Marine and Freshwater Research Marine and Freshwater Research Society
Advances in the aquatic sciences
REVIEW

A DNA barcode database of Australia’s freshwater macroinvertebrate fauna

M. E. Carew A , S. J. Nichols B , J. Batovska C , R. St Clair D G , N. P. Murphy E , M. J. Blacket C and M. E. Shackleton F H
+ Author Affiliations
- Author Affiliations

A School of BioSciences, The University of Melbourne, Parkville, Vic. 3010, Australia.

B Institute for Applied Ecology, University of Canberra, Bruce, ACT 2601, Australia.

C Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Vic. 3083, Australia.

D Environment Protection Authority, 200 Victoria Street, Carlton, Vic. 3053, Australia.

E Department of Ecology, Environment, and Evolution, La Trobe University, Bundoora, Vic. 3086, Australia.

F Murray–Darling Freshwater Research Centre, La Trobe University, 133 McKoy Street, Wodonga, Vic. 3690, Australia.

G Present address: Museums Victoria, GPO Box 666, Melbourne, Vic. 3001, Australia.

H Corresponding author. Email: m.shackleton@latrobe.edu.au

Marine and Freshwater Research 68(10) 1788-1802 https://doi.org/10.1071/MF16304
Submitted: 7 September 2016  Accepted: 6 January 2017   Published: 30 March 2017

Abstract

Macroinvertebrates are widely used for monitoring freshwater ecosystems. In most monitoring programs, identifications take substantial time and expense. Methods that improve the speed, accuracy and cost-effectiveness of macroinvertebrate identification would benefit such programs. Increasingly, DNA barcodes are being used to provide accurate species-level identifications and have the potential to change how macroinvertebrates are routinely identified. Herein we discuss the need for DNA barcodes of freshwater macroinvertebrates with particular reference to Australia. We examine the use of DNA barcodes for species identification and compare DNA barcoding efforts of macroinvertebrates from Australia with those globally. We consider the role of high-throughput sequencing of DNA barcodes in freshwater bioassessment and its potential use in biosurveillance. Finally, we outline a strategy for developing a comprehensive national DNA barcode database for Australian freshwater macroinvertebrates and present the initial efforts in creating this database.

Additional keywords: Barcode of Life Data System, BOLD, biological monitoring, biosecurity, DNA sequences, national database.


References

Alexander, L. C., Delion, M., Hawthorne, D. J., Lamp, W. O., and Funk, D. H. (2009). Mitochondrial lineages and DNA barcoding of closely related species in the mayfly genus Ephemerella (Ephemeroptera: Ephemerellidae). Journal of the North American Benthological Society 28, 584–595.
Mitochondrial lineages and DNA barcoding of closely related species in the mayfly genus Ephemerella (Ephemeroptera: Ephemerellidae).CrossRef |

Andújar, C., Arribas, P., Ruzicka, F., Crampton-Platt, A., Timmermans, M. J. T. N., and Vogler, A. P. (2015). Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics. Molecular Ecology 24, 3603–3617.
Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics.CrossRef |

Australian and New Zealand Environment and Conservation Council & Agriculture and Resource Management Council of Australia and New Zealand (2000). ‘Australian and New Zealand Guidelines for Fresh and Marine Water Quality.’ (Australia Water Association: Artarmon, NSW, Australia.)

Baird, D. J., and Hajibabaei, M. (2012). Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Molecular Ecology 21, 2039–2044.
Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing.CrossRef |

Baird, D. J., Pascoe, T. J., Zhou, X., and Hajibabaei, M. (2011). Building freshwater macroinvertebrate DNA-barcode libraries from reference collection material: formalin preservation vs specimen age. Journal of the North American Benthological Society 30, 125–130.
Building freshwater macroinvertebrate DNA-barcode libraries from reference collection material: formalin preservation vs specimen age.CrossRef |

Baker, A. M., Hughes, J. M., Dean, J. C., and Bunn, S. E. (2004). Mitochondrial DNA reveals phylogenetic structuring and cryptic diversity in Australian freshwater macroinvertebrate assemblages. Marine and Freshwater Research 55, 629–640.
Mitochondrial DNA reveals phylogenetic structuring and cryptic diversity in Australian freshwater macroinvertebrate assemblages.CrossRef | 1:CAS:528:DC%2BD2cXnsleitL8%3D&md5=7de739ac41f6f248805c669249a6cf46CAS |

Balian, E. V., Segers, H., Lévêque, C., and Martens, K. (2008). The freshwater animal diversity assessment: an overview of the results. Hydrobiologia 595, 627–637.
The freshwater animal diversity assessment: an overview of the results.CrossRef |

Ball, S. L., Hebert, P. D. N., Burian, S. K., and Webb, J. M. (2005). Biological identifications of mayflies (Ephemeroptera) using DNA barcoding. Journal of the North American Benthological Society 24, 508–524.
Biological identifications of mayflies (Ephemeroptera) using DNA barcoding.CrossRef |

Barbour, M. T., Gerritsen, J., Snyder, B. D., and Stribling, J. B. (1999). Bioassessment protocols for use in streams and wadeable rivers: periphyton, benthic macroinvertebrates and fish, second edition. EPA 841-B-99-002. (US Environmental Protection Agency, Office of Water: Washington, DC, USA.) Available at http://www.waterboards.ca.gov/water_issues/programs/tmdl/docs/303d_policydocs/161.pdf [Verified 3 February 2017].

Batovska, J., Blacket, M. J., Brown, K., and Lynch, S. E. (2016). Molecular identification of mosquitoes (Diptera: Culicidae) in southeastern Australia. Ecology and Evolution 6, 3001–3011.
Molecular identification of mosquitoes (Diptera: Culicidae) in southeastern Australia.CrossRef |

Bellis, G. A., Gopurenko, D., Cookson, B., Postle, A. C., Halling, L., Harris, N., Yanase, T., and Mitchell, A. (2015). Identification of incursions of Culicoides Latreille species (Diptera: Ceratopogonidae) in Australasia using morphological techniques and DNA barcoding. Australian Entomologist 54, 332–338.
Identification of incursions of Culicoides Latreille species (Diptera: Ceratopogonidae) in Australasia using morphological techniques and DNA barcoding.CrossRef |

Bennett, B. C., and Balick, M. J. (2014). Does the name really matter? The importance of botanical nomenclature and plant taxonomy in biomedical research. Journal of Ethnopharmacology 152, 387–392.
Does the name really matter? The importance of botanical nomenclature and plant taxonomy in biomedical research.CrossRef |

Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Sayers, E. W. (2009). GenBank. Nucleic Acids Research 37, D26–D31.
GenBank.CrossRef | 1:CAS:528:DC%2BD1cXhsFejtLzF&md5=0d290ba92a093b1d06e08a7ff99e3adaCAS |

Blomberg, S., Theodore Garland, J., and Ives, A. (2003). Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57, 717–745.
Testing for phylogenetic signal in comparative data: behavioral traits are more labile.CrossRef |

Bonada, N., Prat, N., Resh, V. H., and Statzner, B. (2006). Developments in aquatic insect biomonitoring: a comparative analysis of recent approaches. Annual Review of Entomology 51, 495–523.
Developments in aquatic insect biomonitoring: a comparative analysis of recent approaches.CrossRef | 1:CAS:528:DC%2BD28XptlCmtQ%3D%3D&md5=df34607b963eace8847dd360d7423718CAS |

Boonsoong, B., Sangpradub, N., and Barbour, M. T. (2009). Development of rapid bioassessment approaches using benthic macroinvertebrates for Thai streams. Environmental Monitoring and Assessment 155, 129–147.
Development of rapid bioassessment approaches using benthic macroinvertebrates for Thai streams.CrossRef | 1:CAS:528:DC%2BD1MXotlOrur4%3D&md5=f0cd2a2833dbb8494fa14ceafc59fbbeCAS |

Bortolus, A. (2008). Error cascades in the biological sciences: the unwanted consequences of using bad taxonomy in ecology. BioOne 37, 114–118.

