BIBLIOGRAPHY: CONCEPTS AND PRINCIPLES

BIOLOGICAL MONITORING AND ASSESSMENT

Selected Bibliography; FISH/BIOL 438; June 2002

CONCEPTS AND PRINCIPLES 1

Definition of Concepts 1

Regionalization and Classification 4

Assessment 5

State of Environment Reports 7

Statistics and Analyses 8

Manuals and Web Sites (State and Fed) 10

Books 11

Special Journal Issues 12

TYPES OF ENVIRONMENTS 13

Streams 13

Wetlands and Riparian Areas 15

Lakes and Ponds 17

Coastal and Marine 17

TAXONOMIC GROUPS 20

Stream Invertebrates 20

Fish 21

Algae and Diatoms 22

Birds 22

Amphibians and Reptiles 23

Terrestrial Invertebrates 23

Plants 23

Definition of Concepts

Angermeier, P. L. 1997. Conceptual roles of biological integrity and diversity. Pages 49-65 in J. E. Williams, C. A. Wood, and M. P. Dombeck, editors. Watershed Restoration: Principles and Practices. American Fisheries Society, Bethesda, MD.

Angermeier, P. L. 2000. The natural imperative for biological conservation. Conservation Biology 14: 373-381.

Angermeier, P. L. 2001. Reply to Povilitis: Another conservation conundrum. Conservation Biology 15: 536-538.

Angermeier, P. L., and J. R. Karr. 1994. Biological integrity versus biological diversity as policy directives. BioScience 44: 690-697.

Barkmann, J., and W. Windhorst. 2000. Hedging our bets: The utility of ecological integrity. Pages 497-517 in S. E. Jorgensen and F. Muller. Handbook of Ecosystem Theories and Management. Lewis Publishers, Boca Raton, Florida.

Boulton, A. J. 1999. An overview of river health assessment: philosophies, practice, problems and prognosis. Freshwater Biology 41: 469-479.

Callicott, J. B. 1995. A review of some problems with the concept of ecosystem health. Ecosystem Health 1: 101-112.

Callicott, J. B., L. B. Crowder, and K. Mumford. 1999. Current normative concepts in conservation. Conservation Biology 13: 22-35.

Regionalization and Classification

Abell, R. A., D. M. Olson, E. Dinerstein, P. T. Hurley, J. T. Diggs, W. Eichbaum, S. Walters, W. Wettengel, T. Allnutt, C. J. Loucks, and P. Hedao. 1999. Freshwater Ecoregions of North America: A Conservation Assessment. Washington, DC: Island Press.

Angermeier, P. L., R. A. Smogor, and J. R. Stauffer. 2000. Regional frameworks and candidate metrics for assessing biotic integrity in Mid-Atlantic highland streams. Transactions American Fisheries Society 129:962-981.

Frissell, C. A., W. J. Liss, C. E. Warren, and M. D. Hurley. 1986. A hierarchical framework for stream habitat classification: viewing streams in a watershed context. Environmental Management 10: 199-214.

Jepson, P.&R. J. Whittaker. 2002. Ecoregions in context: a critique with special reference to Indonesia.Conservation Biology 16:42-57.

Maddock, I. 1999. The importance of physical habitat assessment for evaluating river health. Freshwater Biology 41: 373-391.

Maxwell, J. R., C. J. Edwards, M. E. Jensen, S. J. Paustian, H. Parrott, and D. M. Hill. 1995. A hierarchical framework of aquatic ecological units in North America (Nearctic Zone). General Technical Report NC-176. US Forest Service, St. Paul, Minnesota.

McCormick, F. H., D. V. Peck, and D. P. Larsen. 2000. Comparison of geographic classification schemes for Mid-Atlantic stream fish assemblages. Journal of the North American Benthological Society 19:385-404.

Nature Conservancy. 1997. A classification framework for freshwater communities: Proceedings of the Nature Conservancy’s Aquatic Community Classification Workshop. New Haven Missouri, April 9-11, 1996. The Nature Conservancy, Arlington, Virginia.

Omernik, J. M. 1987. Ecoregions of the conterminus United States. Annals Association American Geographers 77:118-125

Omernik, J. M. 1995. Ecoregions: A spatial framework for environmental management. Pages 49-62 in W. S. Davis and T. P. Simon, eds. Biological Assessment and Criteria: Tools for Water Resource Planning and Decision Making. Lewis, Boca Raton, FL.

Omernik, J. M., and R. G. Bailey. 1997. Distinguishing between watersheds and ecoregions. Journal American Water Resources Association 33: 935-949.

Rabeni, C. F., and K. E. Doisy. 2000. Correspondence of stream benthic invertebrate assemblages to regional classification schemes in Missouri. Journal of the North American Benthological Society 19:419-428.

Rabeni, C. F., K. E. Doisy, and D. L. Galat. 2002. Testing the biological basis of a stream habatat classification using benthic invertebrates. Ecological Applications 12: 782-796.

Ricketts, T. H., E. Dinerstein, D. M. Olson, C. L. Loucks, W. Eichbaum, D. DellaSala, K. Kavanagh, P. Hedao, P. Hurley, K. Carney, R. Abell, and S. Walters. 1999. Terrestrial Ecoregions of North America: A Conservation Assessment. Washington, DC: Island Press.

Smogor, R. A., and P. L. Angermeier. 2001. Determining a regional framework for assessing biotic integrity of Virginia streams. Transactions American Fisheries Society 130:18-35.

Van Sickle, J. K., and R. J. Hughes. 2000. Classification strengths of ecoregions, catchments, and geographic clusters for aquatic vertebrates in Oregon. Journal of the North American Benthological Society 19:370-384.

Waite, I. R., A. T. Herlihy, D. P. Larsen, and D. J. Klemm. 2000. Comparing strengths of geographic and nongeographic classifications of stream benthic macroinvertebrates in the Mid-Atlantic Highlands, USA. Journal of the North American Benthological Society 19:429-441.

Wikramanayake, W., E. Dinerstein, C. Loucks, D. Olson, J. Morrison, J. Lamoreux, M. McKnight, and P. Hedao. 2002. Ecoregions in ascendance: Reply to Jepson and Whittaker. Conservation Biology 16: 238-243.

Assessment

Ayensu, E., and 25 other authors. 1999. International ecosystem assessment. Science 286: 685-686. See also responses and counter responses: Science 2000. 287:234-235.

Canadian Environmental Advisory Council. 1991. Economic, Ecological, and Decision Theories: Indicators of Ecologically Sustainable Development. Ottawa, Ontario: Canadian Environmental Advisory Council.

Crossley, J. W. 1996. Managing ecosystems for integrity: theoretical considerations for resource and environmental managers. Society and Natural Resources 9: 465-481.

Dufrene, M., and P. Legendre. 1997. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecological Monographs 67: 345-366.

Fore, L. S. 2001. Evaluation of alternative sampling designs for biological monitoring of streams. Report prepared for Washington Department of Ecology. Statistical Design, Seattle, Washington.

Gibbs, J. P., S. Droege, and P. Eagle. 1998. Monitoring populations of plants and animals. BioScience 48: 935-940.

Heinz Center. 1999. Designing a report on the state of the nation’s ecosystems: Selected measurements for croplands, forests and coasts and oceans. Washington, DC: H. John Heinz III Center for Science, Economics and the Environment.

Johnson, N., Revenga, C., and Echeverria, J. 2001. Managing water for people and nature. Science 292: 1071–1072.

Keeler, A. G. and D. McLemore. 1996. The value of incorporating bioindicators in economic approaches to water pollution. Ecological Economics 19: 237-245.

Kremen, C. 1992. Assessing the indicator properties of species assemblages for natural areas monitoring. Ecological Applications 2: 203-217.

