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

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

Rare dental trait provides morphological evidence of archaic introgression in Asian fossil record.

The recently described Denisovan hemimandible from Xiahe, China [F. Chen et al., (2019) Nature 569, 409-412], possesses an unusual dental feature: a 3-rooted lower second molar. A survey of the clinical and bioarchaeological literature demonstrates that the 3-rooted lower molar is rare (less than 3.5% occurrence) in non-Asian Homo sapiens In contrast, its presence in Asian-derived populations can exceed 40% in China and the New World. It has long been thought that the prevalence of 3-rooted lower molars in Asia is a relatively late acquisition occurring well after the origin and dispersal of H. sapiens However, the presence of a 3-rooted lower second molar in this 160,000-y-old fossil hominin suggests greater antiquity for the trait. Importantly, it also provides morphological evidence of a strong link between archaic and recent Asian H. sapiens populations. This link provides compelling evidence that modern Asian lineages acquired the 3-rooted lower molar via introgression from Denisovans.

New fossils from Koobi Fora in northern Kenya confirm taxonomic diversity in early Homo.

Since its discovery in 1972 (ref. 1), the cranium KNM-ER 1470 has been at the centre of the debate over the number of species of early Homo present in the early Pleistocene epoch of eastern Africa. KNM-ER 1470 stands out among other specimens attributed to early Homo because of its larger size, and its flat and subnasally orthognathic face with anteriorly placed maxillary zygomatic roots. This singular morphology and the incomplete preservation of the fossil have led to different views as to whether KNM-ER 1470 can be accommodated within a single species of early Homo that is highly variable because of sexual, geographical and temporal factors, or whether it provides evidence of species diversity marked by differences in cranial size and facial or masticatory adaptation. Here we report on three newly discovered fossils, aged between 1.78 and 1.95 million years (Myr) old, that clarify the anatomy and taxonomic status of KNM-ER 1470. KNM-ER 62000, a well-preserved face of a late juvenile hominin, closely resembles KNM-ER 1470 but is notably smaller. It preserves previously unknown morphology, including moderately sized, mesiodistally long postcanine teeth. The nearly complete mandible KNM-ER 60000 and mandibular fragment KNM-ER 62003 have a dental arcade that is short anteroposteriorly and flat across the front, with small incisors; these features are consistent with the arcade morphology of KNM-ER 1470 and KNM-ER 62000. The new fossils confirm the presence of two contemporary species of early Homo, in addition to Homo erectus, in the early Pleistocene of eastern Africa.

Race and diversity in U.S. Biological Anthropology: A decade of AAPA initiatives.

Biological Anthropology studies the variation and evolution of living humans, non-human primates, and extinct ancestors and for this reason the field should be in an ideal position to attract scientists from a variety of backgrounds who have different views and experiences. However, the origin and history of the discipline, anecdotal observations, self-reports, and recent surveys suggest the field has significant barriers to attracting scholars of color. For a variety of reasons, including quantitative research that demonstrates that diverse groups do better science, the discipline should strive to achieve a more diverse composition. Here we discuss the background and underpinnings of the current and historical dearth of diversity in Biological Anthropology in the U.S. specifically as it relates to representation of minority and underrepresented minority (URM) (or racialized minority) scholars. We trace this lack of diversity to underlying issues of recruitment and retention in the STEM sciences generally, to the history of Anthropology particularly around questions of race-science, and to the absence of Anthropology at many minority-serving institutions, especially HBCUs, a situation that forestalls pathways to the discipline for many minority students. The AAPA Committee on Diversity (COD) was conceived as a means of assessing and improving diversity within the discipline, and we detail the history of the COD since its inception in 2006. Prior to the COD there were no systematic AAPA efforts to consider ethnoracial diversity in our ranks and no programming around questions of diversity and inclusion. Departmental survey data collected by the COD indicate that undergraduate majors in Biological Anthropology are remarkably diverse, but that the discipline loses these scholars between undergraduate and graduate school and systematically up rank. Our analysis of recent membership demographic survey data (2014 and 2017) shows Biological Anthropology to have less ethnoracial diversity than even the affiliated STEM disciplines of Biology and Anatomy; nearly 87% of AAPA members in the United States identify as white and just 7% as URM scholars. These data also suggest that the intersection of race and gender significantly influence scholarly representation. In response to these data, we describe a substantial body of programs that have been developed by the COD to improve diversity in our ranks. Through these programs we identify principal concerns that contribute to the loss of scholars of color from the discipline at different stages in their careers, propose other directions that programming for recruitment should take, and discuss the beginnings of how to develop a more inclusive discipline at all career stages.

