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Three sub-regions of the Indian Ocean in which SSTs significantly influence the equatorial East African short rains on interannual timescales are identified, and the physical processes of this influence are studied using regional climate model simulations from the Weather Research and Forecasting model (WRF). Five 20-year ensemble integrations are generated to represent a control climate and to simulate the individual and combined effects of SSTAs in the influential regions. SSTAs in the western Indian Ocean exert a stronger influence on the equatorial East African short rains than central and eastern Indian Ocean SSTAs both in terms of the coverage of significantly-changed precipitation and the magnitude of the precipitation response. Positive western Indian Ocean SSTAs significantly increase the short rains over 95% of the equatorial East Africa domain (30°–40°E, 5°S–5°N), while only 30% of the region responds to central and eastern Indian Ocean SSTAs. Evidence of an influential Indian Ocean dipole mode does not emerge from the analysis. The mechanisms of this influence are diagnosed using atmospheric moisture budget and moist static energy analyses, with reference to Kelvin and Rossby wave generation as in the Gill model, but in the presence of complicated topography and nonzero background flows. Wind convergence anomalies in a moist environment primarily support precipitation anomalies in all cases, while changes in atmospheric instability are largely controlled by low-level moisture. Central and eastern Indian Ocean SSTAs change circulations and precipitation locally, but the remote influence on East Africa is weaker than that of the western Indian Ocean SSTAs.