Ludwig, D., M. Mangel, and B. Haddad. 2001. Ecology, conservation, and public policy. Annual Review Ecology and Systematics 32: 481-517.

Mac Nally, R., A. F. Bennett, G. W. Brown, L. F. Lumsden, A. Yen, S. Hinkley, P. Lillywhite, and D. Ward. 2002. How well do ecosystem-based planning units represent different components of biodiversity? Ecological Applications 12: 900-912.

Matthews, R. A., W. G. Landis, and G. B. Matthews. The community conditioning hypothesis and its application to environmental toxicology. Environmental Toxicology and Chemistry 15: 597-603.

Monaghan, K. A., and A. M. Milner. 1999. Alternative methods for the biological classification of rivers. R&D Technical Report E57. Environment Agency, Bristol, UK. (classification here means “assessment”)

McCarron, E., and R. Frydenborg. 1997. The Florida Bioassessment Program: An agent of change. Human and Ecological Risk Assessment 3: 967-977.

National Council for Science and the Environment. 2000. Recommendations for improving the scientific basis for environmental decisionmaking. National Council for Science and the Environment, Washington, DC.

National Research Council (NRC). 2000. Ecological Indicators for the Nation. National Academy of Sciences Press, Washington, DC.

National Research Council (NRC). 2001. Assessing the TMDL Approach to Water Quality Management. National Academy Press, Washington, DC.

Norton, B. G. 1998. Improving ecological communication: The role of ecologists in environmental policy formation. Ecological Applications 8:350-364.

Paulsen, S. G., R. M. Hughes, and D. P. Larsen. 1998. Critical elements in describing and understanding our nation’s aquatic resources. Journal American Water Resources Association 34: 995-1005.

PCAST (President’s Committee of Advisers on Science and Technology). 1998. Teaming with life: investing in science to understand and use America’s living capital. President’s Committee of Advisers on Science and Technology, Washington, DC.

Poff, N. L., M. M. Brinson, and J. W. Day, Jr. 2002. Aquatic ecosystems and global climate change: Potential impacts on inland freshwater and coastal wetland ecosystems in the United States. Prepared for the Pew Center on Global Climate Change.

Reid, W. V. 2000. Ecosystem data to guide hard choices. Issues in Science and Technology (http://www.nap.edu/issues/16.3/reid.htm) See comments on this paper at http://www.nap.edu/issues/16.4/forum.htm.

Schindler, D. W. 1987. Determining ecosystem responses to anthropogenic stress. Canadian Journal Fisheries Aquatic Sciences 44(suppl. 1): 6-25.

Schindler, D. W. 1990. Experimental perturbations of whole lakes as tests of hypotheses concerning ecosystem structure and function. Oikos 57: 25-41.

Schmitt, R. J., and C. W. Osenberg, eds. 1996. Detecting Ecological Impacts: Concepts and Applications in Coastal Habitats. Academic Press, San Diego, CA.

Stewart-Oaten, A., and J. R. Bence. 2001. Temporal and spatial variation in environmental impact assessment. Ecological Monographs 71: 305-339.

Stewart‑Oaten, A., W. W. Murdoch, and K. R. Parker. 1986. Environmental impact assessment: "Pseudoreplication" in time? Ecology 67: 929-940.

Suter, II, G. W. 2001. Applicability of indicator monitoring to ecological risk assessment. Ecological Indicators 1: 101-112.

Tenenbaum, D. J. 2001. Global ecosystems assessments: Ask The big question. Environmental Health Perspectives 109(12): A588-A592.

Treweek, J. 1999. Ecological Impact Assessment. Oxford: Blackwell Science.

Walther, G-R., E. Post, P. Convey, A. Menzel, C. Parmesan, T. J. C. Beebee, J-M. Fromentin, O Hoegh-Guldberg, and F. Barlien. 2002. Ecological responses to recent climate change. Nature: 416: 389-395.

Whitfield, J. 2001. Vital signs. Nature 411: 989-990.

Williams, P., J. Biggs., L. Dodds, M. Whitfield, A. Corfield, and G. Fox. 1996. Biological techniques of still water assessment: Phase I Scoping Study. R&D Technical Report E7, Bristol, England; Environmnet Agency.

Williams, P., J. Biggs, M. Whitfield, A. Corfield, G. Fox, and K. Adare. 1998. Biological techniques of still water quality assessment: 2. Method Development. R&D Technical Report E56. Bristol, England: Environment Agency.

Yoder, C. O., and Rankin, E. T. 1998. The role of biological indicators in a state water quality management process. Environmental Monitoring and Assessment 51: 61–88.

Yoder, C. O., and E. T. Rankin. 1999. Biological criteria for water resource management. Pages 227-259 in P. Schulze, editor. Measures of Environmental Performance and Ecosystem Condition. National Academy Press, Washington, DC.

State of Environment Reports

Anielski, M. 2001. Towards a measurement of ecological integrity. Prepared for; The National Round Table on the Environment and the Economy, Canada. Pembina Institute for Appropriate Development, Edmonton, Alberta, Canada.

British Columbia Ministry of Environment, Lands and Parks. 2000. Environmental trends in Briticah Columbia 2000. Ministry of Environment, Lands and Parks, British Columbia, Victoria, British Columbia.

Cincotta, R. P., and R. Engelman. 2000. Nature’s place: human population and the future of biological diversity. Population Action International, Washington, DC. Available at: http://www.populationaction.org.

Commission for Environmental Cooperation. 2001. The North American Mosaic: A State of the Environment Report. Montreal, Quebec. Available online from the Commission.

European Environment Agency. 2001. Environmental signals 2001. European Environment Agency, Copenhagen, Denmark. Available on the web at http://reports.eea.eu.int/signals-2001/en. This site has microsoft powerpoint presentations available as well.

Hannah, L., D. Lohse, C. Hutchinson, J. L. Carr, and A. Lankerani. 1994. A preliminary inventory of human disturbance of world ecosystems. Ambio 23: 246-250.

Heinz Center. 2001. The State of the Nation’s Ecosystems: Measuring the Lands, Waters, and Living Resources of the United States. The H. J. Heinz III Center for Science, Economics, and the Environment, Washington, DC.

Jones, K. B., K. H. Riitters, J. D. Wickham, R. D. Tankersley, Jr., R. V. O’Neill, D. J. Chaloud, E. R. Smith, and A. C. Neale. 1997. An ecological assessment of the United States Mid-Atlantic Region. EPA/600/R-97/130. Office of Research and Development. Washington, DC: U.S. Environmental Protection Agency.

LaRoe, E. T., G. S. Farris, C. E. Puckett, P. D. Doran, and M. J. Mac, editors. 1995. Our living resources: A report to the nation on the distribution, abundance, and health of U. S. plants, animals, and ecosystems. Department of the Interior, Washington, DC.

Mac, M. J., P. J. Opler, C. E. Puckett Haecker, and P. D. Doran. 1998. Status and trends of the nation’s biological resources. 2 vols. U. S. Department of Interior, U. S. Geological Service, Reston, Virginia.

Millennium Ecosystem Assessment. A major new international effort to assess the condition of Earth’s ecosystems. For more details see:

http://www.ma-secretariat.org/en/about/index.htm

National Intelligence Council. 2000. Global Trends 2015: A Dialogue About the Future With Nongovernment Experts. NIC 2000-02. National Intelligence Council, Washington, DC. Available at http://www.odci.gov/cia/publications/globaltrends2015/globaltrends2015.pdf

Noss, R. F., E. T. LaRoe, III, and J. M. Scott. 1995. Endangered ecosystems of the United States: a preliminary assessment of loss and degradation. Biological Report 28, US Department of Interior, Washington, DC.

