The environmental clades were originally hypothesized to be ecologically distinct from gut-associated E. coli, both from their surprising habitat associations and because they fell into sequence clusters quite distinct from classical E. coli in the multilocus analysis. While sequence clustering has proved an important tool for identifying ecologically distinct populations, we note that it is not straightforward to identify the sequence clusters that correspond to the fundamental units of ecology and evolution, owing to the hierarchical nature of sequence diversity, with subclusters within clusters and so on