A 3-D geometric morphometric study of intraspecific variation in the ontogeny of the temporal bone in modern Homo sapiens

Investigating temporal bone variation of colonial populations from St-Lawrence Valley, Quebec: A 3D geometric morphometric approach

OBJECTIVES

In Quebec, genetic and genealogical research are used to document migratory events and family structures since colonial times, because bioarchaeological analysis is limited by poor skeletal preservation. This article aims to fill this gap by exploring past population structure in the St-Lawrence Valley from the French (1683-1760) and British (1760-1867) regimes using morphological variation of well-preserved temporal bones.

MATERIALS AND METHODS

3D geometric morphometrics shape data from seven populations (five Catholics of French descent and two Protestants of British descent; n = 214) were collected from temporal bones. Using Procrustes distances and both MANOVA and Discriminant Function Analysis, morphological differences were measured to calculate affinities patterns among populations. Shape variations were explored with between-group analysis, Mahalanobis distances and quantified by means of Fst estimates using Relethford-Blangero analysis.

RESULTS

Despite strong affinities between all Catholic cemeteries, all show divergent morphological regional diversity -especially Montreal and the fortified villages dedicated to its defense. Montreal exhibits low increase in morphological variance over three centuries. As our results show no morphological differences between the Catholic and the Protestant cemeteries in Montreal, this fact may highlight the potential presence of Irish or admixed individuals in Montreal cemeteries after the British takeover.

DISCUSSION

Patterns of morphological diversity highlighted that French colonists did not equally contribute to the descendant populations as reflected by significant interregional variation. Although historical records show that French and English-speaking populations did not tend to admix, morphological affinities between Protestants and Catholics in the beginning of the industrial era in Montreal could reflect the genetic contribution of Catholic Irish migrants.

RESEARCH HIGHLIGHTS

All Catholic cemeteries display distinct morphologies, highlighting differential contributions from French colonists and founder effects, which have increased regional differences. Montreal Catholic (French descent) and Protestant (English colonists) cemeteries show significant morphological affinities at the beginning of the industrial era. The Irish migration following the British conquest may explain morphological similarities observed between Catholic and Protestant cemeteries.

Three-dimensional geometric morphometric study of the Xuchang 2 cranium

Results of traditional metric and nonmetric assessments suggest that the Xuchang hominin shares features with Neanderthals. To comprehensively compare the nuchal morphology of XC 2 to those of the genus Homo, we conduct a three-dimensional geometric morphometric study with 35 cranial landmarks and surface semilandmarks of XC 2, Homo erectus, Middle Pleistocene humans, Neanderthals, and early and recent modern humans. Results reveal that the centroid size of XC 2 is larger than that of early and recent modern humans and can only be compared to that of Middle Pleistocene humans and H. erectus. Early and recent modern humans share a nuchal morphology distinct from archaic hominins (Ngandong H. erectus, Middle Pleistocene humans, and Neanderthals), except for SM 3, Sangiran 17, and Asian and African H. erectus. Although Ngandong specimens differ from the other H. erectus, it is unclear whether this represents a temporal or spatial trend in the process of evolution of this species. The nuchal morphological resemblance between Middle Pleistocene humans and Neanderthals may be attributed to similar cranial architecture and cerebellar shape. The great nuchal morphological variation shared by recent modern humans may indicate a particular developmental pattern. In conclusion, the nuchal morphology of different human groups is highly variable and may be caused by different factors including brain globularization and developmental plasticity. XC 2 shares similar nuchal morphology with Middle Pleistocene humans and Neanderthals, but these results are insufficient to fully resolve the taxonomic status of XC 2.

Morphometric Analysis of the Neurocranium in an Adult South African Cadaveric Sample

Craniometric studies of South Africans yield high accuracies of sex and ancestry classification, but most assess only inter-group variation of Black and White individuals, excluding the highly heterogeneous Colored group, which constitute a significant proportion of the population. This study applied a geometric morphometric approach to the neurocrania of 774 Black, Colored, and White individuals to assess sex and ancestry estimation accuracy based on the detected morphological variation. Accuracies of 70% and 83% were achieved for sex and ancestry, respectively, with ancestry-related variation contributing the largest proportion of overall observed variation. Even when comparing the closely related Black and Colored groups, relatively high accuracies were obtained. It is thus recommended that a similar approach be used to develop a contemporary three-dimensional database, which can be used to objectively, reliably, and accurately classify unknown remains in the South African forensic context.

