In South China, both crustal reworking and crust–mantle interaction were important geological processes during the Paleozoic and Mesozoic eras. However, the relationships between these two processes and metal mineralization are still unknown. Here we report rhenium and osmium isotopic data for pyrite grains from a pyrite deposit associated with a granite intrusion in the Shangbao area, southeastern Hunan Province (South China). Two pyrite samples, both containing many euhedral pyrite grains, were collected from the same locality, but the samples yield distinct ages. Six euhedral pyrite grains from one sample yield an isochronal age of 279 ± 12 Ma, with an initial 187Os/188Os ratio of 0.39 ± 0.71, and Re and Os concentrations of 0.12–63.5 ppb and 2.14–185 ppt, respectively. This Early Permian age is in good agreement with the age of the strata that host the pyrite deposit. Five euhedral pyrite grains from the other sample yield an isochronal age of 75.2 ± 4.3 Ma, with an initial 187Os/188Os ratio of 0.141 ± 0.030 and Re and Os concentrations of 0.15–0.43 ppb and 1.0–39.9 ppt, respectively. If one pyrite grain with the highest 187Re/188Os and 187Os/188Os ratios is excluded, other four pyrite grains give an isochronal age of 85 ± 13 Ma. The Late Cretaceous age (75–85 Ma) is consistent with the zircon U–Pb age of the Shangbao granites (80.1 ± 0.3 Ma) to within uncertainties. Considering also the relatively lower radiogenic initial 187Os/188Os ratio of this sample, we suggest that the later stage pyrite ore was probably formed through crystallization from the magmatic hydrothermal fluids. Combined with other geological and associated magmatic data, we propose a skarn-related fluid–ore interaction process to explain the second stage of metallogenesis in the Shangbao pyrite deposit. The Early Permian pyrite ore was deposited in a brine basin with evaporites during the Early Permian. Later magmatic hydrothermal fluids originating from the Shangbao granites, which included mantle components, interacted with the strata and the Early Permian pyrite ore during the Late Cretaceous and precipitated a later stage pyrite ore. During the Late Mesozoic, the roll-back of subducted Paleo-Pacific plate caused lithospheric extension in South China, triggering the upwelling and partial melting of the asthenosphere. The resulting underplating of mantle-derived magmas provided a vast amount of heat and materials for the formation of the granites and polymetallic deposits in South China. Given that the multiple mineralization events were spatially and temporally associated with the Paleozoic–Mesozoic magmatism, the Re–Os isotopic dating of euhedral pyrite grains has been shown to be a viable method for unveiling the evolutionary history of ore-deposits. Skarn development caused by granite and mafic dike emplacement resulting from crust–mantle interaction explains the occurrence of two mineralization episodes at the same locality.

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