The shaping of human diversity: filters, boundaries and transitions

Quantifying hominin morphological diversity at the end of the middle Pleistocene: Implications for the origin of Homo sapiens

OBJECTIVES

The Middle Pleistocene (MP) saw the emergence of new species of hominins: Homo sapiens in Africa, H. neanderthalensis, and possibly Denisovans in Eurasia, whose most recent common ancestor is thought to have lived in Africa around 600 ka ago. However, hominin remains from this period present a wide range of morphological variation making it difficult to securely determine their taxonomic attribution and their phylogenetic position within the Homo genus. This study proposes to reconsider the phenetic relationships between MP hominin fossils in order to clarify evolutionary trends and contacts between the populations they represent.

MATERIALS AND METHODS

We used a Geometric Morphometrics approach to quantify the morphological variation of the calvarium of controversial MP specimens from Africa and Eurasia by using a comparative sample that can be divided into 5 groups: H. ergaster, H. erectus, H. neanderthalensis, and H. sapiens, as well as individuals from current modern human populations. We performed a Generalized Procrustes Analysis, a Principal Component Analysis, and Multinomial Principal Component Logistic Regressions to determine the phenetic affinities of the controversial Middle Pleistocene specimens with the other groups.

RESULTS

MP African and Eurasian specimens represent several populations, some of which show strong affinities with H. neanderthalensis in Europe or H. sapiens in Africa, others presenting multiple affinities.

DISCUSSION

These MP populations might have contributed to the emergence of these two species in different proportions. This study proposes a new framework for the human evolutionary history during the MP.

Ancient DNA and deep population structure in sub-Saharan African foragers

Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa^1–4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations^3,5. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80–20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.

DNA analysis of 6 individuals from eastern and south-central Africa spanning the past approximately 18,000 years, and of 28 previously published ancient individuals, provides genetic evidence supporting hypotheses of increasing regionalization at the end of the Pleistocene.

Ostrich eggshell beads reveal 50,000-year-old social network in Africa

Humans evolved in a patchwork of semi-connected populations across Africa1,2; understanding when and how these groups connected is critical to interpreting our present-day biological and cultural diversity. Genetic analyses reveal that eastern and southern African lineages diverged sometime in the Pleistocene epoch, approximately 350-70 thousand years ago (ka)3,4; however, little is known about the exact timing of these interactions, the cultural context of these exchanges or the mechanisms that drove their separation. Here we compare ostrich eggshell bead variations between eastern and southern Africa to explore population dynamics over the past 50,000 years. We found that ostrich eggshell bead technology probably originated in eastern Africa and spread southward approximately 50-33 ka via a regional network. This connection breaks down approximately 33 ka, with populations remaining isolated until herders entered southern Africa after 2 ka. The timing of this disconnection broadly corresponds with the southward shift of the Intertropical Convergence Zone, which caused periodic flooding of the Zambezi River catchment (an area that connects eastern and southern Africa). This suggests that climate exerted some influence in shaping human social contact. Our study implies a later regional divergence than predicted by genetic analyses, identifies an approximately 3,000-kilometre stylistic connection and offers important new insights into the social dimension of ancient interactions.

Age of the oldest known Homo sapiens from eastern Africa

Efforts to date the oldest modern human fossils in eastern Africa, from Omo-Kibish1-3 and Herto4,5 in Ethiopia, have drawn on a variety of chronometric evidence, including 40Ar/39Ar ages of stratigraphically associated tuffs. The ages that are generally reported for these fossils are around 197 thousand years (kyr) for the Kibish Omo I3,6,7, and around 160-155 kyr for the Herto hominins5,8. However, the stratigraphic relationships and tephra correlations that underpin these estimates have been challenged6,8. Here we report geochemical analyses that link the Kamoya's Hominid Site (KHS) Tuff9, which conclusively overlies the member of the Omo-Kibish Formation that contains Omo I, with a major explosive eruption of Shala volcano in the Main Ethiopian Rift. By dating the proximal deposits of this eruption, we obtain a new minimum age for the Omo fossils of 233 ± 22 kyr. Contrary to previous arguments6,8, we also show that the KHS Tuff does not correlate with another widespread tephra layer, the Waidedo Vitric Tuff, and therefore cannot anchor a minimum age for the Herto fossils. Shifting the age of the oldest known Homo sapiens fossils in eastern Africa to before around 200 thousand years ago is consistent with independent evidence for greater antiquity of the modern human lineage10.

