Aim:We propose a novel approach that considers taxonomic uniqueness, functional uniqueness and environmental uniqueness and show how it can be used in guiding conservation planning. We illustrate the approach using data for lake biota and environment.Location: Lake Puruvesi, Finland. Methods:We sampled macrophytes and macroinvertebrates from the same 18 littoral sites. By adapting the original "ecological uniqueness" approach, we used distancebased methods to calculate measures of taxonomic (LCBD-t), functional (LCBD-f) and environmental (LCEH) uniqueness for each site. We also considered the numbers and locations of the sites needed to protect up to 70% of total variation in taxonomic, functional or environmental features in the studied part of the lake.Results: Relationships between taxonomic (LCBD-t), functional (LCBD-f) and environmental (LCEH) uniqueness were generally weak, and only the relationship between macrophyte LCBD-t and LCBD-f was statistically significant. Overall, however, if the whole biotic dataset was considered, macroinvertebrate LCBD-f values showed a consistent positive relationship with macrophyte LCBD-f. Depending on the measure of site uniqueness, between one-third to one half of the sites could help protect up to 70% of the ecological uniqueness of the studied part of Lake Puruvesi. Main conclusions:Although the dataset examined originated from a large lake system, the approach we proposed here can be applied in different ecosystems and at various spatial scales. An important consideration is that a set of sites has been sampled using the same methods, resulting in species and environmental matrices that can be analysed using the methodological approach proposed here. This framework can be easily applied to grid-based data, sets of islands or sets of forest fragments. We suggest that the approach based on taxonomic, functional and environmental uniqueness will be a useful tool in guiding nature conservation and ecosystem management, especially if associated with meta-system ideas or network thinking.

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Eutrophication, pollution, habitat fragmentation, intense cultivation and global warming are increasingly causing deterioration of continental waters, and lentic ecosystems (here, lakes and ponds) are especially vulnerable to these changes, resulting in a critical situation that threatens their biodiversity in unparalleled rate. Aquatic macrophytes are the dominant element of most lentic ecosystems, and therefore, better understanding the patterns and mechanisms that structure their distributions would be valuable from basic and applied perspectives. Since the assessment of structures emerging from spatial organisation is now widely recognised as a cornerstone paradigm to interpret ecological phenomena, research has notably steered towards multi-scale perspectives on the assembly of biological diversity. This progress has been closely intertwined with recent developments in population genetics, metacommunity ecology and macroecology. However, their most recent conceptual advances are usually not fully operational because these empirical areas of research are usually considered independent of each other.The main aim of this thesis was to examine patterns and mechanisms of aquatic macrophyte diversity at regional and global scales using distinct organisation levels, from genes to species. Specifically, we (i) established a novel combination of robust mathematical methods capable of identifying the processes -including biotic interactions-and most important spatial scales involved in community assembly; (ii) built several phylogenies comprising most aquatic plant lineages and exploited a wide array of functional traits to determine whether different diversity facets (i.e. taxonomic, functional and phylogenetic) explain idiosyncratic patterns of macrophyte species distributions that would otherwise be missed in a traditional analysis of community turnover; (iii) used microsatellite loci to explore the spatial genetic variation of the aquatic macrophyte Myriophyllum alterniflorum DC. and examine if the results obtained through molecular estimates match modern perspectives of metacommunity theory at regional scales; and (iv) retrieved regional data from six continents to untangle if macroecological processes have left a footprint in the current patterns of compositional variation and community-environment relationships of aquatic macrophytes at global scales.