Australian freshwater genetic bibliography

Australian freshwater genetic bibliography

Peter J. Unmack

Welcome to the Australian freshwater genetic bibliography. The papers below are organised into several sections based on specific taxa: fishes, turtles, crayfishes, other decapods, molluscs and arthropods (I will add more groups if I find papers on them). I have tried to limit it to papers that are primarily concerned with genetic patterns within Australia, and/or papers dealing with Australian species that have involved genetic research, but have not simply included a phylogeny paper because it had an Australian species in it. However, if that paper discusses aspects relating to biogeographic patterns within Australia, then it would be included.

If you happen to find any errors or typos please let me know. And if you know of any papers that I have not included, I would greatly appreciate being informed about them. Alternatively, if you have suggestions on better ways to present these references I'll happily consider them.

Please feel free to contact Peter Unmack at

Genetic references for fishes

Adams, M. & Humphreys, W.F. (1993) Patterns of genetic diversity within selected subterranean fauna of the North West Cape peninsula, Western Australia: systematic and biogeographic implications. Records of the Western Australian Museum Supplement, 45, 145–164.

Berra, T.M. & Weatherley, A.H. (1972) A systematic study of the Australian freshwater serranid fish genus Maccullochella. Copeia, 1971, 53–64.

Berra, T.M., Crowley, L.E.L.M., Ivantsoff, W. & Fuerst, P.A. (1996) Galaxias maculatus: an explanation of its biogeography. Marine and Freshwater Research, 47, 845–849.

Bertozzi, T. Adams, M. & Walker, K.F. (2000) Species boundaries in carp gudgeons (Eleotridae: Hypseleotris) from the River Murray, South Australia: evidence for multiple species and extensive hybridization. Marine and Freshwater Research, 51, 805–815.

Bostock, B.M., Adams, M., Laurenson. L.J.B. & Austin, C.M. (2006) The molecular systematics of Leiopotherapon unicolor (Gunther, 1859): testing for cryptic speciation in Australia's most widespread freshwater fish. Biological Journal of the Linnean Society, 87, 537–552.

Chenoweth, S.F. & Hughes, J.M. (1997) Genetic population structure of the catadromous perciform: Macquaria novemaculeata (Percichthyidae). Journal of Fish Biology, 50, 721–723.

Chenoweth, S.F., Hughes, J.M., Keenan, C.P. & Lavery, S. (1998) Concordance between dispersal and mitochondrial gene flow: isolation by distance in a tropical teleost, Lates calcarifer (Australian barramundi). Heredity, 80, 187–197.

Chenoweth, S.F., Hughes, J.M., Keenan, C.P. & Lavery, S. (1998) When oceans meet: a teleost shows secondary intergradation at an Indian-Pacific interface. Proceedings of the Royal Society of London Series B, 265, 415–420.

Cook, B.D., Ma, J., Hillyer, M. J., Song, S. D. & Hughes, J.M. (2006) Polymorphic microsatellite markers in an Australian freshwater fish, southern pygmy perch Nannoperca australis. Molecular Ecology Notes, 6,.

Cook, B.D., Bunn, S.E. & Hughes, J.M. (2007) Molecular genetic and stable isotope signatures reveal complementary patterns of population connectivity in the regionally vulnerable southern pygmy perch (Nannoperca australis). Biological Conservation, 138, 60–72.

Crowley, L.E.L.M., Ivantsoff, W. & Allen, G.R. (1986) Taxonomic position of two crimson-spotted rainbowfish, Melanotaenia duboulayi and Melanotaenia fluviatilis (Pisces: Melanotaeniidae), from eastern Australia, with special reference to their early life-history stages. Australian Journal of Marine and Freshwater Research, 37, 385–398.

Crowley, L.E.L.M. & Ivantsoff, W. (1990) A review of species previously identified as Craterocephalus eyresii (Pisces: Atherinidae). Proceedings of the Linnean Society of New South Wales, 112, 87–103.

Crowley, L.E.L.M. & Ivantsoff, W. (1991) Genetic similarity among populations of rainbowfishes (Pisces: Melanotaeniidae) from Atherton Tableland, northern Queensland. Ichthyological Exploration of Freshwaters, 2, 129–137.

Crowley, L.E.L.M. & Ivantsoff, W. (1992) Redefinition of the freshwater fish genus Craterocephalus (Teleostei: Atherinidae) of Australia and New Guinea with an analysis of three species. Ichthyological Exploration of Freshwaters, 3, 273–287.

Douglas, J.W., Gooley, G.J., Ingram, B.A., Murray, N.D. & Brown, L.D. (1995) Natural hybridization between Murray cod, Maccullochella peelii peelii (Mitchell), and trout cod, M. macquariensis (Cuvier) (Percichthyidae), in the Murray River, Australia. Marine and Freshwater Research, 46, 729–734.

Doupé, R.G., Horwitz, P. & Lymbery, A.J. (1999) Mitochondrial genealogy of Western Australian barramundi: applications of inbreeding coefficients and coalescent analysis for separating temporal population processes. Journal of Fish Biology, 54, 1197–1209.

Frentiu, F.D., Ovenden, J.R. & Street, R. (2001) Australian lungfish (Neoceratodus forsteri: Dipnoi) have low genetic variation at allozyme and mitochondrial DNA loci: a conservation alert? Conservation Genetics, 2, 63–67.

Hammer, M., Adams, M., Unmack, P.J. & Walker, K.F. (2007) A rethink on Retropinna: conservation implications of new taxa and significant genetic sub-structure in Australian smelts (Pisces: Retropinnidae). Marine and Freshwater Research, 58, 327–341.

Hillyer, M.J., Woods, R.J. & Hughes, J.M. (2006) Isolation and characterization of polymorphic microsatellite loci in the Australian smelt, Retropinna semoni. Molecular Ecology Notes, 6, 224–226.

