REFERENCES

• Abell , R. , Thieme , M. L. , Revenga , C. , Bryer , M. , Kottelat , M. , Bogutskaya , N. , Coad , B. , Mandrak , N. , Balderas , S. C. , Bussing , W. , Stiassny , M. L. J. , Skelton , P. , Allen , G. R. , Unmack , P. , Naseka , A. , Ng , R. , Sindorf , N. , Robertson , J. , Armijo , E. , Higgins , J. V. , Heibel , T. J. , Wikramanayake , E. , Olson , D. , López , H. L. , Reis , R. E. , Lundberg , J. G. , Pérez , M. H. S. and Petry , P. 2008 . Freshwater ecoregions of the world: a new map of biogeographic units for freshwater biodiversity conservation . Bio Science , 58 : 403 – 414 .
   Web of Science ®Google Scholar
• Angermeier , P. L. and Smogor , R. A. 1995 . Estimating number of species and relative abundances in stream-fish communities: effects of sampling effort and discontinuous spatial distributions . Canadian Journal of Fisheries and Aquatic Sciences , 52 : 936 – 949 .
   Web of Science ®Google Scholar
• Araújo , F. G. 1998 . Adaptation of the index of biotic integrity based on fish assemblages in the Paraíba do Sul River, RJ, Brazil . Brazilian Journal of Biology , 58 : 547 – 558 .
   Google Scholar
• Araújo , F. G. , Fichberg , I. , Pinto , B. C. and Peixoto , M. G. 2003 . A preliminary index of biotic integrity for monitoring condition of the Rio Paraíba do Sul, Southeast Brazil . Environmental Management , 32 : 516 – 526 .
   PubMed Web of Science ®Google Scholar
• Baptista , D. F. , Buss , D. F. , Egler , M. , Giovanelli , A. , Silveira , M. P. and Nessimian , J. 2007 . A multimetric index based on benthic macroinvertebrates for evaluation of Atlantic Forest streams at Rio de Janeiro State, Brazil . Hydrobiologia , 575 : 83 – 94 .
   Web of Science ®Google Scholar
• Bonar , S. , Hubert , W. and Willis , D. , eds. 2009 . Standard methods for sampling North American freshwater fishes , Bethesda , Maryland : American Fisheries Society .
   Google Scholar
• Bozzetti , M. and Schulz , U. H. 2004 . An index of biotic integrity based on fish assemblages for subtropical streams in southern Brazil . Hydrobiologia , 529 : 133 – 144 .
   Web of Science ®Google Scholar
• Cao , Y. , Larsen , D. P. and Hughes , R. M. 2001 . Evaluating sampling sufficiency in fish assemblages: a similarity-based approach . Canadian Journal of Fisheries and Aquatic Sciences , 58 : 1782 – 1793 .
   Web of Science ®Google Scholar
• Casatti , L. , Ferreira , C. P. and Langeani , F. 2009 . A fish-based biotic integrity index for assessment of lowland streams in southeastern Brazil . Hydrobiologia , 623 : 173 – 189 .
   Web of Science ®Google Scholar
• Chao , A. 1984 . Non-parametric estimation of the number of classes in a population . Scandinavian Journal of Statistics , 11 : 265 – 270 .
   Web of Science ®Google Scholar
• Chao , A. 1987 . Estimating the population size for capture–recapture data with unequal catchability . Biometrics , 43 : 783 – 791 .
   PubMed Web of Science ®Google Scholar
• Clarke , K. R. and Gorley , R. N. 2006 . PRIMER v6: user manual/tutorial , Plymouth , , UK : PRIMER-E .
   Google Scholar
• Comite Europeen de Normalisation . 2003 . Water quality—sampling of fish with electricity , CEN . European Standard EN 14011:2003 E, Brussels, Belgium
   Google Scholar
• Dauwalter , D. C. and Pert , E. J. 2003a . Effect of electrofishing effort on an index of biotic integrity . North American Journal of Fisheries Management , 23 : 1247 – 1252 .
