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 crustaceans, molluscs and arthropods, miscellaneous (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, or if you know of any papers that I have not included then please let me know, .

 

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.

Adams, M., Wedderburn, S.D., Unmack, P.J., Hammer, M.P., & Johnson, J.B. (2011) Congeneric assessment demonstrates the linked genetic histories of two threatened fishes (Atherinidae: Craterocephalus) in Australia's Murray-Darling Basin. Conservation Biology, 25, 767–776.

Adams, M., Page, T.J., Hurwood, D.A. & Hughes J.M. (2013) A molecular assessment of species boundaries and phylogenetic affinities in Mogurnda (Eleotridae): a case study of cryptic biodiversity in the Australian freshwater fishes. Marine and Freshwater Research, 64, 920–931.

Austin, C.M., Tan, M.H., Lee, Y.P., Croft, L.J. & Gan, H.M. (2014) The complete mitogenome of the Murray Cod, Maccullochella peelii (Mitchell, 1838) (Teleostei: Percichthyidae). Mitochondrial DNA, (0), 1–2.

Ayres, R.M., Pettigrove, V.J. & Hoffmann, A.A. (2010) Low diversity and high levels of population genetic structuring in introduced eastern mosquitofish (Gambusia holbrooki) in the greater Melbourne area, Australia. Biological Invasions, 12, 3727–3744.

Ayres, R.M., Pettigrove, V.J. & Hoffmann, A.A. (2013) Genetic structure and diversity of introduced eastern mosquitofish (Gambusia holbrooki) in south-eastern Australia. Marine and Freshwater Research, 63, 1206–1214.

Brauer, C.J., Unmack, P.J., Hammer, M.P., Adams, M. & Beheregaray, L.B. (2013) Catchment-scale conservation units identified for the threatened Yarra pygmy perch (Nannoperca obscura) in highly modified river systems. PLoS One, in press

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.

Betancur-R., R. (2009) Molecular phylogenetics and evolutionary history of ariid catfishes revisited: a comprehensive sampling.BMC Evolutionary Biology, 9, 175.

Betancur-R., R. (2010) Molecular phylogenetics supports multiple evolutionary transitions from marine to freshwater habitats in ariid catfishes. Molecular Phylogenetics and Evolution, 55, 249–258.

Betancur-R., R., Ortν, G., Stein, A. M., Marceniuk, A. P. & Pyron, R.A. (2012) Apparent signal of competition limiting diversification after ecological transitions from marine to freshwater habitats. Ecology Letters, doi: 10.1111/j.1461-0248.2012.01802.x

Bloom, D.B., Unmack, P.J., Gosztonyi, A.E., Piller K.R. & Lovejoy, N.R. (2012) It's a family matter: molecular phylogenetics of Atheriniformes and the polyphyly of the surf silversides (Family: Notocheiridae). Molecular Phylogenetics and Evolution, 62, 1025–1030.

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.

Brauer, C.J., Unmack, P.J., Hammer, M.P., Adams, M. & Beheregaray, L.B. (2013) Catchment-scale conservation units identified for the threatened Yarra pygmy perch (Nannoperca obscura) in highly modified river systems. PLoS One, 8(12), e82953.

Brown, C., Aksoy, Y., Varinli, H. & Gillings, M. (2013) Identification of the rainbowfish in Lake Eacham using DNA sequencing. Australian Journal of Zoology, 60, 334–339.

Burridge, C.P., McDowall, R.M., Craw, D., Wilson, M.V.H. & Waters, J.M. (2012) Marine dispersal as a pre-requisite for Gondwanan vicariance among elements of the galaxiid fish fauna. Journal of Biogeography, 39, 306–321.

Carvalho, D.C., Hammer, M.P. & Beheregaray, L.B. (2011) Isolation and PCR multiplex genotyping of 18 novel microsatellite markers for the threatened southern pygmy perch (Nannoperca australis). Conservation Genetics Resources, DOI: 10.1007/s12686-011-9462-z.

Carvalho, D.C., Rodriguez-Zarate, C.J., Hammer, M.P. & Beheregaray, L.B. (2011) Development of 21 microsatellite markers for the threatened Yarra pygmy perch (Nannoperca obscura) through 454 shot-gun pyrosequencing. Conservation Genetics Resources, doi: 10.1007/s12686-011-9413-8.

Chakrabarty, P. (2010) Status and phylogeny of Milyeringidae (Teleostei: Gobiiformes), with the description of a new blind cave-fish from Australia, Milyeringa brooksi, n. sp. Zootaxa, 2557, 19–28.