Brandon-Mong, G. J., Gan, H. M., Sing, K. W., Lee, P. S., Lim, P. E., and Wilson, J. J. (2015). DNA metabarcoding of insects and allies: an evaluation of primers and pipelines. Bulletin of Entomological Research 105, 717–727.
DNA metabarcoding of insects and allies: an evaluation of primers and pipelines.CrossRef | 1:CAS:528:DC%2BC2MXhvVSlsbrN&md5=1bd32f2e9d5dce415ab2901c650fba2cCAS |

Bridge, P. D., Roberts, P. J., Spooner, B. M., and Panchal, G. (2003). On the unreliability of published DNA sequences. New Phytologist 160, 43–48.
On the unreliability of published DNA sequences.CrossRef | 1:CAS:528:DC%2BD3sXot1WitLc%3D&md5=308456c99f4aba36560e6d4f1e6ddc70CAS |

Buchwalter, D. B., Cain, D. J., Martin, C. A., Xie, L., Luoma, S. N., and Garland, T. (2008). Aquatic insect ecophysiological traits reveal phylogenetically based differences in dissolved cadmium susceptibility. Proceedings of the National Academy of Sciences of the United States of America 105, 8321–8326.
Aquatic insect ecophysiological traits reveal phylogenetically based differences in dissolved cadmium susceptibility.CrossRef | 1:CAS:528:DC%2BD1cXnvVKktLc%3D&md5=2541f6e5417fc8804613fcd74032cac5CAS |

Carew, M. E., and Hoffmann, A. A. (2015). Delineating closely related species with DNA barcodes for routine biological monitoring. Freshwater Biology 60, 1545–1560.
Delineating closely related species with DNA barcodes for routine biological monitoring.CrossRef | 1:CAS:528:DC%2BC2MXht1WrsLfP&md5=5aa2b085ddb79cd2ea92e2049aea5f6fCAS |

Carew, M. E., Pettigrove, V., Cox, R. L., and Hoffmann, A. A. (2007a). DNA identification of urban Tanytarsini chironomids (Diptera: Chironomidae). Journal of the North American Benthological Society 24, 586–599.

Carew, M. E., Pettigrove, V., Cox, R. L., and Hoffmann, A. A. (2007b). The response of Chironomidae to sediment pollution and other environmental characteristics in urban wetlands. Freshwater Biology 52, 2444–2462.
The response of Chironomidae to sediment pollution and other environmental characteristics in urban wetlands.CrossRef | 1:CAS:528:DC%2BD1cXls1SmtQ%3D%3D&md5=2d3fbe73bbd01eab4726b6ec105bef1cCAS |

Carew, M. E., Marshall, S. E., and Hoffmann, A. A. (2011a). A combination of molecular and morphological approaches resolves species in the taxonomically difficult genus Procladius Skuse (Diptera: Chironomidae) despite high intra-specific morphological variation. Bulletin of Entomological Research 101, 505–519.
A combination of molecular and morphological approaches resolves species in the taxonomically difficult genus Procladius Skuse (Diptera: Chironomidae) despite high intra-specific morphological variation.CrossRef | 1:STN:280:DC%2BC3MfgvVGksA%3D%3D&md5=2f818e819fddb54536d74ae69feab7f5CAS |

Carew, M. E., Miller, A. D., and Hoffmann, A. A. (2011b). Phylogenetic signals and ecotoxicological responses: potential implications for aquatic biomonitoring. Ecotoxicology (London, England) 20, 595–606.
Phylogenetic signals and ecotoxicological responses: potential implications for aquatic biomonitoring.CrossRef | 1:CAS:528:DC%2BC3MXltFGntLw%3D&md5=a6f5209564f82327b8e8aea105c53b7fCAS |

Carew, M. E., Pettigrove, V. J., Metzeling, L., and Hoffmann, A. A. (2013). Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species. Frontiers in Zoology 10, 45.
Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species.CrossRef |

Castalanelli, M. A., Severtson, D. L., Brumley, C. J., Szito, A., Foottit, R. G., Grimm, M., Munyard, K., and Groth, D. M. (2010). A rapid non-destructive DNA extraction method for insects and other arthropods. Journal of Asia-Pacific Entomology 13, 243–248.
A rapid non-destructive DNA extraction method for insects and other arthropods.CrossRef | 1:CAS:528:DC%2BC3cXhsFelsrvJ&md5=dd386bcae27593827113ad70ffb16701CAS |

Chessman, B. 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, 122–129.
Rapid assessment of rivers using macroinvertebrates: a procedure based on habitat-specific sampling, family level identification and a biotic index.CrossRef |

Chessman, B. C., Growns, J. E., and Kotlash, A. R. (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, 159–172.
Objective derivation of macroinvertebrate family sensitivity grade numbers for the SIGNAL biotic index: application to the Hunter River system, New South Wales.CrossRef |

Chessman, B., Williams, S., and Besley, C. (2007). Bioassessment of streams with macroinvertebrates: effect of sampled habitat and taxonomic resolution. Journal of the North American Benthological Society 26, 546–565.
Bioassessment of streams with macroinvertebrates: effect of sampled habitat and taxonomic resolution.CrossRef |

Clarke, L. J., Soubrier, J., Weyrich, L. S., and Cooper, A. (2014). Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias. Molecular Ecology Resources 14, 1160–1170.
Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias.CrossRef | 1:CAS:528:DC%2BC2cXhslCqsbfK&md5=778082dded4422fbac46e2d0300f0b05CAS |

Cook, R., and Hawking, J. (2014). Capturing the legacy of the Murray and Mitta Mitta biological monitoring program. (The Murray–Darling Basin Authority: Wodonga, Vic., Australia.) Available at http://www.mdba.gov.au/publications/independent-reports/capturing-legacy-murray-mitta-mitta-biological-macroinvertebrate [Verified 6 February 2017].