Oregon Progress Board. 2000. Oregon State of the Environment Report 2000: Statewide summary. Oregon Progress Board, Salem, Oregon.

Washington State Department of Natural Resources. 1998. Our changing nature: natural resource trends in Washington State. Washington State Department of Natural Resources, Olympia, Washington.

Statistics and Analyses

First a few general introductions to statistical issues and concepts:

The USEPA bioindicators web site (http://www.epa.gov/bioindicators/index.html) has an excellent primer on statistics and statistical concepts in monitoring See: (http://www.epa.gov/bioindicators/primer/html/primer.html)

Elzinga, C. L., D. W. Salzer, J. W. Willoughby, and J. B. Gibbs. 2001. Chapters 7 (Basic Principles of Sampling, pp 75-100), 8 (Sampling Design, 101-148), 9 (Statistical Analysis, 149-184), 10 (Analysis of Trends, 185-193), and 11 (Selection of Random Samples, 195-204) in Monitoring Plant and Animal Populations. Blackwell Science, Malden, Massachusetts.

Feinsinger, P. 2001. Chapter 5: Small Samples and Big Questions: The Role of Statistical Inference (pages 57-86) in Designing Field Studies for Biodiversity Conservation. Island Press, Washington, DC.

Cao, Y., D. P. Larsen, and R. M. Hughes. 2001. Evaluating sampling sufficiency in fish assemblage surveys: a similarity-based approach. Canadian Journal Fisheries Aquatic Sciences 58: 1782-1793.

Caughlan, L., and K. L. Oakley. 2001. Cost considerations for long-term ecological monitoring. Ecological Indicators 1: 123-134.

Fore, L. S., J. R. Karr, and L. L. Conquest. 1994. Statistical properties of an index of biotic integrity used to evaluate water resources. Canadian Journal Fisheries Aquatic Sciences 51: 1077–1087.

Fryer, G. 1987. Quantitative and qualitative: numbers and reality in the study of living organisms. Freshwater Biology 17: 177-189.

Hilborn, R. 1997. Statistical hypothesis testing and decision theory in fisheries science. Fisheries 22(10): 19–20.

Hyman, J. B., and S. G. Leibowitz. 2001. JSEM: A framework for identifying and evaluating indicators. Environmental Monitoring and Assessment 66: 207-232.

Johnson, G. D., B. D. Nussbaum, G. P. Patil, and N. P. Ross. 1996. Designing cost-effective environmental sampling using concomitant information. Chance 9(1): 4-11.

Larsen, D. P. 1997. Sample survey design issues for bioassessment of inland aquatic ecosystems. Human and Ecological Risk Assessment 3: 979-991.

Larsen, D. P., K. W. Thornton, N. S. Urquhart, and S. G. Paulsen. 1994. The role of sample surveys for monitoring the condition of the nation’s lakes. Environmental Monitoring and Assessment 32: 101–134.

Larsen, D. P., T. M. Kincaid, S. E. Jacobs, and N. S. Urquhart. 2001. Designs for evaluating local and regional scale trends. BioScience 51: 1069-1078.

Norris, R. H. 1995. Biological monitoring: the dilemma of data analysis. Journal North American Benthological Society 14: 440-450.

Olsen, A. R., J. Sedransk, D. Edwards, C. A. Gotway, W. Liggett, S. Rathbun, K. E. Reckhow, and L. J. Young. 1999. Statistical issues for monitoring ecological and natural resources in the United States. Environmental Monitoring and Assessment 54: 1-45.

Osenberg, C. W. and R. J. Schmitt. 1996. Detecting ecological impacts caused by human activities. Pages 3-16 in R. J. Schmitt and C. W. Osenberg, editors. Detecting ecological impacts: Concepts and applications in coastal habitats. San Diego, California: Academic Press.

Osenberg, C. W., R. J. Schmitt, S. J. Holbrook, K. E. Abu‑Saba, and A. R. Flegal. 1994. Detection of environmental impacts: Natural variability, effect size, and power analysis. Ecological Applications 4: 16–30.

Parkhurst, D. F. 2001. Statistical significance tests: Equivalence and reverse tests should reduce misinterpretation. BioScience 51: 1051-1057

Regan, H. M., M. Colyvan, and M. A. Burgman. 2002. A taxonomy and treatment of uncertainty for ecology and conservation biology. Ecological Applications 12: 618-628.

Smith, E. P. 1994. Biological monitoring: Statistical issues and models. Pages 243-261 in G. P. Patil and C. R. Rao, editors. Handbook of Statistics, Vol 12. Elsevier Science.

Suter, III, G. W., 1996. Abuse of hypothesis testing statistics in ecological risk assessment. Human and Ecological Risk Assessment 2: 331-347.

Ter Braak, C. J. F., and P. F. M. Verdonschot. 1995. Canonical correspondence analysis and related multivariate methods in aquatic ecology. Aquatic Sciences 57: 255-289.

Thomson, J. D., G. Weiblen, B. A. Thomson, S. Alfaro, and P. Legendre. 1996. Untangling multiple factors in spatial distributions: Lilies, gophers, and rocks. Ecology 77:1698–1715.

Underwood, A. J. 1991. Beyond BACI: Experimental designs for detecting human environmental impacts on temporal variations in natural populations. Australian Journal Marine Freshwater Research 42: 569-587.

Underwood, A. J. 1994. On beyond BACI: Sampling designs that might reliably detect environmental disturbances. Ecological Application 4: 3-15.

Yoccoz, N. G. 1991. Use, overuse, and misuse of significance tests in evolutionary biology and ecology. Bulletin Ecological Society America 71: 106–111.

Yoccoz, N. G., J. D. Nichols, and T. Boulinier. 2001. Monitoring of biological diversity in space and time. Trends in Ecology and Evolution 16: 446-453.

Federal and State Manuals and Web Sites

Many guidance and technical documents from USEPA (with links to USGS and state agencies) can be found at the following site:

http://www.epa.gov/bioindicators/html/publications.html

Biological Indicators of Watershed Health. Available on line at http://www.epa.gov/bioindicators/html/about.html

Bioassessment and Biocriteria website on line at

http://www.epa.gov/ost/biocriteria/index.html

Barbour, M. T., J. Gerritsen, B. D. Snyder, and J. B. Stribling. 1999. Rapid bioassessment protocols for use in streams and wadeable rivers: Periphyton, benthic macroinvertebrates and fish. Second edition. EPA 841-B-99-002. Washington, DC: Office of Water, US Environmental Protection Agency.

Bowman, M. L., J. Gerritsen, G. R. Gibson, Jr., and B. D. Snyder. 2000. Estuarine and coastal marine waters: Bioassessment and biocriteria technical guidance. EPA-822-B-00-024. Office of Water, U. S. Environmental Protection Agency, Washington, DC.

Coastal Research and Monitoring Strategy Workgroup. 2000. Clean Water Action Plan:
Coastal Research and Monitoring Strategy. Available at: http://cleanwater.gov/coastalresearch/index.html.

Davis, W. S., Snyder, B. D., Stribling, J. B. and Stoughton, C. (1996) Summary of State Biological Assessment Programs for Streams and Rivers. EPA 230-R-96-007. Office of Policy, Planning, and Evaluation, US Environmental Protection Agency, Washington, DC.

EPA. 1997. Biological Criteria: Technical Guidance for Survey Design and Statistical Evaluation of Biosurvey Data. EPA 822-B97-002. US Environmental Protection Agency, Washington, DC.

