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Summary: Multi-indicator palaeoecological studies have become increasingly popular over the last decade as the need for a more complete understanding of lake ecological histories has increased. However, the true potential of the full biological record for assessing the potential drivers of observed ecological shifts in lake sediment records has rarely been demonstrated. Here, we examine the remains of a range of food-web components including algae (diatoms), macrophytes (plant macrofossils), zooplankton (chitinous and ephippial Cladocera remains), invertebrates (including chironomids, bryozoans, Mollusca) and fish (fish scales and fish leech egg cocoons) in multiple sediment cores from Groby Pool, an enriched English shallow lake, to assess whole-ecosystem response to eutrophication over the last two centuries. We focus on three striking changes in the palaeorecord, namely the post-1900 increase in Daphnia spp., the post-1840 decline in Cristatella mucedo and the post-1940 increase in Cocconeis placentula, and utilise the multi-indicator palaeoecological data to evaluate possible explanations for these patterns. Principal curves analysis revealed marked and broadly simultaneous changes in the plant macrofossils, cladocerans, diatoms and chironomids (as well as in other animal remains such as bryozoans and Mollusca), indicating an early period of enrichment most likely associated with land-use change in the late 18th century, followed by a more recent eutrophication phase coincident with the discharge of sewage effluent to the lake from 1935. Ecological change, resulting from eutrophication, was shown to have progressed slowly and steadily and to have occurred at all trophic levels with a shift from a relatively diverse 'mesotrophic' macrophyte assemblage, dominance by benthic diatoms and plant-associated Chydoridae and chironomids towards a relatively species-poor, 'eutrophic' macrophyte community with dominance by planktonic algae (e.g. Cyclostephanoid diatom taxa), planktonic Cladocera (Bosmina, Daphnia) and a chironomid fauna dominated by mud-associated taxa. The inferred shift in the macrophyte community from charophyte to fine-leaved pondweed and Callitriche truncata suggests a reduction in the seasonal duration of plant dominance. The multi-indicator analysis indicates that a combination of increased phytoplankton biomass and low zooplanktivorous fish predation is likely to explain the recent increases in Daphnia spp., while loss of plant habitat and increased competition for food appear to be the most likely causes of the observed decline in C. mucedo, and resistance to increased grazing pressure from invertebrates is the most probable driver of the C. placentula increase. Our study illustrates the potential of using the full array of fossil groups preserved in lake sediment cores to infer ecosystem dynamics over centennial timescales and to contribute to our understanding of the mechanisms that may link biological assemblages to a range of forcing factors. Further, this paper provides methodological guidance by demonstrating the ability of amalgamated records from three cores to reveal a strong sequence of events and coherent patterns.

SUMMARY 1. We investigate long-term (>200 years) changes to the composition and spatial structure of macrophyte communities in a shallow, eutrophic lake (Barton Broad, eastern England) and consider the implications for lake restoration. 2. Historical macrophyte data were assembled from a variety of sources: existing plant databases, museum herbaria, journal articles, old photographs and eyewitness accounts. Additionally, two types of sediment core sample were analysed for plant macro-remains and pollen; bulk basal samples from multiple core sites analysed to provide information on ‘pre-disturbance’ macrophyte communities and two whole cores analysed to determine historical change. 3. Prior to the late 1800s, macrophyte communities were diverse and included a multilayered mosaic of short-stature submerged taxa and taller submerged and floatingleaved species. With the progression of eutrophication after around 1900, the former community was displaced by the latter. Diversity was maintained, however, since an encroaching Schoenoplectus–nymphaeid swamp generated extensive patches of low-energy habitat affording refugia for several macrophytes otherwise unable to withstand the hydraulic forces associated with open water conditions. When this swamp vegetation disappeared in the 1950s, many of the ‘dependent’ aquatic macrophytes also declined leaving behind a sparse, species-poor community (as today) resilient to both eutrophication and turbulent open waters. 4. The combination of historical and palaeolimnological data sources offers considerable benefits for reconstructing past changes to the aquatic vegetation of lakes and for setting restoration goals. In this respect, our study suggests that successful restoration might often be better judged by reinstatement of the characteristic structure of plant communities than the fine detail of species lists; when nutrients are low and the structure is right, the right species will follow.