Morphometric analysis of the humerus in an adult South African cadaveric sample

Recent studies using geometric morphometrics have shown that estimations of demographic parameters can be made using skeletal elements previously not thought useful for such purposes. This study used geometric morphometrics to assess humeral morphological variation in an adult South African sample, and evaluated the accuracy of sex and ancestry estimations based on this variation. Humeri of 1046 adult South African individuals (464 females, 582 males) were digitized. Data sets were rotated and scaled to a common centroid using Generalized Procrustes Analysis. Mean centroid sizes between groups were compared using parametric tests, while morphological variation was evaluated using multivariate analyses. Discriminant Function Analysis coupled with leave-one-out cross-validation tests were used to assess the reliability of sex and ancestry classifications based on this variation. Male humeri were relatively larger and presented with morphological features indicative of larger muscle mass and smaller carrying angles than females. White individuals had relatively larger but morphologically less robust humeri than Black or Coloured individuals, likely a reflection of both genetic and socio-economic differences between the groups as enforced under Apartheid law. When sex and ancestry were assessed together, similar variations were detected than when either parameter was individually assessed. Classification accuracy was relatively low when sex was independently assessed (73.3%), but increased when considered in conjunction with ancestry, indicating greater variation between-groups (ancestry) than within-groups. Ancestry estimation accuracies exceeded 80%, even for the highly diverse Coloured group. Classification accuracies of sex-ancestry groups all exceeded 76%. These results show that humerus morphological variation is present and may be used to estimate parameters, such as sex and ancestry, even in complex groups such as the Coloured sample of this study.

Human bony labyrinth is an indicator of population history and dispersal from Africa

The cavity system of the inner ear—the so-called bony labyrinth—houses the senses of balance and hearing. This structure is embedded in dense petrous bone, fully formed by birth and generally well preserved in human skeletal remains, thus providing a rich source of morphological information about past populations. Here we show that labyrinthine morphology tracks genetic distances and geography in an isolation-by-distance model with dispersal from Africa. Because petrous bones have become prime targets of ancient DNA recovery, we propose that all destructive studies first acquire high-resolution 3D computed-tomography data prior to any invasive sampling. Such data will constitute an important archive of morphological variation in past and present populations, and will permit individual-based genotype–phenotype comparisons.

The dispersal of modern humans from Africa is now well documented with genetic data that track population history, as well as gene flow between populations. Phenetic skeletal data, such as cranial and pelvic morphologies, also exhibit a dispersal-from-Africa signal, which, however, tends to be blurred by the effects of local adaptation and in vivo phenotypic plasticity, and that is often deteriorated by postmortem damage to skeletal remains. These complexities raise the question of which skeletal structures most effectively track neutral population history. The cavity system of the inner ear (the so-called bony labyrinth) is a good candidate structure for such analyses. It is already fully formed by birth, which minimizes postnatal phenotypic plasticity, and it is generally well preserved in archaeological samples. Here we use morphometric data of the bony labyrinth to show that it is a surprisingly good marker of the global dispersal of modern humans from Africa. Labyrinthine morphology tracks genetic distances and geography in accordance with an isolation-by-distance model with dispersal from Africa. Our data further indicate that the neutral-like pattern of variation is compatible with stabilizing selection on labyrinth morphology. Given the increasingly important role of the petrous bone for ancient DNA recovery from archaeological specimens, we encourage researchers to acquire 3D morphological data of the inner ear structures before any invasive sampling. Such data will constitute an important archive of phenotypic variation in present and past populations, and will permit individual-based genotype–phenotype comparisons.

Reconstructing human population history from dental phenotypes

Dental phenotypic data are often used to reconstruct biological relatedness among past human groups. Teeth are an important data source because they are generally well preserved in the archaeological and fossil record, even when associated skeletal and DNA preservation is poor. Furthermore, tooth form is considered to be highly heritable and selectively neutral; thus, teeth are assumed to be an excellent proxy for neutral genetic data when none are available. However, to our knowledge, no study to date has systematically tested the assumption of genetic neutrality of dental morphological features on a global scale. Therefore, for the first time, this study quantifies the correlation of biological affinities between worldwide modern human populations, derived independently from dental phenotypes and neutral genetic markers. We show that population relationship measures based on dental morphology are significantly correlated with those based on neutral genetic data (on average r = 0.574, p < 0.001). This relatively strong correlation validates tooth form as a proxy for neutral genomic markers. Nonetheless, we suggest caution in reconstructions of population affinities based on dental data alone because only part of the dental morphological variation among populations can be explained in terms of neutral genetic differences.

