Divergence-time estimates for hominins provide insight into encephalization and body mass trends in human evolution

The genetic architecture of and evolutionary constraints on the human pelvic form

Human pelvic evolution following the human-chimpanzee divergence is thought to result in an obstetrical dilemma, a mismatch between large infant brains and narrowed female birth canals, but empirical evidence has been equivocal. By using deep learning on 31,115 dual-energy x-ray absorptiometry scans from UK Biobank, we identified 180 loci associated with seven highly heritable pelvic phenotypes. Birth canal phenotypes showed sex-specific genetic architecture, aligning with reproductive function. Larger birth canals were linked to slower walking pace and reduced back pain but increased hip osteoarthritis risk, whereas narrower birth canals were associated with reduced pelvic floor disorder risk but increased obstructed labor risk. Lastly, genetic correlation between birth canal and head widths provides evidence of coevolution between the human pelvis and brain, partially mitigating the dilemma.

Evolution of long scalp hair in humans

The ability to grow long scalp hair is a distinct human characteristic. It probably originally evolved to aid in cooling the sun-exposed head, although the genetic determinants of long hair are largely unknown. Despite ancestral variations in hair growth, long scalp hair is common to all extant human populations, which suggests its emergence before or concurrently with the emergence of anatomically modern humans (AMHs), approximately 300 000 years ago. Long scalp hair in AMHs was also a trait that was selected because it conveyed essential signals related to an individual's age, sexual maturity, health and social status. Biologically, hair length is primarily determined by the amount of time that a hair follicle spends in the active growth phase (anagen). While anagen duration is typically tightly regulated in most mammals, the inherent ability of a hair follicle to continuously recruit new dividing progenitors to its base, where hair fibre is generated, theoretically removes limits on maximal anagen duration. We propose a model wherein hair cycle progression into and out of anagen is regulated by evolutionary malleable molecular checkpoints. Several animal species and domesticated animal breeds display long body hair, which suggests that extremely long scalp hair in humans emerged via attenuation of an existing out-of-anagen checkpoint mechanism rather than via a newly evolved molecular programme. Studying congenital and somatic mosaicism conditions featuring altered hair length could potentially unveil the currently unknown molecular basis underlying this human trait.

The morphology of the oval window in Paranthropus robustus compared to humans and other modern primates

The oval window (OW) is an opening connecting the inner and middle ear. Its area has been shown to consistently scale with body mass (BM) in primates, and has been used alongside semi-circular canal (SCC) size to differentiate Homo sapiens and fossil hominins, including Paranthropus robustus. However, while the morphology of other inner ear elements, such as cochlea and SCCs, has been extensively studied in primates, OW shape has received little attention. In this study, we assess OW morphological variability in extant primates, and compare P. robustus to extant hominids. The potential of OW size to predict BM is also assessed. For this, measurements were performed on 3D scans from extant primate species and of P. robustus from the sites of Kromdraai, Swartkrans, and Drimolen. Size was assessed using perimeter (OWP), area (OWA), and centroid size (OWCS). Shape was assessed using geometric morphometric methods. The OW has no sexual dimorphism; there is no size difference between juveniles and adults, but there is a slight shape difference between human juveniles and adults, with a seemingly opposite ontogenetic trajectory compared to other primates. P. robustus has an intermediary OW shape between apes and humans, with more ape-like specimens from Kromdraai and more human-like ones from Drimolen. Overall, OW morphology discriminates primate species well enough, especially H. sapiens. BM is well explained by OWA, but OWA is not reliable as a BM proxy due to high prediction errors. Nonetheless, the OWA of P. robustus suggests a BM close to that of a chimpanzee.

Hominin brain size increase has emerged from within-species encephalization

The fact that rapid brain size increase was clearly a key aspect of human evolution has prompted many studies focusing on this phenomenon, and many suggestions as to the underlying evolutionary patterns and processes. No study to date has however separated out the contributions of change through time within vs. between hominin species while simultaneously incorporating effects of body size. Using a phylogenetic approach never applied before to paleoanthropological data, we show that relative brain size increase across ~7 My of hominin evolution arose from increases within individual species which account for an observed overall increase in relative brain size. Variation among species in brain size after accounting for this effect is associated with body mass differences but not time. In addition, our analysis also reveals that the within-species trend escalated in more recent lineages, implying an overall pattern of accelerating relative brain size increase through time.

