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Genetic and fragmented palaeoanthropological data suggest that Denisovans were once widely distributed across eastern Eurasia 1-3 . Despite limited archaeological evidence, this indicates that Denisovans were capable of adapting to a highly diverse range of environments. Here we integrate zooarchaeological and proteomic analyses of the late Middle to Late Pleistocene faunal assemblage from Baishiya Karst Cave on the Tibetan Plateau, where a Denisovan mandible and Denisovan sedimentary mitochondrial DNA were found 3,4 . Using zooarchaeology by mass spectrometry, we identify a new hominin rib specimen that dates to approximately 48-32 thousand years ago (layer 3). Shotgun proteomic analysis taxonomically assigns this specimen to the Denisovan lineage, extending their presence at Baishiya Karst Cave well into the Late Pleistocene. Throughout the stratigraphic sequence, the faunal assemblage is dominated by Caprinae, together with megaherbivores, carnivores, small mammals and birds. The high proportion of anthropogenic modifications on the bone surfaces suggests that Denisovans were the primary agent of faunal accumulation. The chaîne opératoire of carcass processing indicates that animal taxa were exploited for their meat, marrow and hides, while bone was also used as raw material for the production of tools. Our results shed light on the behaviour of Denisovans and their adaptations to the diverse and fluctuating environments of the late Middle and Late Pleistocene of eastern Eurasia., (© 2024. The Author(s).)

Sahelanthropus tchadensis has raised much debate since its initial discovery in Chad in 2001, given its controversial classification as the earliest representative of the hominin lineage. This debate extends beyond the phylogenetic position of the species, and includes several aspects of its habitual behavior, especially in what regards its locomotion. The combination of ancestral and derived traits observed in the fossils associated with the species has been used to defend different hypotheses related to its relationship to hominins. Here, the cranial morphology of Sahelanthropus tchadensis was assessed through 16 linear craniometric measurements, and compared to great apes and hominins through Principal Component Analysis based on size and shape and shape information alone. The results show that S. tchadensis share stronger morphological affinities with hominins than with apes for both the analysis that include size information and the one that evaluates shape alone. Since TM 266-01-060-1 shows a strong morphological affinity with the remaining hominins represented in the analysis, our results support the initial interpretations that S. tchadensis represents an early specimen of our lineage or a stem basal lineage more closely related to hominins than to Panini.

The Kocabaş specimen comes from a travertine quarry near the homonymous village in the Denizli basin (Turkey). The specimen comprises three main fragments: portions of the right and left parietal and left and right parts of the frontal bone. The fossil was assumed to belong to the Homo erectus s.l. hypodigm by some authors, whereas others see similarities with Middle Pleistocene fossils (Broken Hill 1/Kabwe, Bodo, or Ceprano). Here, we present the first attempt to make a complete reconstruction of the missing medial portion of the frontal bone and a comprehensive geometric morphometric analysis of this bone. We restored the calotte by aligning and mirroring the three preserved fragments. Afterward, we restored the missing portion by applying the thin-plate spline interpolation algorithm of target fossils onto the reconstructed Kocabaş specimen. For the geometric morphometric analyses, we collected 80 landmarks on the frontal bone (11 osteometric points, 14 bilateral curve semilandmarks, and 41 surface semilandmarks). The comparative sample includes 21 fossils from different chronological periods and geographical areas and 30 adult modern humans from different populations. Shape analyses highlighted the presence in Kocabaş of features usually related to Middle Pleistocene Homo, such as a developed supraorbital torus associated with a relatively short frontal squama and reduced post-toral sulcus. Cluster analysis and linear discriminant analysis classification procedure suggest Kocabaş being part of the same taxonomic unit of Eurasian and African Middle Pleistocene Homo. In light of our results, we consider that attributing the Kocabaş hominin to H. erectus s.l. may be unwarranted. Results of our analyses are compatible with different evolutionary scenarios, but a more precise chronological framework is needed for a thorough discussion of the evolutionary significance of this specimen. Future work should clarify its geological age, given uncertainties regarding its stratigraphic provenance., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Apes possess two sex chromosomes-the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked to infertility 1 . The X chromosome is vital for reproduction and cognition 2 . Variation in mating patterns and brain function among apes suggests corresponding differences in their sex chromosomes. However, owing to their repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (bonobo (Pan paniscus), chimpanzee (Pan troglodytes), western lowland gorilla (Gorilla gorilla gorilla), Bornean orangutan (Pongo pygmaeus) and Sumatran orangutan (Pongo abelii)) and a lesser ape (the siamang gibbon (Symphalangus syndactylus)), and untangled the intricacies of their evolution. Compared with the X chromosomes, the ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements-owing to the accumulation of lineage-specific ampliconic regions, palindromes, transposable elements and satellites. Many Y chromosome genes expand in multi-copy families and some evolve under purifying selection. Thus, the Y chromosome exhibits dynamic evolution, whereas the X chromosome is more stable. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of more than 100 individual great apes. These reference assemblies are expected to inform human evolution and conservation genetics of non-human apes, all of which are endangered species., (© 2024. The Author(s).)

The largest ever primate and one of the largest of the southeast Asian megafauna, Gigantopithecus blacki 1 , persisted in China from about 2.0 million years until the late middle Pleistocene when it became extinct 2-4 . Its demise is enigmatic considering that it was one of the few Asian great apes to go extinct in the last 2.6 million years, whereas others, including orangutan, survived until the present 5 . The cause of the disappearance of G. blacki remains unresolved but could shed light on primate resilience and the fate of megafauna in this region 6 . Here we applied three multidisciplinary analyses-timing, past environments and behaviour-to 22 caves in southern China. We used 157 radiometric ages from six dating techniques to establish a timeline for the demise of G. blacki. We show that from 2.3 million years ago the environment was a mosaic of forests and grasses, providing ideal conditions for thriving G. blacki populations. However, just before and during the extinction window between 295,000 and 215,000  years ago there was enhanced environmental variability from increased seasonality, which caused changes in plant communities and an increase in open forest environments. Although its close relative Pongo weidenreichi managed to adapt its dietary preferences and behaviour to this variability, G. blacki showed signs of chronic stress and dwindling populations. Ultimately its struggle to adapt led to the extinction of the greatest primate to ever inhabit the Earth., (© 2024. The Author(s).)

