Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis

There
are two basic forms of animal development: mosaic (as found in roundworms and
sea squirts) and regulative (as found in amphibians and mammals). How might one
distinguish between each type of development? Using a four-dimensional spatial
representation (x,y,z,t), major
features of the developmental process are revealed. To establish the role of
mosaic mechanisms, we can map the cell division process to a computational
representation of C. elegans
embryogenesis using a directed, acyclic graph (DAG) and a differentiation code.
Mosaic development is identifiable by observing spatial localization of
progenitor and descendent cells. This three-dimensional compartmentalization
should be consistent with nesting in the cell lineage tree. Regulative
development should demonstrate spatial “smearing”, or deviations from the
compartmentalization of the mosaic process. In a complementary manner, complex
network statistics should confirm this by providing an approximation of embryo
geometry. Characterizing the spatial organization and geometry of embryos in
this way allows for heuristic indicators of developmental patterns both within
and between organisms.

All raw data used in this study are available at Github.

Lineage Tree Raw Data: https://github.com/balicea/DevoWorm/tree/master/Lineage Tree DB, Differentiation Tree

Raw Data: https://github.com/balicea/DevoWorm/tree/master/Differentiation Tree Dataset.

All processed data (used in the analyses) are available from the Open Science Framework: https://osf.io/q9jvb/