Chakrabarty, P., Davis, M.P. & Sparks, J.S. (2012) The first record of a trans-oceanic sister-group relationship between obligate vertebrate troglobites. PLoS ONE, 7(8), e44083.

Chen, X., Liu, M., Grewe, P.M., Kyne, P.M. & Feutry, P. (2014) Complete mitochondrial genome of the critically endangered speartooth shark Glyphis glyphis (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA, 0(0), 1-2. doi: doi:10.3109/19401736.2013.809443

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.

Congdon, B.C. (1995) Unidirectional gene flow and maintenance of genetic diversity in mosquitofish Gambusia holbrooki (Teleostei: Poeciliidae). Copeia, 1995, 162–172.

Coleman, R.A., Pettigrove, V., Raadik, T.A., Hoffmann, A.A., Miller A.D. & Carew, M.E. (2010) Microsatellite markers and mtDNA data indicate two distinct groups in dwarf galaxias, Galaxiella pusilla (Mack) (Pisces: Galaxiidae), a threatened freshwater fish from south-eastern Australia. Conservation Genetics, 11, 1911–1928.

Coleman, R.A., Weeks, A.R. & Hoffmann, A.A. (2013) Balancing genetic uniqueness and genetic variation in determining conservation and translocation strategies: a comprehensive case study of threatened dwarf galaxias, Galaxiella pusilla (Mack) (Pisces: Galaxiidae). Molecular Ecology, 22, 1820–1835.

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.

Cook, B.D. & Hughes, J.M. (2010) Historical population connectivity and fragmentation in a tropical freshwater fish with a disjunct distribution (pennyfish, Denariusa bandata). Journal of the North American Benthological Society, 29, 1119–1131.

Cook, B.D., Kennard, M.J, Real, K, Pusey, B.J & Hughes, J.M. (2011) Landscape genetic analysis of the tropical freshwater fish Mogurnda mogurnda (Eleotridae) in a monsoonal river basin: importance of hydrographic factors and population history. Freshwater Biology, 56, 812–827.

Cook, B.D., Adams, M., Mather, P. & Hughes, J.M. (2012) Statistical phylogeographic tests of competing 'Lake Carpentaria hypotheses' in the mouth-brooding freshwater fish, Glossamia aprion (Apogonidae). Marine and Freshwater Research, 63, 450–456.

Cook, B.D., Unmack, P.J., Huey, J.A. & Hughes, J.M. (2014) Do common disjunct populations of freshwater fishes in northern Australia form from the same biogeographic events? Freshwater Science, 33, 263–272.

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.

Davis, A.M., Unmack, P.J., Pusey, B.J., Johnson, J.B. & Pearson, R.G. (2012) Marine-freshwater transitions are associated with the evolution of dietary diversification in terapontid grunters (Teleostei: Terapontidae). Journal of Evolutionary Biology, 25, 1163–1179.

Davis, A.M., Unmack, P.J., Pusey, B.J., Pearson, R.G. & Morgan, D.L. (2013) Ontogenetic development of intestinal length and relationships to diet in an Australasian fish family (Terapontidae). BMC Evolutionary Biology, 13, 53.

Davis, A.M., Unmack, P.J., Pusey, B.J., Pearson, R.G. & Morgan, D.L (2013) Effects of an adaptive zone shift on morphological and ecological diversification in terapontid fishes. Evolutionary Ecology.

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.

Doupι, 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.

Farrington, L.W., Lintermans, M. & Ebner, B.C. (2014) Characterising genetic diversity and effective population size in one reservoir and two riverine populations of the threatened Macquarie perch. Conservation Genetics, in press.

Faulks, L.K, Gilligan, D.M. & Beheregaray, L.B. (2008) Phylogeography of a threatened freshwater fish (Mogurnda adspersa) in eastern Australia: conservation implications. Marine and Freshwater Research, 59, 89–96.

Faulks, L.K, Gilligan, D.M. & Beheregaray, L.B. (2009) Evolution and maintenance of divergent lineages in an endangered freshwater fish, Macquaria australasica. Conservation Genetics, 11, 921–934.

Faulks, L.K, Gilligan, D.M. & Beheregaray, L.B. (2010) Clarifying an ambiguous evolutionary history: range-wide phylogeography of an Australian freshwater fish, golden perch (Macquaria ambigua). Journal of Biogeography, 37, 1329–1340.

Faulks, L.K, Gilligan, D.M. & Beheregaray, L.B. (2010) Islands of water in a sea of dry land: hydrological regime predicts genetic diversity and dispersal in a widespread fish from Australia’s arid zone, the golden perch (Macquaria ambigua). Molecular Ecology, 19, 4723–4737.

