40 research outputs found

    Revisiting probabilistic neural networks: a comparative study with support vector machines and the microhabitat suitability for the Eastern Iberian chub (Squalius valentinus)

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    [EN] Probabilistic Neural Networks (PNNs) and Support Vector Machines (SVMs) are flexible classification techniques suited to render trustworthy species distribution and habitat suitability models. Although several alternatives to improve PNNs¿ reliability and performance and/or to reduce computational costs exist, PNNs are currently not well recognised as SVMs because the SVMs were compared with standard PNNs. To rule out this idea, the microhabitat suitability for the Eastern Iberian chub (Squalius valentinus Doadrio & Carmona, 2006) was modelled with SVMs and four types of PNNs (homoscedastic, heteroscedastic, cluster and enhanced PNNs); all of them optimised with differential evolution. The fitness function and several performance criteria (correctly classified instances, true skill statistic, specificity and sensitivity) and partial dependence plots were used to assess respectively the performance and reliability of each habitat suitability model. Heteroscedastic and enhanced PNNs achieved the highest performance in every index but specificity. However, these two PNNs rendered ecologically unreliable partial dependence plots. Conversely, homoscedastic and cluster PNNs rendered ecologically reliable partial dependence plots. Thus, Eastern Iberian chub proved to be a eurytopic species, presenting the highest suitability in microhabitats with cover present, low flow velocity (approx. 0.3 m/s), intermediate depth (approx. 0.6 m) and fine gravel (64¿256 mm). PNNs outperformed SVMs; thus, based on the results of the cluster PNN, which also showed high values of the performance criteria, we would advocate a combination of approaches (e.g., cluster & heteroscedastic or cluster & enhanced PNNs) to balance the trade-off between accuracy and reliability of habitat suitability models.The study has been partially funded by the national Research project IMPADAPT (CGL2013-48424-C2-1-R) with MINECO (Spanish Ministry of Economy) and Feder funds and by the Confederacion Hidrografica del Near (Spanish Ministry of Agriculture and Fisheries, Food and Environment). This study was also supported in part by the University Research Administration Center of the Tokyo University of Agriculture and Technology. Thanks to Maria Jose Felipe for reviewing the mathematical notation and to the two anonymous reviewers who helped to improve the manuscript.Muñoz Mas, R.; Fukuda, S.; Portolés, J.; Martinez-Capel, F. (2018). Revisiting probabilistic neural networks: a comparative study with support vector machines and the microhabitat suitability for the Eastern Iberian chub (Squalius valentinus). Ecological Informatics. 43:24-37. https://doi.org/10.1016/J.ECOINF.2017.10.008S24374

    Shifts in the suitable habitat available for brown trout (Salmo trutta L.) under short-term climate change scenarios

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    The impact of climate change on the habitat suitability for large brown trout (Salmo trutta L.) was studied in a segment of the Cabriel River (Iberian Peninsula). The future flow and water temperature patterns were simulated at a daily time step with M5 models' trees (NSE of 0.78 and 0.97 respectively) for two short-term scenarios (2011 2040) under the representative concentration pathways (RCP 4.5 and 8.5). An ensemble of five strongly regularized machine learning techniques (generalized additive models, multilayer perceptron ensembles, random forests, support vector machines and fuzzy rule base systems) was used to model the microhabitat suitability (depth, velocity and substrate) during summertime and to evaluate several flows simulated with River2D©. The simulated flow rate and water temperature were combined with the microhabitat assessment to infer bivariate habitat duration curves (BHDCs) under historical conditions and climate change scenarios using either the weighted usable area (WUA) or the Boolean-based suitable area (SA). The forecasts for both scenarios jointly predicted a significant reduction in the flow rate and an increase in water temperature (mean rate of change of ca. −25% and +4% respectively). The five techniques converged on the modelled suitability and habitat preferences; large brown trout selected relatively high flow velocity, large depth and coarse substrate. However, the model developed with support vector machines presented a significantly trimmed output range (max.: 0.38), and thus its predictions were banned from the WUA-based analyses. The BHDCs based on the WUA and the SA broadly matched, indicating an increase in the number of days with less suitable habitat available (WUA and SA) and/or with higher water temperature (trout will endure impoverished environmental conditions ca. 82% of the days). Finally, our results suggested the potential extirpation of the species from the study site during short time spans.The study has been partially funded by the IMPADAPT project (CGL2013-48424-C2-1-R) - Spanish MINECO (Ministerio de Economia y Competitividad) - and FEDER funds and by the Confederacion Hidrografica del Jucar (Spanish Ministry of Agriculture, Food and Environment). We are grateful to the colleagues who worked in the field and in the preliminary data analyses, especially Juan Diego Alcaraz-Henandez, David Argibay, Aina Hernandez and Marta Bargay. Thanks to Matthew J. Cashman for the academic review of English. Finally, the authors would also to thank the Direccion General del Agua and INFRAECO for the cession of the trout data. The authors thank AEMET and UC by the data provided for this work (dataset Spain02).Muñoz Mas, R.; López Nicolás, AF.; Martinez-Capel, F.; Pulido-Velazquez, M. (2016). Shifts in the suitable habitat available for brown trout (Salmo trutta L.) under short-term climate change scenarios. Science of the Total Environment. 544:686-700. https://doi.org/10.1016/j.scitotenv.2015.11.14768670054

    Length weight relationships of two endemic fish species in the Júcar River Basin, Iberian Peninsula

