References
AWT. 1999. “Merri and Darebin Creeks Biological
Monitoring Program.” {AWT} report {No}. 437/00. Melbourne,
Australia: Australian Water Technologies.
Benson, D. A., M. Cavanaugh, K. Clark, I. Karsch-Mizrachi, D. J. Lipman,
J. Ostell, and E. W. Sayers. 2012. “GenBank.” Nucleic
Acids Research 41 (D1): D36–42. https://doi.org/10.1093/nar/gks1195.
Bond, N., J. Thomson, and P. Reich. 2012. “Macroinvertebrate
Responses to Antecedent Flow, Long-Term Flow Regime Characteristics and
Landscape Context in Victorian Rivers.” Report. National Water
Commission. http://archive.nwc.gov.au/__data/assets/word_doc/0016/23083/Victorian-Rivers.doc.
Butcher, R. 2003. “Developing a Long-Term Environmental Fixed
Sites Monitoring Program for Melbourne
Water.” Melbourne: Biological Sciences, Monash
University.
Callahan, B.J., P. J. McMurdie, M. J. Rosen, A. W. Han, A. J. A.
Johnson, and S. P. Holmes. 2016. “DADA2: High-Resolution Sample
Inference from Illumina Amplicon Data.” Nature Methods
13 (7): 581–83. https://doi.org/10.1038/nmeth.3869.
Cameron, A, and D Vertessy. 1995. “Macroinvertebrate Survey of the
Diamond Creek Basin and Stony
Creek, May 1994.” WES Scientific Report 11060095.
Melbourne: Water EcoScience.
———. 1999. “Aquatic Macroinvertebrate Survey of the
Diamond Creek Basin. Final
Report.” Melbourne: ALS Consultants.
Carew, M E, W K Yow, K L Robinson, R A Coleman, and A A Hoffmann. 2022.
“DNA Barcoding and Metabarcoding of Highly Diverse
Aquatic Mites (Acarina) Can Improve Their Use in Routine
Biological Monitoring.” Marine and Freshwater Research
73 (7): 900–914. https://doi.org/10.1071/MF21291.
Carew, M, A Hoffman, C Kellar, C J Walsh, K Stevenson, and R Coleman.
2019. “Integrating DNA Metabarcoding into Melbourne Water’s Macroinvertebrate Monitoring
Program.” Report to {{Melbourne Water}}. School of
Biosciences, The University of Melbourne.
Chessman, B C. 2003. “New Sensitivity Grades for Australian River
Macroinvertebrates.” Journal Article. Marine and Freshwater
Research 54 (2): 95–103.
Coleman, R. 2006. “Ecological and Physical Responses to Large
Woody Debris Reintroduction in the Little
Yarra River, Victoria,
Australia.” Master’s thesis, Melbourne: Monash
University.
Coleman, R, and V Pettigrove. 1998a. Waterway Assessment in the
Yarra Catchment: The Health of the Andersons
and Jumping Creeks. Melbourne: Waterways;
Drainage, Melbourne Water Corporation.
———. 1998b. Waterway Assessment in the Yarra Catchment:
The Health of the Watts River. Melbourne:
Waterways; Drainage, Melbourne Water Corporation.
———. 2001. Waterway Assessment in the Western
Port Catchment: The Health of the Lang
Lang River. Melbourne: Waterways Group,
Melbourne Water Corporation.
Crowther, D, G Canale, and P Papas. 2001. “Melbourne
Water Biological Monitoring Program 2000-2001.”
Melbourne: Arthur Rylah Institute for Environmental Research, Department
of Sustainability; Environment.
Crowther, D, P Papas, and S MacKay. 2003. “Melbourne
Water Biological Monitoring Program 2002-2003.”
Melbourne: Arthur Rylah Institute for Environmental Research, Department
of Sustainability; Environment.
Elbrecht, V., and F. Leese. 2017. “Validation and Development of
COI Metabarcoding Primers for Freshwater Macroinvertebrate
Bioassessment.” Frontiers in Environmental Science 5. https://doi.org/10.3389/fenvs.2017.00011.
EPA Victoria. 2004. “Biological Objectives for Rivers and
Streams–Ecosystem Protection.” Report 793.2. Environment
Protection Authority Victoria.
