The evolution of hominoid cranial diversity: A quantitative genetic approach

Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes

To quantify selection acting on a trait, methods have been developed using either within or between-species variation. However, methods using within-species variation do not integrate the changes at the macro-evolutionary scale. Conversely, current methods using between-species variation usually discard within-species variation, thus not accounting for processes at the micro-evolutionary scale. The main goal of this study is to define a neutrality index for a quantitative trait, by combining within- and between-species variation. This neutrality index integrates nucleotide polymorphism and divergence for normalizing trait variation. As such, it does not require estimation of population size nor of time of speciation for normalization. Our index can be used to seek deviation from the null model of neutral evolution, and test for diversifying selection. Applied to brain mass and body mass at the mammalian scale, we show that brain mass is under diversifying selection. Finally, we show that our test is not sensitive to the assumption that population sizes, mutation rates and generation time are constant across the phylogeny, and automatically adjust for it.

Evaluating modularity in the hominine skull related to feeding biomechanics

OBJECTIVES

Modular architecture of traits in complex organisms can be important for morphological evolution at micro- and sometimes macroevolutionary scales as it may influence the tempo and direction of changes to groups of traits that are essential for particular functions, including food acquisition and processing. We tested several distinct hypotheses about craniofacial modularity in the hominine skull in relation to feeding biomechanics.

MATERIALS AND METHODS

First, we formulated hypothesized functional modules for craniofacial traits reflecting specific demands of feeding biomechanics (e.g., masseter leverage/gape or tooth crown mechanics) in Homo sapiens, Pan troglodytes, and Gorilla gorilla. Then, the pattern and strength of modular signal was quantified by the covariance ratio coefficient and compared across groups using covariance ratio effect size. Hierarchical clustering analysis was then conducted to examine whether a priori-defined functional modules correspond to empirically recovered clusters.

RESULTS

There was statistical support for most a priori-defined functional modules in the cranium and half of the functional modules in the mandible. Modularity signal was similar in the cranium and mandible, and across the three taxa. Despite a similar strength of modularity, the empirically recovered clusters do not map perfectly onto our priori functional modules, indicating that further work is needed to refine our hypothesized functional modules.

CONCLUSION

The results suggest that modular structure of traits in association with feeding biomechanics were mostly shared with humans and the two African apes. Thus, conserved patterns of functional modularity may have facilitated evolutionary changes to the skull during human evolution.

Rules of teeth development align microevolution with macroevolution in extant and extinct primates

Macroevolutionary biologists have classically rejected the notion that higher-level patterns of divergence arise through microevolutionary processes acting within populations. For morphology, this consensus partly derives from the inability of quantitative genetics models to correctly predict the behaviour of evolutionary processes at the scale of millions of years. Developmental studies (evo-devo) have been proposed to reconcile micro- and macroevolution. However, there has been little progress in establishing a formal framework to apply evo-devo models of phenotypic diversification. Here we reframe this issue by asking whether using evo-devo models to quantify biological variation can improve the explanatory power of comparative models, thus helping us bridge the gap between micro- and macroevolution. We test this prediction by evaluating the evolution of primate lower molars in a comprehensive dataset densely sampled across living and extinct taxa. Our results suggest that biologically informed morphospaces alongside quantitative genetics models allow a seamless transition between the micro- and macroscales, whereas biologically uninformed spaces do not. We show that the adaptive landscape for primate teeth is corridor like, with changes in morphology within the corridor being nearly neutral. Overall, our framework provides a basis for integrating evo-devo into the modern synthesis, allowing an operational way to evaluate the ultimate causes of macroevolution.

Functional morphological integration related to feeding biomechanics in the hominine skull

Quantifying and characterizing the pattern of trait covariances is crucial for understanding how population-level patterns of integration might constrain or facilitate craniofacial evolution related to the feeding system. This study addresses an important gap in our knowledge by investigating magnitudes and patterns of morphological integration of biomechanically informative traits in the skulls of Homo sapiens, Pan troglodytes, and Gorilla gorilla. We predicted a lower magnitude of integration among human biomechanical traits since humans eat a softer, less biomechanically challenging diet than apes. Indeed, compared to African apes, the magnitudes of integration were lower in H. sapiens skulls for form data (raw dimensions) but were similar or higher for shape data (raw dimensions scaled by geometric mean). Patterns of morphological integration were generally similar, but not identical, across the three species, particularly for the form data compared to the shape data. Traits that load heavily on the primary axis of variation in morphospace are generally associated with size and/or shape of the temporalis and masseter muscles and with dimensions related to the constrained lever model of jaw biomechanics. Given the conserved nature of morphological integration, skull adaptations for food processing in African apes and humans may have been constrained to occur along certain paths of high evolvability. The conserved pattern of functional integration also indicates that extant hominine species can operate as reasonable analogues for extinct hominins in studies that require population-level patterns of trait variance/covariance.

