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U.S. GEOLOGICAL SURVEY
Scientific Investigations Report 2006–5101–D

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References Cited

Alberti, M., and Marzluff, J.M., 2004, Ecological resilience in urban ecosystems—Linking urban patterns to human and ecological functions: Urban Ecosystems, v. 7, p. 241-265.

Anderson, C.W., Wood, T.M., and Morace, J.L., 1997, Distribution of dissolved pesticides and other water-quality constituents in small streams, and their relation to land use, in the Willamette River Basin, Oregon, 1996: U.S. Geological Survey Water-Resources Investigations Report 97-4268, 78 p.

Arar, E.J., and Collins, G.B., 1997, U.S. Environmental Protection Agency method 445.0, in vitro determination of chlorophyll-a and pheophytin a in marine and freshwater algae by fluorescence, revision 1.2: Cincinnati, Ohio, U.S. Environmental Protection Agency, National Exposure Research Laboratory, Office of Research and Development, 22 p.

Arnold, C.L., and Gibbons, C.J., 1996, Impervious surface coverage—The emergence of a key environmental indicator: American Planners Association Journal, v. 62, p. 243–258.

Bahls, L.L., 1993, Periphyton bioassessment methods for Montana Streams: Helena, Mont., Water Quality Bureau, Department of Health and Environmental Sciences, 69 p.

Baker, D.B., Richards, R.P., Loftus, T.T., and Kramer, J.W., 2004, A new Flashiness Index—Characteristics and applications to Midwestern rivers and streams: Journal of the American Water Resources Association, v. 40, no. 2, p. 503–522.

Barbour, M.T., Gerritsen, J., Snyder, B.D., and Stribling, J.B., 1999, Rapid bioassessment protocols for use in streams and wadeable rivers—Periphyton, benthic macroinvertebrates, and fish, (2d ed.): Washington, D.C., U.S. Environmental Protection Agency, Office of Water, EPA 841-B-99-002, 226 p.

Biggs, B.J., 1990, Periphyton communities and their environments in New Zealand rivers: New Zealand Journal of Marine and Freshwater Research, v. 24, p. 367–386.

Biggs, B.J., 1996, Patterns in benthic algae in streams, in Stevenson, J.R., Bothwell, M.L., and Lowe, R.L., eds., Algal ecology—Freshwater benthic ecosystems: San Diego, Calif., Academic Press Inc., p. 31–56.

Booth, D.B., and Jackson, C.R., 1997, Urbanization of aquatic systems—Degradation thresholds, stormwater detention, and the limits of mitigation: Journal of the American Water Resources Association, v. 22, no. 5, p. 1–20.

Britton, L.J., and Greeson, P.W., eds., 1987, Methods for collection and analyses of aquatic biological and microbiological samples: U.S. Geological Survey Techniques of Water-Resources Investigations, book 5, chap. A4, p. 139–140.

Brown, L.R., Gray, R.H., Hughes, R.M., and Meador, M.R., 2005, Introduction to effects of urbanization on stream ecosystems, in Brown, L.R., Hughes, R.M., Gray, R., and Meador, M.R., eds., Effects of urbanization on stream ecosystems: American Fisheries Society Symposium 47, p. 1–8.

Bryant, W.L., Goodbred, S.L., Leiker, T.L., Inuoye, Laura, and Johnson, B.T., 2007, Use of chemical analysis and assays of semi-permeable membrane devices extracts to assess the response of bioavailable organic pollutants in streams to urbanization in six metropolitan areas of the United States: U.S. Geological Survey Scientific Investigations Report 2007-5113, 46 p., 2 app., accessed May 17, 2007, at https://pubs.water.usgs.gov/sir2007-5113

Carpenter, K.D., 2003, Water-quality and algal conditions in the Clackamas River Basin, Oregon, and their relations to land and water management: U.S. Geological Survey Water‑Resources Investigations Report 02–4189, 114 p.

Carpenter, K.D., and Waite, I.R., 2000, Relations of habitat-specific algal assemblages to land use and water chemistry in the Willamette Basin, Oregon: Environmental Monitoring and Assessment, v. 64, no. 1, p. 247–257.

Charles, D.F., Candia, K., and Davis, R.S., eds., 2002, Protocols for the analysis of the algae collected as part of the U.S. Geological Survey National Water-Quality Assessment Program: Academy of Natural Sciences Report 02-06, 124 p.

Clarke, K.R., and Ainsworth, M., 1993, A method of linking multivariate community structure to environmental variables: Marine Ecological Progress Series, v. 92, p. 205–219.