Government of Victoria. 2001. “Variation to State
Environment Protection Policy
(Waters of Victoria): Insertion of
Schedule F8, Waters of the
Western Port and
Catchment.” Report. The Craftsman Press. http://www.craftpress.com.au/gazette/Gazettes1999/GG1999S089.pdf.
———. 2004. “State Environment Protection
Policy (Waters of Victoria)
23/2/1988, No. S13 Gazette
26/2/1988, as Varied to 2004.” https://www.epa.vic.gov.au/about-us/legislation/water-legislation/~/media/Files/About%20us/Legislation/Water/Consolidated%20SEPP%20Waters%20of%20Victoria%20PDF.pdf.
Grace Detailed-GIS Services. 2012. “Directly Connected
Imperviousness Compilation for Melbourne Water Selected
Catchments.” Report.
Hajibabaei, M., J. L. Spall, S. Shokralla, and S. Van Konynenburg. 2012.
“Assessing Biodiversity of a Freshwater Benthic Macroinvertebrate
Community Through Non-Destructive Environmental Barcoding of DNA from
Preservative Ethanol.” BMC Ecology 12 (1): 28. https://doi.org/10.1186/1472-6785-12-28.
Hardwick, R. 1998. “Waterway Assessment in the
Western Port Catchment: The Environmental
Health of Western Port Peninsula
Streams.” {AWT} {Report} {No}. 267/98 for {Waterways} and
{Drainage}, {Melbourne} {Water}. Melbourne: Australian Water
Technologies.
Hardwick, R, and K Lewin. 1999. “Autumn 1996-Spring
1997 Macroinvertebrate and Sediment Toxicants Monitoring
Program.” {AWT} report {No}. 274/99. Melbourne, Australia:
Australian Water Technologies.
Hardwick, R, and K Waller. 1999a. “1998-1999
Melbourne Water Monitoring Program.”
{AWT} report {No}. 327/99. Melbourne, Australia: Australian Water
Technologies.
———. 1999b. “Plenty River Ecological
Assessment.” {AWT} report {No}. 309/99. Melbourne, Australia:
Australian Water Technologies.
Hebert, P. D. N., A. Cywinska, S. L. Ball, and J. R. DeWaard. 2003.
“Biological Identifications Through DNA Barcodes.”
Proceedings of the Royal Society of London. Series B: Biological
Sciences 270 (1512): 313–21.
Hebert, P. D. N., E. H. Penton, J. M. Burns, D. H. Janzen, and W.
Hallwachs. 2004. “Ten Species in One: DNA Barcoding Reveals
Cryptic Species in the Neotropical Skipper Butterfly Astraptes
Fulgerator.” Proceedings of the National Academy of
Sciences 101 (41): 14812–17. https://doi.org/10.1073/pnas.0406166101.
Kunapo, J, C J Walsh, and M J Sammonds. 2019. “Melbourne Water
Stream Network. Version 1.0.” Report. School of Ecosystem; Forest
Sciences, The University of Melbourne.
Leray, M., J. Y. Yang, C. P. Meyer, S. C. Mills, N. Agudelo, V. Ranwez,
J. T. Boehm, and R. J. Machida. 2013. “A New Versatile Primer Set
Targeting a Short Fragment of the Mitochondrial COI Region for
Metabarcoding Metazoan Diversity: Application for Characterizing Coral
Reef Fish Gut Contents.” Frontiers in Zoology 10 (1):
34. https://doi.org/10.1186/1742-9994-10-34.
McCasker, N. 2002. “Macroinvertebrate Colonization of
Re-Introduced Large Woody Debris in the Little Yarra River.”
Thesis.
Müller, Kirill, Hadley Wickham, David A. James, and Seth Falcon. 2022.
RSQLite: SQLite Interface for r. https://CRAN.R-project.org/package=RSQLite.
Norris, R H, and K R Norris. 1995. “The Need for Biological
Assessment of Water Quality: Australian
Perspective.” Journal Article. Australian Journal of
Ecology 20 (1): 1–6.
Papas, P, D Crowther, M Nicol, G Canale, S McKay, and S Schreiber. 2002.
“Melbourne Water Biological Monitoring Program -
2001-2002.” Melbourne, Australia: Arthur Rylah Institute for
Environmental Research, Department of Natural Resources; Environment,
Victoria.