Quantifying the relationship between bone and soft tissue measures within the rhesus macaques of Cayo Santiago.

OBJECTIVES: Interpretations of the primate and human fossil record often rely on the estimation of somatic dimensions from bony measures. Both somatic and skeletal variation have been used to assess how primates respond to environmental change. However, it is unclear how well skeletal variation matches and predicts soft tissue. Here, we empirically test the relationship between tissues by comparing somatic and skeletal measures using paired measures of pre- and post-mortem rhesus macaques from Cayo Santiago, Puerto Rico. MATERIALS AND METHODS: Somatic measurements were matched with skeletal dimensions from 105 rhesus macaque individuals to investigate paired signals of variation (i.e., coefficients of variation, sexual dimorphism) and bivariate codependence (reduced major axis regression) in measures of: (1) limb length; (2) joint breadth; and (3) limb circumference. Predictive models for the estimation of soft tissue dimensions from skeletons were built from Ordinary Least Squares regressions. RESULTS: Somatic and skeletal measurements showed statistically equivalent coefficients of variation and sexual dimorphism as well as high epiphyses-present ordinary least square (OLS) correlations in limb lengths (R2 >0.78, 0.82), joint breadths (R2 >0.74, 0.83) and, to a lesser extent, limb circumference (R2 >0.53, 0.68). CONCLUSION: Skeletal measurements are good substitutions for somatic values based on population signals of variation. OLS regressions indicate that skeletal correlates are highly predictive of somatic dimensions. The protocols and regression equations established here provide a basis for reliable reconstruction of somatic dimension from catarrhine fossils and validate our ability to compare or combine results of studies based on population data of either hard or soft tissue proxies.

Evolutionary and biomedical implications of sex differences in the primate brain transcriptome.

Humans exhibit sex differences in the prevalence of many neurodevelopmental disorders and neurodegenerative diseases. Here, we generated one of the largest multi-brain-region bulk transcriptional datasets for the rhesus macaque and characterized sex-biased gene expression patterns to investigate the translatability of this species for sex-biased neurological conditions. We identify patterns similar to those in humans, which are associated with overlapping regulatory mechanisms, biological processes, and genes implicated in sex-biased human disorders, including autism. We also show that sex-biased genes exhibit greater genetic variance for expression and more tissue-specific expression patterns, which may facilitate rapid evolution of sex-biased genes. Our findings provide insights into the biological mechanisms underlying sex-biased disease and support the rhesus macaque model for the translational study of these conditions.

Mechanical and morphometric approaches to body mass estimation in rhesus macaques: A test of skeletal variables.

OBJECTIVES: Estimation of body mass from skeletal metrics can reveal important insights into the paleobiology of archeological or fossil remains. The standard approach constructs predictive equations from postcrania, but studies have questioned the reliability of traditional measures. Here, we examine several skeletal features to assess their accuracy in predicting body mass. MATERIALS AND METHODS: Antemortem mass measurements were compared with common skeletal dimensions from the same animals postmortem, using 115 rhesus macaques (male: n = 43; female: n = 72). Individuals were divided into training (n = 58) and test samples (n = 57) to build and assess Ordinary Least Squares or multivariate regressions by residual sum of squares (RSS) and AIC weights. A leave-one-out approach was implemented to formulate the best fit multivariate models, which were compared against a univariate and a previously published catarrhine body-mass estimation model. RESULTS: Femur circumference represented the best univariate model. The best model overall was composed of four variables (femur, tibia and fibula circumference and humerus length). By RSS and AICw, models built from rhesus macaque data (RSS = 26.91, AIC = -20.66) better predicted body mass than did the catarrhine model (RSS = 65.47, AIC = 20.24). CONCLUSION: Body mass in rhesus macaques is best predicted by a 4-variable equation composed of humerus length and hind limb midshaft circumferences. Comparison of models built from the macaque versus the catarrhine data highlight the importance of taxonomic specificity in predicting body mass. This paper provides a valuable dataset of combined somatic and skeletal data in a primate, which can be used to build body mass equations for fragmentary fossil evidence.