Clarke, K.R., and Gorley, R.N., 2006, PRIMER ver. 6—User manual: Plymouth Routines in Multivariate Ecological Research, PRIMER-E, Ltd., 190 p.

Coastal Change and Analysis Program (C-CAP), 2006, Pacific coast land cover—Oregon 2001 land cover data: National Oceanic and Atmospheric Administration, accessed March 2006 at http://www.csc.noaa.gov/crs/lca/pacificcoast.html

Cuffney, T.F., 2003, User’s manual for the National Water-Quality Assessment Program Invertebrate Data Analysis System (IDAS) software—ver. 3: U.S. Geological Survey Open-File Report 03-172, 103 p.

Cuffney, T.F., Meador, M.R., Porter, S.D., and Gurtz, M.E., 2000, Responses of physical, chemical, and biological indicators of water quality to a gradient of agricultural land use in the Yakima River Basin, Washington: Environmental Monitoring and Assessment, v. 64, p. 259-270.

Cuffney, T.F., Zappia, H., Giddings, E.M.P., and Coles, J.F., 2005, Effects of urbanization on benthic macroinvertebrate assemblages in contrasting environmental settings—Boston, Massachusetts, Birmingham, Alabama, and Salt Lake City, Utah: American Fisheries Society Symposium 47, p. 361-408.

Davis, W.S., and Simon, T.P., eds., 1995, Biological assessment and criteria—Tools for water resource planning and decision making: Boca Raton, Fla., Lewis Publishers, 420 p.

Delwiche, L.D., and Slaughter, S.J., 1998, The little SAS book—A primer: Cary, N.C., SAS Institute Inc., 228 p.

Dodds, W.K., Jones, J.R., and Welch, E.B., 1998, Suggested classification of stream trophic state—Distributions of temperate stream types by chlorophyll, total nitrogen, and phosphorus: Water Research, v. 32, no. 5, p. 1455–1462.

Dodds, W.K., Smith, V.H., and Zander, B., 1997, Developing nutrient targets to control benthic chlorophyll levels in streams—A case study of the Clark Fork River: Water Resources Research, v. 31, no. 7, p. 1738–1750.

Falcone, J.A., Stewart, J.S., Sobieszczyk, S., Dupree, J.A., McMahon, G., and Buell, G.R., 2007, A comparison of natural and urban characteristics and the development of Urban Intensity Indices across six geographic settings: U.S. Geological Survey Scientific Investigations Report 2007-5123, 133 p.

Fishman, M.J., 1993, Methods of analysis by the U.S. Geological Survey National Water-Quality Laboratory—Determination of inorganic and organic constituents in water and fluvial sediments: U.S. Geological Survey Open‑File Report 93-125, 217 p.

Fitzpatrick, F.A., Harris, M.A., Arnold, T.L., and Richards, K.D., 2004, Urbanization influences on aquatic communities in northeastern Illinois streams: Journal of the American Water Resources Association, v. 40, p. 461–475.

Fitzpatrick, F.A., Waite, I.R., D’Arconte, P.J., Meador, M.R., Maupin, M.A., and Gurtz, M.E., 1998, Revised methods for characterizing stream habitat in the National Water-Quality Assessment Program: U.S. Geological Survey Water-Resources Investigations Report 98-4052, 67 p.

Gilliom, R.J., Barbash, J.E., Crawford, C.G., Hamilton, P.A., Martin, J.D., Nakagaki, N., Nowell, L.H., Scott, J.C., Stackelberg, P.E., Thelin, G.P., and Wolock, D.M., 2006, Pesticides in the nation’s streams and ground-water, 1992-2001: U.S. Geological Survey Circular 1291, 172 p.

Greenspan Technology, 2006, Greenspan technology user manual, 7th ed., Greenspan Technology: accessed March 2006 at http://www.stevenswater.com/catalog/products/water_quality_sensors/manual/Smart2-manual.pdf

Hoagland, K.D., Roemer, S.C., and Rosowski, R.R., 1982, Colonization and community structure of two periphyton assemblages with emphasis on the diatoms (Bacillariophyceae): American Journal of Botany, v. 69, p. 188–213.

Horner, R.R., Welch, E.B., and Veenstra, R.B., 1983, Development of nuisance periphytic algae in laboratory streams in relation to enrichment and velocity, in Wetzel, R.G., ed., Periphyton of freshwater ecosystems: Boston, Mass., Dr. W. Junk Publishers, p. 122–134.

