Elucidating the evolution of hominid dentition in the age of phenomics, modularity, and quantitative genetics

Human population dynamics in Upper Paleolithic Europe inferred from fossil dental phenotypes

Despite extensive archaeological research, our knowledge of the human population history of Upper Paleolithic Europe remains limited, primarily due to the scarce availability and poor molecular preservation of fossil remains. As teeth dominate the fossil record and preserve genetic signatures in their morphology, we compiled a large dataset of 450 dentitions dating between ~47 and 7 thousand years ago (ka), outnumbering existing skeletal and paleogenetic datasets. We tested a range of competing demographic scenarios using a coalescent-based machine learning Approximate Bayesian Computation (ABC) framework that we modified for use with phenotypic data. Mostly in agreement with but also challenging some of the hitherto available evidence, we identified a population turnover in western Europe at ~28 ka, isolates in western and eastern refugia between ~28 and 14.7 ka, and bottlenecks during the Last Glacial Maximum. Methodologically, this study marks the pioneering application of ABC to skeletal phenotypes, paving the way for exciting future research avenues.

From hunter-gatherers to food producers: New dental insights into the Nile Valley population history (Late Paleolithic-Neolithic)

OBJECTIVES

This study presents biological affinities between the last hunter-fisher-gatherers and first food-producing societies from the Nile Valley. We investigate odontometric and dental tissue proportion changes between these populations from the Middle Nile Valley and acknowledge the biological processes behind them.

MATERIALS AND METHODS

Dental remains of 329 individuals from Nubia and Central Sudan that date from the Late Pleistocene to the mid-Holocene are studied. Using 3D imaging techniques, we investigated outer and inner metric aspects of upper central incisors, and first and second upper molars.

RESULTS

Late Paleolithic and Mesolithic foragers display homogeneous crown dimensions, dental tissue proportions, and enamel thickness distribution. This contrasts with Neolithic trends for significant differences from earlier samples on inner and outer aspects. Finally, within the Neolithic sample differences are found between Nubian and Central Sudanese sites.

DISCUSSION

Substantial dental variation appears to have occurred around 6000 bce in the Nile Valley, coinciding with the emergence of food-producing societies in the region. Archeological and biological records suggest little differences in dietary habits and dental health during this transition. Furthermore, the substantial variations identified here would have happened in an extremely short time, a few centuries at most. This does not support in situ diet-related adaptation. Rather, we suggest these data are consistent with some level of population discontinuity between the Mesolithic and Neolithic samples considered here. Complex settlement processes could also explain the differences between Nubia and Central Sudan, and with previous results based on nonmetric traits.

A tooth crown morphology framework for interpreting the diversity of primate dentitions

Variation in tooth crown morphology plays a crucial role in species diagnoses, phylogenetic inference, and the reconstruction of the evolutionary history of the primate clade. While a growing number of studies have identified developmental mechanisms linked to tooth size and cusp patterning in mammalian crown morphology, it is unclear (1) to what degree these are applicable across primates and (2) which additional developmental mechanisms should be recognized as playing important roles in odontogenesis. From detailed observations of lower molar enamel-dentine junction morphology from taxa representing the major primate clades, we outline multiple phylogenetic and developmental components responsible for crown patterning, and formulate a tooth crown morphology framework for the holistic interpretation of primate crown morphology. We suggest that adopting this framework is crucial for the characterization of tooth morphology in studies of dental development, discrete trait analysis, and systematics.

Moving beyond the adaptationist paradigm for human evolution, and why it matters

The Journal of Human Evolution (JHE) was founded 50 years ago when much of the foundation for how we think about human evolution was in place or being put in place, providing the main framework for how we consider our origins today. Here, we will explore historical developments, including early JHE outputs, as they relate to our understanding of the relationship between phenotypic variation and evolutionary process, and use that as a springboard for considering our current understanding of these links as applied to human evolution. We will focus specifically on how the study of variation itself has shifted us away from taxonomic and adaptationist perspectives toward a richer understanding of the processes shaping human evolutionary history, using literature searches and specific test cases to highlight this. We argue that natural selection, gene exchange, genetic drift, and mutation should not be considered individually when considering the production of hominin diversity. In this context, we offer suggestions for future research directions and reflect on this more complex understanding of human evolution and its broader relevance to society. Finally, we end by considering authorship demographics and practices in the last 50 years within JHE and how a shift in these demographics has the potential to reshape the science of human evolution going forward.

