The Rudny Altai and Gorny Altai regions had different geologic histories and differ in metallogenic patterns. The Vendian–Early Cambrian to Permian–Triassic multistage evolution of Gorny Altai included subduction, accretion–collision, and rifting events accompanied by magmatism and related mineralization. Metallogeny evolved in discrete pulses, with especially abundant Late Paleozoic–earliest Mesozoic mineralization. The Devonian–Carboniferous pulse produced diverse mineral deposits (iron, mercury, gold, silver, molybdenum, tungsten, cobalt, polymetallic ores, and rare earths), some of considerable economic value. The territory of Gorny Altai includes several large ore districts that belong to different zones. They are the Beloretsk–Kholzun iron district in the west, the Kayancha–Sinyukha fluorine–gold district in the northeast, the Kurai gold–mercury and Yustyd rare-metal–silver districts in the southeast, and the Kalguty rare-metal–tungsten and Ulandryk U–REE–Cu districts in the south. The largest mineral deposits are Kholzun (Fe, P2O5), Karakul (Co, Bi), Sinyukha (Au), Aktash and Chagan-Uzun (Hg), Ozernoe and Pogranichnoe (Ag), Kalguty (Mo, W), Alakha (Li, Ta), Rudnyi Log (Y,Fe-specularite), and Urzarsai (W-scheelite). Mineralization in Rudny Altai is mainly pyritic: copper–pyrite, pyrite–polymelallic ore, and barite–polymelallic ore. It resides in suprasubduction basalts and rhyolites and in Emsian to Frasnian island-arc volcanics at different stratigraphic levels of Devonian volcanosedimentary sequences in six ore districts. The Kurchum high-grade metamorphic block hosts copper–pyrite and gold–quartz mineralization related to Hercynian volcanism.

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