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    This study provides length-weight relationship (LWRs) information for two fish species (family Cyprinidae) in two headwater streams of the Júcar River Basin (Eastern Iberian Peninsula). Both species are endemic to the Iberian Peninsula and have no previous LWR estimates.This study was partially funded by the Conselleria d'Infraestructures, Territori y Medi Ambient of the Generalitat Valenciana. The authors would like to thank the Spanish Ministry of Economy and Competitiveness for its financial support through the project SCARCE (Consolider-Ingenio 2010 CSD2009-00065).Alcaraz-Hernández, JD.; Martinez-Capel, F.; Olaya Marín, EJ. (2015). Length weight relationships of two endemic fish species in the Júcar River Basin, Iberian Peninsula. Journal of Applied Ichthyology. 31(1):246-247. https://doi.org/10.1111/jai.12625246247311Clavero, M., Blanco-Garrido, F., & Prenda, J. (2004). Fish fauna in Iberian Mediterranean river basins: biodiversity, introduced species and damming impacts. Aquatic Conservation: Marine and Freshwater Ecosystems, 14(6), 575-585. doi:10.1002/aqc.636Elvira, B., & Almodovar, A. (2001). Freshwater fish introductions in Spain: facts and figures at the beginning of the 21st century. Journal of Fish Biology, 59(sa), 323-331. doi:10.1111/j.1095-8649.2001.tb01393.xFroese, R. (2006). Cube law, condition factor and weight-length relationships: history, meta-analysis and recommendations. Journal of Applied Ichthyology, 22(4), 241-253. doi:10.1111/j.1439-0426.2006.00805.xGarcía-Berthou, E., Alcaraz, C., Pou-Rovira, Q., Zamora, L., Coenders, G., & Feo, C. (2005). Introduction pathways and establishment rates of invasive aquatic species in Europe. Canadian Journal of Fisheries and Aquatic Sciences, 62(2), 453-463. doi:10.1139/f05-01

    Risk of invasion predicted with support vector machines: A case study on northern pike (Esox Lucius, L.) and bleak (Alburnus alburnus, L.)

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    The impacts of invasive species are recognised as a major threat to global freshwater biodiversity. The risk of invasion (probability of presence) of two avowed invasive species, the northern pike (Esox Lucius, L.) and bleak (Alburnus alburnus, L.), was evaluated in the upper part of the Cabriel River (eastern Iberian Peninsula). Habitat suitability models for these invasive species were developed with Support Vector Machines (SVMs), which were trained with data collected downstream the Contreras dam (the last barrier impeding the invasion of the upper river segment). Although SVMs gained visibility in habitat suitability modelling, they cannot be considered widespread in ecology. Thus, with this technique, there is certain controversy about the necessity of performing variable selection procedures. In this study, the parameters tuning and the variable selection for the SVMs was simultaneously performed with a genetic algorithm and, contradicting previous studies in freshwater ecology, the variable selection proved necessary to achieve almost perfect accuracy. Further, the development of partial dependence plots allowed unveiling the relationship between the selected input variables and the probability of presence. Results revealed the preference of northern pike for large and wide mesohabitats with vegetated shores and abundant prey whereas bleak preferred deep and slightly fast flow mesohabitats with fine substrate. Both species proved able to colonize the upper part of the Cabriel River but the habitat suitability for bleak indicated a slightly higher risk of invasion. Altogether may threaten the endemic species that actually inhabit that stretch, especially the Jucar nase (Parachondrostoma arrigonis; Steindachner), which is one of the most critically endangered Iberian freshwater fish species. (C) 2016 Elsevier B.V. All rights reserved.The study has been partially funded by the IMPADAPT project (CGL2013-48424-C2-1-R) with Spanish MINECO (Ministerio de Economia y Competitividad) and by the Confederacion Hidrografica del Jucar (Spanish Ministry of Agriculture, Food and Environment). We also want to thank all the colleagues who worked in the field data collection, especially Rui M. S. Costa and Aina Hernandez. Finally, we are especially grateful to Esther Lopez Fernandez who kindly and selflessly posed for the graphical abstract.Muñoz Mas, R.; Vezza, P.; Alcaraz-Hernández, JD.; Martinez-Capel, F. (2016). Risk of invasion predicted with support vector machines: A case study on northern pike (Esox Lucius, L.) and bleak (Alburnus alburnus, L.). Ecological Modelling. 342:123-134. https://doi.org/10.1016/j.ecolmodel.2016.10.006S12313434

    Spatial variation of the vegetative roughness in Mediterranean torrential streams affected by check dams

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    This is an Accepted Manuscript of an article published in Hydrological Sciences Journal on 2018, available online: http://www.tandfonline.com/10.1080/02626667.2017.1414384[EN] This study focuses on the spatial variations in vegetative roughness associated with morphological channel adjustments due to the presence of check dams in Mediterranean torrential streams. Manning's n values were estimated using methods established by previous studies of submerged and non-submerged vegetation in laboratory flume experiments and field work. The results showed a linear decrease in shrub density and rate of variation of the roughness coefficient versus degree of submergence with increasing distance upstream from the check dam, while downstream, the filling of the check dam and the bed incision had the most influence. A regression analysis was applied by fitting the data to different models: relationships between Manning's n and the flow velocity were found to be of the power type for shrubs in all upstream sections, while relationships of flow velocity versus hydraulic radius in the sections closest to check dams showed a good fit to second-order polynomial equations.This work was supported by project PI/13 (Hydrological and geomorphological response to the fluvial torrential systems affected by forestry-hydrological restoration works in semiarid catchments in southeast of Spain), from the Euromediterranean Institute of Hydrotechnics, European Council, and the Autonomous Community of Murcia, Spain.Conesa-García, C.; Sánchez-Tudela, JL.; Pérez-Cutillas, P.; Martinez-Capel, F. (2018). Spatial variation of the vegetative roughness in Mediterranean torrential streams affected by check dams. Hydrological Sciences Journal. 63(1):114-135. doi:10.1080/02626667.2017.1414384S11413563

    A comparison of artificial neural networks and random forests to predict native fish species richness in Mediterranean rivers

