Pathologies of Between-Groups Principal Components Analysis in Geometric Morphometrics

Quantitative analysis of facial shape in children to support respirator design

The COVID-19 pandemic demonstrated the need for respiratory protection against airborne pathogens. Respirator options for children are limited, and existing designs do not consider differences in facial shape or size. We created a dataset of children's facial images from three cohorts, then used geometric morphometric analyses of dense and sparse facial landmark representations to quantify age, sex and ancestry-related variation in shape. We found facial shape and size in children vary significantly with age from ages 2 to 18, particularly in dimensions relevant to respirator design. Sex differences are small throughout most of the age range of our sample. Ancestry is associated with significant facial shape variation in dimensions that may affect respirator fit. We offer guidance on how to our results can be used for the appropriate design of devices such as respirators for pediatric populations. We also highlight the need to consider ancestry-related variation in facial morphology to promote equitable, inclusive products.

Bioactive proteins and antioxidant peptides from Litsea cubeba fruit meal: Preparation, characterization and ameliorating function on high-fat diet-induced NAFLD through regulating lipid metabolism, oxidative stress and inflammatory response

Non-alcoholic fatty liver disease (NAFLD) plays an increasingly significant threat to human health. In this study, the processing by-products of Litsea cubeba fruit meal were defatted by ultrasound-assisted methods, then the acetone-precipitated protein of L. cubeba (LCP) was obtained and structural analysis was performed. LCP was hydrolyzed by a two-step sequential hydrolysis method using alcalase and papain. Subsequently, antioxidant peptide fraction (IV2) was isolated and identified from the resultant hydrolysate through membrane ultrafiltration, Sephadex G-15 chromatography, and liquid chromatograph mass spectrometer (LC-MS). Animal experimentation indicated the potential of IV2 to mitigate hepatic steatosis. Moreover, IV2 could effectively reduce oxidative stress-induced damage by modulating the Keap1-Nrf2 pathway to activate downstream heme oxygenase-1 (HO-1) and NAD(P) H quinone oxidoreductase 1 (NQO1). Integrating metabolomics and transcriptomics revealed enrichment in pathways associated with glycerolipid metabolism and fatty acid β-oxidation, suggesting the principal mechanisms underlying IV2's ameliorative effects on NAFLD. Transcriptome sequencing identified 3092 up-regulated and 3010 down-regulated genes following IV2 treatment. Interaction analyses based on different lipid compositions (DELs) and differentially expressed genes (DEGs) indicated that IV2 primarily alleviated hepatic steatosis by modulating peroxisome proliferator-activated receptor α (PPAR-α) related pathways, thereby augmenting fatty acid β-oxidation within liver cells. These results indicate that IV2 shows potential in improving high-fat diet (HFD)-induced NAFLD, with improved fatty acid β-oxidation and reduced triglyceride biosynthesis emerging as underlying mechanisms.

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.

Assessing craniofacial growth and form without landmarks: A new automatic approach based on spectral methods

We present a novel method for the morphometric analysis of series of 3D shapes, and demonstrate its relevance for the detection and quantification of two craniofacial anomalies: trigonocephaly and metopic ridges, using CT-scans of young children. Our approach is fully automatic, and does not rely on manual landmark placement and annotations. Our approach furthermore allows to differentiate shape classes, enabling successful differential diagnosis between trigonocephaly and metopic ridges, two related conditions characterized by triangular foreheads. These results were obtained using recent developments in automatic nonrigid 3D shape correspondence methods and specifically spectral approaches based on the functional map framework. Our method can capture local changes in geometric structure, in contrast to methods based, for instance, on global shape descriptors. As such, our approach allows to perform automatic shape classification and provides visual feedback on shape regions associated with different classes of deformations. The flexibility and generality of our approach paves the way for the application of spectral methods in quantitative medicine.

Initial Steps towards a Multilevel Functional Principal Components Analysis Model of Dynamical Shape Changes

In this article, multilevel principal components analysis (mPCA) is used to treat dynamical changes in shape. Results of standard (single-level) PCA are also presented here as a comparison. Monte Carlo (MC) simulation is used to create univariate data (i.e., a single "outcome" variable) that contain two distinct classes of trajectory with time. MC simulation is also used to create multivariate data of sixteen 2D points that (broadly) represent an eye; these data also have two distinct classes of trajectory (an eye blinking and an eye widening in surprise). This is followed by an application of mPCA and single-level PCA to "real" data consisting of twelve 3D landmarks outlining the mouth that are tracked over all phases of a smile. By consideration of eigenvalues, results for the MC datasets find correctly that variation due to differences in groups between the two classes of trajectories are larger than variation within each group. In both cases, differences in standardized component scores between the two groups are observed as expected. Modes of variation are shown to model the univariate MC data correctly, and good model fits are found for both the "blinking" and "surprised" trajectories for the MC "eye" data. Results for the "smile" data show that the smile trajectory is modelled correctly; that is, the corners of the mouth are drawn backwards and wider during a smile. Furthermore, the first mode of variation at level 1 of the mPCA model shows only subtle and minor changes in mouth shape due to sex; whereas the first mode of variation at level 2 of the mPCA model governs whether the mouth is upturned or downturned. These results are all an excellent test of mPCA, showing that mPCA presents a viable method of modeling dynamical changes in shape.