Papas, P, M Nicol, and D Crowther. 2000. “Melbourne
Water Biological Monitoring Program - 1999/2000.”
Melbourne, Australia: Arthur Rylah Institute for Environmental Research,
Department of Natural Resources; Environment, Victoria.
Pettigrove, V, and R Coleman. 1999. “Waterway Assessment in the
Dandenong Valley: The Health of
Corhanwarrabul, Monbulk and Ferny
Creeks.” Melbourne: Melbourne Water Corporation.
R Core Team. 2023. R: A Language and Environment for Statistical
Computing. Vienna, Austria: R Foundation for Statistical Computing.
https://www.R-project.org/.
Ratnasingham, S., and P. D. N. Hebert. 2013. “A DNA-Based Registry
for All Animal Species: The Barcode Index Number (BIN) System.”
Edited by Diego Fontaneto. PLoS ONE 8 (7): e66213. https://doi.org/10.1371/journal.pone.0066213.
Ratnasingham, S., C. Wei, D. Chan, J. Agda, J. Agda, L.
Ballesteros-Mejia, H. A. Boutou, et al. 2024. “BOLD V4: A
Centralized Bioinformatics Platform for DNA-Based Biodiversity
Data.” In DNA Barcoding: Methods and Protocols, 403–41.
Springer.
Smith, T, D Vertessy, and R Hardwick. 1997.
“StreamWatch Biological
Monitoring Program. Annual
Report 1996.” Melbourne: Melbourne Water
Corporation.
Victoria, Government of. 1999. “Variation to State Environment
Protection Policy (Waters of Victoria): Insertion of Schedule F7, Waters
of the Yarra Catchment.” Report No. S89. The Craftsman Press. http://www.craftpress.com.au/gazette/Gazettes1999/GG1999S089.pdf.
Walsh, C J. 2004a. “Impacts of Stormwater Treatment Wetlands on
Stream Macroinvertebrates: A Study of Four Wetlands Constructed by
Melbourne Water on Streams in Eastern
Melbourne.” Report for {Melbourne} {Water}.
Melbourne: Water Studies Centre, Monash University. https://urbanstreams.net/lsc/Docs/NHT_wetland_bugs_Final_report.pdf.
———. 2004b. “Protection of in-Stream Biota from Urban Impacts:
Minimise Catchment Imperviousness or Improve Drainage Design?”
Marine and Freshwater Research 55 (3): 317–26.
———. 2006. “Biological Indicators of Stream Health Using
Macroinvertebrate Assemblage Composition: A Comparison of Sensitivity to
an Urban Gradient.” Marine and Freshwater Research 57
(1): 37–47.
———. 2018. “Melbourne Water Macroinvertebrate Spring 2018
Monitoring Program Proposal.” Report. School of Ecosystem; Forest
Sciences, The University of Melbourne. https://urbanstreams.net/resources/MWSpring2018BugMonitoringProposal.pdf.
———. 2023a. “Melbourne Water Stream Network. Version 1.3.
Melbourne Water Research Practice Partnership Technical Report
19.4d.” Report. School of Agriculture, Food and Ecosystem
Sciences, The University of Melbourne. https://tools.thewerg.unimelb.edu.au/mwstr_manual/.
———. 2023b. “LUMaR: A Sensitive Macroinvertebrate Index of Stream
Condition Combining Observed-to-Expected Ratios and Sensitivity
Weightings.” OSF Preprints. https://doi.org/10.31219/osf.io/392kv.
Walsh, C J, C Bloink, and G Hehir. 2014. “Preliminary Report on
Macroinvertebrate Assemblages of Pyrites and Goodmans Creek in Relation
to the Management of Merrimu Reservoir: Patterns in 2013 in Early Stages
of Flow Manipulation.” {Melbourne} {Waterway}
{Research}-{Practice} {Partnership} Technical Report 14-8. Melbourne:
Waterway Ecosystem Research
Group, The University of
Melbourne. https://urbanstreams.net/lsc/Docs/NHT_wetland_bugs_Final_report.pdf.
Walsh, C J, and P F Breen. 2001. “A Biological Approach to
Assessing the Potential Success of Habitat Restoration in Urban
Streams.” Verhandlungen Internationale Vereinigung Für
Theoretische Und Angewandte Limnologie 27 (6): 3654–58.