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    The original publication is available at www.kmaejournal.org[EN] Machine learning (ML) techniques have become important to support decision making in management and conservation of freshwater aquatic ecosystems. Given the large number of ML techniques and to improve the understanding of ML utility in ecology, it is necessary to perform comparative studies of these techniques as a preparatory analysis for future model applications. The objectives of this study were (i) to compare the reliability and ecological relevance of two predictive models for fish richness, based on the techniques of artificial neural networks (ANN) and random forests (RF) and (ii) to evaluate the conformity in terms of selected important variables between the two modelling approaches. The effectiveness of the models were evaluated using three performance metrics: the determination coefficient (R2), the mean squared error (MSE) and the adjusted determination coefficient (R2adj) and both models were developed using a k-fold crossvalidation procedure. According to the results, both techniques had similar validation performance (R2 = 68% for RF and R2 = 66% for ANN). Although the two methods selected different subsets of input variables, both models demonstrated high ecological relevance for the conservation of native fish in the Mediterranean region. Moreover, this work shows how the use of different modelling methods can assist the critical analysis of predictions at a catchment scale.[FR] Les techniques d’apprentissage automatique (ML) sont devenues importantes pour aider à la décision dans la gestion et la conservation des écosystèmes aquatiques d’eau douce. Étant donné le grand nombre de techniques ML pour améliorer la compréhension de l’utilité des ML en écologie, il est nécessaire de réaliser des études comparatives de ces techniques comme analyse préparatoire pour des applications de modèles futurs. Les objectifs de cette étude étaient : (i) de comparer la fiabilité et la pertinence écologique de deux modèles prédictifs pour la richesse de poisson, basé sur les techniques de réseaux de neurones artifi- ciels (ANN) et les forêts aléatoires (RF) et (ii) d’évaluer la conformité en termes de sélection des variables importantes entre les deux approches de modélisation. L’efficacité des modèles a été évaluée au moyen de trois indicateurs de performance : le coefficient de détermination (R2), l’erreur quadratique moyenne (MSE) et le coefficient de détermination ajusté (R2 adj) et les deux modèles ont été développés en utilisant une procédure de validation croisée k-fold. Selon les résultats, les deux techniques ont des performances de validation similaires (R2 = 68 % pour RF et R2 = 66 % pour ANN). Bien que les deux méthodes aient choisi différents sous-ensembles de variables d’entrée, les deux modèles ont démontré la pertinence écologique pour la conservation des poissons indigènes dans la région méditerranéenne. En outre, ce travail montre comment l’utilisation de différentes méthodes de modélisation peut aider à l’analyse critique des prévisions à l’échelle du bassin versant.This study was partially funded by the Spanish Ministry of Economy and Competitiveness with the projects SCARCE (Consolider-Ingenio 2010 CSD2009-00065) and POTECOL "Evaluacion del Potencial Ecologico de R os Regulados por Embalses y Desarrollo de Criterios para su mejora segun la Directiva Marco del Agua" (CGL2007-66412). In addition, the RF analysis was developed in the frame of the EU-funded HolRiverMed project (IEF, Marie Curie Actions). We thank the Confederacion Hidrografica del Jucar (Spanish Ministry of Agriculture, Food and Environment) for the data provided to develop this study and we also owe our gratitude to Sasa Plestenjak for the collaboration in building the first fish database for this research. We owe our gratitude to Chris Holmquist-Johnson and Leanne Hanson (USGS, Fort Collins Science Center) for the scientific review of the paper.Olaya Marín, EJ.; Martinez-Capel, F.; Vezza, P. (2013). A comparison of artificial neural networks and random forests to predict native fish species richness in Mediterranean rivers. Knowledge and Management of Aquatic Ecosystems. 409(7):1-19. https://doi.org/10.1051/kmae/2013052S1194097Abrahamsson C., Johansson J., Sparén A. and Lindgren F., 2003. Comparison of different variable selection methods conducted on NIR transmission measurements on intact tablets.Chemometrics Intell. Lab. Syst.,69, 3–12.Aertsen W., Kint V., van Orshoven J., Özkan K. and Muys B., 2010. Comparison and ranking of different modelling techniques for prediction of site index in Mediterranean mountain forests.Ecol. Model.,221, 1119–1130.Aertsen W., Kint V., Van Orshoven J. and Muys B., 2011. Evaluation of modelling techniques for forest site productivity prediction in contrasting ecoregions using stochastic multicriteria acceptability analysis (SMAA).Environ. Modell. Softw.,26, 929–937.Alba-Tercedor A., 1996. Macroinvertebrados acuaticos y calidad de las aguas de los ríos, IV Simposio del Agua en Andalucía (SIAGA), Almería, 203–213.Alcaraz-Hernández J.D., Martínez-Capel F., Peredo-Parada M. and Hernández-Mascarell A.B., 2011. Mesohabitat heterogeneity in four mediterranean streams of the Jucar river basin (Eastern Spain).Limnetica,30, 363–378.Allan J.D. and Castillo M.M., 2007. Stream ecology: structure and function of running waters, 2nd edn., Springer, Netherlands, 436 p.Aparicio E., Vargas M.J., Olmo J.M. and de Sostoa A., 2000. Decline of native freshwater fishes in a Mediterranean watershed on the Iberian Peninsula: A quantitative assessment.Environ. Biol. Fishes,59, 11–19.Aparicio E., Carmona-Catot G., Moyle P.B. and García-Berthou E., 2011. Development and evaluation of a fish-based index to assess biological integrity of Mediterranean streams.Aquat. Conserv.: Mar. Freshwat. Ecosyst.,21, 324–337.Armitage D.W. and Ober H.K., 2010. A comparison of supervised learning techniques in the classification of bat echolocation calls.Ecol. Inform.,5, 465–473.Beechie T.J., Sear D.A., Olden J.D., Pess G.R., Buffington J.M., Moir H., Roni P. and Pollock M.M., 2010. Process-based principles for restoring river ecosystems.Bioscience,60, 209–222.Belmar O., Velasco J. and Martinez-Capel F., 2011. Hydrological classification of natural flow regimes to support environmental flow assessments in Intensively regulated Mediterranean Rivers, Segura River Basin (Spain).Environ. Manage.,47, 992–1004.Bernardo J.M., Ilhéu M., Matono P. and Costa A.M., 2003. Interannual variation of fish assemblage structure in a Mediterranean river: implications of streamflow on the dominance of native or exotic species.River Res. Appl.,19, 521–532.Breiman L., 2001a. Random Forests.Mach. Learn.,45, 5–32.Breiman L., 2001b. Statistical modeling: the two cultures.Stat. Sci.,16, 199–231.Breiman L., Friedman J., Olshen R. and Stone C., 1984. Classification and Regression Trees, Wadsworth International Group, Belmont, California, 368 p.Caissie D., 2006. River discharge and channel width relationships for New Brunswick rivers. Canadian Technical Report of Fisheries and Aquatic Sciences, Rept. 2637, 26 p.Carballo R., Cancela J., Iglesias G., Marín A., Neira