Register      Login
Marine and Freshwater Research Marine and Freshwater Research Society
Advances in the aquatic sciences
RESEARCH ARTICLE

DNA barcoding Australian macroinvertebrates for monitoring programs: benefits and current short comings

Michael Shackleton A C and Gavin N. Rees B
+ Author Affiliations
- Author Affiliations

A The Murray–Darling Freshwater Research Centre, La Trobe University, Wodonga, Vic. 3690, Australia.

B The Murray–Darling Freshwater Research Centre and CSIRO Land and Water Flagship, La Trobe University, Wodonga, Vic. 3690, Australia.

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

Marine and Freshwater Research 67(3) 380-390 https://doi.org/10.1071/MF14331
Submitted: 28 August 2014  Accepted: 3 February 2015   Published: 1 July 2015

Abstract

Identification of macroinvertebrates is a key component of monitoring programs that seek to understand the condition of aquatic environments. Classical identification approaches underpin such programs, but molecular approaches are gaining recognition as valuable ways to identify organisms for research and monitoring programs. We applied DNA barcoding data to specimens collected as part of monitoring programs in the Murray–Darling Basin, to investigate the possible informational benefits these data may provide. We also tested the performances of two online DNA databases in assigning taxon names to our sequence data. We found that relying on the online databases to determine species identifications was currently problematic for the Australian freshwater fauna because of a lack of available sequence data. However, we also found that collecting and applying barcode data to our monitoring programs gave considerable informational benefits by providing greater resolution of specimen identity, highlighting the presence of potential cryptic species, providing information on larval and adult associations, demonstrating instances where misidentification had occurred though classical approaches, and providing conformation of the performance of diagnostic characters currently used in keys to determine species identities.

Additional keywords: aquatic macroinvertebrate, molecular biology.


References

Anderson, N. M., and Weir, T. A. (2004). ‘Australian Water Bugs their Biology and Identification (Hemiptera–Heteroptera, Gerromorpha & Nepomorpha).’ (CSIRO Publishing: Melbourne.)

Baldwin, D. S., Colloff, M. J., Rees, G. N., Chariton, A. A., Watson, G. O., Court, L. N., Hartley, D. M., Morgan, M. J., King, A. J., Wilson, J. S., Hodda, M., and Hardy, C. M. (2013). Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils. Molecular Ecology 22, 1746–1758.
Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils.Crossref | GoogleScholarGoogle Scholar | 23379967PubMed |

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, 1–15.

Cartwright, D. I. (1997). ‘Preliminary Guide to the Identification of Late Instar Larvae of Australian Ecnomidae, Philopotamidae and Tasimiidae (Insecta: Trichoptera). Identification Guide Number 10.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

Cartwright, D. I. (1998). ‘Preliminary Guide to the Identification of Late Instar Larvae of Australian Polycentropodidae, Glossosomatidae, Dipsuedopsidae and Psychomyiidae (Insecta: Trichoptera). Identification Guide Number 15.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

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 | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXhsFelsrvJ&md5=22617c6970bd51020fb299db068a6d2cCAS |

Colless, D. H., and McAlpine, D. K. (1991). Diptera. In ‘The Insects of Australia: a Textbook for Students and Research Workers. Vol. 2’. 2nd edn. (Eds I. D. Naumann, P. B. Carne, J. F. Lawrence, E. S. Nielson, J. P. Spradbery, R. W. Taylor, M. J. Whitten and M. J. Littlejohn.) pp. 717–786. (Melbourne University Press: Melbourne.)

Cook, B. D., Baker, A. M., Page, T. J., Grant, S. C., Fawcett, J. H., Hurwood, D. A., and Hughes, J. M. (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 | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XjslWms74%3D&md5=847e6c5385347204d342bb5378e02cbfCAS | 16599968PubMed |

Cook, R., Paul, W., Hawking, J., Davey, C., and Suter, P. (2011). River Murray Biological (Macroinvertebrate) Monitoring Program – Review of monitoring 1980–2009. MDFRC Publication 34/2011. Final report prepared for the Murray–Darling Basin Authority by The Murray–Darling Freshwater Research Centre, Wodonga, Vic.