Faulks, L.K, Gilligan, D.M. & Beheregaray, L.B. (2011) The role of anthropogenic vs. natural in-stream structures in determining connectivity and genetic diversity in an endangered freshwater fish, Macquarie perch (Macquaria australasica). Evolutionary Applications, 19, 4723–4737.

Feutry, P., Grewe, P.M., Kyne, P.M. & Chen, X. (2014) Complete mitogenomic sequence of the critically endangered northern river shark Glyphis garricki (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA, 0(0), 1-2. doi: doi:10.3109/19401736.2013.861428

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.

Galeotti, D., Castalanelli, M., Groth, D., McCullough, C. & Lund, M. (2014) Geneotypic and morphological variation between Galaxiella nigrostriata (Galaxiidae) populations: implications for conservation. Marine and Freshwater Research.

Gan, H.M., Tan, M.H. & Austin, C.M. (2014) The complete mitogenome of the Macquarie perch, Macquaria australasica Cuvier, 1830 (Teleostei: Percichthyidae). Mitochondrial DNA, 0(0), 1–2. doi: doi:10.3109/19401736.2014.895996

Gan, H. M., Tan, M. H., Lee, Y. P. & Austin, C. M. (2014) The complete mitogenome of the river blackfish, Gadopsis marmoratus (Richardson, 1848) (Teleostei: Percichthyidae). Mitochondrial DNA, (0), 1–2.

Hadfield, A.J., Ivantsoff, W. & Johnson, P.G. (1979) Clinal variation in electrophoretic and morphological characters between two nominal species of the genus Pseudomugil (Pisces: Atheriniformes: Pseudomugilidae). Australian Journal of Marine and Freshwater Research, 30, 375–386.

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.

Hammer, M.P., Unmack, P.J., Adams, M., Walker, K.F. & Johnson, J.B. (2010) Phylogeographic structure in the threatened Yarra pygmy perch Nannoperca obscura (Teleostei: Percichthyidae) has major implications for declining populations. Conservation Genetics, 11, 213–223.

Hammer, M.P., Unmack, P.J., Adams, M., Raadik, T.A. & Johnson, J.B. (2014) A multi-gene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of southeastern Australia. Biological Journal of the Linnean Society, 111, 521–540.

Hardy, C.M., Adams, M., Jerry, D.R., Court, L.N., Morgan, M.J. & Hartley, D.M. (2011) DNA barcoding to support conservation: species identification, genetic structure and biogeography of fishes in the Murray-Darling River Basin, Australia.  Marine and Freshwater Research, 62, 887–901.

Hill, E., Ingram, B.A., Rourke, M., Mitchell, J. & Strugnell, J.M. (2014) Genetic diversity and population structure of the threatened freshwater catfish, Tandanus tandanus, in Victoria, Australia. Conservation Genetics, 1–13.

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.

Huey, J.A., Baker, A.M. & Hughes, J.M. (2010) High levels of genetic structure in the Australian freshwater fish, Ambassis macleayi. Journal of the North American Benthological Society, 29, 1148–1160.

Huey, J.A., Schmidt, D.J., Balcombe, S.R., Marshall, J.C. & Hughes, J.M. (2011) High gene flow and metapopulation dynamics detected for three species in a dryland river system. Freshwater Biology, 56, 2378–2390.

Huey, J.A., Baker, A.M. & Hughes, J.M. (2011) Evidence for multiple historical colonizations of an endoreic drainage basin by an Australian freshwater fish. Journal of Fish Biology, 79, 1047–1067.

Huey, J.A., Real, K.M., Mather, P.B., Chand, V., Roberts, D.T., Espinoza, T., McDougall, A., Kind, P.K., Brooks, S. & Hughes, J.M. (2013) Isolation and characterization of 21 polymorphic microsatellite loci in the iconic Australian lungfish, Neoceratodus forsteri, using the Ion Torrent next-generation sequencing platform. Conservation Genetics Resources, 5, 737–740.

Huey, J.A., Espinoza, T. & Hughes, J.M. (2013) Natural and anthropogenic drivers of genetic structure and low genetic variation in the endangered freshwater cod, Maccullochella mariensis. Conservation Genetics, http://dx.doi.org/10.1007/s10592-013-0490-y

Huey, J.A., Cook, B.D., Unmack, P.J. & Hughes, J.M. (2014) Broadscale phylogeographic structure of five freshwater fishes across the Australian Monsoonal Tropics. Freshwater Science, 33, 273–287.