EPA. 1998. Lake and reservoir bioassessment and biocriteria: technical guidance document. EPA 841-B-98-007. US Environmental Protection Agency, Washington, DC. Available on line at http://www.epa.gov/owow/monitoring/tech/lakes.html

EPA. 2000. Mid-Atlantic Highlands Streams Assessment. EPA/903/R-00/015. US Environmetnal Protection Agency Region 3, Philadelphia, Pennsylvania.

EPA. 2000. Stressor identification guidance document. EPA 822-B-97-002. US Environmental Protection Agency, Washington, DC. Available at http://www.epa.gov/ost/biocriteria/stressors/stressorfacts.html

EPA. 2001. National Coastal Condition Report. EPA-620/R-01/005. Office of Research and Development/Office of Water, USEPA, Washington, DC. Available at: http://www.epa.gov/owow/oceans/NCCR/index A 2-page fact sheet (EPA842-F-02-001) is available as well with an excellent summary color graphic.

Jackson, L. E., J. C. Kurtz, and W. S. Fisher. 2000. Evaluation guidelines for ecological indicators. EPA/620/R-99/005. US Environmental Protection Agency, Research Triangle Park, North Carolina. Available on line at http://www.epa.gov/emap/html/pubs/docs/resdocs/ecoind.html

Ohio EPA (Environmental Protection Agency). 1988. Biological Criteria for the Protection of Aquatic Life, vol. 1–3. Columbus, Ecological Assessment Section, Division of Water Quality Monitoring and Assessment, Ohio EPA.

Pellant, M., P. Shaver, D. A. Pyke, and J. E. Herrick. 2000. Interpreting Indicators of Rangeland Health, version 3. Technical Reference 1734-6. Bureau of Land Management, Denver Colorado. Available on the web at www.ftw.nrcs.usda.gov/glti

Books

Crabbé, P., A. Holland, and L. Ryszkowski, editors. Implementing Ecological Integrity: Restoring Regional and Global Environmental and Human Health. NATO Science Series: IV Earth and Environmental Sciences. Kluwer Academic Publishers, The Netherlands.

Davis, W. S. and T. P. Simon, editors. 1995. Biological Assessment and Criteria: Tools for Water Resource Planning and Decision Making. Lewis Publishers, Boca Raton, FL.

Elzinga, C. L., D. W. Salzer, J. W. Willoughby, and J. P. Gibbs. 2001. Monitoring Plant and Animal Populations. Blackwell Science, Malden, Massachusetts.

Karr, J. R., and E. W. Chu. 1999. Restoring Life in Running Waters: Better Biological Monitoring. Washington, DC: Island Press.

Loeb, S. L. and A. Spacie, editors. 1994. Biological Monitoring of Aquatic Systems. Lewis Publishers, Boca Raton, FL.

McKenzie, D. H., D. E. Hyatt, and V. J. McDonald, editors. Ecological Indicators. 2 vols. London: Elsevier Applied Science.

National Research Council (NRC). 1992. Restoration of aquatic ecosystems: Science, technology, and public policy. National Academy Press, Washington, D. C., USA.

Pimentel, D., L. Westra, and R. F. Noss, editors. 2000. Ecological Integrity: Integrating Environment, Conservation, and Health. Island Press, Washington, DC.

Rapport, D., R. Costanza, P. R. Epstein, C. Gaudet, and R. Levins. 1998. Ecosystem Health. Malden, Massachusetts: Blackwell Science

Rosenberg, D. M. and V. H. Resh, editors. 1993. Freshwater biomonitoring and benthic macroinvertebrates. New York: Chapman Hall.

Schmitt, R. J., and C. W. Osenberg, editors. 1996. Detecting ecological impacts: Concepts and applications in coastal habitats. San Diego, California: Academic Press.

Simon, T. P., editor. 1999. Assessing the sustainability and biological integrity of water resources using fish communities. Boca Raton, Florida: CRC Press.

Simon, T. P., editor. 2003. Biological Response Signatures: Indicator Patterns Using Aquatic Communities. Boca Raton, FL: CRC Press.

Spellerberg, I. 1991. Monitoring ecological change. Cambridge, England: Cambridge University Press.

Williams, J. E., C. A. Wood, and M. P. Dombeck, editors. 1997. Watershed Restoration: Principles and Practices. Bethesda, Maryland: American Fisheries Society.

Wright, J. F., D. W. Sutcliffe, and M. T. Furse, editors. 2000. Assessing the Biological Quality of Fresh Waters: RIVPACS and other Techniques. Freshwater Biological Association, Ambleside, Cumbria, UK.

Special Journal Issues

Aquatic Sciences. 1995. 57(3): 181-289. Multivariate statistics for aquatic ecology.

Australian Journal of Ecology. 1995. 20(1): 1-227. Papers from meeting: Use of Biota to Assess Water Quality. 18 papers.

BioScience. 2001. 51: 433-495. Special Issue: Scientific objectivity, value systems, and policymaking.

Ecological Applications. 1996. 6: 33-101. Special paper series: Ecological Issues in Wetland Mitigation: A Forum.

Environmental Monitoring and Assessment. 1998. 51(1): xxx-xxx. Papers from meeting: Ecological Indicators

Environmental Toxicology and Chemistry 1993. 12(9): 1521-1547. Papers from meeting: Management of Ecosystem Quality. 3 papers.

Freshwater Biology. 1999. 41:197-479. Special symposium held in Sydney Australia on River Health.

Human and Ecological Risk Assessment. 1995. 1(4): 337-458. Papers from meeting: Ecological Risk Assessment: Use, Abuse, and Alternatives. 15 papers.

Human and Ecological Risk Assessment.1997. 3(6): 929-1027. Invited Debate/Commentary: Perspectives from North America on the Programmatic and Scientific Elements of an Effective Bioassessment. 8 papers.

Hydrobiologia 2000. 422/423: 1–487. Papers from meeting in Vienna, Austria at symposium titled “Assessing the Ecological Integrity of Running Waters.”

BIBLIOGRAPHY: TYPES OF ENVIRONMENTS

BIOLOGICAL MONITORING AND ASSESSMENT

Selected Bibliography; FISH/BIOL 438; June 2002

Streams

Allan, J. D., D. L. Erickson, and J. Fay. 1997. The influence of catchment land use on stream integrity across multiple spatial scales. Freshwater Biology 37: 149-161.

Barbour, M. T. 1997. The re-invention of biological assessment in the U.S. Human and Ecological Risk Assessment 3: 933-940.

Bash, J. S., and C. M. Ryan. 2002. Stream restoration and enhancment projects: Is anyone monitoring? Environmental Management 29: 877-885.

Boulton, A. J. 2000. River ecosystem health down under: Assessing ecological condition in riverine groundwater zones in Australia. Ecosystem Health 6:108-118.

Cairns, J., Jr., and P. V. McCormick. 1991. The use of community- and ecosystem-level end points in environmental hazard assessment: A scientific and regulatory evaluation. Environmental Auditor 2: 239-248.

Cao, Y., D. P. Larsen, R. M. Hughes, P. L. Angermeier, and T. M. Patton. in press. Sampling effort affects multivariate comparisons of stream assemblages. Journal North American Benthological Society, in press.

Chasan, D. J. 2000. The rusted shield: government’s failure to enforce¾or obey¾our system of environmental law threatens the recovery of Puget Sound’s wild salmon. Report to Bullitt Foundation, Seattle, WA.

Cormier, S. M., E. L. C. Lin, M. R. Millward, M. K. Schubauer-Berigan, D. E. Williams, B. Subramanian, R. Sanders, B. Counts, and D. Altfater. 2000. Using regional exposure criteria and upstream reference data to characterize spatial and temporal exposures to chemical contaminants. Environmental Toxicology and Chemistry 19: 1127-1135.

deBruyn, A. M. H., and J. B. Rasmussen. 2002. Quantifying assimilation of sewage-derived organic matter by riverine benthos. Ecological Applications 12: 511-520.

