References

The works below are cited in the chapters. They fall into three groups: the methods this report uses (rarefaction, PERMANOVA, false discovery rate control, censored-data statistics), the Australian bioassessment literature the rating system descends from (SIGNAL, AUSRIVAS), and the ecological literature against which this report’s findings can be judged — urban stream syndrome, biotic homogenisation, fire effects and fine sediment.

Entries noted as open access in the source bibliography (references.bib) can be read without a journal subscription. These include the AUSRIVAS sampling manual, the ANZECC and ARMCANZ water quality guidelines, the USGS statistical and instrument-comparison reports, and the Australian Museum amphipod monograph. The remainder are behind publisher paywalls; Council may need library access or an author copy.

Anderson, Marti J. 2001. “A New Method for Non-Parametric Multivariate Analysis of Variance.” Austral Ecology 26 (1): 32–46. https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x.

Anderson, Marti J. 2006. “Distance-Based Tests for Homogeneity of Multivariate Dispersions.” Biometrics 62 (1): 245–53. https://doi.org/10.1111/j.1541-0420.2005.00440.x.

Anderson, Marti J., and Daniel C. I. Walsh. 2013. “PERMANOVA, ANOSIM, and the Mantel Test in the Face of Heterogeneous Dispersions: What Null Hypothesis Are You Testing?” Ecological Monographs 83 (4): 557–74. https://doi.org/10.1890/12-2010.1.

ANZECC and ARMCANZ. 2000. Australian and New Zealand Guidelines for Fresh and Marine Water Quality. National Water Quality Management Strategy 4. Australian and New Zealand Environment and Conservation Council, and Agriculture and Resource Management Council of Australia and New Zealand. https://waterquality.gov.au/sites/default/files/documents/anzecc-armcanz-2000-guidelines-vol1.pdf.

Benjamini, Yoav, and Yosef Hochberg. 1995. “Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing.” Journal of the Royal Statistical Society, Series B 57 (1): 289–300. https://doi.org/10.1111/j.2517-6161.1995.tb02031.x.

Blue Mountains City Council. 2018. Leura Falls Catchment Improvement Project: Final Report. Blue Mountains City Council.

Booth, Derek B., and C. Rhett Jackson. 1997. “Urbanization of Aquatic Systems: Degradation Thresholds, Stormwater Detection, and the Limits of Mitigation.” Journal of the American Water Resources Association 33 (5): 1077–90. https://doi.org/10.1111/j.1752-1688.1997.tb04126.x.

Cao, Yong, Charles P. Hawkins, and Mark R. Vinson. 2003. “Measuring and Controlling Data Quality in Biological Assemblage Surveys with Special Reference to Stream Benthic Macroinvertebrates.” Freshwater Biology 48 (10): 1898–911. https://doi.org/10.1046/j.1365-2427.2003.01123.x.

Chessman, Bruce C. 1995. “Rapid Assessment of Rivers Using Macroinvertebrates: A Procedure Based on Habitat-Specific Sampling, Family Level Identification and a Biotic Index.” Australian Journal of Ecology 20 (1): 122–29. https://doi.org/10.1111/j.1442-9993.1995.tb00526.x.

Chessman, Bruce C. 2003. “New Sensitivity Grades for Australian River Macroinvertebrates.” Marine and Freshwater Research 54 (2): 95–103. https://doi.org/10.1071/MF02114.

Chessman, Bruce C. 2021. “What’s Wrong with the Australian River Assessment System (AUSRIVAS)?” Marine and Freshwater Research 72 (8): 1110–17. https://doi.org/10.1071/MF20361.

Chessman, Bruce C., Jane E. Growns, and Amanda R. Kotlash. 1997. “Objective Derivation of Macroinvertebrate Family Sensitivity Grade Numbers for the SIGNAL Biotic Index: Application to the Hunter River System, New South Wales.” Marine and Freshwater Research 48 (2): 159–72. https://doi.org/10.1071/MF96058.