The naming of Australopithecus africanus in 1925, based on the Taung Child, heralded a new era in human evolutionary studies and turned the attention of the then Eurasian-centric palaeoanthropologists to Africa, albeit with reluctance. Almost one hundred years later, Africa is recognized as the cradle of humanity, where the entire evolutionary history of our lineage prior to two million years ago took place-after the Homo-Pan split. This Review examines data from diverse sources and offers a revised depiction of the genus and characterizes its role in human evolution. For a long time, our knowledge of Australopithecus came from both A. africanus and Australopithecus afarensis, and the members of this genus were portrayed as bipedal creatures that did not use stone tools, with a largely chimpanzee-like cranium, a prognathic face and a brain slightly larger than that of chimpanzees. Subsequent field and laboratory discoveries, however, have altered this portrayal, showing that Australopithecus species were habitual bipeds but also practised arboreality; that they occasionally used stone tools to supplement their diet with animal resources; and that their infants probably depended on adults to a greater extent than what is seen in apes. The genus gave rise to several taxa, including Homo, but its direct ancestor remains elusive. In sum, Australopithecus had a pivotal bridging role in our evolutionary history owing to its morphological, behavioural and temporal placement between the earliest archaic putative hominins and later hominins-including the genus Homo., (© 2023. Springer Nature Limited.)

Body and canine size dimorphism in fossils inform sociobehavioral hypotheses on human evolution and have been of interest since Darwin's famous reflections on the subject. Here, we assemble a large dataset of fossil canines of the human clade, including all available Ardipithecus ramidus fossils recovered from the Middle Awash and Gona research areas in Ethiopia, and systematically examine canine dimorphism through evolutionary time. In particular, we apply a Bayesian probabilistic method that reduces bias when estimating weak and moderate levels of dimorphism. Our results show that Ar. ramidus canine dimorphism was significantly weaker than in the bonobo, the least dimorphic and behaviorally least aggressive among extant great apes. Average male-to-female size ratios of the canine in Ar. ramidus are estimated as 1.06 and 1.13 in the upper and lower canines, respectively, within modern human population ranges of variation. The slightly greater magnitude of canine size dimorphism in the lower than in the upper canines of Ar. ramidus appears to be shared with early Australopithecus , suggesting that male canine reduction was initially more advanced in the behaviorally important upper canine. The available fossil evidence suggests a drastic size reduction of the male canine prior to Ar. ramidus and the earliest known members of the human clade, with little change in canine dimorphism levels thereafter. This evolutionary pattern indicates a profound behavioral shift associated with comparatively weak levels of male aggression early in human evolution, a pattern that was subsequently shared by Australopithecus and Homo ., Competing Interests: The authors declare no competing interest.

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

Bipedal trackways discovered in 1978 at Laetoli site G, Tanzania and dated to 3.66 million years ago are widely accepted as the oldest unequivocal evidence of obligate bipedalism in the human lineage 1-3 . Another trackway discovered two years earlier at nearby site A was partially excavated and attributed to a hominin, but curious affinities with bears (ursids) marginalized its importance to the paleoanthropological community, and the location of these footprints fell into obscurity 3-5 . In 2019, we located, excavated and cleaned the site A trackway, producing a digital archive using 3D photogrammetry and laser scanning. Here we compare the footprints at this site with those of American black bears, chimpanzees and humans, and we show that they resemble those of hominins more than ursids. In fact, the narrow step width corroborates the original interpretation of a small, cross-stepping bipedal hominin. However, the inferred foot proportions, gait parameters and 3D morphologies of footprints at site A are readily distinguished from those at site G, indicating that a minimum of two hominin taxa with different feet and gaits coexisted at Laetoli., (© 2021. The Author(s).)

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., (© 2021 The Authors. American Journal of Physical Anthropology published by Wiley Periodicals LLC.)

Wild great apes harbor clades of gut bacteria that are restricted to each host species. Previous research shows the evolutionary relationships among several host-restricted clades mirror those of great-ape species. However, processes such as geographic separation, host-shift speciation, and host-filtering based on diet or gut physiology can generate host-restricted bacterial clades and mimic patterns of co-diversification across host species. To gain insight into the distribution of host-restricted taxa, we examine captive great apes living under conditions where sharing of bacterial strains is readily possible. Here, we show that increased sampling of wild and captive apes identifies additional host-restricted lineages whose relationships are not concordant with the host phylogeny. Moreover, the gut microbiomes of captive apes converge through the displacement of strains that are restricted to their wild conspecifics by human-restricted strains. We demonstrate that host-restricted and co-diversifying bacterial strains in wild apes lack persistence and fidelity in captive environments., (© 2021. The Author(s).)

Insights into potential differences among the bony labyrinths of Plio-Pleistocene hominins may inform their evolutionary histories and sensory ecologies. We use four recently-discovered bony labyrinths from the site of Kromdraai to significantly expand the sample for Paranthropus robustus. Diffeomorphometry, which provides detailed information about cochlear shape, reveals size-independent differences in cochlear shape between P. robustus and Australopithecus africanus that exceed those among modern humans and the African apes. The cochlea of P. robustus is distinctive and relatively invariant, whereas cochlear shape in A. africanus is more variable, resembles that of early Homo, and shows a degree of morphological polymorphism comparable to that evinced by modern species. The curvature of the P. robustus cochlea is uniquely derived and is consistent with enhanced sensitivity to low-frequency sounds. Combined with evidence for selection, our findings suggest that sound perception shaped distinct ecological adaptations among southern African early hominins., (© 2021. The Author(s).)