Evolutionary roots of the risk of hip fracture in humans

The transition to bipedal locomotion was a fundamental milestone in human evolution. Consequently, the human skeleton underwent substantial morphological adaptations. These adaptations are responsible for many of today's common physical impairments, including hip fractures. This study aims to reveal the morphological changes in the proximal femur, which increase the risk of intracapsular hip fractures in present-day populations. Our sample includes chimpanzees, early hominins, early Homo Neanderthals, as well as prehistoric and recent humans. Using Geometric Morphometric methods, we demonstrate differences in the proximal femur shape between hominids and populations that practiced different lifestyles. We show that the proximal femur morphology is a risk factor for intracapsular hip fracture independent of osteoporosis. Changes in the proximal femur, such as the shortening of the femoral neck and an increased anterolateral expansion of the greater trochanter, are associated with an increased risk for intracapsular hip fractures. We conclude that intracapsular hip fractures are a trade-off for efficient bipedal walking in humans, and their risk is exacerbated by reduced physical activity.

Endostructural and periosteal growth of the human humerus

The growth and development of long bones are of considerable interests in the fields of comparative anatomy and palaeoanthropology, as evolutionary changes and adaptations to specific physical activity patterns are expected to be revealed during bone ontogeny. Traditionally, the cross-sectional geometry of long bones has been examined at discrete locations usually placed at set intervals or fixed percentage distances along the midline axis of the bone shaft. More recently, the technique of morphometric mapping has enabled the continuous analysis of shape variation along the shaft. Here we extend this technique to the full sequence of late fetal and postnatal development of the humeral shaft in a modern human population sample, with the aim of establishing the shape changes during growth and their relationship with the development of the arm musculature and activity patterns. A sample of modern human humeri from individuals of age ranging from 24 weeks in utero to 18 years was imaged using microtomography at multiple resolutions and custom Matlab scripts. Standard biomechanical properties, cortical thickness, surface curvature, and pseudo-landmarks were extracted along radial vectors spaced at intervals of 1° at each 0.5% longitudinal increment measured along the shaft axis. Heat maps were also generated for cortical thickness and surface curvature. The results demonstrate that a whole bone approach to analysis of cross-sectional geometry is more desirable where possible, as there is a continuous pattern of variation along the shaft. It is also possible to discriminate very young individuals and adolescents from other groups by relative cortical thickness, and also by periosteal surface curvature.

The prognostic value of neonatal conventional-EEG monitoring in hypoxic-ischemic encephalopathy during therapeutic hypothermia

AIM

To determine the prognostic value of conventional electroencephalography (EEG) monitoring in neonatal hypoxic-ischemic encephalopathy (HIE).

METHOD

In this multicentre retrospective study, 95 full-term neonates (mean of 39.3wks gestational age [SD  1.4], 36 [38%] females, 59 [62%] males) with HIE (2013-2016) undergoing therapeutic hypothermia were divided between favourable or adverse outcomes. Background EEG activity (French classification scale: 0-1-2-3-4-5) and epileptic seizure burden (epileptic seizure scale: 0-1-2) were graded for seven 6-hour periods. Conventional EEG monitoring was investigated by principal component analysis (PCA), with clustering methods to extract prognostic biomarkers of development at 2 years and infant death.

RESULTS

Eighty-one per cent of infants with an adverse outcome had a French classification scale equal to or greater than 3 after H48 (100% at H6-12). The H6-12 epileptic seizure scale was equal to or greater than 1 for 39%, increased to 52% at H30-36 and then remained equal to or greater than 1 for 39% after H48. Forty-five per cent of infants with a favourable outcome had a H6-12 French classification scale equal to or greater than 3, which dropped to 5% after H48; 13% had a H6-12 epileptic seizure scale equal to or greater than 1 but no seizures after H48. Clustering methods based on PCA showed the high efficiency (96%) of conventional EEG monitoring for outcome prediction and allowed the definition of three prognostic EEG biomarkers: H6-78 French classification scale mean, H6-78 French classification scale slope, and H30-78 epileptic seizure scale mean.

INTERPRETATION

Early lability and recovery of physiological features is prognostic of a favourable outcome. Seizure onset from the second day should also be considered to accurately predict neurodevelopment in HIE and support the importance of conventional EEG monitoring in HIE in infants cooled with therapeutic hypothermia.

WHAT THIS PAPER ADDS

Comprehensive analysis showed the high prognostic efficiency (96%) of conventional electroencephalography (EEG) monitoring. Prognostic EEG biomarkers consist of the grade of background EEG activity, its evolution, and the mean seizure burden. Persistent seizures (H48) without an improvement in background EEG activity were consistently associated with an adverse outcome.