Morphology, evolution, and the whole organism imperative: Why evolutionary questions need multi-trait evolutionary quantitative genetics

Since Washburn's New Physical Anthropology, researchers have sought to understand the complexities of morphological evolution among anatomical regions in human and non-human primates. Researchers continue, however, to preferentially use comparative and functional approaches to examine complex traits, but these methods cannot address questions about evolutionary process and often conflate function with fitness. Moreover, researchers also tend to examine anatomical elements in isolation, which implicitly assumes independent evolution among different body regions. In this paper, we argue that questions asked in primate evolution are best examined using multiple anatomical regions subjected to model-bound methods built from an understanding of evolutionary quantitative genetics. A nascent but expanding number of studies over the last two decades use this approach, examining morphological integration, evolvability, and selection modeling. To help readers learn how to use these methods, we review fundamentals of evolutionary processes within a quantitative genetic framework, explore the importance of neutral evolutionary theory, and explain the basics of evolutionary quantitative genetics, namely the calculation of evolutionary potential for multiple traits in response to selection. Leveraging these methods, we demonstrate their use to understand non-independence in possible evolutionary responses across the limbs, limb girdles, and basicranium of humans. Our results show that model-bound quantitative genetic methods can reveal unexpected genetic covariances among traits that create a novel but measurable understanding of evolutionary complexity among multiple traits. We advocate for evolutionary quantitative genetic methods to be a standard whenever appropriate to keep studies of primate morphological evolution relevant for the next seventy years and beyond.

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.

Human maxillary sinus size, shape, and surface area: Implications for structural and functional hypotheses

OBJECTIVES

Although research into human maxillary sinus (MS) morphology has overwhelmingly focused on sinus volume, other aspects of morphology (e.g., overall shape, mucosal surface area) factor prominently in hypotheses regarding MS form and function. Here, we investigate MS volume in conjunction with measures of MS shape and surface area in a large, diverse sample of modern humans. We test whether variation in MS volume is associated with predictable changes in MS shape (i.e., allometry) and investigate the influence of MS size-shape scaling on mucosal surface area dynamics.

MATERIALS AND METHODS

Measures of MS volume and surface area were obtained from computed tomographic (CT) scans of 162 modern human crania from three ancestral backgrounds-Equatorial Africa, Europe, and East Asia. 3D coordinate landmarks and linear measurements were also collected. Multivariate analyses were employed to test for associations between MS volume and other morphological variables.

RESULTS

Significant associations between MS volume and 3D shape were identified both across and within the subsamples. Variation in MS volume was found to predominantly relate to differences in MS height and width dimensions relative to MS length. This pattern of allometric scaling was found to differentially influence total mucosal surface area and the SAV ratio.

CONCLUSION

This study suggests that variation in MS volume is disproportionately mediated by MS width and height dimensions. This finding has implications for hypotheses which structurally link MS morphology to craniofacial ontogeny and those which suggest that MS morphology may perform adaptive physiological functions.

Morphological modularity in the anthropoid axial skeleton

Previous research has found that hominoids have stronger modularity between limb elements than other anthropoids, suggesting that there is less constraint on morphological diversification (e.g., limb proportions) in hominoids in terms of evolutionary independence. However, degrees of modularity in the axial skeleton have not been investigated across a broad range of anthropoid taxa. Thus, it is unknown whether hominoids also have stronger modularity in the axial skeleton than other anthropoids, which has implications for the evolution of diverse torso morphologies in Miocene apes as well as the evolution of novel characteristics in the skull and vertebrae of fossil hominins. In this study, 12 anthropoid genera were sampled to examine degrees of modularity between axial skeletal elements (i.e., cranium, mandible, vertebrae, and sacrum). Covariance ratio coefficients were calculated using variance/covariance matrices of interlandmark distances for each axial skeletal element to evaluate degrees of modularity. The results showed that Alouatta, Hylobates, Gorilla, Pan, and Homo showed generally stronger modularity than other anthropoid taxa when considering all axial skeletal elements. When only considering the vertebral elements (i.e., vertebrae and sacrum), Alouatta, Hylobates, Gorilla, and Pan showed generally stronger modularity than other anthropoid taxa. Humans showed stronger modularity between the skull and vertebrae than other hominoids. Thus, the evolution of novel characteristics in the skull and vertebral column may have been less constrained in fossil hominins due to the dissociation of trait covariation between axial skeletal elements in hominoid ancestors, thus fostering more evolutionary independence between the skull and vertebral column.