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.

Hughes, J.M., Schmidt, D.J. & Finn, D.S. (2009) Genes in streams: a molecular approach to understanding movement of freshwater fauna and their riverine habitat. Bioscience, 59, 573–583.

Hughes, J.M., Real, K.M., Marshall, J.C. & Schmidt, D.J. (2012) Extreme genetic structure in a small-bodied freshwater fish, the purple spotted gudgeon, Mogurnda adspersa (Eleotridae). PLoS ONE, 7(7), e40546.

Hughes, J.M., Huey, J.A. And Schmidt, D.J. (2013) Is realised connectivity among populations of aquatic fauna predictable from potential connectivity? Freshwater Biology, doi: 10.1111/fwb.12099

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.

Ingram, B., Hayes, B. & Rourke, M. (2011) Impacts of stock enhancement strategies on the effective population size of Murray cod, Maccullochella peelii, a threatened Australian fish. Fisheries Management and Ecology, 18, 467–481.

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. (2008) 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.

Johnson, C.R., White, R.W.G. & Bick, Y.A.E. (1981) Cytotaxonomy of seven species of Galaxias (Pisces: Galaxiidae) in Tasmania. Genetica, 56, 17–21.

Kadarusman, Hubert, N., Hadiaty, R. K., Paradis, E. & Pouyaud, L. (2012) Cryptic diversity in Indo-Australian rainbowfishes revealed by DNA barcoding: implications for conservation in a biodiversity hotspot candidate. PloS one, 7(7), e40627.

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.

Knight, J. T., Nock, C.J., Elphinstone, M.S. & Baverstock, P.R. (2009) Conservation implications of distinct genetic structuring in the endangered freshwater fish Nannoperca oxleyana (Percichthyidae). Marine and Freshwater Research, 60, 34–44.

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.

Loh, W.K.W., Bond, P., Ashton, K.J., Roberts, D.T. & Tibbetts, I.R. (2014) DNA barcoding of freshwater fishes and the development of a quantitative qPCR assay for the speciesspecific detection and quantification of fish larvae from plankton samples. Journal of Fish Biology, 85, 30–328.

Loughnan, S.R., Baranski, M.D., Robinson, N.A., Jones, P.L. & Burridge, C.P. (2004) Microsatellite loci for studies of wild and hatchery Australian Murray cod Maccullochella peelii peelii (Percichthyidae). Molecular Ecology Notes, 4, 382–384.

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.

Masci, K.D., Ponniah, M. & Hughes, J.M. (2008) Patterns of connectivity between the Lake Eyre and Gulf drainages, Australia: a phylogeographic approach. Marine and Freshwater Research, 59, 761–760.

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.

Miller, A.D., van Rooyen, A., Ayres, R.M., Raadik, T.A., Fairbrother, P. & Weeks, A.R. (2012) The development of 24 polymorphic microsatellite loci for the endangered barred galaxias, Galaxias fuscus, through next generation DNA sequencing. Conservation Genetics Resources, DOI 10.1007/s12686-012-9605-x

Mills, C.E., Hadwen, W.L. & Hughes, J.M. (2008) Looking through glassfish: marine genetic structure in an estuarine species. Marine and Freshwater Research, 59, 627–637.

Mondol, MR..K., Schmidt, D.J., Huey, J.A. & Hughes, J.M. (2014) Development of microsatellite markers for western rainbowfish (Melanotaenia australis) using the Ion Torrent second generation sequencing approach. Conservation Genetics Resources, DOI 10.1007/s12686-014-0271-z

Mu, X.-D., Yang, Y.-X., Liu, Y., Song, H.-M., Luo, J.-R., & Hu, Y.-C. (2014) Complete mitochondrial genome of northern spotted barramundi, Scleropages jardinii. Mitochondrial DNA, 0(0), 1-2. doi: doi:10.3109/19401736.2013.843080

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.

Near, T.J., Sandel, M., Kuhn, K.L., Unmack, P.J., Wainwright, P.C. & Smith, W.M. (2012) Nuclear gene inferred phylogenies resolve the relationships of the enigmatic pygmy sunfishes, Elassoma (Teleostei: Percomorpha). Molecular Phylogenetics and Evolution, 63, 388–395.

Nock, C.J. & Baverstock, P.R. (2008) Polymorphic microsatellite loci for species of Australian freshwater cod, Maccullochella. Conservation Genetics, 9, 1353–1356.