Clarke, K. Robert. 1993. “Non-Parametric Multivariate Analyses of Changes in Community Structure.” Australian Journal of Ecology 18 (1): 117–43. https://doi.org/10.1111/j.1442-9993.1993.tb00438.x.

Davies, Peter J., Ian A. Wright, Sophia J. Findlay, Olof J. Jonasson, and Shelley Burgin. 2010. “Impact of Urban Development on Aquatic Macroinvertebrates in South Eastern Australia: Degradation of in-Stream Habitats and Comparison with Non-Urban Streams.” Aquatic Ecology 44 (4): 685–700. https://doi.org/10.1007/s10452-009-9307-y.

Davies, Robert B. 1987. “Hypothesis Testing When a Nuisance Parameter Is Present Only Under the Alternative.” Biometrika 74 (1): 33–43. https://doi.org/10.1093/biomet/74.1.33.

De Cáceres, Miquel, and Pierre Legendre. 2009. “Associations Between Species and Groups of Sites: Indices and Statistical Inference.” Ecology 90 (12): 3566–74. https://doi.org/10.1890/08-1823.1.

Doberstein, Craig P., James R. Karr, and Loveday L. Conquest. 2000. “The Effect of Fixed-Count Subsampling on Macroinvertebrate Biomonitoring in Small Streams.” Freshwater Biology 44 (2): 355–71. https://doi.org/10.1046/j.1365-2427.2000.00575.x.

Dufrêne, Marc, and Pierre Legendre. 1997. “Species Assemblages and Indicator Species: The Need for a Flexible Asymmetrical Approach.” Ecological Monographs 67 (3): 345–66. https://doi.org/10.1890/0012-9615(1997)067[0345:SAAIST]2.0.CO;2.

Gallant, John, Nicholas Wilson, Trevor Dowling, Arthur Read, and Craig Inskeep. 2011. SRTM-Derived 1 Second Digital Elevation Models Version 1.0. Dataset, Geoscience Australia, Canberra. https://data.gov.au/dataset/ds-dga-9a9284b6-eb45-4a13-97d0-91bf25f1187b.

Gomez Isaza, Daniel F., Rebecca L. Cramp, and Craig E. Franklin. 2022. “Fire and Rain: A Systematic Review of the Impacts of Wildfire and Associated Runoff on Aquatic Fauna.” Global Change Biology 28 (8): 2578–95. https://doi.org/10.1111/gcb.16088.

Gotelli, Nicholas J., and Robert K. Colwell. 2001. “Quantifying Biodiversity: Procedures and Pitfalls in the Measurement and Comparison of Species Richness.” Ecology Letters 4 (4): 379–91. https://doi.org/10.1046/j.1461-0248.2001.00230.x.

Growns, Jane E., Bruce C. Chessman, Jean E. Jackson, and David G. Ross. 1997. “Rapid Assessment of Australian Rivers Using Macroinvertebrates: Cost and Efficiency of 6 Methods of Sample Processing.” Journal of the North American Benthological Society 16 (3): 682–93. https://doi.org/10.2307/1468153.

Growns, Jane E., Bruce C. Chessman, Paul K. McEvoy, and Ian A. Wright. 1995. “Rapid Assessment of Rivers Using Macroinvertebrates: Case Studies in the Nepean River and Blue Mountains, NSW.” Australian Journal of Ecology 20 (1): 130–41. https://doi.org/10.1111/j.1442-9993.1995.tb00527.x.

Hack, John T. 1957. Studies of Longitudinal Stream Profiles in Virginia and Maryland. Professional Paper 294-B. U.S. Geological Survey. https://doi.org/10.3133/pp294b.

Harvey, Mark S. 2002. “Short-Range Endemism Amongst the Australian Fauna: Some Examples from Non-Marine Environments.” Invertebrate Systematics 16 (4): 555–70. https://doi.org/10.1071/IS02009.