Cook, B. D., Baker, A., Page, T., Grant, S. C., Fawcett, J., Hurwood, D., and Hughes, J. (2006). Biogeographic history of an Australian freshwater shrimp, Paratya australiensis (Atyidae): the role life history transition in phylogeographic diversification. Molecular Ecology 15, 1083–1093.
Biogeographic history of an Australian freshwater shrimp, Paratya australiensis (Atyidae): the role life history transition in phylogeographic diversification.CrossRef | 1:CAS:528:DC%2BD28XjslWms74%3D&md5=0b461c67e42f7d0c7c70a67ebe76e258CAS |

Dafforn, K. A., Johnston, E. L., Ferguson, A., Humphrey, C. L., Monk, W., Nichols, S. J., Simpson, S. L., Tulbure, M. G., and Baird, D. J. (2016). Big data opportunities and challenges for assessing multiple stressors across scales in aquatic ecosystems. Marine and Freshwater Research 67, 393–413.
Big data opportunities and challenges for assessing multiple stressors across scales in aquatic ecosystems.CrossRef |

Dai, Q. Y., Gao, Q., Wu, C. S., Chesters, D., Zhu, C. D., and Zhang, A. B. (2012). Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers. PLoS One 7, e32544.
Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.CrossRef | 1:CAS:528:DC%2BC38XlsFyqt7s%3D&md5=330f0c6bbd93c295a71e321c54284361CAS |

Davies, P. E. (2000). Development of a national river bioassessment system (AUSRIVAS) in Australia. In ‘Assessing the Biological Quality of Fresh Waters: RIVPACS and Other Techniques’. (Eds J. F. Wright, D. W. Sutcliffe and M. T. Furse.) pp. 113–124. (Freshwater Biological Association: Ambleside, UK.)

Dawson, M. N., Raskoff, K. A., and Jacobs, D. K. (1998). Field preservation of marine invertebrate tissue for DNA analyses. Molecular Marine Biology and Biotechnology 7, 145–152.
| 1:CAS:528:DyaK1cXjslCrsr0%3D&md5=9c3f5738f2e40dd566a8b94608ac496bCAS |

de Moraes, G. J. (1987). Importance of taxonomy in biological control. International Journal of Tropical Insect Science 8, 841–844.
Importance of taxonomy in biological control.CrossRef |

Debach, P. (1960). The importance of taxonomy to biological control as illustrated by the cryptic history of Aphytis holoxanthus n. sp. (Hymenoptera: Aphelinidae), a parasite of Chrysomphalus aonidum, and Aphytis coheni n. sp., a parasite of Aonidiella aurantii. Annals of the Entomological Society of America 53, 701–705.
The importance of taxonomy to biological control as illustrated by the cryptic history of Aphytis holoxanthus n. sp. (Hymenoptera: Aphelinidae), a parasite of Chrysomphalus aonidum, and Aphytis coheni n. sp., a parasite of Aonidiella aurantii.CrossRef |

DeSalle, R., Egan, M. G., and Siddall, M. (2005). The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philosophical Transactions of the Royal Society of London – B. Biological Sciences 360, 1905–1916.
The unholy trinity: taxonomy, species delimitation and DNA barcoding.CrossRef | 1:CAS:528:DC%2BD2MXhtlSjsrnE&md5=7de30c37698fe48beedf27f748456bcaCAS |

DeWalt, R. E. (2011). DNA barcoding: a taxonomic point of view. Journal of the North American Benthological Society 30, 174–181.
DNA barcoding: a taxonomic point of view.CrossRef |

Dickens, C. W., and Graham, P. (2002). The South African scoring system (SASS) version 5 rapid bioassessment method for rivers. African Journal of Aquatic Science 27, 1–10.
The South African scoring system (SASS) version 5 rapid bioassessment method for rivers.CrossRef |

Ekrem, T., Willassen, E., and Stur, E. (2007). A comprehensive DNA sequence library is essential for identification with DNA barcodes. Molecular Phylogenetics and Evolution 43, 530–542.
A comprehensive DNA sequence library is essential for identification with DNA barcodes.CrossRef | 1:CAS:528:DC%2BD2sXlt1altrk%3D&md5=423682b4b8e180291b3ad6cd56fcce97CAS |

Elbrecht, V., and Leese, F. (2015). Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass–sequence relationships with an innovative metabarcoding protocol. PLoS One 10, e0130324.
Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass–sequence relationships with an innovative metabarcoding protocol.CrossRef |

Elias, M., Hill, R. I., Willmott, K. R., Dasmahapatra, K. K., Brower, A. V. Z., Malllet, J., and Jiggins, C. D. (2007). Limited performance of DNA barcoding in a diverse community of tropical butterflies. Proceedings of the Royal Society – B. Biological Sciences 274, 2881–2889.
Limited performance of DNA barcoding in a diverse community of tropical butterflies.CrossRef | 1:CAS:528:DC%2BD2sXhtlOhtr%2FF&md5=0b180a2c495a29a3f38b895003292b69CAS |

Feng, Y., Zhang, Y., Ying, C., Wang, D., and Du, C. (2015). Nanopore-based fourth-generation DNA sequencing technology. Genomics, Proteomics & Bioinformatics 13, 4–16.
Nanopore-based fourth-generation DNA sequencing technology.CrossRef |

Ferri, E., Barbuto, M., Bain, O., Galimberti, A., Uni, S., Guerrero, R., Ferté, H., Bandi, C., Martin, C., and Casiraghi, M. (2009). Integrated taxonomy: traditional approach and DNA barcoding for the identification of filarioid worms and related parasites (Nematoda). Frontiers in Zoology 6, 1–12.
Integrated taxonomy: traditional approach and DNA barcoding for the identification of filarioid worms and related parasites (Nematoda).CrossRef | 1:CAS:528:DC%2BD1MXntFWltr0%3D&md5=8a1598a862007b819ad2de70517cc9e6CAS |

Ferro, M. L., and Park, J.-S. (2013). Effect of propylene glycol concentration on mid-term DNA preservation of Coleoptera. Coleopterists Bulletin 67, 581–586.
Effect of propylene glycol concentration on mid-term DNA preservation of Coleoptera.CrossRef |

Ficetola, G. F., Miaud, C., Pompanon, F., and Taberlet, P. (2008). Species detection using environmental DNA from water samples. Biology Letters 4, 423–425.
Species detection using environmental DNA from water samples.CrossRef |

Foote, A. D., Thomsen, P. F., Sveegaard, S., Wahlberg, M., Kielgast, J., Kyhn, L. A., Salling, A. B., Galatius, A., Orlando, L., and Gilbert, M. T. P. (2012). Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS One 7, e41781.
Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals.CrossRef | 1:CAS:528:DC%2BC38Xht12htLzI&md5=5257844d7ce057dd512f139c8102521eCAS |

Fujisawa, T., Vogler, A. P., and Barraclough, T. G. (2015). Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles. Proceedings of the Royal Society – B. Biological Sciences 282, 1–9.