Huey, J.A., Hughes, J.M. & Baker, A.M. (2006) Patterns of gene flow in two species of eel-tailed catfish, Neosilurus hyrtlii and Porochilus argenteus (Siluriformes: Plotosidae), in western Queensland's dryland rivers. Biological Journal of the Linnean Society, 87, 457–467.

Huey, J.A., Baker, A.M. & Hughes, J.M. (2008) The effect of landscape processes upon gene flow and genetic diversity in an Australian freshwater fish, Neosilurus hyrtlii. Freshwater Biology, 53, 1393-1408.

Hughes, J., Ponniah, M., Hurwood, D., Chenoweth, S. & Arthington, A. (1999) Strong genetic structuring in a habitat specialist, the Oxleyan pygmy perch Nannoperca oxleyana. Heredity, 83, 5–14.

Hughes, J.M. & Hillyer, M.J. (2006) Mitochondrial DNA and allozymes reveal high dispersal abilities and historical movement across drainage boundaries in two species of freshwater fishes from inland rivers in Queensland, Australia. Journal of Fish Biology, 68 (Suppl. B), 270-291.

Hughes, J.M. (2007) Constraints on recovery: using molecular methods to study connectivity of aquatic biota in rivers and streams. Freshwater Biology, 52, 616–631.

Hurwood, D.A. & Hughes, J.M. (1998) Phylogeography of the freshwater fish, Mogurnda adspersa, in streams of northeastern Queensland, Australia: evidence for altered drainage patterns. Molecular Ecology, 7, 1507–1517.

Hurwood, D.A & Hughes, J.M. (2001) Historical interdrainage dispersal of eastern rainbowfish from the Atherton Tableland, north-eastern Australia. Journal of Fish Biology, 58, 1125–1136.

Jerry, D.R. (1997) Population genetic structure of the catadromous Australian bass from throughout its range. Journal of Fish Biology, 51, 909–920.

Jerry, D.R. & Woodland, D.J. (1997) Electrophoretic evidence for the presence of the undescribed ‘Bellinger’ catfish (Tandanus sp.) (Teleostei: Plotosidae) in four New South Wales mid-northern coastal rivers. Marine and Freshwater Research, 48, 235–240.

Jerry, D.R. & Baverstock, P.R. (1998) Consequences of a catadromous life-strategy for levels of mitochondrial DNA differentiation among populations of the Australian bass, Macquaria novemaculeata. Molecular Ecology, 7, 1003–1013.

Jerry, D.R., Raadik, T.A., Cairns, S.C. & Baverstock, P.R. (1999) Evidence for natural interspecific hybridization between Australian bass (Macquaria novemaculeata) and estuary perch (M. colonorum). Marine and Freshwater Research, 50, 661–666.

Jerry, D.R., Elphinstone, M.S. & Baverstock, P.R. (2001) Phylogenetic relationships of Australian members of the family Percichthyidae inferred from mitochondrial 12S rRNA sequence data. Molecular Phylogenetics and Evolution, 18, 335–347.

Jerry, D.R. (2005) Elucidation of the range of Tandanus tandanus in south-eastern Australian coastal drainages. Proceedings of the Linnean Society of New South Wales, 126, 121–124.

Jerry, D.R. (2005) Phylogeography of the freshwater catfish Tandanus tandanus (Plotosidae): a model species to understand evolution of the eastern Australian freshwater fish fauna. Marine and Freshwater Research, 59, 351-360.

Keenan, C.P. (1994) Recent evolution of population structure in Australian barramundi, Lates calcarifer (Bloch): an example of isolation by distance in one dimension. Australian Journal of Marine and Freshwater Research, 45, 1123–1148.

Keenan, C. (1999) Should we allow human-induced migration of the Indo-West Pacific fish, barramundi Lates calcarifer (Bloch) within Australia? Aquaculture Research, 31, 121–131.

Kumazawa, Y. & Nishida, M. (2000) Molecular phylogeny of osteoglossoids: a new model for Gondwanian origin and plate tectonic transportation of the Asian arowana. Molecular Phylogenetics and Evolution, 17, 1869–1878.

MacDonald, C.M. (1978) Morphological and biochemical systematics of Australian freshwater and estuarine percichthyid fishes. Australian Journal of Marine and Freshwater Research, 29, 667–698.

McDowall, R.M. & Waters, J.M. (2004) Phylogenetic relationships in a small group of diminutive galaxiid fishes and the evolution of sexual dimorphism. Journal of the Royal Society of New Zealand, 34, 23–57.

McGlashan, D.J. & Hughes, J.M. (2000) Reconciling patterns of genetic variation with stream structure, earth history and biology in the Australian freshwater fish Craterocephalus stercusmuscarum (Atherinidae). Molecular Ecology, 9, 1737–1751.

McGlashan, D.J. & Hughes, J.M. (2001) Low levels of genetic differentiation among populations of the freshwater fish Hypseleotris compressa (Gobiidae: Eleotridinae): implications for its biology, population connectivity and history. Heredity, 86, 222–233.

McGlashan, D.J. & Hughes, J.M. (2001) Genetic evidence for historical continuity between populations of the Australian freshwater fish Craterocephalus stercusmuscarum (Atherinidae) east and west of the Great Dividing Range. Journal of Fish Biology, 59 (Supplement A), 55–67.

McGlashan, D.J., Hughes, J.M. & Bunn, S.E. (2001) Within-drainage population genetic structure of the freshwater fish Pseudomugil signifer (Pseudomugilidae) in northern Australia. Canadian Journal of Fisheries and Aquatic Sciences, 58, 1842–1852.

McGlashan, D.J. & Hughes, J.M. (2002) Extensive genetic divergence among populations of the Australian freshwater fish, Pseudomugil signifer (Pseudomugilidae), at different hierarchical scales. Marine and Freshwater Research, 53, 897-907.

McGuigan, K., Zhu, D., Allen, G.R. & Moritz, C. (2000) Phylogenetic relationships and historical biogeography of melanotaeniid fishes in Australia and New Guinea. Marine and Freshwater Research, 51, 713–723.

