Description of methods used for collection/generation of data: Data have been collected by researchers from Irkutsk State University at least monthly, usually every 7-10 days, in depth profiles from the surface to at least 250 m at a single main station approximately 2.7 km offshore from Bol’shie Koty in the Southern Basin. Ice conditions prevent collection in some months, usually January and May. Phytoplankton were sampled along depth profiles with the Van Dorn bottle at 0, 10, 50, 100, and 200 m depths and were preserved before settling in Utermöhl chambers. In 1973 there was a change in the preservation methods from the use of formalin to a Lugol’s solution. Counts from samples before 1973 are considered representative for diatoms because they are equally well preserved in both, but not for other phytoplankton groups. Only diatom counts from the upper 50m are included in this dataset. Single zooplankton samples were collected with a closing plankton net (37.5 cm diameter, 100 μm mesh) from depth layers of 0-10, 10-25, 25-50, 50-100, 100-150, 150-250, and 250-500 m. Zooplankton samples were fixed in formalin throughout the duration of the long-term monitoring program with greatest consistency of temporal and spatial sampling occurring from 1955 forward. Both phytoplankton and zooplankton were identified and counted at the species level, and copepods were enumerated by age class. Only Epischurella baikalensis counts from the upper 25 m are included in this dataset, samples from the 25–50 m depth layer were excluded from our analyses because sampling frequency was not consistent at this depth layer across the time series. See also Hampton SE, Gray DK, Izmest’eva LR, Moore MV, Ozersky T (2014) The Rise and Fall of Plankton: Long-Term Changes in the Vertical Distribution of Algae and Grazers in Lake Baikal, Siberia. PLoS ONE 9(2): e88920. doi:10.1371/journal.pone.0088920 Methods for processing the data: For the analysis, diatom cell count data were converted to corresponding biovolume values (µm³/L) based on reported cell sizes (Rioual & Mackay 2005, Olenina et al. 2006, Belykh et al. 2006, Genkal & Bondarenko 2006, Kremer et al. 2014 and Database on Biovolume Metrics from Academy of Natural Sciences of Drexel University 2001). Count data (ind/m²) for nauplii, copepodite and adult stages of the Lake Baikal dominant zooplankton species Epischurella baikalensis were converted to (ind/L). Count data were then converted to corresponding biomass data (mg dry weight/L) based on body size reported by Afanasyeva (1998), multiplying number of individuals by 0.00027 for nauplii, by 0.008 for copepodites and by 0.1 for adults. Total diatom biovolume and total Epischurella biomass per sampling date were calculated for data from the upper layer (0-50m and 0-25m respectively).

Predicting how food webs will respond to global environmental change is difficult because of the complex interplay between the abiotic forcing and biotic interactions. Mechanistic models of species interactions in seasonal environments can help understand the effects of global change in different ecosystems. Seasonally ice-covered lakes are warming faster than many other ecosystems and undergoing pronounced food web changes, making the need to forecast those changes especially urgent. Using a seasonally forced food web model with a generalist zooplankton grazer and competing cold-adapted winter and warm-adapted summer phytoplankton, we show that with declining ice cover, the food web moves through different dynamic regimes, from annual to biennial cycles, with decreasing and then disappearing winter phytoplankton blooms and a shift of maximum biomass to summer season. Interestingly, when predator-prey interactions were not included, a declining ice cover did not cause regime shifts, suggesting that both are needed for regime transitions. A cluster analysis of long-term data from Lake Baikal, Siberia supports model results, revealing a change from regularly occurring winter blooms of endemic diatoms to less-frequent winter bloom years with decreasing ice cover. Together, the results show that even gradual environmental change, such as declining ice cover duration, may cause discontinuous or abrupt transitions between dynamic regimes in food webs.

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