Hatt, Belinda E., Tim D. Fletcher, Christopher J. Walsh, and Sally L. Taylor. 2004. “The Influence of Urban Density and Drainage Infrastructure on the Concentrations and Loads of Pollutants in Small Streams.” Environmental Management 34 (1): 112–24. https://doi.org/10.1007/s00267-004-0221-8.

Helsel, Dennis R. 2006. “Fabricating Data: How Substituting Values for Nondetects Can Ruin Results, and What Can Be Done about It.” Chemosphere 65 (11): 2434–39. https://doi.org/10.1016/j.chemosphere.2006.04.051.

Helsel, Dennis R. 2012. Statistics for Censored Environmental Data Using Minitab and R. 2nd ed. John Wiley; Sons. https://doi.org/10.1002/9781118162729.

Helsel, Dennis R., Robert M. Hirsch, Karen R. Ryberg, Stacey A. Archfield, and Edward J. Gilroy. 2020. Statistical Methods in Water Resources. Techniques and Methods Nos. 4-A3. U.S. Geological Survey. https://doi.org/10.3133/tm4a3.

Hering, Daniel, Christian K. Feld, Otto Moog, and Thomas Ofenböck. 2006. “Cook Book for the Development of a Multimetric Index for Biological Condition of Aquatic Ecosystems: Experiences from the European AQEM and STAR Projects and Related Initiatives.” Hydrobiologia 566 (1): 311–24. https://doi.org/10.1007/s10750-006-0087-2.

Hirsch, Robert M., and James R. Slack. 1984. “A Nonparametric Trend Test for Seasonal Data with Serial Dependence.” Water Resources Research 20 (6): 727–32. https://doi.org/10.1029/WR020i006p00727.

Hurlbert, Stuart H. 1971. “The Nonconcept of Species Diversity: A Critique and Alternative Parameters.” Ecology 52 (4): 577–86. https://doi.org/10.2307/1934145.

Johnston, Matthew W., and John S. Williams. 2006. Field Comparison of Optical and Clark Cell Dissolved Oxygen Sensors in the Tualatin River, Oregon, 2005. Open-File Report Nos. 2006-1047. U.S. Geological Survey. https://doi.org/10.3133/ofr20061047.

Jones, J. I., J. F. Murphy, A. L. Collins, D. A. Sear, P. S. Naden, and P. D. Armitage. 2012. “The Impact of Fine Sediment on Macroinvertebrates.” River Research and Applications 28 (8): 1055–71. https://doi.org/10.1002/rra.1516.

Karr, James R. 1981. “Assessment of Biotic Integrity Using Fish Communities.” Fisheries 6 (6): 21–27. https://doi.org/10.1577/1548-8446(1981)006<0021:AOBIUF>2.0.CO;2.

Kaushal, Sujay S., Gene E. Likens, Norbert A. Jaworski, et al. 2010. “Rising Stream and River Temperatures in the United States.” Frontiers in Ecology and the Environment 8 (9): 461–66. https://doi.org/10.1890/090037.

King, Ryan S., Matthew E. Baker, Paul F. Kazyak, and Donald E. Weller. 2011. “How Novel Is Too Novel? Stream Community Thresholds at Exceptionally Low Levels of Catchment Urbanization.” Ecological Applications 21 (5): 1659–78. https://doi.org/10.1890/10-1357.1.

Legendre, Pierre, and Marti J. Anderson. 1999. “Distance-Based Redundancy Analysis: Testing Multispecies Responses in Multifactorial Ecological Experiments.” Ecological Monographs 69 (1): 1–24. https://doi.org/10.1890/0012-9615(1999)069[0001:DBRATM]2.0.CO;2.

McKee, Thomas B., Nolan J. Doesken, and John Kleist. 1993. “The Relationship of Drought Frequency and Duration to Time Scales.” Proceedings of the 8th Conference on Applied Climatology, 17–22 January 1993, Anaheim, California (Boston), 179–84. https://climate.colostate.edu/pdfs/relationshipofdroughtfrequency.pdf.

