Use of a natural hybrid zone for genomewide association mapping of craniofacial traits in the house mouse

The identification of the genes involved in morphological variation in nature is still a major challenge. Here, we explore a new approach: we combine 178 samples from a natural hybrid zone between two subspecies of the house mouse (Mus musculus domesticus and Mus musculus musculus), and high coverage of the genome (~ 145K SNPs) to identify loci underlying craniofacial shape variation. Due to the long history of recombination in the hybrid zone, high mapping resolution is anticipated. The combination of genomes from subspecies allows the mapping of both, variation within subspecies and inter‐subspecific differences, thereby increasing the overall amount of causal genetic variation that can be detected. Skull and mandible shape were measured using 3D landmarks and geometric morphometrics. Using principal component axes as phenotypes, and a linear mixed model accounting for genetic relatedness in the mapping populations, we identified nine genomic regions associated with skull shape and 10 with mandible shape. High mapping resolution (median size of significant regions = 148 kb) enabled identification of single or few candidate genes in most cases. Some of the genes act as regulators or modifiers of signalling pathways relevant for morphological development and bone formation, including several with known craniofacial phenotypes in mice and humans. The significant associations combined explain 13% and 7% of the skull and mandible shape variation, respectively. In addition, a positive correlation was found between chromosomal length and proportion of variation explained. Our results suggest a complex genetic architecture for shape traits and support a polygenic model.     

A genome-wide association study of facial morphology identifies novel genetic loci in Han Chinese

The human face is a heritable surface with many complex sensory organs. In recent years, many genetic loci associated with facial features have been reported in different populations, yet there is a lack of studies on the Han Chinese population. Here, we report a genome-wide association study of 3 D normal human faces of 2,659 Han Chinese with autosegment phenotypes of facial morphology. We identify singlenucleotide polymorphisms(SNPs) encompassing four genomic regions showing significant associations with different facial regions, including SNPs in DENND1 B associated with the chin, SNPs among PISRT1 associated with eyes, SNPs between DCHS2 and SFRP2 associated with the nose, and SNPs in VPS13 B associated with the nose. We replicate 24 SNPs from previously reported genetic loci in different populations, whose candidate genes are DCHS2, SUPT3 H, HOXD1, SOX9, PAX3, and EDAR. These results provide a more comprehensive understanding of the genetic basis of variation in human facial morphology.     

A Genome-Wide Association Study Identifies Five Loci Influencing Facial Morphology in Europeans

Inter-individual variation in facial shape is one of the most noticeable phenotypes in humans, and it is clearly under genetic regulation; however, almost nothing is known about the genetic basis of normal human facial morphology. We therefore conducted a genome-wide association study for facial shape phenotypes in multiple discovery and replication cohorts, considering almost ten thousand individuals of European descent from several countries. Phenotyping of facial shape features was based on landmark data obtained from three-dimensional head magnetic resonance images (MRIs) and two-dimensional portrait images. We identified five independent genetic loci associated with different facial phenotypes, suggesting the involvement of five candidate genes—PRDM16, PAX3, TP63, C5orf50, and COL17A1—in the determination of the human face. Three of them have been implicated previously in vertebrate craniofacial development and disease, and the remaining two genes potentially represent novel players in the molecular networks governing facial development. Our finding at PAX3 influencing the position of the nasion replicates a recent GWAS of facial features. In addition to the reported GWA findings, we established links between common DNA variants previously associated with NSCL/P at 2p21, 8q24, 13q31, and 17q22 and normal facial-shape variations based on a candidate gene approach. Overall our study implies that DNA variants in genes essential for craniofacial development contribute with relatively small effect size to the spectrum of normal variation in human facial morphology. This observation has important consequences for future studies aiming to identify more genes involved in the human facial morphology, as well as for potential applications of DNA prediction of facial shape such as in future forensic applications.     

Ontogeny of facial dimorphism and patterns of individual development within one human population

Based on a longitudinal study of radiographs of the Denver Growth Study, we investigated the morphological development of individual and gender differences in the anterior neurocranium, face, and basicranium. In total, 500 X-rays of 14 males and 14 females, each with 18 landmarks and semilandmarks, were digitized and analyzed using geometric morphometric methods. Sexual dimorphism in shape and form is already present at the earliest age stage included in the analysis. However, the nature of dimorphism changes with age. Four factors apper to contribute to cranial sexual dimorphism in human postnatal development: 1) initial, possibly prenatal, differences in shape; 2) differences in the association of size and shape; 3) male hypermorphosis; and 4) some degree of difference in the direction of male and female growth trajectories. Studying changes in individuals, we find a low correlation between newborn and adult morphology, while 3-year-olds already show a high correlation with their adult form. We conclude that the adult pattern of interindividual difference in facial form in a single human population is established within the first few years of life.     

