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Background: Male cones of modern Ephedraceae are compound and compact. No fossil evidence has so far been found to support an origin of the compact compound male cone from a hypothetical loosely-arranged shoot system.

Results: Here we describe a new macrofossil taxon, Eamesia chinensis Yang, Lin, Ferguson et Wang, gen. et sp. nov., from the Early Cretaceous of western Liaoning, northeastern China. It was an ephedroid shrub bearing male spikes terminal to twigs, but differs from modern Ephedraceae by its loosely-arranged male cones, the axillary male shoot consisting of an elongated synangiophore on which leaf-like foliar organs were inserted, and four sessile synangia terminal to the apex.

Conclusions: The morphology of this fossil suggests that the modern compact male cone of Ephedra was indeed derived from a once loosely-arranged shoot system, and the male reproductive unit originated from a once elongated axillary male shoot This new fossil species thus provides a transitional link from the hypothetical ancestral shoot system to the modern compact morphology. Changes of habitat from closed humid forests to open dry deserts and shifts of the pollination syndrome may have acted as the driving forces behind this morphological evolution.