface of the site leaves some room for doubt. KNM-ER 64060 is one of fewer than ten hominin specimens from the Early Pleistocene of East Africa that comprises a full or nearly complete mandibular dentition. Its taxonomic attribution is potentially significant, especially if the postcranial elements are related. At least three, and probably four hominin species, including Paranthropus boisei and Homo erectus (= H. ergaster), are known at about this time in East Africa. Other penecontemporaneous fossils have been referred to a single, highly variable species, H. habilis, or two taxa, namely H. habilis and H. rudolfensis. Although the weight of evidence supports the attribution of these specimens to two species, there is notable lack of agreement over the assignation of individual fossils. We take a conservative approach and group all such specimens under the designation "early Homo sp." for comparative purposes. KNM-ER 64060 is clearly attributable to Homo rather than Paranthropus. The preponderance of the evidence suggests that the affinities of KNM-ER 64060 are with fossils assigned to the early Homo sp. category rather than with H. erectus. This is indicated by the overall sizes of the KNM-ER 64060 canine, premolar and molar crowns, the size relationships of the P₃ to P₄, the relative narrowness of its premolar crowns, the cusp proportions of the M₁ and especially those of the M₂ and M₃, and seemingly the possession of a two-rooted P₄. Some of these comparisons suggest further that among the fossils comprising the early Homo sp. sample, the KNM-ER 64060 dentition exhibits greater overall similarity to specimens such as OH 7 and OH 16 that represent Homo habilis sensu stricto.

Morphological trends in arcade shape and size in Middle Pleistocene Homo

OBJECTIVES

Middle Pleistocene fossil hominins, often summarized as Homo heidelbergensis sensu lato, are difficult to interpret due to a fragmentary fossil record and ambiguous combinations of primitive and derived characters. Here, we focus on one aspect of facial shape and analyze shape variation of the dental arcades of these fossils together with other Homo individuals.

MATERIALS AND METHODS

Three-dimensional landmark data were collected on computed tomographic scans and surface scans of Middle Pleistocene fossil hominins (n = 8), Homo erectus s.l. (n = 4), Homo antecessor (n = 1), Homo neanderthalensis (n = 13), recent (n = 52) and fossil (n = 19) Homo sapiens. To increase sample size, we used multiple multivariate regression to reconstruct complementary arches for isolated mandibles, and explored size and shape differences among maxillary arcades.

RESULTS

The shape of the dental arcade in H. erectus s.l. and H. antecessor differs markedly from both Neanderthals and H. sapiens. The latter two show subtle but consistent differences in arcade length and width. Shape variation among Middle Pleistocene fossil hominins does not exceed the amount of variation of other species, but includes individuals with more primitive and more derived morphology, all more similar to Neanderthals and H. sapiens than to H. erectus s.l.

DISCUSSION

Although our results cannot reject the hypothesis that the Middle Pleistocene fossil hominins belong to a single species, their shape variation comprises a more primitive morph that represents a likely candidate for the shape of the last common ancestor of Neanderthals and H. sapiens, and a more derived morph resembling Neanderthals. The arcade shape difference between Neanderthals and H. sapiens might be related to different ways to withstand mechanical stress.

Amplio, Ergo Sum

This article aims to explore the idea that enhancement technologies have been and will continue to be an essential element of what we might call the "human continuum," and are indeed key to our existence and evolution into persons. Whereas conservative commentators argue that enhancement is likely to cause us to lose our humanity and become something other, it is argued here that the very opposite is true: that enhancement is the core of what and who we are. Using evidence from paleoanthropology to examine the nature of our predecessor species, and their proclivities for tool use, we can see that there is good reason to assume that the development of Homo sapiens is a direct result of the use of enhancement technologies. A case is also made for broad understandings of the scope of enhancement, based on the significant evolutionary results of acts that are usually dismissed as "unremarkable." Furthermore, the use of enhancement by modern humans is no different than these prehistoric applications, and is likely to ultimately have similar results. There is no good reason to assume that whatever we may become will not also consider itself human.