X. and Cuesta T., 2009. WFD indicators and definition of the ecological status of rivers.Water Resour. Manag.,23, 2231–2247.Cheng L., Lek S., Lek-Ang S. and Li Z., 2012. Predicting fish assemblages and diversity in shallow lakes in the Yangtze River basin.Limnologica,42, 127–136.CHJ, 2007. Estudio general sobre la Demarcación Hidrográfica del Júcar, Confederación Hidrográfica del Júcar, Madrid, 206 p.Corbacho C. and Sánchez J.M., 2001. Patterns of species richness and introduced species in native freshwater fish faunas of a Mediterranean-type basin: the Guadiana River (southwest Iberian Peninsula).Regul. River.,17, 699–707.Costa R.M.S., Martínez-Capel F., Muñoz-Mas R., Alcaraz-Hernández J.D. and Garófano-Gómez V., 2012. Habitat suitability modelling at mesohabitat scale and effects of dam operation on the endangered Júcar nase,Parachondrostoma arrigonis(river Cabriel, Spain).River Res. Appl.,28, 740–752.Cutler D.R., Edwards T.C., Beard K.H., Cutler A., Hess K.T., Gibson J. and Lawler J.J., 2007. Random Forests for classification in ecology.Ecology,88, 2783–2792.Demuth H., Beale M. and Hagan M., 2010. Neural network toolbox user’s guide, The MathWorks Inc, Natick, Massachusetts, 901 p.Dimopoulos Y., Bourret P. and Lek S., 1995. Use of some sensitivity criteria for choosing networks with good generalization ability.Neural Process. Lett.,2, 1–4.Doadrio I., 2001. Atlas y libro rojo de los peces continentales de España, Ministerio de Medio Ambiente, Madrid, 358 p.Doadrio I., 2002. Origen y Evolución de la Ictiofauna Continental Española.En: Atlas y libro rojo de los peces continentales de España. 2da ed, CSIC y Ministerio del Medio Ambiente, Madrid, 20–34.Dolloff C.A., Hankin D.G. and Reeves G.H., 1993. Basinwide estimation of habitat and fish populations in streams, U.S. Department of Agriculture, Blacksburg, Virginia, 25 p.Dormann C.F., 2011. Modelling species’ distributions.In: Jopp F., Reuter H. and Breckling B. (eds.), Modelling complex ecological dynamics: an Introduction into ecological modelling for students, teachers and scientists, Springer-Verlag, Berlin, 179–196.Drew C.A., Wiersma Y. and Huettmann F., 2011. Predictive species and habitat modeling in landscape ecology: concepts and applications, Springer, New York, 328 p.Estrela T., Fidalgo A., Fullana J., Maestu J., Pérez M.A. and Pujante A.M., 2004. Júcar Pilot River Basin, provisional article 5 report Pursuant to the Water Framework Directive, Confederación Hidrográfica del Júcar, Valencia, 200 p.Evans J. and Cushman S., 2009. Gradient modeling of conifer species using random forests.Landsc. Ecol.,24, 673–683.Evans J.S., Murphy M.A., Holden Z.A. and Cushman S.A., 2011. Modeling species distribution and change using Random Forest.In: Drew C.A., Wiersma Y.F. and Huettmann F. (eds.), Predictive Species and Habitat Modeling in Landscape Ecology, Springer New York, 139–159.Fausch K., Torgersen C., Baxter C. and Li H., 2002. Landscapes to riverscapes: bridging the gap between research and conservation of stream fishes.Bioscience,52, 483–498.Ferreira T., Oliveira J., Caiola N., De Sostoa A., Casals F., Cortes R., Economou A., Zogaris S., Garcia de Jalón D., Ilhéu M., Martinez-Capel F., Pont D., Rogers C. and Prenda J., 2007. Ecological traits of fish assemblages from Mediterranean Europe and their responses to human disturbance.Fisheries Manag. Ecol.,14, 473–481.Filipe A.F., Magalhães M.F. and Collares-Pereira M.J., 2010. Native and introduced fish species richness in Mediterranean streams: the role of multiple landscape influences.Divers. Distrib.,16, 773–785.Franklin J., 2010. Mapping species distributions: spatial inference and prediction, Cambridge University Press, New York, 338 p.García-Berthou E., Alcaraz C., Pou-Rovira Q., Zamora L., Coenders G. and Feo C., 2005. Introduction pathways and establishment rates of invasive aquatic species in Europe.Can. J. Fish. Aquat. Sci.,62, 453–463.Garófano-Gómez V., Martínez-Capel F., Peredo-Parada M., Olaya-Marín E.J., Muñoz-Mas R., Costa R. and Pinar-Arenas L., 2011. Assessing hydromorphological and floristic patterns along a regulated Mediterranean river: The Serpis River (Spain).Limnetica,30, 307–238.Gevrey M., Dimopoulos I. and Lek S., 2003. Review and comparison of methods to study the contribution of variables in artificial neural network models.Ecol. Model.,160, 249–264.Goethals P., Dedecker A., Gabriels W., Lek S. and De Pauw N., 2007. Applications of artificial neural networks predicting macroinvertebrates in freshwaters.Aquat. Ecol.,41, 491–508.Granado-Lorencio C., 1996. Ecología de peces, Universidad de Sevilla, Sevilla, 353 p.Granado-Lorencio C., 2000. Ecología de comunidades: el paradigma de los peces de agua dulce, Universidad de Sevilla, Sevilla, 284 p.Guisan A. and Zimmermann N.E., 2000. Predictive habitat distribution models in ecology.Ecol. Model.,135, 147–186.Gutiérrez-Estrada J.C. and Bilton D.T., 2010. A heuristic approach to predicting water beetle diversity in temporary and fluctuating waters.Ecol. Model.,221, 1451–1462.Hastie T., Tibshirani R. and Friedman J., 2009. The Elements of Statistical Learning: data mining, Inference and prediction, Springer, 768 p.Hauser-Davis R.A., Oliveira T.F., Silveira A.M., Silva T.B. and Ziolli R.L., 2010. Case study: Comparing the use of nonlinear discriminating analysis and Artificial Neural Networks in the classification of three fish species: acaras (Geophagus brasiliensis), tilapias (Tilapia rendalli) and mullets (Mugil liza).Ecol. Inform.,5, 474–478.He Y., Wang J., Lek-Ang S. and Lek S., 2010. Predicting assemblages and species richness of endemic fish in the upper Yangtze River.Sci. Total Environ.,408, 4211–4220.Hermoso V. and Clavero M., 2011. Threatening processes and conservation management of endemic freshwater fish in the Mediterranean basin: a review.Mar. Freshwater Res.,62, 244–254.Hooten M.B., 2011. The state of spatial and spatio-temporal statistical modeling.In: Drew C., Wiersma Y. and Huettmann F. (eds.), Predictive Species and Habitat Modeling in Landscape Ecology, Springer New York, 29–41.Ibarra A.A., Gevrey M., Park Y.-S., Lim P. and Lek S., 2003. Modelling the factors that influence fish guilds composition using a back-propagation network: assessment of metrics for indices of biotic integrity.Ecol. Model.,160, 281–290.Isa I.S., Omar S., Saad Z. and Osman M.K., 2010. Performance comparison of different multilayer perceptron network activation functions in automated weather classification. Proceedings of the 2010 Fourth Asia International Conference on Mathematical/Analytical Modelling and Computer Simulation, Kota Kinabalu, Malaysia, 71–75.Jackson D.A., Peres-Neto P.R. and Olden J.D., 2001. What controls who is where in freshwater fish communities the roles of biotic, abiotic, and spatial factors.Can. J. Fish. Aquat. Sci.,58, 157–170.Jorgensen S.E. and Fath B.D., 2011. Fundamentals of ecological modelling: applications in environmental management and research. 