Genetic evidence for facial variation being a composite phenotype of cranial variation and facial soft tissue thickness

Facial and cranial variation represent a multidimensional set of highly correlated and heritable phenotypes. Little is known about the genetic basis explaining this correlation. We develop a software package ALoSFL for simultaneous localization of facial and cranial landmarks from head computed tomography (CT) images, apply it in the analysis of head CT images of 777 Han Chinese women, and obtain a set of phenotypes representing variation in face, skull and facial soft tissue thickness (FSTT). Association analysis of 301 single nucleotide polymorphisms (SNPs) from 191 distinct genomic loci previously associated with facial variation reveals an unexpected larger number of loci showing significant associations (P < 1e–3) with cranial phenotypes than expected under the null (O/E = 3.39), suggesting facial and cranial phenotypes share a substantial proportion of genetic components. Adding FSTT to a SNP-only model shows a large impact in explaining facial variance. A gene ontology analysis reveals that bone morphogenesis and osteoblast differentiation likely underlie our cranial-significant findings. Overall, this study simultaneously investigates the genetic effects on both facial and cranial variation of the same sample, supporting that facial variation is a composite phenotype of cranial variation and FSTT.     

Modeling 3D Facial Shape from DNA

Human facial diversity is substantial, complex, and largely scientifically unexplained. We used spatially dense quasi-landmarks to measure face shape in population samples with mixed West African and European ancestry from three locations (United States, Brazil, and Cape Verde). Using bootstrapped response-based imputation modeling (BRIM), we uncover the relationships between facial variation and the effects of sex, genomic ancestry, and a subset of craniofacial candidate genes. The facial effects of these variables are summarized as response-based imputed predictor (RIP) variables, which are validated using self-reported sex, genomic ancestry, and observer-based facial ratings (femininity and proportional ancestry) and judgments (sex and population group). By jointly modeling sex, genomic ancestry, and genotype, the independent effects of particular alleles on facial features can be uncovered. Results on a set of 20 genes showing significant effects on facial features provide support for this approach as a novel means to identify genes affecting normal-range facial features and for approximating the appearance of a face from genetic markers.     

GEOMETRIC MORPHOMETRICS OF DEVELOPMENTAL INSTABILITY: ANALYZING PATTERNS OF FLUCTUATING ASYMMETRY WITH PROCRUSTES METHODS

Although fluctuating asymmetry has become popular as a measure of developmental instability, few studies have examined its developmental basis. We propose an approach to investigate the role of development for morphological asymmetry by means of morphometric methods. Our approach combines geometric morphometrics with the two-way ANOVA customary for conventional analyses of fluctuating asymmetry and can discover localized features of shape variation by examining the patterns of covariance among landmarks. This approach extends the notion of form used in studies of fluctuating asymmetry from collections of distances between morphological landmarks to an explicitly geometric concept of shape characterized by the configuration of landmarks. We demonstrate this approach with a study of asymmetry in the wings of tsetse flies (Glossina palpalis gambiensis). The analysis revealed significant fluctuating and directional asymmetry for shape as well as ample shape variation among individuals and between the offspring of young and old females. The morphological landmarks differed markedly in their degree of variability but multivariate patterns of landmark covariation identified by principal component analysis were generally similar between fluctuating asymmetry (within-individual variability) and variation among individuals. Therefore there is no evidence that special developmental processes control fluctuating asymmetry. We relate some of the morphometric patterns to processes known to be involved in the development of fly wings.     

Getting into Shape: An Empirical Comparison of Traditional Truss-Based Morphometric Methods with a Newer Geometric Method Applied to New World Cichlids

Body shape is a difficult, but important, trait to quantify. Researchers have traditionally used multivariate analysis of several linear measures ('trusses') across the body form to quantify shape. Newer geometric morphometric methods claim to better estimate shape because they analyze the geometry among the locations of all landmarks simultaneously rather than the linear distances between pairs of landmarks. We tested this claim by comparing the results of several traditional morphometric analyses against a newer geometric analysis involving thin-plate splines (TPS), all applied to a common data set of morphologically variable new world cichlids Amphilophus citrinellus and A. zaliosus. The TPS method yielded slightly stronger evidence of morphological differences among forms, although traditional methods also distinguished the two species. Perhaps our most important result was the idiosyncratic interpretation of shape variation among the traditional truss-based methods, whereas the generation of deformation grids using the TPS approach yielded clear and visually interpretable figures. Our results indicate that geometric morphometrics can be a more effective way to analyze and interpret body form, but also that traditional methods can be relied upon to provide statistical evidence of shape differences, although not necessarily accurate information about the nature of variation in shape.     