Miller, A.D., Waggy, G., Ryan, S.G. & Austin, C.M. (2004) Mitochondrial 12S rRNA sequences support the existence of a third species of freshwater blackfish (Percichthyidae: Gadopsis) from south-eastern Australia. Memoirs of Museum of Victoria, 61, 121–127.

Musyl, M.K. & Keenan, C.P. (1992) Population genetics and zoogeography of Australian freshwater golden perch, Macquaria ambigua (Richardson 1845) (Teleostei: Percichthyidae), and electrophoretic identification of a new species from the Lake Eyre Basin. Australian Journal of Marine and Freshwater Research, 43, 1585–1601.

Musyl, M.K. & Keenan, C.P. (1996) Evidence for cryptic speciation in Australian freshwater eel-tailed catfish, Tandanus tandanus (Teleostei: Plotosidae). Copeia, 1996, 526–534.

Ovenden, J.R., White, R.W.G. & Sanger, A.C. (1988) Evolutionary relationships of Gadopsis spp. inferred from restriction enzyme analysis of their mitochondrial DNA. Journal of Fish Biology, 32, 137–148.

Ovenden, J.R. & White, R.W.G. (1990) Mitochondrial and allozyme genetics of incipient speciation in a landlocked population of Galaxias truttaceus (Pisces: Galaxiidae). Genetics, 124, 701–716.

Ovenden, J.R., White, R.W.G. & Adams, M. (1993) Mitochondrial and allozyme genetics of two Tasmanian galaxiids (Galaxias auratus and G. tanycephalus, Pisces: Galaxiidae) with restricted lacustrine distributions. Heredity, 70, 223–230.

Page, T.J., Sharma, S. & Hughes, J.M. (2004) Deep phylogenetic structure has conservation implications for ornate rainbowfish (Melanotaeniidae: Rhadinocentrus ornatus) in Queensland, eastern Australia. Marine and Freshwater Research, 55, 165–172.

Rourke, M., Nheu, J., Mountford, H., Lade, J., Ingram, B. & McPartlan, H. (2007) Isolation and characterization of 102 new microsatellite loci in Murray cod, Maccullochella peelii peelii (Percichthyidae), and assessment of cross-amplification in 13 Australian native and six introduced freshwater species. Molecular Ecology Notes, 7, 1258-1264. doi:10.1111/j.1471-8286.2007.01849.x

Rowland, S.J. (1993) Maccullochella ikei, an endangered species of freshwater cod (Pisces: Percichthyidae) from the Clarence River system, NSW, and M. peeli mariensis, a new subspecies from the Mary River System, Qld. Records of the Australian Museum, 45, 121–145.

Shaklee, J.B. & Salini, J. (1985) Genetic variation and population subdivision in Australian barramundi, Lates calcarifer (Bloch). Australian Journal of Marine and Freshwater Research, 36, 203–218.

Smith, K.D., Pen, L.J. & Knott, B. (2002) Genetic and morphological study of the black-stripe minnow, Galaxiella nigrostriata (Salmoniformes: Galaxiidae), including a disjunct population near Perth, Western Australia. Records of the Western Australian Museum, 21, 285–290.

Sparks, J.S. & Smith, W.L. (2004) Phylogeny and biogeography of the Malagasy and Australasian rainbowfishes (Teleostei: Melanotaenioidei): Gondwanan vicariance and evolution in freshwater. Molecular Phylogenetics and Evolution, 33, 719–734.

Thacker, C. & Unmack, P.J. (2005) Phylogeny and biogeography of the eleotrid genus Hypseleotris (Teleostei: Gobioidei: Eleotridae). Records of the Australian Museum, 57, 1–13.

Thacker, C., Unmack, P.J., Matsui, L. & Rifenbark, N. (2007) Comparative phylogeography of five sympatric Hypseleotris species (Teleostei: Eleotridae) in southeastern Australia reveals a complex pattern of drainage basin exchanges with little congruence across species. Journal of Biogeography, 34, 1518-1533.

Thacker, C., Unmack, P.J., Matsui, L., Duong, P. & Huang, E. (in press) Phylogeography of Philypnodon species (Teleostei: Eleotridae) across eastern Australia: comparative evolution of a sister pair. Journal of the Linnean Society.

Waters, J.M., Lintermans, M. & White, R.W.G. (1994) Mitochondrial DNA variation suggests river capture as a source of vicariance in Gadopsis bispinosus (Pisces: Gadopsidae). Journal of Fish Biology, 44, 549–551.

Waters, J.M. & Burridge, C.P. (1999) Extreme intraspecific mitochondrial DNA sequence divergence in Galaxias maculatus (Osteichthyes: Galaxiidae), one of the world’s most widespread freshwater fish. Molecular Phylogenetics and Evolution, 11, 1–12.

Waters, J.M., Dijkstra, L.H. & Wallis, G.P. (2000) Biogeography of a southern hemisphere freshwater fish: how important is marine dispersal? Molecular Ecology, 9, 1815–1821.

Waters, J.M., López, J.A. & Wallis, G.P. (2000) Molecular phylogenetics and biogeography of galaxiid fishes (Osteichthyes: Galaxiidae): dispersal, vicariance, and the position of Lepidogalaxias salamandroides. Systematic Biology, 49, 777–795.

Waters, J.M., Shirley, M. & Closs, G.P. (2002) Hydroelectric development and translocation of Galaxias brevipinnis: a cloud at the end of the tunnel? Canadian Journal of Fisheries and Aquatic Sciences, 59, 49–56.

Watts, R.J., Storey, A.W., Hebbert, D.R. & Edward, D.H.D. (1995) Genetic and morphological differences between populations of the western minnow, Galaxias occidentalis, from two river systems in south-western Australia. Journal of Marine and Freshwater Research, 46, 769–777.

Wong, B.B.M., Keogh, J.S. & Jennions, M.D. (2004) Mate recognition in a freshwater fish: geographic distance, genetic differentiation, and variation in female preference for local over foreign males. Journal of Evolutionary Biology, 17, 701–708.