Geometric morphometric variability in the supraorbital and orbital region of Middle Pleistocene hominins: Implications for the taxonomy and evolution of later Homo

This study assessed variation in the supraorbital and orbital region of the Middle Pleistocene hominins (MPHs), sometimes called Homo heidelbergensis s.l., to test whether it matched the expectations of intraspecific variation. The morphological distinctiveness and relative variation of this region, which is relatively well represented in the hominin fossil record, was analyzed quantitatively in a comparative taxonomic framework. Coordinates of 230 3D landmarks (20) and sliding semilandmarks (210) were collected from 704 specimens from species of Homo, Australopithecus, Paranthropus, Gorilla, Pan, Papio, and Macaca. Results showed that the MPHs had expected levels of morphological distinctiveness and intragroup and intergroup variation in supraorbital and orbital morphology, relative to commonly recognized non-hominin catarrhine species. However, the Procrustes distances between this group and H. sapiens were significantly higher than expected for two closely related catarrhine species. Furthermore, this study showed that variation within the MPH could be similarly well contained within existing hypodigms of H. sapiens, H. neanderthalensis, and H. erectus s.l. Although quantitative assessment of supraorbital and orbital morphology did not allow differentiation between taxonomic hypotheses in later Homo, it could be used to test individual taxonomic affiliation and identify potentially anomalous individuals. This study confirmed a complicated pattern of supraorbital and orbital morphology in the MPH fossil record and raises further questions over our understanding of the speciation of H. sapiens and H. neanderthalensis and taxonomic diversity in later Homo.

Human burials at the Kisese II rockshelter, Tanzania

OBJECTIVES

The Late Pleistocene and early Holocene in eastern Africa are associated with complex evolutionary and demographic processes that contributed to the population variability observed in the region today. However, there are relatively few human skeletal remains from this time period. Here we describe six individuals from the Kisese II rockshelter in Tanzania that were excavated in 1956, present a radiocarbon date for one of the individuals, and compare craniodental morphological diversity among eastern African populations.

MATERIALS AND METHODS

This study used standard biometric analyses to assess the age, sex, and stature of the Kisese II individuals. Eastern African craniodental morphological variation was assessed using measures of dental size and a subset of Howells' cranial measurements for the Kisese II individuals as well as early Holocene, early pastoralist, Pastoral Neolithic, and modern African individuals.

RESULTS

Our results suggest a minimum of six individuals from the Kisese II collections with two adults and four juveniles. While the dating for most of the burials is uncertain, one individual is directly radiocarbon dated to ~7.1 ka indicating that at least one burial is early Holocene in age. Craniodental metric comparisons indicate that the Kisese II individuals extend the amount of human morphological diversity among Holocene eastern Africans.

CONCLUSIONS

Our findings contribute to a growing body of evidence that Late Pleistocene and early Holocene eastern Africans exhibited relatively high amounts of morphological diversity. However, the Kisese II individuals suggest morphological similarity at localized sites potentially supporting increased regionalization during the early Holocene.