Huckins, J.N., Manuweera, G.K., Petty, J.D., Mackay, D., and Lebo, J.A., 1993, Lipid-containing semi-permeable membrane devices for monitoring organic contaminants in water: Environmental Science and Technology, v. 27, p. 2489–2496.

Huckins, J.N., Tubergen, M.W., and Manuweera, G.K., 1990, Semi-permeable membrane devices containing model lipid—A new approach to monitoring the availability of lipophilic contaminants and estimating their bioconcentration potential: Chemosphere, v. 20, p. 533–552.

Jacobson, R.B., Femmer, S.R., McKenney, R.A., 2001, Land use changes and the physical habitat of streams—A review with emphasis on studies within the U.S. Geological Survey Federal-State cooperative program: U.S. Geological Survey Circular 1175, 63 p.

Johnson, B.T., 1998, Microtox toxicity test system—New developments and application, in Wells, P.G., Lee, K., and Blaise, C., eds., Microscale testing in aquatic toxicology—Advances, techniques and practice: Boca Raton, Fla., CRC Lewis Publishers, p. 201–218.

Johnson, B.T., Petty, J.D., Huckins, J.N., Lee, K., and Gauthier, J., 2004, Hazard assessment of a simulated oil spill on intertidal areas of the St. Lawrence River with SPMD-TOX: Environmental Toxicology, v. 19, p. 329–335.

Konrad, C.P., and Booth, D.B., 2005, Hydrologic changes in urban streams and their ecological significance: American Fisheries Society Symposium 47, p. 157–178.

Koplin, D.W., Barbash, J.E., and Gilliom, R.J., 1998, Occurrence of pesticides in shallow ground-water of the United States—Initial results from the National Water-Quality Assessment Program: Environmental Science & Technology, v. 32, no. 3, p. 558-566.

LeBlanc, R.T., Brown, R.D., and FitzGibbon, J.E., 1997, Modeling the effects of land use change on the water temperature in unregulated urban streams: Journal of Environmental Management, v. 49, p. 445–469.

Legendre, P., and Legendre, L., 1998, Numerical ecology 2d ed—Developments in Environmental Modeling 20: Amsterdam, The Netherlands, Elsevier Science, 853 p.

Lyons, J., Wang, L., and Simonson, T.D., 1996, Development and validation of an index of biotic integrity for coldwater streams in Wisconsin: North American Fish Management, v. 16, p. 241–256.

McDonnell, M.J., and Pickett, S.T.A., 1990, Ecosystem structure and function along urban-rural gradients—An unexploited opportunity for ecology: Ecology, v. 71, p. 1231–1237.

McGarigal, Kevin, and Marks, B.J., 1995, FRAGSTATS—Spatial pattern analysis program for quantifying landscape structure: U.S. Department of Agriculture Forest Service Technical Report PNW-352, 134 p.

McGarigal, Kevin, Cushman, S.A., Neel, M.C., and Ene, E., 2002, FRAGSTATS—Spatial pattern analysis program for categorical maps, FRAGSTATS 3.1: Amhurst, Mass., University of Massachusetts, accessed March 2006 at http://www.umass.edu/landeco/research/fragstats/fragstats.html

McMahon, G., Bales, J.D., Coles, J.F., Giddings, E.M.P., and Zappia, H., 2003, Use of stage data to characterize hydrologic conditions in an urbanizing environment: Journal of the American Water Resources Association, v. 39, no. 6, p. 1529–1546.

McMahon, G., and Cuffney, T.F., 2000, Quantifying urban intensity in drainage basins for assessing stream ecological conditions: Journal of the American Water Resources Association, v. 36, p. 1247–1261.

Meador, M.R., Coles, J.F., and Zappia, H., 2005, Fish assemblage responses to urban intensity gradients in contrasting metropolitan areas—Birmingham, Alabama and Boston, Massachusetts: American Fisheries Society Symposium 47, p. 409–423.

Moulton, S.R. II, Kennen, J.G., Goldstein, R.M., and Hambrook, J.A., 2002, Revised protocols for sampling algal, invertebrate and fish communities as part of the National Water-Quality Assessment Program: U.S. Geological Survey Open-File Report 02-150, 75 p.

Munn, M.D., and Gilliom, R.J., 2001, Pesticide toxicity index for freshwater aquatic organisms: U.S. Geological Survey Water-Resources Investigation Report 01-4077, 55 p.

