Genetic architecture of mandible shape in mice: effects of quantitative trait loci analyzed by geometric morphometrics

Shape variation in cranium, mandible and teeth in selected mouse strains

There are different strains of laboratory mouse used in many different fields. These strains differ anatomically. In order to determine these anatomical differences, shape analysis was conducted according to species. CD-1, C57bl/6 and Balb-c strains were preferred to study these differences. Forty-eight adult mouse strains belonging to these strains were utilized. The bones were photographed and geometric morphometry was applied to these photographs. Principal Component Analysis was applied to determine shape variations. In Principal component 1 for cranium, CD-1 and C57bl/6 strain groups showed different shape variations, while Balb-c strain group showed similar shape variations to the other strain groups. Principal Component 1 for the mandible separated the CD-1 and C57bl/6 strain groups in terms of shape variation. Principal Component 2 explained most of the variation between the C57bl/6 and CD-1 lineage groups. In PC1 for molars, the CD-1 group showed a different shape variation from the other groups. Mahalanobis distances and Procrustes distances were measured using Canonical variance analysis to explain the differences between the lineage groups. These measurements were statistically significant. For cranium, in canonical variate 1, CD-1 group of mouse and Balb-c group of mouse were separated from each other. In canonical variate 2, C57bl/6 group of mouse were separated from the other groups. For mandible, Balb-c group of mouse in canonical variate 1 and CD-1 group of mouse in canonical variate 2 were separated from the other groups. For molars, CD-1 group of mouse in canonical variate 1 and Balb-c group of mouse in canonical variate 2 were separated from the other groups. It was thought that these anatomical differences could be caused by genotypic factors as well as dietary differences and many different habits that would affect the way their muscles work.

Leveraging Descriptor Learning and Functional Map-based Shape Matching for Automatic Landmark Acquisition

Geometric morphometrics is widely employed across the biological sciences for the quantification of morphological traits. However, the scalability of these methods to large datasets is hampered by the requisite placement of landmarks, which can be laborious and time consuming if done manually. Additionally, the selected landmarks embody a particular hypothesis regarding the critical geometry pertinent to the biological inquiry at hand. Modifying this hypothesis lacks flexibility, necessitating the acquisition of an entirely new set of landmarks on the entire dataset to reflect any theoretical adjustments. In our research, we investigate the precision and accuracy of landmarks derived from the comprehensive set of functional correspondences acquired through the functional map framework of geometry processing. We use a deep functional map network to learn shape descriptors that effectively yield functional map-based and point-to-point correspondences between the specimens in our dataset. We then interrogate these maps to identify corresponding landmarks given manually placed landmarks from the entire dataset. We assess our method by automating the landmarking process on a dataset comprising mandibles from various rodent species, comparing its efficacy against MALPACA, a cutting-edge technique for automatic landmark placement. Compared to MALPACA, our model is notably faster and maintains competitive accuracy. The Root Mean Square Error (RMSE) analysis reveals that while MALPACA generally exhibits the lowest RMSE, our models perform comparably, especially with smaller training datasets, suggesting strong generalizability. Visual evaluations confirm the precision of our landmark placements, with deviations remaining within an acceptable range. These findings underscore the potential of unsupervised learning models in anatomical landmark placement, providing a viable and efficient alternative to traditional methods.

Evo-Devo Mechanobiology: The Missing Link

While the modern framework of evolutionary development (evo-devo) has been decidedly genetic, historic analyses have also considered the importance of mechanics in the evolution of form. With the aid of recent technological advancements in both quantifying and perturbing changes in the molecular and mechanical effectors of organismal shape, how molecular and genetic cues regulate the biophysical aspects of morphogenesis is becoming increasingly well studied. As a result, this is an opportune time to consider how the tissue-scale mechanics that underlie morphogenesis are acted upon through evolution to establish morphological diversity. Such a focus will enable a field of evo-devo mechanobiology that will serve to better elucidate the opaque relations between genes and forms by articulating intermediary physical mechanisms. Here, we review how the evolution of shape is measured and related to genetics, how recent strides have been made in the dissection of developmental tissue mechanics, and how we expect these areas to coalesce in evo-devo studies in the future.

Skeletal Class II Malocclusion: From Clinical Treatment Strategies to the Roadmap in Identifying the Genetic Bases of Development in Humans with the Support of the Collaborative Cross Mouse Population

Depending on how severe it is, malocclusion, which may involve misaligned teeth, jaws, or a combination of the two, can hurt a person's overall facial aesthetics. The maxillary molar develops before the mandibular molar in class II malocclusion, which affects 15% of the population in the United States. With a retrusive mandible, patients typically have a convex profile. The goal of this study is to classify the skeletal and dental variability present in class II malocclusion, to reduce heterogeneity, present the current clinical treatment strategies, to summarize the previously published findings of genetic analysis, discuss these findings and their constraints, and finally, propose a comprehensive roadmap to facilitate investigations aimed at determining the genetic bases of malocclusion development using a variety of genomic approaches. To further comprehend the hereditary components involved in the onset and progression of class II malocclusion, a novel animal model for class II malocclusion should be developed while considering the variety of the human population. To overcome the constraints of the previous studies, here, we propose to conduct novel research on humans with the support of mouse models to produce contentious findings. We believe that carrying out a genome-wide association study (GWAS) on a large human cohort to search for significant genes and their modifiers; an epigenetics-wide association study (EWAS); RNA-seq analysis; integrating GWAS and the expression of quantitative trait loci (eQTL); and the testing of microRNAs, small RNAs, and long noncoding RNAs in tissues related to the skeletal class II malocclusion (SCIIMO) phenotype, such as mandibular bone, gum, and jaw in humans and the collaborative cross (CC) mouse model, will identify novel genes and genetic factors affecting this phenotype. We anticipate discovering novel genetic elements to advance our knowledge of how this malocclusion phenotype develops and open the venue for the early identification of patients carrying the susceptible genetic factors so that we can offer early prevention treatment strategies.

Characterization of Triatoma infestans (Klug, 1834) (Hemiptera: Heteroptera, Reduviidae) from Residual Foci in the States of Bahia and Rio Grande do Sul, Brazil, Using Geometric Morphology

Triatoma infestans is one of the main vectors of Chagas disease in Latin America. Although the species is under control in most Latin countries, it is still necessary to maintain epidemiological surveillance. The present study aims to characterize T. infestans populations from residual foci in Bahia and Rio Grande do Sul, Brazil, comparing them with natural populations in Argentina and Bolivia. For this, we adopt the geometric morphometry of the heads. It is possible to report the morphometric variety of the studied populations. In addition, we show that the size of the heads contributes to the differentiation between populations, while the shape has less power to discriminate groups. Furthermore, we show that some natural populations have morphometric proximity to residual populations, suggesting a relationship between these triatomines. Our data do not support the origin of residual populations but demonstrate the importance of new studies with other techniques to understand the dynamics of distribution and reintroduction of these vectors in Brazilian territory.

