Ghosts of extinct apes: genomic insights into African hominid evolution.

We are accustomed to regular announcements of new hominin fossils. There are now some 6000 hominin fossils, and up to 31 species. However, where are the announcements of African ape fossils? The answer is that there are almost none. Our knowledge of African ape evolution is based entirely on genomic analyses, which show that extant diversity is very young. This contrasts with the extensive and deep diversity of hominins known from fossils. Does this difference point to low and late diversification of ape lineages, or high rates of extinction? The comparative evolutionary dynamics of African hominids are central to interpreting living ape adaptations, as well as understanding the patterns of hominin evolution and the nature of the last common ancestor.

The Distribution and Biogenic Origins of Zinc in the Mineralised Tooth Tissues of Modern and Fossil Hominoids: Implications for Life History, Diet and Taphonomy.

Zinc is incorporated into enamel, dentine and cementum during tooth growth. This work aimed to distinguish between the processes underlying Zn incorporation and Zn distribution. These include different mineralisation processes, the physiological events around birth, Zn ingestion with diet, exposure to the oral environment during life and diagenetic changes to fossil teeth post-mortem. Synchrotron X-ray Fluorescence (SXRF) was used to map zinc distribution across longitudinal polished ground sections of both deciduous and permanent modern human, great ape and fossil hominoid teeth. Higher resolution fluorescence intensity maps were used to image Zn in surface enamel, secondary dentine and cementum, and at the neonatal line (NNL) and enamel-dentine-junction (EDJ) in deciduous teeth. Secondary dentine was consistently Zn-rich, but the highest concentrations of Zn (range 197-1743 ppm) were found in cuspal, mid-lateral and cervical surface enamel and were similar in unerupted teeth never exposed to the oral environment. Zinc was identified at the NNL and EDJ in both modern and fossil deciduous teeth. In fossil specimens, diagenetic changes were identified in various trace element distributions but only demineralisation appeared to markedly alter Zn distribution. Zinc appears to be tenacious and stable in fossil tooth tissues, especially in enamel, over millions of years.

Brain evolution and language: A comparative 3D analysis of Wernicke's area in extant and fossil hominids.

The spoken word does not fossilize. Despite this, scientists have long sought to unearth the origins of language within the human lineage. One of the lines of evidence they have pursued is functional brain areas, such as Broca's and Wernicke's areas, which are associated with speech production and comprehension, respectively. Sulcal layout of Broca's area clearly differs between humans and our closest living relatives, the chimpanzees, enabling its homolog in fossil hominins to be deemed more chimpanzee-like (i.e., closer to the ancestral form) or more human-like (i.e., derived form) with relative ease. Yet, no such differences have been found for Wernicke's area. This study compares sulcal and gyral organization of Wernicke's area across extant human brains (n=4), extant chimpanzee brains (n=5) and fossil hominin endocasts (n=4). Some chimpanzee brains had indications of leftward Wernicke's area asymmetry in the form of a shorter Sylvian fissure and/or caudal superior temporal gyral bulging in the left hemisphere. Overlap between the superior and middle temporal sulci in human but not chimpanzee brains may be due to a relatively larger Wernicke's area in humans. Fragmentation of the main body of the superior temporal sulcus exclusively in human left hemispheres was ascribed to a leftward Wernicke's area asymmetry in this species. Endocast examination found that, while Paranthropus robustus exhibit human-like overlap between the superior and middle temporal sulci, Australopithecus africanus do not, although they do exhibit chimpanzee-like caudal superior temporal gyral bulging. Such findings signal, albeit loosely, a more human-like Wernicke's area in Paranthropus than Australopithecus.

Applying dental microwear texture analysis to the living: Challenges and prospects.

OBJECTIVES: The food that people and animals consume leaves microscopic traces on teeth in predictable ways, and analyses of these markings-known as dental microwear analyses-allow us to reverse engineer the characteristics of diet. However, the microwear features of modern human diets are most often interpreted through the lens of ethnographic records. Given the subtle variation within human diets when compared to other species, we need better models of how foods and processing techniques produce marks on teeth. Here, we report on the second study to target the occlusal surface microwear of living human populations, and the first to target populations other than foragers. METHODS: We collected 150 dental impressions from five Kenyan communities: El Molo, Turkana (Kerio), Luhya (Webuye), Luhya (Port Victoria), and Luo (Port Victoria), representing a range of subsistence strategies and associated staple diets-fishing, pastoralism, and agriculture. Our results suggest that the occlusal microwear of these groups records differences in diet. However, biofilm obscured most of the molds obtained despite the steps taken to remove it, resulting in only 38 usable surfaces. RESULTS: Due to the biofilm problem and final sample size, the analysis did not have enough power to demonstrate the differences observed statistically. The results and problems encountered are here explained. CONCLUSIONS: Considering that in vivo studies of dental microwear texture analysis have the potential to increase our understanding of the association between patterns of dental microwear and complex, mixed human diets, resolution of the current pitfalls of the technique is critical.