Efforts to name and classify Middle Pleistocene Homo, often referred to as "Homo heidelbergensis" are hampered by confusing patterns of morphology but also by conflicting paleoanthropological ideologies that are embedded in approaches to hominin taxonomy, nomenclature, and the species concept. We deconstruct these issues to show how the field's search for a "real" species relies on strict adherence to pre-Darwinian essentialist naming rules in a post-typological world. We then examine Middle Pleistocene Homo through the framework of ethnobiology, which examines on how Indigenous societies perceive, classify, and name biological organisms. This research reminds us that across human societies, taxonomies function to (1) identify and classify organisms based on consensus pattern recognition and (2) construct a stable nomenclature for effective storage, retrieval and communication of information. Naming Middle Pleistocene Homo as a "real" species cannot be verified with the current data; and separating regional groups into distinct evolutionary lineages creates taxa that are not defined by readily perceptible or universally salient differences. Based on ethnobiological studies of this kind of patterning, referring to these hominins above the level of the species according to their generic category with modifiers (e.g., "European Middle Pleistocene Homo") is consistent with observed human capabilities for cognitive differentiation, is both necessary and sufficient given the current data, and will allow for the most clear communication across ideologies going forward., (© 2021 The Authors. American Journal of Physical Anthropology published by Wiley Periodicals LLC.)

The middle Miocene stem kenyapithecine Nacholapithecus kerioi (16-15 Ma; Nachola, Kenya) is represented by a large number of isolated fossil remains and one of the most complete skeletons in the hominoid fossil record (KNM-BG 35250). Multiple fieldwork seasons performed by Japanese-Kenyan teams during the last part of the 20th century resulted in the discovery of a large sample of Nacholapithecus fossils. Here, we describe the new femoral remains of Nacholapithecus. In well-preserved specimens, we evaluate sex differences and within-species variation using both qualitative and quantitative traits. We use these data to determine whether these specimens are morphologically similar to the species holotype KNM-BG 35250 (which shows some plastic deformation) and to compare Nacholapithecus with other Miocene hominoids and extant anthropoids to evaluate the distinctiveness of its femur. The new fossil evidence reaffirms previously reported descriptions of some distal femoral traits, namely the morphology of the patellar groove. However, results also show that relative femoral head size in Nacholapithecus is smaller, relative neck length is longer, and neck-shaft angle is lower than previously reported for KNM-BG 35250. These traits have a strong functional signal related to the hip joint kinematics, suggesting that the morphology of the proximal femur in Nacholapithecus might be functionally related to quadrupedal-like behaviors instead of more derived antipronograde locomotor modes. Results further demonstrate that other African Miocene apes (with the exception of Turkanapithecus kalakolensis) generally fall within the Nacholapithecus range of variation, whose overall femoral shape resembles that of Ekembo spp. and Equatorius africanus. Our results accord with the previously inferred locomotor repertoire of Nacholapithecus, indicating a combination of generalized arboreal quadrupedalism combined with other antipronograde behaviors (e.g., vertical climbing)., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine-platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo -specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

Humans diverged from apes (chimpanzees, specifically) toward the end of the Miocene ~9.3 million to 6.5 million years ago. Understanding the origins of the human lineage (hominins) requires reconstructing the morphology, behavior, and environment of the chimpanzee-human last common ancestor. Modern hominoids (that is, humans and apes) share multiple features (for example, an orthograde body plan facilitating upright positional behaviors). However, the fossil record indicates that living hominoids constitute narrow representatives of an ancient radiation of more widely distributed, diverse species, none of which exhibit the entire suite of locomotor adaptations present in the extant relatives. Hence, some modern ape similarities might have evolved in parallel in response to similar selection pressures. Current evidence suggests that hominins originated in Africa from Miocene ape ancestors unlike any living species., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

The origin and evolution of hominin mortuary practices are topics of intense interest and debate 1-3 . Human burials dated to the Middle Stone Age (MSA) are exceedingly rare in Africa and unknown in East Africa 1-6 . Here we describe the partial skeleton of a roughly 2.5- to 3.0-year-old child dating to 78.3 ± 4.1 thousand years ago, which was recovered in the MSA layers of Panga ya Saidi (PYS), a cave site in the tropical upland coast of Kenya 7,8 . Recent excavations have revealed a pit feature containing a child in a flexed position. Geochemical, granulometric and micromorphological analyses of the burial pit content and encasing archaeological layers indicate that the pit was deliberately excavated. Taphonomical evidence, such as the strict articulation or good anatomical association of the skeletal elements and histological evidence of putrefaction, support the in-place decomposition of the fresh body. The presence of little or no displacement of the unstable joints during decomposition points to an interment in a filled space (grave earth), making the PYS finding the oldest known human burial in Africa. The morphological assessment of the partial skeleton is consistent with its assignment to Homo sapiens, although the preservation of some primitive features in the dentition supports increasing evidence for non-gradual assembly of modern traits during the emergence of our species. The PYS burial sheds light on how MSA populations interacted with the dead.

Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus., (© 2021 The Authors. Evolutionary Anthropology published by Wiley Periodicals LLC.)

The KNM-ER 2598 occipital is among the oldest fossils attributed to Homo erectus but questions have been raised about whether it may derive from a younger horizon. Here we report on efforts to relocate the KNM-ER 2598 locality and investigate its paleontological and geological context. Although located in a different East Turkana collection area (Area 13) than initially reported, the locality is stratigraphically positioned below the KBS Tuff and the outcrops show no evidence of deflation of a younger unit, supporting an age of >1.855 Ma. Newly recovered faunal material consists primarily of C 4 grazers, further confirmed by enamel isotope data. A hominin proximal 3rd metatarsal and partial ilium were discovered <50 m from the reconstructed location where KNM-ER 2598 was originally found but these cannot be associated directly with the occipital. The postcrania are consistent with fossil Homo and may represent the earliest postcrania attributable to Homo erectus.