Description and analysis of three Homo naledi incudes from the Dinaledi Chamber, Rising Star cave (South Africa)

This study describes three incudes recovered from the Dinaledi Chamber in the Rising Star cave system in South Africa. All three bones were recovered during sieving of excavated sediments and likely represent three Homo naledi individuals. Morphologically and metrically, the Dinaledi ossicles resemble those of chimpanzees and Paranthropus robustus more than they do later members of the genus Homo, and fall outside of the modern human range of variation in several dimensions. Despite this, when overall size is considered, the functional lengths in H. naledi and P. robustus are very similar to those predicted for a human with a similar-sized incus. In this sense, both taxa seem to show a relatively elongated functional length, distinguishing them from chimpanzees. The functional length in H. naledi is slightly longer in absolute terms than in P. robustus, suggesting H. naledi may already show a slight increase in functional length compared with early hominins. While H. naledi lacks the more open angle between the long and short processes found in modern humans, considered a derived feature within the genus Homo, the value in H. naledi is similar to that predicted for a hominoid with a similar-sized incus. Principal components analysis of size-standardized variables shows H. naledi falling outside of the recent human range of variation, but within the confidence ellipse for gorillas. Phylogenetic polarity is complicated by the absence of incus data from early members of the genus Homo, but the generally primitive nature of the H. naledi incudes is consistent with other primitive features of the species, such as the very small cranial capacity. These ossicles add significantly to the understanding of incus variation in hominins and provide important new data on the morphology and taxonomic affinities of H. naledi.

Endocast morphology of Homo naledi from the Dinaledi Chamber, South Africa

The new species Homo naledi was discovered in 2013 in a remote cave chamber of the Rising Star cave system, South Africa. This species survived until between 226,000 and 335,000 y ago, placing it in continental Africa at the same time as the early ancestors of modern humans were arising. Yet, H. naledi was strikingly primitive in many aspects of its anatomy, including the small size of its brain. Here, we have provided a description of endocast anatomy of this primitive species. Despite its small brain size, H. naledi shared some aspects of human brain organization, suggesting that innovations in brain structure were ancestral within the genus Homo.

Hominin cranial remains from the Dinaledi Chamber, South Africa, represent multiple individuals of the species Homo naledi. This species exhibits a small endocranial volume comparable to Australopithecus, combined with several aspects of external cranial anatomy similar to larger-brained species of Homo such as Homo habilis and Homo erectus. Here, we describe the endocast anatomy of this recently discovered species. Despite the small size of the H. naledi endocasts, they share several aspects of structure in common with other species of Homo, not found in other hominins or great apes, notably in the organization of the inferior frontal and lateral orbital gyri. The presence of such structural innovations in a small-brained hominin may have relevance to behavioral evolution within the genus Homo.

Mixture of Probabilistic Principal Component Analyzers for Shapes from Point Sets

Inferring a probability density function (pdf) for shape from a population of point sets is a challenging problem. The lack of point-to-point correspondences and the non-linearity of the shape spaces undermine the linear models. Methods based on manifolds model the shape variations naturally, however, statistics are often limited to a single geodesic mean and an arbitrary number of variation modes. We relax the manifold assumption and consider a piece-wise linear form, implementing a mixture of distinctive shape classes. The pdf for point sets is defined hierarchically, modeling a mixture of Probabilistic Principal Component Analyzers (PPCA) in higher dimension. A Variational Bayesian approach is designed for unsupervised learning of the posteriors of point set labels, local variation modes, and point correspondences. By maximizing the model evidence, the numbers of clusters, modes of variations, and points on the mean models are automatically selected. Using the predictive distribution, we project a test shape to the spaces spanned by the local PPCA's. The method is applied to point sets from: i) synthetic data, ii) healthy versus pathological heart morphologies, and iii) lumbar vertebrae. The proposed method selects models with expected numbers of clusters and variation modes, achieving lower generalization-specificity errors compared to state-of-the-art.