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

Syst Biol. 2016 Mar;65(2):194-211. doi: 10.1093/sysbio/syv067. Epub 2015 Sep 16.


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.

Keywords: Elliptical Fourier analysis; Hoxa genes; Procrustes-based semilandmark; gene domain; limb morphogenesis; whole-mount in situ hybridization.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Classification / methods*
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental*
  • Homeodomain Proteins / genetics
  • Limb Buds / anatomy & histology
  • Limb Buds / embryology*
  • Mice
  • Phenotype*


  • Homeodomain Proteins
  • Hoxa11 protein, mouse
  • homeobox protein HOXA13