Physical habitat assessment in the Tajuna river (Spain) by means of the MesoHABSIM approach

Physical habitat was assessed in the Tajuña river (Tagus basin, Spain) by means of the MesoHABSIM approach. Long reaches of the Tajuña river are altered by agricultural use of the riverside. The main impacts are river rectification (straightening), channel entrenchment and incision, and degradation of riparian vegetation, along with important flow depletion and regulation. To our knowledge, this is the first application in Spain of MesoHABSIM, which is a physical habitat model based on the identification of habitat attributes - depth, water velocity, substrate, types of hydromorphologic units (HMU), and types of cover - on the mesohabitat scale. The river was stratified into 16 segments with similar habitat characteristics. Mesohabitats were mapped in one representative site (1-2 km long) within each segment to provide a hydromorphologic model of the river. Biological models were developed for fry, juvenile, and adult brown trout. To do this, preliminary models were generated based on literature about trout habitat requirements, and then they were calibrated with electrofishing data. These models were applied to the hydromorphologic model of the river to quantify the available habitat for brown trout in the current conditions. Finally, restoration action was designed to decrease channel entrenchment, increase river sinuosity, and recover its riparian vegetation. The physical changes after restoration were estimated by expert opinion, and the quantification of the available habitat was done with MesoHABSIM at each site. These results can be used to select the segments that are the best candidates for restoration.Se ha evaluado el hábitat físico en el río Tajuña (cuenca del Tajo, España) mediante la metodología MesoHABSIM. Una parte importante del río Tajuña está alterada por los usos agrícolas de las riberas. Los principales impactos son la rectificación, el encajonamiento e incisión del cauce, y la degradación de la vegetación riparia, junto con una importante extracción y regulación del caudal. Hasta donde conocemos, ésta es la primera aplicación de MesoHABSIM en España. Se trata de un modelo de hábitat físico, basado en la identificación de los atributos del h'abitat -profundidad, velocidad del agua, sustrato, tipo de unidad hidromorfológica (HMU) y tipo de cobertura o refugio- en la escala del mesohábitat. Se estratificó el río en 16 segmentos con características similares de hábitat. En cada segmento se muestrearon los mesohábitats en un tramo representativo de 1-2 km de largo, construyendo así un modelo hidromorfológico del río. Se generaron modelos biológicos para alevines, juveniles y adultos de trucha común. Para ello, se construyeron unos modelos preliminares a partir de bibliografía acerca de los requerimientos de hábitat de la trucha, y después se calibraron con datos obtenidos mediante pesca eléctrica. Estos modelos fueron aplicados al modelo hidromorfológico para cuantificar el hábitat disponible para la trucha común en las condiciones actuales. Finalmente se diseño una acción de restauración con el objetivo de disminuir el encajonamiento del cauce, aumentar su sinuosidad y recuperar su vegetación riparia. Los cambios tras la restauración se estimaron por opinión de experto, y la evaluación del hábitat resultante se realizó mediante MesoHABSIM. Estos resultados pueden emplearse para elegir los segmentos más apropiados para realizar la restauración propuesta

River-Wide Habitat Availability for Fish Habitat Guilds: Implications for In-Stream Flow Protection

The variation in river discharge alters habitat heterogeneity with implications for the distribution of fish species with different habitat requirements. Assessments of habitat availability following changes in river discharge are difficult to apply at broad spatial scales and with relevance to multiple species. We used a MesoHABSIM modeling approach to quantify river-wide changes in habitat availability for five fish habitat guilds under three river discharge levels along the Niobrara River, NE, USA.We used a time-series of river discharge (1958–2010) to create uniform continuous under-threshold habitat duration curves that identified habitat conditions that may result in periods of stress for fish communities along the Niobrara River. Habitat availability for each fish habitat guild was dependent on river discharge and location along the river. Habitat availability for fish habitat guilds ranged from 5% to 49% of the total channel area suggesting habitat availability may, at times, be limited. We provide river discharge guidelines for bioperiods that limit the frequency and duration of stressful habitat conditions. Understanding interactions between river discharge and habitat availability through time and at river-wide scales may aid in managing for ecological integrity by including protection of river discharge variability to support multiple fish habitat guilds

Spatio-temporal patterns of fish assemblages in a large regulated alluvial river

1. The River Durance, the last alpine tributary of the River Rhone, is a large, braided alluvial hydrosystem. Following large-scale regulation, flow downstream of the Serre-Poncon dam has been maintained at 1⁄40th of previous annual mean discharge. To assess the effects of historical disturbances, fish assemblages and habitat use were analysed during five summers in a representative reach of the middle Durance. 2. Habitat availability and use were assessed with a multi-scale approach including the variables water depth, current velocity, roughness height of substratum, amount of woody debris and lateral⁄longitudinal location. Eighteen fish species were sampled by electrofishing in 289 habitat sample units. 3. Partial least square (PLS) regression showed that taxa were mainly distributed according to relationships between their total length and water depth⁄velocity variables. Fish assemblage composition was also related to roughness height as well as distance from the bank or to the nearest large woody debris. However, PLS regression revealed no significant differences in habitat selection between two periods of varying hydromorphological stability. 4. Fish distribution patterns and density were related to proximity to the bank and cover, indicating that local scale variables need to be considered in conservation and restoration programmes