1. A long-term monitoring programme on phytoplankton and physicochemical characteristics of Esthwaite Water (England) that started in 1945 provides a rare opportunity to understand the effects of climate and nutrients on a lake ecosystem. 2. Monitoring records show that the lake experienced nutrient enrichment from the early 1970s, particularly after 1975, associated with inputs from a local sewage treatment plant, resulting in marked increases in concentration of soluble reactive phosphorus (SRP). Climatic variables, such as air temperature (AirT) and rainfall, exhibit high variability with increasing trends after 1975. 3. Diatom analyses of an integrated 210Pb-dated lake sediment core from Esthwaite Water, covering the period from 1945 to 2004, showed that fossil diatoms exhibited distinct compositional change in response to nutrient enrichment. 4. Redundancy analysis (RDA) based on diatom and environmental data sets over the past 60 years showed that the most important variables explaining diatom species composition were winter concentrations of SRP, followed by AirT, independently explaining 22% and 8% of the diatom variance, respectively. 5. Additive models showed that winter SRP was the most important factor controlling the diatom assemblages for the whole monitoring period. AirT had little effect on the diatom assemblages when nutrient levels were low prior to 1975. With the increase in nutrient availability during the eutrophication phase after 1975, climate became more important in regulating the diatom community, although SRP was still the major controlling factor. 6. The relative effects of climate and nutrients on diatom communities vary depending on the timescale. RDA and additive model revealed that climate contributed little to diatom dynamics at an annual or decadal scale. 7. The combination of monitoring and palaeolimnological records employed here offers the opportunity to explore how nutrients and climate have affected a lake ecosystem over a range of timescales. This dual approach can potentially be extended to much longer timescales (e.g. centuries), where long-term, reliable observational records exist.

1. Changes in nutrients and climate have occurred over approximately the same timescales in many European lake catchments. Here, we attempt to interpret the sedimentary diatom record of a large shallow lake, Loch Leven, in relation to these pressures using information gained from analysis of long-term data sets of water quality, climate and planktonic diatoms. 2. The core data indicate the enrichment of Loch Leven starting in c. 1800–1850, most likely from agricultural practices in the catchment, with a more marked phase since c. 1940–1950 caused by increased phosphorus inputs from sewage treatment works, land drainage and a woollen mill. 3. While the recent diatom plankton remains are dominated by taxa associated with nutrient-rich conditions, an increase in Aulacoseira subarctica relative to Stephanodiscus taxa since the mid-1980s suggests that reductions in external catchment sources of nutrients (since 1985) may have resulted in partial recovery. This observation accords well with the long-term monitoring series of water chemistry and phytoplankton. 4. On a decadal-centennial scale, the eutrophication signal in the sediment record outweighs any evidence of climate as a control on the diatom community. However, at an inter-annual scale, while the diatom data exhibit high variability, there are several changes in species composition in the recent fossil record that may be attributed to climatic controls. 5. The study highlights the value of a palaeolimnological approach, particularly when coupled with long-term data sets, for developing our understanding of environmental change at a range of temporal scales. The diatom record in the sediment can be used effectively to track recovery from eutrophication, but requires greater understanding of contemporary ecology to fully interpret climate impacts. 6. The study illustrates the complexity of ecosystem response to synchronous changes in nutrients and climate, and the difficulty of disentangling the effects of these multiple, interacting pressures.

1. The low-Mg calcite shells of Ostracoda (Crustacea) are often well preserved in the sediments of alkaline lakes. In coastal waters that have undergone large temporal changes in salinity, ostracod assemblages preserved in the sediment record have been used to reconstruct palaeosalinity, often assuming that salinity is the only significant control on the faunas.2. We evaluate the performance of ostracods as palaeosalinity indicators in Hickling Broad, a shallow brackish coastal lake in Norfolk, U.K., by comparing fossil ostracod assemblages covering two centuries with geochemical inferences and instrumental records of past salinity and water composition along with other palaeolimnological indicators.3. Despite large changes in the salinity of the lake and the supposed salinity sensitivity of ostracods, the fossil ostracod assemblages do not clearly reflect the salinity trends inferred from the other independent data. Rather, a complex series of changes has occurred in the lake over the past 200 years and factors other than salinity, including eutrophication, toxicity and associated complex alterations in habitat availability have probably influenced ostracod assemblages. In contrast, there is a good broad agreement between inferred or measured salinity and the trace-element chemistry of ostracod shells.4. We conclude that ostracod faunas may not always provide unambiguous palaeosalinity records and should therefore not be used to reconstruct salinity changes except as part of a multi-proxy investigation that includes other palaeoecological and /or geochemical indicators.