4th ed., Elsevier, Amsterdam, 432 p.Kampichler C., Wieland R., Calmé S., Weissenberger H. and Arriaga-Weiss S., 2010. Classification in conservation biology: a comparison of five machine-learning methods.Ecol. Inform.,5, 441–450.Karul C., Soyupak S., Çilesiz A.F., Akbay N. and Germen E., 2000. Case studies on the use of neural networks in eutrophication modeling.Ecol. Model.,134, 145–152.Knudby A., LeDrew E. and Brenning A., 2010. Predictive mapping of reef fish species richness, diversity and biomass in Zanzibar using IKONOS imagery and machine-learning techniques.Remote Sens. Environ.,114, 1230–1241.Kroes M.J., Gough P.P., Wanningen H., Schollema P., Ordeix M. and Vesely D., 2006. From sea to source. Practical guidance for the restoration of fish migration in European Rivers. Interreg IIIC Project “Community Rivers”, Groningen, The Netherlands, 119 p.Kurková V., 1992. Kolmogorov’s theorem and multilayer neural networks.Neural Netw.,5, 501-506.Leclere J., Oberdorff T., Belliard J. and Leprieur F., 2011. A comparison of modeling techniques to predict juvenile 0 + fish species occurrences in a large river system.Ecol. Inform.,6, 276–285.Lek S., Scardi M., Verdonschot P., Descy J.P. and Park Y.S. (eds.), 2005. Modelling community structure in freshwater ecosystems, Springer-Verlag, Berlin.Leopold L.B., Wolman M.G. and Miller J.P., 1964. Fluvial processes in geomorphology, W.H. Freeman, San Francisco, 544 p.Leprieur F., Brosse S., García-Berthou E., Oberdorff T., Olden J.D. and Townsend C.R., 2009. Scientific uncertainty and the assessment of risks posed by non-native freshwater fishes.Fish. Fish.,10, 88–97.Liaw A. and Wiener M., 2002. Classification and regression by Random Forest.R News,2, 18–22.Magalhães M.F., Beja P., Schlosser I.J. and Collares-Pereira M.J., 2007. Effects of multi-year droughts on fish assemblages of seasonally drying Mediterranean streams.Freshw. Biol.,52, 1494–1510.Maier H.R. and Dandy G.C., 2000. Neural networks for the prediction and forecasting of water resources variables: A review of modelling issues and applications.Environ. Modell. Softw.,15, 101–124.Mastrorillo S., Dauba F., Oberdorff T., Guégan J.-F. and Lek S., 1998. Predicting local fish species richness in the garonne river basin.C.R. Acad. Sci. - Ser. III - Sciences de la Vie,321, 423–428.MMARM, 2008. Orden MARM/2656/2008 de 10 septiembre, por la que se aprueba la instrucción de planificación hidrológica. BOE núm. 229, de 22 de septiembre de 2008., Ministerio de Medio Ambiente, y Medio Rural y Marino (MMARM), Madrid.Mouton A.M., Alcaraz-Hernández J.D., De Baets B., Goethals P.L.M. and Martínez-Capel F., 2011. Data-driven fuzzy habitat suitability models for brown trout in Spanish Mediterranean rivers.Environ. Modell. Softw.,26, 615–622.Munné A., Prat N., Solà C., Bonada N. and Rieradevall M., 2003. A simple field method for assessing the ecological quality of riparian habitat in rivers and streams: QBR index.Aquat. Conserv.: Mar. Freshwat. Ecosyst.,13, 147–163.Murphy M.A., Evans J.S. and Storfer A., 2010. QuantifyingBufo boreasconnectivity in Yellowstone National Park with landscape genetics.Ecology,91, 252–261.Naiman R.J., Decamps H. and Pollock M., 1993. The role of riparian corridors in maintaining regional biodiversity.Ecol. Appl.,3, 209–212.Oberdorff T., Guégan J.-F. and Hugueny B., 1995. Global scale patterns of fish species richness in rivers.Ecography,18, 345–352.Olaya-Marín E.J., Martínez-Capel F., Soares Costa R.M. and Alcaraz-Hernández J.D., 2012. Modelling native fish richness to evaluate the effects of hydromorphological changes and river restoration (Júcar River Basin, Spain).Sci. Total Environ.,440, 95–105.Olden J.D. and Jackson D.A., 2002. Illuminating the “black box”: a randomization approach for understanding variable contributions in artificial neural networks.Ecol. Model.,154, 135–150.Olden J.D., Poff N.L. and Bledsoe B.P., 2006. Incorporating ecological knowledge into ecoinformatics: An example of modeling hierarchically structured aquatic communities with neural networks.Ecol. Inform.,1, 33–42.Olden J.D., Lawler J.J. and Poff N.L., 2008. Machine learning methods without tears: A primer for ecologists.Q. Rev. Biol.,83, 171–193.Ollero A., Ibisate A., Gonzalo L., Acín V., Ballarín D., Díaz E., Gimeno M., Domenech S., Granado D., García H., Mora D. and Sánchez M. 2011. The IHG index for hydromorphological quality assessment of rivers and streams: updated versionLimnetica,30, 255–262.Özesmi S.L., Tan C.O. and Özesmi U., 2006. Methodological issues in building, training, and testing artificial neural networks in ecological applications.Ecol. Model.,195, 83–93.Paredes-Arquiola J., Martinez-Capel F., Solera A. and Aguilella V., 2013. Implementing environmental flows in complex water resources systems–case study: the Duero river basin, Spain.River Res. Appl.,29, 451–468.Paredes-Arquiola J., Solera-Solera A., Martínez-Capel F., Momblanch-Benavent A. and Andreu-Álvarez J. Integrating water management, habitat modelling and water quality at basin scale environmental flow assessment – Tormes River (Spain).Hydrol. Sci. J.-J. Sci. Hydrol., in press.Poff N.L., Allan J.D., Bain M.B., Karr J.R., Prestegaard K.L., Richter B.D., Sparks R.E. and Stromberg J.C., 1997. The natural klow regime.Bioscience,47, 769–784.Poff N.L., Richter B.D., Arthington A.H., Bunn S.E., Naiman R.J., Kendy E., Acreman M., Apse C., Bledsoe B.P., Freeman M.C., Henriksen J., Jacobson R.B., Kennen J.G., Merritt D.M., O’Keeffe J.H., Olden J.D., Rogers K., Tharme R.E. and Warner A., 2010. The ecological limits of hydrologic alteration (ELOHA): a new framework for developing regional environmental flow standards.Freshw. Biol.,55, 147–170.R Development Core Team, 2009. R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria, 409 p.Reunanen J., 2003. Overfitting in making comparisons between variable selection methods.J. Mach. Learn. Res.,3, 1371–1382.Reyjol Y., Hugueny B., Pont D., Bianco P.G., Beier U., Caiola N., Casals F., Cowx I., Economou A., Ferreira T., Haidvogl G., Noble R., De Sostoa A., Vigneron T. and Virbickas T., 2007. Patterns in species richness and endemism of European freshwater fish.Glob. Ecol. Biogeogr.,16, 65–75.Sánchez-Montoya M.M., Vidal-Abarca M.R. and Suárez M.L., 2010. Comparing the sensitivity of diverse macroinvertebrate metrics to a multiple stressor gradient in Mediterranean streams and its influence on the assessment of ecological status.Ecol. Indic.,10, 896–904.Singh K.P., Basant A., Malik A. and Jain G., 2009. Artificial neural network modeling of the river water quality–A case study.Ecol. Model.,220, 888–895.Siroky D.S., 2009. Navigating Random Forests and related advances in algorithmic modeling.Statist. Surv.,3, 147–163.Smith K.G. and Darwall W.R.T., 2006. The status and distribution of freshwater fish endemic to the mediterranean basin, IUCN – The World Conservation Union, Gland, Switzerland/Cambridge, UK., 41 p.Strayer D.L. and Dudgeon D., 2010. Freshwater biodiversity conservation: recent progress and future challenges.J. N. Am. Benthol. Soc.,29, 344–358.Tirelli T. and Pessani D., 2009. Use of decision tree and artificial neural network approaches to model presence/absence ofTelestes muticellusin piedmont (North-Western Italy).River Res. Appl.,25, 1001–1012.Tirelli T. and Pessani D., 2011. Importance of feature selection in decision-tree and artificial-neural-network ecological applications.Alburnus alburnus alborella: A practical example.Ecol. Inform.,6, 309-315.Tirelli T., Pozzi L. and Pessani D., 2009. Use of differen