The allometry of brain size in Euarchontoglires: clade-specific patterns and their impact on encephalization quotients

The timing and nature of evolutionary shifts in the relative brain size of Primates have been extensively studied. Less is known, however, about the scaling of the brain-to-body size in their closest living relatives, i.e., among other members of Euarchontoglires (Dermoptera, Scandentia, Lagomorpha, Rodentia). Ordinary least squares (OLS), reduced major axis (RMA), and phylogenetic generalized least squares (PGLS) regressions were fitted to the largest euarchontogliran data set of brain and body mass, comprising 715 species. Contrary to previous inferences, lagomorph brain sizes (PGLS slope = 0.465; OLS slope = 0.593) scale relative to body mass similarly to rodents (PGLS = 0.526; OLS = 0.638), and differently than primates (PGLS = 0.607; OLS = 0.794). There is a shift in the pattern of the scaling of the brain in Primates, with Strepsirrhini occupying an intermediate stage similar to Scandentia but different from Rodentia and Lagomorpha, while Haplorhini differ from all other groups in the OLS and RMA analyses. The unique brain-body scaling relationship of Primates among Euarchontoglires illustrates the need for clade-specific metrics for relative brain size (i.e., encephalization quotients; EQs) for more restricted taxonomic entities than Mammalia. We created clade-specific regular and phylogenetically adjusted EQ equations at superordinal, ordinal, and subordinal levels. When using fossils as test cases, our results show that generalized mammalian equations underestimate the encephalization of the stem lagomorph Megalagus turgidus in the context of lagomorphs, overestimate the encephalization of the stem primate Microsyops annectens and the early euprimate Necrolemur antiquus, but provide similar EQ values as our new strepsirrhine-specific EQ when applied to the early euprimate Adapis parisiensis.

Diversity-dependent speciation and extinction in hominins

The search for drivers of hominin speciation and extinction has tended to focus on the impact of climate change. Far less attention has been paid to the role of interspecific competition. However, research across vertebrates more broadly has shown that both processes are often correlated with species diversity, suggesting an important role for interspecific competition. Here we ask whether hominin speciation and extinction conform to the expected patterns of negative and positive diversity dependence, respectively. We estimate speciation and extinction rates from fossil occurrence data with preservation variability priors in a validated Bayesian framework and test whether these rates are correlated with species diversity. We supplement these analyses with calculations of speciation rate across a phylogeny, again testing whether these are correlated with diversity. Our results are consistent with clade-wide diversity limits that governed speciation in hominins overall but that were not quite reached by the Australopithecus and Paranthropus subclade before its extinction. Extinction was not correlated with species diversity within the Australopithecus and Paranthropus subclade or within hominins overall; this is concordant with climate playing a greater part in hominin extinction than speciation. By contrast, Homo is characterized by positively diversity-dependent speciation and negatively diversity-dependent extinction-both exceedingly rare patterns across all forms of life. The genus Homo expands the set of reported associations between diversity and macroevolution in vertebrates, underscoring that the relationship between diversity and macroevolution is complex. These results indicate an important, previously underappreciated and comparatively unusual role of biotic interactions in Homo macroevolution, and speciation in particular. The unusual and unexpected patterns of diversity dependence in Homo speciation and extinction may be a consequence of repeated Homo range expansions driven by interspecific competition and made possible by recurrent innovations in ecological strategies. Exploring how hominin macroevolution fits into the general vertebrate macroevolutionary landscape has the potential to offer new perspectives on longstanding questions in vertebrate evolution and shed new light on evolutionary processes within our own lineage.

Genomic Diversity in the Endosymbiotic Bacteria of Human Head Lice

Insects have repeatedly forged symbioses with heritable microbes, gaining novel traits. For the microbe, the transition to symbioses can lead to the degeneration of the symbiont's genome through transmission bottlenecks, isolation, and the loss of DNA repair enzymes. However, some insect-microbial symbioses have persisted for millions of years, suggesting that natural selection slows genetic drift and maintains functional consistency between symbiont populations. By sampling in multiple countries, we examine genomic diversity within a symbiont species, a heritable symbiotic bacterium found only in human head lice. We find that human head louse symbionts contain genetic diversity that appears to have arisen contemporaneously with the appearance of anatomically modern humans within Africa and/or during the colonization of Eurasia by humans. We predict that the observed genetic diversity underlies functional differences in extant symbiont lineages, through the inactivation of genes involved in symbiont membrane construction. Furthermore, we find evidence of additional gene losses prior to the appearance of modern humans, also impacting the symbiont membrane. From this, we conclude that symbiont genome degeneration is proceeding, via gene inactivation and subsequent loss, in human head louse symbionts, while genomic diversity is maintained. Collectively, our results provide a look into the genomic diversity within a single symbiont species and highlight the shared evolutionary history of humans, lice, and bacteria.