Gibson, J., Shokralla, S., Porter, T. M., King, I., van Konynenburg, S., Janzen, D. H., Hallwachs, W., and Hajibabaei, M. (2014). Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. Proceedings of the National Academy of Sciences of the United States of America 111, 8007–8012.
Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics.CrossRef | 1:CAS:528:DC%2BC2cXnsFWlt7w%3D&md5=790f0c7040af751fe291c65339d04915CAS |

Gibson, J. F., Shokralla, S., Curry, C., Baird, D. J., Monk, W. A., King, I., and Hajibabaei, M. (2015). Large-scale biomonitoring of remote and threatened ecosystems via high-throughput sequencing. PLoS One 10, e0138432.
Large-scale biomonitoring of remote and threatened ecosystems via high-throughput sequencing.CrossRef |

Gwiazdowski, R. A., Foottit, R. G., Maw, H. E., and Hebert, P. D. (2015). The Hemiptera (Insecta) of Canada: constructing a reference library of DNA barcodes. PLoS One 10, e0125635.
The Hemiptera (Insecta) of Canada: constructing a reference library of DNA barcodes.CrossRef |

Haase, P., Pauls, S. U., Schindehutte, K., and Sundermann, A. (2010). First audit of macroinvertebrate samples from an EU Water Framework Directive monitoring program: human error greatly lowers precision of assessment results. Journal of the North American Benthological Society 29, 1279–1291.
First audit of macroinvertebrate samples from an EU Water Framework Directive monitoring program: human error greatly lowers precision of assessment results.CrossRef |

Hajibabaei, M., DeWaard, J. R., Ivanova, N. V., Ratnasingham, S., Dooh, R. T., Kirk, S. L., Mackie, P. M., and Hebert, P. D. N. (2005). Critical factors for assembling a high volume of DNA barcodes. Philosophical Transactions of the Royal Society of London – B. Biological Sciences 360, 1959–1967.
Critical factors for assembling a high volume of DNA barcodes.CrossRef | 1:CAS:528:DC%2BD2MXhtlSjsrbE&md5=c18b097d98c12a075db5fe5ce64689e3CAS |

Hajibabaei, M., Shokralla, S., Zhou, X., Singer, G. A. C., and Baird, D. J. (2011). Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One 6, e17497.
Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos.CrossRef | 1:CAS:528:DC%2BC3MXltV2rt7c%3D&md5=8f8671568ac2a04dd343ecef1cad1298CAS |

Hajibabaei, M., Spall, J., Shokralla, S., and van Konynenburg, S. (2012). Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol. BMC Ecology 12, 28.
Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol.CrossRef | 1:CAS:528:DC%2BC3sXht1yrsb0%3D&md5=0d36c692e79fed50cc4618aeb6a4e413CAS |

Hebert, P. D. N., Cywinska, A., Ball, S. L., and deWaard, J. R. (2003a). Biological identification through DNA barcodes. Proceedings of the Royal Society of London – B. Biological Sciences 270, 313–321.
Biological identification through DNA barcodes.CrossRef | 1:CAS:528:DC%2BD3sXktVWiu7g%3D&md5=1587680ffcfb74f947272ac0c4689374CAS |

Hebert, P. D., Ratnasingham, S., and deWaard, J. R. (2003b). Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London – B. Biological Sciences 270, S96–S99.
Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species.CrossRef | 1:CAS:528:DC%2BD3sXns1Smsbo%3D&md5=6b30a5e3c729ecc7e14b489c0a1da25aCAS |

Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D. H., and Hallwachs, W. (2004). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences of the United States of America 101, 14812–14817.
Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator.CrossRef | 1:CAS:528:DC%2BD2cXovVyju7g%3D&md5=164a12f10767ba86c7b0e4901e31c146CAS |

Hebert, P. D. N., Zakharov, E. V., Prosser, S. W., Sones, J. E., McKeown, J. T., Mantle, B., and La Salle, J. (2013). A DNA ‘barcode blitz’: rapid digitization and sequencing of a natural history collection. PLoS One 8, e68535.
A DNA ‘barcode blitz’: rapid digitization and sequencing of a natural history collection.CrossRef | 1:CAS:528:DC%2BC3sXhtFymt7rE&md5=9a29c59618de0aebc99313039b89896bCAS |

Hernández-Triana, L. M., Prosser, S. W., Rodriguez-Perez, M. A., Chaverri, L. G., Hebert, P. D., and Gregory, T. R. (2014). Recovery of DNA barcodes from blackfly museum specimens (Diptera: Simuliidae) using primer sets that target a variety of sequence lengths. Molecular Ecology Resources 14, 508–518.
Recovery of DNA barcodes from blackfly museum specimens (Diptera: Simuliidae) using primer sets that target a variety of sequence lengths.CrossRef |

Hollingsworth, P. M., Forrest, L. L., Spouge, J. L., Hajibabaei, M., Ratnasingham, S., van der Bank, M., Chase, M. W., Cowan, R. S., Erickson, D. L., Fazekas, A. J., Graham, S. W., James, K. E., Kim, K.-J., Kress, W. J., Schneider, H., van AlphenStahl, J., Barrett, S. C. H., van den Berg, C., Bogarin, D., Burgess, K. S., Cameron, K. M., Carine, M., Chacón, J., Clark, A., Clarkson, J. J., Conrad, F., Devey, D. S., Ford, C. S., Hedderson, T. A. J., Hollingsworth, M. L., Husband, B. C., Kelly, L. J., Kesanakurti, P. R., Kim, J. S., Kim, Y.-D., Lahay, R., Lee, H.-L., Long, D. G., Madriñán, S., Maurin, O., Meusnier, I., Newmaster, S. G., Park, C.-W., Percy, D. M., Petersen, G., Richardson, J. E., Salazar, G. A., Savolainen, V., Seberg, O., Wilkinson, M. J., Yi, D.-K., and Little, D. P. (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America 106, 12794–12797.
A DNA barcode for land plants.CrossRef | 1:CAS:528:DC%2BD1MXhtVKlt77J&md5=9ef2eb4f9fadabe70f314a34283bed0dCAS |

Huber, J. T. (1998). The importance of voucher specimens, with practical guidelines for preserving specimens of the major invertebrate phyla for identification. Journal of Natural History 32, 367–385.
The importance of voucher specimens, with practical guidelines for preserving specimens of the major invertebrate phyla for identification.CrossRef |

Jackson, J. K., Battle, J. M., White, B. P., Pilgrim, E. M., Stein, E. D., Miller, P. E., and Sweeney, B. W. (2014). Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications. Freshwater Science 33, 312–324.
Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications.CrossRef |

Janda, J. M., and Abbott, S. L. (2002). Bacterial identification for publication: when is enough enough? Journal of Clinical Microbiology 40, 1887–1891.
Bacterial identification for publication: when is enough enough?CrossRef |

Jerde, C. L., Mahon, A. R., Chadderton, W. L., and Lodge, D. M. (2011). ‘Sight-unseen’ detection of rare aquatic species using environmental DNA. Conservation Letters 4, 150–157.
‘Sight-unseen’ detection of rare aquatic species using environmental DNA.CrossRef |

Jiang, F., Jin, Q., Liang, L., Zhang, A. B., and Li, Z. H. (2014). Existence of species complex largely reduced barcoding success for invasive species of Tephritidae: a case study in Bactrocera spp. Molecular Ecology Resources 14, 1114–1128.
Existence of species complex largely reduced barcoding success for invasive species of Tephritidae: a case study in Bactrocera spp.CrossRef | 1:CAS:528:DC%2BC2cXhslCqtr%2FM&md5=17035ebecd355b3a3e0b1102905e4809CAS |

Jones, J. I., Davy-Bowker, J., Murphy, J. F., and Pretty, J. L. (2010). Ecological monitoring and assessment of pollution in rivers. In ‘Ecology of Industrial Pollution’. (Eds L. C. Batty and K. B. Hallberg.) pp. 126–146. (Cambridge University Press: Cambridge, UK.)