Deciphering African late middle Pleistocene hominin diversity and the origin of our species.

The origin of Homo sapiens remains a matter of debate. The extent and geographic patterning of morphological diversity among Late Middle Pleistocene (LMP) African hominins is largely unknown, thus precluding the definition of boundaries of variability in early H. sapiens and the interpretation of individual fossils. Here we use a phylogenetic modelling method to predict possible morphologies of a last common ancestor of all modern humans, which we compare to LMP African fossils (KNM-ES 11693, Florisbad, Irhoud 1, Omo II, and LH18). Our results support a complex process for the evolution of H. sapiens, with the recognition of different, geographically localised, populations and lineages in Africa - not all of which contributed to our species' origin. Based on the available fossils, H. sapiens appears to have originated from the coalescence of South and, possibly, East-African source populations, while North-African fossils may represent a population which introgressed into Neandertals during the LMP.

Carbon and nitrogen isotopic signatures of hair, nail, and breath from tropical African human populations.

RATIONALE: Stable isotopic analyses are increasingly used to study the diets of past and present human populations. Yet, the carbon and nitrogen isotopic data of modern human diets collected so far are biased towards Europe and North America. Here, we address this gap by reporting on the dietary isotopic signatures of six tropical African communities: El Molo, Turkana (Kerio), Luhya (Webuye), Luhya (Port Victoria), and Luo (Port Victoria) from Kenya, and Baka from Cameroon; representing four subsistence strategies: fishing, pastoralism, agriculturalism, and hunter-gatherer. METHODS: We used an elemental analyser coupled in continuous-flow mode to an isotope ratio mass spectrometer to measure the carbon and nitrogen isotopic ratios of hair (n = 134) and nail (n = 80) and the carbon isotopic ratios of breath (n = 184) from these communities, as well as the carbon and nitrogen isotopic ratios of some food samples from the Kenyan communities. RESULTS: We expand on the known range of δ13 C values in human hair through the hunter-gatherer Baka, with a diet based on C3 plants, and through the agriculturalist Luhya (Webuye), with a diet based on C4 plants. In addition, we found that the consumption of fish from East African lakes is difficult to detect isotopically due to the combined effects of high nitrogen isotopic ratios of plants and the low nitrogen isotopic ratios of fish. Finally, we found that some of the communities studied are markedly changing their diets through increasing sedentism and urbanisation. CONCLUSIONS: Our findings contribute substantially to the understanding of the environmental, demographic, and economic dynamics that affect the dietary landscape of different tropical populations of Africa. These results highlight the importance of studying a broader sample of human populations and their diet, with a focus on their precise context - from both isotopic and more general anthropological perspectives.

Upper Paleolithic cultural diversity in the Iranian Zagros Mountains and the expansion of modern humans into Eurasia.

This paper aims to understand the cultural diversity among the first modern human populations in the Iranian Zagros and the implications of this diversity for evolutionary and ecological models of human dispersal through Eurasia. We use quantitative data and technotypological attributes combined with physiogeographic information to assess if the Zagros Upper Paleolithic (UP) developed locally from the Middle Paleolithic (MP), as well as to contextualize the variation in lithics from four UP sites of Warwasi, Yafteh, Pasangar, and Ghar-e Boof. Our results demonstrate (1) that the Zagros UP industries are intrusive to the region, and (2) that there is significant cultural diversity in the early UP across different Zagros habitat areas, and that this diversity clusters in at least three groups. We interpret this variation as parallel developments after the initial occupation of the region shaped by the relative geotopographical isolation of different areas of the Zagros, which would have favored different ecological adaptations. The greater similarity of lithic traditions and modes of production observed in the later phases of the UP across all sites indicates a marked increase in inter-group contact throughout the West-Central Zagros mountain chain. Based on the chronological and geographical patterns of Zagros UP variability, we propose a model of an initial colonization phase leading to the emergence of distinct local traditions, followed by a long phase of limited contact among these first UP groups. This has important implications for the origins of biological and cultural diversity in the early phases of modern human colonization of Eurasia. We suggest that the mountainous arc that extends from Anatolia to the Southern Zagros preserves the archaeological record of different population trajectories. Among them, by 40 ka, some would have been transient, whereas others would have left no living descendants. However, some would have led to longer term local traditions, including groups who share ancestry with modern Europeans and modern East/Southeast Asians.