   Web of Science ®Google Scholar
• Dauwalter , D. C. and Pert , E. J. 2003b . Electrofishing effort and fish species richness and relative abundance in Ozark Highland streams of Arkansas . North American Journal of Fisheries Management , 23 : 1152 – 1166 .
   Web of Science ®Google Scholar
• Dolph , C. L. , Sheshukov , A. Y. , Chizinski , C. J. , Vondracek , B. and Wilson , B. 2010 . The index of biological integrity and the bootstrap: can random sampling error affect stream impairment decisions . Ecological Indicators , 10 : 527 – 537 .
   Web of Science ®Google Scholar
• Dos Anjos , M. B. and Zuanon , J. 2007 . Sampling effort and fish species richness in small terra firme forest streams of central Amazonia, Brazil . Neotropical Ichthyology , 5 : 45 – 52 .
   Web of Science ®Google Scholar
• Dußling , U. , Berg , R. , Klinger , H. , Wolter , C. and Wilken , R.-D. 2004 . “ Assessing the ecological status of river systems using fish assemblages ” . In Handbuch angewandte limnologie, VIII-7.4, 20 , Edited by: Steinberg , C. , Calmano , W. and Klapper , H. 1 – 84 . Bavaria : Ecomed, Landsberg am Lech .
   Google Scholar
• Efron , B. 1979 . Bootstrap methods: another look at the jackknife . Annals of Statistics , 7 : 1 – 26 .
   Web of Science ®Google Scholar
• Efron , B. 1981 . Nonparametric estimates of standard error: the jackknife, the bootstrap and other methods . Biometrika , 68 : 589 – 599 .
   Web of Science ®Google Scholar
• Erős , T. , Tóth , B. , Sevcsik , A. and Schmera , D. 2008 . Comparison of fish assemblage diversity in natural and artificial rip-rap habitats in the littoral zone of a large river (River Danube, Hungary) . International Review of Hydrobiology , 93 : 88 – 105 .
   Web of Science ®Google Scholar
• Ferreira , C. P. and Casatti , L. 2006a . Influence of habitat structure on fish from a stream in a micro-watershed pasture, São Paulo, Brazil . Brazilian Journal of Zoology , 23 : 642 – 651 .
   Google Scholar
• Ferreira , C. P. and Casatti , L. 2006b . Stream biotic integrity assessed by fish assemblages in the Upper Rio Paraná basin . Biota Neotropica , 6 : 1 – 25 .
   Google Scholar
• Fischer , J. R. and Paukert , C. P. 2009 . Effects of sampling effort, assemblage similarity, and habitat heterogeneity on estimates of species richness and relative abundance of stream fishes . Canadian Journal of Fisheries and Aquatic Sciences , 66 : 277 – 290 .
   Web of Science ®Google Scholar
• Froese , R. and Pauly , D. , eds. 2012 . FishBase Available: http://www.fishbase.org. (April, 2012)
   Google Scholar
• Ganasan , V. and Hughes , R. M. 1998 . Application of an index of biological integrity to fish assemblages of the rivers Khan and Kshipra, India . Freshwater Biology , 40 : 367 – 383 .
   Web of Science ®Google Scholar
• Gerhard , P. , Moraes , R. and Molander , S. 2004 . Stream fish communities and their associations to habitat variables in a rainforest reserve in southeastern Brazil . Environmental Biology of Fishes , 71 : 321 – 340 .
   Web of Science ®Google Scholar
• Gotelli , N. and Colwell , R. K. 2001 . Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness . Ecology Letters , 4 : 379 – 391 .
   Web of Science ®Google Scholar
• Hammer , Ø. , Harper , D. A. T. and Ryan , P. D. 2001 . PAST: Paleontological statistics software package for education and data analysis . Palaeontologia Electronica , 4 ( 1 )
   Google Scholar
• Hellman , J. J. and Fowler , G. W. 1999 . Bias, precision, and accuracy of four measures of species richness . Ecological Applications , 9 : 824 – 834 .
