Understanding the functioning of extinct ecosystems is a complicated knot of ecological, evolutionary, and preservational strands that must be untangled. For instance, anatomical and behavioral differences can profoundly alter fossilization pathways. This is particularly true in exceptionally preserved soft-bodied biotas that record the earliest phases of animal evolution during the Cambrian Explosion and the Ordovician Radiation. Herein, a novel method of data partitioning based on probabilistic modelling is developed to examine these processes for the Walcott Quarry, Burgess Shale, Canada (510Ma), and the Fezouata Shale, Morocco (c. 475Ma). The modelling shows that the mechanism for soft-tissue preservation in the Walcott Quarry is ecologically selective, favoring the endobenthos. This is not found in the Fezouata Shale. Taken in concert with bioturbation data, a new model of comparative preservation is developed based on sedimentary flow dynamics. This suggests that during the Cambrian Explosion and Ordovician Radiation the most exceptional fossils sites must still be calibrated against each other to understand the unfolding evolutionary events and the ecological structuring of ancient animal communities.