The ontogeny of sexual dimorphism in free-ranging rhesus macaques.

Objective: Reconstructing the social lives of extinct primates is possible only through an understanding of the interplay between morphology, sexual selection pressures, and social behavior in extant species. Somatic sexual dimorphism is an important variable in primate evolution, in part because of the clear relationship between the strength and mechanisms of sexual selection and the degree of dimorphism. Here, we examine body size dimorphism across ontogeny in male and female rhesus macaques to assess whether it is primarily achieved via bimaturism as predicted by a polygynandrous mating system, faster male growth indicating polygyny, or both. Methods: We measured body mass in a cross-sectional sample of 364 free-ranging rhesus macaques from Cayo Santiago, Puerto Rico to investigate size dimorphism: 1) across the lifespan; and 2) as an outcome of sex-specific growth strategies, including: a) age of maturation; b) growth rate; and c) total growth duration, using regression models fit to sex-specific developmental curves. Results: Significant body size dimorphism was observed by prime reproductive age with males 1.51 times the size of females. Larger male size resulted from a later age of maturation (males: 6.8-7.8 years versus females: 5.5-6.5 years; logistic model) and elevated growth velocity through the pre-prime period (LOESS model). Though males grew to larger sizes overall, females maintained adult size for longer before senescence (quadratic model). Discussion: The ontogeny of size dimorphism in rhesus macaques is achieved by bimaturism and a faster male growth rate. Our results provide new data for understanding the development and complexities of primate dimorphism.

Multiregion transcriptomic profiling of the primate brain reveals signatures of aging and the social environment.

Aging is accompanied by a host of social and biological changes that correlate with behavior, cognitive health and susceptibility to neurodegenerative disease. To understand trajectories of brain aging in a primate, we generated a multiregion bulk (N = 527 samples) and single-nucleus (N = 24 samples) brain transcriptional dataset encompassing 15 brain regions and both sexes in a unique population of free-ranging, behaviorally phenotyped rhesus macaques. We demonstrate that age-related changes in the level and variance of gene expression occur in genes associated with neural functions and neurological diseases, including Alzheimer's disease. Further, we show that higher social status in females is associated with younger relative transcriptional ages, providing a link between the social environment and aging in the brain. Our findings lend insight into biological mechanisms underlying brain aging in a nonhuman primate model of human behavior, cognition and health.

Social connections predict brain structure in a multidimensional free-ranging primate society.

Reproduction and survival in most primate species reflects management of both competitive and cooperative relationships. Here, we investigated the links between neuroanatomy and sociality in free-ranging rhesus macaques. In adults, the number of social partners predicted the volume of the mid-superior temporal sulcus and ventral-dysgranular insula, implicated in social decision-making and empathy, respectively. We found no link between brain structure and other key social variables such as social status or indirect connectedness in adults, nor between maternal social networks or status and dependent infant brain structure. Our findings demonstrate that the size of specific brain structures varies with the number of direct affiliative social connections and suggest that this relationship may arise during development. These results reinforce proposed links between social network size, biological success, and the expansion of specific brain circuits.

Craniometric measures during development using MRI.

Developmental changes in brain volume and shape in infants, children, and adolescents were ascertained with MRI, using craniometric (linear brain) measures in 118 individuals, ages 1 postnatal week to 18.7years. Collected clinical data included age, sex, weight, height, body mass index, occipito-frontal circumference (OFC), and diagnosis prompting the MRI scan. Twenty craniometric measures were obtained to allow for the determination of specific ratios as well as sex and age-related changes in brain shape and size. Analysis of the cohort showed that OFC is larger today than 40years ago, likely related to a concomitant increase in body stature. The data indicated a wide variation in the maturational pattern of several specific craniometric ratios, which reflects changes in the volume and configuration of the brain with advancing age. The increases in brain volume and changes in brain shape were most dramatic during infancy, with continued minor escalations in volume and reshaping during childhood and adolescence. Sex differences existed both in brain volume and shape, as well as evidence of sexual dimorphism. Changes in cerebellar volume and shape lagged behind the corresponding changes in the cerebral hemispheres. These collective data in living developing individuals allow for comparisons of clinical or craniometric measures in distant and more recent humans.