Humans harbor diverse communities of microorganisms, the majority of which are bacteria in the gastrointestinal tract. These gut bacterial communities in turn host diverse bacteriophage (hereafter phage) communities that have a major impact on their structure, function, and, ultimately, human health. However, the evolutionary and ecological origins of these human-associated phage communities are poorly understood. To address this question, we examined fecal phageomes of 23 wild nonhuman primate taxa, including multiple representatives of all the major primate radiations. We find relatives of the majority of human-associated phages in wild primates. Primate taxa have distinct phageome compositions that exhibit a clear phylosymbiotic signal, and phage-superhost codivergence is often detected for individual phages. Within species, neighboring social groups harbor compositionally and evolutionarily distinct phageomes, which are structured by superhost social behavior. Captive nonhuman primate phageome composition is intermediate between that of their wild counterparts and humans. Phage phylogenies reveal replacement of wild great ape-associated phages with human-associated ones in captivity and, surprisingly, show no signal for the persistence of wild-associated phages in captivity. Together, our results suggest that potentially labile primate-phage associations have persisted across millions of years of evolution. Across primates, these phylosymbiotic and sometimes codiverging phage communities are shaped by transmission between groupmates through grooming and are dramatically modified when primates are moved into captivity., Competing Interests: The authors declare no competing interest.

The presence of multiple Australopithecus species at Sterkfontein Member 4, South Africa (2.07-2.61 Ma), is highly contentious, and quantitative assessments of craniodental and postcranial variability remain inconclusive. Using geometric morphometrics, we compared the sacrum of the small-bodied, presumed female subadult Australopithecus africanus skeleton Sts 14 to the large, alleged male adult StW 431 against a geographically diverse sample of modern humans, and two species of Pan, Gorilla, and Pongo. The probabilities of sampling morphologies as distinct as Sts 14 and StW 431 from a single species ranged from 1.3 to 2.5% for the human sample, and from 0.0 to 4.5% for the great apes, depending on the species and the analysis. Sexual dimorphism and developmental or geologic age could not adequately explain the differences between StW 431 and Sts 14, suggesting that they are unlikely to be conspecific. This supports earlier claims of taxonomic heterogeneity at Sterkfontein Member 4.

Late Miocene great apes are key to reconstructing the ancestral morphotype from which earliest hominins evolved. Despite consensus that the late Miocene dryopith great apes Hispanopithecus laietanus (Spain) and Rudapithecus hungaricus (Hungary) are closely related (Hominidae), ongoing debate on their phylogenetic relationships with extant apes (stem hominids, hominines, or pongines) complicates our understanding of great ape and human evolution. To clarify this question, we rely on the morphology of the inner ear semicircular canals, which has been shown to be phylogenetically informative. Based on microcomputed tomography scans, we describe the vestibular morphology of Hispanopithecus and Rudapithecus , and compare them with extant hominoids using landmark-free deformation-based three-dimensional geometric morphometric analyses. We also provide critical evidence about the evolutionary patterns of the vestibular apparatus in living and fossil hominoids under different phylogenetic assumptions for dryopiths. Our results are consistent with the distinction of Rudapithecus and Hispanopithecus at the genus rank, and further support their allocation to the Hominidae based on their derived semicircular canal volumetric proportions. Compared with extant hominids, the vestibular morphology of Hispanopithecus and Rudapithecus most closely resembles that of African apes, and differs from the derived condition of orangutans. However, the vestibular morphologies reconstructed for the last common ancestors of dryopiths, crown hominines, and crown hominids are very similar, indicating that hominines are plesiomorphic in this regard. Therefore, our results do not conclusively favor a hominine or stem hominid status for the investigated dryopiths., Competing Interests: The authors declare no competing interest.

Objectives: The purpose of this study is to help elucidate the taxonomic relationship between Homo naledi and other hominins., Materials and Methods: Homo naledi deciduous maxillary and mandibular molars from the Dinaledi Chamber, South Africa were compared to those of Australopithecus africanus, Australopithecus afarensis, Paranthropus robustus, Paranthropus boisei, early Homo sp., Homo erectus, early Homo sapiens, Upper Paleolithic H. sapiens, recent southern African H. sapiens, and Neanderthals by means of morphometric analyses of crown outlines and relative cusp areas. The crown shapes were analyzed using elliptical Fourier analyses followed by principal component analyses (PCA). The absolute and relative cusp areas were obtained in ImageJ and compared using PCA and cluster analyses., Results: PCA suggests that the crown shapes and relative cusp areas of mandibular molars are more diagnostic than the maxillary molars. The H. naledi deciduous mandibular first and second molar (dm 1 and dm 2 ) do not have a strong affinity to any taxon in the comparative sample in all analyses. While the H. naledi dm 2 plots as an outlier in the relative cusp analysis, the H. naledi specimen fall closest to Australopithecus due to their relatively large metaconid, a primitive trait for the genus Homo. Although useful for differentiating Neanderthals from recent southern African H. sapiens and UP H. sapiens, the PCA of the relative cusp areas suggests that the deciduous maxillary second molars (dm 2 ) do not differentiate other groups. The three H. naledi dm 2 cuspal areas are variable and fall within the ranges of other Homo, as well as Australopithecus, and Paranthropus suggesting weak diagnostic utility., Discussion: This research provides another perspective on the morphology of, and variation within, H. naledi. The H. naledi deciduous molars do not consistently align with any genus or species in the comparative sample in either the crown shape or relative cusp analyses. This line of inquiry is consistent with other cranial and postcranial studies suggesting that H. naledi is unique., (© 2020 Wiley Periodicals LLC.)

The discovery of the nearly complete Plio-Pleistocene skeleton StW 573 Australopithecus prometheus from Sterkfontein Member 2, South Africa, has intensified debates as to whether Sterkfontein Member 4 contains a hominin species other than Australopithecus africanus. For example, it has recently been suggested that the partial skeleton StW 431 should be removed from the A. africanus hypodigm and be placed into A. prometheus. Here we re-evaluate this latter proposition, using published information and new comparative data. Although both StW 573 and StW 431 are apparently comparable in their arboreal (i.e., climbing) and bipedal adaptations, they also show significant morphological differences. Surprisingly, StW 431 cannot be unequivocally aligned with either StW 573 or other hominins from Sterkfontein commonly attributed to A. africanus (nor with Paranthropus robustus and Australopithecus sediba). This finding, together with considerations about the recent dating of Plio-Pleistocene hominin-bearing sites in South Africa and palaeoecological/palaeoclimatic conditions, raises questions whether it is justified to subsume hominins from Taung, Makapansgat and Sterkfontein (and Gladysvale) within a single taxon. Given the wealth of fossil material and analytical techniques now available, we call for a re-evaluation of the taxonomy of South African Plio-Pleistocene hominins. Such an endeavour should however go beyond the current (narrow) focus on establishing an A. africanus-A. prometheus dichotomy.