Munn, M.D., Gilliom, R.J., Moran, P.W., and Nowell, L.H., 2006, Pesticide toxicity index for freshwater aquatic organisms (2d ed).: U.S. Geological Survey Scientific Investigations Report 2006-5148, 81 p.

Murk, A.J., Legler, J., Penison, M.S., Giesy, J.P., Vande Guchte, C., and Brouwer, A., 1996, Chemical activated luciferase gene expression, CALUX—A novel in vitro bioassay for AH receptor active compounds in sediment and pore water: Fundamental and Applied Toxicology, v. 33, p. 149–160.

Newall, P., and Walsh, C.J., 2005, Response of epilithic diatom assemblages to urbanization influences: Hydrobiologia, v. 532, p. 53–67.

Omernik, J.M., 1987, Ecoregions of the conterminous United States: Annals—Association of American Geographers, v. 77, no. 1, p. 118–125.

Paul, M.J., and Meyer, J.L., 2001, Streams in the urban landscape: Annual Review of Ecology and Systems, v. 32, p. 333–365.

Porter, S.D., 2008, Algal attributes—An autecological classification of algal taxa collected by the National Water-Quality Assessment Program: U.S. Geological Survey Data Series 329, https://pubs.usgs.gov/ds/ds329/.

Potapova, M., Coles, J.F., Giddings, E.M.P., and Zappia, H., 2005, A comparison of the influences of urbanization in contrasting environmental settings on stream benthic algal assemblages: American Fisheries Society Symposium 47, p. 333–359.

Roy, A.H., Freeman, M.C., Freeman, B.J., Wenger, S.J., Ensign, W.E., and Meyer, J.L., 2005, Investigating hydrologic alteration as a mechanism of fish assemblage shifts in urbanizing streams: Journal of the North American Benthological Society, v. 24, no. 3, p. 656–678.

Sala, O.E., Chapin, F.S. III, Armesto, J.J., Berlow, E., Bloomfield, J., Dirzo, R., Huber-Sanwald, E., Huenneke, L.F., Jackson, R.B., Kinzig, A., Leemans, R., Lodge, D.M., Mooney, H.A., Oesterheld, M., Poff, N.L., Sykes, M.T., Walker, B.H., Walker, M., and Wall, D.H., 2000, Global biodiversity scenarios for the year 2100: Science, v. 287, p. 1770–1774.

Sauer, V.B., 2002, Standards for the analysis and processing of surface-water data and information using electronic methods: U.S. Geological Survey Water-Resources Investigations Report 01–4044, 92 p.

Short, T.M., Giddings, E.M.P., Zappia, H., and Coles, J.F., 2005, Urbanization effects on habitat characteristics in Boston, Massachusetts; Birmingham, Alabama; and Salt Lake City, Utah: American Fisheries Society Symposium 47, p. 317–332.

Simon, T.P., and Lyons, J., 1995, Application of the index of biotic integrity to evaluate water resource integrity in freshwater ecosystems, in Davis, W.S., and Simon, T.P., eds., Biological assessment and criteria—Tools for water resource planning and decision making: Boca Raton, Fla., Lewis Publishers, p. 245–262.

Sinokrot, B.A., and Stefan, H.G., 1993, Stream temperature dynamics—Measurements and modeling: Water Resources Research, v. 29, p. 2299–2312.

Sprague, L.A., Zuelling, R.E., and Dupree, J.A., 2006, Effects of urbanization on stream ecosystems in the South Platte River Basin, Colorado and Wyoming: U.S. Geological Survey Scientific Investigations Report 2006-5101-A, 139 p.

Sprouffske, K., Mellott, D., Charles, D.F., and Potapova, M., 2006, Phyco-AIDE—Algal indicators and data exploration, ver. 2.0: Philadelphia, Pa., Academy of Natural Sciences, Phycology Section, Patrick Center for Environmental Research (computer program).

Tate, C.M., Cuffney, T.F., McMahon, G., Giddings, E.M.P., Coles, J.F., and Zappia, H., 2005, Use of an urban intensity index to assess urban effects on streams in three contrasting environmental settings, in Brown, L.R., Hughes, R.M., Gray, R., and Meador, M.R., eds., Effects of urbanization on stream ecosystems: American Fisheries Society Symposium 47, p. 291-315.