Dissecting the Complexity of Skeletal-Malocclusion-Associated Phenotypes: Mouse for the Rescue

Skeletal deformities and malocclusions being heterogeneous traits, affect populations worldwide, resulting in compromised esthetics and function and reduced quality of life. Skeletal Class III prevalence is the least common of all angle malocclusion classes, with a frequency of 7.2%, while Class II prevalence is approximately 27% on average, varying in different countries and between ethnic groups. Orthodontic malocclusions and skeletal deformities have multiple etiologies, often affected and underlined by environmental, genetic and social aspects. Here, we have conducted a comprehensive search throughout the published data until the time of writing this review for already reported quantitative trait loci (QTL) and genes associated with the development of skeletal deformation-associated phenotypes in different mouse models. Our search has found 72 significant QTL associated with the size of the mandible, the character, shape, centroid size and facial shape in mouse models. We propose that using the collaborative cross (CC), a highly diverse mouse reference genetic population, may offer a novel venue for identifying genetic factors as a cause for skeletal deformations, which may help to better understand Class III malocclusion-associated phenotype development in mice, which can be subsequently translated to humans. We suggest that by performing a genome-wide association study (GWAS), an epigenetics-wide association study (EWAS), RNAseq analysis, integrating GWAS and expression quantitative trait loci (eQTL), micro and small RNA, and long noncoding RNA analysis in tissues associated with skeletal deformation and Class III malocclusion characterization/phenotypes, including mandibular basic bone, gum, and jaw, in the CC mouse population, we expect to better identify genetic factors and better understand the development of this disease.

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).

Complex adaptive landscape for a "Simple" structure: The role of trade-offs in the evolutionary dynamics of mandibular shape in ground squirrels

Trade-offs are inherent features of many biomechanical systems and are often seen as evolutionary constraints. Structural decoupling may provide a way to escape those limits in some systems but not for structures that transmit large forces, such as mammalian mandibles. For such structures to evolve in multiple directions on a complex adaptive landscape, different regions must change shape while maintaining structural integrity. We evaluated the complexity of the adaptive landscape for mandibular shape in Marmotini, a lineage of ground squirrels that varies in the proportions of seeds and foliage in their diets, by comparing the fit of models based on traits that predict changes in mandibular loading. The adaptive landscape was more complex than predicted by a two-peak model with a single dietary shift. The large number of adaptive peaks reflects a high diversity of directions of shape evolution. The number of adaptive peaks also reflects a multiplicity of functional trade-offs posed by the conflicting demands of processing foods with various combinations of material properties. The ability to balance trade-offs for diets with different proportions of the same foods may account for diversification and disparity of lineages in heterogeneous environments. Rather than constraints, trade-offs may be the impetus of evolutionary change.

A complex genetic architecture underlies mandibular evolution in big mice from Gough Island

Some of the most compelling examples of morphological evolution come from island populations. Alterations in the size and shape of the mandible have been repeatedly observed in murid rodents following island colonization. Despite this pattern and the significance of the mandible for dietary adaptation, the genetic basis of island-mainland divergence in mandibular form remains uninvestigated. To fill this gap, we examined mandibular morphology in 609 F2s from a cross between Gough Island mice, the largest wild house mice on record, and mice from a mainland reference strain (WSB). Univariate genetic mapping identifies 3 quantitative trait loci (QTL) for relative length of the temporalis lever arm and 2 distinct QTL for relative condyle length, 2 traits expected to affect mandibular function that differ between Gough Island mice and WSB mice. Multivariate genetic mapping of coordinates from geometric morphometric analyses identifies 27 QTL contributing to overall mandibular shape. Quantitative trait loci show a complex mixture of modest, additive effects dispersed throughout the mandible, with landmarks including the coronoid process and the base of the ascending ramus frequently modulated by QTL. Additive effects of most shape quantitative trait loci do not align with island-mainland divergence, suggesting that directional selection played a limited role in the evolution of mandibular shape. In contrast, Gough Island mouse alleles at QTL for centroid size and QTL for jaw length increase these measures, suggesting selection led to larger mandibles, perhaps as a correlated response to the evolution of larger bodies.

Genetic, morphometric, and molecular analyses of interspecies differences in head shape and hybrid developmental defects in the wasp genus Nasonia

Males in the parasitoid wasp genus Nasonia have distinct, species-specific, head shapes. The availability of fertile hybrids among the species, along with obligate haploidy of males, facilitates analysis of complex gene interactions in development and evolution. Previous analyses showed that both the divergence in head shape between Nasonia vitripennis and Nasonia giraulti, and the head-specific developmental defects of F2 haploid hybrid males, are governed by multiple changes in networks of interacting genes. Here, we extend our understanding of the gene interactions that affect morphogenesis in male heads. Use of artificial diploid male hybrids shows that alleles mediating developmental defects are recessive, while there are diverse dominance relationships among other head shape traits. At the molecular level, the sex determination locus doublesex plays a major role in male head shape differences, but it is not the only important factor. Introgression of a giraulti region on chromsome 2 reveals a recessive locus that causes completely penetrant head clefting in both males and females in a vitripennis background. Finally, a third species (N. longicornis) was used to investigate the timing of genetic changes related to head morphology, revealing that most changes causing defects arose after the divergence of N. vitripennis from the other species, but prior to the divergence of N. giraulti and N. longicornis from each other. Our results demonstrate that developmental gene networks can be dissected using interspecies crosses in Nasonia, and set the stage for future fine-scale genetic dissection of both head shape and hybrid developmental defects.

Sensitivity to expression levels underlies differential dominance of a putative null allele of the Drosophila tβh gene in behavioral phenotypes

The biogenic amine octopamine (OA) and its precursor tyramine (TA) are involved in controlling a plethora of different physiological and behavioral processes. The tyramine-β-hydroxylase (tβh) gene encodes the enzyme catalyzing the last synthesis step from TA to OA. Here, we report differential dominance (from recessive to overdominant) of the putative null tβh^nM18 allele in 2 behavioral measures in Buridan’s paradigm (walking speed and stripe deviation) and in proboscis extension (sugar sensitivity) in the fruit fly Drosophila melanogaster. The behavioral analysis of transgenic tβh expression experiments in mutant and wild-type flies as well as of OA and TA receptor mutants revealed a complex interaction of both aminergic systems. Our analysis suggests that the different neuronal networks responsible for the 3 phenotypes show differential sensitivity to tβh gene expression levels. The evidence suggests that this sensitivity is brought about by a TA/OA opponent system modulating the involved neuronal circuits. This conclusion has important implications for standard transgenic techniques commonly used in functional genetics.