Wong, B.B.M., Keogh, J.S. & McGlashan, D.J. (2004) Current and historical patterns of drainage connectivity in eastern Australia inferred from population genetic structuring in a widespread freshwater fish Pseudomugil signifer (Pseudomugilidae). Molecular Ecology, 13, 391–401.

Zhu, D., Jamieson, B.G.M., Moritz, C. & Hugall, A. (1994) Sequence evolution and phylogenetic signal in control-region and cytochrome b sequences of rainbow fishes (Melanotaeniidae). Molecular Biology and Evolution, 11, 672–683.

Zhu, D., Degnan, S. & Moritz, C. (1998) Evolutionary distinctiveness and status of the endangered Lake Eacham rainbowfish (Melanotaenia eachamensis). Conservation Biology, 12, 80–93.

Genetic references for turtles

Georges, A. & Adams, M. (1992) A phylogeny for the Australian chelid turtles based on allozyme electrophoresis. Australian Journal of Zoology, 40, 453–476.

Georges, A. & Adams, M. (1996) Electrophoretic delineation of species boundaries within the short-necked freshwater turtles of Australia (Testudines: Chelidae). Zoological Journal of the Linnean Society, 118, 241–260.

Georges, A., Birrell, J., Saint, K.M., McCord, W. & Donnellan, S.C. (1998) A phylogeny for side-necked turtles (Chelonia: Pleurodira) based on mitochondrial and nuclear gene sequence variation. Biological Journal of the Linnean Society, 67, 213–246.

Georges, A., Adams, M. & McCord, W. (2002) Electrophoretic delineation of species boundaries within the genus Chelodina (Testudines: Chelidae) of Australia, New Guinea, and Indonesia. Zoological Journal of the Linnean Society, 134, 401–421.

Seddon, J.M., Georges, A., Baverstock, P.R. & McCord, W. (1997) Phylogenetic relationships of chelid turtles (Pleurodira: Chelidae) based on mitochondrial 12S rRNA gene sequence variation. Molecular Phylogenetics and Evolution, 7, 55–61.

Genetic references for crayfishes

Austin, C.M. (1995) Evolution in the genus Cherax (Decapoda: Parastacidae) in Australia: a numerical cladistic analyses of allozyme and morphological data. Freshwater Crayfish, 8, 32–50.

Austin, C.M. (1995) The definition and phylogenetic position of the genus Cherax (Decapoda: Parastacidae). Freshwater Crayfish, 8, 12–31.

Austin, C.M. (1996) Systematics of the freshwater crayfish genus Cherax Erichson (Decapoda: Parastacidae) in northern and eastern Australia: electrophoretic and morphological variation. Australian Journal of Zoology, 44, 259–296.

Austin, C.M. & Knott, B. (1996) Systematics of the freshwater crayfish genus Cherax (Decapoda: Parastacidae) in southwestern Australia: electrophoretic, morphological and habitat variation. Australian Journal of Zoology, 44, 223–258.

Austin, C.M. & Ryan, S.R. (2002) Allozyme evidence for a new species of freshwater crayfish of the genus Cherax Erichson (Decapoda: Parastacidae) from the south-west of Western Australia. Invertebrate Systematics, 16, 357–367.

Austin, C.M., Nguyen, T.T.T., Meewan, M. & Jerry, D.R. (2003) The taxonomy and evolution of the Cherax destructor complex (Decapoda: Parastacidae) re-examined using mitochondrial 16S sequences. Australian Journal of Zoology, 51, 99–110.

Avery, L. & Austin, C.M. (1997) A biochemical taxonomic study of spiny crayfish of the genera Astacopsis and Euastacus (Decapoda: Parastacidae) in south-eastern Australia. Memoirs of the Museum of Victoria, 56, 543–555.

Baker, A.M., Hughes, J.M., Dean, J.C. & Bunn, S.E. (2004) Mitochondrial DNA reveals phylogenetic structuring and cryptic diversity in Australian freshwater macroinvertebrate assemblages. Marine and Freshwater Research, 55, 629–640.

Baker, N., Byrne, K., Noor, S. & Mather, P.B. (2000) Characterization of microsatellite loci in the redclaw crayfish, Cherax quadricarinatus. Molecular Ecology, 9, 494.

Baker, N., De Bruyn, M. & Mather, P.B. (2008) Patterns of molecular diversity in wild stocks of the redclaw crayfish (Cherax quadricarinatus) from northern Australia and Papua New Guinea: impacts of Plio-Pleistocene landscape evolution. Freshwater Biology.

Campbell, N.J.H., Geddes, M.C. & Adams, M. (1994) Genetic variation in yabbies (Cherax destructor Clark and C. albidus Clark (Crustacea: Decapoda: Parastacidae)) indicates the presence of a single, highly sub-structured, species. Australian Journal of Zoology, 42, 745–760.

Crandall, K.A., Lawler, S.H. & Austin, C.M. (1995) A preliminary examination of the molecular phylogenetic relationships of some crayfish genera from Australia (Decapoda: Parastacidae). Freshwater Crayfish, 10, 18–30.

Crandall, K.A., Fetzner, J.W., Lawler, S.H., Kinnersley, M. & Austin, C.M. (1999) Phylogenetic relationships among the Australian and New Zealand genera of freshwater crayfishes (Decapoda: Parastacidae). Australian Journal of Zoology, 47, 199–214.

Geddes, M.C., Musgrove, R.J. & Campbell, N.J.H. (1993) The feasibility of re-establishing the River Murray crayfish, Euastacus armatus, in the lower River Murray. Freshwater Crayfish, 9, 368–379.

Gouws, G., Stewart, B.A. & Daniels, S.R. (2006) Phylogeographic structure of a freshwater crayfish (Decapoda: Parastacidae: Cherax preissii) in south-western Australia. Marine and Freshwater Research, 57, 837–848.

Hansen, B., Adams, M., Krasnicki, T. & Richardson, A.M.M. (2001) Substantial allozyme diversity in the freshwater crayfish Parastacoides tasmanicus supports extensive cryptic speciation. Invertebrate Taxonomy, 15, 667–679.

