Reconstructing development of the earliest seed integuments raises a new hypothesis for the evolution of ancestral seed‐bearing structures.

Summary: How plant seeds originated remains unresolved, in part due to disconnects between fossil intermediates and developmental genetics in extant species. The Carboniferous fossil Genomosperma is considered among the most primitive known seeds, with highly lobed integument and exposed nucellus. We have used this key fossil taxon to investigate the evolutionary origins of seed development.We examined sectioned Genomosperma specimens using modern digital 3D reconstruction techniques and established population‐level measurements of Genomosperma ovules for quantitative analysis.Genomosperma ovules show significant variation in integumentary lobe fusion and curvature. Our analysis suggests that this variation represents a single species with significant variations in lobe number and fusion, reminiscent of floral development in extant species. We conclude that changes in lobe flexure occurred late in development, consistent with a previously hypothesized function in pollen guidance/retention. We also identify seeds of Genomosperma within cupules for the first time.The presence of a cupule adds evidence towards the plesiomorphy of cupules within seed plants. Together with the similarities identified between the Genomosperma lobed integument and floral organs, we propose that the cupule, integument and nucellus together developed in a shoot‐like fashion, potentially ancestral to extant seed plant reproductive shoots. See also the Commentary on this article by Hetherington, 229: 1189–1191. [ABSTRACT FROM AUTHOR]