Brachiopods dominated the seafloor as a primary member of the Paleozoic fauna. Despite the devastating effects of the end-Permian extinction, the group recovered during the early Mesozoic only to gradually decline from the Jurassic to today. This decline likely had multiple causes, including increased predation and bioturbation-driven substrate disruption, but the role of changing substrate is not well understood. Given the importance of substrate for extant brachiopod habitat, we documented Mesozoic-Cenozoic lithological preferences and morphological changes to assess how decreasing firm-substrate habitat may have contributed to the brachiopod decline. Compared to bivalves, Mesozoic brachiopods occurred more frequently and were disproportionately abundant in carbonate lithologies. Although patterns in glauconitic or ferruginous sediments are equivocal, brachiopods became more abundant in coarser-grained carbonates and less abundant in fine-grained siliciclastics. During the Jurassic, brachiopod species rarely had abraded beaks but tended to be more convex with a high beak, potentially consistent with a non-analogue lifestyle resting on the seafloor. However, those highly-convex morphotypes largely disappeared by the Cenozoic, when more terebratulides had abraded beaks, suggesting closer attachment to hard substrates. Rhynchonellides disproportionately declined to become a minor component of Cenozoic faunas, perhaps because of less pronounced morphological shifts. Trends in lithological preferences and morphology are consistent with bioturbation-driven substrate disruption, with brachiopods initially using firmer carbonate sediments as refugia before adapting to live primarily attached to hard surfaces. This progressive habitat restriction likely played a role in the final brachiopod decline, as bioturbating ecosystem engineers transformed benthic habitats in the Mesozoic and Cenozoic.

Contains measurements and descriptive categorization of shell morphology, especially related to the pedicle foramen and beak, for Jurassic-Recent terebratulide and rhynchonellide species. These include:

Width of pedical foramen opening, as a proportion of shell length (foramen_width). Based on a single individual, either the holotype or a representative specimen.

Height of umbo (linear distance), as a proportion of shell length (umbo_height). Based on a single individual, either the holotype or a representative specimen.

Angle of umbo, measured relative to commissure in lateral view. An angle of 0 represents a straight umbo that is parallel to the commissure, while an angle of 90 degrees represents an erect/incurved umbo that is perpendicular to the commissure. Based on a single individual, either the holotype or a representative specimen.

Shell width/length (WL) and height/length (HL). Based on the mean of all measurements in the Paleobiology Database.

The file also notes whether the pedicle foramen is labiate, whether the beak is abraded (beak_weathering), and whether there is shell thickening, usually in the dorsal valve. Traits were assigned based on published descriptions and illustrations, and represent the typical condition for each species. In these columns, blank entries typically mean that the feature is not present, but some of the features vary among specimens or during ontogeny.