McKinney, Michael L. 2006. “Urbanization as a Major Cause of Biotic Homogenization.” Biological Conservation 127 (3): 247–60. https://doi.org/10.1016/j.biocon.2005.09.005.

Muggeo, Vito M. R. 2003. “Estimating Regression Models with Unknown Break-Points.” Statistics in Medicine 22 (19): 3055–71. https://doi.org/10.1002/sim.1545.

Nichols, Susan J., Leon A. Barmuta, Bruce C. Chessman, et al. 2017. “The Imperative Need for Nationally Coordinated Bioassessment of Rivers and Streams.” Marine and Freshwater Research 68 (4): 599–613. https://doi.org/10.1071/MF15329.

Olden, Julian D., and Thomas P. Rooney. 2006. “On Defining and Quantifying Biotic Homogenization.” Global Ecology and Biogeography 15 (2): 113–20. https://doi.org/10.1111/j.1466-822X.2006.00214.x.

Ostermiller, Jeffrey D., and Charles P. Hawkins. 2004. “Effects of Sampling Error on Bioassessments of Stream Ecosystems: Application to RIVPACS-Type Models.” Journal of the North American Benthological Society 23 (2): 363–82. https://doi.org/10.1899/0887-3593(2004)023<0363:EOSEOB>2.0.CO;2.

Peres-Neto, Pedro R., Pierre Legendre, Stéphane Dray, and Daniel Borcard. 2006. “Variation Partitioning of Species Data Matrices: Estimation and Comparison of Fractions.” Ecology 87 (10): 2614–25. https://doi.org/10.1890/0012-9658(2006)87[2614:VPOSDM]2.0.CO;2.

Robson, B. J., E. T. Chester, T. G. Matthews, and K. Johnston. 2018. “Post-Wildfire Recovery of Invertebrate Diversity in Drought-Affected Headwater Streams.” Aquatic Sciences 80 (2): 21. https://doi.org/10.1007/s00027-018-0570-7.

St Lawrence, Amy, Ian A. Wright, Robert B. McCormack, Christina Day, Geoffrey Smith, and Brian Crane. 2014. “Bifenthrin Pesticide Contamination: Impacts and Recovery at Jamison Creek, Wentworth Falls.” In Proceedings of the 7th Australian Stream Management Conference, edited by G. Vietz, I. D. Rutherfurd, and R. Hughes. Townsville, Queensland. https://www.bmcc.nsw.gov.au/sites/default/files/docs/Bifenthrin%20pesticide%20contamination%20at%20Jamison%20Creek%20%28Conference%20Paper%29_0.PDF.

Stewart-Oaten, Allan, William W. Murdoch, and Keith R. Parker. 1986. “Environmental Impact Assessment: ‘Pseudoreplication’ in Time?” Ecology 67 (4): 929–40. https://doi.org/10.2307/1939815.

Stoddard, John L., Alan T. Herlihy, David V. Peck, Robert M. Hughes, Thomas R. Whittier, and Ellen Tarquinio. 2008. “A Process for Creating Multimetric Indices for Large-Scale Aquatic Surveys.” Journal of the North American Benthological Society 27 (4): 878–91. https://doi.org/10.1899/08-053.1.

Suter, Glenn W. 1993. “A Critique of Ecosystem Health Concepts and Indexes.” Environmental Toxicology and Chemistry 12 (9): 1533–39. https://doi.org/10.1002/etc.5620120903.

Sutherland, R. C. 2000. “Methods for Estimating the Effective Impervious Area of Urban Watersheds.” Chap. 32 in The Practice of Watershed Protection, edited by Thomas R. Schueler and Heather K. Holland. Center for Watershed Protection. https://yourcleanwater.org/wp-content/uploads/2021/10/CWP-Sutherland-DCIA-Paper.pdf.