Heterochronies and allometries in the evolution of the hominid cranium: a morphometric approach using classical anthropometric variables

This article studies the evolutionary change of allometries in the relative size of the two main cranial modules (neurocranium and splanchnocranium) in the five living hominid species and a diverse sample of extinct hominins. We use six standard craniometric variables as proxies for the length, width and height of each cranial module. Factor analysis and two-block partial least squares (2B-PLS) show that the great apes and modern humans share a pervasive negative ontogenetic allometry in the neurocranium and a positive one in the splanchnocranium. This developmental constraint makes it possible to interpret the cranial heterochronies in terms of ontogenetic scaling processes (i.e., extensions or truncations of the ancestral ontogenetic trajectory) and lateral transpositions (i.e., parallel translations of the entire trajectory starting from a different shape for a given cranial size). We hypothesize that ontogenetic scaling is the main evolutionary modality in the australopithecines while in the species of Homo it is also necessary to apply transpositions. Both types of processes are coordinated in Homo, which result in an evolutionary trend toward an increase in brain size and in the degree of paedomorphosis from the earliest habilines.

Thirty years of geometric morphometrics: Achievements, challenges, and the ongoing quest for biological meaningfulness

The foundations of geometric morphometrics were worked out about 30 years ago and have continually been refined and extended. What has remained as a central thrust and source of debate in the morphometrics community is the shared goal of meaningful biological inference through a tight connection between biological theory, measurement, multivariate biostatistics, and geometry. Here we review the building blocks of modern geometric morphometrics: the representation of organismal geometry by landmarks and semilandmarks, the computation of shape or form variables via superimposition, the visualization of statistical results as actual shapes or forms, the decomposition of shape variation into symmetric and asymmetric components and into different spatial scales, the interpretation of various geometries in shape or form space, and models of the association between shape or form and other variables, such as environmental, genetic, or behavioral data. We focus on recent developments and current methodological challenges, especially those arising from the increasing number of landmarks and semilandmarks, and emphasize the importance of thorough exploratory multivariate analyses rather than single scalar summary statistics. We outline promising directions for further research and for the evaluation of new developments, such as "landmark-free" approaches. To illustrate these methods, we analyze three-dimensional human face shape based on data from the Avon Longitudinal Study of Parents and Children (ALSPAC).

Skull variation in Afro-Eurasian monkeys results from both adaptive and non-adaptive evolutionary processes

Afro-Eurasian monkeys originated in the Miocene and are the most species-rich modern primate family. Molecular and fossil data have provided considerable insight into their evolutionary divergence, but we know considerably less about the evolutionary processes that underlie these differences. Here, we apply tests developed from quantitative genetics theory to a large (n > 3000) cranio-mandibular morphometric dataset, investigating the relative importance of adaptation (natural selection) and neutral processes (genetic drift) in shaping diversity at different taxonomic levels, an approach applied previously to monkeys of the Americas, apes, hominins, and other vertebrate taxa. Results indicate that natural selection, particularly for differences in size, plays a significant role in diversifying Afro-Eurasian monkeys as a whole. However, drift appears to better explain skull divergence within the subfamily Colobinae, and in particular the African colobine clade, likely due to habitat fragmentation. Small and declining population sizes make it likely that drift will continue in this taxon, with potentially dire implications for genetic diversity and future resilience in the face of environmental change. For the other taxa, many of whom also have decreasing populations and are threatened, understanding adaptive pressures similarly helps identify relative vulnerability and may assist with prioritising scarce conservation resources.

The pre-eminent role of directional selection in generating extreme morphological change in glyptodonts (Cingulata; Xenarthra)

The prevalence of stasis on macroevolution has been classically taken as evidence of the strong role of stabilizing selection in constraining morphological change. Rates of evolution calculated over longer timescales tend to fall below the expected under genetic drift, suggesting that directional selection signals are erased at longer timescales. Here, we investigated the rates of morphological evolution of the skull in a fossil lineage that underwent extreme morphological modification, the glyptodonts. Contrary to what was expected, we show here that directional selection was the primary process during the evolution of glyptodonts. Furthermore, the reconstruction of selection patterns shows that traits selected to generate a glyptodont morphology are markedly different from those operating on extant armadillos. Changes in both direction and magnitude of selection are probably tied to glyptodonts' invasion of a specialist-herbivore adaptive zone. These results suggest that directional selection might have played a more critical role in the evolution of extreme morphologies than previously imagined.

