1. Submerged macrophyte and phytoplankton components of eutrophic, shallow lakes have frequently undergone dynamic changes in composition and abundance with important consequences for lake functioning and stability. However, because of a paucity of long-term survey data, we know little regarding the nature, direction and sequencing of such changes over decadal-centennial or longer timescales. 2. To circumvent this problem, we analysed multiple (n = 5) chronologically correlated sediment cores for plant macro-remains and a single core for pollen and diatoms from one small, shallow, English lake (Felbrigg Hall Lake, Norfolk, U.K.), documenting 250 years of change to macrophyte and algal communities. 3. All five cores showed broadly similar stratigraphic changes in macrophyte remains with three distinct phases of macrophyte development: Myriophyllum-Chara-Potamogeton (c. pre-1900), to Ceratophyllum-Chara- Potamogeton (c. 1900Potamogeton (c. -1960 and finally to Zannichellia-Potamogeton (c. post-1960). Macrophyte species richness declined from at least 10 species pre-1900 to just four species at the present day. Additionally, in the final Zannichellia-Potamogeton phase, a directional shift between epi-benthic and phytoplanktonbased primary production was indicated by the diatom data. 4. Based on macrophyte-seasonality relationships established for the region, concomitant with the final shift to Zannichellia-Potamogeton, we infer a reduction in the seasonal duration of plant dominance (plant-covered period). Furthermore, we hypothesise that this change in species composition resulted in a situation whereby macrophyte populations were seasonally 'sandwiched' between two phytoplankton peaks in spring and late summer as observed in the contemporary lake. 5. We suggest that eutrophication-induced reductions in macrophyte species richness, especially if the number of plant-seasonal strategies is reduced, may constrict the plant growing season. In turn, this may render a shallow lake increasingly vulnerable to seasonal invasions of phytoplankton resulting in further species losses in the plant community. Thus, as part of a slow (over perhaps 10-100s of years) and self-perpetuating process, macrophytes may be gradually pushed out by phytoplankton without the need for a perturbation as required in the alternative stable states model of plant loss.

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Summary 1. Eutrophication has a profound effect on the biological structure and function of shallow lakes, altering the composition and abundance of submerged macrophyte and fish assemblages. Relatively little is known, however, about decadal to centennial‐scale change in these important aspects of shallow lake ecology. 2. Established palaeolimnological inference models are limited to reconstructing a single variable. As macrophyte and zooplanktivorous fish abundance exert dual and interacting controls on cladoceran assemblages a single variable inference model may contain significant error. To obviate this problem, we applied a new cladoceran‐based multivariate regression tree (MRT) model to cladoceran subfossil assemblages from dated cores from a small shallow lake (Felbrigg Lake, U.K.) to assess long‐term change in fish and submerged macrophyte abundance. Plant macrofossil, chironomid and mollusc subfossil assemblages were also analysed to track changes in biological structure and function and to evaluate the inferences of the MRT model. 3. Over the 200+ year period covered by the sediment cores, there was good agreement in the timing and nature of ecological change reflected by the plant macrofossil, mollusc, chironomid and cladoceran data. The sediment sequence was divided into three dated zones: c. 1797–1890, c. 1890–1954 and c. 1954–present. Prior to 1890 plant‐associated mollusc, cladoceran and chironomid assemblages indicated a species‐rich macrophyte community; a scenario confirmed by the plant macrofossil data. From c. 1890 to 1954 macrophyte‐associated species of all three invertebrate groups remained abundant but the proportion of pelagic cladocerans rose. Post‐1954 mollusc and chironomid assemblages changed to sediment associated detrital feeders and the proportion of pelagic cladoceran taxa increased further. 4. The cladoceran‐based MRT model indicated a long period of stability, c. 1790–1927, characterised by abundant submerged macrophytes and zooplanktivorous fish. From c. 1927 to 1980, the MRT model inferred a decline in zooplanktivorous fish density (ZF) but relative stability in August macrophyte abundance. From 1980 to 2000, an increase in zooplanktivorous fish was inferred tallying well with available data on the fish population (since the 1970s), which indicated extirpation of perch in the 1970s and a subsequent increase in the rudd population. The model inferred little change in August macrophyte abundance until post‐c. 1980 at which point it indicated a decline. The surface sediment assemblage was placed in MRT group A, where submerged plants are absent or very rare in late summer in good agreement with current conditions at the site. 5. The MRT model, applied here for the first time, appears to have successfully tracked changes in macrophyte abundance and ZF over the last 200 years at Felbrigg Lake. The inferences agreed with historical observations on the fish community and the supporting palaeolimnological data. Given that multiple structuring forces shape most biological communities, ...

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The EU's Water Framework Directive requires all surface water bodies to be classified according to their ecological status. As biological communities show both spatial and temporal heterogeneity, expressions of ecological status will, inevitably, have an element of uncertainty associated with them. A consequence of this environmental heterogeneity is that there is a risk that status inferred from one or more samples is different to the true status of that water body. In order to quantify the scale of temporal uncertainty associated with benthic diatoms, replicate samples were collected from sites across the ecological status gradient in lakes and rivers in the UK. Variability (expressed as standard deviation of temporal replicate samples from a single site) could be described using a polynomial function and this was then used to calculate the risk of placing a water body in the wrong ecological status class. This risk varied depending on the distance from the class boundaries and the number of replicates. Based on these data, we recommend that ecological status is determined from a number of samples collected from a site over a period of time.