Background: The molecular out of Africa hypothesis, OOAH, has been considered as an established fact amid population geneticists for some 25-30 years despite the early concern with it among phylogeneticists with experience beyond that of Homo. The palaeontological support for the hypothesis is also questionable, a circumstance that in the light of expanding Eurasian palaeontological knowledge has become accentuated through the last decades., Results: The direction of evolution in the phylogenetic tree of modern humans (Homo sapiens sapiens, Hss) was established inter alia by applying progressive phylogenetic analysis to an mtDNA sampling that included a Eurasian, Lund, and the African Mbuti, San and Yoruba. The examination identified the African populations as paraphyletic, thereby compromising the OOAH. The finding, which was consistent with the out of Eurasia hypothesis, OOEH, was corroborated by the mtDNA introgression from Hss into Hsnn (Neanderthals) that demonstrated the temporal and physical Eurasian coexistence of the two lineages. The results are consistent with the palaeontologically established presence of H. erectus in Eurasia, a Eurasian divergence between H. sapiens and H. antecessor ≈ 850,000 YBP, an Hs divergence between Hss and Hsn (Neanderthals + Denisovans) ≈ 800,000 YBP, an mtDNA introgression from Hss into Hsnn* ≈ 500,000 YBP and an Eurasian divergence among the ancestors of extant Hss ≈ 250,000 YBP at the exodus of Mbuti/San into Africa., Conclusions: The present study showed that Eurasia was not the receiver but the donor in Hss evolution. The findings that Homo left Africa as erectus and returned as sapiens sapiens constitute a change in the understanding of Hs evolution to one that conforms to the extensive Eurasian record of Hs palaeontology and archaeology.

A partial left femur (TM 266-01-063) was recovered in July 2001 at Toros-Menalla, Chad, at the same fossiliferous location as the late Miocene holotype of Sahelanthropus tchadensis (the cranium TM 266-01-060-1). It was recognized as a probable primate femur in 2004 when one of the authors was undertaking a taphonomic survey of the fossil assemblages from Toros-Menalla. We are confident the TM 266 femoral shaft belongs to a hominid. It could sample a hominid hitherto unrepresented at Toros-Menalla, but a more parsimonious working hypothesis is that it belongs to S. tchadensis. The differences between TM 266 and the late Miocene Orrorin tugenensis partial femur BAR 1002'00, from Kenya, are consistent with maintaining at least a species-level distinction between S. tchadensis and O. tugenensis. The results of our preliminary functional analysis suggest the TM 266 femoral shaft belongs to an individual that was not habitually bipedal, something that should be taken into account when considering the relationships of S. tchadensis. The circumstances of its discovery should encourage researchers to check to see whether there is more postcranial evidence of S. tchadensis among the fossils recovered from Toros-Menalla., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

A late Middle Pleistocene mandible from Baishiya Karst Cave (BKC) on the Tibetan Plateau has been inferred to be from a Denisovan, an Asian hominin related to Neanderthals, on the basis of an amino acid substitution in its collagen. Here we describe the stratigraphy, chronology, and mitochondrial DNA extracted from the sediments in BKC. We recover Denisovan mitochondrial DNA from sediments deposited ~100 thousand and ~60 thousand years ago (ka) and possibly as recently as ~45 ka. The long-term occupation of BKC by Denisovans suggests that they may have adapted to life at high altitudes and may have contributed such adaptations to modern humans on the Tibetan Plateau., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Phylogenetic systematics (e.g., cladistics) is one of the most important analytical frameworks of modern Biology. It seems to be common knowledge that within phylogenetics, 'groups' must be defined based solely on the synapomorphies or on the "derived" characters that unite two or more taxa in a clade or monophyletic group. Thus, the idea of synapomorphy seems to be of fundamental influence and importance. Here I will show that the most common and straightforward understanding of synapomorphy as a shared derived character is not sufficient and eventually must be rejected in favor of Nelson's relational interpretation of such term. Arguing for this point and using three examples from previously published Apes' genomic matrices, I explicitly demonstrate that the relationship (Pongo (Gorilla (Homo, Pan))) with Hylobatidae as a sister taxon, may be successfully recovered by three-taxon statement analysis (3TA) and three-taxon statement average consensus analysis (3TS-ACA) even if all of the evident standard shared derived molecular characters of the relationship (Pongo (Gorilla (Homo, Pan))) with Hylobatidae as a sister taxon, have been excluded from the molecular alignments. Neither conventional Maximum Parsimony nor Maximum Likelihood or Bayesian Inference can do this in such situation. Thus, our results show that the relationship (Pongo (Gorilla (Homo, Pan))) with Hylobatidae as a sister taxon has appeared, in some way, behind standard shared derived characters: the last ones could be excluded, but the relationship remains the same.

Paleontology has long relied on assumptions about the genetic and developmental influences on skeletal variation. The last few decades of developmental genetics have elucidated the genetic pathways involved in making teeth and patterning the dentition. Quantitative genetic analyses have refined this genotype:phenotype map even more, especially for primates. We now have the ability to define dental traits with a fair degree of fidelity to the underlying genetic architecture; for example, the molar module component (MMC) and the premolar-molar module (PMM) that have been defined through quantitative genetic analyses. We leverage an extensive dataset of extant and extinct hominoid dental variation to explore how these two genetically patterned phenotypes have evolved through time. We assess MMC and PMM to test the hypothesis that these two traits reveal a more biologically informed taxonomy at the genus and species levels than do more traditional measurements. Our results indicate that MMC values for hominids fall into two categories and that Homo is derived compared with earlier taxa. We find a more variable, species-level pattern for PMM. These results, in combination with previous research, demonstrate that MMC reflects the phenotypic output of a more evolutionarily stable, or phylogenetically congruent, genetic mechanism, and PMM is a reflection of a more evolutionarily labile mechanism. These results suggest that the human lineage since the split with chimpanzees may not represent as much genus-level variation as has been inferred from traits whose etiologies are not understood.