Tracking modern human population history from linguistic and cranial phenotype

Languages and genes arguably follow parallel evolutionary trajectories, descending from a common source and subsequently differentiating. However, although common ancestry is established within language families, it remains controversial whether language preserves a deep historical signal. To address this question, we evaluate the association between linguistic and geographic distances across 265 language families, as well as between linguistic, geographic, and cranial distances among eleven populations from Africa, Asia, and Australia. We take advantage of differential population history signals reflected by human cranial anatomy, where temporal bone shape reliably tracks deep population history and neutral genetic changes, while facial shape is more strongly associated with recent environmental effects. We show that linguistic distances are strongly geographically patterned, even within widely dispersed groups. However, they are correlated predominantly with facial, rather than temporal bone, morphology, suggesting that variation in vocabulary likely tracks relatively recent events and possibly population contact.

The relative correspondence of cranial and genetic distances in papionin taxa and the impact of allometric adjustments

The reconstruction of phylogenetic relationships in the primate fossil record is dependent upon a thorough understanding of the phylogenetic utility of craniodental characters. Here, we test three previously proposed hypotheses for the propensity of primate craniomandibular data to exhibit homoplasy, using a study design based on the relative congruence between cranial distance matrices and a consensus genetic distance matrix ("genetic congruence") for papionin taxa: 1) matrices based on cranial regions subjected to less masticatory strain are more genetically congruent than high-strain cranial matrices; 2) matrices based on cranial regions developing earlier in ontogeny are more genetically congruent than matrices based on regions that develop later; and 3) matrices based on cranial regions with greater anatomical/functional complexity are more genetically congruent than matrices based on anatomically simpler regions. Morphological distance matrices based on the shape of 15 different cranial regions, delineated on the basis of previous catarrhine studies, were statistically compared to a matrix of known genetic distances in papionins. Since sexual dimorphism and allometry are known to characterize this clade, several analytical iterations were conducted: 1) mixed-sex, male-only, and female-only analyses and 2) with and without an allometric scaling adjustment. Across all datasets, the chondrocranium matrix was the most consistently correlated with genetic distances, which is also consistent with previous studies of cercopithecoid taxa; however, there was no support for the internal predictions of the three hypotheses tested. Allometric scaling corrections had the largest impact on the genetic congruence of facial shape matrices, a result consistent with previous studies that have described facial homoplasy in papionin taxa. These findings differ from patterns described for hominoid taxa, suggesting that no single predictive criterion can explain phylogenetic utility of cranial datasets across catarrhine primate taxa. Many of the differences in morphological-genetic matrix correlations could result from different levels of phenotypic integration and evolvability in cercopithecoids and hominoids, suggesting that further study of these phenomena in extant primates is warranted.

Morphological Covariation between the Maxillary Sinus and Midfacial Skeleton among Sub-Saharan and Circumpolar Modern Humans

OBJECTIVES

Maxillary sinus volume tracks ecogeographic differences in nasal form and may serve as a zone of accommodation for ontogenetic and evolutionary changes in nasal cavity breadth. However, little is known regarding how sinus volume is distributed within the midface. This study investigates morphological covariation between midfacial and sinus shape to better understand structural and functional relationships between the sinus, midface, and nasal cavity.

METHODS

Cranial and sinus models were rendered from CT scans of modern human samples from two disparate climates: sub-Saharan (South Africans [n = 15], West Africans [n = 17]), and circumpolar (Siberian Buriats [n = 18], Alaskan Inuit [n = 20]). Twenty-five 3D coordinate landmarks were placed on the models and subjected to generalized Procrustes analysis. Two-block partial least squares (2B-PLS) analysis was employed to identify patterns of covariation.