Early human dispersals within the Americas.

Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning from Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans, including those from an Ancient Beringian individual and two morphologically distinct "Paleoamericans." We found evidence of rapid dispersal and early diversification that included previously unknown groups as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, as well as a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America.

Who were the Nataruk people? Mandibular morphology among late Pleistocene and early Holocene fisher-forager populations of West Turkana (Kenya).

Africa is the birthplace of the species Homo sapiens, and Africans today are genetically more diverse than other populations of the world. However, the processes that underpinned the evolution of African populations remain largely obscure. Only a handful of late Pleistocene African fossils (∼50-12 Ka) are known, while the more numerous sites with human fossils of early Holocene age are patchily distributed. In particular, late Pleistocene and early Holocene human diversity in Eastern Africa remains little studied, precluding any analysis of the potential factors that shaped human diversity in the region, and more broadly throughout the continent. These periods include the Last Glacial Maximum (LGM), a moment of extreme aridity in Africa that caused the fragmentation of population ranges and localised extinctions, as well as the 'African Humid Period', a moment of abrupt climate change and enhanced connectivity throughout Africa. East Africa, with its range of environments, may have acted as a refugium during the LGM, and may have played a critical biogeographic role during the heterogene`ous environmental recovery that followed. This environmental context raises a number of questions about the relationships among early Holocene African populations, and about the role played by East Africa in shaping late hunter-gatherer biological diversity. Here, we describe eight mandibles from Nataruk, an early Holocene site (∼10 Ka) in West Turkana, offering the opportunity of exploring population diversity in Africa at the height of the 'African Humid Period'. We use 3D geometric morphometric techniques to analyze the phenotypic variation of a large mandibular sample. Our results show that (i) the Nataruk mandibles are most similar to other African hunter-fisher-gatherer populations, especially to the fossils from Lothagam, another West Turkana locality, and to other early Holocene fossils from the Central Rift Valley (Kenya); and (ii) a phylogenetic connection may have existed between these Eastern African populations and some Nile Valley and Maghrebian groups, who lived at a time when a Green Sahara may have allowed substantial contact, and potential gene flow, across a vast expanse of Northern and Eastern Africa.

Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans.

Recent studies have reported evidence suggesting that portions of contemporary human genomes introgressed from archaic hominin populations went to high frequencies due to positive selection. However, no study to date has specifically addressed the postintrogression population dynamics of these putative cases of adaptive introgression. Here, for the first time, we specifically define cases of immediate adaptive introgression (iAI) in which archaic haplotypes rose to high frequencies in humans as a result of a selective sweep that occurred shortly after the introgression event. We define these cases as distinct from instances of selection on standing introgressed variation (SI), in which an introgressed haplotype initially segregated neutrally and subsequently underwent positive selection. Using a geographically diverse data set, we report novel cases of selection on introgressed variation in living humans and shortlist among these cases those whose selective sweeps are more consistent with having been the product of iAI rather than SI. Many of these novel inferred iAI haplotypes have potential biological relevance, including three that contain immune-related genes in West Siberians, South Asians, and West Eurasians. Overall, our results suggest that iAI may not represent the full picture of positive selection on archaically introgressed haplotypes in humans and that more work needs to be done to analyze the role of SI in the archaic introgression landscape of living humans.

Estimating mobility using sparse data: Application to human genetic variation.

Mobility is one of the most important processes shaping spatiotemporal patterns of variation in genetic, morphological, and cultural traits. However, current approaches for inferring past migration episodes in the fields of archaeology and population genetics lack either temporal resolution or formal quantification of the underlying mobility, are poorly suited to spatially and temporally sparsely sampled data, and permit only limited systematic comparison between different time periods or geographic regions. Here we present an estimator of past mobility that addresses these issues by explicitly linking trait differentiation in space and time. We demonstrate the efficacy of this estimator using spatiotemporally explicit simulations and apply it to a large set of ancient genomic data from Western Eurasia. We identify a sequence of changes in human mobility from the Late Pleistocene to the Iron Age. We find that mobility among European Holocene farmers was significantly higher than among European hunter-gatherers both pre- and postdating the Last Glacial Maximum. We also infer that this Holocene rise in mobility occurred in at least three distinct stages: the first centering on the well-known population expansion at the beginning of the Neolithic, and the second and third centering on the beginning of the Bronze Age and the late Iron Age, respectively. These findings suggest a strong link between technological change and human mobility in Holocene Western Eurasia and demonstrate the utility of this framework for exploring changes in mobility through space and time.

Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers.

Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. To investigate whether the contemporary HG strategy was already present in the Upper Paleolithic, we used complete genome sequences from Sunghir, a site dated to ~34,000 years before the present, containing multiple anatomically modern human individuals. We show that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that Upper Paleolithic social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.

Newly discovered Neanderthal remains from Shanidar Cave, Iraqi Kurdistan, and their attribution to Shanidar 5.

The Neanderthal remains from Shanidar Cave, excavated between 1951 and 1960, have played a central role in debates concerning diverse aspects of Neanderthal morphology and behavior. In 2015 and 2016, renewed excavations at the site uncovered hominin remains from the immediate area where the partial skeleton of Shanidar 5 was found in 1960. Shanidar 5 was a robust adult male estimated to have been aged over 40 years at the time of death. Comparisons of photographs from the previous and recent excavations indicate that the old and new remains were directly adjacent to one another, while the disturbed arrangement and partial crushing of the new fossils is consistent with descriptions and photographs of the older discoveries. The newly discovered bones include fragments of several vertebrae, a left hamate, part of the proximal left femur, a heavily crushed partial pelvis, and the distal half of the right tibia and fibula and associated talus and navicular. All these elements were previously missing from Shanidar 5, and morphological and metric data are consistent with the new elements belonging to this individual. A newly discovered partial left pubic symphysis indicates an age at death of 40-50 years, also consistent with the age of Shanidar 5 estimated previously. Thus, the combined evidence strongly suggests that the new finds can be attributed to Shanidar 5. Ongoing analyses of associated samples, including for sediment morphology, palynology, and dating, will therefore offer new evidence as to how this individual was deposited in the cave and permit new analyses of the skeleton itself and broader discussion of Neanderthal morphology and variation.

New evidence suggesting a dissociated etiology for cribra orbitalia and porotic hyperostosis.

OBJECTIVES: Porotic hyperostosis (PH), characterized by porotic lesions on the cranial vault, and cribra orbitalia (CO), a localized appearance of porotic lesions on the roof of the orbits, are relatively common osteological conditions. Their etiology has been the focus of several studies, and an association with anemia has long been suggested. Anemia often causes bone marrow hypertrophy or hyperplasia, leading to the expansion in trabecular or cranial diploic bone as a result of increased hematopoiesis. Hypertrophy and/or hyperplasia is often coupled with a disruption of the remodeling process of outer cortical bone, cranially and/or postcranially, leading to the externally visible porotic lesions reported in osteological remains. In this article, we investigate whether individuals with CO have increased thickness of the diploë, the common morphological direct effect of increased hematopoiesis, and thus test the relationship between the two conditions, as well as explore the type of anemia that underlie it. METHODS: An analysis of medical CT scans of a worldwide sample of 98 complete, young to middle-aged adult dry skulls from the Duckworth Collection was conducted on male and female cribrotic individuals (n = 23) and noncribrotic individuals (n = 75), all of whom lacked any evidence of porotic lesions on the vault. Measurements of total and partial cranial thickness were obtained by virtual landmark placement, using the Amira 5.4 software; all analyses were conducted in IBM SPSS 21. RESULTS: Cribriotic individuals have significantly thinner diploic bone and thicker outer and inner tables than noncribriotic individuals, contrary to the expected diploic expansion that would result from anemic conditions associated to bone marrow hypertrophy or hyperplasia. Additionally, individuals without CO and those with the condition have distinctive cranial thickness at particular locations across the skull and the severity to which CO is expressed also differentiates between those with mild and those with a moderate to severe form of the condition. CONCLUSIONS: Our results suggest a complex pattern of causality in relation to the pathologies that may lead to the formation of porotic lesions on the vault and the roof of the orbits. A form of anemia may be behind the osteological changes observed in PH and CO, but it is unlikely to be the same type of anemic condition that underlies both types of osteological lesions. We suggest that CO may be associated to anemias that lead to diploic bone hypocellularity and hypoplasia, such as those caused by anemia of chronic disease and, to a lesser extent, of renal failure, aplastic anemia, protein deficiency, and anemia of endocrine disorders, and not those that lead to bone marrow hypercellularity and hyperplasia and potential PH. This leads us to the conclusion that the terms PH and CO should be used to reflect different underlying conditions.

