Summary 1. The spatial patterns of groundwater biodiversity in Europe remain poorly known, yet their knowledge is essential to understand local variation in groundwater assemblages and to develop sound conservation policies. We explore here the broad‐scale distribution of groundwater biodiversity across Europe, focussing on obligate subterranean species. 2. We compiled published distributional data of obligate subterranean aquatic taxa for six European countries (Belgium, France, Italy, Portugal, Slovenia and Spain), and conducted a detailed biological survey of six regions (one in Belgium, two in France, one in Italy, one in Slovenia and one in Spain). Based on this data set, we mapped spatial patterns of biodiversity in Europe on a cell grid with 0.2 × 0.2 ° resolution. 3. As of mid‐2006, the total number of described stygobiotic species in the six countries was 930 and the total number of genera with at least one described stygobiotic species was 191. The total number of sampling sites where at least one stygobiont had been collected was 4709, distributed in 1228 of the 4668 grid cells covering the study area. 4. Groundwater stygobiotic biodiversity was dominated by Crustacea with 757 species in 122 genera. Insects were represented by only two species of a single genus of dytiscid beetles restricted to south‐eastern France. 5. The geographic distribution of stygobionts was extremely heterogeneous. Stygobionts were recorded in 26% of the 4668 grid cells and only 33 cells had more than 20 stygobiotic species. These 33 ‘hot‐cells’ of groundwater species richness clustered in seven hotspots. 6. Endemicity was very high, with 43% of the total number of stygobiotic species restricted to a single cell, i.e. <500 km2. 7. Hotspots defined by rarity, number of genera, number of genera with only one species known in Europe, or number of monospecific genera differed markedly in ranking from those based on species richness. However, a core of four hotspots emerged in all cases: one stretching across Slovenia and northeastern Italy, one in the French Pyrenees, one in the Cévennes in southern France and one in the Rhine River valley in northeastern France. 8. Unevenness in stygobiont distribution cannot be explained solely by unevenness in sampling effort. This is indicated in particular by the fact that our comprehensive sampling survey roughly matched the level of taxonomic richness of the studied regions based on previously published information. 9. With sampling effort continuing, a twofold or higher increase in species richness can be expected in several Mediterranean areas, with a potential to discover up to 50% more new species than are currently known in the region.

Summary 1. Species assemblages of diatoms, rotifers, chydorids, planktonic crustaceans and chironomids were studied in 235 alpine lakes in the Alps, Pyrenees, Tatras (Western Carpathians), Retezat (Southern Carpathians) and Rila Mountains (Balkans). 2. For all taxonomic groups we found a hierarchical structure in the community assemblage using distinct scales of lake clustering (number of k‐means groups) based on species composition similarity (Hellinger distance). We determined the optimal partition in assemblage types (i.e. number of lake clusters) for each taxonomic group by maximising the sum of the taxon indicative value (IndVal) and performed discriminant analyses, using environmental variables not conditioned by geographical patterns. Relevant environmental variables differed among and within taxonomic groups. Therefore the assemblages respond to a complex environmental mosaic, with the exception of diatom assemblages, which followed an acid–base gradient. 3. The significant environmental variables could be grouped into four general factors: lake size, tropho‐dynamic status, acid–base balance and ice‐cover duration (i.e., altitudinal gradient). Lake size was significant for the highest number of assemblage types; however, the most significant factor differed among taxonomic groups: acid–base balance for diatoms, lake size for rotifers, ice‐cover duration for chydorids and planktonic crustaceans and tropho‐dynamic status for chironomids. No single environmental typology accounted for the assemblage structure of all taxonomic groups. 4. However, defining ecological thresholds as values within environmental gradients at which the rate of change in assemblages is accelerated relative to points distant from that threshold, we were able to find specific threshold values for each of the four main general environmental factors identified, which were relevant across several taxonomic groups: 3 ha for lake area; 0.6 mg L−1 for dissolved organic carbon; 190 days for ice‐cover duration and 200 μeq L−1 for acid neutralising capacity. Above and below these values ecosystem organisation change substantially. They have direct applications in establishing lake typologies for environmental quality and biodiversity conservation programmes, and in improving predictions about global change impacts.

1.A survey of c. 350 remote high altitude and high latitude lakes from 11 different mountain regions was undertaken to explore species distribution across Europe at a scale not previously attempted. 2. Lakes were sampled for planktonic crustaceans, rotifers, littoral invertebrates and subfossil chironomids, diatoms and cladocerans. Each lake was characterised in terms of water chemistry, morphology, catchment attributes and geographical location. 3. Separate TWI NSPAN TWI NSPAN analyses were undertaken on diatom, chironomid, planktonic crustacean, littoral invertebrate and cladoceran (chydorids only) data to classify sites according to taxonomic composition. For most datasets there was a spatial component to the classification with distinct geographical groups emerging -Norway and Scotland, Finland and Central ⁄ Eastern Europe. 4. Constrained ordination methods were employed to examine how species responded to a range of environmental factors, which were aggregated into a series of component groups -proximal environment (the chemical, trophic and physical attributes of the lake), catchment characteristics and geographical location. Several key environmental gradients were identified, which explained significant levels of the variance across several of the biological groups including dissolved organic carbon (chironomids, planktonic crustaceans), temperature (chironomids and littoral invertebrates), chloride ⁄ sea-salt (littoral invertebrates, diatoms and rotifers), lake morphology (all groups), calcium ⁄ pH (diatoms), nitrate (chydorids, littoral invertebrates, rotifers and planktonic crustaceans) and fish (littoral invertebrates). In some cases these statistical relationships are likely to represent direct ecological constraints and, in others, it is probable that the environmental variable is acting as a surrogate for some other attribute or process. 5. Variance partitioning was undertaken to quantify how much of the variation in each biological group could be uniquely attributed to variables representing the proximal environment, catchment characteristics and geographical location. For most groups the Correspondence: Martin Kernan, Environmental

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