Waigeo occupies a critical position between the Halmahera-Philippine arcs to the northwest and Australia-New Guinea to the southeast. The island consists of a deformed ophiolitic basement of supra-subduction zone type overlain by probable Paleogene forearc sedimentary rocks. The forerarc basement is cut by mylonite shear zones and the basement and sedimentary cover rocks were deformed by southward-directed thrusts and associated folds during the Oligocene. The deformed sequences are intruded by basic dykes, thought to be coeval with basalts and andesites of Late Oligocene age. The entire Paleogene sequence is overlain unconformably by a thick (up to 2000 m) sequence of Miocene limestones which accumulated during a tectonically quiet period. A final phase of deformation occurred during the Pliocene which caused the development of two very large anticlines and an intervening syncline, associated with left-lateral wrench faults. Waigeo is interpreted to have been situated in a forearc position in an intra-oceanic island arc during the early Paleogene, forming part of the East Halmahera-Waigeo forearc terrane. The Waigeo arc terrane collided with a continental block in about the Middle Oligocene, contemporaneous with similar arc-continent collision in northern New Guinea. A period of tectonic quiescence during the Miocene was followed by Pliocene deformation in Waigeo related to a left-lateral wrench faulting on splays of the Sorong Fault in northern New Guinea. The Pliocene deformation is interpreted as resulting from compression on a right-stepping restraining bend in this wrench fault system.
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