Green Tea Catechins Modulate Skeletal Development with Effects Dependent on Dose, Time, and Structure in a down Syndrome Mouse Model

Altered skeletal development in Down syndrome (DS) results in a brachycephalic skull, flattened face, shorter mandibular ramus, shorter limbs, and reduced bone mineral density (BMD). Our previous study showed that low doses of green tea extract enriched in epigallocatechin-3-gallate (GTE-EGCG), administered continuously from embryonic day 9 to postnatal day 29, reduced facial dysmorphologies in the Ts65Dn (TS) mouse model of DS, but high doses could exacerbate them. Here, we extended the analyses to other skeletal structures and systematically evaluated the effects of high and low doses of GTE-EGCG treatment over postnatal development in wild-type (WT) and TS mice using in vivo µCT and geometric morphometrics. TS mice developed shorter and wider faces, skulls, and mandibles, together with shorter and narrower humerus and scapula, and reduced BMD dynamically over time. Besides facial morphology, GTE-EGCG did not rescue any other skeletal phenotype in TS treated mice. In WT mice, GTE-EGCG significantly altered the shape of the skull and mandible, reduced the length and width of the long bones, and lowered the BMD. The disparate effects of GTE-EGCG depended on the dose, developmental timepoint, and anatomical structure analyzed, emphasizing the complex nature of DS and the need to further investigate the simultaneous effects of GTE-EGCG supplementation.

Morphology of the Bony Labyrinth Supports the Affinities of Paradolichopithecus with the Papionina

Discoveries in recent decades indicate that the large papionin monkeys Paradolipopithecus and Procynocephalus are key members of the Late Pliocene - Early Pleistocene mammalian faunas of Eurasia. However, their taxonomical status, phylogenetic relationships, and ecological profile remain unclear. Here we investigate the two latter aspects through the study of the inner ear anatomy, as revealed by applying micro-CT scan imaging techniques on the cranium LGPUT DFN3-150 of Paradolichopithecus from the lower Pleistocene (2.3 Ma) fossil site Dafnero-3 in Northwestern Greece. Using geometric morphometric methods, we quantified shape variation and the allometric and phylogenetic signals in extant cercopithecines (n = 80), and explored the morphological affinities of the fossil specimen with extant taxa. LGPUT DFN3-150 has a large centroid size similar to that of baboons and their relatives. It shares several shape features with Macacina and Cercopithecini, which we interpret as probable retention of a primitive morphology. Overall, its inner ear morphology is more consistent with a stem Papionini more closely related to Papionina than Macacina, or to a basal crown Papionina. Our results, along with morphometrical and ecological features from previous studies, call into question the traditional hypothesis of a Paradolichopithecus-Macacina clade, and provide alternative perspectives in the study of Eurasian primate evolution during the late Neogene-Quaternary.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10764-022-00329-4.

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.

Endocranial ontogeny and evolution in early Homo sapiens: The evidence from Herto, Ethiopia

Fossils and artifacts from Herto, Ethiopia, include the most complete child and adult crania of early Homo sapiens. The endocranial cavities of the Herto individuals show that by 160,000 y ago, brain size, inferred from endocranial size, was similar to that seen in modern human populations. However, endocranial shape differed from ours. This gave rise to the hypothesis that the brain itself evolved substantially during the past ∼200,000 y, possibly in tandem with the transition from Middle to Upper Paleolithic techno-cultures. However, it remains unclear whether evolutionary changes in endocranial shape mostly reflect changes in brain morphology rather than changes related to interaction with maxillofacial morphology. To discriminate between these effects, we make use of the ontogenetic fact that brain growth nearly ceases by the time the first permanent molars fully erupt, but the face and cranial base continue to grow until adulthood. Here we use morphometric data derived from digitally restored immature and adult H. sapiens fossils from Herto, Qafzeh, and Skhul (HQS) to track endocranial development in early H. sapiens. Until the completion of brain growth, endocasts of HQS children were similar in shape to those of modern human children. The similarly shaped endocasts of fossil and modern children indicate that our brains did not evolve substantially over the past 200,000 y. Differences between the endocranial shapes of modern and fossil H. sapiens adults developed only with continuing facial and basicranial growth, possibly reflecting substantial differences in masticatory and/or respiratory function.

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).

Geometric morphometrics of mandibles for dietary differentiation of Bovidae (Mammalia: Artiodactyla)

The mammalian family Bovidae has been widely studied in ecomorphological research, with important applications to paleoecological and paleohabitat reconstructions. Most studies of bovid craniomandibular features in relation to diet have used linear measurements. In this study, we conduct landmark-based geometric-morphometric analyses to evaluate whether different dietary groups can be distinguished by mandibular morphology. Our analysis includes data for 100 species of extant bovids, covering all bovid tribes and 2 dietary classifications. For the first classification with 3 feeding categories, we found that browsers (including frugivores), mixed feeders, and grazers are moderately well separated using mandibular shape. A finer dietary classification (frugivore, browser, browser-grazer intermediate, generalist, variable grazer, and obligate grazer) proved to be more useful for differentiating dietary extremes (frugivores and obligate grazers) but performed equally or less well for other groups. Notably, frugivorous bovids, which belong in tribe Cephalophini, have a distinct mandibular shape that is readily distinguished from all other dietary groups, yielding a 100% correct classification rate from jackknife cross-validation. The main differences in mandibular shape found among dietary groups are related to the functional needs of species during forage prehension and mastication. Compared with browsers, both frugivores and grazers have mandibles that are adapted for higher biomechanical demand of chewing. Additionally, frugivore mandibles are adapted for selective cropping. Our results call for more work on the feeding ecology and functional morphology of frugivores and offer an approach for reconstructing the diet of extinct bovids.