    Simulation of retrospective morphological channel adjustments using high-resolution differential digital elevation models versus predicted sediment delivery and stream power variations

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    [EN] This work proposes a methodological approach applied to ephemeral gravel-bed streams to verify the change in the magnitude and frequency of hydrological events affecting the morphological dynamics and sediment budget in this type of channel. For the case study, the Azohia Rambla, located in southeastern Spain, was chosen, emphasizing the research on two reference riverbed sections (RCRs): an upper one, with a predominance of erosion, and a middle one, where processes of incision, transport, and deposition were involved. First, this approach focuses on relationships between peak discharges and sediment budgets during the period 2018-2022. For this purpose, water level measurements from pressure sensors, a One-Dimensional Hydrodynamic model, and findings from comparative analyses of high-resolution differential digital elevation models (HRDEM of Difference-HRDoD) based on SfM-MVS and LiDAR datasets were used. In a second phase, the GeoWEPP model was applied to the period 1996-2022 in order to simulate runoff and sediment yield at the event scale for the watersheds draining into both RCRs. During the calibration phase, a sensitivity analysis was carried out to detect the most influential parameters in the model and confirm its capacity to simulate peak flow and sediment delivery in the area described above. Values of NS (Nash-Sutcliffe efficiency) and PBIAS (percent bias) equal to 0.86 and 7.81%, respectively, were found in the calibration period, while these indices were 0.81 and -4.1% in the validation period. Finally, different event class patterns (ECPs) were established for the monitoring period (2018-2022), according to flow stage and morphological channel adjustments (overtopping, bankfull and sub-bankfull, and half-sub-bankfull), and then retrospectively extrapolated to stages of the prior simulated period (1996-2018) from their typical sequences (PECPs). The results revealed a significant increase in the number of events and PECPs leading to lower bed incision rates and higher vertical accretion, which denotes a progressive increase in bed armoring and bank erosion processes.This research was funded by ERDF/Spanish Ministry of Science, Innovation and Universities-State Research Agency (AEI)/Project CGL2017-84625-C2-1-R. State Program for Research, Develop-ment and Innovation focused on the Challenges of SocietyConesa-García, C.; Martínez-Salvador, A.; Puig-Mengual, C.; Martinez-Capel, F.; Pérez-Cutillas, P. (2023). Simulation of retrospective morphological channel adjustments using high-resolution differential digital elevation models versus predicted sediment delivery and stream power variations. Water. 15(15):1-35. https://doi.org/10.3390/w15152697135151