Kaila, L., and Ståhls, G. (2006). DNA barcodes: evaluating the potential of COI to diffentiate closely related species of Elachista (Lepidoptera: Gelechioidea: Elachistidae) from Australia. Zootaxa 1170, 1–26.

Kermarrec, L., Franc, A., Rimet, F., Chaumeil, P., Frigerio, J. M., Humbert, J. F., and Bouchez, A. (2014). A next-generation sequencing approach to river biomonitoring using benthic diatoms. Freshwater Science 33, 349–363.
A next-generation sequencing approach to river biomonitoring using benthic diatoms.CrossRef |

Kim, S., Song, K. H., Ree, H. I., and Kim, W. (2012). A DNA barcode library for Korean Chironomidae (Insecta: Diptera) and indexes for defining barcode gap. Molecules and Cells 33, 9–17.
A DNA barcode library for Korean Chironomidae (Insecta: Diptera) and indexes for defining barcode gap.CrossRef | 1:CAS:528:DC%2BC38XhvVOhs7o%3D&md5=8cf307824512132281bb78bb5bf1107eCAS |

Kocher, A., Gantier, J. C., Gaborit, P., Zinger, L., Holota, H., Valiere, S., Dusfour, I., Girod, R., Banuls, A. L., and Murienne, J. (2017). Vector soup: high-throughput identification of Neotropical phlebotomine sand flies using metabarcoding. Molecular Ecology Resources 17, 172–182.
Vector soup: high-throughput identification of Neotropical phlebotomine sand flies using metabarcoding.CrossRef | 1:CAS:528:DC%2BC2sXislKqsL0%3D&md5=7dc89073fbcc8e622ccb2de132b1cf59CAS |

Krosch, M. N., and Cranston, P. S. (2012). Non-destructive DNA extraction from Chironomidae, including of fragile pupal exuviae, extends analysable collections and enhances vouchering. CHIRONOMUS Journal of Chironomidae Research 25, 22–27.

Lake, P. S., Bond, N., and Reich, P. (2007). Linking ecological theory with stream restoration. Freshwater Biology 52, 597–615.
Linking ecological theory with stream restoration.CrossRef |

Likens, G. E. (2010). ‘Lake Ecosystem Ecology: a Global Perspective.’ (Academic Press: Millbrook, NY, USA.)

Mächler, E., Deiner, K., Steinmann, P., and Altermatt, F. (2014). Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species. Freshwater Science 33, 1174–1183.
Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species.CrossRef |

Marchant, R., and Hehir, G. (2002). The use of AUSRIVAS predictive models to assess the response of lotic macroinvertebrates to dams in south-east Australia. Freshwater Biology 47, 1033–1050.
The use of AUSRIVAS predictive models to assess the response of lotic macroinvertebrates to dams in south-east Australia.CrossRef |

Marshall, J. C., Steward, A. L., and Harch, B. D. (2006). Taxonomic resolution and quantification of freshwater macroinvertebrate samples from an Australian dryland river: the benefits and costs of using species abundance data. Hydrobiologia 572, 171–194.
Taxonomic resolution and quantification of freshwater macroinvertebrate samples from an Australian dryland river: the benefits and costs of using species abundance data.CrossRef |

Masese, F. O., Omukoto, J. O., and Nyakeya, K. (2013). Biomonitoring as a prerequisite for sustainable water resources: a review of current status, opportunities and challenges to scaling up in East Africa. Ecohydrology and Hydrobiology 13, 173–191.
Biomonitoring as a prerequisite for sustainable water resources: a review of current status, opportunities and challenges to scaling up in East Africa.CrossRef |

Meier, R., Shiyang, K., Vaidya, G., and Ng, P. K. L. (2006). DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology 55, 715–728.
DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success.CrossRef |

Meier, R., Zhang, G., and Ali, F. (2008). The use of mean instead of smallest interspecific distances exaggerates the size of the ‘barcoding gap’ and leads to misidentification. Systematic Biology 57, 809–813.
The use of mean instead of smallest interspecific distances exaggerates the size of the ‘barcoding gap’ and leads to misidentification.CrossRef |

Metzeling, L. (2002). Australia-wide assessment of river health: Victorian bio-assessment report (final report). Monitoring River Health Initiative Technical Report Number 4. (Environment Australia: Canberra, ACT, Australia.) Available at http://www.environment.gov.au/water/publications/environmental/rivers/nrhp/vic.html [Verified 6 February 2017].

Meyer, C. P., and Paulay, G. (2005). DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 3, e422.
DNA barcoding: error rates based on comprehensive sampling.CrossRef |

Monaghan, M. T., Balke, M., Gregory, T. R., and Vogler, A. P. (2005). DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers. Philosophical Transactions of the Royal Society of London – B. Biological Sciences 360, 1925–1933.
DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers.CrossRef | 1:CAS:528:DC%2BD2MXhtlSjsrbN&md5=d6a4b55843a3d026110de6de29612534CAS |

Moreau, C. S., Wray, B. D., Czekanski-Moir, J. E., and Rubin, B. E. (2013). DNA preservation: a test of commonly used preservatives for insects. Invertebrate Systematics 27, 81–86.
DNA preservation: a test of commonly used preservatives for insects.CrossRef | 1:CAS:528:DC%2BC3sXktVOgs78%3D&md5=ccc060dd5d644c94d6a310a543d1e97aCAS |

Moritz, C., and Cicero, C. (2004). DNA barcoding: promise and pitfalls. PLoS Biology 2, e354.
DNA barcoding: promise and pitfalls.CrossRef |

Murphy, N. P., Adams, M., and Austin, A. D. (2009). Independent colonization and extensive cryptic speciation of freshwater amphipods in the isolated groundwater springs of Australia’s Great Artesian Basin. Molecular Ecology 18, 109–122.
| 1:CAS:528:DC%2BD1MXit1Grsr0%3D&md5=1045fc5f3b4d3ac17cd7f67acfd8adf9CAS |

Mynott, J. H. (2015). Mitochondrial DNA allows the association of life stages to facilitate species recognition and delimitation in Australian stoneflies (Plecoptera: Gripopterygidae: Newmanoperla). Invertebrate Systematics 29, 223–238.
Mitochondrial DNA allows the association of life stages to facilitate species recognition and delimitation in Australian stoneflies (Plecoptera: Gripopterygidae: Newmanoperla).CrossRef | 1:CAS:528:DC%2BC2MXhtVOktL%2FK&md5=66a53d2e6921bc38b01636a97b0e163aCAS |