Dynesius, M. and C. Nilsson. 1994. Fragmentation and flow regulation of river systems in the northern third of the world. Science 266: 753–762.

Falkenmark, M. 1997. Society’s interaction with the water cycle: A conceptual framework for a more holistic approach. Hydrological Sciences Journal 42: 451–466.

Fore, L. S., J. R. Karr, and R. W. Wisseman. 1996. Assessing invertebrate responses to human activities: evaluating alternative approaches. Journal North American Benthological Society 15:212–231.

Gatz, A. J., Jr., A. L.Harig. 1993. Decline in the index of biotic integrity of Delaware Run, Ohio, over 50 years. Ohio Journal Science 93: 95-100.

Gerritsen, J., M. T. Barbour, and K. King. 2000. Apples, oranges, and ecoregions: on determining pattern in aquatic assemblages. Journal of the North American Benthological Society 19:487-496.

Gessner, M. O., and E. Chauvet. 2002. A case study for using litter breakdown to assess functional stream integrity. Ecological Applications 12: 498-510.

Hawkins, C. P., and R. H. Norris. 2000. Performance of different landscape classifications for aquatic bioassessments: Introduction to the series. Journal of the North American Benthological Society 19:367-369.

Hession, W. C., and 15 other authors. 2000. Ecological benefits of riparian reforestation in urban watersheds: study design and preliminary results. Environmental Monitoring and Assessment 63: 211-222.

Karr, J. R. 1999. Defining and measuring river health. Freshwater Biology 41: 221–234.

Karr, J. R. and E. W. Chu. 2000. Sustaining living rivers. Hydrobiologia 422/423:1-14.

Karr, J. R. and E. M. Rossano. 2001. Applying public health lessons to protect river health. Ecology and Civil Engineering 4: 3-18.

Keeler, A. G. and D. McLemore. 1996. The value of incorporating bioindicators in economic approaches to water pollution control. Ecological Economics 19: 237-245.

Lammert, M. and J. D. Allan. 1999. Assessing biotic integrity of streams: effects of scale in measuring the influence of land use/cover and habitat structure on fish and macroinvertebrates. Environmental Management 23: 257-270.

Lang, C., and P. Reymond. 1995. An improved index of environmental quality for Swiss rivers based on benthic invertebrates. Aquatic Sciences 57: 172-180.

Larson, M. G., D. B. Booth, and S. A. Morley. 2001. Effectiveness of large woody debris in stream rehabilitation projects in urban basins. Ecological Engineering 18: 211-226.

Mallin, M. A. 2000. Impacts of industrial animal production on rivers and estuaries. American Scientist 88: 26-37. Also letter re this paper: 88: 100.

McMahon, G., and T. F. Cuffney. 2000. Quantifying urban intensity in drainage basins for assessing stream ecological condition. Journal American Water Resources Association 36: 1247-1260.

Mebane, C. A. 2001. Testing bioassessment metrics: macroinvertebrate, sculpin, and salmonid responses to stream habitat, sediment, and metals. Environmental Monitoring and Assessment 67: 293-322.

Miltner, R. J., and E. T. Rankin. 1998. Primary nutrients and the biotic integrity of rivers and streams. Freshwater Biology 40: 145-158.

Monaghan, K. A. and A. M. Milner. 1999. Alternative methods for the biological classification of rivers. R&D Technical Report E57. Bristol, England: Environment Agency.

Parsons, M., and R. H. Norris. 1996. The effect of habitat-specific sampling on biological assessment of water quality using a predictive model. Freshwater Biology 36: 419-434.

Penrose, D., and S. M. Call. 1995. Volunteer monitoring of benthic macroinvertebrates: regulatory biologists’ perspective. Journal North American Benthological Society 14: 203-209.

Richards, C., L. B. Johnson, and G. E. Hart. 1996. Landscape-scale influence on stream habitats and biota. Canadian Journal of Fisheries and Aquatic Sciences 53 (supple 1): 295-311.

Rodriguez, M. A., and P. Magnan. 1995. Application of multivariate analyses in studies of the organization and structure of fish and invertebrate communities. Aquatic Sciences 57: 199-216.

Roth, N. E., J. D. Allan, and D. L. Erickson. 1996. Landscape influences on stream biotic integrity assessed at multiple scales. Landscape Ecology 11: 141-156.

Roth, N. E., M. T. Southerland, G. Mercurio, J. C. Chaillou, P. F. Kazyak, S. S. Stranko, A. P. Prochaska, D. G. Heimbuch, and J. C. Seibel. 1999. State of Streams: 1995–1997 Maryland Biological Stream Survey Results. Maryland Department of Natural Resources, Annapolis, Maryland, USA.

Rothrock, J. A., P. K. Barten, and G. L. Ingram. 1998. Land use and aquatic biointegrity in the Blackfoot River watershed, Montana. Journal American Water Resources Association 34: 565-581.

Sanders, R. E., editor. A guide to Ohio streams. Streams Committee, Ohio Chapter, American Fisheries Society, Columbus, Ohio.

Statzner, B., H. Capra, L. W. G. Higler, and A. L. Roux. 1997. Focusing environmental management budgets on nonlinear system responses: potential for significant improvements to freshwater ecosystems. Freshwater Biology 37: 463-472.

Steedman, R. J. 1988. Modification and assessment of an index of biotic integrity to quantify stream quality in southern Ontario. Canadian Journal Fisheries and Aquatic Sciences 45: 492–501.

Wang, X. 2001. Integrating water-quality management and land-use planning in a watershed context. Journal of Environmental Management 61: 25–36.

Wright, J. F. 1995. Development and use of a system for predicting the macroinvertebrate fauna in flowing waters. Australian Journal of Ecology 20: 181-197.

Wright, J. F., D. Moss, R. T. Clarke, and M. T. Furse. 1997. Biological assessment of river quality using the new version of RIVPACS (RIVPACS III). Pages 102-108 P. J. Boon and D. L. Howell, editors. Freshwater Quality: Defining the Indefinable? Scottish Natural Heritage, Edinburgh.

Yoder, C. O., R. J. Miltner, and D. White. 2000. Using biological criteria to assess and classify urban streams and develop improved landscape indicators. Page 32-44 in S. Minamyer, J. Dye, and S. Wilson, editors. National Conference on Tools for Urban Water Resources Management and Protection. EPA/625/R-00/001. U. S. Environmental Protection Agency, Cincinnati, Ohio.

Wetlands and Riparian Areas

EPA websites:

Methods for Evaluating Wetland Condition. http://www.epa.gov/waterscience/criteria/wetlands/

Biological Assessment of Wetlands Working Group

http://www.epa.gov/owow/wetlands/bawwg/whatsnew/html

http://www.epa.gov/owow/wetlands/bawwg/biobasics.html

Bertness, M. D., P. J. Ewanchuk, and B. R. Silliman. 2002. Anthropogenic modification of New England salt marsh landscapes. Proceedings National Academy of Sciences (USA) 99: 1395-1398.

Brinson, M. 1996. Assessing wetland functions using HGM. National Wetlands Newsletter 18: 10-16.

Brinson, M. M., and R. Rheinhardt. 1996. The role of reference wetlands in functional assessment and mitigation. Ecological Applications 6:69-76.

Brooks, R. P., T. J. O’Connell, D. H. Wardrop, and L. E. Jackson. 1998. Towards a regional index of biological integrity. Environmental Monitoring and Assessment 51: 131-143.

Euliss, Jr., N. H., D. M. Mushet, and D. H. Johnson. 2001. Use of macroinvertebrates to identify cultivated wetlands in the prairie pothole region. Wetlands 21: 223-231.