   Web of Science ®Google Scholar
• Hughes , R. M. and Gammon , J. R. 1987 . Longitudinal changes in fish assemblages and water quality in the Willamette River, Oregon . Transactions of the American Fisheries Society , 116 : 196 – 209 .
   Web of Science ®Google Scholar
• Hughes , R. M. and Herlihy , A. T. 2007 . Electrofishing distance needed to estimate consistent index of biotic integrity (IBI) scores in raftable Oregon rivers . Transactions of the American Fisheries Society , 136 : 135 – 141 .
   Web of Science ®Google Scholar
• Hughes , R. M. , Herlihy , A. T. , Gerth , W. J. and Pan , Y. 2012 . Estimating vertebrate, benthic macroinvertebrate, and diatom taxa richness in raftable Pacific Northwest rivers for bioassessment purposes . Environmental Monitoring Assessment , 184 : 3185 – 3198 .
   PubMed Web of Science ®Google Scholar
• Hughes , R. M. , Kaufmann , P. R. , Herlihy , A. T. , Intelmann , S. S. , Corbett , S. C. , Arbogast , M. C. and Hjort , R. C. 2002 . Electrofishing distance needed to estimate fish species richness in raftable Oregon rivers . North American Journal of Fisheries Management , 22 : 1229 – 1240 .
   Web of Science ®Google Scholar
• Hughes , R. M. and Peck , D. V. 2008 . Acquiring data for large aquatic resource surveys: the art of compromise among science, logistics, and reality . Journal of the North American Benthological Society , 27 : 837 – 859 .
   Web of Science ®Google Scholar
• Japan International Cooperation Agency . 1994 . The study on recuperation of Guanabara Bay ecosystem , Tokyo : Kokusai Kogyo Co. .
   Google Scholar
• Kanno , Y. , Vokoun , J. C. , Dauwalter , D. C. , Hughes , R. M. , Herlihy , A. T. , Maret , T. R. and Patton , T. M. 2009 . Influence of rare species on electrofishing distance when estimating species richness of stream and river reaches . Transactions of the American Fisheries Society , 138 : 1240 – 1251 .
   Web of Science ®Google Scholar
• Lyons , J. 1992 . The length of stream to sample with a towed electrofishing unit when fish species richness is estimated . North American Journal of Fisheries Management , 12 : 198 – 203 .
   Google Scholar
• Magalhães , M. F. , Ramalho , C. E. and Collares-Pereira , M. J. 2008 . Assessing biotic integrity in a Mediterranean watershed: development and evaluation of a fish-based index . Fisheries Management and Ecology , 15 : 273 – 289 .
   Web of Science ®Google Scholar
• Magurran , A. E. 2004 . Measuring biological diversity , London : Blackwell Publishing .
   Google Scholar
• Mazzoni , R. , Fenerich-Verani , N. and Caramasch , E. P. 2000 . Electrofishing as a sampling technique for coastal stream fish populations in the southeast of Brazil . Revista Brasileira de Biologia , 60 ( 2 ) : 205 – 216 .
   PubMedGoogle Scholar
• Mazzoni , R. , Fenerich-Verani , N. , Caramaschi , E. P. and Iglesias–Rios , R. 2006 . Stream-dwelling fish communities from an Atlantic rainforest drainage . Brazilian Archives of Biology and Technology , 49 : 249 – 256 .
   Google Scholar
• Mebane , C. A. , Maret , T. R. and Hughes , R. M. 2003 . An index of biological integrity (IBI) for Pacific Northwest rivers . Transactions of the American Fisheries Society , 132 : 239 – 261 .
   Web of Science ®Google Scholar
• Ministério do Meio Ambiente, Conservation International do Brasil, Fundação SOS Mata Atlǎntica, Fundação Biodiversitas, Instituto de Pesquisas Ecológicas, Secretaria do Meio Ambiente do Estado de São Paulo, and SEMAD/ Instituto Estadual de Florestas-MG . 2000 . Assessment and Priority Actions for Conservation of Atlantic Rain Forest and Southern Fields Biodiversity. Ministério do Meio Ambiente, Brasília
   Google Scholar
• Mugnai , R. , Oliveira , R. B. S. , Carvalho , A. L. and Baptista , D. F. 2008 . Adaptation of the indice biotico esteso (IBE) for water quality assessment in rivers of Serra do Mar, Rio de Janeiro State, Brazil . Tropical Zoology , 21 : 57 – 74 .