Dean, J. C. (1997). ‘Larvae of the Australian Hydrobiosidae (Insecta: Trichoptera). Identification Guide Number 11.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

Dean, J. C. (1999a). ‘Preliminary Keys for the Identification of Australian Mayfly Nymphs of the Family Leptophlebiidae. Identification Guide Number 20.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

Dean, J. C. (1999b). ‘Preliminary Keys for the Identification of Australian Trichoptera Larvae of the Lamily Hydropsychidae. Identification Guide Number 22.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

Dean, J. C. (2011). ‘A Key to the Australian Genera of Mayfly Nymphs of the Family Leptophlebiidae (Ephemeroptera).’ (La Trobe University: Wodonga, Vic.)

Dean, J. C., St Clair, R. M., and Cartwright, D. I. (2004). ‘Identification Keys to Australian Families and Genera of Caddis-fly Larvae (Trichoptera). Identification Guide Number 50.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

DNABaser (2012). ‘DNA Baser Sequence Assembler.’ 2.75 edn. (Heracle Biosoft S.R.L.: Romania.) Available at www.DnaBaser.com [Verified 6 May 2015]

Folmer, O., Black, M., Hoeh, W., Lutz, R., and Vrijenhoek, R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3, 294–299.
| 1:CAS:528:DyaK2MXjt12gtLs%3D&md5=6840b5af5c40a6be526f2a641c6404abCAS | 7881515PubMed |

Glaister, A. (1999). ‘Guide to the Identification of Australian Elmidae Larvae, (Insecta: Coleoptera). Identification Guide Number 21.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

Greenslade, P. (1991). Collembola. In ‘The Insects of Australia: a Textbook for Students and Research Workers’. 2nd edn. (Eds I. D. Naumann, P. B. Carne, J. F. Lawrence, E. S. Nielson, J. P. Spradbery, R. W. Taylor, M. J. Whitten and M. J. Littlejohn.) pp. 252–264. (Melbourne University Press: Melbourne.)

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 | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXltV2rt7c%3D&md5=23f6dee6ab0a1f1b54a9bd753f7f003eCAS | 21533287PubMed |

Harvey, M. S. (1998). ‘The Australian Water Mites: a Guide to Families and Genera.’ (CSIRO Publishing: Melbourne.)

Harvey, M. S., and Growns, J. E. (1997). ‘A Guide to the Identification of Families of Australian Water Mites (Arachnida: Acarina). Identification Guide Number 18.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

Hebert, P. D. N., Cywinska, A., and Ball, S. L. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London – B. Biological Sciences 270, 313–321.
Biological identifications through DNA barcodes.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3sXktVWiu7g%3D&md5=0a3c55121aec562c77fd37481bd37253CAS |

Horwitz, P. (1995). ‘A Preliminary Key to the Species of Decapoda (Crustacea: Malacostraca) found in Australian Inland Waters. Identification Guide Number 5.’ (Cooperative Rresearch Centre for Freshwater Ecology: Thurgoona, NSW.)

Ivanova, N. V., deWaard, J., and Hebert, P. D. N. (2006). An inexpensive, automation-friendly protocol for recovering high-quality DNA. Molecular Ecology Notes 6, 998–1002.
An inexpensive, automation-friendly protocol for recovering high-quality DNA.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXmsl2ksw%3D%3D&md5=b2df6af94847835e11f102fc3549fc5fCAS |

Jackson, J. (1998). ‘Preliminary Guide to the Identification of Late Instar Larvae of Australian Calocidae, Helicophidae and Conoesucidae (Insecta: Trichoptera). Identification Guide Number 16.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

Johanson, K. A., and Keijsner, M. (2008). Phylogeny of the Helicophidae (Trichoptera), with emphasis on the New Caledonian species of Helicopha. Systematic Entomology 33, 451–483.
Phylogeny of the Helicophidae (Trichoptera), with emphasis on the New Caledonian species of Helicopha.Crossref | GoogleScholarGoogle Scholar |

Johanson, K. A., Kjer, K., and Malm, T. (2009). Testing the monophyly of the New Zealand and Australian endemic family Conoesucidae Ross based on combined molecular and morphological data (Insecta: Trichoptera: Sericostomatoidea). Zoologica Scripta 38, 563–573.
Testing the monophyly of the New Zealand and Australian endemic family Conoesucidae Ross based on combined molecular and morphological data (Insecta: Trichoptera: Sericostomatoidea).Crossref | GoogleScholarGoogle Scholar |

Lawrence, J. F. (1992). ‘Coleoptera Workshop.’ (Murray–Darling Freshwater Research Centre: Albury, NSW.)

