The question of whether the high U and Th concentrations in zircon are primary or secondary is often difficult to resolve, and a clear understanding of the modification processes of secondary U- and Th-rich zircon is lacking. Zircon crystals from two well-studied, highly evolved granites, the Jiangjunshan muscovite granite in the Chinese Altai Mountains and the Cuonadong leucogranite in the Eastern Tethyan Himalaya, have been investigated and classified into two types. Type I exhibits typical igneous growth zoning, and type II has “diffuse” or “spongy” internal structures. These textures, along with compositional data, indicate that the type II zircon crystals formed through hydrothermal modification of magmatic zircon (type I) by infiltrating hydrothermal fluids. During hydrothermal modification, the U and Th concentrations increase from type I to type II in the Jiangjunshan muscovite granite but decrease from type I to type II in the Cuonadong leucogranite. The Raman spectra of type II zircon crystals from Jiangjunshan muscovite granite have broader peaks (i.e., measured as the full width at half maximum, FWHM) with decreased intensities than their type I counterparts, which indicates that the former are affected by significant accumulated radiation damage. However, the preserved radiation damage in both the type I and II zircon measured by Raman spectroscopy is less than that expected from the total dose of alpha particles calculated from the U and Th contents, which indicates variable degrees of annealing. We propose that late magmatic-hydrothermal alteration was responsible for the modification of magmatic zircon grains in highly evolved granites and resulted in the enrichment or redistribution of U and Th. The calculated radiation dose of the Cuonadong leucogranite zircon is far below that required for metamictization, which indicates that metamictization is not always responsible for diffuse and spongy textures.

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