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 P 4 and M 3 compared with the M 1 , 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., Competing Interests: Disclosure of competing interest The authors declare that there is no conflict of interest., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

The major histocompatibility complex (MHC) is one of the most gene-dense regions of the mammalian genome. Multiple genes within the human MHC (HLA) show extensive polymorphism, and currently, more than 26,000 alleles divided over 39 different genes are known. Nonhuman primate (NHP) species are grouped into great and lesser apes and Old and New World monkeys, and their MHC is studied mostly because of their important role as animal models in preclinical research or in connection with conservation biology purposes. The evolutionary equivalents of many of the HLA genes are present in NHP species, and these genes may also show abundant levels of polymorphism. This review is intended to provide a comprehensive comparison relating to the organization and polymorphism of human and NHP MHC regions., (© 2020 John Wiley & Sons Ltd.)

Objectives: The aim of this study is to understand whether the shape of three sub-regions of the mandibular corpus (the alveolar arch, corpus at M 1 and posterior symphysis) are useful for making taxonomic assessments at the genus and species levels in extant hominids., Materials and Methods: We use data taken from 3D surface scans of the mandibular corpus of seven extant hominid taxa: Gorilla gorilla gorilla, Gorilla beringei graueri, Homo sapiens, Pan paniscus, Pan troglodytes schweinfurthii, Pongo abelii, and Pongo pygmaeus pygmaeus to generate four shape variables: alveolar arch shape (AAS), corpus shape at M 1 (CSM 1 ), posterior symphysis shape at the midline (PSSM), and posterior symphysis shape (PSS). To ascertain how reliable each mandibular shape variable is for assessing taxonomy, we ran canonical discriminant and discriminant function analysis, reporting cross-validated results., Results: Using a combination of three mandibular corpus shape variables, 99% of specimens were classified correctly for genus-level analyses. A maximum of 100% of Pan specimens, 94% of Gorilla specimens and 96% of Pongo specimens were classified correctly at the species level when up to three mandibular shape variables were included in the analyses. When mandibular corpus variables were considered in isolation, posterior symphysis shape yielded the highest overall correct classification results., Discussion: The high taxonomic classification rates at both the genus and species level, using 3D surface data and advanced quantification techniques, show that the shape of the alveolar arch, corpus at M 1 and symphysis can distinguish extant hominid taxa. These findings have implications for assessing the taxonomy of extinct hominid specimens which preserve these mandibular sub-regions., (© 2020 Wiley Periodicals, Inc.)

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., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Introgressive hybridization results in the transfer of genetic material between species, often with fitness implications for the recipient species. The development of statistical methods for detecting the signatures of historical introgression in whole-genome data has been a major area of focus. Although existing techniques are able to identify the taxa that exchanged genes during introgression using a four-taxon system, most methods do not explicitly distinguish which taxon served as donor and which as recipient during introgression (i.e., polarization of introgression directionality). Existing methods that do polarize introgression are often only able to do so when there is a fifth taxon available and that taxon is sister to one of the taxa involved in introgression. Here, we present divergence-based introgression polarization (DIP), a method for polarizing introgression using patterns of sequence divergence across whole genomes, which operates in a four-taxon context. Thus, DIP can be applied to infer the directionality of introgression when additional taxa are not available. We use simulations to show that DIP can polarize introgression and identify potential sources of bias in the assignment of directionality, and we apply DIP to a well-described hominin introgression event., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Functional morphology of the atlas reflects multiple aspects of an organism's biology. More specifically, its shape indicates patterns of head mobility, while the size of its vascular foramina reflects blood flow to the brain. Anatomy and function of the early hominin atlas, and thus, its evolutionary history, are poorly documented because of a paucity of fossilized material. Meticulous excavation, cleaning and high-resolution micro-CT scanning of the StW 573 ('Little Foot') skull has revealed the most complete early hominin atlas yet found, having been cemented by breccia in its displaced and flipped over position on the cranial base anterolateral to the foramen magnum. Description and landmark-free morphometric analyses of the StW 573 atlas, along with other less complete hominin atlases from Sterkfontein (StW 679) and Hadar (AL 333-83), confirm the presence of an arboreal component in the positional repertoire of Australopithecus. Finally, assessment of the cross-sectional areas of the transverse foramina of the atlas and the left carotid canal in StW 573 further suggests there may have been lower metabolic costs for cerebral tissues in this hominin than have been attributed to extant humans and may support the idea that blood perfusion of these tissues increased over the course of hominin evolution.

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 ., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)

Oreopithecus bambolii (8.3-6.7 million years old) is the latest known hominoid from Europe, dating to approximately the divergence time of the Pan -hominin lineages. Despite being the most complete nonhominin hominoid in the fossil record, the O. bambolii skeleton IGF 11778 has been, for decades, at the center of intense debate regarding the species' locomotor behavior, phylogenetic position, insular paleoenvironment, and utility as a model for early hominin anatomy. Here we investigate features of the IGF 11778 pelvis and lumbar region based on torso preparations and supplemented by other O. bambolii material. We correct several crucial interpretations relating to the IGF 11778 anterior inferior iliac spine and lumbar vertebrae structure and identifications. We find that features of the early hominin Ardipithecus ramidus torso that are argued to have permitted both lordosis and pelvic stabilization during upright walking are not present in O. bambolii However, O. bambolii also lacks the complete reorganization for torso stiffness seen in extant great apes (i.e., living members of the Hominidae), and is more similar to large hylobatids in certain aspects of torso form. We discuss the major implications of the O. bambolii lower torso anatomy and how O. bambolii informs scenarios of hominoid evolution., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)