Major transitions in human evolution.

Evolutionary problems are often considered in terms of 'origins', and research in human evolution seen as a search for human origins. However, evolution, including human evolution, is a process of transitions from one state to another, and so questions are best put in terms of understanding the nature of those transitions. This paper discusses how the contributions to the themed issue 'Major transitions in human evolution' throw light on the pattern of change in hominin evolution. Four questions are addressed: (1) Is there a major divide between early (australopithecine) and later (Homo) evolution? (2) Does the pattern of change fit a model of short transformations, or gradual evolution? (3) Why is the role of Africa so prominent? (4) How are different aspects of adaptation-genes, phenotypes and behaviour-integrated across the transitions? The importance of developing technologies and approaches and the enduring role of fieldwork are emphasized.This article is part of the themed issue 'Major transitions in human evolution'.

The shaping of human diversity: filters, boundaries and transitions.

The evolution of modern humans was a complex process, involving major changes in levels of diversity through time. The fossils and stone tools that record the spatial distribution of our species in the past form the backbone of our evolutionary history, and one that allows us to explore the different processes-cultural and biological-that acted to shape the evolution of different populations in the face of major climate change. Those processes created a complex palimpsest of similarities and differences, with outcomes that were at times accelerated by sharp demographic and geographical fluctuations. The result is that the population ancestral to all modern humans did not look or behave like people alive today. This has generated questions regarding the evolution of human universal characters, as well as the nature and timing of major evolutionary events in the history of Homo sapiens The paucity of African fossils remains a serious stumbling block for exploring some of these issues. However, fossil and archaeological discoveries increasingly clarify important aspects of our past, while breakthroughs from genomics and palaeogenomics have revealed aspects of the demography of Late Quaternary Eurasian hominin groups and their interactions, as well as those between foragers and farmers. This paper explores the nature and timing of key moments in the evolution of human diversity, moments in which population collapse followed by differential expansion of groups set the conditions for transitional periods. Five transitions are identified (i) at the origins of the species, 240-200 ka; (ii) at the time of the first major expansions, 130-100 ka; (iii) during a period of dispersals, 70-50 ka; (iv) across a phase of local/regional structuring of diversity, 45-25 ka; and (v) during a phase of significant extinction of hunter-gatherer diversity and expansion of particular groups, such as farmers and later societies (the Holocene Filter), 15-0 ka.This article is part of the themed issue 'Major transitions in human evolution'.

Virtual ancestor reconstruction: Revealing the ancestor of modern humans and Neandertals.

The timing and geographic origin of the common ancestor of modern humans and Neandertals remain controversial. A poor Pleistocene hominin fossil record and the evolutionary complexities introduced by dispersals and regionalisation of lineages have fuelled taxonomic uncertainty, while new ancient genomic data have raised completely new questions. Here, we use maximum likelihood and 3D geometric morphometric methods to predict possible morphologies of the last common ancestor of modern humans and Neandertals from a simplified, fully resolved phylogeny. We describe the fully rendered 3D shapes of the predicted ancestors of humans and Neandertals, and assess their similarity to individual fossils or populations of fossils of Pleistocene age. Our results support models of an Afro-European ancestral population in the Middle Pleistocene (Homo heidelbergensis sensu lato) and further predict an African origin for this ancestral population.

The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent.

Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22-28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India.

Variation at diabetes- and obesity-associated Loci may mirror neutral patterns of human population diversity and diabetes prevalence in India.

South Asian populations harbor a high degree of genetic diversity, due in part to demographic history. Two studies on genome-wide variation in Indian populations have shown that most Indian populations show varying degrees of admixture between ancestral north Indian and ancestral south Indian components. As a result of this structure, genetic variation in India appears to follow a geographic cline. Similarly, Indian populations seem to show detectable differences in diabetes and obesity prevalence between different geographic regions of the country. We tested the hypothesis that genetic variation at diabetes- and obesity-associated loci may be potentially related to different genetic ancestries. We genotyped 2977 individuals from 61 populations across India for 18 SNPs in genes implicated in T2D and obesity. We examined patterns of variation in allele frequency across different geographical gradients and considered state of origin and language affiliation. Our results show that most of the 18 SNPs show no significant correlation with latitude, the geographic cline reported in previous studies, or by language family. Exceptions include KCNQ1 with latitude and THADA and JAK1 with language, which suggests that genetic variation at previously ascertained diabetes-associated loci may only partly mirror geographic patterns of genome-wide diversity in Indian populations.