Danielson, T. J. 1998. Indicators for Monitoring and Assessing Biological Integrity of Inland, Freshwater wetlands: A Review of the Technical Literature (1989-1996). EPA843-R-98-002. Office of Wetlands, Oceans, and Watersheds, US Environmental Protection Agency, Washington, DC.

Danielson, T. J. 1998. Wetlands bioassessment fact sheets. EPA 843-F-98-001. US Environmental Protection Agency, Washington, DC. Available at the following site: http://www.epa.gov/owow/wetlands/wqual/bio_fact/index.html

Gernes, M. C., and J. C. Helgen. 1999. Indexes of biotic integrity (IBI) for wetlands: Vegetation and invertebrate IBIs. Final Report to USEPA. St. Paul, Minnesota: Minnesota Pollution Control Agency, Environmental Outcomes Division.

Hauer, F. R., and R. D. Smith. 1998. The hydrogeomorphic approach to functional assessment of riparian wetlands: evaluating impacts and mitigation on river floodplains in the U.S.A. Freshwater Biology 40: 517-530.

Karr, J. R. 1998. Seeking Suitable Endpoints: Biological Monitoring For Wetland Assessment. Report to USEPA, Region 10, Seattle, Washington.

Kantrud, H. A., and W. E. Newton. 1996. A test of vegetation-realted indicators of wetland quality in the prairie pothole region. Journal of Aquatic Ecosystem Health 5: 177-191.

Kusler, J. and W. Niering. 1998. Wetland assessment: Have we lost our way? National Wetlands Newsletter 20(2): 8-14.

Lemly, A. D., and R. S.King. 2000. An insect-bacteria indicator for assessing detrimental nutrient enrichment in wetlands. Wetlands 20: 91-100.

Lopez, R. D., and M. S. Fennessy. 2002. Testing the floristic quality assessment index as an indicator of wetland condition. Ecological Applications 12: 487-497.

Lougheed, V. L., and P. Chow-Fraser. 2002. Development and use of a zooplankton index of wetland quality in the Laurentian Great Lakes basin. Ecological Applications 12: 474-486.

Ludden, V. E., and F. R. Hauer. 2000. The effects of natural variability on the use of macroinvertebrates as bioindicators of disturbance in intermontane depressional wetlands in Northwestern Montana, USA. Flathead Lake Biological Station, University of Montana, Polson, Montana.

Mack, J. J. 2001. Vegetation index of biotic integrity (VIBI) for wetlands: ecoregional, hydrogeomorphic, and plant community comparisons with preliminary wetland aquatic life use designations. Final Report to US EPA. Ohio EPA, Columbus Ohio. Available at: http://www.epa.state.oh.us/dsw/wetlands/FINAL_RPT_G833.pdf

Malakoff, D. 1998. Restored wetlands flunk real-world test. Science 280: 371-372.

Spaling, H. and B. Smit. 1995. Agroecosystem health and cumulative effects assessment: An application to land drainage and wetlands. Ecosystem Health 1: 260-272.

USEPA. 1997. Pilot Test of Wetland Condition Indicators in the Prairie Pothole Region of the United States. EPA/620/R-97/002. Office of Research and Development, US Environmental Protection Agency, Washington, DC.

Lakes and Ponds

Ohio EPA. 1998(?). Biological criteria for the protection of aquatic life: Volume IV: Fish and macroinvertebrates indicies for Ohio’s Lake Erie nearshore waters, harbors, and lacustuaries. Division of Surface Waters, Ecological Assessment Unit, Ohio EPA, Columbus, Ohio.

Ohio EPA. 1996(?). Development of biological indices using macroinvertebrates in Ohio nearshore waters, harbors, and lacustuaries of Lake Erie in order to evaluate water quality. Division of Surface Waters, Ecological Assessment Unit, Ohio EPA, Columbus, Ohio.

Harig, A. L., and M. B. Bain. 1998. Defining and restoring biological integrity in wilderness lakes. Ecological Applications 8: 71–87.

Verschuren, D., and 7 other authors. 2001. History and timing of human impact on Lake Victoria, East Africa. Proceedings Royal Society London, B published online DOI 10.1098/rspb.2001.1850.

Whittier, T. R., S. G. Paulsen, D. P. Larsen, S. A. Peterson, A. T. Herlihy, and P. R. Kaufmann. 2002. Indicators of ecological stress and their extent in the population of Northeastern lakes: A regional-scale assessment. BioScience 52: 235-247.

Williams, P., J. Biggs, L. Dodds, M. Whitfield, A. Corfield, and G. Fox. 1996. Biological techniques of still water quality assessment: Phase 1 Scoping Study. R&D Technical Report E7. Environment Agency, Bristol, UK.

Williams, P., J. Biggs, M. Whitfield, A. Corfield, G. Fox, K. Adare. 1998. Biological techniques of still water quality assessment. 2. method development. R&D Technical Report E56. Environmenta Agency, Bristol, UK.

Coastal and Marine

Camhi, M. 1995. Industrial fisheries threaten ecological integrity of the Galapagos Islands. Conservation Biology 9: 715-724.

Carroll, G. 1998. Are our coastal waters turning deadly? National Wildlife (April/May 1998, pages 42-46.

Coleman, F. C., and S. L. Williams. 2002. Overexploiting marine ecosystem engineers: potential consequences for biodiversity. Trends in Ecology and Evolution 17(1): 40-44.

Deegan, L. A., and J. T. Finn, and J. Buonaccorsi. 1997. Development and validation of an estuarine biotic integrity index. Estuaries 20: 601-617.

Done, T. J., and R. E. Reichelt. 1998. Integrated coastal zone and fisheries ecosystem management: Generic goals and performance indices. Ecological Applications 8: S110-S118.

Engle, V. D., J. K. Summers, and G. R. Gaston. 1994. A benthic index of environmental condition of Gulf of Mexico estuaries. Estuaries 17: 372-284.

Engle, V. D., and J. K. Summers. 1998. Determining the causes of benthic conditions. Environmental Monitoring and Assessment 51: 381-397.

France, R., and M. Sharp. 1992. Polynyas as centers of organization for structuring the integrity of arctic marine communities. Conservation Biology 6: 442-446.

Hartwell, S. I., editor. 1997. Workshop Proceedings: Biological Habitat Quality Indicators for Essential Fish Habitat. National Marine Fisheries Service, Charleston, SC.

Jackson, J. B. C. 1997. Reefs since Columbus. Coral Reefs 16 (suppl): S23-S32.

Jackson, J. B. C. 2001. What was natural in the coastal oceans? Proceedings of the National Academy of Sciences 98: 5411-5418.

Jackson, J. B. C., and E. Sala. 2001. Unnatural oceans. Scientia Marina 65 (suppl. 2): 273-281.

Jackson, J. B. C., and 18 other authors. 2001. Historical overfishing and the recent collapse of coastal ecosystems. Science 293: 629-638.

Jameson, S. C., M. V. Erdmann, G. R. Gibson Jr., K. W. Potts. 1998. Development of biological criteria for coral reef ecosystem assessment. Atoll Research Bulletin, September 1998, No. 450, Smithsonian Institution, Washington, DC.

Jameson, S. C., M. S. A. Ammar, E. Saadalla, H. M. Mostafa, B. Reigl. 1999. A coral damage index and its application to diving sites in the Egyptian Red Sea. Coral Reefs 18: 333-339.

Jameson, S.C., M.V. Erdmann, J.R. Karr and K.W. Potts. 2001. Charting a course toward diagnostic monitoring: A continuing review of coral reef attributes and a research strategy for creating coral reef indexes of biotic integrity. Bulletin of Marine Science 69: 701-744.