Effects of hybridization on pelvic morphology: A macaque model

Ancient DNA analyses have shown that interbreeding between hominin taxa occurred multiple times. Although admixture is often reflected in skeletal phenotype, the relationship between the two remains poorly understood, hampering interpretation of the hominin fossil record. Direct study of this relationship is often impossible due to the paucity of hominin fossils and difficulties retrieving ancient genetic material. Here, we use a sample of known ancestry hybrids between two closely related nonhuman primate taxa (Indian and Chinese Macaca mulatta) to investigate the effect of admixture on skeletal morphology. We focus on pelvic shape, which has potential fitness implications in hybrids, as mismatches between maternal pelvic and fetal cranial morphology are often fatal to mother and offspring. As the pelvis is also one of the skeletal regions that differs most between Homo sapiens and Neanderthals, investigating the pelvic consequences of interbreeding could be informative regarding the viability of their hybrids. We find that the effect of admixture in M. mulatta is small and proportional to the relatively small morphological difference between the parent taxa. Sexual dimorphism appears to be the main determinant of pelvic shape in M. mulatta. The lack of difference in pelvic shape between Chinese and Indian M. mulatta is in contrast to that between Neanderthals and H. sapiens, despite a similar split time (in generations) between the hybridizing pairs. Greater phenotypic divergence between hominins may relate to adaptations to disparate environments but may also highlight how the unique degree of cultural buffering in hominins allowed for greater neutral divergence. In contrast to some previous work identifying extreme morphologies in first- and second-generation hybrids, here the relationship between pelvic shape and admixture is linear. This linearity may be because most sampled animals have a multigenerational admixture history or because of relatively high constraints on the pelvis compared with other skeletal regions.

Reconstructing the ancestral phenotypes of great apes and humans (Homininae) using subspecies-level phylogenies

Owing to their close affinity, the African great apes are of interest in the study of human evolution. Although numerous researchers have described the ancestors we share with these species with reference to extant great apes, few have done so with phylogenetic comparative methods. One obstacle to the application of these techniques is the within-species phenotypic variation found in this group. Here, we leverage this variation, modelling common ancestors using ancestral state reconstructions (ASRs) with reference to subspecies-level trait data. A subspecies-level phylogeny of the African great apes and humans was estimated from full-genome mitochondrial DNA sequences and used to implement ASRs for 14 continuous traits known to vary between great ape subspecies. Although the inclusion of within-species phenotypic variation increased the phylogenetic signal for our traits and improved the performance of our ASRs, whether this was done through the inclusion of subspecies phylogeny or through the use of existing methods made little difference. Our ASRs corroborate previous findings that the last common ancestor of humans, chimpanzees and bonobos was a chimp-like animal, but also suggest that the last common ancestor of humans, chimpanzees, bonobos and gorillas was an animal unlike any extant African great ape.

Morphological integration affects the evolution of midline cranial base, lateral basicranium, and face across primates

OBJECTIVES

The basicranium and face are two integrated bony structures displaying great morphological diversity across primates. Previous studies in hominids determined that the basicranium is composed of two independent modules: the midline basicranium, mostly influenced by brain size, and the lateral basicranium, predominantly associated with facial shape. To better assess how morphological integration impacts the evolution of primate cranial shape diversity, we test to determine whether the relationships found in hominids are retained across the order.

MATERIALS AND METHODS

Three-dimensional landmarks (29) were placed on 143 computed tomography scans of six major clades of extant primate crania. We assessed the covariation between midline basicranium, lateral basicranium, face, and endocranial volume using phylogenetically informed partial least squares analyses and phylogenetic generalized least squares models.

RESULTS

We found significant integration between lateral basicranium and face and between midline basicranium and face. We also described a significant correlation between midline basicranium and endocranial volume but not between lateral basicranium and endocranial volume.

DISCUSSION

Our findings demonstrate a significant and pervasive integration in the craniofacial structures across primates, differing from previous results in hominids. The uniqueness of module organization in hominids may explain this distinction. We found that endocranial volume is significantly integrated to the midline basicranium but not to the lateral basicranium. This finding underlines the significant effect of brain size on the shape of the midline structures of the cranial base in primates. With the covariations linking the studied features defined here, we suggest that future studies should focus on determining the causal links between them.

