The habitability and ecology of Earth is fundamentally shaped by surface temperature, but the temperature history of our planet is not easily reconstructed, especially before the evolution of early biomineralizing animals. This work presents a billion-year-long, high-resolution, mineral-specific record of oxygen isotope measurements in shallow marine rocks. Clumped isotope paleothermometry results from four minerals resolves previous ambiguity in seawater oxygen isotope composition and confirms that long-term cooling punctuated by short-lived temperature extremes are dominant components of this record. We consider post-depositional effects by comparing Phanerozoic rock and fossil records, and identify temporal and spatial controls on alteration. Furthermore, this record is suggestive of key differences in dolomite (CaMg(CO3)2) formation processes between the Neoproterozoic (1000–538.8 Ma) and Phanerozoic (538.8–0 Ma), consistent with previous suggestions based on petrographic and sedimentological observations. This record, when viewed alongside the fossil record, suggests temperature change is tightly coupled to extinction and origination in the history of life and carbon cycle perturbations over the last billion years.

The potential for carbonate clumped isotope thermometry to independently constrain both the formation temperature (T∆47 ) of carbonate minerals and fluid oxygen isotope composition allows insight into long-standing questions in the Earth sciences, but remaining discrepancies between calibration schemes hamper interpretation of T∆47 measurements. To address discrepancies between calibrations, we designed and analyzed a sample suite (41 total samples) with broad applicability across the geosciences, with an exceptionally wide range of formation temperatures, precipitation methods, and mineralogies. We see no statistically significant offset between sample types, although comparison of calcite and dolomite remains inconclusive. When data are reduced identically, the regression defined by this study is nearly identical to that defined by four previous calibration studies that used carbonate-based standardization; we combine these data to present a composite carbonate-standardized regression equation. Agreement across a wide range of temperature and sample types demonstrates a unified, broadly applicable clumped isotope thermometer calibration.

Carbonate rocks on continental crust are one of Earth’s largest reservoirs of CO2 and yet the controls on their volume through time are poorly understood. Here we quantify temporal changes in preserved continental carbonate rocks over the last billion years in both global and North America-specific datasets within paleogeographic context. We find the preserved area of continental carbonate rocks increases by ~175% across the Neoproterozoic-Phanerozoic boundary ca. 539 million years ago, coincident with the rise of macroscopic, multicellular life and the evolutionary innovation of carbonate biomineralization in shallow water reefs. We demonstrate that crustal loading from carbonate sediments on one tropical paleo-continent (North America) contributes to an increase in continent-scale accommodation in the early Phanerozoic, expanding shallow marine environments. We predict this feedback between enhanced carbonate accumulation and subsidence was an important component of the termination of the Great Unconformity. These results are combined into a new conceptual model that links the changes in preserved carbonate rock volumes to the evolutionary innovation of carbonate biomineralization in a range of complex organisms. Our model implies evolutionary controls on the carbonate rock reservoir enhanced CO2 sequestration at the beginning of the Phanerozoic, with consequences for Earth’s carbon cycle, climate and habitability.