Jamieson, G., and R. O’Boyle, co-chairs. 2001. Proceedings of the national workshop on objectives and indicators for ecosystem-based management. Sydney, British Columbia, 27 February – 2 March 2001. Department of Fisheries and Oceans, Ottawa, Ontario.

Knowlton, N. 2001. The future of coral reefs. Proceedings of the National Academy of Sciences (USA) 98: 5419-5425.

Nelson, W. G. 1990. Prospects for development of an index of biotic integrity for evaluating habitat degradation in coastal systems. Chemistry and Ecology 4: 197-210.

Paul, J. F., and 8 coauthors. 2001. Developing and applying a benthic index of estuarine condition for the Virginian biogeographic province. Ecological Indicators 1: 83-99.

Pauly, D., V. Christensen, R. Froese, and M. L. Palomares. 2000. Fishing down aquatis food webs. American Scientist 88: 46-51.

Puget Sound Water Quality Action Team. 2002. Puget Sound’s Health 2002. Puget Sound Water Quality Action Team, Olympia, WA. Available at: www.wa.gov/Puget_sound/Publications/pshealth2002/pshealth_pdf.html

Ramm, A. E. L. 1990. Application of the community degradation index to South African estuaries. Water Res. 24: 383-389.

Roberts, C. M., J. A. Bohnsack, F. Gell, J. P. Hawkins, and R. Goodridge. 2001. Effects of marine researves on adjacent fisheries. Science 294: 1920-1923.

Van Dolah, R. F., J. L. Hyland, A. F. Holland, J. S. Rosen, and T. R. Snoots. 1999. A benthic index of biological integrity for assessing habitat quality in estuaries of the southeastern USA. Marine Environmental Research 48: 269-283.

Watson, R. and D. Pauly. 2001. Systematic distortions in world fisheries catch trends. Nature 414: 534-536.

Weisberg, S. B., J. A. Ranasinghe, L. C. Schaffner, R. M. Diaz, D. M. Dauer, and J. B. Frithsen. 1997. An estuarine benthic index of biotic integrity (B-IBI) for Chesapeake Bay. Estuaries 20: 149-158.

BIBLIOGRAPHY: TAXONOMIC GROUPS

BIOLOGICAL MONITORING AND ASSESSMENT

Selected Bibliography; FISH/BIOL 438; June 2002

Stream Invertebrates

Angradi, T. R. 1999. Fine sediment and macroinvertebrate assemblages in Appalachian streams: a field experiment with biomonitoring applications. Journal North American Benthological Society 18: 49-66.

Black, R. W., and D. E. MacCoy. 2000. The development and evaluation of a benthic index of biological integrity for the Cedar River watershed, Washington. Water Resources Investigations Report 99-4203. Tacoma, Washington: U.S. Geological Survey.

Clayton, J. L. and R. Menendez. 1996. Macroinvertebrate responses to mitigative liming of Dogway Fork, West Virginia. Restoration Ecology 4: 234-246.

Fore, L. S., J. R. Karr, and R. W. Wisseman. 1996. Assessing invertebrate responses to human activities: Evaluating alternative approaches. Journal North American Benthological Society 15: 212–231.

Harding, J. S., E. F. Benfield, P. V. Bolstad, G. S. Helfman, and E. B. D. Jones, III. 1998. Stream biodiversity: The ghost of land use past. Proceedings of the National Academy of Sciences USA 95: 14843-14847.

Karr, J. R., and E. W. Chu. 1999. Restoring Life in Running Waters: Better Biological Monitoring. Island Press, Washington, DC.

Kennen, J. G. 1999. Relation of macroinvertebrate community impairment to catchment characteristics in New Jersey streams. Journal American Water Resources Association 35: 939-955.

Maret, T. R., D. E. MacCoy, K. D. Skinner, S. E. Moore, and I. O’Dell. 2001. Evaluation of macroinvertebrate assemblages in Idaho rivers using multimetric and multivariate techniques, 1996-98. Water-Resources Investigations Report 01-4145, US Geological Survey, Boise, Idaho.

Morley, S. A., and J. R. Karr. 2002. Assessing and restoring the health of urban streams in the Puget Sound basin. Conservation Biology, in press.

Pontasch, K. W., and M. A. Brusven. 1988. Diversity and community comparison indices: Assessing macroinvertebrate recovery following a gasoline spill. Water Res. 22: 619-626.

Sponseller, R. A., E. F. Benfield, and H. M. Valett. 2001. Relationships between land use, spatial scale and stream macroinvertebrate communities. Freshwater Biology 46: 1409-1424.

Thomson, J. R., P. S. Lake, and B. J. Downes. 2002. 83: 628-642.

Thorne, R. St. J., and W. P. Williams. 1997. The response of benthic macroinvertebrates to pollution in developing countries: a multimetric system for bioassessment. Freshwater Biology 37: 671-686.

Voshell, J. R., E. P. Smith, S. K. Evans, and M. Hudy. 1997. Effective and scientifically sound bioassessment: Opinions and corroboration from academe. Human and Ecological Risk Assessment 3: 941-954.

Wallace, J. B., J. W. Grubaugh, and M. R. Whiles. 1996. Biotic indices and stream ecosystem processes: Results from an experimental study. Ecological Applications 6: 140-151.

Fish

Allan, J. D., D. L. Erickson, and J. Fay. 1997. The influences of catchment land use on stream integrity across multiple spatial scales. Freshwater Biology 37: 149-161.

Edwards, C. J., R. A. Ryder, and T. R. Marshall. 1990. Using lake trout as a surrogate of ecosystem health for oligotrophic waters of the Great Lakes. Journal of Great Lakes Research 16: 591-608.

Fausch, K. D., J. Lyons, J. R. Karr, and P. L. Angermeier. 1990. Fish communities as indicators of environmental degradation. American Fisheries Society Symposium 8: 123–144.

Fore, S. A., S. I. Guttman, A. J. Bailer, D. J. Altfater, and B. V. Counts. 1995. Exploratory analysis of population genetic assessment as a water quality indicator: II Campostoma anomalum. Ecotoxicology and Environmental Safety 30: 36-46.

Ganasan, V., and R. M. Hughes. 1998. Application of an index of biological integrity (IBI) to fish assemblages of the rivers Khan and Kshipra (Madhya Pradesh), India. Freshwater Biology 40: 367-383.

Hay, C. J., B. J. van Zyl, and G. J. Steyn. 1996. A quantitative assessment of the biotic integrity of the Okavango River, Namibia, based on fish. Water SA 22: 263-284.

Hughes, R. M., P. R. Kaufmann, A. T. Herlihy, T. M. Kincaid, L. Reynolds, and D. P. Larsen. 1998. A process for developing and evaluating indices of fish assemblage integrity. Canadian Journal Fisheries and Aquatic Sciences 55: 1618-1631.

Hughes, R. M., and T. Oberdorff. 1999. Applications of IBI concepts and metrics to waters outside the United States. Pages 79-93 in T. P. Simon, editor. Assessing the sustainability and biological integrity of water resources using fish communities. Boca Raton, Florida: CRC Press.

Karr, J. R., Fausch, K. D., Angermeier, P. L., Yant, P. R., and Schlosser, I. J. 1986. Assessment of biological integrity in running waters: A method and its rationale. Special Publication No. 5. Champaign, Illinois: Illinois Natural History Survey.

Kleynhans, C. J. 1999. The development of a fish index to assess the biological integrity of South African rivers. Water SA 25: 265-278.

Kovacs, T. G., P. H. Martel, and R. H. Voss. 2002. Assessing the biological status of fish in a river receiving pulp and paper mill effluents. Environmental Pollution 118: 123-140.