Allometry, sexual selection and evolutionary lines of least resistance shaped the evolution of exaggerated sexual traits within the genus Tyrannus

Variational properties hold a fundamental role in shaping biological evolution, exerting control over the magnitude and direction of evolutionary change elicited by microevolutionary processes that sort variation, such as selection or drift. We studied the genus Tyrannus as a model for examining the conditions and drivers that facilitate the repeated evolution of exaggerated, secondary sexual traits in the face of significant functional limitations. In particular, we explore the role of allometry, sexual selection and their interaction, on the diversification of tail morphology in the genus, assessing whether and how they promoted or constrained phenotypic evolution. Non-deep-forked species tend to show reduced sexual dimorphism and moderate allometric variation in tail shape. The exaggerated and functionally constrained long feathers of deep-forked species, T. savana and T. forficatus, which show both marked sexual dimorphism and allometric tail shape variation, independently diverged from the rest of the genus following the same direction of main interspecific variation accrued during the evolution of non-deep-forked species. Moreover, the latter direction is also aligned with axes summarising sexual dimorphism and allometric variation on deep-forked species, a feature lacking in the rest of the species. Thus, exaggerated tail morphologies are interpreted as the result of amplified divergence through reorientation and co-option of allometric variation by sexual selection, repeatedly driving morphology along a historically favoured direction of cladogenetic evolution.

An Exploration of Pathologies of Multilevel Principal Components Analysis in Statistical Models of Shape

3D facial surface imaging is a useful tool in dentistry and in terms of diagnostics and treatment planning. Between-group PCA (bgPCA) is a method that has been used to analyse shapes in biological morphometrics, although various “pathologies” of bgPCA have recently been proposed. Monte Carlo (MC) simulated datasets were created here in order to explore “pathologies” of multilevel PCA (mPCA), where mPCA with two levels is equivalent to bgPCA. The first set of MC experiments involved 300 uncorrelated normally distributed variables, whereas the second set of MC experiments used correlated multivariate MC data describing 3D facial shape. We confirmed results of numerical experiments from other researchers that indicated that bgPCA (and so also mPCA) can give a false impression of strong differences in component scores between groups when there is none in reality. These spurious differences in component scores via mPCA decreased significantly as the sample sizes per group were increased. Eigenvalues via mPCA were also found to be strongly affected by imbalances in sample sizes per group, although this problem was removed by using weighted forms of covariance matrices suggested by the maximum likelihood solution of the two-level model. However, this did not solve problems of spurious differences between groups in these simulations, which was driven by very small sample sizes in one group. As a “rule of thumb” only, all of our experiments indicate that reasonable results are obtained when sample sizes per group in all groups are at least equal to the number of variables. Interestingly, the sum of all eigenvalues over both levels via mPCA scaled approximately linearly with the inverse of the sample size per group in all experiments. Finally, between-group variation was added explicitly to the MC data generation model in two experiments considered here. Results for the sum of all eigenvalues via mPCA predicted the asymptotic amount for the total amount of variance correctly in this case, whereas standard “single-level” PCA underestimated this quantity.

Human semicircular canal form: Ontogenetic changes and variation of shape and size

The semicircular canals (SCCs) transduce angular acceleration of the head into neuronal signals, and their morphology has been used to infer function. Once formed, the bony labyrinth, that surrounds the canals, is tightly regulated and has a very low bone turnover. However, relaxed postnatal inhibition of bone remodelling later in ontogeny may allow for some organised adjustments of shape and size or for greater stochastic variation. In the present study, we test the hypotheses that after birth, the shape and size of the bony canal changes or becomes more variable, or both. We study microCT scans of human perinatal and adult temporal bones using a combination of geometric morphometric analysis and cross-sectional measures. Results revealed marginal differences of size (<5%), of cross-sectional shape and of measurement variability. Geometry of the three canals together and their cross-sectional areas were, however, indistinguishable between perinates and adults. These mixed findings are indicative of diminutive levels of relaxed inhibition superimposed over a constrained template of SCC morphology.