Genetic, Epigenetic and Environmental Factors Influence the Phenotype of Tooth Number, Size and Shape: Anterior Maxillary Supernumeraries and the Morphology of Mandibular Incisors

The aim of this study is to investigate whether the genetic, epigenetic and environmental factors that give rise to supernumeraries in the maxillary incisor region and larger dimensions of the adjacent maxillary incisors are also associated with variations in the morphology of the mandibular incisors. If so, this would contribute to understanding the distribution and interactions of factors during dental development and how these can be modelled. The sample consisted of 34 patients with supernumerary teeth in the maxillary anterior region, matched for gender, age and White Caucasian ethnicity with 34 control subjects. The average ages of the supernumerary and control groups were 12.8 and 12.2 years, respectively. Study models of all subjects were constructed and imaged using a previously validated system. Using custom software, each of the mandibular incisor teeth were measured to obtain 17 parameters from the labial view and 17 from the occlusal view. Principal component analysis (PCA) was used to summarize the measurements into a smaller set representing distinct features of the clinical crowns, followed by a comparison between the supernumerary and control groups using 2-way ANOVA. Seven factors of tooth size of the mandibular central incisors and six factors of the mandibular lateral incisors were identified as major features of the clinical crowns. All parameters of both mandibular incisors were greater in the supernumerary group than in the control, with three of these, located in the incisal and cervical regions of the mandibular lateral incisors, being statistically significantly larger. The findings of this study indicate that the aetiological factors associated with supernumerary teeth in the maxillary anterior region also affect tooth crown dimensions of mandibular incisors. This new evidence enhances several models of the interactions of genetic, epigenetic and environmental components of dental development and supports a multi-model approach to increase understanding of this process and its variations.

The relative impact of evolving pleiotropy and mutational correlation on trait divergence

Both pleiotropic connectivity and mutational correlations can restrict the decoupling of traits under divergent selection, but it is unknown which is more important in trait evolution. To address this question, we create a model that permits within-population variation in both pleiotropic connectivity and mutational correlation, and compare their relative importance to trait evolution. Specifically, we developed an individual-based stochastic model where mutations can affect whether a locus affects a trait and the extent of mutational correlations in a population. We find that traits can decouple whether there is evolution in pleiotropic connectivity or mutational correlation, but when both can evolve, then evolution in pleiotropic connectivity is more likely to allow for decoupling to occur. The most common genotype found in this case is characterized by having one locus that maintains connectivity to all traits and another that loses connectivity to the traits under stabilizing selection (subfunctionalization). This genotype is favored because it allows the subfunctionalized locus to accumulate greater effect size alleles, contributing to increasingly divergent trait values in the traits under divergent selection without changing the trait values of the other traits (genetic modularization). These results provide evidence that partial subfunctionalization of pleiotropic loci may be a common mechanism of trait decoupling under regimes of corridor selection.

Bridging the gap: Using biological data from teeth to comment on social identity of archeological populations from early Anglo-Saxon, England

Human teeth are storytellers, in that, through analysis of their size and shape osteoarchaeologists are able to 'talk' to the dead and translate biological data into social meaning. This concept has been explored in parts of the world through investigations of biological similarity and kinship, but few have focused in depth on early medieval populations who emphasized the importance of family and kinship. This paper presents the results from four early Anglo-Saxon cemeteries which highlight the utility of dental metrics in identifying biological similarity within the skeletal assemblages. 5988 mesiodistal and buccolingual measurements were recorded from the identifiable permanent dentition of adult individuals from early Anglo-Saxon cemeteries in the UK counties of Cambridgeshire and Kent. Results from statistical hierarchical cluster analysis of dental metric data revealed that it was possible to identify individuals within the cemetery sites that were more similar to one another according to their dental metrics. This similarity was not attributed statistically to biological sex or shared familial environment, as similarity between individuals could be found between males and females and few significant differences were found across the sites sampled. It was found that tooth metrics provided a meaningful biological dataset from which current theories regarding the identity of Anglo-Saxon individuals and families could be refined and improved. These types of data are useful as building blocks which help to bridge the gap between social constructs and human skeletal remains in order to substantiate interpretations about past populations in more significant ways. This work supports the need for multidisciplinary approaches to bioarchaeological investigations of past people while highlighting the utility of human dentition to enhance such areas of study.

The genetic architecture of anterior tooth morphology in a longitudinal sample of Australian twins and families

OBJECTIVE

This study presents a quantitative genetic analysis of human anterior dental morphology in a longitudinal sample of known genealogy. The primary aim of this work is to generate a suite of genetic correlations within and between deciduous and permanent characters to access patterns of integration across the diphyodont dental complex.

