Aim Metacommunity assembly mechanisms have been traditionally considered stable through time. However, in highly dynamic systems with varying local environmental conditions and patch connectivity, communities are likely to experience temporal shifts in their assembly mechanisms. Here, we used a set of perennial (PR) and intermittent (IR) rivers to assess if assembly mechanisms vary seasonally in response to flow intermittence. Location Mediterranean climate region (100,000 km2), Spain. Methods We used a modelling approach to assess the relative effect of environmental sorting and dispersal‐based processes on aquatic invertebrate metacommunities within and across river types at four distinct hydrological periods. We used local environmental variables to assess environmental sorting, and considered geographical, network and topographical distances as different dispersal surrogates. Linear mixed effect models accounting for the non‐independence of pairwise distances were used to assess the relationships between community dissimilarity and distance matrices. Results Assembly mechanisms were more temporally stable in PR than in IR. In PR, community dissimilarities were equally related to environmental and geographical distances suggesting codominance of species sorting and dispersal‐based assembly mechanisms. In IR, environmental distance best explained community dissimilarities during the dry period when flow cessation imposes strong environmental sorting, whereas metacommunity organization was much more stochastic during the rewetting period when high flows may randomly reorganize communities. Dispersal processes dominated assembly mechanisms between PR and IR during the rewetting period suggesting an increase in recolonization processes linking both river types following the dry period. Geographical and topographical distances best explained community variability, suggesting that overland dispersal dominates in river networks fragmented by drying events. Main conclusions Aquatic invertebrate metacommunity assembly mechanisms vary seasonally in response to changes in hydrological conditions. The temporal dimension should be better incorporated into metacommunity studies in highly dynamic systems such as intermittent rivers.

SUMMARY1. Contemporary species distributions are determined by a mixture of ecological and historical filters acting on several spatial and temporal scales. Mediterranean climate areas are one of the world's biodiversity hotspots with a high level of endemicity, which is linked to complex ecological and historical factors. 2. This paper explores the ecological and historical factors constraining the distribution of caddisfly species on a large regional scale. A total of 69 taxa were collected from 140 sampling sites in 10 Iberian Mediterranean river basins. Approximately 74% of taxa can be considered rare, with the southern basins (the Baetic-Riffian region) having greater endemicity. The greatest richness, involving a mixture of northern and southern species, was found in the transitional area between the Baetic-Riffian region and the Hesperic Massif. 3. The historical processes occurring during the Tertiary (i.e. the junction of the Eurasian and African plates) explained 3.1% of species distribution, whereas ecological factors accounted for 20.7%. Only 0.3% was explained by the interaction of history and ecology. A set of multi-scale ecological variables (i.e. basin, reach and bedform characteristics) defined five river types with specific caddisfly assemblages. The commonest caddisfly species accounted for the regional distribution pattern, while rare taxa contributed to the explanation of subtle patterns not shown by common species. 4. Despite the importance of historical factors for biogeography and the large scale used in our study, ecological variables better explained caddisfly distribution. This may be explained by the length of time since the historical process we are considering, the high dispersion and colonisation capacity of many caddisfly species, and the strong environmental gradient in the area. Because of the historical and environmental complexity of Mediterranean areas, rare taxa should be included in ecological studies so that the singularity of these ecosystems is not missed.