Can morphotaxa be assessed with photographs? Estimating the accuracy of two-dimensional cranial geometric morphometrics for the study of threatened populations of African monkeys

The classification of most mammalian orders and families is under debate and the number of species is likely greater than currently recognized. Improving taxonomic knowledge is crucial, as biodiversity is in rapid decline. Morphology is a source of taxonomic knowledge, and geometric morphometrics applied to two dimensional (2D) photographs of anatomical structures is commonly employed for quantifying differences within and among lineages. Photographs are informative, easy to obtain, and low cost. 2D analyses, however, introduce a large source of measurement error when applied to crania and other highly three dimensional (3D) structures. To explore the potential of 2D analyses for assessing taxonomic diversity, we use patas monkeys (Erythrocebus), a genus of large, semi-terrestrial, African guenons, as a case study. By applying a range of tests to compare ventral views of adult crania measured both in 2D and 3D, we show that, despite inaccuracies accounting for up to one-fourth of individual shape differences, results in 2D almost perfectly mirror those in 3D. This apparent paradox might be explained by the small strength of covariation in the component of shape variance related to measurement error. A rigorous standardization of photographic settings and the choice of almost coplanar landmarks are likely to further improve the correspondence of 2D to 3D shapes. 2D geometric morphometrics is, thus, appropriate for taxonomic comparisons of patas ventral crania. Although it is too early to generalize, our results corroborate similar findings from previous research in mammals, and suggest that 2D shape analyses are an effective heuristic tool for morphological investigation of small differences.

A spectral theory for Wright's inbreeding coefficients and related quantities

Wright’s inbreeding coefficient, F_ST, is a fundamental measure in population genetics. Assuming a predefined population subdivision, this statistic is classically used to evaluate population structure at a given genomic locus. With large numbers of loci, unsupervised approaches such as principal component analysis (PCA) have, however, become prominent in recent analyses of population structure. In this study, we describe the relationships between Wright’s inbreeding coefficients and PCA for a model of K discrete populations. Our theory provides an equivalent definition of F_ST based on the decomposition of the genotype matrix into between and within-population matrices. The average value of Wright’s F_ST over all loci included in the genotype matrix can be obtained from the PCA of the between-population matrix. Assuming that a separation condition is fulfilled and for reasonably large data sets, this value of F_ST approximates the proportion of genetic variation explained by the first (K − 1) principal components accurately. The new definition of F_ST is useful for computing inbreeding coefficients from surrogate genotypes, for example, obtained after correction of experimental artifacts or after removing adaptive genetic variation associated with environmental variables. The relationships between inbreeding coefficients and the spectrum of the genotype matrix not only allow interpretations of PCA results in terms of population genetic concepts but extend those concepts to population genetic analyses accounting for temporal, geographical and environmental contexts.

Principal component analysis (PCA) is the most-frequently used approach to describe population genetic structure from large population genomic data sets. In this study, we show that PCA not only estimates ancestries of sampled individuals, but also computes the average value of Wright’s inbreeding coefficient over the loci included in the genotype matrix. Our result shows that inbreeding coefficients and PCA eigenvalues provide equivalent descriptions of population structure. As a consequence, PCA extends the definition of those coefficients beyond the framework of allelic frequencies. We give examples on how F_ST can be computed from ancient DNA samples for which genotypes are corrected for coverage, and in an ecological genomic example where a proportion of genetic variation is explained by environmental variables.

A proximal radius of Barberapithecus huerzeleri from Castell de Barberà: Implications for locomotor diversity among pliopithecoids

Pliopithecoids are a diverse group of Miocene catarrhine primates from Eurasia. Their positional behavior is still unknown, and many species are known exclusively from dentognathic remains. Here, we describe a proximal radius (IPS66267) from the late Miocene of Castell de Barberà (Vallès-Penedès Basin, NE Iberian Peninsula) that represents the first postcranial specimen of the pliopithecoid Barberapithecus huerzeleri. A body mass estimate based on the radius is compared with dental estimates, and its morphology is compared with that of extant and fossil anthropoids by qualitative means as well as by landmark-based three-dimensional geometric morphometrics. The estimated body mass of ∼5 kg for IPS66267 closely matches the dental estimates for the (female) holotype, thereby discounting an alternative attribution to the large-bodied hominoid recorded at Castell de Barberà. In multiple features (oval and moderately tilted head with a pronounced lateral lip and a restricted articular area for the capitulum; proximodistally expanded proximal radioulnar joint; and short, robust, and anteroposteriorly compressed neck), the specimen differs from hominoids and resembles instead extant nonateline monkeys and stem catarrhines. The results of the morphometric analysis further indicate that the Barberapithecus proximal radius shows closer similarities with nonsuspensory arboreal cercopithecoids and the dendropithecid Simiolus. From a locomotor viewpoint, the radius of Barberapithecus lacks most of the features functionally related to climbing and/or suspensory behaviors and displays instead a proximal radioulnar joint that would have been particularly stable under pronation. On the other hand, the Barberapithecus radius differs from other stem catarrhines in the less anteroposteriorly compressed and less tilted radial head with a deeper capitular fovea, suggesting a somewhat enhanced mobility at the elbow joint. We conclude that pronograde arboreal quadrupedalism was the main component of the locomotor repertoire of Barberapithecus but that, similar to other crouzeliids, it might have displayed better climbing abilities than pliopithecids.