Thorson, T.D., Bryce, S.A., Lammers, D.A., Woods, A.J., Omernik, J.M., Kagan, J., Pater, D.E., and Comstock, J.A., 2003, Ecoregions of Oregon (color poster with map, descriptive text, summary tables, and photographs): Reston, Va., U.S. Geological Survey (map scale 1:1,500,000), accessed March 2006 at http://www.epa.gov/wed/pages/ecoregions/or_eco.htm

Uhrich, M.A., and Wentz, D.A., 1999, Environmental setting of the Willamette Basin, Oregon: U.S. Geological Survey Water-Resources Investigations Report 97-4082-A, 20 p.

U.S. Census Bureau, 2000, Census 2000 redistricting data summary file: U.S. Census Bureau Technical Documentation Public Law 94-171, 223 p.

U.S. Environmental Protection Agency, 2002, Envirofacts data warehouse: U.S. Environmental Protection Agency, accessed in 2002 at http://www.epa.gov/enviro/index_java.html

U.S. Environmental Protection Agency, 2002, Western ecology division, Level III ecoregions: U.S. Environmental Protection Agency, accessed in 2002 at http://www.epa.gov/wed/pages/ecoregions/level_iii.htm

U.S. Environmental Protection Agency, 2005, Western ecology division, Level IV ecoregions: U.S. Environmental Protection Agency, accessed in 2005 at http://www.epa.gov/wed/pages/ecoregions/level_iv.htm

U.S. Geological Survey, (variously dated), National field manual for the collection of water-quality data: U.S. Geological Survey Techniques of Water-Resources Investigations, book 9, chaps. A1-A9, v. 2, (variously paged). Available at https://pubs.water.usgs.gov/twri9a

U.S. Geological Survey, 1999, National elevation dataset: U.S. Geological Survey Fact Sheet 148-99, accessed March 2006 at http://erg.usgs.gov/isb/pubs/factsheets/fs14899.html

U.S. Geological Survey, 2003, User’s manual for the national water information system of the U.S. Geological Survey—Automated data processing system (ADAPS): U.S. Geological Survey Open-File Report 2003-123, 413 p.

U.S. Geological Survey, 2005, National land cover database 2001 (NLCD 2001): U.S. Geological Survey database, accessed December 2005 at http://www.mrlc.gov/mrlc2k_nlcd.asp

Van Dam, H., Mertens, A., and Sinkeldam, J., 1994, A coded checklist and ecological indicator values of freshwater diatoms from the Netherlands: Netherlands Journal of Equatic Ecology, v. 28, no. 1, p. 117–133.

Waite, I.R., and Carpenter, K.D., 2000, Associations among fish assemblage structure and environmental variables in Willamette Basin streams, Oregon: Transactions of the American Fisheries Society, v. 129, p. 754–770.

Walker, C.E., and Pan, Y., 2006, Using diatom assemblages to assess urban stream conditions: Hydrobiologia, v. 561, p. 179–189.

Walsh, C.J., Roy, A.H., Feminella, J.W., Cottingham, P.D., Groffman, P.M., and Morgan, R.P., 2005, The urban stream syndrome—Current knowledge and the search for a cure: Journal of the North American Benthological Society, v. 24, no. 3, p. 706–723.

Walsh, C.J., Sharpe, A.K., Breen, P.F., and Sonneman, J.A., 2001, Effects of urbanization on streams of the Melbourne region, Victoria, Australia—I. Benthic macroinvertebrate communities: Freshwater Biology, v. 46, p. 535–551.

Wang, L.J., Lyons, J., Kanehl, P., and Bannerman, R., 2001, Impacts of urbanization on stream habitat and fish across multiple scales: Environmental Management, v. 28, p. 255–266.

Welch, E.B., Horner, R.R., and Patmont, C.R., 1989, Prediction of nuisance periphytic biomass—A management approach: Water Resources, v. 23, no. 4, p. 401–405.

Welch, E.B., Jacoby, J.M., Horner, R.R., and Seeley, M.R., 1988, Nuisance biomass levels of periphytic algae in streams: Hydrobiologia, v. 157, p. 161–168.

Winterbourne, M.J., and Townsend, C.R., 1991, Streams and rivers—One-way flow systems, in Barnes, R.S.K., and Mann, K.H., eds., Fundamentals of Aquatic Ecology: Oxford, England, Blackwell Science Ltd., p. 230–242.

Zaugg, S.D., Sandstrom, M.W., Smith, S.G., and Fehlberg, K.M., 1995, Methods of analysis by the U.S. Geological Survey National Water-Quality Laboratory—Determination of pesticides in water by C-18 solid-phase extraction and capillary-column gas chromatography/mass spectrometry with selected-ion monitoring: U.S. Geological Survey Open-File Report 95-181, 60 p.

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