Differential dominance occurs when genes associated with several phenotypes (pleiotropic genes) show different modes of inheritance (e.g., recessive, dominant or overdominant) depending on the phenotype. This study reveals that differential sensitivity to gene expression levels can mediate differential dominance, which can be a significant challenge for standard transgenic techniques commonly used to elucidate gene function.

Genetic analysis of the mandible morphology in DDD.Cg-Ay/Sgn and C57BL/6J inbred mice

Quantitative trait loci (QTL) mapping analysis was performed for the mandible morphology in DDD.Cg-A^y/Sgn and C57BL/6J inbred mice. The size and shape of the mandible was analysed by landmark-based geometric morphometrics as the centroid size and principal components (PCs), respectively. The A^y allele at the agouti locus significantly reduced the mandible size in DDD/Sgn background, and substantially altered the mandible shape in both strain backgrounds. Single-QTL scans, by including the agouti locus genotype (A^y or non-A^y) as an additive covariate, identified three significant QTL for the centroid size on chromosomes 5, 6 and 17, along with four suggestive QTL on chromosomes 2, 12, 18 and 19. These QTLs explained 46.85% of the centroid size variation in F₂ mice. When the F₂A^y and F₂ non-A^y mice were analysed separately, additional significant QTL were identified on chromosomes 12 and 15 in F₂ non-A^y mice. Single-QTL scans also identified 15 significant QTL for the PC1, PC2 and PC3. When the agouti locus genotype was included as an interactive covariate, nine significant QTLs were identified. Unexpectedly, these agouti-interacting QTLs were identified for relatively minor PCs, for which no significant single-QTL were identified. Therefore, it was suggested that the alteration of the mandible shape in A^y mice was the consequence of interactions between the A^y allele and genes that themselves have relatively small phenotypic effect. Although further in vivo studies are required, we postulated Pkd1 as a possible candidate gene underlying QTL for the centroid size on chromosome 17.

Geographical variation in Eurasian red squirrel (Sciurus vulgaris L., 1758) mandibles and the issue of subspecies-level organization: a failure of history?

Sciurus vulgaris is a widespread, highly polytypic tree squirrel species, under which a large number of subspecies have been described. This study tests the robustness of the current subspecific classification by using geometric morphometrics to quantify morphological variation in mandible shape, along with canonical variates analysis to test hypotheses of morphological distinctiveness. Patterns of mandible allometry were examined in eight out of 16 currently recognized subspecies. The significance of the discriminate functions was tested statistically, and the iterative jackknife procedure was applied to evaluate stability of the subspecies-specific discriminant functions. Applying criteria that focus on shape diagnosability, rather than mean group differences, indicates that most regional subspecific groupings show intergradations and continuity in mandible shape and size and that allometric effects on mandible shape are negligible. Evidence of a distinct subspecies confined to the Iberian Peninsula (Sciurus vulgaris infuscatus) and a discrete group originating from an extinct, 19th century population in Dorset, UK were identified based on these mandibular data. All other regional subspecific groupings were not diagnosably different. These results suggest that most red squirrel subspecies might represent non-diagnosable morphological variants whose taxonomic validity seems doubtful. More generally, our results highlight the importance of applying objective, quantitative and reproducible criteria to the issue of subspecies delimitation.

Effects of the Y-chromosome and the dominant hemimelia mutation on the morphology of the mouse mandible

The aims of this study were to test whether the Y-chromosome and the autosomal dominant hemimelia (Dh) mutation can affect mandible morphology in mice. I analyzed mandible size and shape using landmark-based geometric morphometrics in 16 DH-Chr Y^@ -+/+ (@ represents one of the inbred strain names) strains and observed significant differences in mandible size. The largest mandible was identified in strain DH-Chr Y^C3H and the smallest in strain DH-Chr Y^KK . Canonical variate and discriminant function analyses suggested that the mandible shapes of strains DH-Chr Y^C3H and DH-Chr Y^KK differed from those of the other strains. Because seven of the DH-Chr Y^@ -+/+ strains were maintained with dominant hemimelia, I also analyzed the potential influence of dominant hemimelia on mandible morphology because dominant hemimelia is known to cause various skeletal malformations. There were no significant differences in mandible size in seven sets of DH-Chr Y^@ -+/+ and DH-Chr Y^@ -Dh/+ strains. However, canonical variate analysis mapped strains DH-Chr Y^CAS -Dh/+ and DH-Chr Y^CBA -Dh/+ mapped distantly from the rest. Additionally, I observed similar patterns of shape change between DH-Chr Y^CAS -+/+ and DH-Chr Y^CAS -Dh/+, and between DH-Chr Y^CBA -+/+ and DH-Chr Y^CBA -Dh/+. These data indicate that the Y-chromosome affects the size and shape of the mouse mandible. Dominant hemimelia affects mandible shape but not size, and its effects emerge depending on the kinds of Y-chromosomes.

The Development of Integration in Marsupial and Placental Limbs

The morphological interdependence of traits, or their integration, is commonly thought to influence their evolution. As such, study of morphological integration and the factors responsible for its generation form an important branch of the field of morphological evolution. However, most research to date on post-cranial morphological integration has focused on adult patterns of integration. This study investigates patterns of correlation (i.e., morphological integration) among skeletal elements of the fore- and hind limbs of developing marsupial and placental mammals. The goals of this study are to establish how patterns of limb integration vary over development in marsupials and placentals, and identify factors that are likely responsible for their generation. Our results indicate that although the overall pattern of correlation among limb elements is consistent with adult integration throughout mammalian development, correlations vary at the level of the individual element and stage. As a result, the relative integration among fore- and hind limb elements varies dynamically between stages during development in both marsupial and placental mammals. Therefore, adult integration studies of the limbs may not be indicative of developmental integration. Results are also consistent with integration during early limb development being more heavily influenced by genetic and developmental factors, and later by function. Additionally, results are generally consistent with a constraint on marsupial forelimb evolution caused by the functional requirements of the crawl to the teat that operates by limiting morphological variation before and at the time of birth, and not after.

Creating diversity in mammalian facial morphology: a review of potential developmental mechanisms

Mammals (class Mammalia) have evolved diverse craniofacial morphology to adapt to a wide range of ecological niches. However, the genetic and developmental mechanisms underlying the diversification of mammalian craniofacial morphology remain largely unknown. In this paper, we focus on the facial length and orofacial clefts of mammals and deduce potential mechanisms that produced diversity in mammalian facial morphology. Small-scale changes in facial morphology from the common ancestor, such as slight changes in facial length and the evolution of the midline cleft in some lineages of bats, could be attributed to heterochrony in facial bone ossification. In contrast, large-scale changes of facial morphology from the common ancestor, such as a truncated, widened face as well as the evolution of the bilateral cleft possessed by some bat species, could be brought about by changes in growth and patterning of the facial primordium (the facial processes) at the early stages of embryogenesis.

