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Stable isotopes can be used to monitor global and paleoceanographic changes associated with supercontinent formation and breakup. Substantial amounts of isotopic data have been produced for the time interval represented by the evolution of Pangea, but data free of diagenetic effects are uncommon. Thick nonluminescent brachiopod shells and marine cements of original minerology and chemistry are the materials most likely to retain their original isotopic composition. Altered marine cements can be used to infer an original marine signature. Whole rock samples are the least reliable for isotopic study, providing only an approximation of marine δ13C values and diagenetically altered δ18O values. These different techniques have different shortcomings but tend to complement each other.

The isotopic record for Pangea is too sparse for detailed interpretation, but several robust features are evident. Carbon isotopic values of brachiopod shells and former marine cements from Eurasia (Paleotethyan) and Arctic Canada increase by about 2‰ during the mid Carboniferous. This increase is not seen in samples from the central and south-central United States (Panthalassan) and in part reflects changes in ocean circulation with the closing of the equatorial seaway as Gondwana collided with Laurussia. The Paleotethyan-Panthalassan δ13C difference appears to extend into the Permian. Permian δ13C values are high but decrease by roughly 3‰ at or near the Permian-Triassic boundary. This decline in δ13C is attributed to a decrease in the inventory of buried organic carbon. δ13C values remain low in the Triassic (<4‰) compared to Permian values (generally >4‰).

Oxygen isotopic values for the Carboniferous are generally between −3‰ and −1‰ whereas Permian values are between −3‰ and +1‰. The high δ18O values for the Permian are either for latitudes with excess evaporation or for middle to high latitudes with cooler temperatures. No reliable δ18O data are available for the Permian-Triassic boundary.

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