Thinking like a fish: a key ingredient for development of effective fish passage facilities at river obstructions

Worldwide, obstructions on watercourses have interfered with migratory pathways of fish species, reducing life‐cycle success and often eliminating diadromous fish species altogether from river basins. Over the last century, efforts to mitigate these effects were initially directed at developing fishways for upstream, high‐value migrant adult salmon. In more recent years, efforts have turned to developing fishways for other species. Results of past research suggest that the development of effective fishways requires biological knowledge of fish behaviour when encountering variable flows, velocity and turbulence, combined with hydraulic and civil engineering knowledge and expertise to develop facilities that provide ppropriate hydraulic conditions that fish will exploit. Further, it often requires substantial financial resources for biological and hydraulic testing as well as engineering design, particularly where prior knowledge of the behaviour of target fish species does not exist. Where biological or engineering knowledge (or both) is absent, development of effective passage facilities must take on a trial and error approach that will almost certainly require years to attain success. Evaluations of existing adult and juvenile fish passage facilities, where they have been carried out, suggest that migrant fish reject areas with hydraulic conditions they determine unsuitable. Even well designed fish ladders or nature‐like bypass channels for upstream migrants, even those with good attraction flows, will fail if incorrectly sited. Although progress has been made, developing successful installations for downstream migrants remains much more difficult, probably because downstream fish move with the flow and have less time to assess cues at entrances to any bypasses that they encounter

Criteria for identifying free-flowing river stretches for the EU Biodiversity Strategy for 2030

The EU Biodiversity Strategy includes the target that at least 25000 km of rivers should be restored into free-flowing rivers by 2030 through the removal of primarily obsolete barriers and the restoration of floodplains and wetlands. This document proposes criteria for identifying free-flowing rivers, taking into account longitudinal, lateral, and vertical connectivity at local and catchment scales. The aim is to provide a tool that can be used by authorities to determine the length of free-flowing rivers in their catchments. In addition, the tool can be used to predict the increase in free-flowing river length resulting from barrier removal and other restoration measures. This will help prioritising measures that can contribute to the 25,000 km target. Key elements of the method are (1) segmentation of the river into homogeneous reaches; (2) criteria for longitudinal, lateral, and vertical connectivity within a homogeneous reach; (3) a large-scale assessment taking into account sediment connectivity and migration barriers for target fish species; and (4) minimum length criteria to ensure hydromorphological processes and ecological functioning.JRC.D.2 - Ocean and Wate

Over 200,000 kilometers of free-flowing river habitat in Europe is altered due to impoundments

European rivers are disconnected by more than one million man-made barriers that physically limit aquatic species migration and contribute to modification of freshwater habitats. Here, a Conceptual Habitat Alteration Model for Ponding is developed to aid in evaluating the effects of impoundments on fish habitats. Fish communities present in rivers with low human impact and their broad environmental settings enable classification of European rivers into 15 macrohabitat types. These classifications, together with the estimated fish sensitivity to alteration of their habitat are used for assessing the impacts of six main barrier types (dams, weirs, sluices, culverts, fords, and ramps). Our results indicate that over 200,000 km or 10% of previously free-flowing river habitat has been altered due to impoundments. Although they appear less frequently, dams, weirs and sluices cause much more habitat alteration than the other types. Their impact is regionally diverse, which is a function of barrier height, type and density, as well as biogeographical location. This work allows us to foresee what potential environmental gain or loss can be expected with planned barrier management actions in rivers, and to prioritize management actions

Impacts of large and small barriers on fish assemblage composition assessed using environmental DNA metabarcoding

River fragmentation caused by instream barriers is a leading cause of biodiversity loss, particularly for freshwater migratory fish, the vertebrate group that has suffered the steepest decline. However, most studies have tended to focus on the impacts of large dams on only a few taxa. We estimated the cumulative impact of both large and small barriers on fish species richness and relative abundance along an altitudinal gradient in the main stem of the River Allier (France). Using eDNA metabarcoding, we identified 24 fish zero-radius operational taxonomic units (zOTUs), corresponding to 26 species distributed along the main stem of the river. Elevation explained the greatest amount of variation in fish distribution, together with average flow, barrier density and its interaction with cumulative barrier height. Based on eDNA, the largest discontinuity in species richness was not related to the location of Poutès, the largest dam in the system, but located downstream from it. Our results indicate that, in addition to the more obvious effects of large dams on migratory fish such as the Atlantic salmon, the cumulative effects of small barriers can have widespread impacts on fish species richness and relative abundance, which should not be overlooked. We suggest that, as for other fragmented rivers, acting on numerous small barriers might bring about greater benefits in fish species richness than focusing only on the largest dams