Maternal environment and craniofacial growth: geometric morphometric analysis of mandibular shape changes with in utero thyroxine overexposure in mice

An estimated 3% of US pregnancies are affected by maternal thyroid dysfunction, with between one and three of every 1000 pregnancies being complicated by overactive maternal thyroid levels. Excess thyroid hormones are linked to neurological impairment and excessive craniofacial variation, affecting both endochondral and intramembranous bone. Using a geometric morphometric approach, this study evaluates the role of in utero thyroxine overexposure on the growth of offspring mandibles in a sample of 241 mice. Canonical variate analysis utilized 16 unilateral mandibular landmarks obtained from 3D micro-computed tomography to assess shape changes between unexposed controls (n = 63) and exposed mice (n = 178). By evaluating shape changes in the mandible among three age groups (15, 20 and 25 days postnatal) and different dosage levels (low, medium and high), this study found that excess maternal thyroxine alters offspring mandibular shape in both age- and dosage-dependent manners. Group differences in overall shape were significant (P < 0.001), and showed major changes in regions of the mandible associated with muscle attachment (coronoid process, gonial angle) and regions of growth largely governed by articulation with the cranial base (condyle) and occlusion (alveolus). These results compliment recent studies demonstrating that maternal thyroxine levels can alter the cranial base and cranial vault of offspring, contributing to a better understanding of both normal and abnormal mandibular development, as well as the medical implications of craniofacial growth and development.

A population level atlas of Mus musculus craniofacial skeleton and automated image-based shape analysis

Laboratory mice are staples for evo/devo and genetics studies. Inbred strains provide a uniform genetic background to manipulate and understand gene-environment interactions, while their crosses have been instrumental in studies of genetic architecture, integration and modularity, and mapping of complex biological traits. Recently, there have been multiple large-scale studies of laboratory mice to further our understanding of the developmental basis, evolution, and genetic control of shape variation in the craniofacial skeleton (i.e. skull and mandible). These experiments typically use micro-computed tomography (micro-CT) to capture the craniofacial phenotype in 3D and rely on manually annotated anatomical landmarks to conduct statistical shape analysis. Although the common choice for imaging modality and phenotyping provides the potential for collaborative research for even larger studies with more statistical power, the investigator (or lab-specific) nature of the data collection hampers these efforts. Investigators are rightly concerned that subtle differences in how anatomical landmarks were recorded will create systematic bias between studies that will eventually influence scientific findings. Even if researchers are willing to repeat landmark annotation on a combined dataset, different lab practices and software choices may create obstacles for standardization beyond the underlying imaging data. Here, we propose a freely available analysis system that could assist in the standardization of micro-CT studies in the mouse. Our proposal uses best practices developed in biomedical imaging and takes advantage of existing open-source software and imaging formats. Our first contribution is the creation of a synthetic template for the adult mouse craniofacial skeleton from 25 inbred strains and five F1 crosses that are widely used in biological research. The template contains a fully segmented cranium, left and right hemi-mandibles, endocranial space, and the first few cervical vertebrae. We have been using this template in our lab to segment and isolate cranial structures in an automated fashion from a mixed population of mice, including craniofacial mutants, aged 4-12.5 weeks. As a secondary contribution, we demonstrate an application of nearly automated shape analysis, using symmetric diffeomorphic image registration. This approach, which we call diGPA, closely approximates the popular generalized Procrustes analysis (GPA) but negates the collection of anatomical landmarks. We achieve our goals by using the open-source advanced normalization tools (ANT) image quantification library, as well as its associated R library (ANTsR) for statistical image analysis. Finally, we make a plea to investigators to commit to using open imaging standards and software in their labs to the extent possible to increase the potential for data exchange and improve the reproducibility of findings. Future work will incorporate more anatomical detail (such as individual cranial bones, turbinals, dentition, middle ear ossicles) and more diversity into the template.

Methods for Studying Morphological Integration and Modularity

Morphological integration and modularity are closely related concepts about how different traits of an organism are correlated. Integration is the overall pattern of intercorrelation; modularity is the partitioning of integration into evolutionarily or developmentally independent blocks of traits. Modularity and integration are usually studied using quantitative phenotypic data, which can be obtained either from extant or fossil organisms. Many methods are now available to study integration and modularity, all of which involve the analysis of patterns found in trait correlation or covariance matrices. We review matrix correlation, random skewers, fluctuating asymmetry, cluster analysis, Euclidean distance matrix analysis (EDMA), graphical modelling, two-block partial least squares, RV coefficients, and theoretical matrix modelling and discuss their similarities and differences. We also review different coefficients that are used to measure correlations. We apply all the methods to cranial landmark data from and ontogenetic series of Japanese macaques,Macaca fuscatato illustrate the methods and their individual strengths and weaknesses. We conclude that the exploratory approaches (cluster analyses of various sorts) were less informative and less consistent with one another than were the results of model testing or comparative approaches. Nevertheless, we found that competing models of modularity and integration are often similar enough that they are not statistically distinguishable; we expect, therefore, that several models will often be significantly correlated with observed data.

Development Shapes a Consistent Inbreeding Effect in Mouse Crania of Different Line Crosses

Development translates genetic variation into a multivariate pattern of phenotypic variation, distributing it among traits in a nonuniform manner. As developmental processes are largely shared within species, this suggests that heritable phenotypic variation will be patterned similarly, in spite of the different segregating alleles. To investigate developmental effect on the variational pattern in the shape of the mouse skull across genetically differentiated lines, we employed the full set of reciprocal crosses (a.k.a. diallel) between eight inbred mouse strains of the Collaborative Cross Project. We used geometric morphometrics and multivariate analysis to capture cranial size and shape changes in 8 parentals and their 54 F1 crosses. The high heterozygosity generated in the F1 crosses allowed us to compare the multivariate deviations of the F1 phenotypes from the expected midparental phenotypes in different haplotype combinations. In contrast to body weight, we found a high degree of nonadditive deviation in craniofacial shape. Whereas the phenotypic and genetic divergence of parental strains manifested in high dimensionality of additive effects, the nonadditive deviations exhibited lesser dimensionality and in particular a strikingly coherent direction in shape space. We interpret this finding as evidence for a strong structuring effect of a relatively small set of developmental processes on the mapping of genetic to phenotypic variation.