Hansen, B. & Richardson, A.M.M. (2006). A revision of the Tasmanian endemic freshwater crayfish genus Parastacoides (Crustacea: Decapoda: Parastacidae). Invertebrate Systematics, 20, 713–769.

Horwitz, P., Adams, M. & Baverstock, P. (1990) Electrophoretic contributions to the systematics of the freshwater crayfish genus Engaeus Erichson (Decapoda: Parastacidae). Invertebrate Taxonomy, 4, 615–641.

Horwitz, P. & Adams, M. (2000) The systematics, biogeography and conservation status of species in the freshwater crayfish genus Engaewa Riek (Decapoda: Parasticidae) from southwestern Australia. Invertebrate Taxonomy, 14, 655–680.

Hughes, J.M. (2007) Constraints on recovery: using molecular methods to study connectivity of aquatic biota in rivers and streams. Freshwater Biology, 52, 616–631.

Hughes, J.M. & Hillyer, M. (2003) Patterns of connectivity among populations of the freshwater crayfish Cherax destructor (Decapoda: Parastacidae) in western Queensland, Australia. Marine and Freshwater Research, 54, 587–596.

Jerry, D.R., Purvis, I.W. & Piper, L.R. (2002) Genetic differences in growth among wild populations of the yabby, Cherax destructor (Clark). Aquaculture Research, 33, 917–923.

Lawler, S.H. & Crandall, K.A. (1998) The relationship of the Australian freshwater crayfish genera Euastacus and Astacopsis. Proceedings of the Linnean Society of New South Wales, 119, 1–8.

Lawrence, C.S. & Morrissy, N.M. (2000) Genetic improvement of marron Cherax tenuimanus Smith and yabbies Cherax spp. in Western Australia. Aquaculture Research, 31, 69–82.

Macaranas, J.M., Mather, P.B., Hoeben, P. & Capra, M.F. (1995) Assessment of genetic variation in wild populations of the redclaw crayfish (Cherax quadricarinatus, von Martens 1868) by means of allozyme and RAPD-PCR markers. Marine and Freshwater Research, 46, 1217–1228.

Miller, A., Nguyen, T., Burridge, C. & Austin, C. (2004) Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): a novel gene order revealed. Gene, 331, 65–72.

Munasinghe, D.H.N., Murphy, N.P. & Austin C.M. (2003) Utility of mitochondrial DNA sequences from four gene regions for systematic studies of Australian freshwater crayfish of the genus Cherax (Decapoda: Parastacidae). Journal of Crustacean Biology, 23, 402–417.

Munasinghe, D.H.N., Burridge, C.P. & Austin C.M. (2004) Molecular phylogeny and zoogeography of the freshwater crayfish genus Cherax Erichson (Decapoda: Parastacidae) in Australia. Biological Journal of the Linnean Society, 81, 553–563.

Munasinghe, D.H.N., Burridge, C.P. & Austin C.M. (2004) The systematics of freshwater crayfish of the genus Cherax Erichson (Decapoda: Parastacidae) in eastern Australia: re-examined using nucleotide sequences from 12S rRNA and 16S rRNA genes. Invertebrate Systematics, 18, 215–225.

Nguyen, T.T.T. (2005) A genetic investigation on translocation of Australian commercial freshwater crayfish, Cherax destructor. Aquatic Living Resources, 18, 319–323.

Nguyen, T.T.T, Meewan, M. & Austin, C.M. (2002) Genetic diversity and translocation in the marron, Cherax tenuimanus (Smith): implications for management and conservation. Fisheries Management and Ecology, 8, 163–173.

Nguyen, T.T.T., Murphy, N.P. & Austin, C.M. (2002) Amplification of multiple copies of mitochondrial cytochrome b gene fragments in the Australian freshwater crayfish, Cherax destructor Clark (Parastacidae: Decapoda). Animal Genetics, 33, 304–308.

Nguyen, T.T.T. & Austin, C. (2004) Inheritance of molecular markers and sex in the Australian freshwater crayfish, Cherax destructor Clark. Aquaculture Research, 35, 1328–1338.

Nguyen, T.T.T., Austin, C.M., Murphy, N.P., Schultz, M.B. & Jerry, D.R. (2004) Phylogeography of the freshwater crayfish Cherax destructor Clark (Parastacidae) in inland Australia: historical fragmentation and recent range expansion. Biological Journal of the Linnean Society, 83, 539–550.

Nguyen, T.T.T. & Austin, C. (2005) Phylogeny of the Australian freshwater crayfish Cherax destructor-complex (Decapoda : Parastacidae) inferred from four mitochondrial gene regions. Invertebrate Systematics, 19, 209–216.

Nguyen, T.T.T., Burridge, C.P. & Austin, C.M. (2005) Population genetic studies on the Australian freshwater crayfish, Cherax destructor (Parastacidae: Decapoda) using allozyme and RAPD markers. Aquatic Living Resources, 18, 55–64.

Patak, A. & Baldwin, J. (1984) Electrophoretic and immunochemical comparisons of haemocyanins from Australian freshwater crayfish (Family: Parastacidae): phylogenetic implications. Journal of Crustacean Biology, 4, 528–535.

Patak, A., Baldwin, J. & Lake P.S. (1989) Immunochemical comparisons of haemocyanins of Australian freshwater crayfish: phylogenetic implications. Biochemical Systematics and Ecology, 17, 249–252.

Ponniah, M. & Hughes, J.M. (1998) Evolution of Queensland spiny mountain crayfish of the genus Euastacus Clark (Decapoda: Parastacidae): preliminary 16S mtDNA phylogeny. Proceedings of the Linnean Society of New South Wales, 119, 9–19.

Ponniah, M. & Hughes, J.M. (2004) The evolution of Queensland spiny mountain crayfish of the genus Euastacus. I. testing vicariance and dispersal with interspecific mitochondrial DNA. Evolution, 58, 1073–1085.