Small body size phenotypes among Middle and Later Stone Age Southern Africans

Modern humans originated between 300 and 200 ka in structured populations throughout Africa, characterized by regional interaction and diversity. Acknowledgment of this complex Pleistocene population structure raises new questions about the emergence of phenotypic diversity. Holocene Southern African Later Stone Age (LSA) skeletons and descendant Khoe-San peoples have small adult body sizes that may reflect long-term adaptation to the Cape environment. Pleistocene Southern African adult body sizes are not well characterized, but some postcranial elements are available. The most numerous Pleistocene postcranial skeletal remains come from Klasies River Mouth on the Southern Cape coast of South Africa. We compare the morphology of these skeletal elements with globally sampled Holocene groups encompassing diverse adult body sizes and shapes (n = 287) to investigate whether there is evidence for phenotypic patterning. The adult Klasies River Mouth bones include most of a lumbar vertebra, and portions of a left clavicle, left proximal radius, right proximal ulna, and left first metatarsal. Linear dimensions, shape characteristics, and cross-sectional geometric properties of the Klasies River Mouth elements were compared using univariate and multivariate methods. Between-group principal component analyses group Klasies River Mouth elements, except the proximal ulna, with LSA Southern Africans. The similarity is driven by size. Klasies River Mouth metatarsal cross-sectional geometric properties indicate similar torsional and compressive strength to those from LSA Southern Africans. Phenotypic expressions of small-bodied adult morphology in Marine Isotope Stages 5 and 1 suggest this phenotype may represent local convergent adaptation to life in the Cape.

Biocultural diversity in Late Pleistocene/Early Holocene Africa: Olduvai Hominid 1 (Tanzania) biological affinity and intentional body modification

OBJECTIVES

The dentition of Olduvai Hominid 1 (OH1) exhibits an anomalous pattern of dental wear that was originally attributed to either intentional cultural modification (filing) or plant processing behaviors. A differential diagnosis of the wear and assessment of the biological affinity of OH1 is presented.

MATERIALS AND METHODS

Macroscopic and microscopic observations of all labial and buccal tooth surfaces were undertaken to assess wear patterns. A multivariate analysis of mandibular morphology of OH1 compared to other Late Pleistocene, Holocene, and recent modern humans was used to ascertain biological affinity.

RESULTS

The morphological variation of the OH1 mandible is closely aligned with variation in penecontemporaneous fossils from Africa and outside that of recent humans. The concave wear facets exposing dentin on the labial surfaces of all three preserved mandibular incisors is confirmed. Substantial loss of labial/buccal surfaces was documented on the surfaces of all in situ maxillary and mandibular canines, premolars, and molars ranging from distinct facets with well-defined edges, to blunting or "polishing" around areas of maximum buccal curvature. The wear on both the anterior and postcanine teeth closely resemble that caused by adornments ("labrets") worn in lower-lip and buccal facial piercings known from bioarchaeological and ethnographic contexts. The wear pattern suggests that the OH1 wore three facial piercings-two buccal/lateral and a medial one in the lower lip.

DISCUSSION

Our findings suggest that the expression of social identities through intentional body modification is more diverse than previously documented elsewhere in Africa during the Late Pleistocene (i.e., ablation) and Early Holocene (i.e., ablation, chipping, and filing).

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.

Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history

OBJECTIVES

Modern humans are thought to have interbred with Neanderthals in the Near East soon after modern humans dispersed out of Africa. This introgression event likely took place in either the Levant or southern Arabia depending on the dispersal route out of Africa that was followed. In this study, we compare Neanderthal introgression in contemporary Levantine and southern Arabian populations to investigate Neanderthal introgression and to study Near Eastern population history.

MATERIALS AND METHODS

We analyzed genotyping data on >400,000 autosomal SNPs from seven Levantine and five southern Arabian populations and compared these data to those from populations from around the world including Neanderthal and Denisovan genomes. We used f₄ and D statistics to estimate and compare levels of Neanderthal introgression between Levantine, southern Arabian, and comparative global populations. We also identified 1,581 putative Neanderthal-introgressed SNPs within our dataset and analyzed their allele frequencies as a means to compare introgression patterns in Levantine and southern Arabian genomes.

RESULTS

We find that Levantine and southern Arabian populations have similar levels of Neanderthal introgression to each other but lower levels than other non-Africans. Furthermore, we find that introgressed SNPs have very similar allele frequencies in the Levant and southern Arabia, which indicates that Neanderthal introgression is similarly distributed in Levantine and southern Arabian genomes.

DISCUSSION

We infer that the ancestors of contemporary Levantine and southern Arabian populations received Neanderthal introgression prior to separating from each other and that there has been extensive gene flow between these populations.