DESIGN

Data were recorded from casted tooth crowns representing participants of a long-term Australian twin and family study (deciduous n = 290, permanent n = 339). Morphological trait expression was observed and scored following Arizona State University Dental Anthropology System standards. Bivariate genetic correlations were estimated using maximum likelihood variance decomposition models in SOLAR v.8.1.1.

RESULTS

Genetic correlation estimates indicate high levels of integration between antimeres but low to moderate levels among traits within a tooth row. Only 9% of deciduous model comparisons were significant, while pleiotropy was indicated for one third of permanent trait pairs. Canine characters stood out as strongly integrated, especially in the deciduous dentition. For homologous characters across dentitions (e.g., deciduous i¹ shoveling and permanent I¹ shoveling), ∼70% of model comparisons yielded significant genetic correlations.

CONCLUSIONS

Patterns of genetic correlation suggest a morphological canine module that spans the primary and secondary dentition. Results also point to the existence of a genetic mechanism conserving morphology across the diphyodont dental complex, such that paired deciduous and permanent traits are more strongly integrated than characters within individual tooth rows/teeth.

Ancient anomalies: Twinned and supernumerary incisors in a medieval Nubian

During the analysis of a skeletal assemblage from a medieval cemetery in Nubia (c. AD 500-1550), a young adult female with abnormally developed maxillary incisors was discovered. The possible causes of the two dental anomalies found in this individual and their archaeological context are discussed. The remains are from a medieval assemblage from the Fourth Cataract region of Nubia, which forms part of the Nubian collection curated at the British Museum. The left central incisor has a twinned crown with two root canals, and a supernumerary tooth is present on the right side between the central incisor and lateral incisors. Although two different dental anomalies are present, the bilateral expression suggests that the same biological mechanism could be responsible.

An inconstant biorhythm: The changing pace of Retzius periodicity in human permanent teeth

OBJECTIVES

Human tooth enamel retains evidence of growth in the form of Retzius lines. The number of daily growth increments between the regularly occurring lines defines their repeat interval, or periodicity. Retzius periodicity is often incorporated into enamel formation times, age-at-death reconstructions, or used to provide a basis from which to explore an underlying biorhythm. Biological anthropologists typically assume that RP remains constant within an individual and does not vary along the tooth-row. Here, we test that assumption.

MATERIALS AND METHODS

RP was calculated from n = 223 thin sections of human permanent teeth from individuals of British and southern African origin. Forty individuals provided multiple teeth (n = 102 teeth) and a further 121 individuals each provided a single tooth.

RESULTS

We report first evidence that RP of permanent teeth does not always remain constant within an individual. Of those individuals that provided multiple teeth, 42% (n = 17/40) demonstrated a decrease in RP along the tooth row, with most shifting by two or more days (n = 11). Across the entire sample, mean RP of anterior teeth was significantly higher than molars. Mean premolar RP tended to be intermediate between anterior teeth and molars.

DISCUSSION

Our data do not support the assumption that RP invariably remains constant within the permanent teeth of an individual. Transferring RP from molars to incisors within an individual can result in a miscalculation of formation time and age-at-death by up to 1 year. Implications for biological anthropologists and the source of the underlying long period biorhythm are discussed.

Genetic correlations in the rhesus macaque dentition

Quantitative genetic analyses can indicate how complex traits respond to natural selection by demonstrating the genetic relationships between features that constrain their evolution. Genetic correlations between dental measurements have been estimated previously in baboons, humans, and tamarins and indicate variable patterns of modularity by tooth type across these taxa. Here, heritabilities of, and genetic correlations between, linear dental measurements were estimated from the Cayo Santiago rhesus macaques (Macaca mulatta). Relationships between the genetic correlation matrix and matrices designed to test hypotheses of modularity by tooth type, region, function, and development were assessed using a random skewers approach. Dental measurements were found to be moderately to highly heritable, with 24 of 28 heritability estimates differing significantly (p < 0.05) from zero. Almost all genetic correlations between dental dimensions were positive. The genetic correlation matrix was most similar to a regionally modular matrix, with distinct anterior and postcanine tooth modules. This pattern is consistent with previous quantitative genetic analyses of baboons and previous phenotypic analyses of cercopithecoid primates. The existence of a genetic module for the canines and honing premolar was not supported. Ongoing selection pressures, rather than strong genetic constraints, are likely necessary to preserve functional relationships between the canines and honing premolar based on these findings. The genetic correlation matrix of the Cayo Santiago rhesus macaques mirrors patterns of phenotypic correlations observed for cercopithecoid primates broadly and demonstrates that genetic contributions to these patterns may be fairly stable over the course of cercopithecoid evolution. The quantitative genetic study of additional taxa will be necessary to determine whether the regional modularity of baboons and macaques, or the integrated pattern of humans and tamarins, is shared more broadly across primates.