Modern human origins: continuity, replacement, and masticatory robusticity in Australasia.

Morphological evidence for a Multiregional (MR) model of human origins is suggested by a series of "linking traits" seen in the crania of late Javanese Homo erectus from Ngandong and anatomically modern Australian crania. A few studies that consider the genetic, structural, or functional aspects of these regional traits suggest their appearance is heavily influenced not by shared phylogeny but by a common "strong" masticatory pattern. Using dental occlusal areas, external mandibular metrics, internal biomechanical properties of the mandibular corpus measured from CT scans, and nonmetric traits associated with the attachment of masticatory muscles, we test the hypothesis that Australians exhibit evidence of a "strong" masticatory pattern. We use a mixed-sex comparative human sample (n = 415) that includes precontact Alaskans from Point Hope and the Aleutian Islands, Californians, Peruvians, an urban forensic sample, and the late Pleistocene Afalou-Taforalt sample. In comparison with recent humans known to exhibit such patterns, Australian mandibles show none of the expected changes related to producing and dissipating heavy occlusal loads. This is true regardless of whether external or internal mandibular dimensions are considered, albeit Australians show large occlusal areas and relatively large section modulus indices. Thus, a prime functional argument proposed for the origin of some Australian regional features is not supported by these data.

Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques.

BACKGROUND: An individual's microbiome changes over the course of its lifetime, especially during infancy, and again in old age. Confounding factors such as diet and healthcare make it difficult to disentangle the interactions between age, health, and microbial changes in humans. Animal models present an excellent opportunity to study age- and sex-linked variation in the microbiome, but captivity is known to influence animal microbial abundance and composition, while studies of free-ranging animals are typically limited to studies of the fecal microbiome using samples collected non-invasively. Here, we analyze a large dataset of oral, rectal, and genital swabs collected from 105 free-ranging rhesus macaques (Macaca mulatta, aged 1 month-26 years), comprising one entire social group, from the island of Cayo Santiago, Puerto Rico. We sequenced 16S V4 rRNA amplicons for all samples. RESULTS: Infant gut microbial communities had significantly higher relative abundances of Bifidobacterium and Bacteroides and lower abundances of Ruminococcus, Fibrobacter, and Treponema compared to older age groups, consistent with a diet high in milk rather than solid foods. The genital microbiome varied widely between males and females in beta-diversity, taxonomic composition, and predicted functional profiles. Interestingly, only penile, but not vaginal, microbiomes exhibited distinct age-related changes in microbial beta-diversity, taxonomic composition, and predicted functions. Oral microbiome composition was associated with age, and was most distinctive between infants and other age classes. CONCLUSIONS: Across all three body regions, with notable exceptions in the penile microbiome, while infants were distinctly different from other age groups, microbiomes of adults were relatively invariant, even in advanced age. While vaginal microbiomes were exceptionally stable, penile microbiomes were quite variable, especially at the onset of reproductive age. Relative invariance among adults, including elderly individuals, is contrary to findings in humans and mice. We discuss potential explanations for this observation, including that age-related microbiome variation seen in humans may be related to changes in diet and lifestyle. Video abstract.

Climatic influences on the evolution of early Homo?

The nature of the human fossil record is less than ideal for the generation of precise correlations between environmental variables and patterns of evolution in specific lineages. Nonetheless, a critical look at what can and cannot be said from individual fossil morphology and the correlation of specific environmental proxies with specific hominin fossils may lead to a greater understanding of the degree of certainty with which we should embrace environmental hypotheses for the evolution of Homo. Climate shifts have been implicated in both the origin of the genus and its dispersal from Africa. Here, I consider three areas in which a climatic influence has been posited to explain evolutionary shifts in the genus Homo: the origin and dispersal of the genus from Africa; geography, climate and body size in early Homo, and the influence of climate-induced sea level rise on morphological isolation in H. erectus. Each of the data sets is far from ideal, and interpretations of each of the data sets are fraught with issues of equifinality. Of the three hypotheses discussed, the clearest link is seen between latitudinal variation (and presumably temperature) and body size in H. erectus. Similarly, climate-induced sea level change seems a reasonable isolating mechanism to explain the pattern of cranial variation in later Asian H. erectus, but the distribution could also reflect incompletely sampled clinal variation. Alternatively, only equivocal support is found for the influence of climate on the differentiation of H. erectus from H. habilis (as proxied by body/brain size scaling), and therefore the dispersal of the genus Homo cannot be as clearly linked to changes in body size and shape as it has been in the past. These preliminary data suggest that an emphasis on understanding local adaptation before looking at global (and specific) level change is critical to elucidating the importance of climatic factors on the evolution of the genus Homo.