Ontogenetic and in silico models of spatial-packing in the hypermuscular mouse skull

Networks linking single genes to multiple phenotypic outcomes can be founded on local anatomical interactions as well as on systemic factors like biochemical products. Here we explore the effects of such interactions by investigating the competing spatial demands of brain and masticatory muscle growth within the hypermuscular myostatin-deficient mouse model and in computational simulations. Mice that lacked both copies of the myostatin gene (-/-) and display gross hypermuscularity, and control mice that had both copies of the myostatin gene (+/+) were sampled at 1, 7, 14 and 28 postnatal days. A total of 48 mice were imaged with standard as well as contrast-enhanced microCT. Size metrics and landmark configurations were collected from the image data and were analysed alongside in silico models of tissue expansion. Findings revealed that: masseter muscle volume was smaller in -/- mice at day 1 but became, and remained thereafter, larger by 7 days; -/- endocranial volumes begin and remained smaller; -/- enlargement of the masticatory muscles was associated with caudolateral displacement of the calvarium, lateral displacement of the zygomatic arches, and slight dorsal deflection of the face and basicranium. Simulations revealed basicranial retroflexion (flattening) and dorsal deflection of the face associated with muscle expansion and abrogative covariations of basicranial flexion and ventral facial deflection associated with endocranial expansion. Our findings support the spatial-packing theory and highlight the importance of understanding the harmony of competing spatial demands that can shape and maintain mammalian skull architecture during ontogeny.

The pectoral girdle of StW 573 ('Little Foot') and its implications for shoulder evolution in the Hominina

The ca. 3.67 Ma adult skeleton known as 'Little Foot' (StW 573), recovered from Sterkfontein Member 2 breccia in the Silberberg Grotto, is remarkable for its morphology and completeness. Preservation of clavicles and scapulae, including essentially complete right-side elements, offers opportunities to assess morphological and functional aspects of a nearly complete Australopithecus pectoral girdle. Here we describe the StW 573 pectoral girdle and offer quantitative comparisons to those of extant hominoids and selected homininans. The StW 573 pectoral girdle combines features intermediate between those of humans and other apes: a long and curved clavicle, suggesting a relatively dorsally positioned scapula; an enlarged and uniquely proportioned supraspinous fossa; a relatively cranially oriented glenoid fossa; and ape-like reinforcement of the axillary margin by a stout ventral bar. StW 573 scapulae are as follows: smaller than those of some homininans (i.e., KSD-VP-1/1 and KNM-ER 47000A), larger than others (i.e., A.L. 288-1, Sts 7, and MH2), and most similar in size to another australopith from Sterkfontein, StW 431. Moreover, StW 573 and StW 431 exhibit similar structural features along their axillary margins and inferior angles. As the StW 573 pectoral girdle (e.g., scapular configuration) has a greater affinity to that of apes-Gorilla in particular-rather than modern humans, we suggest that the StW 573 morphological pattern appears to reflect adaptations to arboreal behaviors, especially those with the hand positioned above the head, more than human-like manipulatory capabilities. When compared with less complete pectoral girdles from middle/late Miocene apes and that of the penecontemporaneous KSD-VP-1/1 (Australopithecus afarensis), and mindful of consensus views on the adaptiveness of arboreal positional behaviors soliciting abducted glenohumeral joints in early Pliocene taxa, we propose that the StW 573 pectoral girdle is a reasonable model for hypothesizing pectoral girdle configuration of the crown hominin last common ancestor.

An exploration of adolescent facial shape changes with age via multilevel partial least squares regression

BACKGROUND AND OBJECTIVES

Multilevel statistical models represent the existence of hierarchies or clustering within populations of subjects (or shapes in this work). This is a distinct advantage over single-level methods that do not. Multilevel partial-least squares regression (mPLSR) is used here to study facial shape changes with age during adolescence in Welsh and Finnish samples comprising males and females.

METHODS

3D facial images were obtained for Welsh and Finnish male and female subjects at multiple ages from 12 to 17 years old. 1000 3D points were defined regularly for each shape by using "meshmonk" software. A three-level model was used here, including level 1 (sex/ethnicity); level 2, all "subject" variations excluding sex, ethnicity, and age; and level 3, age. The mathematical formalism of mPLSR is given in an Appendix.

RESULTS

Differences in facial shape between the ages of 12 and 17 predicted by mPLSR agree well with previous results of multilevel principal components analysis (mPCA); buccal fat is reduced with increasing age and features such as the nose, brow, and chin become larger and more distinct. Differences due to ethnicity and sex are also observed. Plausible simulated faces are predicted from the model for different ages, sexes and ethnicities. Our models provide good representations of the shape data by consideration of appropriate measures of model fit (RMSE and R2).

CONCLUSIONS

Repeat measures in our dataset for the same subject at different ages can only be modelled indirectly at the lowest level of the model at discrete ages via mPCA. By contrast, mPLSR models age explicitly as a continuous covariate, which is a strong advantage of mPLSR over mPCA. These investigations demonstrate that multivariate multilevel methods such as mPLSR can be used to describe such age-related changes for dense 3D point data. mPLSR might be of much use in future for the prediction of facial shapes for missing persons at specific ages or for simulating shapes for syndromes that affect facial shape in new subject populations.