Lawrence, J. F., and Britton, E. B. (1991). Coleoptera (beetles). In ‘The Insects of Australia: a Textbook for Students and Research Workers’. 2nd edn. (Eds I. D. Naumann, P. B. Carne, J. F. Lawrence, E. S. Nielson, J. P. Spradbery, R. W. Taylor, M. J. Whitten and M. J. Littlejohn.) pp. 543–683. (Melbourne University Press: Melbourne.)

Madden, C. (2009). ‘Key to Genera of Larvae of Australian Chironomidae (Diptera). TRIN Taxonomic Guide 1.’ (La Trobe University: Wodonga, Vic.)

Madden, C. (2013). ‘Identification Key to Families of Diptera Larvae of Australian Inland Waters.’ (La Trobe University, TRIN Taxonomy Workshop: Wodonga, Vic.)

Malm, T., and Johanson, K. A. (2011). A new classification of the long-horned caddisflies (Trichoptera: Leptoceridae) based on molecular data. BMC Evolutionary Biology 11, 1–17.
A new classification of the long-horned caddisflies (Trichoptera: Leptoceridae) based on molecular data.Crossref | GoogleScholarGoogle Scholar |

Mynott, J. (2011). ‘Draft Oreliminary Key to the Larvae of Riekoperla (Plecoptera: Gripopterygidae. Presented at the 3rd TRIN Taxonomy Workshop’. (La Trobe University: Wodonga, Vic.)

Neboiss, A. (1986). ‘Atlas of Trichoptera of the SW Pacific-Australian Region.’ (W. Junk: Dordrecht, the Netherlans.)

Neboiss, A. (1992). ‘Illustrated Keys to the Families and Genera of Australian Trichoptera I. Adults. ASL Special Publication Number 9.’ (Australian Society for Limnology: Melbourne, Vic.)

Neboiss, A., and Wells, A. (1998). Review of Australian species of Trianodes McLachlan (Trichoptera: Leptoceridae). Memoirs of the Museum of Victoria 57, 89–132.

Ogden, T. H. (2008). Molecules, morphology and fossils: a comprehensive approach to odonate phylogeny and the evolution of the odonate wing. Cladistics 23, 1–38.

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 | GoogleScholarGoogle Scholar |

Puillandre, N., Lambert, A., Brouillet, S., and Achaz, G. (2012). ABGD, automatic barcode gap discovery for primary species delimitation. Molecular Ecology 21, 1864–1877.
ABGD, automatic barcode gap discovery for primary species delimitation.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BC38zlsFeltQ%3D%3D&md5=f6b74ce2d678e59181a2264ec65d5d10CAS | 21883587PubMed |

Ruiter, D. E., Boyle, E. E., and Zhou, X. (2013). DNA barcoding facilitates associations and diagnoses for Trichoptera larvae of the Churchill (Manitoba, Canada) area. BMC Biology 13, 1–39.

Russell, R. C. (1993). ‘Mosquitoes and mosquito-borne disease in southeastern Australia.’ Revised edn. (Department of Medical Entomology, Westmead Hospital: Sydney, NSW.)

Schultheis, A. S., Marchant, R., and Hughes, J. M. (2008). Contrasting patterns of genetic structure and disequilibrium in populations of a stone-cased caddisfly (Tasimiidae) from northern and southern Australia. Marine and Freshwater Research 59, 235–245.
| 1:CAS:528:DC%2BD1cXltl2jtL0%3D&md5=c6575ff38a8ba8d4e329d65132378a80CAS |

Shackleton, M. E. (2013). Preliminary keys to the larvae of Australian Calocidae (Trichoptera: Insecta). In ‘Aquatic Macroinvertebrates 2013 Taxonomic Workshop’. (La Trobe University: Albury–Wodonga, Vic.)

Shackleton, M.E., and Webb, J.M. (2013). A new description and association of a larva with the adult male of Pliocaloca fidesria Shackleton (Insecta: Trichoptera: Calocidae) from eastern Australia. Memoirs of the Queensland Museum – Nature 56, 593–600.