Second premolar agenesis is associated with mandibular form: a geometric morphometric analysis of mandibular cross-sections

The aim of this study was to compare mandibular form (i.e., size and shape) between patients with agenesis of the lower second premolar (P2) and a control group with no agenesis. Three hypotheses were tested: (H1) agenesis causes a change in mandibular morphology because of inadequate alveolar ridge development in the area of the missing tooth (mandibular plasticity); (H2) agenesis is caused by spatial limitations within the mandible (dental plasticity); and (H3) common genetic/epigenetic factors cause agenesis and affect mandibular form (pleiotropy). A geometric morphometric analysis was applied to cross-sectional images of computed tomography (CT) scans of three matched groups (n=50 each): (1) regularly erupted P2; (2) agenesis of P2 and the primary second molar in situ; and (3) agenesis of P2 and the primary second molar missing for >3 months. Cross-sections of the three areas of interest (first premolar, P2, first molar) were digitized with 23 landmarks and superimposed by a generalized Procrustes analysis. On average, the mandibular cross-sections were narrower and shorter in patients with P2 agenesis compared with that in the control group. Both agenesis groups featured a pronounced submandibular fossa. These differences extended at least one tooth beyond the agenesis-affected region. Taken together with the large interindividual variation that resulted in massively overlapping group distributions, these findings support genetic and/or epigenetic pleiotropy (H3) as the most likely origin of the observed covariation between mandibular form and odontogenesis. Clinically, reduced dimensions and greater variability of mandibular form, as well as a pronounced submandibular fossa, should be expected during the treatment planning of patients with P2 agenesis.

Human Facial Shape and Size Heritability and Genetic Correlations

The human face is an array of variable physical features that together make each of us unique and distinguishable. Striking familial facial similarities underscore a genetic component, but little is known of the genes that underlie facial shape differences. Numerous studies have estimated facial shape heritability using various methods. Here, we used advanced three-dimensional imaging technology and quantitative human genetics analysis to estimate narrow-sense heritability, heritability explained by common genetic variation, and pairwise genetic correlations of 38 measures of facial shape and size in normal African Bantu children from Tanzania. Specifically, we fit a linear mixed model of genetic relatedness between close and distant relatives to jointly estimate variance components that correspond to heritability explained by genome-wide common genetic variation and variance explained by uncaptured genetic variation, the sum representing total narrow-sense heritability. Our significant estimates for narrow-sense heritability of specific facial traits range from 28 to 67%, with horizontal measures being slightly more heritable than vertical or depth measures. Furthermore, for over half of facial traits, >90% of narrow-sense heritability can be explained by common genetic variation. We also find high absolute genetic correlation between most traits, indicating large overlap in underlying genetic loci. Not surprisingly, traits measured in the same physical orientation (i.e., both horizontal or both vertical) have high positive genetic correlations, whereas traits in opposite orientations have high negative correlations. The complex genetic architecture of facial shape informs our understanding of the intricate relationships among different facial features as well as overall facial development.

The Growth Hormone Receptor Gene is Associated with Mandibular Height in a Chinese Population

Genetic influences are important in the determination of mandibular morphology, and growth hormone receptor ( GHR) is believed to have an important influence on the growth of craniofacial bone. In this study, we used quantitative trait locus methods to evaluate the relationship between craniofacial morphology and single-nucleotide polymorphisms (SNPs) in GHR in an unselected healthy Chinese population. We systematically screened the 10 exons and nearby introns of GHR and identified 6 SNPs. Using 4 SNPs as markers, we studied the relationships between genotypes and craniofacial linear measurements. Individuals with the genotype CC of polymorphism I526L had a significantly greater mandibular ramus length (condylion-gonion/ articulare-gonion) than those with genotype AC or AA. Haplotype analysis showed that there were also significant differences between the long and short mandibular height groups in an extreme population. Our results indicate that the GHR gene polymorphism I526L is associated with mandibular height in the Chinese population.

Genetics of Skeletal Evolution in Unusually Large Mice from Gough Island

Organisms on islands often undergo rapid morphological evolution, providing a platform for understanding mechanisms of phenotypic change. Many examples of evolution on islands involve the vertebrate skeleton. Although the genetic basis of skeletal variation has been studied in laboratory strains, especially in the house mouse Mus musculus domesticus, the genetic determinants of skeletal evolution in natural populations remain poorly understood. We used house mice living on the remote Gough Island-the largest wild house mice on record-to understand the genetics of rapid skeletal evolution in nature. Compared to a mainland reference strain from the same subspecies (WSB/EiJ), the skeleton of Gough Island mice is considerably larger, with notable expansions of the pelvis and limbs. The Gough Island mouse skeleton also displays changes in shape, including elongations of the skull and the proximal vs. distal elements in the limbs. Quantitative trait locus (QTL) mapping in a large F₂ intercross between Gough Island mice and WSB/EiJ reveals hundreds of QTL that control skeletal dimensions measured at 5, 10, and/or 16 weeks of age. QTL exhibit modest, mostly additive effects, and Gough Island alleles are associated with larger skeletal size at most QTL. The QTL with the largest effects are found on a few chromosomes and affect suites of skeletal traits. Many of these loci also colocalize with QTL for body weight. The high degree of QTL colocalization is consistent with an important contribution of pleiotropy to skeletal evolution. Our results provide a rare portrait of the genetic basis of skeletal evolution in an island population and position the Gough Island mouse as a model system for understanding mechanisms of rapid evolution in nature.

Genome-Wide Association Study Reveals Multiple Loci Influencing Normal Human Facial Morphology

Numerous lines of evidence point to a genetic basis for facial morphology in humans, yet little is known about how specific genetic variants relate to the phenotypic expression of many common facial features. We conducted genome-wide association meta-analyses of 20 quantitative facial measurements derived from the 3D surface images of 3118 healthy individuals of European ancestry belonging to two US cohorts. Analyses were performed on just under one million genotyped SNPs (Illumina OmniExpress+Exome v1.2 array) imputed to the 1000 Genomes reference panel (Phase 3). We observed genome-wide significant associations (p < 5 x 10⁻⁸) for cranial base width at 14q21.1 and 20q12, intercanthal width at 1p13.3 and Xq13.2, nasal width at 20p11.22, nasal ala length at 14q11.2, and upper facial depth at 11q22.1. Several genes in the associated regions are known to play roles in craniofacial development or in syndromes affecting the face: MAFB, PAX9, MIPOL1, ALX3, HDAC8, and PAX1. We also tested genotype-phenotype associations reported in two previous genome-wide studies and found evidence of replication for nasal ala length and SNPs in CACNA2D3 and PRDM16. These results provide further evidence that common variants in regions harboring genes of known craniofacial function contribute to normal variation in human facial features. Improved understanding of the genes associated with facial morphology in healthy individuals can provide insights into the pathways and mechanisms controlling normal and abnormal facial morphogenesis.