Cranial airways and the integration between the inner and outer facial skeleton in humans

The cranial airways are in the center of the human face. Therefore variation in the size and shape of these central craniofacial structures could have important consequences for the surrounding midfacial morphology during development and evolution. Yet such interactions are unclear because one school of thought, based on experimental and developmental evidence, suggests a relative independence (modularity) of these two facial compartments, whereas another one assumes tight morphological integration. This study uses geometric morphometrics of modern humans (N = 263) and 40 three‐dimensional‐landmarks of the skeletal nasopharynx and nasal cavity and outer midfacial skeleton to analyze these questions in terms of modularity. The sizes of all facial compartments were all strongly correlated. Shape integration was high between the cranial airways and the outer midfacial skeleton and between the latter and the anterior airway openings (skeletal regions close to and including piriform aperture). However, no shape integration was detected between outer midface and posterior airway openings (nasopharynx and choanae). Similarly, no integration was detected between posterior and anterior airway openings. This may reflect functional modularization of nasal cavity compartments related to respiratory physiology and differential developmental interactions with the face. Airway size likely relates to the energetics of the organism, whereas airways shape might be more indicative of respiratory physiology and climate. Although this hypothesis should be addressed in future steps, here we suggest that selection on morphofunctional characteristics of the cranial airways could have cascading effects for the variation, development, and evolution of the human face. Am J Phys Anthropol 152:287–293, 2013. © 2013 Wiley Periodicals, Inc.     

Cranial morphological variation of Dromiciops gliroides (Microbiotheria) along its geographical distribution in south-central Chile: A three-dimensional analysis

We analyzed the variation in cranial morphology of the marsupial Dromiciops gliroides along its distribution in south-central Chile. We evaluated whether the cranial morphological variation is congruent with the phylogeographic structure previously observed in this species. We built three-dimensional models of 69 crania on which we digitized 30 landmarks. We used standard geometric morphometric methods to extract and analyze the shape and size components of the crania. Our data showed a subtle but consistent cranial size and shape variation along the studied distributional range, suggesting a geographic variation pattern rather than a phylogeographic structuring. Indeed, our multivariate analyses recovered a subtle morphological differentiation between island and mainland populations, contrary to what is suggested by a former phylogeographic study. We detected that either the cranial size variation, as well as the insularity and the latitude could be important factors underlying the cranial shape changes. We suggest that an interplay of historical and contemporary processes could be shaping the morphological pattern observed in this marsupial.     

A genome‐wide association study in Caucasian women suggests the involvement of HLA genes in the severity of facial solar lentigines

Solar lentigines are a common feature of sun‐induced skin ageing. Little is known, however, about the genetic factors contributing to their development. In this genome‐wide association study, we aimed to identify genetic loci associated with solar lentigines on the face in 502 middle‐aged French women. Nine SNPs, gathered in two independent blocks on chromosome 6, exhibited a false discovery rate below 25% when looking for associations with the facial lentigine score. The first block, in the 6p22 region, corresponded to intergenic SNPs and also exhibited a significant association with forehead lentigines (P = 1.37 × 10^?8). The second block, within the 6p21 HLA region, was associated with decreased HLA‐C expression according to several eQTL databases. Interestingly, these SNPs were also in high linkage disequilibrium with the HLA‐C*0701 allele (r² = 0.95). We replicated an association recently found by GWAS in the IRF4 gene. Finally, a complementary study on 44 selected candidate SNPs revealed novel associations in the MITF gene. Overall, our results point to several mechanisms involved in the severity of facial lentigines, including HLA/immunity and the melanogenesis pathway.     

Exploring a Tomato Landraces Collection for Fruit-Related Traits by the Aid of a High-Throughput Genomic Platform