Landsberg, J. H., B. A. Blakesley, R. O. Reese, G. McRae, and P. R. Forstchen. 1998. Parasites of fish as indicators of environmental stress. Environmental Monitoring and Assessment 51: 211-232.

Lyons, J. 1992a. Using the index of biotic integrity (IBI) to measure environmental quality in warmwater streams of Wisconsin. US Forest Service, General Technical Report NC‑149. U. S. Forest Service, St. Paul. Minnesota.

Lyons, J., S. Navarro-Perez, P. A. Cochran, E. Santana C., and M. Guzman-Arroyo. 1995. Index of biotic integrity based on fish assemblages for the conservation of streams and rivers in West-central Mexico. Conservation Biology 9: 569-584.

McCormick, F. H., R. M. Hughes, P. R. Kaufmann, D. V. Peck, J. L. Stoddard, and A. T. Herlihy. 2001. Development of an index of biotic integrity for the mid-Atlantic highlands region. Transactions American Fisheries Society 130:857-877.

Niemala, S., and M. Feist. 2000. Index of biotic integrity (IBI) guidance for coolwater rivers and streams of the St. Croix basin in Minnesota. Biological Monitoring Program, Minnesota Pollution Control Agency, St. Paul, Minnesota.

Ricciardi, A. and J.B. Rasmussen. 1999. Extinction rates of North American freshwater fauna. Conservation Biology 13:1220-1222.

Scott, M. C., and G. S. Helfman. 2001. Native invasions, homogenization, and the mismeasure of integrity in fish assemblages. Fisheries 26(11): 6-15

Wang, L., J. Lyons, P. Kanehl, and R. Gatti. 1997. Influences of watershed land use on habitat quality and biotic integrity in Wisconsin streams. Fisheries 22(6): 6-12.

Wang, L., J. Lyons, P. Kanehl, R. Bannerman, and E. Emmons. 2000. Watershed urbanization and changes in fish communities in southeastern Wisconsin streams. Journal Water Resources Association 36:1173–1189.

Whittier, T. R., D. B. Halliwell, and S. G. Paulsen. 1997. Cyprinid distributions in Northeast lakes: Evidence of regional-scale minnow biodiversity losses. Canadian Journal of Fisheries and Aquatic Sciences 54: 1593-1607.

Yoder, C. O., and M. A. Smith. 1999. Using fish assemblages in a state biological assessment and criteria program: Essential concepts and considerations. Pages 17-56 in T. P. Simon, editor. Assessing the sustainability and biological integrity of water resources using fish communities. Boca Raton, Florida: CRC Press.

Algae and Diatoms

Fore, L. S. 2001. Development and testing of diatom metrics for the mid-appalachian region. Report prepared for USEPA. Statistical Design, Seattle, Washington.

Birds

Austin, J. E., T. K. Buhl, G. R. Guntenspergen, W. Norling, and H. T. Sklebar. 2001. Duck populations as indicators of landscape condition in the prairie pothole region. Environmental Monitoring and Assessment 69: 29-47.

Blair, R. B. 1996. Land use and avian species diversity along an urban gradient. Ecological Applications 6: 506-519.

Blair, R. B. 1999. Birds and butterflies along an urban gradient: Surrogate taxa for assessing biodiversity? Ecological Applications 9: 164-170.

Bradford, D. F., S. E. Franson, A. C. Neale, D. T. Heggem, G. R. Miller, and G. E. Canterbury. 1998. Bird species assemblages as indicators of biological integrity in Great Basin rangeland. Environmental Monitoring and Assessment 49: 1-22.

Canaday, C. 1996. Loss of insectivorous birds along a gradient of human impact in Amazonia. Biological Conservation 77: 63-77.

Koskimies, P. 1989. Birds as a tool in environmental monitoring. Annals Zoologica Fennici 26: 153-166.

Lichstein, J. W., T. R. Simons, and K. E. Franzreb. 2002. Landscape effects on breeding songbird abundance in managed forest. Ecological Applications 12: 836-857.

O’Connell, T. J., L. E. Jackson, and R. P. Brooks. 2000. Bird guilds as indicators of ecological condition in the central Appalachians. Ecological Applications 10: 1706-1721.

Sekercioglu, C. H., P. R. Ehrlich, G. C. Daily, D. Aygen, D. Goehring, and R. F. Sandi. 2002. Disappearance of insectivorous birds from tropical forest fragments. Proceedings National Academy of Sciences (USA) 99: 263-267.

Amphibians and Reptiles

Lehtinen, R. M., S. M. Galatowitsch, and J. R. Tester. 1999. Consequences of habitat loss and fragmentation for wetland amphibian assemblages. Wetlands 19: 1-12.

Micacchion, M. 2002. Amphibian Index of Biotic Integrity (AmphIBI) for Wetlands. Final Repoirt to USEPA Grant No. CD985875-01. Wetland Ecology Group, Division of Water, Ohio Environmental Protection Agency, Columbus, Ohio. Available at: http://www.epa.state.oh.us/dsw/wetlands/wetland_bioasses.html

Terrestrial Invertebrates

Davis, A. J., J. D. Holloway, H. Huijbrets, J. Krikken, A. H. Kirk-Spriggs, and S. L. Sutton. 2001. Dung beetles as indicators of change in the forest of Northern Borneo. Journal of Applied Ecology 38: 593-616.

Kimberling, D. N., J. R. Karr, and L. S. Fore. 2001. Measuring human disturbance using terrestrial invertebrates in the shrub-steppe of eastern Washington (USA). Ecological Indicators 1: 63-81.

Summerville, K. S., and T. O. Crist. 2002. Effects of timber harvest on forest Lepidoptera: Community, guild, and species responses. Ecological Applications 12:820-835.

Plants

Dennison, W. C., R. J. Orth, K. A. Moore, J. C. Stevenson, V. Carter, S. Kollar, P. Bergstrom, and R. A. Batiuk. 1993. Assessing water quality with submerged aquatic vegetation. BioScience 43: 86-94.

Elzinga, C. L., D. W. Salzer, and J. W. Willoughby. 1998. Measuring and monitoring plant populations. BLM Technical Reference 1730-1. Denver, CO: Bureau of Land Management.

Herman, K. D., A. A. Reznicek, L. A. Masters, G. S. Wilhelm, M. R. Penskar, and W. W. Brodowicz. 1997. Floristic quality assessment: Development and application in the state of Michigan (USA). Natural Areas Journal 17: 265-279.

Hylander, K., B. G. Jonsson, and C. Nilsson. 2002. Evaluating buffer strips along boreal streams using bryophytes as indicators. Ecological Applications 12: 797-806.

Loucks, O. L. 2000. Forest wildland integrity in the Eastern U.S. and Canada: Measuring systems loss. Pages 177-190 in D. Pimentel, L. Westra, and R. F. Noss, editors. Ecological Integrity: Integrating Environment, Conservation, and Health. Washington, DC: Island Press.

Loucks, O. L. 2000. Ecological functions and integrity: Approaches to valuation. Pages 157-176 in P. Crabbé, A. Holland, and L. Ryszkowski, editors. Implementing Ecological Integrity: Restoring Regional and Global Environmental and Human Health. NATO Science Series: IV Earth and Environmental Sciences. . Kluwer Academic Publishers, The Netherlands.

Lundquist, J. E., and J. S. Beatty. 1999. A conceptual model for defining and assessing condition of forest stands. Environmental Management 23: 519-525.

Medley, K. E., M. J. McDonnell, and S. T. A. Pickett. 1995. Forest-landscape structure along an urban-to-rural gradient. Professional Geographer 47: 159-168.