There is a great deal of evidence that genes influence facial appearance. This is perhaps most apparent when we look at our own families, since we are more likely to share facial features in common with our close relatives than with unrelated individuals. Nevertheless, little is known about how variation in specific regions of the genome relates to the kinds of distinguishing facial characteristics that give us our unique identities, e.g., the size and shape of our nose or how far apart our eyes are spaced. In this paper, we investigate this question by examining the association between genetic variants across the whole genome and a set of measurements designed to capture key aspects of facial form. We found evidence of genetic associations involving measures of eye, nose, and facial breadth. In several cases, implicated regions contained genes known to play roles in embryonic face formation or in syndromes in which the face is affected. Our ability to connect specific genetic variants to ubiquitous facial traits can inform our understanding of normal and abnormal craniofacial development, provide potential predictive models of evolutionary changes in human facial features, and improve our ability to create forensic facial reconstructions from DNA.

Patterns of morphological integration in the dental arches of individuals with malocclusion

OBJECTIVES

In humans, there is a large range of variation in the form of the maxillary and mandibular dental arches. This variation can manifest as either prognathism or retrognathism in either or both arches, which can cause malocclusion and lead to abnormal masticatory function. This study aims to identify aspects of variation and morphological integration existing in the dental arches of individuals with different types of malocclusion.

METHODS

Coordinate landmark data were collected along the gingival margins of 397 scanned dental casts and then analyzed using geometric morphometric techniques to explore arch form variation and patterns of morphological integration within each malocclusion type.

RESULTS

Significant differences were identified between Class II forms (increased projection of upper arch relative to the lower arch) and Class III forms (lower arch projection beyond the upper arch) in symmetrical shape variation, including anteroposterior arch discrepancies and abnormal anterior arch divergence or convergence. Partial least squares analysis demonstrated that Class III dental arches have higher levels of covariance between upper and lower arches (RV = 0.91) compared to the dental arches of Class II (RV = 0.78) and Class I (RV = 0.73). These high levels of covariance, however, are on the lower end of the overall range of possible masticatory blocks, indicating weaker than expected levels of integration.

CONCLUSIONS

This study provides evidence for patterns of variation in dental arch shape found in individuals with Class II and Class III malocclusions. Moreover, differences in integration found between malocclusion types have ramifications for how such conditions should be studied and treated. Am. J. Hum. Biol. 28:879-889, 2016. © 2016Wiley Periodicals, Inc.

Quantitative trait locus analysis of body shape divergence in nine-spined sticklebacks based on high-density SNP-panel

Heritable phenotypic differences between populations, caused by the selective effects of distinct environmental conditions, are of commonplace occurrence in nature. However, the actual genomic targets of this kind of selection are still poorly understood. We conducted a quantitative trait locus (QTL) mapping study to identify genomic regions responsible for morphometric differentiation between genetically and phenotypically divergent marine and freshwater nine-spined stickleback (Pungitius pungitius) populations. Using a dense panel of SNP-markers obtained by restriction site associated DNA sequencing of an F2 recombinant cross, we found 22 QTL that explained 3.5-12.9% of phenotypic variance in the traits under investigation. We detected one fairly large-effect (PVE = 9.6%) QTL for caudal peduncle length-a trait with a well-established adaptive function showing clear differentiation among marine and freshwater populations. We also identified two large-effect QTL for lateral plate numbers, which are different from the lateral plate QTL reported in earlier studies of this and related species. Hence, apart from identifying several large-effect QTL in shape traits showing adaptive differentiation in response to different environmental conditions, the results suggest intra- and interspecific heterogeneity in the genomic basis of lateral plate number variation.

Does 3D Phenotyping Yield Substantial Insights in the Genetics of the Mouse Mandible Shape?

We describe the application of high-resolution 3D microcomputed tomography, together with 3D landmarks and geometric morphometrics, to validate and further improve previous quantitative genetic studies that reported QTL responsible for variation in the mandible shape of laboratory mice using a new backcross between C57BL/6J and A/J inbred strains. Despite the increasing availability of 3D imaging techniques, artificial flattening of the mandible by 2D imaging techniques seems at first an acceptable compromise for large-scale phenotyping protocols, thanks to an abundance of low-cost digital imaging systems such as microscopes or digital cameras. We evaluated the gain of information from considering explicitly this additional third dimension, and also from capturing variation on the bone surface where no precise anatomical landmark can be marked. Multivariate QTL mapping conducted with different landmark configurations (2D vs. 3D; manual vs. semilandmarks) broadly agreed with the findings of previous studies. Significantly more QTL (23) were identified and more precisely mapped when the mandible shape was captured with a large set of semilandmarks coupled with manual landmarks. It appears that finer phenotypic characterization of the mandibular shape with 3D landmarks, along with higher density genotyping, yields better insights into the genetic architecture of mandibular development. Most of the main variation is, nonetheless, preferentially embedded in the natural 2D plane of the hemi-mandible, reinforcing the results of earlier influential investigations.

Developmental basis of phenotypic integration in two Lake Malawi cichlids

Background

Cichlid fishes from the Rift Lakes of East Africa have undergone the most spectacular adaptive radiations in vertebrate history. Eco-morphological adaptations in lakes Victoria, Malawi and Tanganyika have resulted in a vast array of skull shapes and sizes, yet primary axes of morphological variation are conserved in all three radiations, prominently including the size of the preorbital region of the skull. This conserved pattern suggests that development may constrain the trajectories of cichlid head morphological evolution.

Results

Here, we (1) present a comparative analysis of adult head morphology in two sand-dweller cichlids from Lake Malawi with preorbital size differences representative of the main axis of variation among the three lakes and (2) analyze the ontogeny of shape and size differences by focusing on known developmental modules throughout the head. We find that (1) developmental differences between the two species correlate with known developmental modules; (2) differences in embryonic cartilage development result in phenotypically integrated changes among all bones derived from a single cartilage, while differences in dermal bone development tend to influence isolated regions within a bone; and lastly (3) species-specific morphologies appear in the embryo as subtle differences, which become progressively amplified throughout ontogeny. We propose that this amplification takes place at skeletal growth zones, the locations and shapes of which are patterned during embryogenesis.

Conclusions

This study is the most anatomically comprehensive analysis of the developmental differences underlying cichlid skull evolution in the Rift Lakes of East Africa. The scale of our analysis reveals previously unnoticed correlations between developmental modules and patterns of phenotypic integration. We propose that the primary axes of morphological variation among East African cichlid adaptive radiations are constrained by the hierarchical modularity of the teleost head skeleton.

