The Tyuya-Muyun massif in SW Kyrgyzstan hosts a number of caves some of which contain Ra- and U-bearing minerals that were extensively mined in the early 20th century. Previous studies have suggested that the caves of the Tyuya-Muyun have experienced a complex speleogenetic history, including epigene and hypogene processes. Here, we reconstruct the late stages of hypogene processes by studying subaqueous (calcite and barite spars, cave clouds), near-water table (rafts, folia) and vadose (flowstone) mineral deposits in Great Barite and Surprise caves. We determined the chronology (230Th dating), stable isotope composition (δ18O, δ13C and Δ47), and formation temperature (fluid inclusion microthermometry and Δ47) of these minerals and reconstructed the oxygen isotopic composition of the paleo-water (δ18Ow). In contrast to previous hypotheses about cave evolution, we found no evidence of an initial epigenic karst phase. The earliest mineral deposits suggest already hydrothermal conditions, with calcite and barite forming at ∼40–50 °C prior to 600 ka. Cave clouds in Great Barite Cave mark the beginning of the lowering of the groundwater table and also record a decrease in water temperature from 29.7 ± 8.3 °C to 12.7 ± 5.6 °C, as shown by Δ47 thermometry. The latter temperature remained stable, within analytical uncertainties, during the past 600 ka, as indicated by Δ47 results of near-water table and vadose speleothems in Surprise Cave. At the same time, the decrease in δ18Ow suggests a reduced contribution of thermal water and an increased input of colder meteoric water. By around 540–450 ka Surprise Cave emerged from the phreatic zone, as indicated by 230Th ages of the highest folia and flowstone. This lowering of the water table continued until 84 ka and may have been related to the final uplift phase of the Tyuya-Muyun massif and the concomitant incision of the Aravan River forming the Dangi Gorge.
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