On species distribution modelling, spatial scales and environmental flow assessment with Multi Layer Perceptron Ensembles: A case study on the redfin barbel (Barbus haasi; Mertens, 1925)

Inconsistent performance of Species Distribution Models (SDMs), which may depend on several factors such as the initial conditions or the applied modelling technique, is one of the greatest challenges in ecological modelling. To overcome this problem, ensemble modelling combines the forecasts of several individual models. A commonly applied ensemble modelling technique is the Multi Layer Perceptron (MLP) Ensemble, which was envisaged in the 1990s. However, despite its potential for ecological modelling, it has received little attention in the development of SDMs for freshwater fish. Although this approach originally included all the developed MLPs, Genetic Algorithms (GA) now allow selection of the optimal subset of MLPs and thus substantial improvement of model performance. In this study, MLP Ensembles were used to develop SDMs for the redfin barbel (Barbus haasi; Mertens, 1925) at two different spatial scales: the micro scale and the meso scale. Finally, the potential of the MLP Ensembles for environmental flow (e flow) assessment was tested by linking model results to hydraulic simulation. MLP Ensembles with a candidate selection based on GA outperformed the optimal single MLP or the ensemble of the whole set of MLPs. The micro scale model complemented previous studies, showing high suitability of relatively deep areas with coarse substrate and corroborating the need for cover and the rheophilic nature of the redfin barbel. The meso scale model highlighted the advantages of using cross scale variables, since elevation (a macro scale variable) was selected in the optimal model. Although the meso scale model also demonstrated that redfin barbel selects deep areas, it partially contradicted the micro scale model because velocity had a clearer positive effect on habitat suitability and redfin barbel showed a preference for fine substrate in the meso scale model. Although the meso scale model suggested an overall higher habitat suitability of the test site, this did not result in a notable higher minimum environmental flow. Our results demonstrate that MLP Ensembles are a promising tool in the development of SDMs for freshwater fish species and proficient in e flow assessment.This study was funded by the Spanish Ministry of Economy and Competitiveness with the projects SCARCE (Consolider-Ingenio 2010 CSD2009-00065). We thank to Confederacion Hidrografica del Jucar (Spanish Ministry of Agriculture, Food and Environment), especially to the Office for Water Planning and Teodoro Estrela for the data provided to develop the SDMs. Finally we would like to thank TECNOMA S.A. for the development of the hydraulic model in the Mijares River and all the people who participated in the field data collection.Muñoz Mas, R.; Martinez-Capel, F.; Alcaraz-Hernández, JD.; Mouton, A. (2017). On species distribution modelling, spatial scales and environmental flow assessment with Multi Layer Perceptron Ensembles: A case study on the redfin barbel (Barbus haasi; Mertens, 1925). Limnologica. 62. https://doi.org/10.1016/j.limno.2016.09.004S6

Application of Probabilistic Neural Networks to microhabitat suitability modelling for adult brown trout (Salmo trutta L.) in Iberian rivers

Probabilistic Neural Networks (PNN) have been tested for the first time in microhabitat suitability modelling for adult brown trout (Salmo trutta L.). The impact of data prevalence on PNN was studied. The PNN were evaluated in an independent river and the applicability of PNN to assess the environmental flow was analysed. Prevalence did not affect significantly the results. However PNN presented some limitations regarding the output range. Our results agreed previous studies because trout preferred deep microhabitats with medium-to-coarse substrate whereas velocity showed a wider suitable range. The 0.5 prevalence PNN showed similar classificatory capability than the 0.06 prevalence counterpart and the outputs covered the whole feasible range (from 0 to 1), but the 0.06 prevalence PNN showed higher generalisation because it performed better in the evaluation and it allowed a better modulation of the environmental flow. PNN has demonstrated to be a tool to be into consideration.The authors would like to thank the Spanish Ministry of Economy and Competitiveness for its financial support through the SCARCE project (Consolider-Ingenio 2010 CSD2009-00065). We are grateful to the colleagues who worked in the field and in the preliminary data analyses, especially Marta Bargay, Aina Hernandez and David Argibay. The works were partially funded by the Confederacion Hidrografica del Jucar (Spanish Ministry of Agriculture, Food and Environment), that also provided hydrological and environmental information about the study sites. The authors also thank the Direccion General del Agua and INFRAECO for the cession of the microhabitat data. Finally, we also thank Javier Ferrer, Teodoro Estrela and Onofre Gabaldo (Confederacion Hidrografica del Jucar) for their help and the data provided. Thanks to Grieg Davies for the academic review of English.Muñoz Mas, R.; Martinez-Capel, F.; Garófano-Gómez, V.; Mouton, A. (2014). Application of Probabilistic Neural Networks to microhabitat suitability modelling for adult brown trout (Salmo trutta L.) in Iberian rivers. Environmental Modelling and Software. 59:30-43. https://doi.org/10.1016/j.envsoft.2014.05.003S30435