RESULTS

The 2B-PLS analysis indicates PLS1 (58.6% total covariation) relates to height and breadth relationships between the midface, nasal cavity, and maxillary sinus. Significant regional differences in PLS1 scores are evident: circumpolar samples possess taller/narrower noses with taller/wider sinuses compared to sub-Saharan samples. Importantly, PLS1 indicates that sinus breadth is not exclusively related to nasal cavity breadth; variation in lateral sinus expansion toward the zygoma represents an important contributing factor. PLS2 (16%) relates to supero-inferior positioning of the sinus within the midface. Allometric trends, while statistically significant, explain only a small portion of these covariation patterns.

CONCLUSIONS

These results suggest that the maxillary sinus serves as a zone of accommodation at the confluence of multiple facial components, potentially minimizing effects of morphological alterations to certain components on adjacent structures. Am J Phys Anthropol 160:483-497, 2016. © 2016 Wiley Periodicals, Inc.

Developmental Changes in Morphology of the Middle and Posterior External Cranial Base in Modern Homo sapiens

The basicranium has been described as phylogenetically informative, developmentally stable, and minimally affected by external factors and consequently plays an important role in cranial size and shape in subadult humans. Here basicranial variation of subadults from several modern human populations was investigated and the impact of genetic relatedness on basicranial morphological similarities was investigated. Three-dimensional landmark data were digitized from subadult basicrania from seven populations. Published molecular data on short tandem repeats were statistically compared to morphological data from three ontogenetic stages. Basicranial and temporal bone morphology both reflect genetic distances in childhood and adolescence (5–18 years), but not in infancy (<5 years). The occipital bone reflects genetic distances only in adolescence (13–18 years). The sphenoid bone does not reflect genetic distances at any ontogenetic stage but was the most diagnostic region evaluated, resulting in high rates of correct classification among populations. These results suggest that the ontogenetic processes driving basicranial development are complex and cannot be succinctly summarized across populations or basicranial regions. However, the fact that certain regions reflect genetic distances suggests that the morphology of these regions may be useful in reconstructing population history in specimens for which direct DNA evidence is unavailable, such as archaeological sites.

Ecogeography, genetics, and the evolution of human body form

Genetic resemblances among groups are non-randomly distributed in humans. This population structure may influence the correlations between traits and environmental drivers of natural selection thus complicating the interpretation of the fossil record when modern human variation is used as a referential model. In this paper, we examine the effects of population structure and natural selection on postcranial traits that reflect body size and shape with application to the more general issue of how climate - using latitude as a proxy - has influenced hominin morphological variation. We compare models that include terms reflecting population structure, ascertained from globally distributed microsatellite data, and latitude on postcranial phenotypes derived from skeletal dimensions taken from a large global sample of modern humans. We find that models with a population structure term fit better than a model of natural selection along a latitudinal cline in all cases. A model including both latitude and population structure terms is a good fit to distal limb element lengths and bi-iliac breadth, indicating that multiple evolutionary forces shaped these morphologies. In contrast, a model that included only a population structure term best explained femoral head diameter and the crural index. The results demonstrate that population structure is an important part of human postcranial variation, and that clinally distributed natural selection is not sufficient to explain among-group differentiation. The distribution of human body form is strongly influenced by the contingencies of modern human origins, which calls for new ways to approach problems in the evolution of human variation, past and present.

Genomic and cranial phenotype data support multiple modern human dispersals from Africa and a southern route into Asia

Despite broad consensus on Africa as the main place of origin for anatomically modern humans, their dispersal pattern out of the continent continues to be intensely debated. In extant human populations, the observation of decreasing genetic and phenotypic diversity at increasing distances from sub-Saharan Africa has been interpreted as evidence for a single dispersal, accompanied by a series of founder effects. In such a scenario, modern human genetic and phenotypic variation was primarily generated through successive population bottlenecks and drift during a rapid worldwide expansion out of Africa in the Late Pleistocene. However, recent genetic studies, as well as accumulating archaeological and paleoanthropological evidence, challenge this parsimonious model. They suggest instead a "southern route" dispersal into Asia as early as the late Middle Pleistocene, followed by a separate dispersal into northern Eurasia. Here we test these competing out-of-Africa scenarios by modeling hypothetical geographical migration routes and assessing their correlation with neutral population differentiation, as measured by genetic polymorphisms and cranial shape variables of modern human populations from Africa and Asia. We show that both lines of evidence support a multiple-dispersals model in which Australo-Melanesian populations are relatively isolated descendants of an early dispersal, whereas other Asian populations are descended from, or highly admixed with, members of a subsequent migration event.