Reliable estimates of when hominin taxa originated and went extinct are central to addressing many paleoanthropological questions, including those relating to macroevolutionary patterns. The timing of hominin temporal ranges can be used to test chronological predictions generated from phylogenetic hypotheses. For example, hypotheses of phyletic ancestor-descendant relationships, based on morphological data, predict no temporal range overlap between the two taxa. However, a fossil taxon's observed temporal range is almost certainly underestimated due to the incompleteness of both the fossil record itself and its sampling, and this decreases the likelihood of observing temporal overlap. Here, we focus on a well-known and widely accepted early hominin lineage, Australopithecus anamensis-afarensis, and place 95% confidence intervals (CIs) on its origination and extinction dates. We do so to assess whether its temporal range is consistent with it being a phyletic descendant of Ardipithecus ramidus and/or a direct ancestor to the earliest claimed representative of Homo (i.e., Ledi-Geraru). We find that the last appearance of Ar. ramidus falls within the origination CI of Au. anamensis-afarensis, whereas the claimed first appearance of Homo postdates the extinction CI. These results are consistent with Homo evolving from Au. anamensis-afarensis, but temporal overlap between Ar. ramidus and Au. anamensis-afarensis cannot be rejected at this time. Though additional samples are needed, future research should extend our initial analyses to incorporate the uncertainties surrounding the range endpoints of Ar. ramidus and earliest Homo. Overall, our findings demonstrate the need for quantifying the uncertainty surrounding the appearances and disappearances of hominin taxa in order to better understand the timing of evolutionary events in our clade's history., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

The great apes play an important role as model organisms. They are our closest living relatives, allowing us to identify the genetic basis of phenotypic traits that we think of as characteristically human. However, the most significant asset of great apes as model organisms is that they share with humans most of their genetic makeup. This means that we can extend our vast knowledge of the human genome, its genes, and the associated phenotypes to these species. Comparative genomic studies of humans and apes thus reveal how very similar genomes react when exposed to different population genetic regimes. In this way, each species represents a natural experiment, where a genome highly similar to the human one, is differently exposed to the evolutionary forces of demography, population structure, selection, recombination, and admixture/hybridization. The initial sequencing of reference genomes for chimpanzee, orangutan, gorilla, the bonobo, each provided new insights and a second generation of sequencing projects has provided diversity data for all the great apes. In this chapter, we will outline some of the findings that population genomic analysis of great apes has provided, and how comparative studies have helped us understand how the fundamental forces in evolution have contributed to shaping the genomes and the genetic diversity of the great apes.

In paleoanthropological literature, the use of the term "mosaic" (mosaic evolution, mosaic trait, mosaic species, and so on) is becoming more and more frequent. In order to promote a clarification of the use of the concept in literature, we propose here a classification in three different meanings of the notion of mosaic in human evolution: 1) morphological (inter-specific and intra-specific) instability in a certain phase of a branched phylogeny; 2) multiple trajectories and versions of the same adaptive trait in a branched phylogeny; 3) the trait itself as a complex mosaic of sub-traits with different phylogenetic stories (as is the case in language). We argue that the relevance of such mosaic patterns needs a macro-evolutionary interpretation, which takes into consideration the interaction between general selective pressures (promoting different versions of the same adaptation) and a cladogenetic approach in which speciation played a crucial role, due to ecological instability, habitat fragmentation, and geographical dispersals in human evolution.

Objectives: The taxonomic status of isolated hominoid teeth from the Asian Pleistocene has long been controversial due to difficulties distinguishing between pongine and hominin molars given their high degree of morphometrical variation and overlap. Here, we combine nonmetric and geometric morphometric data to document a dental pattern that appears to be taxonomically diagnostic among Pongo. We focus on the protoconule, a cuspule of well-documented evolutionary history, as well as on shape differences of the mesial fovea of the upper molars., Materials and Methods: We examined 469 upper molars of eight hominid genera (Australopithecus, Paranthropus, Homo, Meganthropus, Sivapithecus, Pan, Gorilla, and Pongo), including representatives of Homo erectus and extinct and recent Pongo. Analyses were conducted at the enamel-dentine junction to overcome the limitations introduced by dental wear., Results: We found that a moderate or large protoconule is present in ~80% of Pleistocene and extant Pongo. Conversely, a moderate to pronounced protoconule in hominins, Meganthropus, and African great apes occurs in low frequencies (~0-20%). Canonical variate analyses for the mesial fovea show that Pleistocene and extant Pongo cluster together and are clearly differentiated from all other groups, except for Sivapithecus., Discussion: This study suggests that the protoconule and the shape of the mesial fovea in upper molars are useful features for the taxonomic identification of isolated hominid teeth. By identifying these new features, our results can contribute to the better understanding of hominoid evolutionary history and biogeography during the Asian Pleistocene. However, we emphasize that the reported features should be used in combination with other diagnostic variables for the most accurate taxonomic assessments., (© 2019 Wiley Periodicals, Inc.)

To evaluate the taxonomic position of the Neandertal and Homo erectus within the hominid clade, the variation among and within the hominid taxa was assessed based on the craniodental morphology and integrated with molecular analyses of the whole mt DNA genomes. Ordination and clustering of the Procrustes craniodental landmarks have showed a notable shape transformation from the earliest hominid species to the modern humans. Although levels of distinction between the analyzed taxa ( Homo, Pan, Gorilla , and Pongo ) are generally corresponding to probable expectations based on their taxonomic rank, few exceptions were found. Notably, the craniodental morphology of Homo erectus showed a greater dissimilarity to other Homo species, where it consistently overlapped or grouped with Pan species on all ordination plots and clustering. In addition, the direct link between European humans and Neandertals, which is well-characterized on all of the phylogenetic trees based on maximum parsimony and maximum likelihood methods, was not outlined in the morphologic-based clustering. Both morphological and molecular distances between Neandertal and modern humans were consistently greater than the distances among modern humans, however, the distances are still smaller than those between any two distinct species (so they are subspecies). The topology of the phylogenetic trees based on the whole mt DNA has shown a minor discrepancy with the results obtained from the craniodental morphologies.