Turak, Eren, Lloyd K. Flack, Richard H. Norris, Justen Simpson, and Natacha Waddell. 1999. “Assessment of River Condition at a Large Spatial Scale Using Predictive Models.” Freshwater Biology 41 (2): 283–98. https://doi.org/10.1046/j.1365-2427.1999.00431.x.

Turak, Eren, Natacha Waddell, and Glenn Johnstone. 2004. New South Wales (NSW) Australian River Assessment System (AUSRIVAS) Sampling and Processing Manual. Department of Environment; Conservation (NSW), for the National River Health Program. https://ausrivas.ewater.org.au/index.php/resources2/category/10-manuals?download=15:nsw-sampling-and-processing-manual-pdf-32mb.

Underwood, A. J. 1994. “On Beyond BACI: Sampling Designs That Might Reliably Detect Environmental Disturbances.” Ecological Applications 4 (1): 3–15. https://doi.org/10.2307/1942110.

Verkaik, Iraima, Maria Rieradevall, Scott D. Cooper, John M. Melack, Tom L. Dudley, and Narcís Prat. 2013. “Fire as a Disturbance in Mediterranean Climate Streams.” Hydrobiologia 719 (1): 353–82. https://doi.org/10.1007/s10750-013-1463-3.

Vinson, Mark R., and Charles P. Hawkins. 1996. “Effects of Sampling Area and Subsampling Procedure on Comparisons of Taxa Richness Among Streams.” Journal of the North American Benthological Society 15 (3): 392–99. https://doi.org/10.2307/1467286.

Walsh, Christopher J., Tim D. Fletcher, and Anthony R. Ladson. 2005. “Stream Restoration in Urban Catchments Through Redesigning Stormwater Systems: Looking to the Catchment to Save the Stream.” Journal of the North American Benthological Society 24 (3): 690–705. https://doi.org/10.1899/04-020.1.

Walsh, Christopher J., and Joshphar Kunapo. 2009. “The Importance of Upland Flow Paths in Determining Urban Effects on Stream Ecosystems.” Journal of the North American Benthological Society 28 (4): 977–90. https://doi.org/10.1899/08-161.1.

Walsh, Christopher J., Allison H. Roy, Jack W. Feminella, Peter D. Cottingham, Peter M. Groffman, and Raymond P. Morgan. 2005. “The Urban Stream Syndrome: Current Knowledge and the Search for a Cure.” Journal of the North American Benthological Society 24 (3): 706–23. https://doi.org/10.1899/04-028.1.

Wang, Yi, Ulrike Naumann, Stephen T. Wright, and David I. Warton. 2012. “mvabund – an R Package for Model-Based Analysis of Multivariate Abundance Data.” Methods in Ecology and Evolution 3 (3): 471–74. https://doi.org/10.1111/j.2041-210X.2012.00190.x.

Warton, David I., Stephen T. Wright, and Yi Wang. 2012. “Distance-Based Multivariate Analyses Confound Location and Dispersion Effects.” Methods in Ecology and Evolution 3 (1): 89–101. https://doi.org/10.1111/j.2041-210X.2011.00127.x.

Williams, W. D., and J. Laurens Barnard. 1988. “The Taxonomy of Crangonyctoid Amphipoda (Crustacea) from Australian Fresh Waters: Foundation Studies.” Records of the Australian Museum, Supplement 10: 1–180. https://doi.org/10.3853/j.0812-7387.10.1988.94.

Wood, Paul J., and Patrick D. Armitage. 1997. “Biological Effects of Fine Sediment in the Lotic Environment.” Environmental Management 21 (2): 203–17. https://doi.org/10.1007/s002679900019.

Wright, Ian A., and Shelley Burgin. 2009. “Comparison of Sewage and Coal-Mine Wastes on Stream Macroinvertebrates Within an Otherwise Clean Upland Catchment, Southeastern Australia.” Water, Air, and Soil Pollution 204 (1–4): 227–41. https://doi.org/10.1007/s11270-009-0040-x.