A genotype:phenotype approach to testing taxonomic hypotheses in hominids

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

Testing the utility of dental morphological trait combinations for inferring human neutral genetic variation

Researchers commonly rely on human dental morphological features in order to reconstruct genetic affinities among past individuals and populations, particularly since teeth are often the best preserved part of a human skeleton. Tooth form is considered to be highly heritable and selectively neutral and, therefore, to be an excellent proxy for DNA when none is available. However, until today, it remains poorly understood whether certain dental traits or trait combinations preserve neutral genomic signatures to a greater degree than others. Here, we address this long-standing research gap by systematically testing the utility of 27 common dental traits and >134 million possible trait combinations in reflecting neutral genomic variation in a worldwide sample of modern human populations. Our analyses reveal that not all traits are equally well-suited for reconstructing population affinities. Whereas some traits largely reflect neutral variation and therefore evolved primarily as a result of genetic drift, others can be linked to nonstochastic processes such as natural selection or hominin admixture. We also demonstrate that reconstructions of population affinity based on many traits are not necessarily more reliable than those based on only a few traits. Importantly, we find a set of highly diagnostic trait combinations that preserve neutral genetic signals best (up to [Formula: see text] _r = 0.580; 95% r range = 0.293 to 0.758; P = 0.001). We propose that these trait combinations should be prioritized in future research, as they allow for more accurate inferences about past human population dynamics when using dental morphology as a proxy for DNA.

Evidence of strong stabilizing effects on the evolution of boreoeutherian (Mammalia) dental proportions

The dentition is an extremely important organ in mammals with variation in timing and sequence of eruption, crown morphology, and tooth size enabling a range of behavioral, dietary, and functional adaptations across the class. Within this suite of variable mammalian dental phenotypes, relative sizes of teeth reflect variation in the underlying genetic and developmental mechanisms. Two ratios of postcanine tooth lengths capture the relative size of premolars to molars (premolar-molar module, PMM), and among the three molars (molar module component, MMC), and are known to be heritable, independent of body size, and to vary significantly across primates. Here, we explore how these dental traits vary across mammals more broadly, focusing on terrestrial taxa in the clade of Boreoeutheria (Euarchontoglires and Laurasiatheria). We measured the postcanine teeth of N = 1,523 boreoeutherian mammals spanning six orders, 14 families, 36 genera, and 49 species to test hypotheses about associations between dental proportions and phylogenetic relatedness, diet, and life history in mammals. Boreoeutherian postcanine dental proportions sampled in this study carry conserved phylogenetic signal and are not associated with variation in diet. The incorporation of paleontological data provides further evidence that dental proportions may be slower to change than is dietary specialization. These results have implications for our understanding of dental variation and dietary adaptation in mammals.

Variation of 3D outer and inner crown morphology in modern human mandibular premolars

Objectives

This study explores the outer and inner crown of lower third and fourth premolars (P₃, P₄) by analyzing the morphological variation among diverse modern human groups.

Materials and Methods

We studied three‐dimensional models of the outer enamel surface and the enamel–dentine junction (EDJ) from μCT datasets of 77 recent humans using both an assessment of seven nonmetric traits and a standard geometric morphometric (GM) analysis. For the latter, the dental crown was represented by four landmarks (dentine horns and fossae), 20 semilandmarks along the EDJ marginal ridge, and pseudolandmarks along the crown and cervical outlines.

Results

Certain discrete traits showed significantly different regional frequencies and sexual dimorphism. The GM analyses of both P₃s and P₄s showed extensive overlap in shape variation of the various populations (classification accuracy 15–69%). The first principal components explained about 40% of shape variance with a correlation between 0.59 and 0.87 of the features of P₃s and P₄s. Shape covariation between P₃s and P₄s expressed concordance of high and narrow or low and broad crowns.

Conclusions

Due to marked intragroup and intergroup variation in GM analyses of lower premolars, discrete traits such as the number of lingual cusps and mesiolingual groove expression provide better geographic separation of modern human populations. The greater variability of the lingual region suggests a dominance of functional constraints over geographic provenience or sex. Additional information about functionally relevant aspects of the crown surface and odontogenetic data are needed to unravel the factors underlying dental morphology in modern humans.