Substantial differences among the pelves of anthropoids have been central to interpretations of the selection pressures that shaped extant hominoids, yet the evolution of the hominoid pelvis has been poorly understood due to the scarcity of fossil material. A recently discovered partial hipbone attributed to the 10 million-year-old fossil ape Rudapithecus hungaricus from Rudabánya, Hungary, differs from the hipbones of cercopithecids and earlier apes in functionally significant ways. Comparisons were made to extant and other fossil anthropoids using combination of non-landmark-based and linear metrics. Measurements were taken on 3D polygonal models of hipbones collected using laser scans. These metrics capture functionally relevant morphology given the incomplete preservation of the Rudapithecus specimen. This fossil displays features that reflect changes in spinal musculature and torso structure found only in extant great and lesser apes among hominoids. Rudapithecus has an expanded cranial acetabular lunate surface related to orthograde positional behaviors, a shallow acetabulum and relatively short ischium like orangutans and hylobatids. It displays evidence of moderately coronally-oriented iliac blades as in all extant apes and Ateles, and flaring iliac blade shape of siamangs and great apes, associated with some level of spinal stiffness. However, this fossil lacks the long lower ilium that characterizes chimpanzees, gorillas and orangutans, associated with their reduction of the number of lumbar vertebrae. The R. hungaricus pelvis demonstrates that the extreme elongation of the lower ilium seen in extant great apes does not necessarily accompany adaptation to orthograde posture and forelimb-dominated arboreal locomotion in hominoid evolution. Lower iliac elongation appears to have occurred independently in each lineage of extant great apes, supporting the hypothesis that the last common ancestor of Pan and Homo may have been unlike extant great apes in pelvic length and lower back morphology., (Copyright © 2019. Published by Elsevier Ltd.)

Mobile elements (MEs), making ∼50% of primate genomes, are known to be responsible for generating inter- and intra-species genomic variations and play important roles in genome evolution and gene function. Using a bioinformatics comparative genomics approach, we performed analyses of species-specific MEs (SS-MEs) in eight primate genomes from the families of Hominidae and Cercopithecidae, focusing on retrotransposons. We identified a total of 230,855 SS-MEs, with which we performed normalization based on evolutionary distances, and we also analyzed the most recent SS-MEs in these genomes. Comparative analysis of SS-MEs reveals striking differences in ME transposition among these primate genomes. Interesting highlights of our results include: 1) the baboon genome has the highest number of SS-MEs with a strong bias for SINEs, while the crab-eating macaque genome has a sustained extremely low transposition for all ME classes, suggesting the existence of a genome-wide mechanism suppressing ME transposition; 2) while SS-SINEs represent the dominant class in general, the orangutan genome stands out by having SS-LINEs as the dominant class; 3) the human genome stands out among the eight genomes by having the largest number of recent highly active ME subfamilies, suggesting a greater impact of ME transposition on its recent evolution; and 4) at least 33% of the SS-MEs locate to genic regions, including protein coding regions, presenting significant potentials for impacting gene function. Our study, as the first of its kind, demonstrates that mobile elements evolve quite differently among these primates, suggesting differential ME transposition as an important mechanism in primate evolution., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Many ideas have been proposed to explain the origin of bipedalism in hominins and suspension in great apes (hominids); however, fossil evidence has been lacking. It has been suggested that bipedalism in hominins evolved from an ancestor that was a palmigrade quadruped (which would have moved similarly to living monkeys), or from a more suspensory quadruped (most similar to extant chimpanzees) 1 . Here we describe the fossil ape Danuvius guggenmosi (from the Allgäu region of Bavaria) for which complete limb bones are preserved, which provides evidence of a newly identified form of positional behaviour-extended limb clambering. The 11.62-million-year-old Danuvius is a great ape that is dentally most similar to Dryopithecus and other European late Miocene apes. With a broad thorax, long lumbar spine and extended hips and knees, as in bipeds, and elongated and fully extended forelimbs, as in all apes (hominoids), Danuvius combines the adaptations of bipeds and suspensory apes, and provides a model for the common ancestor of great apes and humans.

Present-day African ecosystems serve as referential models for conceptualizing the environmental context of early hominin evolution, but the degree to which modern ecosystems are representative of those in the past is unclear. A growing body of evidence from eastern Africa's rich and well-dated late Cenozoic fossil record documents communities of large-bodied mammalian herbivores with ecological structures differing dramatically from those of the present day, implying that modern communities may not be suitable analogs for the ancient ecosystems of hominin evolution. To determine when and why the ecological structure of eastern Africa's herbivore faunas came to resemble those of the present, here we analyze functional trait changes in a comprehensive dataset of 305 modern and fossil herbivore communities spanning the last ∼7 Myr. We show that nearly all communities prior to ∼700 ka were functionally non-analog, largely due to a greater richness of non-ruminants and megaherbivores (species >1,000 kg). The emergence of functionally modern communities precedes that of taxonomically modern communities by 100,000s of years, and can be attributed to the combined influence of Plio-Pleistocene C 4 grassland expansion and pulses of aridity after ∼1 Ma. Given the disproportionate ecological impacts of large-bodied herbivores on factors such as vegetation structure, hydrology, and fire regimes, it follows that the vast majority of early hominin evolution transpired in the context of ecosystems that functioned unlike any today. Identifying how past ecosystems differed compositionally and functionally from those today is key to conceptualizing ancient African environments and testing ecological hypotheses of hominin evolution., Competing Interests: The authors declare no competing interest.

Background: Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. Here, in an effort to improve our understanding of the human microbiome, we compare gut microbiome composition and functional potential in 14 populations of humans from ten nations and 18 species of wild, non-human primates., Results: Contrary to expectations from host phylogenetics, we find that human gut microbiome composition and functional potential are more similar to those of cercopithecines, a subfamily of Old World monkey, particularly baboons, than to those of African apes. Additionally, our data reveal more inter-individual variation in gut microbiome functional potential within the human species than across other primate species, suggesting that the human gut microbiome may exhibit more plasticity in response to environmental variation compared to that of other primates., Conclusions: Given similarities of ancestral human habitats and dietary strategies to those of baboons, these findings suggest that convergent ecologies shaped the gut microbiomes of both humans and cercopithecines, perhaps through environmental exposure to microbes, diet, and/or associated physiological adaptations. Increased inter-individual variation in the human microbiome may be associated with human dietary diversity or the ability of humans to inhabit novel environments. Overall, these findings show that diet, ecology, and physiological adaptations are more important than host-microbe co-diversification in shaping the human microbiome, providing a key foundation for comparative analyses of the role of the microbiome in human biology and health.