Mynott, J. H., Webb, J. M., and Suter, P. J. (2011). Adult and larval associations of the alpine stonefly genus Riekoperla McLellan (Plecoptera: Gripopterygidae) using mitochondrial DNA. Invertebrate Systematics 25, 11–21.
Adult and larval associations of the alpine stonefly genus Riekoperla McLellan (Plecoptera: Gripopterygidae) using mitochondrial DNA.CrossRef |

Nichols, S. J., Barmuta, L. A., Chessman, B. C., Davies, P. E., Dyer, F. J., Harrison, E. T., Hawkins, C. P., Jones, I., Kefford, B. J., Linke, S., Marchant, R., Metzeling, L., Moon, K., Ogden, R., Peat, M., Reynoldson, T. B., and Thompson, R. M. (2016). The imperative need for nationally coordinated bioassessment of rivers and streams. Marine and Freshwater Research 68, 599–613.
The imperative need for nationally coordinated bioassessment of rivers and streams.CrossRef |

Nilsson, R. H., Ryberg, M., Kristiansson, E., Abarenkov, K., Larsson, K. H., and Kõljalg, U. (2006). Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS One 1, e59.
Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective.CrossRef |

Norris, R. H., Liston, P., Davies, N., Coysh, J., Dyer, F., Linke, S., Prosser, I., and Young, B. (2001). Snapshot of the Murray–Darling basin river condition. Murray–Darling Basin Commission, Canberra. Available at http://www.mdba.gov.au/sites/default/files/archived/mdbc-tlm-reports/455_Snapshot_of_the_MDB_river_condition_2001.pdf [Verified 6 February 2017].

Norris, R. H., Linke, S., Prosser, I., Young, W. J., Liston, P., Bauer, N., Sloane, N., Dyer, F., and Thoms, M. (2007). Very-broad-scale assessment of human impacts on river condition. Freshwater Biology 52, 959–976.
Very-broad-scale assessment of human impacts on river condition.CrossRef |

Oliver, P. M., Couper, P. J., and Pepper, M. (2014). Independent transitions between monsoonal and arid biomes revealed by systematic revison of a complex of Australian geckos (Diplodactylus; Diplodactylidae). PLoS One 9, e111895.
Independent transitions between monsoonal and arid biomes revealed by systematic revison of a complex of Australian geckos (Diplodactylus; Diplodactylidae).CrossRef |

Page, T. J., Choy, S. C., and Hughes, J. M. (2005). The taxonomic feedback loop: symbiosis of morphology and molecules. Biology Letters 1, 139–142.
The taxonomic feedback loop: symbiosis of morphology and molecules.CrossRef | 1:CAS:528:DC%2BD2MXpsVaqu74%3D&md5=791829b8713fd8906c21c0de42b9abe1CAS |

Pentinsaari, M., Hebert, P. D. N., and Mutanen, M. (2014). Barcoding beetles: a regional survey of 1872 species reveals high identification success and unusually deep interspecific divergences. PLoS One 9, e108651.
Barcoding beetles: a regional survey of 1872 species reveals high identification success and unusually deep interspecific divergences.CrossRef |

Pettigrove, V., and Hoffmann, A. A. (2005). A field-based microcosm method to assess the effect of polluted urban stream sediments on aquatic macroinvertebrates. Environmental Toxicology and Chemistry 24, 170–180.
A field-based microcosm method to assess the effect of polluted urban stream sediments on aquatic macroinvertebrates.CrossRef | 1:CAS:528:DC%2BD2MXivVGns70%3D&md5=f0c415cd81b6889daee49f7df7d358f1CAS |

Pilgrim, E. M., Jackson, S. A., Swenson, S., Turcsanyi, I., Friedman, E., Weigt, L., and Bagley, M. J. (2011). Incorporation of DNA barcoding into a large-scale biomonitoring program: opportunities and pitfalls. Journal of the North American Benthological Society 30, 217–231.
Incorporation of DNA barcoding into a large-scale biomonitoring program: opportunities and pitfalls.CrossRef |

Plant Health Australia (2009). Contingency Plan: Golden Apple Snail. Available at http://www.planthealthaustralia.com.au/wp-content/uploads/2013/03/Golden-apple-snail-CP-2008.pdf [Verified 6 February 2017].

Porco, D., Rougerie, R., Deharveng, L., and Hebert, P. N. (2010). Coupling non-destructive DNA extraction and voucher retrieval for small soft-bodied arthropods in a high-throughput context: the example of Collembola. Molecular Ecology Resources 10, 942–945.
Coupling non-destructive DNA extraction and voucher retrieval for small soft-bodied arthropods in a high-throughput context: the example of Collembola.CrossRef | 1:CAS:528:DC%2BC3cXhsVGmtrjP&md5=c3f80f6cab289cf99c41bc9430d324dbCAS |

Ratnasingham, S., and Hebert, P. D. N. (2013). A DNA-based registry for all animal species: the barcode index number (BIN) system. PLoS One 8, e66213.
A DNA-based registry for all animal species: the barcode index number (BIN) system.CrossRef | 1:CAS:528:DC%2BC3sXhtFOmt7%2FK&md5=2c9250b50a36e629705e0a013d071d70CAS |

Regis, L., Monteiro, A. M., Melo-Santos, M. A., Silveira, J. C., Furtado, A. F., Acioli, R. V., Santos, G. M., Nakazawa, M., Carvalho, M. S., Ribeiro, P. J., and Souza, W. V. (2008). Developing new approaches for detecting and preventing Aedes aegypti population outbreaks: basis for surveillance, alert and control system. Memorias do Instituto Oswaldo Cruz 103, 50–59.
Developing new approaches for detecting and preventing Aedes aegypti population outbreaks: basis for surveillance, alert and control system.CrossRef |

Reynoldson, T. B., Bailey, R. C., Day, K. E., and Norris, R. H. (1995). Biological guidelines for freshwater sediment based on BEnthic Assessment of SedimenT (the BEAST) using a multivariate approach for predicting biological state. Australian Journal of Ecology 20, 198–219.
Biological guidelines for freshwater sediment based on BEnthic Assessment of SedimenT (the BEAST) using a multivariate approach for predicting biological state.CrossRef |

Rosenberg, D. M., and Resh, V. H. (1993). ‘Freshwater Biomonitoring and Benthic Macroinvertebrates.’ (Chapman & Hall: New York, NY, USA.)