Ontogenetic divergence generates novel phenotypes in hybrid cichlids

Hybridization is suggested to contribute to ecomorphological and taxonomic diversity in lacustrine East African cichlids. This is supported by studies demonstrating that genetic diversity within lake radiations has been influenced by hybridization events, leading to extensive phenotypic differentiation of genetically closely related species. Hybrid persistence and speciation in sympatry with gene flow can be explained by pleiotropy in traits involved in reproductive isolation; however, little attention has been given to how trait differentiation is established during hybrid ontogeny, and how this may relate to trophic and locomotor specialization. This study compares body shape changes in a Lake Victoria cichlid hybrid throughout its post-hatch ontogeny to those of its parental species. Across the considered age/size categories, hybrids occupy a distinct and intermediate morphological space, yet where several transgressive traits emerge. A between-group principal component analysis on body shapes across size categories reveals axes of shape variation exclusive to the hybrids in the youngest/smallest size categories. Shape differences in the hybrids involved morphological traits known to be implicated in trophic and locomotor specializations in the parental species. Combined, our findings suggest that phenotypic divergence in the hybrid can lead to functional differences that may potentially release them to some degree from competition with the parental species. These findings agree with recent literature that addresses the potential importance of hybridization for the unusually recent origin of the Lake Victoria cichlid super-species flock.

A comparative analysis of the vestibular apparatus in Epipliopithecus vindobonensis: Phylogenetic implications

Pliopithecoids are an extinct group of catarrhine primates from the Miocene of Eurasia. More than 50 years ago, they were linked to hylobatids due to some morphological similarities, but most subsequent studies have supported a stem catarrhine status, due to the retention of multiple plesiomorphic features (e.g., the ectotympanic morphology) relative to crown catarrhines. More recently, some morphological similarities to hominoids have been noted, raising the question of whether they could be stem members of this clade. To re-evaluate these competing hypotheses, we examine the morphology of the semicircular canals of the bony labyrinth of the middle Miocene pliopithecid Epipliopithecus vindobonensis. The semicircular canals are suitable to test between these hypotheses because (1) they have been shown to embed strong phylogenetic signal and reliably discriminate among major clades; (2) several potential hominoid synapomorphies have been identified previously in the semicircular canals; and (3) semicircular canal morphology has not been previously described for any pliopithecoid. We use a deformation-based (landmark-free) three-dimensional geometric morphometric approach to compare Epipliopithecus with a broad primate sample of extant and extinct anthropoids. We quantify similarities in semicircular canal morphology using multivariate analyses, reconstruct ancestral morphotypes by means of a phylomorphospace approach, and identify catarrhine and hominoid synapomorphies based on discrete characters. Epipliopithecus semicircular canal morphology most closely resembles that of platyrrhines and Aegyptopithecus due to the retention of multiple anthropoid symplesiomorphies. However, Epipliopithecus is most parsimoniously interpreted as a stem catarrhine more derived than Aegyptopithecus due to the possession of a crown catarrhine synapomorphy (i.e., the rounded anterior canal), combined with the lack of other catarrhine and any hominoid synapomorphies. Some similarities with hylobatids and atelids are interpreted as homoplasies likely related to positional behavior. The semicircular canal morphology of Epipliopithecus thus supports the common view that pliopithecoids are stem catarrhines.

Optimizing digitalization effort in morphometrics

Quantifying phenotypes is a common practice for addressing questions regarding morphological variation. The time dedicated to data acquisition can vary greatly depending on methods and on the required quantity of information. Optimizing digitization effort can be done either by pooling datasets among users, by automatizing data collection, or by reducing the number of measurements. Pooling datasets among users is not without risk since potential errors arising from multiple operators in data acquisition prevent combining morphometric datasets. We present an analytical workflow to estimate within and among operator biases and to assess whether morphometric datasets can be pooled. We show that pooling and sharing data requires careful examination of the errors occurring during data acquisition, that the choice of morphometric approach influences amount of error, and that in some cases pooling data should be avoided. The demonstration is based on a worked example (Sus scrofa teeth) using a combinations of 18 morphometric approaches and datasets for which we identified and quantified several potential sources of errors in the workflow. We show that it is possible to estimate the analytical power of a study using a small subset of data to select the best morphometric protocol and to optimize the number of variables necessary for analysis. In particular, we focus on semi-landmarks, which often produce an inflation of variables in contrast to the number of available observations use in statistical testing. We show how the workflow can be used for optimizing digitization efforts and provide recommendations for best practices in error management.