   Web of Science ®Google Scholar
• Myers , N. , Mittermeier , R. A. , Mittermeier , C. G. , Fonseca , G. A. B. and Kent , J. 2000 . Biodiversity hotspots for conservation priorities . Nature , 403 : 853 – 858 .
   PubMed Web of Science ®Google Scholar
• Oberdorff , T. , Pont , D. , Hugueny , B. and Porcher , J. P. 2002 . Development and validation of a fish-based index (FBI) for the assessment of French rivers: a framework for environmental assessment . Freshwater Biology , 46 : 399 – 415 .
   Web of Science ®Google Scholar
• Oliveira , R. B. , Baptista , D. F. , Mugnai , R. , Castro , C. M. and Hughes , R. M. 2011 . Towards rapid bioassessment of wadeable streams in Brazil: development of the Guapiaçu-Macacu multimetric index (GMMI) based on benthic macroinvertebrates . Ecological Indicators , 11 : 1584 – 1593 .
   Web of Science ®Google Scholar
• Paller , M. H. 1995 . Relationships among number of fish species sampled, reach length surveyed, and sampling effort in South Carolina coastal plain streams . North American Journal of Fisheries Management , 15 : 110 – 120 .
   Google Scholar
• Patton , T. M. , Hubert , W. A. , Rahel , F. J. and Gerow , K. G. 2000 . Effort needed to estimate species richness in small streams on the Great Plains in Wyoming . North American Journal of Fisheries Management , 20 : 394 – 398 .
   Google Scholar
• Peck , D. V. , Herlihy , A. T. , Hill , B. H. , Hughes , R. M. , Kaufmann , P. R. , Klemm , D. J. , Lazorchak , J. M. , McCormick , F. H. , Peterson , S. A. , Ringold , P. L. , Magee , T. and Cappaert , M. R. 2006 . Environmental Monitoring and Assessment Program—Surface Waters Western Pilot Study: field operations manual for wadeable streams , U.S. Environmental Protection Agency, Office of Research and Development . EPA 600/R-06/003, Washington, D.C.
   Google Scholar
• Pinto , B. C. and Araújo , F. G. 2007 . Assessing of biotic integrity of the fish community in a heavily impacted segment of a tropical river in Brazil . Brazilian Archives of Biology and Technology , 50 ( 3 ) : 489 – 502 .
   Web of Science ®Google Scholar
• Pinto , B. C. , Araújo , F. G. and Hughes , R. M. 2006 . Effects of landscape and riparian condition on a fish index of biotic integrity in a large southeastern Brazil river . Hydrobiologia , 556 : 69 – 83 .
   Web of Science ®Google Scholar
• Pont , D. , Hughes , R. M. , Whittier , T. R. and Schmutz , S. 2009 . A predictive index of biotic integrity model for aquatic-vertebrate assemblages of Western U.S. streams . Transactions of the American Fisheries Society , 138 : 292 – 305 .
   Web of Science ®Google Scholar
• Pont , D. , Hugueny , B. , Beir , U. , Goffaux , D. , Melcher , A. , Noble , R. , Rogers , C. , Roset , N. and Schmutz , S. 2006 . Assessing river biotic condition at the continental scale: a European approach using functional metrics and fish assemblages . Journal of Applied Ecology , 43 : 70 – 80 .
   Web of Science ®Google Scholar
• Rabeni , C. F. , Lyons , J. , Mercado-Silva , N. and Peterson , J. T. 2009 . “ Warmwater fish in wadeable streams ” . In Standard methods for sampling North American freshwater fishes , Edited by: Bonar , S. A. , Hubert , W. A. and Willis , D. W. 43 – 58 . Bethesda , Maryland : American Fisheries Society .