Evolutionary History of Periodontitis and the Oral Microbiota—Lessons for the Future

Purpose of Review

Currently, periodontal disease is the sixth most prevalent disease in the world. Emerging evidence suggests the possibility of pre-historic humans having relatively low occurrences of oral diseases, particularly periodontitis when compared to modern humans. In this review, we look back into the history of Homo sapiens and explore the emerging scientific literature to discuss the evolution of the human oral microbiota and the prevalence of periodontitis from pre-historic to modern times.

Recent Findings

Most of the scientific literature points to a more health-associated, eubiotic oral microbiota and a seemingly lower prevalence of periodontitis in pre-historic humans compared to modern times. The oral microbiome has evolved along with humans. Humans of the contemporary era are exposed to a far greater number of risk factors for periodontal disease. Also, major lifestyle changes induced by the agricultural revolution and the industrial revolution have led to the development of a more dysbiotic oral microbiota and a rise in the prevalence of periodontitis in modern humans.

Summary

An understanding of the prevalence of periodontitis across human history, the evolution of the oral microbiota, and the factors that influenced its nature and complexity helps identify and modify the disease-associated lifestyle factors acquired through modernization to manage the common worldwide problem of periodontitis.

The Genome of Plasmodium gonderi: Insights into the Evolution of Human Malaria Parasites

Plasmodium species causing malaria in humans are not monophyletic, sharing common ancestors with nonhuman primate parasites. Plasmodium gonderi is one of the few known Plasmodium species infecting African old-world monkeys that are not found in apes. This study reports a de novo assembled P. gonderi genome with complete chromosomes. The P. gonderi genome shares codon usage, syntenic blocks, and other characteristics with the human parasites Plasmodium ovale s.l. and Plasmodium malariae, also of African origin, and the human parasite Plasmodium vivax and species found in nonhuman primates from Southeast Asia. Using phylogenetically aware methods, newly identified syntenic blocks were found enriched with conserved metabolic genes. Regions outside those blocks harbored genes encoding proteins involved in the vertebrate host-Plasmodium relationship undergoing faster evolution. Such genome architecture may have facilitated colonizing vertebrate hosts. Phylogenomic analyses estimated the common ancestor between P. vivax and an African ape parasite P. vivax-like, within the Asian nonhuman primates parasites clade. Time estimates incorporating P. gonderi placed the P. vivax and P. vivax-like common ancestor in the late Pleistocene, a time of active migration of hominids between Africa and Asia. Thus, phylogenomic and time-tree analyses are consistent with an Asian origin for P. vivax and an introduction of P. vivax-like into Africa. Unlike other studies, time estimates for the clade with Plasmodium falciparum, the most lethal human malaria parasite, coincide with their host species radiation, African hominids. Overall, the newly assembled genome presented here has the quality to support comparative genomic investigations in Plasmodium.

The estimation and evolution of hominin body mass

Body mass is a critical variable in many hominin evolutionary studies, with implications for reconstructing relative brain size, diet, locomotion, subsistence strategy, and social organization. We review methods that have been proposed for estimating body mass from true and trace fossils, consider their applicability in different contexts, and the appropriateness of different modern reference samples. Recently developed techniques based on a wider range of modern populations hold promise for providing more accurate estimates in earlier hominins, although uncertainties remain, particularly in non-Homo taxa. When these methods are applied to almost 300 Late Miocene through Late Pleistocene specimens, the resulting body mass estimates fall within a 25-60 kg range for early non-Homo taxa, increase in early Homo to about 50-90 kg, then remain constant until the Terminal Pleistocene, when they decline.

From fossils to mind

Fossil endocasts record features of brains from the past: size, shape, vasculature, and gyrification. These data, alongside experimental and comparative evidence, are needed to resolve questions about brain energetics, cognitive specializations, and developmental plasticity. Through the application of interdisciplinary techniques to the fossil record, paleoneurology has been leading major innovations. Neuroimaging is shedding light on fossil brain organization and behaviors. Inferences about the development and physiology of the brains of extinct species can be experimentally investigated through brain organoids and transgenic models based on ancient DNA. Phylogenetic comparative methods integrate data across species and associate genotypes to phenotypes, and brains to behaviors. Meanwhile, fossil and archeological discoveries continuously contribute new knowledge. Through cooperation, the scientific community can accelerate knowledge acquisition. Sharing digitized museum collections improves the availability of rare fossils and artifacts. Comparative neuroanatomical data are available through online databases, along with tools for their measurement and analysis. In the context of these advances, the paleoneurological record provides ample opportunity for future research. Biomedical and ecological sciences can benefit from paleoneurology's approach to understanding the mind as well as its novel research pipelines that establish connections between neuroanatomy, genes and behavior.