Ponniah, M. & Hughes, J.M. (2006) The evolution of Queensland spiny mountain crayfish of the genus Euastacus. II. Investigating simultaneous vicariance with intraspecific genetic data. Marine and Freshwater Research, 57, 349–362.

Shull, H.C., Perez-Losada, M., Blair, D., Sewell, K., Sinclair, E.A., Lawler, S., Ponniah, M. & Crandall, K.A. (2005) Phylogeny and biogeography of the freshwater crayfish Euastacus (Decapoda: Parastacidae) based on nuclear and mitochondrial DNA. Molecular Phylogeny and Evolution, 37, 249–263.

Versteegen, M. & Lawler, S. (1996) Population genetics of the Murray River crayfish Euastacus armartus. Freshwater Crayfish, 11, 146–157.

Walker, M.L., Austin, C.M. & Meewan, M. (2000) Evidence for the inheritance of a blue variant of the Australian fresh-water crayfish Cherax destructor (Decapoda: Parastacidae) as an autosomal recessive. Journal of Crustacean Biology, 20, 25–30.

Zeidler, W. and Adams, M. (1990) Revision of the Australian Genus of freshwater crayfish Gramastacus Riek (Decapoda, Parastacidae). Invertebrate Taxonomy, 3, 913–924.

Genetic references for decapods minus crayfishes

Baker, A.M., Hurwood, D.A., Krogh, M. & Hughes, J.M. (2004) Mitochondrial DNA signatures of restricted gene flow within divergent lineages of an atyid shrimp (Paratya australiensis). Heredity, 93, 196–207.

Boulton, A.J. & Knott, B. (1984) Morphological and electrophoretic studies of the Palaemonidae (Crustacea) of the Perth region, Western Australia. Australian Journal of Marine and Freshwater Research, 35, 769–783.

Carini, G. & Hughes, J.M. (2004) Population structure of Macrobrachium australiense (Decapoda: Palaemonidae) in Western Queensland, Australia: the role of contemporary and historical processes. Heredity, 93, 350–363.

Carini, G., Hughes, J.M. & Bunn, S.E. (2006) The role of waterholes as 'refugia' in sustaining genetic diversity and variation of two freshwater species in dryland river systems (Western Queensland, Australia). Freshwater Biology, 51, 1434–1446.

Chand, V., de Bruyn, M. & Mather, P.B. (2005) Microsatellite loci in the eastern form of the giant freshwater prawn (Macrobrachium rosenbergii). Molecular Ecology Notes, 5, 308–310.

Chenoweth, S.F. & 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.

Cook, B.D., Bunn, S.E. & Hughes, J.M. (2002) Genetic structure and dispersal of Macrobrachium australiense (Decapoda: Palaemonidae) in western Queensland, Australia. Freshwater Biology, 47, 2098–2112.

Cook, B.D., Baker, A.M., Page, T.J., Grant, S.C., Fawcett, J.H., Hurwood, D.A. & 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.

Cook, B.D., Bunn, S.E. & Hughes, J.M. (2007) A comparative analysis of population subdivision in sympatric species of freshwater shrimp (Atyidae: Paratya): concerted or independent responses to hydrographic factors? Freshwater Biology, 52, 2156-2171.

Cooper, S.J.B., Bradbury, J.H., Saint, K.M., Leys, R., Austin, A.D. & Humphreys, W.F. (2007) Subterranean archipelago in the Australian arid zone: mitochondrial DNA phylogeography of amphipods from central Western Australia. Molecular Ecology, 16, 1533–1544.

Cooper, S.J.B., Saint, K.M., Taiti, S., Austin, A.D. & Humphreys, W.F. (2008) Subterranean archipelago: mitochondrial DNA phylogeography of stygobitic isopods (Oniscidea: Haloniscus) from the Yilgarn region of Western Australia. Invertebrate Systematics, 22, 195-203.

de Bruyn, M., Wilson, J.C. & Mather, P.B. (2004) Huxley’s Line demarcates extensive genetic divergence between eastern and western forms of the giant freshwater prawn, Macrobrachium rosenbergii. Molecular Phylogenetics and Evolution, 30, 251–257.

de Bruyn, M., Wilson, J.C. & Mather, P.B. (2004) Reconciling geography and genealogy: phylogeography of giant freshwater prawns from the Lake Carpentaria region. Molecular Ecology, 13, 3515–3526.

Finston, T.L., Bradbury, J.H., Johnson, M.S. & Knott, B. (2004) When morphology and molecular markers conflict: a case history of subterranean amphipods from the Pilbara, Western Australia. Animal Biodiversity and Conservation, 27, 83–94.

Finston, T.L. & Johnson, M.S. (2004) Geographic patterns of genetic diversity in subterranean amphipods of the Pilbara, Western Australia. Marine and Freshwater Research, 55, 619–628.

Finston, T.L., Johnson, M.S., Humphreys, W.S., Eberhard, S.M. & Halse, S.A. (2007) Cryptic speciation in two widespread subterranean amphipod genera reflects historical drainage patterns in an ancient landscape. Molecular Ecology, 16, 355–365.

Gouws, G. & Stewart, B.A. (2007) From genetic structure to wetland conservation: a freshwater isopod Paramphisopus palustris (Phreatoicidea: Amphisopidae) from the Swan Coastal Plain, Western Australia. Hydrobiologia, 589, 249–263.

Guzik, M.T., Abrams, K.M., Cooper, S.J.B., Humphreys, W.F., Cho, J.-L. & Austin, A.D. (2008) Phylogeography of the ancient Parabathynellidae (Crustacea: Bathynellacea) from the Yilgarn region of Western Australia. Invertebrate Systematics, 22, 205-216.

Hancock, M.A. & Hughes, J.M. (1999) Direct measures of instream movement in a freshwater shrimp using a genetic marker. Hydrobiologia, 416, 23–32.

