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In botany, in addition to a memoir on the minute structure of Volvox (1852), his work on the structure of fossil plants established British palaeobotany on a scientific basis; Williamson ranks with Adolphe Theodore Brongniart as one of its founders.
A number of plant, animal and fungal species have been named to his honour, e.g. Saxifraga nathorstii (Dusén) Hayek (East Greenland saxifrage) and a suite of fossil plant species, Williamsonia nathorstii Carruthers (a fossil dragonfly) and Laestadites nathorstii Mesch. (a fossil fungus).