A global catalog of whole-genome diversity from 233 primate species

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.

Homo medicus: The transition to meat eating increased pathogen pressure and the use of pharmacological plants in Homo

The human lineage transitioned to a more carnivorous niche 2.6 mya and evolved a large body size and slower life history, which likely increased zoonotic pathogen pressure. Evidence for this increase includes increased zoonotic infections in modern hunter-gatherers and bushmeat hunters, exceptionally low stomach pH compared to other primates, and divergence in immune-related genes. These all point to change, and probably intensification, in the infectious disease environment of Homo compared to earlier hominins and other apes. At the same time, the brain, an organ in which immune responses are constrained, began to triple in size. We propose that the combination of increased zoonotic pathogen pressure and the challenges of defending a large brain and body from pathogens in a long-lived mammal, selected for intensification of the plant-based self-medication strategies already in place in apes and other primates. In support, there is evidence of medicinal plant use by hominins in the middle Paleolithic, and all cultures today have sophisticated, plant-based medical systems, add spices to food, and regularly consume psychoactive plant substances that are harmful to helminths and other pathogens. We propose that the computational challenges of discovering effective plant-based treatments, the consequent ability to consume more energy-rich animal foods, and the reduced reliance on energetically-costly immune responses helped select for increased cognitive abilities and unique exchange relationships in Homo. In the story of human evolution, which has long emphasized hunting skills, medical skills had an equal role to play.

Evolutionary history of hominin brain size and phylogenetic comparative methods

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

The Biological Roots of Music and Dance : Extending the Credible Signaling Hypothesis to Predator Deterrence

After they diverged from panins, hominins evolved an increasingly committed terrestrial lifestyle in open habitats that exposed them to increased predation pressure from Africa's formidable predator guild. In the Pleistocene, Homo transitioned to a more carnivorous lifestyle that would have further increased predation pressure. An effective defense against predators would have required a high degree of cooperation by the smaller and slower hominins. It is in the interest of predator and potential prey to avoid encounters that will be costly for both. A wide variety of species, including carnivores and apes and other primates, have therefore evolved visual and auditory signals that deter predators by credibly signaling detection and/or the ability to effectively defend themselves. In some cooperative species, these predator deterrent signals involve highly synchronized visual and auditory displays among group members. Hagen and Bryant (Human Nature, 14(1), 21-51, 2003) proposed that synchronized visual and auditory displays credibly signal coalition quality. Here, this hypothesis is extended to include credible signals to predators that they have been detected and would be met with a highly coordinated defensive response, thereby deterring an attack. Within-group signaling functions are also proposed. The evolved cognitive abilities underlying these behaviors were foundations for the evolution of fully human music and dance.

Postcranial evidence of late Miocene hominin bipedalism in Chad

Bipedal locomotion is one of the key adaptations that define the hominin clade. Evidence of bipedalism is known from postcranial remains of late Miocene hominins as early as 6 million years ago (Ma) in eastern Africa^1-4. Bipedality of Sahelanthropus tchadensis was hitherto inferred about 7 Ma in central Africa (Chad) based on cranial evidence^5-7. Here we present postcranial evidence of the locomotor behaviour of S. tchadensis, with new insights into bipedalism at the early stage of hominin evolutionary history. The original material was discovered at locality TM 266 of the Toros-Ménalla fossiliferous area and consists of one left femur and two, right and left, ulnae. The morphology of the femur is most parsimonious with habitual bipedality, and the ulnae preserve evidence of substantial arboreal behaviour. Taken together, these findings suggest that hominins were already bipeds at around 7 Ma but also suggest that arboreal clambering was probably a significant part of their locomotor repertoire.

Rocks and clocks revised: New promises and challenges in dating the primate tree of life

In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.

Decreases in Brain Size and Encephalization in Anatomically Modern Humans

Growth in human brain size and encephalization is well documented throughout much of prehistory and believed to be responsible for increasing cognitive faculties. Over the past 50,000 years, however, both body size and brain mass have decreased but little is known about the scaling relationship between the two. Here, changes to the human brain are examined using matched body remains to determine encephalization levels across an evolutionary timespan. The results find decreases to encephalization levels in modern humans as compared to earlier Holocene H. sapiens and Late Pleistocene anatomically modern Homo. When controlled for lean body mass, encephalization changes are isometric, suggesting that much of the declines in encephalization are driven by recent increases in obesity. A meta-review of genome-wide association studies finds some evidence for selective pressures acting on human cognitive ability, which may be an evolutionary consequence of the more than 5% loss in brain mass over the past 50,000 years.