When the regime of a river is not perennial, there are four main difficulties with the use of hydrographs for assessing hydrological alteration: i) the main hydrological features relevant for biological communities are not quantitative (discharges) but qualitative (phases such as flowing water, stagnant pools or lack of surface water), ii) stream flow records do not inform on the temporal occurrence of stagnant pools, iii) as most of the temporary streams are ungauged, their regime has to be evaluated by alternative methods such as remote sensing or citizen science, and iv) the biological quality assessment of the ecological status of a temporary stream must follow a sampling schedule and references adapted to the flow- pool-dry regime. To overcome these challenges within an operational approach, the freely available software tool TREHS has been developed within the EU LIFE TRIVERS project. This software permits the input of information from flow simulations obtained with any rainfall-runoff model (to set an unimpacted reference stream regime) and compares this with the information obtained from flow gauging records (if available) and interviews with local people, as well as instantaneous observations by individuals and interpretation of ground-level or aerial photographs. Up to six metrics defining the permanence of water flow, the presence of stagnant pools and their temporal patterns of occurrence are used to determine natural and observed river regimes and to assess the degree of hydrological alteration. A new regime classification specifically designed for temporary rivers was developed using the metrics that measure the relative permanence of the three main phases: flow, disconnected pools and dry stream bed. Finally, the software characterizes the differences between the natural and actual regimes, diagnoses the hydrological status (degree of hydrological alteration), assesses the significance and robustness of the diagnosis and recommends the best periods for biological quality samplings.

For the European Parliament and Commission to implement the Water Framework Directive (WFD), the water-quality indices that are currently used in Europe need to be compared and calibrated. This will facilitate the comparative assessment of ecological status throughout the European Union. According to the WFD, biologic indices should respond consistently to human impacts, using multimetric approaches and water-quality classification boundaries adjusted to a common set of normative definitions. The European Commission has started an intercalibration exercise to review biologic indices and harmonize class boundaries. We used data from rivers in Spain to compare the IBMWP (Iberian Biological Monitoring Working Party) index, which is commonly used by water authorities in Spain and by several research centers, with the Intercalibration Common Multimetric Index (ICM-Star), which was used as a standard in the intercalibration exercise. We also used data from Spanish rivers to compare the multimetric indices ICM-7 (based on quantitative data) and ICM-9 (based on qualitative data) with the IBMWP. ICM-7 and ICM-9 were proposed by the Mediterranean Geographical Intercalibration Group (Med-GIG). Additionally, we evaluated two new multimetric indices, developed specifically for macroinvertebrate communities inhabiting Mediterranean river systems. One of these is based on quantitative data (ICM-10), while the other is based on qualitative data (ICM-11a). The results show that the IBMWP index responds well to the stressor gradient present in our data, and correlates well with ICM-Star. Moreover, the IBMWP quality class boundaries were consistent with the intercalibration requirements of the WFD. However, multimetric indices showed a more linear relation with the stressor gradient in our data, and less variation in reference values. In addition, they may provide more statistical power for detecting potential environmental impacts. Multimetric indices produced similar results for quantitative and qualitative data. Thus, ICM-10 (also named IMMi-T) and ICM-11a (also named IMMi-L) indices could be used to meet European Commission requirements for assessing the water quality in Spanish Mediterranean rivers.

The assessment of the ecological status of water bodies, as requires by the European Water Framework Directive, can raise a number of problems when applied to temporary streams. These problems are because of the particular physical, chemical and biological conditions resulting from the recurrent cessation of flow or even the complete drying of the stream beds. In such non‐permanent water bodies, the reference quality standards developed for permanent streams may only be applicable under certain circumstances or may not be applicable at all. Work conducted within the collaborative EU‐funded project Mediterranean Intermittent River ManAGEment (MIRAGE) has addressed most of these difficulties and has used diverse approaches to solve them. These approaches have been brought together in the so‐called MIRAGE Toolbox. This toolbox consists of a series of methodologies that are designed to be used in a sequential manner to allow the establishment of the ecological and chemical status of temporary streams and to relate these findings to the hydrological status of the streams. The toolbox is intended to serve the following purposes: (i) the determination of the hydrological regime of the stream; (ii) the design of adequate schedules for biological and chemical sampling according to the aquatic state of the stream; (iii) the fulfillment of criteria for designing reference condition stations; (iv) the analysis of hydrological modifications of the stream regime (with the definition of the hydrological status); and (v) the development of new methods to measure the ecological status (including structural and functional methods) and chemical status when the stream's hydrological conditions are far from those in permanent streams. Copyright © 2014 John Wiley & Sons, Ltd.