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Study of the distribution of the age-populations of detrital zircons in the Snake River system suggest that specific stream systems can be identified based on the detrital-zircon age-population signature (“barcode”) of ancient and Holocene sand deposits. Detrital zircon studies can be used on regional and local scales to determine changes in drainage patterns using both surface and subsurface data.

Regional study of drainage patterns using detrital zircons found in Neogene strata of Idaho and southwest Montana suggest northeastward late Miocene to Holocene migration of the Continental Divide from the western side of the Pioneer Mountains to the current position in southwest Montana. Specifically, mixed populations of recycled Proterozoic detrital zircons that define the Wood River drainage are not found in the western Snake River Plain until after 7 Ma. Late Miocene eastward drainage from the central Snake River Plain to southwest Montana is suggested by 9–12 Ma detrital zircons found in fluvial strata less than 6 million years old, of the Sixmile Creek Formation

Basalt eruptions of the Eastern Snake River Plain during the Pliocene and Pleistocene also caused drainage diversion. Detrital zircons in Pliocene sands from coreholes at Wendell and Mountain Home Air Force Base contain Big Lost River zircon provenance, suggesting that during the Pliocene, the Big Lost River flowed west along the central Snake River Plain.

Late Pliocene and early Pleistocene basaltic volcanoes and rhyolite dome eruptions resulted in volcanic highlands, the Axial Volcanic Zone of the eastern Snake River Plain and the northwest-trending Arco Volcanic Rift Zone (which includes Craters of the Moon volcanic center). The development of these volcanic highlands disrupted the ancestral drainage of the Pliocene Big Lost River system, confining it to the Big Lost Trough, a volcanically dammed basin of internal drainage on the Idaho National Laboratory.

After the Big Lost Trough was cut off from the main Snake River, basalt eruptions, local subsidence, and climate controlled the courses of the rivers that flowed into it. Detrital-zircon populations in core samples reveal the provenance of specific sand beds from the Big or Little Lost River systems.

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