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

Mitochondrial DNA reveals phylogenetic structuring and cryptic diversity in Australian freshwater macroinvertebrate assemblages

Andrew M. Baker A C , Jane M. Hughes A , John C. Dean B and Stuart E. Bunn A
+ Author Affiliations
- Author Affiliations

A Cooperative Research Centre for Freshwater Ecology, Centre for Riverine Landscapes, Griffith University, Nathan Campus, Qld 4111, Australia.

B Environment Protection Authority, Freshwater Sciences Unit, Ernest Jones Drive, Macleod, Vic. 3085, Australia.

C Corresponding author. Email:

Marine and Freshwater Research 55(6) 629-640
Submitted: 12 March 2004  Accepted: 7 June 2004   Published: 14 September 2004


Freshwater catchments of south-east Australia possess generally rich and diverse macroinvertebrate faunas, although the genetic structuring of these assemblages is poorly known. In this study, we assessed mitochondrial phylogenetic structure within four genera of macroinvertebrates from the Sydney Water Supply Catchment, south-east Australia: Euastacus (parastacid crayfish), Cheumatopsyche (hydropsychid caddisflies), Atalophlebia (leptophlebiid mayflies) and Paratya (atyid shrimp), with a view to prioritising areas of high diversity for future conservation efforts. We found extremely divergent (≈4–19%) cytochrome c oxidase subunit I (COI) lineages within all surveyed groups, many of which corresponded to recognised taxa, although there was also evidence of cryptic species within three genera; Euastacus, Atalophlebia and Paratya. Distributions of these three genera were associated with high altitude streams, above dam impoundments. Our results have important implications for management of the Sydney Water Supply Catchment. Future disturbance in this region is likely to be high and priority should be directed towards preserving the diversity of fauna in these upland areas. This comparative phylogenetic approach may have value as a means to focus and direct conservation efforts in other areas supporting high biodiversity.

Extra keywords: Atalophlebia, Cheumatopsyche, cryptic diversity, Euastacus, mitochondrial DNA, Paratya, phylogenetic.


We thank Keith Crandall for use of his unpublished Euastacus sequences, Arlene Wheatley for unpublished Sclerocyphon data and Jemma Somerville for laboratory work. Peter Davie kindly provided access to Queensland Museum Euastacus specimens. James Fawcett, Mia Hillyer, Amanda Kotlash, Martin Krogh, Tim Page and Simon Williams provided invaluable field assistance. This research forms a component of a large project on connectivity of macroinvertebrates in the SWSC, funded by the Cooperative Research Centre for Freshwater Ecology.


Avise, J. C. (1994). ‘Molecular Markers, Natural History and Evolution.’ (Chapman and Hall: New York, USA.)

Baker, A. M. , Hurwood, D. A. , Krogh, M. , and Hughes, J. M. (in press). Mitochondrial DNA signatures of restricted gene flow within divergent lineages of an atyid shrimp (Paratya australiensis). Heredity ,

Baker, A. M. , Williams, S. A. , and Hughes, J. M. (2003). Patterns of spatial genetic structuring in a hydropsychid caddisfly (Cheumatopsyche sp. AV1) from southeastern Australia. Molecular Ecology 12, 3313–3324.
CrossRef | PubMed |

Barker, G. M. (2002). Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation. Biological Journal of the Linnean Society 76, 165–194.
CrossRef |

Bininda-Emonds, O. R. P. , Vazquez, D. , and Manne, L. L. (2000). The calculus of biodiversity: integrating phylogeny and conservation. Trends in Ecology & Evolution 15, 92–94.
CrossRef | PubMed |

Boyero, L. (2002). Insect biodiversity in freshwater ecosystems: is there any latitudinal gradient? Marine and Freshwater Research 53, 753–755.
CrossRef |

Bunn, S. E. , and Davies, P. M. (1990). Why is the stream fauna of south-western Australia so impoverished. Hydrobiologia 194, 169.

Chenoweth, S. F. , and Hughes, J. M. (2003). Speciation and phylogeography in Caridina indistincta, a complex of freshwater shrimps from Australian heathland streams. Marine and Freshwater Research 54, 807–812.
CrossRef |

Chessman, B. C. , and Williams, S. A. (1999). Biodiversity and conservation of river macroinvertebrates on an expanding urban fringe: western Sydney, New South Wales, Australia. Pacific Conservation Biology 5, 36–55.

Dean, J. C. (1999a). ‘Preliminary Keys for the Identification of Australian Trichoptera Larvae of the Family Hydropsychidae.’ (Cooperative Research Centre for Freshwater Ecology: Albury, Australia.)

Dean, J. C. (1999b). ‘Preliminary Keys for the Identification of Australian Mayfly Nymphs of the Family Leptophlebiidae.’ (Cooperative Research Centre for Freshwater Ecology: Albury, Australia.)

Doyle, J. J. , and Doyle, J. L. (1987). A rapid DNA isolation procedure for small quantities of leaf tissue. Phytochemistry Bulletin 19, 11–15.

Eck, R. V., and  Dayhoff, M. O. (1966). ‘Atlas of Protein Sequence and Structure 1966.’ (National Biomedical Research Foundation: Silver Spring, MD, USA.)

Faith, D. P. (1992). Conservation evaluation and phylogenetic diversity. Biological Conservation 61, 1–10.
CrossRef |

Faith, D. P. (2002). Quantifying biodiversity: a phylogenetic perspective. Conservation Biology 16, 248–252.
CrossRef |

Faith, D. P. , Reid, C. A. M. , and Hunter, J. (2004). Integrating phylogenetic diversity, complementarity, and endemism for conservation assessment. Conservation Biology 18, 255–261.