Shen, Y.-Y., Chen, X., and Murphy, R. W. (2013). Assessing DNA barcoding as a tool for species identification and data quality control. PLoS ONE 8, e57125.
Assessing DNA barcoding as a tool for species identification and data quality control.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXjsF2jsrw%3D&md5=11b85deda630672303304f97eedce905CAS | 23431400PubMed |

Short, J. W. (2004). A revision of Australian river prawns, Macrobrachium (Crustacea: Decapoda: Palaemonidae). Hydrobiologia 525, 1–100.
A revision of Australian river prawns, Macrobrachium (Crustacea: Decapoda: Palaemonidae).Crossref | GoogleScholarGoogle Scholar |

St Clair, R. M. (1997). ‘Preliminary Guide to the Identification of Late Instar Larvae of Australian Philorheithridae, Calamoceratidae and Helicopsychidae (Insecta: Trichoptera). Identification Guide Number 12.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

St Clair, R. M. (2000). ‘Preliminary Keys for the Identification of Australian Larvae of the Family Leptoceridae. Identification Guide Number 27.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

Suter, P. J. (1999). ‘Illustrated Key to the Australian Caenid Nymphs (Ephemeroptera: Caenidae). Identification Guide Number 23.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

Suter, P. J., Webb, J. M., and Rowe, D. (2009). Key to the mature nymphs of Coloburiscoides (Lestage) (Ephemeroptera: Coloburiscidae). Museum Victoria Science Reports 14, 1–24.

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 | GoogleScholarGoogle Scholar |

Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28, 2731–2739.
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXht1eiu73K&md5=887c0fd611631fa5076e3aa6bcbb4e32CAS | 21546353PubMed |

Theischinger, G. (2000). ‘Australian Alderfly Larvae and Adults (Insecta: Megaloptera): a Preliminary Guide to the Identification of Larvae and Survey of Adults of Australian Alderflies. Identification Guide Number 29.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

Theischinger, G., and Hawking, J. H. (2003). ‘Dragonflies of Victoria: an Identification Guide to Adult and Larval Dragonflies (Odonata). Identification and Ecology Guide Number 46.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

Thomas, D. (2012). ‘Key to Larvae of Victorian Dinotoperla (Plecoptera). TRIN Taxonomic Workshop.’ (La Trobe University: Wodonga, Vic.)

Tixier, M.-S., Hernandes, F. A., Guichou, S., and Kreiter, S. (2012). The puzzle of DNA sequences of Phytoseiidae (Acari: Mesostigmata) in the public GenBank database. Invertebrate Systematics 25, 389–406.
The puzzle of DNA sequences of Phytoseiidae (Acari: Mesostigmata) in the public GenBank database.Crossref | GoogleScholarGoogle Scholar |

Watts, C. H. S. (1978). A revision of the Australian Dytiscidae (Coleoptera). Australian Journal of Zoology Supplementary Series 26, 1–166.
A revision of the Australian Dytiscidae (Coleoptera).Crossref | GoogleScholarGoogle Scholar |

Watts, C. H. S. (1999). Revision of the Australian Hydrochus (Coleoptera: Hydrochidae). Records of the South Australia Museum 32, 1–43.

Watts, C. H. S. (2002). ‘Checklists & Guides to the Identification, to Genus, of Adult and Larval Australian Water Beetles of the Families Dytiscidae, Noteridae, Hygrobiidae, Haliplidae, Gyrinidae, Hydraenidae and the Superfamily Hydrophiloidea (Insecta: Coleoptera). Identification and Ecology Guide Number 43.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

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

Webb, J. M., and Suter, P. J. (2011). Identification of larvae of Australian Baetidae. Museum Victoria Science Reports 15, 1–24.

Wells, A. (1997). ‘A Preliminary Guide to the Identification of Larval Hydroptilidae (Insecta: Trichoptera). Identification Guide Number 13.’ (Cooperative Research Centre for Freshwater Ecology: Thurgoona, NSW.)

Wiemers, M., and Fiedler, K. (2007). Does the DNA barcoding gap exist? A case study in blue butterflies (Lepidoptera: Lycaenidae). Frontiers in Zoology 4, 1–16.

Yule, C. (1997). ‘Identification Guide to the Stonefly Nymphs of NSW and Northern Victoria. AWT Identification Guide Number 2.’ (Australian Water Technologies: Sydney.)

Zhou, X., Kjer, K.M., and Morse, J.C. (2007). Associating larvae and adults of Chinese Hydropsychidae caddisflies (Insecta:Trichoptera) using DNA sequences. Journal of the North American Benthological Society 26, 719–742.

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 | GoogleScholarGoogle Scholar |