Rowley, D. L., Coddington, J. A., Gates, M. W., Norrbom, A. L., Ochoa, R. A., Vandenberg, N. J., and Greenstone, M. H. (2007). Vouchering DNA-barcoded specimens: test of a nondestructive extraction protocol for terrestrial arthropods. Molecular Ecology Notes 7, 915–924.
Vouchering DNA-barcoded specimens: test of a nondestructive extraction protocol for terrestrial arthropods.CrossRef | 1:CAS:528:DC%2BD1cXls12lsA%3D%3D&md5=270f2e4219fbee8a887518312c8c8d8fCAS |

Saito, V. S., Siqueira, T., and Fonseca-Gessner, A. A. (2015). Should phylogenetic and functional diversity metrics compose macroinvertebrate multimetric indices for stream biomonitoring? Hydrobiologia 745, 167–179.
Should phylogenetic and functional diversity metrics compose macroinvertebrate multimetric indices for stream biomonitoring?CrossRef |

Sanger, F., Nicklen, S., and Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America 74, 5463–5467.
DNA sequencing with chain-terminating inhibitors.CrossRef | 1:CAS:528:DyaE1cXhtlaru7Y%3D&md5=5f2bc1d10cb524b5c1113c41647d4dffCAS |

Schmidt-Kloiber, A., and Nijboer, R. C. (2004). The effect of taxonomic resolution on the assessment of ecological water quality classes. Hydrobiologia 516, 269–283.
The effect of taxonomic resolution on the assessment of ecological water quality classes.CrossRef |

Schoch, C. L., Seifert, K. A., Huhndorf, S., Robert, V., Spouge, J. L., Levesque, C. A., Chen, W., and Consortium, F. B. (2012). Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America 109, 6241–6246.
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.CrossRef | 1:CAS:528:DC%2BC38Xmt12mu7o%3D&md5=2bd1ceadcb3aead6acca62b0dd4e0ed5CAS |

Shackleton, M., and Rees, G. (2016). DNA barcoding Australian macroinvertebrates for monitoring programs: benefits and current short comings. Marine and Freshwater Research 67, 380–390.
DNA barcoding Australian macroinvertebrates for monitoring programs: benefits and current short comings.CrossRef |

Shackleton, M. E., and Webb, J. M. (2014). Two new species of Calocoides Neboiss 1984 (Trichoptera: Calocidae) from eastern Australia, with descriptions of the immature stages. Australian Entomologist 53, 444–457.
Two new species of Calocoides Neboiss 1984 (Trichoptera: Calocidae) from eastern Australia, with descriptions of the immature stages.CrossRef |

Shaw, K. L. (2002). Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: what mtDNA reveals and conceals about modes of speciation in Hawaiian crickets. Proceedings of the National Academy of Sciences of the United States of America 99, 16122–16127.
Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: what mtDNA reveals and conceals about modes of speciation in Hawaiian crickets.CrossRef | 1:CAS:528:DC%2BD38Xps1ens7c%3D&md5=fa5009c3f60ac1db283f0e952917f20dCAS |

Shea, C. P., Peterson, J. T., Wisniewski, J. M., and Johnson, N. A. (2011). Misidentification of freshwater mussel species (Bivalvia: Unionidae): contributing factors, management implications, and potential solutions. Journal of the North American Benthological Society 30, 446–458.
Misidentification of freshwater mussel species (Bivalvia: Unionidae): contributing factors, management implications, and potential solutions.CrossRef |

Shokralla, S., Spall, J. L., Gibson, J. F., and Hajibabaei, M. (2012). Next-generation sequencing technologies for environmental DNA research. Molecular Ecology 21, 1794–1805.
Next-generation sequencing technologies for environmental DNA research.CrossRef | 1:CAS:528:DC%2BC38XptVGksLo%3D&md5=2b7a0c161a30df560060b347dc26fc1fCAS |

Shokralla, S., Gibson, J. F., Nikbakht, H., Janzen, D. H., Hallwachs, W., and Hajibabaei, M. (2014). Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens. Molecular Ecology Resources 14, 892–901.
| 1:CAS:528:DC%2BC2cXhtlKlu7rN&md5=26223b46a16eb1ff3fbf42eb90ec8819CAS |

Shokralla, S., Porter, T. M., Gibson, J. F., Dobosz, R., Janzen, D. H., Hallwachs, W., Golding, G. B., and Hajibabaei, M. (2015). Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Scientific Reports 5, 9687.
Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform.CrossRef | 1:CAS:528:DC%2BC2MXhtFOrs7vN&md5=91acfc5a10dd68a4d999efe565d26cb5CAS |

Simpson, J. C., and Norris, R. H. (2000). Biological assessment of river quality: development of AUSRIVAS models and outputs. In ‘Assessing the Biological Quality of Fresh Waters: RIVPACS and Other Techniques’. (Eds J. F. Wright, D. W. Sutcliffe and M. T. Furse.) pp. 125–142. (Freshwater Biological Association: Ambleside, UK.)

Smith, M. A., Woodley, N. E., Janzen, D. H., Hallwachs, W., and Hebert, P. D. N. (2006). DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae). Proceedings of the National Academy of Sciences of the United States of America 103, 3657–3662.
DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae).CrossRef | 1:CAS:528:DC%2BD28XivFWju7k%3D&md5=baa2abd1efd5332873117b21181ccc75CAS |

Srivathsan, A., and Meier, R. (2012). On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature. Cladistics 28, 190–194.
On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature.CrossRef |

Stein, E. D., White, B. P., Mazor, R. D., Miller, P. E., and Pilgrim, E. M. (2013). Evaluating ethanol-based sample preservation to facilitate use of DNA barcoding in routine freshwater biomonitoring programs using benthic macroinvertebrates. PLoS One 8, e51273.
Evaluating ethanol-based sample preservation to facilitate use of DNA barcoding in routine freshwater biomonitoring programs using benthic macroinvertebrates.CrossRef | 1:CAS:528:DC%2BC3sXpsFKmsw%3D%3D&md5=75d8d845012e52f2fd2cc4a07fd1192fCAS |

Stein, E. D., Martinez, M. C., Stiles, S., Miller, P. E., and Zakharov, E. V. (2014). Is DNA barcoding actually cheaper and faster than traditional morphological methods: results from a survey of freshwater bioassessment efforts in the United States? PLoS One 9, e95525.
Is DNA barcoding actually cheaper and faster than traditional morphological methods: results from a survey of freshwater bioassessment efforts in the United States?CrossRef |

Steininger, S., Storer, C., Hulcr, J., and Lucky, A. (2015). Alternative preservatives of insect DNA for citizen science and other low-cost applications. Invertebrate Systematics 29, 468–472.
Alternative preservatives of insect DNA for citizen science and other low-cost applications.CrossRef | 1:CAS:528:DC%2BC2MXhsl2htL%2FJ&md5=901a8c0964d55f883af22158c2c38b1eCAS |

Stribling, J. B., Pavlik, K. L., Holdsworth, S. M., and Leppo, E. W. (2008). Data quality, performance, and uncertainty in taxonomic identification for biological assessments. Journal of the North American Benthological Society 27, 906–919.
Data quality, performance, and uncertainty in taxonomic identification for biological assessments.CrossRef |

Stubauer, I., Hering, D., Korte, T., Hoffmann, A., Brabec, K., Sharma, S., Shrestha, M., Kahlown, M. A., Tahir, M. A., Kumar, A., Sharma, M. P., Bari, M. F., Badruzzaman, A. B. M., Chhopel, G. K., and Moog, O. (2010). The development of an assessment system to evaluate the ecological status of rivers in the Hindu Kush–Himalayan region: introduction to the special feature. Hydrobiologia 651, 1–15.
The development of an assessment system to evaluate the ecological status of rivers in the Hindu Kush–Himalayan region: introduction to the special feature.CrossRef |

