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Exogenous drivers may cause a gradual and reversible change in a lake equilibrium, or they may force it over a threshold to a persistent alternative stable state, described as a regime shift in the ecosystem. In the mid-and-lower Yangtze River Basin (MLYB), major environmental problems in shallow lakes have been eutrophication and abrupt algal blooms under anthropogenic disturbances for the recent century. Much value is therefore placed on understanding the changes in shallow-lake ecosystems that characteristically precede changes in the state of the lake. Here, we describe a case study of the paleolimnological signature in diatom assemblages of various types of regime shifts caused by historically documented anthropogenic drivers in a temperate shallow lake: Taibai Lake. We evaluate the effectiveness of paleolimnological data as a surrogate for long-term monitoring. Algorithms using sequential t and F statistics detected breakpoints in the time series of diatom assemblages, in 1994–1996, 1974–1977, 1952–1956, and 1931–1934, respectively. The regression statistics suggest that the hydrodynamic–ecosystem and aquacultural–ecosystem relationships fit better in the breakpoint regression model, and the relationship between nutrient loading and ecosystem state suits the linear model. Feedback loops help reconstruct dynamic changes in Taibai influenced by major stressors. Our study exemplifies the value of system approaches to identifying regime shifts and their possible causes in shallow lakes from paleolimnological records. The case study of Taibai set an example of reconstructing the ecological regime shifts in shallow lakes in the MLYB and understanding the state changes in lake ecosystems, which will benefit effective lake management.

Reconstruction of Ecological Transitions in a Temperate Shallow Lake of the Middle Yangtze River Basin in the Last Century