Multivariate morphometrics, quantitative genetics, and neutral theory: Developing a "modern synthesis" for primate evolutionary morphology

Anthropologists are increasingly turning to explicit model-bound evolutionary approaches for understanding the morphological diversification of humans and other primate lineages. Such evolutionary morphological analyses rely on three interconnected conceptual frameworks; multivariate morphometrics for quantifying similarity and differences among taxa, quantitative genetics for modeling the inheritance and evolution of morphology, and neutral theory for assessing the likelihood that taxon diversification is due to stochastic processes such as genetic drift. Importantly, neutral theory provides a framework for testing more parsimonious explanations for observed morphological differences before considering more complex adaptive scenarios. However, the consistency with which these concepts are applied varies considerably, which mirrors some of the theoretical obstacles faced during the "modern synthesis" of classical population genetics in the early 20th century. Here, each framework is reviewed and some potential stumbling blocks to the full conceptual integration of multivariate morphometrics, quantitative genetics, and neutral theory are considered.

Hominoid intraspecific cranial variation mirrors neutral genetic diversity

In humans, patterns of cranial variation mirror genetic diversity globally, implicating population history as a key driver of cranial disparity. Here, we demonstrate that the magnitude of genetic diversity within 12 extant ape taxa explains a large proportion of cranial shape variation. Taxa that are more genetically diverse tend to be more cranially diverse also. Our results suggest that neutral evolutionary processes such as mutation, genetic drift, and gene flow are reflected in both genetic and cranial diversity in apes. This work provides a perspective on intraspecific cranial variation in apes which has important implications for interpreting selective and developmental pressures on the cranium and for understanding shape variation in fossil hominin crania.

Natural selection, developmental constraint, and plasticity have all been invoked as explanations for intraspecific cranial variation in humans and apes. However, global patterns of human cranial variation are congruent with patterns of genetic variation, demonstrating that population history has influenced cranial variation in humans. Here we show that this finding is not unique to Homo sapiens but is also broadly evident across extant ape species. Specifically, taxa that exhibit greater intraspecific cranial shape variation also exhibit greater genetic diversity at neutral autosomal loci. Thus, cranial shape variation within hominoid taxa reflects the population history of each species. Our results suggest that neutral evolutionary processes such as mutation, gene flow, and genetic drift have played an important role in generating cranial variation within species. These findings are consistent with previous work on human cranial morphology and improve our understanding of the evolutionary processes that generate intraspecific cranial shape diversity within hominoids. This work has implications for the analysis of selective and developmental pressures on the cranium and for interpreting shape variation in fossil hominin crania.

Look in the trees: Hylobatids as evolutionary models for extinct hominins

Studying extant apes is of central importance to paleoanthropology. This approach is informative in inferring how hominin skeletal morphology reflects phylogeny, behavior, development, and ecological context. Traditionally, great apes have dominated the paleoanthropological literature as extant analogs for extinct hominins, to the exclusion of their phylogenetic sister group, the hylobatids. Phylogenetic proximity, large body size, and high encephalization quotients may have contributed to decisions to use great apes as models for hominins. However, if we reexamine hylobatids as extant models for extinct hominins-using modern phylogenetic, behavioral, and ecological data-this clade is uniquely poised to inform future frameworks in paleoanthropology. The following features make hylobatids strong analogs for extinct hominins: taxonomic diversity, the timing of diversification, hybridization between species, small body size, and reduced sexual dimorphism. Based on these shared features, hylobatids offer future opportunities to paleoanthropology, and provide a much richer extant analog than is currently recognized.

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.

Using geometric morphometric visualizations of directional selection gradients to investigate morphological differentiation

Researchers studying extant and extinct taxa are often interested in identifying the evolutionary processes that have lead to the morphological differences among the taxa. Ideally, one could distinguish the influences of neutral evolutionary processes (genetic drift, mutation) from natural selection, and in situations for which selection is implicated, identify the targets of selection. The directional selection gradient is an effective tool for investigating evolutionary process, because it can relate form (size and shape) differences between taxa to the variation and covariation found within taxa. However, although most modern morphometric analyses use the tools of geometric morphometrics (GM) to analyze landmark data, to date, selection gradients have mainly been calculated from linear measurements. To address this methodological gap, here we present a GM approach for visualizing and comparing between-taxon selection gradients with each other, associated difference vectors, and "selection" gradients from neutral simulations. To exemplify our approach, we use a dataset of 347 three-dimensional landmarks and semilandmarks recorded on the crania of 260 primate specimens (112 humans, 67 common chimpanzees, 36 bonobos, 45 gorillas). Results on this example dataset show how incorporating geometric information can provide important insights into the evolution of the human braincase, and serve to demonstrate the utility of our approach for understanding morphological evolution.