Hedgecock, D., Stelmach, D.J., Nelson, K., Lindenfelser, M.E. & Malecha, S.R. (1979) Genetic divergence and biogeography of natural populations of Macrobrachium rosenbergii. Proceedings of the World Mariculture Society, 10, 873–879.

Hughes, J.M. (2007) Constraints on recovery: using molecular methods to study connectivity of aquatic biota in rivers and streams. Freshwater Biology, 52, 616–631.

Hughes, J.M., Bunn, S.E., Kingston, D.M. & Hurwood, D.A. (1995) Genetic differentiation and dispersal among populations of Paratya australiensis (Atyidae) in rainforest streams in south-east Queensland, Australia. Journal of the North American Benthological Society, 14, 158–173.

Hughes, J.M., Bunn, S.E., Hurwood, D.A., Choy, S. & Pearson, R.G. (1996) Genetic differentiation among populations of Caridina zebra (Decapoda: Atyidae) in tropical rainforest streams, northern Australia. Freshwater Biology, 36, 289–296.

Hughes, J.M., Goudkamp, K., Hurwood, D.A., Hancock, M. & Bunn, S.E. (2003) Translocation causes extinction of a local population of the glass shrimp, Paratya australiensis. Conservation Biology, 17, 1007–1012.

Humphreys, W.F. & Adams, M. (1991) The subterranean aquatic fauna of the North West Cape peninsula, Western Australia. Records of the Western Australian Museum, 15, 383–411.

Hurwood, D.A. & Hughes, J.M. (2001) Nested clade analysis of the freshwater shrimp, Caridina zebra (Decapoda: Atyidae), from north-eastern Australia. Molecular Ecology, 10, 113–126.

Hurwood, D.A., Hughes, J.M., Bunn, S.E. & Cleary, C. (2003) Population structure in the freshwater shrimp (Paratya australiensis) inferred from allozymes and mitochondrial DNA. Heredity, 90, 64–70.

Lindenfelser, M.E. (1984) Morphometric and allozymic congruence: evolution in the prawn Macrobrachium rosenbergii (Decapoda: Palaemonidae). Systematic Zoology, 33, 195–204.

Murphy, N.P. & Austin. C.M. (2002) A preliminary study of 16S rRNA sequence variation in Australian Macrobrachium shrimps (Palaemonidae: Decapoda) reveals inconsistencies in their current classification. Invertebrate Systematics, 16, 697–701.

Murphy, N.P. & Austin, C.M. (2003) Molecular taxonomy and phylogenetics of some Australian palaemonid shrimps. Journal of Crustacean Biology, 23, 169–177.

Murphy, N.P. & Austin, C.M. (2004) Phylogeography of the widespread Australian freshwater prawn, Macrobrachium australiense (Decapoda, Palaemonidae). Journal of Biogeography, 31, 1065–1072.

Murphy, N. & Austin, C. (2004) Multiple origins of the endemic Australian Macrobrachium (Descapoda: Palaemonidae) based on 16S rRNA mitochondrial sequences. Australian Journal of Zoology, 52, 549–559.

Murphy, N.P., Short, J.W. & Austin, C.M. (2004) Re-examination of the taxonomy of the Macrobrachium australiense Holthuis (Decapoda: Palaemonidae) species-complex: molecular evidence for a single species. Invertebrate Systematics, 18, 227–232.

Murphy, N. & Austin, C. (2005) Phylogenetic relationships of the globally distributed freshwater prawn genus Macrobrachium (Crustacea: Decapoda: Palaemonidae): biogeography, taxonomy and the convergent evolution of abbreviated larval development. Zoologica Scripta, 34, 187–197.

Page, T.J., Baker, A.M., Cook, B.D. & Hughes, J.M. (2005) Historical transoceanic dispersal of a freshwater shrimp: the colonization of the South Pacific by the genus Paratya (Atyidae). Journal of Biogeography, 32, 581–593.

Page, T.J., Choy, S.C. & Hughes, J.M. (2005) The taxonomic feedback loop: symbiosis of morphology & molecules. Biology Letters, 1, 139–142.

Page, T.J., von Rintelen, K. & Hughes, J.M. (2007) An Island in the stream: Australia's place in the cosmopolitan world of Indo-West Pacific freshwater shrimp (Decapoda: Atyidae: Caridina). Molecular Phylogenetics and Evolution, 43, 645–659. doi:10.1016/j.ympev.2006.08.007

Page, T.J. & Hughes, J.M. (2007) Phylogeographic structure in an Australian freshwater shrimp largely pre-dates the geological origins of its landscape. Heredity, 98, 222–231. doi:10.1038/sj.hdy.6800932

Page, T.J. & Hughes, J.M. (2007) Radically different scales of phylogeographic structuring within cryptic species of freshwater shrimp (Atyidae: Caridina). Limnology and Oceanography, 52, 1055–1056.

Page, T.J. von Rintelen, K. & Hughes, J.M. (2007) Phylogenetic and biogeographic relationships of subterranean and surface genera of Australian Atyidae (Crustacea: Decapoda: Caridea) inferred with mitochondrial DNA. Invertebrate Systematics, 21, 137–145.

Page, T.J., Short, J.W., Humphrey, C.L., Hillyer, M.J. & Hughes, J.M. (in press) Molecular systematics of the Kakaducarididae (Crustacea: Decapoda: Caridea). Molecular Phylogenetics and Evolution, DOI:10.1016/j.ympev.2007.12.020

Woolschot, L., Hughes, J.M. & Bunn, S.E. (1999) Dispersal among populations of Caridina sp. (Decapoda : Atyidae) in coastal lowland streams, south-eastern Queensland, Australia. Marine and Freshwater Research, 50, 681–688.

Genetic references for molluscs

Baker, A.M., Bartlett, C., Bunn, S.E., Goudkamp, K., Sheldon, F. & Hughes, J.M. (2003) Cryptic species and morphological plasticity in long-lived bivalves (Unionoida: Hyriidae) from inland Australia. Molecular Ecology, 12, 2707–2717.