    Habitat evaluation for the endangered fish species Lefua echigonia in the Yagawa River, Japan

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    This is an Accepted Manuscript of an article published by Taylor & Francis in Journal of Ecohydraulics on 2019, available online: http://www.tandfonline.com/10.1080/24705357.2019.1614886[EN] Spring-fed streams in Tokyo are important habitats for various aquatic species, whereas urbanization as well as introduction of invasive species is threatening the sustainability of such aquatic ecosystems. This study applies the System for Environmental Flow Analysis (SEFA) in a small urban river in Tokyo to assess the dynamics of the suitable habitats for the endangered freshwater fish Lefua echigonia (Jordan and Richardson 1907). A set of Habitat Suitability Curves (HSCs) for water depth, velocity and substrate was developed to evaluate the suitable habitats. The habitat assessment indicated that the Area Weighted Suitability (AWS) reached the maximum at 0.02 m3/s, which is close to the base flow of the target river; a gradual decrease in AWS was observed for higher flows. The temporal distribution of AWS, during forty-one consecutive months, showed that, on average, the best habitat conditions for adult L. echigonia occur during the period between January and July, whereas the worst situation occurs during the period between August and December. This work presents information and tools for instream habitat analysis that should help managers to conserve this aquatic species and prioritize actions to further rehabilitate urban rivers, using L. echigonia as a case study.We thank Dr. Masaomi Kimura, Masato Kondo, Taichi Kasahara, and Akihiro Tanaka for their support in the field survey. This study was made in part with the support of the JSPS Grants-in-Aid for Scientific Research (Grant number: 17H03886 and 17H04631) and the PROMOE grant for Marina de Miguel Gallo, funded by the Universitat Politecnica de Valencia, between April and August 2018.De-Miguel-Gallo, M.; Martinez-Capel, F.; Muñoz Mas, R.; Aihara, S.; Matsuzawa, Y.; Fukuda, S. (2019). Habitat evaluation for the endangered fish species Lefua echigonia in the Yagawa River, Japan. Journal of Ecohydraulics. 4(2):147-157. https://doi.org/10.1080/24705357.2019.1614886S14715742Bovee KD, Lamb BL, Bartholow JM, Stalnaker CB, Taylor J, Henriksen J. 1998. Stream habitat analysis using the instream flow incremental methodology. U.S. Geological Survey, Biological Resources Division Information and Technology Report USGS/BRD-1998-0004. Fort Collins: U.S. Geological Survey.Bovee KD. 1986. Development and evaluation of habitat suitability criteria for use in the instream flow incremental methodology. Washington, D.C.: U.S. Fish and Wildlife Service Biological Report, 86/7.Lambert TR. 1994. Evaluation of factors causing variability in habitat suitability criteria for Sierra Nevada trout. Environment, Health & Safety. Report 009.4-94.5. San Francisco: Pacific Gas and Electric Company.Martínez-Capel F. 2000. Preferencias de microhábitat de Barbus bocagei, Chondrostoma polylepis y Leuciscus pyrenaicus en la cuenca del río Tajo [PhD Dissertation]. Madrid: Universidad Politécnica de Madrid. (In Spanish)Matsuzawa Y, Aoki K, Fukuda S. 2017a. Critical swimming speed of Lefua echigonia in a laboratory open channel. Proceedings of the Annual Meeting of the Japanese Society of Irrigation Drainage and Reclamation Engineering (JSIDRE). ID: 4-30. Tokyo: Japanese Society of Irrigation Drainage and Reclamation Engineering.Matsuzawa Y, Ohira M, Fukuda S. 2017b. Microhabitat Modelling for an Endangered Freshwater Fish, Lefua Echigonia, in a Spring-Fed Urban Stream. E-Proceedings of the 37th IAHR World Congress. Kuala Lumpur: International Association for Hydro-environment Research and Engineering (IAHR).Poff NL. 2018. Beyond the natural flow regime? Broadening the hydro-ecological foundation to meet environmental flows challenges in a non-stationary world. Freshwater Biol. 63(8):1011–1021