During its evolution and domestication Solanum lycopersicum has undergone various genetic ‘bottlenecks’ and extreme inbreeding of limited genotypes. In Europe the tomato found a secondary centre for diversification, which resulted in a wide array of fruit shape variation given rise to a range of landraces that have been cultivated for centuries. Landraces represent a reservoir of genetic diversity especially for traits such as abiotic stress resistance and high fruit quality. Information about the variation present among tomato landrace populations is still limited. A collection of 123 genotypes from different geographical areas was established with the aim of capturing a wide diversity. Eighteen morphological traits were evaluated, mainly related to the fruit. About 45% of morphological variation was attributed to fruit shape, as estimated by the principal component analysis, and the dendrogram of relatedness divided the population in subgroups mainly on the basis of fruit weight and locule number. Genotyping was carried out using the tomato array platform SolCAP able to interrogate 7,720 SNPs. In the whole collection 87.1% markers were polymorphic but they decreased to 44–54% when considering groups of genotypes with different origin. The neighbour-joining tree analysis clustered the 123 genotypes into two main branches. The STRUCTURE analysis with K = 3 also divided the population on the basis of fruit size. A genomic-wide association strategy revealed 36 novel markers associated to the variation of 15 traits. The markers were mapped on the tomato chromosomes together with 98 candidate genes for the traits analyzed. Six regions were evidenced in which candidate genes co-localized with 19 associated SNPs. In addition, 17 associated SNPs were localized in genomic regions lacking candidate genes. The identification of these markers demonstrated that novel variability was captured in our germoplasm collection. They might also provide a viable indirect selection tool in future practical breeding programs.     

Finding associations in dense genetic maps: a genetic algorithm approach

Large-scale association studies hold promise for discovering the genetic basis of common human disease. These studies will consist of a large number of individuals, as well as large number of genetic markers, such as single nucleotide polymorphisms (SNPs). The potential size of the data and the resulting model space require the development of efficient methodology to unravel associations between phenotypes and SNPs in dense genetic maps. Our approach uses a genetic algorithm (GA) to construct logic trees consisting of Boolean expressions involving strings or blocks of SNPs. These blocks or nodes of the logic trees consist of SNPs in high linkage disequilibrium (LD), that is, SNPs that are highly correlated with each other due to evolutionary processes. At each generation of our GA, a population of logic tree models is modified using selection, cross-over and mutation moves. Logic trees are selected for the next generation using a fitness function based on the marginal likelihood in a Bayesian regression frame-work. Mutation and cross-over moves use LD measures to pro pose changes to the trees, and facilitate the movement through the model space. We demonstrate our method and the flexibility of logic tree structure with variable nodal lengths on simulated data from a coalescent model, as well as data from a candidate gene study of quantitative genetic variation.     

Sexual dimorphism in the baboon facial skeleton

Baboons exhibit marked sexual dimorphism in many aspects of their morphology. Dimorphism is especially pronounced in the face. We use finite-element analysis to investigate the ontogeny of sexual dimorphism in a cross-sectional sample of baboon (Papio sp.) faces. This method provides detailed quantitative information about size and shape changes at anatomical landmarks in the face during growth. Allometric results suggest that sexual dimorphism in facial size and shape is produced by ontogenetic scaling: males and females share a common ontogenetic trajectory. Analyses of growth in time, which complement allometric analyses, show that female growth slows much earlier than male growth, accounting for the differences between sexes. Local size and local shape follow similar patterns of growth, but changes in these variables are slower in females. Local and global facial size are much more dimorphic than local and global facial shape.     

Genome-wide association analysis of host genotype and plastic wing morphological variation of an endoparasitoid wasp <Emphasis Type="Italic">Asobara japonica</Emphasis> (Hymenoptera: Braconidae)

Accumulating evidence suggests that genotype of host insects influences the development of koinobiont endoparasitoids. Although there are many potential genetic variations that lead to the internal body environmental variations of host insects, association between the host genotype and the parasitoid development has not been examined in a genome-wide manner. In the present study, we used highly inbred whole genome sequenced strains of Drosophila melanogaster to associate single nucleotide polymorphisms (SNPs) of host flies with morphological traits of Asobara japonica, a larval-pupal parasitoid wasp that infected those hosts. We quantified the outline shape of the forewings of A. japonica with two major principal components (PC1 and PC2) calculated from Fourier coefficients obtained from elliptic Fourier analysis. We also quantified wing size and estimated wasp survival. We then examined the association between the PC scores, wing size and 1,798,561 SNPs and  the association between the estimated wasp survival and 1,790,544 SNPs. As a result, we obtained 22, 24 and 14 SNPs for PC1, PC2 and wing size and four SNPs for the estimated survival with P values smaller than 10^?5. Based on the location of the SNPs, 12, 17, 11 and five protein coding genes were identified as potential candidates for PC1, PC2, wing size and the estimated survival, respectively. Based on the function of the candidate genes, it is suggested that the host genetic variation associated with the cell growth and morphogenesis may influence the wasp’s morphogenetic variation.     