Baker, A.M., Sheldon, F., Somerville, J., Walker, K.F. & Hughes, J.M. (2004) Mitochondrial DNA phylogenetic structuring suggests similarity between two morphologically plastic genera of Australian freshwater mussels (Unionoida: Hyriidae). Molecular Phylogenetics and Evolution, 32, 902–912.

Carini, G. & Hughes, J.M. (2006) Subdivided population structure and phylogeography of an endangered freshwater snail, Notopala sublineata (Conrad, 1850) (Gastropoda: Viviparidae), in western Queensland, Australia. Biological Journal of the Linnean Society, 88, 1–16.

Colgan, D.J. & Ponder, W.F. (2000) Incipient speciation in aquatic snails in an arid-zone spring complex. Biological Journal of the Linnean Society, 71, 625–641.

Graf, D.L. & O’Foighil, D. (2000) Molecular phylogenetic analysis of 28S rDNA supports a Gondwanan origin for Australasian Hyriidae (Mollusca: Bivalvia: Unionoida). Vie Milieu, 50, 245–254.

Hill, A., Johnson, M.S. & Merrifield, H. (1983) An electrophoretic and morphological examination of Bothriembryon kendricki (Pulmonata: Bulimulidae), a new species previously considered conspecific with B. bulla (Menke). Australian Journal of Zoology, 31, 227–242.

Hughes, J.M. (2007) Constraints on recovery: using molecular methods to study connectivity of aquatic biota in rivers and streams. Freshwater Biology, 52, 616–631.

Hughes, J.M., Baker, A.M., Bartlett, C., Bunn, S., Goudkamp, K. & Somerville, J. (2004) Past and present patterns of connectivity among populations of four cryptic species of freshwater mussels Velesunio spp. (Hyriidae) in central Australia. Molecular Ecology, 13, 3197–3212.

Pereza, K.E., Ponder, W.F., Colgan, D.J. Clark, S.A. & Lydeard, C. (2005) Molecular phylogeny and biogeography of spring-associated hydrobiid snails of the Great Artesian Basin, Australia. Molecular Phylogenetics and Evolution, 34, 545–556.

Ponder, W.F., Colgan, D.J., Clark, G.A., Miller, A.C. & Terzis, T. (1994) Microgeographic genetic and morphological differentiation of freshwater snails-a study on the Hydrobiidae of Wilsons Promontory, Victoria, south eastern Australia. Australian Journal of Zoology, 42, 557–678.

Ponder, W.F., Eggler, P. & Colgan, D.J. (1995) Genetic differentiation of aquatic snails (Gastropoda: Hydrobiidae) from artesian springs in arid Australia. Biological Journal of the Linnean Society, 56, 553–596.

Ponder, W.F., Colgan, D.J., Terzis, T., Clark, S.A. & Miller, A.C. (1996) Three new morphologically and genetically determined species of hydrobiid gastropods from Dalhousie Springs, northern South Australia, with the description of a new genus. Molluscan Research, 17, 49–109.

Wilmer, J.W., Hughes, J.M., Ma, J. & C. Wilcox, C. (2005) Characterization of microsatellite loci in the endemic mound spring snail Fonscochlea accepta and cross species amplification in four other hydrobiid snails. Molecular Ecology Notes, 5, 205–207.

Wilmer, J.W. & Wilcox, C. (2007) Fine scale patterns of migration and gene flow in the endangered mound spring snail, Fonscochlea accepta (Mollusca:Hydrobiidae) in arid Australia. Conservation Genetics, 8, 617–628. doi:10.1007/s10592-006-9206-x

Genetic references for arthropods

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

Bunn, S.E. & Hughes, J.M. (1997) Dispersal and recruitment in streams: evidence from genetic studies. Journal of the North American Benthological Society, 16, 338–346.

Cooper, S.J.B., Hinze, S., Leys, R., Watts, C.H.S. & Humphreys, W.F. (2002) Islands under the desert: molecular systematics and evolutionary origins of stygobitic water beetles (Coleoptera: Dytiscidae) from central Western Australia. Invertebrate Systematics, 16, 589–598.

Hughes, J.M. (2007) Constraints on recovery: using molecular methods to study connectivity of aquatic biota in rivers and streams. Freshwater Biology, 52, 616–631.

Hughes, J.M., Bunn, S.E., Hurwood, D.A. & Cleary, C. (1998) Dispersal and recruitment of Tasiagma ciliata (Trichoptera: Tasimiidae) in rainforest streams, south east Queensland, Australia. Freshwater Biology, 39, 117–127.

Hughes, J.M., Bunn, S.E., Cleary, C. & Hurwood, D.A. (2000) A hierarchical analysis of the genetic structure of an aquatic insect Bungona (Baetidae: Ephemeroptera). Heredity, 85, 561–570.

Hughes, J.M., Hillyer, M. & Bunn, S.E. (2003) Small-scale patterns of genetic variation in the mayfly Bungona narilla (Ephemeroptera: Baetidae) in rainforest streams, south-east Queensland. Freshwater Biology, 48, 709–717.

Leys, R., Watts, C.H.S., Cooper, S.J.B. & Humphreys, W.F. (2003) Evolution of subterranean diving beetles (Coleoptera: Dytiscidae: Hydroporini, Bidessini) in the arid zone of Australia. Evolution, 57, 2819–2834.

Leys, R. & Watts, C.H.S. (2008) Systematics and evolution of the Australian subterranean hydroporine diving beetles (Dytiscidae), with notes on Carabhydrus. Invertebrate Systematics, 22, 217-225.

Schultheis, A.S. & Hughes, J.M. (2005) Spatial patterns of genetic structure among populations of a stone-cased caddis (Trichoptera: Tasimiidae) in south-east Queensland, Australia. Freshwater Biology, 50, 2002–2010.

Scmidt, S.K., Hughes, J.M. & Bunn, S.E. (1995) Gene flow among conspecific populations of Baetis sp. (Ephemeroptera): adult flight and larval drift. Journal of the North American Benthological Society, 14, 147–157.