Clarifying distinct models of modern human origins in Africa

Accumulating genomic, fossil and archaeological data from Africa have led to a renewed interest in models of modern human origins. However, such discussions are often discipline-specific, with limited integration of evidence across the different fields. Further, geneticists typically require explicit specification of parameters to test competing demographic models, but these have been poorly outlined for some scenarios. Here, we describe four possible models for the origins of Homo sapiens in Africa based on published literature from paleoanthropology and human genetics. We briefly outline expectations for data patterns under each model, with a special focus on genetic data. Additionally, we present schematics for each model, doing our best to qualitatively describe demographic histories for which genetic parameters can be specifically attached. Finally, it is our hope that this perspective provides context for discussions of human origins in other manuscripts presented in this special issue.

Harnessing ancient genomes to study the history of human adaptation

The past several years have witnessed an explosion of successful ancient human genome-sequencing projects, with genomic-scale ancient DNA data sets now available for more than 1,100 ancient human and archaic hominin (for example, Neandertal) individuals. Recent 'evolution in action' analyses have started using these data sets to identify and track the spatiotemporal trajectories of genetic variants associated with human adaptations to novel and changing environments, agricultural lifestyles, and introduced or co-evolving pathogens. Together with evidence of adaptive introgression of genetic variants from archaic hominins to humans and emerging ancient genome data sets for domesticated animals and plants, these studies provide novel insights into human evolution and the evolutionary consequences of human behaviour that go well beyond those that can be obtained from modern genomic data or the fossil and archaeological records alone.

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'.

Mosaic evolution and the pattern of transitions in the hominin lineage

Humans are uniquely unique, in terms of the extreme differences between them and other living organisms, and the impact they are having on the biosphere. The evolution of humans can be seen, as has been proposed, as one of the major transitions in evolution, on a par with the origins of multicellular organisms or the eukaryotic cell (Maynard Smith & Szathmáry 1997 Major transitions in evolution). Major transitions require the evolution of greater complexity and the emergence of new evolutionary levels or processes. Does human evolution meet these conditions? I explore the diversity of evidence on the nature of transitions in human evolution. Four levels of transition are proposed-baseline, novel taxa, novel adaptive zones and major transitions-and the pattern of human evolution considered in the light of these. The primary conclusions are that changes in human evolution occur continuously and cumulatively; that novel taxa and the appearance of new adaptations are not clustered very tightly in particular periods, although there are three broad transitional phases (Pliocene, Plio-Pleistocene and later Quaternary). Each phase is distinctive, with the first based on ranging and energetics, the second on technology and niche expansion, and the third on cognition and cultural processes. I discuss whether this constitutes a 'major transition' in the context of the evolutionary processes more broadly; the role of behaviour in evolution; and the opportunity provided by the rich genetic, phenotypic (fossil morphology) and behavioural (archaeological) record to examine in detail major transitions and the microevolutionary patterns underlying macroevolutionary change. It is suggested that the evolution of the hominin lineage is consistent with a mosaic pattern of change.This article is part of the themed issue 'Major transitions in human evolution'.

Network analysis of the hominin origin of Herpes Simplex virus 2 from fossil data

Herpes simplex virus 2 (HSV2) is a human herpesvirus found worldwide that causes genital lesions and more rarely causes encephalitis. This pathogen is most common in Africa, and particularly in central and east Africa, an area of particular significance for the evolution of modern humans. Unlike HSV1, HSV2 has not simply co-speciated with humans from their last common ancestor with primates. HSV2 jumped the species barrier between 1.4 and 3 MYA, most likely through intermediate but unknown hominin species. In this article, we use probability-based network analysis to determine the most probable transmission path between intermediate hosts of HSV2, from the ancestors of chimpanzees to the ancestors of modern humans, using paleo-environmental data on the distribution of African tropical rainforest over the last 3 million years and data on the age and distribution of fossil species of hominin present in Africa between 1.4 and 3 MYA. Our model identifies Paranthropus boisei as the most likely intermediate host of HSV2, while Homo habilis may also have played a role in the initial transmission of HSV2 from the ancestors of chimpanzees to P.boisei.