Genetics of murine craniofacial morphology: diallel analysis of the eight founders of the Collaborative Cross

Using eight inbred founder strains of the mouse Collaborative Cross (CC) project and their reciprocal F1 hybrids, we quantified variation in craniofacial morphology across mouse strains, explored genetic contributions to craniofacial variation that distinguish the founder strains, and tested whether specific or summary measures of craniofacial shape display stronger additive genetic contributions. This study thus provides critical information about phenotypic diversity among CC founder strains and about the genetic contributions to this phenotypic diversity, which is relevant to understanding the basis of variation in standard laboratory strains and natural populations. Craniofacial shape was quantified as a series of size-adjusted linear dimensions (RDs) and by principal components (PC) analysis of morphological landmarks captured from computed tomography images from 62 of the 64 reciprocal crosses of the CC founder strains. We first identified aspects of skull morphology that vary between these phenotypically 'normal' founder strains and that are defining characteristics of these strains. We estimated the contributions of additive and various non-additive genetic factors to phenotypic variation using diallel analyses of a subset of these strongly differing RDs and the first eight PCs of skull shape variation. We find little difference in the genetic contributions to RD measures and PC scores, suggesting fundamental similarities in the magnitude of genetic contributions to both specific and summary measures of craniofacial phenotypes. Our results indicate that there are stronger additive genetic effects associated with defining phenotypic characteristics of specific founder strains, suggesting these distinguishing measures are good candidates for use in genotype-phenotype association studies of CC mice. Our results add significantly to understanding of genotype-phenotype associations in the skull, which serve as a foundation for modeling the origins of medically and evolutionarily relevant variation.

Performance of single and multi-atlas based automated landmarking methods compared to expert annotations in volumetric microCT datasets of mouse mandibles

BACKGROUND

Here we present an application of advanced registration and atlas building framework DRAMMS to the automated annotation of mouse mandibles through a series of tests using single and multi-atlas segmentation paradigms and compare the outcomes to the current gold standard, manual annotation.

RESULTS

Our results showed multi-atlas annotation procedure yields landmark precisions within the human observer error range. The mean shape estimates from gold standard and multi-atlas annotation procedure were statistically indistinguishable for both Euclidean Distance Matrix Analysis (mean form matrix) and Generalized Procrustes Analysis (Goodall F-test). Further research needs to be done to validate the consistency of variance-covariance matrix estimates from both methods with larger sample sizes.

CONCLUSION

Multi-atlas annotation procedure shows promise as a framework to facilitate truly high-throughput phenomic analyses by channeling investigators efforts to annotate only a small portion of their datasets.

Mapping of Craniofacial Traits in Outbred Mice Identifies Major Developmental Genes Involved in Shape Determination

The vertebrate cranium is a prime example of the high evolvability of complex traits. While evidence of genes and developmental pathways underlying craniofacial shape determination is accumulating, we are still far from understanding how such variation at the genetic level is translated into craniofacial shape variation. Here we used 3D geometric morphometrics to map genes involved in shape determination in a population of outbred mice (Carworth Farms White, or CFW). We defined shape traits via principal component analysis of 3D skull and mandible measurements. We mapped genetic loci associated with shape traits at ~80,000 candidate single nucleotide polymorphisms in ~700 male mice. We found that craniofacial shape and size are highly heritable, polygenic traits. Despite the polygenic nature of the traits, we identified 17 loci that explain variation in skull shape, and 8 loci associated with variation in mandible shape. Together, the associated variants account for 11.4% of skull and 4.4% of mandible shape variation, however, the total additive genetic variance associated with phenotypic variation was estimated in ~45%. Candidate genes within the associated loci have known roles in craniofacial development; this includes 6 transcription factors and several regulators of bone developmental pathways. One gene, Mn1, has an unusually large effect on shape variation in our study. A knockout of this gene was previously shown to affect negatively the development of membranous bones of the cranial skeleton, and evolutionary analysis shows that the gene has arisen at the base of the bony vertebrates (Eutelostomi), where the ossified head first appeared. Therefore, Mn1 emerges as a key gene for both skull formation and within-population shape variation. Our study shows that it is possible to identify important developmental genes through genome-wide mapping of high-dimensional shape features in an outbred population.

Formation of the face, mandible, and skull is determined in part by genetic factors, but the relationship between genetic variation and craniofacial development is not well understood. We demonstrate how recent advances in mouse genomics and statistical methods can be used to identify genes involved in craniofacial development. We use outbred mice together with a dense panel of genetic markers to identify genetic loci affecting craniofacial shape. Some of the loci we identify are also known from past studies to contribute to craniofacial development and bone formation. For example, the top candidate gene identified in this study, Mn1, is a gene that appeared at a time when animals started to form bony skulls, suggesting that it may be a key gene in this evolutionary innovation. This further suggests that Mn1 and other genes involved in head formation are also responsible for more fine-grained regulation of its shape. Our results confirm that the outbred mouse population used in this study is suitable to identify single genetic factors even under conditions where many genes cooperate to generate a complex phenotype.

Cranial symmetry in baleen whales (Cetacea, Mysticeti) and the occurrence of cranial asymmetry throughout cetacean evolution

Odontoceti and Mysticeti (toothed and baleen whales) originated from Eocene archaeocetes that had evolved from terrestrial artiodactyls. Cranial asymmetry is known in odontocetes that can hear ultrasound (>20,000 Hz) and has been linked to the split function of the nasal passage in breathing and vocalization. Recent results indicate that archaeocetes also had asymmetric crania. Their asymmetry has been linked to directional hearing in water, although hearing frequencies are still under debate. Mysticetes capable of low-frequency and infrasonic hearing (<20 Hz) are assumed to have symmetric crania. This study aims to resolve whether mysticete crania are indeed symmetric and whether mysticete cranial symmetry is plesiomorphic or secondary. Cranial shape was analyzed applying geometric morphometrics to three-dimensional (3D) cranial models of fossil and modern mysticetes, Eocene archaeocetes, modern artiodactyls, and modern odontocetes. Statistical tests include analysis of variance, principal components analysis, and discriminant function analysis. Results suggest that symmetric shape difference reflects general trends in cetacean evolution. Asymmetry includes significant fluctuating and directional asymmetry, the latter being very small. Mysticete crania are as symmetric as those of terrestrial artiodactyls and archaeocetes, without significant differences within Mysticeti. Odontocete crania are more asymmetric. These results indicate that (1) all mysticetes have symmetric crania, (2) archaeocete cranial asymmetry is not conspicuous in most of the skull but may yet be conspicuous in the rostrum, (3) directional cranial asymmetry is an odontocete specialization, and (4) directional cranial asymmetry is more likely related to echolocation than hearing.