Sudduth, E. B., and Meyer, J. L. (2006). Effects of bioengineered streambank stabilization on bank habitat and macroinvertebrates in urban streams. Environmental Management 38, 218–226.
Effects of bioengineered streambank stabilization on bank habitat and macroinvertebrates in urban streams.CrossRef |

Sweeney, B. W., Battle, J. M., Jackson, J. K., and Dapkey, T. (2011). Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality? Journal of the North American Benthological Society 30, 195–216.
Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality?CrossRef |

Thompson, R. M., and Townsend, C. R. (1999). The effect of seasonal variation on the community structure and food-web attributes of two streams: implications for food-web science. Oikos 87, 75–88.
The effect of seasonal variation on the community structure and food-web attributes of two streams: implications for food-web science.CrossRef |

Trewick, S. A. (2008). DNA barcoding is not enough: mismatch of taxonomy and genealogy in New Zealand grasshoppers (Orthoptera: Acrididae). Cladistics 24, 240–254.
DNA barcoding is not enough: mismatch of taxonomy and genealogy in New Zealand grasshoppers (Orthoptera: Acrididae).CrossRef |

Vij, R., Harbach, R. E., Service, M. W., Crampton, J. M., and Molynuex, D. H. (1997). Identification of dry-pinned museum specimens of the sibling species Anopheles gambiae and A. arabiensis (Diptera: Culicidae) using non-radioactively labelled probes. Systematic Entomology 22, 173–180.
Identification of dry-pinned museum specimens of the sibling species Anopheles gambiae and A. arabiensis (Diptera: Culicidae) using non-radioactively labelled probes.CrossRef |

Vink, C. J., Thomas, S. M., Paquin, P., Hayashi, C. Y., and Hedin, M. (2005). The effects of preservatives and temperatures on arachnid DNA. Invertebrate Systematics 19, 99–104.
The effects of preservatives and temperatures on arachnid DNA.CrossRef | 1:CAS:528:DC%2BD2MXls1SlsL8%3D&md5=737203ed4415ab4d9fbfa19b62f34dc4CAS |

Virgilio, M., Backeljau, T., Nevado, B., and De Meyer, M. (2010). Comparative performances of DNA barcoding across insect orders. BMC Bioinformatics 11, 206.
Comparative performances of DNA barcoding across insect orders.CrossRef |

Vivien, R., Wyler, S., Lafont, M., and Pawlowski, J. (2015). Molecular barcoding of aquatic oligochaetes: implications for biomonitoring. PLoS One 10, e0125485.
Molecular barcoding of aquatic oligochaetes: implications for biomonitoring.CrossRef |

Vivien, R., Lejzerowicz, F., and Pawlowski, J. (2016). Next-generation sequencing of aquatic Oligochaetes: comparison of experimental communities. PLoS One 11, e0148644.
Next-generation sequencing of aquatic Oligochaetes: comparison of experimental communities.CrossRef |

Wallace, J. B., and Webster, J. R. (1996). The role of macroinvertebrates in stream ecosystem function. Annual Review of Entomology 41, 115–139.
The role of macroinvertebrates in stream ecosystem function.CrossRef | 1:CAS:528:DyaK28XksVyrsw%3D%3D&md5=c52541eed1d2bc976b773cdf0cd46843CAS |

Walsh, C. J. (2006). Biological indicators of stream health using macroinvertebrate assemblage composition: a comparison of sensitivity to an urban gradient. Marine and Freshwater Research 57, 37–47.
Biological indicators of stream health using macroinvertebrate assemblage composition: a comparison of sensitivity to an urban gradient.CrossRef |

Webb, J., and Suter, P. (2010). Revalidation and redescription of Bungona illiesi Lugo-Ortiz & McCafferty (Ephemeroptera: Baetidae) from Australia, based on mitochondrial and morphological evidence. Zootaxa 2481, 37–51.

Webb, J. M., Jacobus, L. M., Funk, D. H., Zhou, X., Kondratieff, B., Geraci, C. J., DeWalt, R. E., Baird, D. J., Richard, B., Phillips, I., and Hebert, P. D. N. (2012). A DNA barcode library for North American Ephemeroptera: progress and prospects. PLoS One 7, e38063.
A DNA barcode library for North American Ephemeroptera: progress and prospects.CrossRef | 1:CAS:528:DC%2BC38Xot12qsbc%3D&md5=222be3fbe8e62a3b235c2f9d09b22219CAS |

Whitworth, T. L., Dawson, R. D., Magalon, H., and Baudry, E. (2007). DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae). Proceedings of the Royal Society of London – B. Biological Sciences 274, 1731–1739.
DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae).CrossRef | 1:CAS:528:DC%2BD2sXosVans7k%3D&md5=1f4c64b3e504f2ab34c02cc9f3fa81e4CAS |

Will, K. W., Mishler, B. D., and Wheeler, Q. D. (2005). The perils of DNA barcoding and the need for integrative taxonomy. Systematic Biology 54, 844–851.
The perils of DNA barcoding and the need for integrative taxonomy.CrossRef |

Wright, J. F., Sutcliffe, D. W., and Furse, M. T. (Eds) (2000). An introduction to RIVPACS. In ‘Assessing the Biological Quality of Fresh Waters: RIVPACS and Other Techniques’. pp. 1–24. (Freshwater Biological Association: Ambleside, UK.) Available at https://core.ac.uk/download/files/331/11020774.pdf [Verified 6 February 2017].

Yu, D. W., Ji, Y. Q., Emerson, B. C., Wang, X. Y., Ye, C. X., Yang, C. Y., and Ding, Z. L. (2012). Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution 3, 613–623.
Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring.CrossRef |

Zhou, X., Adamowicz, S., Jacobus, L., DeWalt, R., and Hebert, P. D. N. (2009). Towards a comprehensive barcode library for arctic life – Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada. Frontiers in Zoology 6, 30–38.
Towards a comprehensive barcode library for arctic life – Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada.CrossRef |

Zhou, X., Robinson, J. L., Geraci, C. J., Parker, C. R., Flint, O. S., Etnier, D. A., Ruiter, D., DeWalt, R. E., Jacobus, L. M., and Hebert, P. D. N. (2011). Accelerated construction of a regional DNA-barcode reference library: caddisflies (Trichoptera) in the Great Smoky Mountains National Park. Journal of the North American Benthological Society 30, 131–162.
Accelerated construction of a regional DNA-barcode reference library: caddisflies (Trichoptera) in the Great Smoky Mountains National Park.CrossRef |

Zhou, X., Li, Y., Liu, S., Yang, Q., Su, X., Zhou, L., Tang, M., Fu, R., Li, J., and Huang, Q. (2013). Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. GigaScience 2, 1–12.
Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification.CrossRef |

Zimmermann, J., Hajibabaei, M., Blackburn, D. C., Hanken, J., Cantin, E., Posfai, J., and Evans, T. C. (2008). DNA damage in preserved specimens and tissue samples: a molecular assessment. Frontiers in Zoology 5, 1–13.

Zimmermann, J., Abarca, N., Enke, N., Skibbe, O., Kusber, W. H., and Jahn, R. (2014). Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research. PLoS One 9, e108793.
Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.CrossRef |



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