Early Homo, plasticity and the extended evolutionary synthesis.

The Modern Synthesis led to fundamental advances in understandings of human evolution. For human palaeontology, a science that works from ancestral phenotypes (i.e. the fossil record), particularly important have been perspectives used to help understand the heritable aspects of phenotypes and how fossil individuals might then be aggregated into species, and relationships among these groups understood. This focus, coupled with the fragmentary nature of the fossil record, however, means that individual phenotypic variation is often treated as unimportant 'noise', rather than as a source of insight into population adaptation and evolutionary process. The emphasis of the extended evolutionary synthesis on plasticity as a source of phenotypic novelty, and the related question of the role of such variation in long-term evolutionary trends, focuses welcome attention on non-genetic means by which novel phenotypes are generated and in so doing provides alternative approaches to interpreting the fossil record. We review evidence from contemporary human populations regarding some of the aspects of adult phenotypes preserved in the fossil record that might be most responsive to non-genetic drivers, and we consider how these perspectives lead to alternate hypotheses for interpreting the fossil record of early genus Homo. We conclude by arguing that paying closer attention to the causes and consequences of intraspecific phenotypic variation in its own right, as opposed to as noise around a species mean, may inspire a new generation of hypotheses regarding species diversity in the Early Pleistocene and the foundations for dispersal and regional diversification in Homo erectus and its descendants.

Morphological variation in Homo erectus and the origins of developmental plasticity.

Homo erectus was the first hominin to exhibit extensive range expansion. This extraordinary departure from Africa, especially into more temperate climates of Eurasia, has been variously related to technological, energetic and foraging shifts. The temporal and regional anatomical variation in H. erectus suggests that a high level of developmental plasticity, a key factor in the ability of H. sapiens to occupy a variety of habitats, may also have been present in H. erectus. Developmental plasticity, the ability to modify development in response to environmental conditions, results in differences in size, shape and dimorphism across populations that relate in part to levels of resource sufficiency and extrinsic mortality. These differences predict not only regional variations but also overall smaller adult sizes and lower levels of dimorphism in instances of resource scarcity and high predator load. We consider the metric variation in 35 human and non-human primate 'populations' from known environmental contexts and 14 time- and space-restricted paleodemes of H. erectus and other fossil Homo Human and non-human primates exhibit more similar patterns of variation than expected, with plasticity evident, but in differing patterns by sex across populations. The fossil samples show less evidence of variation than expected, although H. erectus varies more than Neandertals.This article is part of the themed issue 'Major transitions in human evolution'.

Natural history of Homo erectus.

Our view of H. erectus is vastly different today than when Pithecanthropus erectus was described in 1894. Since its synonimization into Homo, views of the species and its distribution have varied from a single, widely dispersed, polytypic species ultimately ancestral to all later Homo, to a derived, regional isolate ultimately marginal to later hominin evolution. A revised chronostratigraphic framework and recent work bearing either directly or indirectly on reconstructions of life-history patterns are reviewed here and, together with a review of the cranial and postcranial anatomy of H. erectus, are used to generate a natural history of the species. Here I argue that H. erectus is a hominin, notable for its increased body size, that originates in the latest Pliocene/earliest Pleistocene of Africa and quickly disperses into Western and Eastern Asia. It is also an increasingly derived hominin with several regional morphs sustained by intermittent isolation, particularly in Southeast Asia. This view differs from several current views, most especially that which recognizes only a single hominin species in the Pleistocene, H. sapiens, and those which would atomize H. erectus into a multiplicity of taxa. Following Jolly ([2001] Yrbk Phys Anthropol 44:177-204), the regional morphs of H. erectus may be productively viewed as geographically replacing allotaxa, rather than as the focus of unresolvable species debates. Such a view allows us to focus on the adaptations and biology of local groups, including questions of biogeographic isolation and local adaptation. A number of issues remain unresolved, including the significance of diversity in size and shape in the early African and Georgian records.