   Google Scholar
• Reynolds , L. , Herlihy , A. T. , Kaufmann , P. R. , Gregory , S. V. and Hughes , R. M. 2003 . Electrofishing effort requirements for assessing species richness and biotic integrity in western Oregon streams . North American Journal of Fisheries Management , 23 : 450 – 461 .
   Web of Science ®Google Scholar
• Rezende , C. F. , Moraes , M. , Manna , L. R. , Leitão , R. P. , Caramaschi , E. P. and Mazzoni , R. 2010 . Mesohabitat indicator species in a coastal stream of the Atlantic rainforest, Rio de Janeiro-Brazil . Revista de Biología Tropical , 58 : 1479 – 1487 .
   PubMed Web of Science ®Google Scholar
• Sály , P. , Erős , T. , Takács , P. , Specziár , A. , Kiss , I. and Bíró , P. 2009 . Assemblage level monitoring of stream fishes: the relative efficiency of single-pass vs. double-pass electrofishing . Fisheries Research , 99 : 226 – 233 .
   Web of Science ®Google Scholar
• Segurado , P , Santos , J. M. , Pont , D. , Melcher , A. , Garcia Jalon , D. , Hughes , R. M. and Ferreira , M. T. 2011 . Estimating species tolerance to human perturbation: expert judgment versus quantitative approaches . Ecological Indicators , 11 : 1623 – 1635 .
   Web of Science ®Google Scholar
• Secretaria de Estado de Meio Ambiente e Desenvolvimento Sustenável . 2001 . Fluminense Watershed and Rivers—Informational Summary by Macro Region , Brazil : Planágua, Rio de Janeiro .
   Google Scholar
• Smith , E. P. and van Belle , G. 1984 . Nonparametric estimation of species richness . Biometrics , 40 : 119 – 129 .
   Web of Science ®Google Scholar
• Smith , K. L. and Jones , M. L. 2008 . Allocation of sampling effort to optimize efficiency of watershed-level ichthyofaunal inventories . Transactions of the American Fisheries Society , 137 : 1500 – 1506 .
   Web of Science ®Google Scholar
• Terra , B. F. and Araújo , F. G. 2011 . A preliminary fish assemblage index for a transitional river reservoir system in southeastern Brazil . Ecological Indicators , 11 : 874 – 881 .
   Web of Science ®Google Scholar
• Van Liefferinge , C. , Simoens , I. , Vogt , C. , Cox , T. J. S. , Breine , J. , Ercken , D. , Goethals , P. , Belpaire , C. and Meire , P. 2010 . Impact of habitat diversity on the sampling effort required for the assessment of river fish communities and IBI . Hydrobiologia , 644 : 169 – 183 .
   Web of Science ®Google Scholar
• Vaux , P. D. , Whittier , T. R. , DeCesare , G. and Kurtenbach , J. P. 2000 . Evaluation of a backpack electrofishing unit for multiple-lake surveys of fish assemblage structure . North American Journal of Fisheries Management , 20 : 168 – 179 .
   Google Scholar
• Wan , H. , Chizinski , C. J. , Dolph , C. L. , Vondracek , B. and Wilson , B. N. 2010 . The impact of rare taxa on a fish index of biotic integrity . Ecological Indicators , 10 : 781 – 788 .
   Web of Science ®Google Scholar
• Whittier , T. R. , Hughes , R. M. , Lomnicky , G. A. and Peck , D. V. 2007a . Fish and amphibian tolerance values and an assemblage tolerance index for streams and rivers in the Western USA . Transactions of the American Fisheries Society , 136 : 254 – 271 .
   Web of Science ®Google Scholar
• Whittier , T. R. , Hughes , R. M. , Stoddard , J. L. , Lomnicky , G. A. , Peck , D. V. and Herlihy , A. T. 2007b . A structured approach to developing indices of biotic integrity: three examples from Western USA streams and rivers . Transactions of the American Fisheries Society , 136 : 718 – 735 .
   Web of Science ®Google Scholar