山顶洞101号男性头骨的三维颅面复原

山顶洞101号头骨化石是东亚地区保存最为完整的化石之一,是探讨东亚地区现代人起源的重要研究材料。本文依据数据集中现生人的面部软组织平均分布,提出了计算机三维颅面复原方法,实现了101号头骨生前面貌的预测复原。主要包括三个步骤：首先使用CT完成了101号男性头骨和下颌骨仿制模型的三维重建。然后,利用计算机技术将现生人的面部软组织分布作为101号头骨的面部软组织分布,实现了颅面虚拟复原,并采用手工绘画技巧再现了复原面貌的形态特征。最后,提出了一种基于面部软组织分布和面貌统计形状模型的形态分析方法,实现了颅面复原结果的评估。山顶洞101号头骨的复原面貌具有头部较长、额头前倾、眉弓粗壮等特征,与101号头骨的几何形态基本一致。该技术再现了更新世晚期人类的脑颅及面部的形态特征,为古人类颅面复原的研究提供了技术支持和参考资料。     

The evolutionary role of modularity and integration in the hominoid cranium

Patterns of morphological integration and modularity among shape features emerge from genetic and developmental factors with varying pleiotropic effects. Factors or processes affecting morphology only locally may respond to selection more easily than common factors that may lead to deleterious side effects and hence are expected to be more conserved. We briefly review evidence for such global factors in primate cranial development as well as for local factors constrained to either the face or the neurocranium. In a sample comprising 157 crania of Homo sapiens, Pan troglodytes, and Gorilla gorilla, we statistically estimated common and local factors of shape variation from Procrustes coordinates of 347 landmarks and semilandmarks. Common factors with pleiotropic effects on both the face and the neurocranium account for a large amount of shape variation, but mainly by extension or truncation of otherwise conserved developmental pathways. Local factors (modular shape characteristics) have more degrees of freedom for evolutionary change than mere ontogenetic scaling. Cranial shape is similarly integrated during development in all three species, but human evolution involves dissociation among several characteristics. The dissociation has probably been achieved by evolutionary alterations and by the novel emergence of local factors affecting characteristics that are controlled at the same time by the common factors.     

Craniofacial variation,body size and ecological factors in aboriginal populations from central Patagonia (2000–200 years B.P.)

Previous studies have shown that ecological factors had a significant role in shaping the patterns of craniofacial variation among South American populations. Here, we evaluate whether temperature and diet contributed to facial diversification in small geographic areas. Facial size and shape of 9 osteological samples from central Patagonia (Argentina) were described using 2D landmarks and semilandmarks. Data on mean annual temperature, diet composition (δ¹³C and δ¹⁵N values) and femoral head maximum breadth, used as a proxy of body mass, were obtained for each sample. We then tested the association of body mass and the ecological variables with facial morphology using spatial regression techniques and a model selection approach. Akaike Information Criterion produced disparate results for both components of facial morphology. The best model for facial size included temperature and body mass proxy, and accounted for more than 80% of variation in size. Lower temperatures were related to larger facial sizes. Body mass was negatively associated with facial size and showed no relationship with the temperature. This suggests a relatively independent variation of cranial traits and body mass at the spatial scale studied here. Facial shape was not associated with the temperature or diet composition, contrasting with the patterns observed at larger spatial scales. Our results point out that the effect of climatic variables on cranial traits might be a source of morphological differentiation not only at large scales but also in small geographic areas, and that size and shape display a differential preservation of environmental signals.     

A quantitative genetic analysis of localized morphology in mandibles of inbred mice using finite element scaling analysis.

We analyzed patterns of mandibular genetic and phenotypic morphological integration and the relationship of genealogy to interstrain molecular and morphological differences in ten inbred strains of mice. Positions of mandibular landmarks in two-dimensional space were used to construct a finite element mesh for each individual, then all individuals from the ten strains were compared to the average mandible from a standard strain (SEA/GnJ). Measures of size and shape associated with finite element scaling analysis were then used in a quantitative genetic analysis of mandibular variation. Significant genetic variation for mandibular size and shape was uncovered. Patterns of both genetic and phenotypic correlation for measures of landmark-specific sizes were consistent with models of morphological integration based on the developmental origin of parts of the mandible and on the effects of muscle attachment on mandibular morphology. Shape differences local to particular landmarks did not show these forms of morphological integration. Although interstrain distances based on local shape magnitudes were significantly correlated with genealogical relationship, distances based on local size differences were not. Even higher than the correlation of genealogy with distances based on local shape magnitude was the genealogical-molecular distance correlation. Patterns of morphometric mandibular variation corresponded to expected effects of epigenetic developmental processes. Also, when detailed shape differences were considered, morphology served as a rough guide to genealogy, although molecular distances showed a stronger relationship.