SUMMARY 1. Shallow lakes are often cited as classic examples of systems that exhibit trophic cascades but, whilst they provide good model systems with which to test general ecological theory and to assess long-term community change, their food web linkages have rarely been resolved, so changes associated with the structure and dynamics of the ecological network as a whole are still poorly understood. 2. We sought to redress this, and to demonstrate the potential benefits of integrating palaeolimnological and contemporary data, by constructing highly resolved food webs and stable isotope derived measures of trophic interactions and niche space, for the extant communities of two shallow U.K. lakes from different positions along a gradient of eutrophication. The contemporary surface sediment cladoceran and submerged macrophyte assemblages in the less enriched site, Selbrigg Pond, matched the palaeolimnological assemblages of the more enriched site, Felbrigg Hall Lake, in its more pristine state during the 1920s. Thus, Selbrigg was a temporal analogue for Felbrigg, from which the consequences of long-term eutrophication on food web structure could be inferred. These data represent the first steps towards reconstructing not only past assemblages (i.e. nodes within a food web), but also past interactions (i.e. links within a food web): a significant departure from much of the previous research in palaeolimnology. 3. The more eutrophic food web had far fewer nodes and links, and thus a less reticulate network, than was the case for the more pristine system. In isotopic terms, there was vertical compression in d 15 N range (NR) and subsequent increased overlap in isotopic niche space, indicating increased trophic redundancy within Felbrigg. This structural change, which was associated with a greater channelling of energy through a smaller number of nodes as alternative feeding pathways disappear, could lead to reduced dynamic stability, pushing the network towards further simplification. These changes reflected a general shift from a benthic-dominated towards a more pelagic system, as the plant-associated subweb eroded. 4. Although these data are among the first of their kind, the palaeo-analogue approach used here demonstrates the huge potential for applying food web theory to understand how and why these ecological networks change during eutrophication. Furthermore, because of the rich biological record preserved in their sediments, shallow lakes represent potentially important models for examining long-term intergenerational dynamics

1. To correctly interpret chironomid faunas for palaeoenvironmental reconstruction, it is essential that we improve our understanding of the relative influence of ecosystem variables, biotic as well as physicochemical, on chironomid larvae. To address this, we analysed the surface sediments from 39 shallow lakes (29 Norfolk, U.K., 10 Denmark) for chironomid head capsules, and 70 chironomid taxa (including Chaoborus) were identified. 2. The shallow lakes were selected over large environmental gradients of aquatic macrophytes, total phosphorus (TP) and fish communities. Redundancy analysis (RDA) identified two significant variables that explained chironomid distribution: macrophyte species richness (P identified specific taxa that had significant relationships with both these variables. Macrophyte percentage volume infested (PVI) and species richness were significant in classifying the lake types based on chironomid communities under TWINSPAN analysis, although other factors, notably nutrient concentrations and fish communities, were also important, illustrating the complexities of classifying shallow lake ecosystems. Lakes with plant species richness >10 all had relatively diverse (Hill’s N2) chironomid assemblages, and lakes with Hill’s N2 >10 all had TP 3. Plant density (PVI), and perhaps more importantly species richness, were primary controls on the distribution of chironomid communities within these lakes. This clearly has implications for palaeoenvironmental reconstructions using zoobenthos remains (i.e. chironomids) and suggests that they could be used to track changes in benthic/pelagic production and could be used as indicators of changing macrophyte habitat. 4. Measuring key biological gradients, in addition to physicochemical gradients, allowed the major controls on chironomid distribution to be assessed more directly, in terms of plant substrate, food availability, competition and predation pressure, rather than implying indirect mechanisms through relationships with nutrients. Many of these variables, notably macrophyte abundance and species richness, are not routinely measured in such studies, despite their importance in determining zoobenthos in temperate shallow lakes. 5. When physical, chemical and ecological gradients are considered, as is often the case with palaeo-reconstructions rather than training sets chosen to maximise one gradient, complex relationships exist, and attempting to reconstruct a single trophic variable quantitatively may not be appropriate or reliable.