    Investigating the influence of habitat structure and hydraulics on tropical macroinvertebrate communities

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    [EN] The influences of habitat structure and hydraulics on tropical macroinvertebrate communities were investigated in two foothill rivers of the Udzungwa Mountains (United Republic of Tanzania) to assist future Environmental Flow Assessments (EFAs). Macroinvertebrate samples, hydraulic variables and habitat structure were collected at the microhabitat scale (n = 90). Macroinvertebrate communities were first delineated (i.e. clustered) through Poisson and negative binomial mixture models for count data in a semi-supervised mode by taking into account the sampled river. Then, genetically optimised Multi-Layer Perceptrons (MLPs) were used to identify the relationship of the most relevant variables with the delineated communities. Between the three delineated communities exclusively one community was shared between both rivers. The first and third communities presented similar values of richness (i.e. number of families) and diversity but the first was characterised by high abundance and was dominated by Baetidae (43.2%) while Hydropsychidae (36.3%) dominated the third community. The second community was dominated by Baetidae (33.4%), but it involved low abundance, richness and diversity samples and encompassed the microhabitats where no-macroinvertebrates were found. The performance of the MLP acknowledged the quality of the delineation and it indicated that the first community shows a clear affinity for microhabitats with aquatic vegetation and woody debris and the third for unshaded, fast flowing and shallow microhabitats on intermediate-sized substrate. Conversely, the second community occurred in deep and shaded microhabitats with low flow velocity and coarse substrate. We demonstrated that habitat structure and hydraulics are able to properly discriminate the macroinvertebrate communities, which, in turn, underlines their importance as drivers of community composition and abundance. Aquatic vegetation, woody debris, velocity and substrate index, followed by depth and shade, emerged as the most discriminant variables to understand macroinvertebrate communities in these tropical running waters. These results should enhance the implementation of ongoing and future EFA studies. (C) 2018 European Regional Centre for Ecohydrology of the Polish Academy of Sciences. Published by Elsevier B.V. All rights reserved.This study was financed by the United States Agency for International Development (USAID) as part of the Technical Assistance to Support the Development of Irrigation and Rural Roads Infrastructure Project (IRRIP2), implemented by CDM International Inc. J. Sanchez-Hernandez was supported by a postdoctoral grant from the Galician Plan for Research, Innovation, and Growth (Plan I2C, Xunta de Galicia).Muñoz Mas, R.; Sánchez-Hernández, J.; Mcclain, M.; Tamatamah, R.; Mukama, SC.; Martinez-Capel, F. (2019). Investigating the influence of habitat structure and hydraulics on tropical macroinvertebrate communities. Ecohydrology & Hydrobiology. 19(3):339-350. https://doi.org/10.1016/j.ecohyd.2018.07.005S33935019

    Determining the macroinvertebrate community indicators and relevant environmental predictors of the Hun-Tai River Basin (Northeast China): A study based on community patterning

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    [EN] It is essential to understand the patterning of biota and environmental influencing factors for proper rehabilitation and management at the river basin scale. The Hun-Tai River Basin was extensively sampled four times for macroinvertebrate community and environmental variables during one year. Self-Organizing Maps (SOMs) were used to reveal the aggregation patterns of the 355 samples. Three community types (i.e., clusters) were found (at the family level) based on the community composition, which showed a clearly gradient by combining them with the representative environmental variables: minimally impacted source area, intermediately anthropogenic impacted sites, and highly anthropogenic impacted downstream area, respectively. This gradient was corroborated by the decreasing trends in density and diversity of macroinvertebrates. Distance from source, total phosphorus and water temperature were identified as the most important variables that distinguished the delineated communities. In addition, the sampling season, substrate type, pH and the percentage of grassland were also identified as relevant variables. These results demonstrated that macroinvertebrates communities are structured in a hierarchical manner where geographic and water quality prevail over temporal (season) and habitat (substrate type) features at the basin scale. In addition, it implied that the local-scale environment variables affected macroinvertebrates under the longitudinal gradient of the geographical and anthropogenic pressure. More than one family was identified as the indicator for each type of community. Abundance contributed significantly for distinguishing the indicators, while Baetidae with higher density indicated minimally and intermediately impacted area and lower density indicated highly impacted area. Therefore, we suggested the use of abundance data in community patterning and classification, especially in the identification of the indicator taxa. (C) 2018 Elsevier B.V. All rights reserved.This work was supported by the National Natural Science Foundation of China (51779275, 41501204, 51479219) and the IWHR Research & Development Support Program (WE0145B532017).Zhang, M.; Muñoz Mas, R.; Martinez-Capel, F.; Qu, X.; Zhang, H.; Peng, W.; Liu, X. (2018). Determining the macroinvertebrate community indicators and relevant environmental predictors of the Hun-Tai River Basin (Northeast China): A study based on community patterning. The Science of The Total Environment. 634:749-759. https://doi.org/10.1016/j.scitotenv.2018.04.021S74975963
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