Small changes, big results: evolution of morphological discontinuity in mammals

Quantification of gene expression patterns to reveal the origins of abnormal morphogenesis

The earliest developmental origins of dysmorphologies are poorly understood in many congenital diseases. They often remain elusive because the first signs of genetic misregulation may initiate as subtle changes in gene expression, which are hard to detect and can be obscured later in development by secondary effects. Here, we develop a method to trace back the origins of phenotypic abnormalities by accurately quantifying the 3D spatial distribution of gene expression domains in developing organs. By applying Geometric Morphometrics to 3D gene expression data obtained by Optical Projection Tomography, we determined that our approach is sensitive enough to find regulatory abnormalities that have never been detected previously. We identified subtle but significant differences in the gene expression of a downstream target of a Fgfr2 mutation associated with Apert syndrome, demonstrating that these mouse models can further our understanding of limb defects in the human condition. Our method can be applied to different organ systems and models to investigate the etiology of malformations.

Our development in the womb is complex. Genes need to switch on and off in a precise order, controlling the activity of millions of cells as they work together to form different tissues. For everything to happen smoothly, cells must use instructions provided by each gene exactly at the correct moment and in the correct place. In this biological assembly line, the slightest change can lead to a defect.

Certain genetic mutations can change when and where cells use particular genes, and this can cause errors in development. These kinds of mutations are a common cause of birth defects, but we cannot always pinpoint how they begin. For example, a single mutation in a gene called FGFR2 causes malformations in the head, the heart and the limbs in a rare disease called Apert syndrome.

The first signs that development has gone wrong can be subtle changes in the use of certain genes, impossible to detect with standard methods. As development continues, other processes can mask the impact of problems with certain genes. Ultimately, changes alter the shape of the developing embryo.

Genetically engineered mouse models can mimic the gene defects that cause disease in humans. But current methods are not sensitive enough to detect the very first signs of defects. Now, Martínez-Abadías et al. developed a new method to detect these subtle changes and reveal the precise moment when development starts to go wrong.

In mice, a specific mutation in the FGFR2 gene affects the activity of a series of other genes. To track the levels of one of these genes, Martínez-Abadías et al. marked mouse embryos using a chemical label. Scanning the embryos then revealed the pattern of the cells using the gene during the earliest stages of development. In mice carrying a mutation in the FGFR2 gene, subtle changes in gene expression began just a few hours after their limbs start to develop. But it took another half a day to see the effects of these changes on the shape and size of the growing limbs. This approach revealed changes in gene expression before any problems with development were visible by eye.

Tracking subtle changes in the way cells use genes could allow us to detect the origins of embryo malformations before they appear, pointing at the best moment to start a treatment. With further development, the model could extend to other genes, proteins, animal models and diseases.

Geometric Morphometrics on Gene Expression Patterns Within Phenotypes: A Case Example on Limb Development

How the genotype translates into the phenotype through development is critical to fully understand the evolution of phenotypes. We propose a novel approach to directly assess how changes in gene expression patterns are associated with changes in morphology using the limb as a case example. Our method combines molecular biology techniques, such as whole-mount in situ hybridization, with image and shape analysis, extending the use of Geometric Morphometrics to the analysis of nonanatomical shapes, such as gene expression domains. Elliptical Fourier and Procrustes-based semilandmark analyses were used to analyze the variation and covariation patterns of the limb bud shape with the expression patterns of two relevant genes for limb morphogenesis, Hoxa11 and Hoxa13. We devised a multiple thresholding method to semiautomatically segment gene domains at several expression levels in large samples of limb buds from C57Bl6 mouse embryos between 10 and 12 postfertilization days. Besides providing an accurate phenotyping tool to quantify the spatiotemporal dynamics of gene expression patterns within developing structures, our morphometric analyses revealed high, non-random, and gene-specific variation undergoing canalization during limb development. Our results demonstrate that Hoxa11 and Hoxa13, despite being paralogs with analogous functions in limb patterning, show clearly distinct dynamic patterns, both in shape and size, and are associated differently with the limb bud shape. The correspondence between our results and already well-established molecular processes underlying limb development confirms that this morphometric approach is a powerful tool to extract features of development regulating morphogenesis. Such multilevel analyses are promising in systems where not so much molecular information is available and will advance our understanding of the genotype–phenotype map. In systematics, this knowledge will increase our ability to infer how evolution modified a common developmental pattern to generate a wide diversity of morphologies, as in the vertebrate limb.

The developmental renaissance in adaptationism

From an adaptation perspective, unoccupied patches of morphological space are inferred to be empty because they are of low fitness and selected against. These inferences hinge on venturesome assumptions, because emptiness is explained by low fitness and low fitness is inferred from emptiness. Moreover, non-adaptive factors, such as developmental constraint, could also plausibly account for empty morphospace. In response, biologists increasingly study ontogeny to test the assumption that unobserved phenotypes could be produced if selection were to favor them; finding that empty space morphologies can be readily produced in development helps reject constraint and lends support to adaptive hypotheses. This developmental approach to adaptation calls on manifold techniques, including embryology, artificial selection and comparative methods. Belying their diversity, all of these methods examine the causes of empty morphospace and mark a return of development, long excluded from traditional evolutionary biology, to adaptationist practice.

Evolutionary trends of the pharyngeal dentition in Cypriniformes (Actinopterygii: Ostariophysi)

Background

The fish order Cypriniformes is one of the most diverse ray-finned fish groups in the world with more than 3000 recognized species. Cypriniformes are characterized by a striking distribution of their dentition: namely the absence of oral teeth and presence of pharyngeal teeth on the last gill arch (fifth ceratobranchial). Despite this limited localisation, the diversity of tooth patterns in Cypriniformes is astonishing. Here we provide a further description of this diversity using X-ray microtomography and we map the resulting dental characters on a phylogenetic tree to explore evolutionary trends.

Results

We performed a pilot survey of dental formulae and individual tooth shapes in 34 adult species of Cypriniformes by X-ray microtomography (using either conventional X-ray machine, or synchrotron microtomography when necessary) or by dissecting. By mapping morphological results in a phylogenetic tree, it emerges that the two super-families Cobitoidea and Cyprinoidea have followed two distinct evolutionary pathways. Furthermore, our analysis supports the hypothesis of a three-row dentition as ancestral for Cyprinoidea and a general trend in tooth row reduction in most derived lineages. Yet, this general scheme must be considered with caution as several events of tooth row gain and loss have occurred during evolutionary history of Cyprinoidea.

Significance

Dentition diversity in Cypriniformes constitutes an excellent model to study the evolution of complex morphological structures. This morphological survey clearly advocates for extending the use of X-ray microtomography to study tooth morphology in Cypriniformes. Yet, our survey also underlines that improved knowledge of Cypriniformes life traits, such as feeding habits, is required as current knowledge is not sufficient to conclude on the link between diet and dental morphology.