P>1. Quantitative palaeolimnology has traditionally sought to quantify species-environment relationships to use alterations in biological assemblages to reflect past environmental change. Transfer functions have used regression techniques, such as weighted averaging, to define taxon optima and tolerance for a single chemical or biological variable.2. Cladoceran assemblages and their sub-fossil remains in shallow lakes are shaped by a combination of interacting factors. Partial constrained ordination of sub-fossil cladoceran assemblages from 39 shallow lakes (29 in Norfolk, U.K. and 10 in Denmark) indicated that both zooplanktivorous fish (ZF) density and submerged macrophyte abundance significantly influenced community composition. These dual structuring forces precluded the use of a transfer function as one of the key assumptions of this approach was not met, namely that environmental variables apart from the variable being modelled have negligible influence on species distribution or that there is a linear relationship between the two. Separate transfer functions for ZF and macrophyte abundance were developed but had poor performance diagnostics with low bootstrapped r2, high root mean square error of prediction (RMSEP) and large bias.3. To obviate the problem of multiple structuring forces a multivariate regression tree (MRT) was employed, which allows for more than one explanatory variable within a model. The MRT analysis defined six groups with discrete ranges of ZF and macrophyte densities. The technique identified critical values or 'break points' in ZF and macrophyte abundances which result in significant alterations in the sub-fossil cladoceran assemblage. In addition, the MRT groups had different summer mean values for chlorophyll-a, Secchi depth, total phosphorus and nitrate-nitrogen.4. The predictive abilities of the model were assessed by comparing the observed versus predicted MRT group membership. In general group membership was reliably predicted, suggesting sub-fossil cladoceran assemblages reliably reflect ZF and macrophyte density in shallow lakes. For a relatively small number of sites there were differences between the observed and predicted MRT group membership. These failures of prediction may result, at least in part, from the disparity of the time period represented by the environmental data and the surface sediment cladoceran assemblage.

1. Palaeolimnology and contemporary ecology are complementary disciplines but are rarely combined. By reviewing the literature and using a case study, we show how linking the timescales of these approaches affords a powerful means of understanding ecological change in shallow lakes. 2. Recently, palaeolimnology has largely been pre-occupied with developing transfer functions which use surface sediment-lake environment datasets to reconstruct a single environmental variable. Such models ignore complex controls over biological structure and can be prone to considerable error in prediction. Furthermore, by reducing species assemblage data to a series of numbers, transfer functions neglect valuable ecological information on species’ seasonality, habitat structure and food web interactions. These elements can be readily extracted from palaeolimnological data with the interpretive assistance of contemporary experiments and surveys. For example, for one shallow lake, we show how it is possible to infer long-term seasonality change from plant macrofossil and fossil diatom data with the assistance of seasonal datasets on macrophyte and algal dynamics. 3. On the other hand, theories on shallow lake functioning have generally been developed from short-term ( timescales (decades–centuries) of shallow lake response to stressors such as eutrophication and climate change. Palaeolimnological techniques can track long-term dynamics in lakes whilst smoothing out short-term variability and thus provide a unique and important means of not only developing ecological theories, but of testing them. 4. By combining contemporary ecology and palaeolimnology, it should be possible to gain a fuller understanding of changing ecological patterns and processes in shallow lakes on multiple timescales.

Summary 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. 1900–1960) 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 phytoplankton-based 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.

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 acrophyte 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, the application of a model capable of allowing for this represents a significant advance in palaeolimnology.

1. A diatom-total phosphorus transfer function has been applied to a sedimentary diatom sequence from Groby Pool, a small shallow lake in Leicestershire, U.K.2. Extensive aquatic plant records exist for Groby Pool dating back over two centuries. These records, in conjunction with selected aquatic pollen and herbarium diatom data, provide independent, qualitative evidence for the progression of eutrophication and its effects on aquatic plant communities and habitat structure.3. Before 1800, Groby Pool was probably mesotrophic with clear water and a diverse submerged macrophyte community, but subsequently it experienced considerable nutrient enrichment. Key evidence for this includes: (i) historical plant records indicating the loss of species associated with mesotrophic waters and their replacement by others typical of eutrophic conditions, (ii) a significant increase in the percentage of planktonic diatoms in the lake sediment record (particularly Cyclostephanos dubius) after 1890, and (iii) increases in percentages of Stephanodiscus parvus and Cocconeis placentula in the second half of the twentieth century.4. Diatom-inferred total phosphorus (DI-TP) estimates were inconsistent with the qualitative evidence for eutrophication at Groby Pool. In particular the DI-TP profile was thought to overestimate phosphorus during the period of dominance by small Fragilaria spp. before 1890, and to misjudge the timing and direction of subsequent changes in nutrient loading.5. This study highlights some of the problems associated with the application of diatom-TP transfer functions to sedimentary diatom sequences from shallow lakes. The major problem relates to the frequent dominance of non-planktonic diatoms in the sediments of these systems, many species of which (particularly small Fragilaria spp.) appear to be more sensitive to changes in habitat availability than to phosphorus. Potential ways of improving diatom-TP models via altered approaches to sampling are suggested.