Heritability of the Human Craniofacial Complex

Quantifying normal variation and the genetic underpinnings of anatomical structures is one of the main goals of modern morphological studies. However, the extent of genetic contributions to normal variation in craniofacial morphology in humans is still unclear. The current study addresses this gap by investigating the genetic underpinnings of normal craniofacial morphology. The sample under investigation consists of 75 linear and angular measurements spanning the entire craniofacial complex, recorded from lateral cephalographs of 1,379 participants in the Fels Longitudinal Study. Heritabilities for each trait were estimated using SOLAR, a maximum-likelihood variance components approach utilizing all pedigree information for parameter estimation. Trait means and mean effects of the covariates age, sex, age(2) , sex × age, and sex × age(2) were simultaneously estimated in the analytic models. All traits of the craniofacial complex were significantly heritable. Heritability estimates ranged from 0.10 to 0.60, with the majority being moderate. It is important to note that we found similar ranges of heritability occurring across the different functional/developmental components of the craniofacial complex, the splanchnocranium, the basicranium, and the neurocranium. This suggests that traits from different regions of the craniofacial complex are of comparable utility for the purposes of population history and phylogeny reconstruction. At the same time, this genetic influence on craniofacial morphology signals a caution to researchers of nongenetic studies to consider the implications of this finding when selecting samples for study given their project design and goals.

Genetic architecture of pollination syndrome transition between hummingbird-specialist and generalist species in the genus Rhytidophyllum (Gesneriaceae)

Adaptation to pollinators is a key factor of diversification in angiosperms. The Caribbean sister genera Rhytidophyllum and Gesneria present an important diversification of floral characters. Most of their species can be divided in two major pollination syndromes. Large-open flowers with pale colours and great amount of nectar represent the generalist syndrome, while the hummingbird-specialist syndrome corresponds to red tubular flowers with a less important nectar volume. Repeated convergent evolution toward the generalist syndrome in this group suggests that such transitions rely on few genes of moderate to large effect. To test this hypothesis, we built a linkage map and performed a QTL detection for divergent pollination syndrome traits by crossing one specimen of the generalist species Rhytidophyllum auriculatum with one specimen of the hummingbird pollinated R. rupincola. Using geometric morphometrics and univariate traits measurements, we found that floral shape among the second-generation hybrids is correlated with morphological variation observed between generalist and hummingbird-specialist species at the genus level. The QTL analysis showed that colour and nectar volume variation between syndromes involve each one major QTL while floral shape has a more complex genetic basis and rely on few genes of moderate effect. Finally, we did not detect any genetic linkage between the QTLs underlying those traits. This genetic independence of traits could have facilitated evolution toward optimal syndromes.

Using whole-genome sequences of the LG/J and SM/J inbred mouse strains to prioritize quantitative trait genes and nucleotides

Background

The laboratory mouse is the most commonly used model for studying variation in complex traits relevant to human disease. Here we present the whole-genome sequences of two inbred strains, LG/J and SM/J, which are frequently used to study variation in complex traits as diverse as aging, bone-growth, adiposity, maternal behavior, and methamphetamine sensitivity.

Results

We identified small nucleotide variants (SNVs) and structural variants (SVs) in the LG/J and SM/J strains relative to the reference genome and discovered novel variants in these two strains by comparing their sequences to other mouse genomes. We find that 39% of the LG/J and SM/J genomes are identical-by-descent (IBD). We characterized amino-acid changing mutations using three algorithms: LRT, PolyPhen-2 and SIFT. We also identified polymorphisms between LG/J and SM/J that fall in regulatory regions and highly informative transcription factor binding sites (TFBS). We intersected these functional predictions with quantitative trait loci (QTL) mapped in advanced intercrosses of these two strains. We find that QTL are both over-represented in non-IBD regions and highly enriched for variants predicted to have a functional impact. Variants in QTL associated with metabolic (231 QTL identified in an F₁₆ generation) and developmental (41 QTL identified in an F₃₄ generation) traits were interrogated and we highlight candidate quantitative trait genes (QTG) and nucleotides (QTN) in a QTL on chr13 associated with variation in basal glucose levels and in a QTL on chr6 associated with variation in tibia length.

Conclusions

We show how integrating genomic sequence with QTL reduces the QTL search space and helps researchers prioritize candidate genes and nucleotides for experimental follow-up. Additionally, given the LG/J and SM/J phylogenetic context among inbred strains, these data contribute important information to the genomic landscape of the laboratory mouse.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1592-3) contains supplementary material, which is available to authorized users.

Quantitative trait loci affecting the 3D skull shape and size in mouse and prioritization of candidate genes in-silico

We describe the first application of high-resolution 3D micro-computed tomography, together with 3D landmarks and geometric morphometrics, to map QTL responsible for variation in skull shape and size using a backcross between C57BL/6J and A/J inbred strains. Using 433 animals, 53 3D landmarks, and 882 SNPs from autosomes, we identified seven QTL responsible for the skull size (SCS.qtl) and 30 QTL responsible for the skull shape (SSH.qtl). Size, sex, and direction-of-cross were all significant factors and included in the analysis as covariates. All autosomes harbored at least one SSH.qtl, sometimes up to three. Effect sizes of SSH.qtl appeared to be small, rarely exceeding 1% of the overall shape variation. However, they account for significant amount of variation in some specific directions of the shape space. Many QTL have stronger effect on the neurocranium than expected from a random vector that will parcellate uniformly across the four cranial regions. On the contrary, most of QTL have an effect on the palate weaker than expected. Combined interval length of 30 SSH.qtl was about 315 MB and contained 2476 known protein coding genes. We used a bioinformatics approach to filter these candidate genes and identified 16 high-priority candidates that are likely to play a role in the craniofacial development and disorders. Thus, coupling the QTL mapping approach in model organisms with candidate gene enrichment approaches appears to be a feasible way to identify high-priority candidates genes related to the structure or tissue of interest.

The macroevolutionary consequences of phenotypic integration: from development to deep time

Phenotypic integration is a pervasive characteristic of organisms. Numerous analyses have demonstrated that patterns of phenotypic integration are conserved across large clades, but that significant variation also exists. For example, heterochronic shifts related to different mammalian reproductive strategies are reflected in postcranial skeletal integration and in coordination of bone ossification. Phenotypic integration and modularity have been hypothesized to shape morphological evolution, and we extended simulations to confirm that trait integration can influence both the trajectory and magnitude of response to selection. We further demonstrate that phenotypic integration can produce both more and less disparate organisms than would be expected under random walk models by repartitioning variance in preferred directions. This effect can also be expected to favour homoplasy and convergent evolution. New empirical analyses of the carnivoran cranium show that rates of evolution, in contrast, are not strongly influenced by phenotypic integration and show little relationship to morphological disparity, suggesting that phenotypic integration may shape the direction of evolutionary change, but not necessarily the speed of it. Nonetheless, phenotypic integration is problematic for morphological clocks and should be incorporated more widely into models that seek to accurately reconstruct both trait and organismal evolution.

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.