Felsenstein, J. (1993). PHYLIP – Phylogeny Inference Package (Version 3.2). Cladistics 5, 164–166.

Felsenstein, J. , and Churchill, G. A. (1996). A hidden Markov model approach to variation among sites in rate of evolution. Molecular Biology and Evolution 13, 93–104.
PubMed |

Feral, J. P. (2002). How useful are the genetic markers in attempts to understand and manage marine biodiversity. Journal of Experimental Marine Biology and Ecology 268, 121–145.
CrossRef |

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.
PubMed |

Growns, I. O. , and Growns, J. E. (2001). Ecological effects of flow regulation on macroinvertebrate and periphytic diatom assemblages in the Hawkesbury-Nepean River, Australia. Regulated Rivers  Research Management 17, 275–293.
CrossRef |

Hall, T. A. (1999) Ecological effects of flow regulation on macroinvertebrate and periphytic diatom assemblages in the Hawkesbury-Nepean River, Australia. Regulated Rivers Nucleic Acids Symposium Series 41, 95–98.

Horwitz, P. (1995). ‘A Preliminary Key to the Species of Decapoda (Crustacea: Malacostraca) Found in Australian Inland Waters.’ (Cooperative Research Centre for Freshwater Ecology: Albury, Australia.)

Huelsenbeck, J. P. , and Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Biometrics 17, 754–755.
CrossRef |

Kumar, S. , Tamura, T. , Jakobsen, I. B. , and Nei, M. (2001). MEGA2: molecular evolutionary genetics analysis software. Bioinformatics (Oxford, England) 17, 1244–1245.
CrossRef | PubMed |

Lake, P. S. , Barmuta, L. A. , Boulton, A. J. , Campbell, I. C. , and StClair, R. M. (1985). Australian streams and Northern Hemisphere: comparisons and problems. Proceedings of the Ecological Society of Australia 14, 61–82.

Lee, M. S. Y. (2003). Species concepts and species reality: salvaging a Linnaean rank. Journal of Evolutionary Biology 16, 179–188.
CrossRef | PubMed |

Meegaskumbura, M. , Bossuyt, F. , Pethiyagoda, R. , Manamendra-Arachchi, K. , Bahir, M. , Milinkovitch, M. C. , and Schneider, C. J. (2002). Sri Lanka: an amphibian hotspot. Science 298, 379.
CrossRef | PubMed |

Merrick, J. R. (1993). ‘Freshwater Crayfishes of New South Wales.’ (Linnean Society of New South Wales: Milson’s Point, New South Wales, USA.)

Mishler, B. , and Brandon, R. N. (1987). Individuality, pluralism and the phylogenetic species concept. Biology and Philosophy 2, 397–414.

Mishler, B. and  Theriot, E. C. (2000). The phylogenetic species concept: monophyly, apomorphy and phylogenetic species concepts. In ‘Species Concepts and Phylogenetic Theory: a Debate’. (Eds. Q. D.Wheeler and R. Meier)  pp. 44–54. (Columbia University Press: New York, USA.)

Morgan, G. J. (1997). Freshwater crayfish of the genus Euastacus Clark (Decapoda: Parastacidae) from New South Wales, with a key to all species of the genus. Records of the Australian Museum Supplement 23, 1–110.

Moritz, C. , and Faith, D. P. (1998). Comparative phylogeography and the identification of genetically divergent areas for conservation. Molecular Ecology 7, 419–429.
CrossRef |

Palumbi, S. R., Martin, A., Romano, S., McMillan, W. O., Stice, L., and  Grabowski, G. (1991). ‘The Simple Fools Guide PCR.’ (Kewalo Marine Laboratory: University of Hawaii)

Posada, D. , and Crandall, K. A. (1998). Modeltest: testing the model of DNA substitution. Bioinformatics (Oxford, England) 14, 817–818.
CrossRef | PubMed |

de Queiroz, K. , and Donoghue, M. J. (1988). Phylogenetic systematics and the species problem. Cladistics 4, 317–338.

Rannala, B. , and Yang, Z. H. (1996). Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution 43, 304–311.
PubMed |

Recher, H. F. , Hutchings, P. A. , and Rosen, S. (1993). The biota of the Hawkesbury-Nepean catchment: reconstruction and restoration. Australian Journal of Zoology 29, 3–41.

Saitou, N. , and Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406–425.
PubMed |

Sechrest, W. , Brooks, T. M. , da Fonseca, G. A. B. , Konstant, W. R. , Mittermeier, R. A. , Purvis, A. , Rylands, A. B. , and Gittleman, J. L. (2002). Hotspots and the conservation of evolutionary diversity. Proceedings of the National Academy of Sciences of the United States of America 99, 2067–2071.
CrossRef | PubMed |

Swofford, D. L. (2001). ‘PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4.’ (Sinauer Associates: Sunderland, MA, USA.)

Sydney Catchment Authority (2002). ‘Draft Bulk Water Network Delivery Plan.’ (Bulk Water Division: Sydney, Australia)

Williams, W. D. (1977). Some aspects of the ecology of Paratya australiensis (Crustacea: Decapoda: Atyidae). Australian Journal of Marine and Freshwater Research 28, 403–415.

Rent Article (via Deepdyve) Export Citation Cited By (32)