The geodynamic process from the evolution of supercontinent has distinct isotope characteristics explorable using zircon Hf isotopic composition. Since Peninsular Malaysia associates with Gondwana dispersal and Pangaea formation, analyzing the U-Pb and Hf-isotopic content of its 500–200 Ma magmatic zircon could reveal the signal left by the transitional geodynamic process between the supercontinents. We collected two groups of magmatic rocks from West Malaya: Ordovician meta-volcanics (n = 8), and Triassic Main Range granitoid province (MRGP) (n = 6); and three groups from East Malaya: Carboniferous meta-volcanics (n = 2), Permian-Triassic Eastern granite province (EGP) (n = 6), and Permian-Triassic EGP volcanics (n = 8). Difference in magmatic zircon Hf isotopic crustal model ages uphold the previous rationale which separates Peninsular into two blocks: West Malaya (part of Sibumasu terrane) magmatic zircon Hf isotopic crustal model ages (Average TDM2: 1.3 Ga) are older than East Malaya (part of Chanthaburi-Sukhothai-Lincang arc of Indochina terrane) (Average TDM2: 0.9 Ga). During the final assembly of Gondwana from 500 to 450 Ma, West Malaya and East Malaya were at the outboard of Gondwana Proto-Tethys margin. The shift of East Malaya zircon Hf array towards higher εHf(t) (external orogenic system) after ca.370 Ma may infers Paleo-Tethys ocean broadening and East Malaya separation from Gondwana. The 370–350 Ma juvenile zircon Hf isotopic composition in East Malaya is a significant improvement over radiolarian age to show the broadening and subduction of the Paleo-Tethys ocean between the two terranes. After ca.280 Ma, East Malaya zircon Hf array shifted towards lower εHf(t) (internal orogenic system). Coinciding with the Indosinian collision at ca.230 Ma, crustal reworking signal increases in both blocks, signifying the end in Peninsular Malaysia Gondwana to Pangaea transitional geodynamic process. As the Paleo-Tethys segment was completely subducted after 230 Ma, the peninsular crustal thickening starts from 230 to 218 Ma. The post-collision phase would begin at ca.215 Ma.
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