Walsh, C J, M J Burns, T D Fletcher, D G Bos, J Kunapo, P Poelsma, and M
Imberger. 2022. “Linking Stormwater Control Performance to Stream
Ecosystem Outcomes: Incorporating a Performance Metric into Effective
Imperviousness.” PLOS Water 1 (2): e0000004. https://doi.org/10.1371/journal.pwat.0000004.
Walsh, C J, Y E Chee, N Bond, and Coleman R. 2019. “Assessing and
Understanding in-Stream Habitat Suitability for Invertebrate Families,
Fish Species and Platypus of the Melbourne Region with the
Melbstreambiota Package (Version 0.1.2).” https://osf.io/v2tda.
Walsh, C J, T D Fletcher, D G Bos, and S J Imberger. 2015.
“Restoring a Stream Through Retention of Urban Stormwater Runoff:
A Catchment-Scale Experiment in a Social-Ecological System.”
Journal Article. Freshwater Science 34 (3): 1161–68. http://www.jstor.org/stable/pdfplus/10.1086/682422.pdf.
Walsh, C J, M Imberger, M J Burns, D G Bos, and T D Fletcher. 2022.
“Dispersed Urban-Stormwater Control Improved
Stream Water Quality in a Catchment-Scale
Experiment.” Water Resources Research 58 (12). https://doi.org/10.1029/2022WR032041.
Walsh, C J, and N McCasker. 2002. “Melbourne Water
Macroinvertebrate Database 1994 – 2002. A Report on Its Compilation,
with Recommendations for Its Use and for Future Biological
Monitoring.” Report. CRC for Freshwater Ecology.
Walsh, C J, M J Sammonds, and J Kunapo. 2020. “The Melbourne
Water Macroinvertebrate Database.” Melbourne {{Waterway
Research-Practice Partnership Report}} 20.1. School of Ecosystem
and Forest Sciences, The University of Melbourne, Melbourne.
Walsh, C J, A K Sharpe, P F. Breen, and J A Sonneman. 2001.
“Effects of Urbanization on Streams of the Melbourne
Region, Victoria, Australia. I.
Benthic Macroinvertebrate Communities.”
Freshwater Biology 46 (4): 535–51.
Walsh, C J, K A Waller, J Gehling, and R Mac Nally. 2007.
“Riverine Invertebrate Assemblages Are Degraded More by Catchment
Urbanization Than by Riparian Deforestation.” Freshwater
Biology 52: 574–87. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.631.6082&rep=rep1&type=pdf.
Walsh, C J, J A Webb, Gwinn D C, and P F Breen. 2023. “Constructed
Rock Riffles Increase Habitat Heterogeneity but Not Biodiversity in
Streams Constrained by Urban Impacts.” Ecosphere, in
review.
Water Technology, GHD, and Streamline Research. 2014. “Capital
Works Monitoring Program.” Linked site summary tool. Melbourne,
Australia: Melbourne Water.
White, J Y. 2018. “The Effects of Urban Land Use, Riparian Forest
Cover, and Instream Habitat Complexity on Macroinvertebrate
Assemblages.” {PhD} {Thesis}, Melbourne Australia: The University
of Melbourne.
White, J Y, and C J Walsh. 2020. “Catchment-Scale Urbanization
Diminishes Effects of Habitat Complexity on Instream Macroinvertebrate
Assemblages.” Journal Article. Ecological Applications.
WSL. 2004. “Melbourne Water Biological
Monitoring Program–2003/2004.” Report for {Melbourne} {Water}
{Catchment} and {Waterways}. Melbourne: WSL consultants Pty Ltd.
———. 2005. “Melbourne Water Biological
Monitoring Program–2004/2005.” Report for {Melbourne} {Water}
{Catchment} and {Waterways}. Melbourne: WSL consultants Pty Ltd.
Yu, D. W., Y. Ji, B. C. Emerson, X. Wang, C. Ye, C. Yang, and Z. Ding.
2012. “Biodiversity Soup: Metabarcoding of Arthropods for Rapid
Biodiversity Assessment and Biomonitoring.” Methods in
Ecology and Evolution 3 (4): 613–23. https://doi.org/10.1111/j.2041-210X.2012.00198.x.