Initial Investigations of the Cranial Size and Shape of Adult Eurasian Otters (Lutra lutra) in Great Britain

Three-dimensional (3D) surface scans were carried out in order to determine the shapes of the upper sections of (skeletal) crania of adult Eurasian otters (Lutra lutra) from Great Britain. Landmark points were placed on these shapes using a graphical user interface (GUI) and distance measurements (i.e., the length, height, and width of the crania) were found by using the landmark points. Male otters had significantly larger skulls than females (P < 0.001). Differences in size also occurred by geographical area in Great Britain (P < 0.05). Multilevel Principal Components Analysis (mPCA) indicated that sex and geographical area explained 31.1% and 9.6% of shape variation in "unscaled" shape data and that they explained 17.2% and 9.7% of variation in "scaled" data. The first mode of variation at level 1 (sex) correctly reflected size changes between males and females for "unscaled" shape data. Modes at level 2 (geographical area) also showed possible changes in size and shape. Clustering by sex and geographical area was observed in standardized component scores. Such clustering in a cranial shape by geographical area might reflect genetic differences in otter populations in Great Britain, although other potentially confounding factors (e.g., population age-structure, diet, etc.) might also drive regional differences. This work provides a successful first test of the effectiveness of 3D surface scans and multivariate methods, such as mPCA, to study the cranial morphology of otters.

Hominin diversity in East Asia during the Middle Pleistocene: A premolar endostructural perspective

Following the recent studies of East Asian mid-Middle to early Late Pleistocene hominin material, a large spectrum of morphological diversity has been recognized and the coexistence of archaic ('Homo erectus-like') and derived ('modern-like') dental morphological patterns has been highlighted. In fact, for most of these Chinese fossils, generally categorized as 'archaic Homo sapiens' or 'post-H. erectus Homo', the taxonomic attribution is a matter of contention. With the help of μCT techniques and a deformation-based 3D geometric morphometric approach, we focused on the morphological variation in the enamel-dentine junction (EDJ) of 18 upper and lower premolars from Chinese Middle Pleistocene hominins. We then compared our results with a number of fossil and modern human groups, including Early Pleistocene H. erectus from Sangiran; late Early Pleistocene hominins from Tighenif, Algeria; classic Neanderthals; and modern humans. Our results highlight an evolutionary/chronological trend of crown base reduction, elevation of EDJ topography, and EDJ surface simplification in the hominin groups studied here. Moreover, this study brings insights to the taxonomy/phylogeny of 6 late Middle Pleistocene specimens whose evolutionary placement has been debated for decades. Among these specimens, Changyang premolars show features that can be aligned with the Asian H. erectus hypodigm, whereas Panxian Dadong and Tongzi premolars are more similar to Late Pleistocene Homo. Compared with early to mid-Middle Pleistocene hominins in East Asia, late Middle Pleistocene hominins evince an enlarged morphological variation. A persistence of archaic morphotypes and possible admixture among populations during the late Middle Pleistocene are discussed.

Morphological evidence for early dog domestication in the European Pleistocene: New evidence from a randomization approach to group differences

The antiquity of the wolf/dog domestication has been recently pushed back in time from the Late Upper Paleolithic (~14,000 years ago) to the Early Upper Paleolithic (EUP; ~36,000 years ago). Some authors questioned this early dog domestication claiming that the putative (EUP) Paleolithic dogs fall within the morphological range of recent wolves. In this study, we reanalyzed a data set of large canid skulls using unbalanced- and balanced-randomized discriminant analyses to assess whether the putative Paleolithic dogs are morphologically unique or whether they represent a subsample of the wolf morpho-population. We evaluated morphological differences between 96 specimens of the 4 a priori reference groups (8 putative Paleolithic dogs, 41 recent northern dogs, 7 Pleistocene wolves, and 40 recent northern wolves) using discriminant analysis based on 5 ln-transformed raw and allometrically size-adjusted cranial measurements. Putative Paleolithic dogs are classified with high accuracies (87.5 and 100.0%, cross-validated) and randomization experiment suggests that these classification rates cannot be exclusively explained by the small and uneven sample sizes of reference groups. It indicates that putative Upper Paleolithic dogs may represent a discrete canid group with morphological signs of domestication (a relatively shorter skull and wider palate and braincase) that distinguish them from sympatric Pleistocene wolves. The present results add evidence to the view that these specimens could represent incipient Paleolithic dogs that were involved in daily activities of European Upper Paleolithic forager groups.

Modern morphometrics and the study of population differences: Good data behind clever analyses and cool pictures?

The study of phenotypic variation in time and space is central to evolutionary biology. Modern geometric morphometrics is the leading family of methods for the quantitative analysis of biological forms. This set of techniques relies heavily on technological innovation for data acquisition, often in the form of 2D or 3D digital images, and on powerful multivariate statistical tools for their analysis. However, neither the most sophisticated device for computerized imaging nor the best statistical test can produce accurate, robust and reproducible results, if it is not based on really good samples and an appropriate use of the 'measurements' extracted from the data. Using examples mostly from my own work on mammal craniofacial variation and museum specimens, I will show how easy it is to forget these most basic assumptions, while focusing heavily on analytical and visualization methods, and much less on the data that generate potentially powerful analyses and visually appealing diagrams.