Recent insights into the evolution of quantitative traits in non-human primates

The past few years of genetic research on primate quantitative trait variation have been notable in the diversity of phenotypes explored, ranging from classic skeletal measurements to behavior, through to levels of gene expression, and with observations from both captive and wild populations. These studies demonstrate the importance of captive pedigreed breeding colonies, populations that can be matched to their wild counterparts to enable comparison of genetic architectures. Non-human primate genotype:phenotype maps are essential for placing human variation within an evolutionary framework as well as for gaining insight to human biology. While the demographic history of most primates has been fairly stable since the Late Pleistocene, humans experienced a dramatic population expansion that increased the number of rare, mildly deleterious mutations. These rare genetic variants complicate the genotype:phenotype association because they account for a disproportionate amount of the genetic variance and are harder to detect. The similar physiologies of our closest living relatives may prove to be key for overcoming the hurdles posed by humans' peculiar demographic explosion.

The Integrated Genomic Architecture and Evolution of Dental Divergence in East African Cichlid Fishes (Haplochromis chilotes x H. nyererei)

The independent evolution of the two toothed jaws of cichlid fishes is thought to have promoted their unparalleled ecological divergence and species richness. However, dental divergence in cichlids could exhibit substantial genetic covariance and this could dictate how traits like tooth numbers evolve in different African Lakes and on their two jaws. To test this hypothesis, we used a hybrid mapping cross of two trophically divergent Lake Victoria species (Haplochromis chilotes × Haplochromis nyererei) to examine genomic regions associated with cichlid tooth diversity. Surprisingly, a similar genomic region was found to be associated with oral jaw tooth numbers in cichlids from both Lake Malawi and Lake Victoria. Likewise, this same genomic location was associated with variation in pharyngeal jaw tooth numbers. Similar relationships between tooth numbers on the two jaws in both our Victoria hybrid population and across the phylogenetic diversity of Malawi cichlids additionally suggests that tooth numbers on the two jaws of haplochromine cichlids might generally coevolve owing to shared genetic underpinnings. Integrated, rather than independent, genomic architectures could be key to the incomparable evolutionary divergence and convergence in cichlid tooth numbers.

Internal Tooth Structure and Burial Practices: Insights into the Neolithic Necropolis of Gurgy (France, 5100-4000 cal. BC)

Variations in the dental crown form are widely studied to interpret evolutionary changes in primates as well as to assess affinities among human archeological populations. Compared to external metrics of dental crown size and shape, variables including the internal structures such as enamel thickness, tissue proportions, and the three-dimensional shape of enamel-dentin junction (EDJ), have been described as powerful measurements to study taxonomy, phylogenetic relationships, dietary, and/or developmental patterns. In addition to providing good estimate of phenotypic distances within/across archeological samples, these internal tooth variables may help to understand phylogenetic, functional, and developmental underlying causes of variation. In this study, a high resolution microtomographic-based record of upper permanent second molars from 20 Neolithic individuals of the necropolis of Gurgy (France) was applied to evaluate the intrasite phenotypic variation in crown tissue proportions, thickness and distribution of enamel, and EDJ shape. The study aims to compare interindividual dental variations with burial practices and chronocultural parameters, and suggest underlying causes of these dental variations. From the non-invasive characterization of internal tooth structure, differences have been found between individuals buried in pits with alcove and those buried in pits with container and pits with wattling. Additionally, individuals from early and recent phases of the necropolis have been distinguished from those of the principal phase from their crown tissue proportions and EDJ shape. The results suggest that the internal tooth structure may be a reliable proxy to track groups sharing similar chronocultural and burial practices. In particular, from the EDJ shape analysis, individuals buried in an alcove shared a reduction of the distolingual dentin horn tip (corresponding to the hypocone). Environmental, developmental and/or functional underlying causes might be suggested for the origin of phenotypic differences shared by these individuals buried in alcoves.

The integration of quantitative genetics, paleontology, and neontology reveals genetic underpinnings of primate dental evolution

Developmental genetics research on mice provides a relatively sound understanding of the genes necessary and sufficient to make mammalian teeth. However, mouse dentitions are highly derived compared with human dentitions, complicating the application of these insights to human biology. We used quantitative genetic analyses of data from living nonhuman primates and extensive osteological and paleontological collections to refine our assessment of dental phenotypes so that they better represent how the underlying genetic mechanisms actually influence anatomical variation. We identify ratios that better characterize the output of two dental genetic patterning mechanisms for primate dentitions. These two newly defined phenotypes are heritable with no measurable pleiotropic effects. When we consider how these two phenotypes vary across neontological and paleontological datasets, we find that the major Middle Miocene taxonomic shift in primate diversity is characterized by a shift in these two genetic outputs. Our results build on the mouse model by combining quantitative genetics and paleontology, and thereby elucidate how genetic mechanisms likely underlie major events in primate evolution.