Nock, C.J., Elphinstone, M.S., Rowland, S.J. & Baverstock, P.R. (2010) Phylogenetics and revised taxonomy of the Australian freshwater cod genus, Maccullochella (Percichthyidae). Marine and Freshwater Research, 61, 980–991.

Nock, C.J., Ovenden, J.R., Butler, G.L., Wooden, I., Moore A. & Baverstock, P.R. (2011) Population structure, effective population size and adverse effects of stocking in the endangered Australian eastern freshwater cod Maccullochella ikei. Journal of Fish Biology, 78, 303–321.

Ovenden, J.R. & White, R.W.G. (1988) Mitochondrial DNA restriction site map for Gadopsis marmoratus. Biochemical Systematics and Ecology, 16, 355–357.

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.

Page, T.J. & Hughes, J.M. (2010) Comparing the performance of multiple mitochondrial genes in the analysis of Australian freshwater fishes. Journal of Fish Biology, 77, 2093–2122.

Page, T.J., Marshall, J.C. & Hughes, J.M. (2012) The world in a grain of sand: evolutionarily relevant, small-scale freshwater bioregions on subtropical dune islands. Freshwater Biology, 57, 612–627.

Page, T.J. & Hughes, J.M. (2014) Contrasting insights provided by single and multispecies data in a regional comparative phylogeographic study. Biological Journal of the Linnean Society, 111, 554–569.

Perini, V.d.R., de Carvalho, D.C., Beheregaray, L.B., & Prosdocimi, F. (2014) The complete mitochondrial genome of the southern purple-spotted gudgeon Mogurnda adspersa (Perciformes: Eleotridae) through pyrosequencing. Mitochondrial DNA, 0(0), 1-3. doi: doi:10.3109/19401736.2014.895995

Peters, M.B., Ovenden, J., Broderick, D., Lance, S.L., Hagen, C. & Glenn, T. (2009) Fifteen microsatellite loci for the jungle perch, Kuhlia ruprestris. Molecular Ecology Resources, 9, pp. 1467–1469.

Phillips, R.D., Storey, A.W. & Johnson, M.S. (2009) Genetic structure of Melanotaenia australis at local and regional scales in the east Kimberley, Western Australia. Journal of Fish Biology, 74, 437–451.

Pouyaud, L., Carman, O., Widyastuti, U. & Avarre, J. C. (2014) Development of twelve novel polymorphic microsatellite DNA markers for the Boeseman’s rainbowfish (Melanotaenia boesemani) and tests for their cross-utility in 21 rainbowfish species from West Papua (Indonesia). European Journal of Wildlife Research, 1–6.

Prosdocimi, F., Carvalho, D.C., Almeida, R.N. & Beheregaray, L.B. (2012) The complete mitochondrial genome for two recently derived species of the fish genus Nannoperca (Perciformes, Percichthyidae). Molecular Biology Reports, 39, 2767–2772.

Real, K.M., Schmidt, D.J. & Hughes, J.M. (2009) Mogurnda adspersa microsatellite markers: multiplexing and multi-tailed primer tagging. Conservation Genetics Resources, 1, 411–414.

Rodriguez-Zarate, C.J., Carvalho, D.C., Hammer, M.P. & Beheregaray, L.B. (2014) A set of microsatellite markers for the threatened Murray hardyhead, Craterocephalus fluviatilis (Pisces: Atherinidae) from the southern Murray–Darling Basin. Conservation Genetics Resources, 6, 473–475. DOI 10.1007/s12686-013-0131-2.

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

Rourke, M.L., McPartlan, H.C., Ingram, B.A. & Taylor, C.A. (2009) Polygamy and low effective population size in a captive Murray cod (Maccullochella peelii peelii) population: genetic implications for wild restocking programs. Marine and Freshwater Research, 60, 873–883.

Rourke, M.L., Teske, P.R., Attard, C.R.M., Gilligan, D.M. & Beheregaray, L.B. (2009) Isolation and characterisation of microsatellite loci in the Australian freshwater catfish (Tandanus tandanus). Conservation Genetics Resources, DOI 10.1007/s12686-009-9161-1

Rourke, M.L., McPartlan, H.C., Ingram, B.A. & Taylor, C.A. (2010) Biogeography and life history ameliorate the potentially negative genetic effects of stocking on Murray cod (Maccullochella peelli peelii). Marine and Freshwater Research, 61, 918–927.

Rourke, M.L., McPartlan, H.C., Ingram, B.A. & Taylor, C.A. (2011) Variable stocking effect and endemic population genetic structure in Murray cod Maccullochella peelli peelii. Journal of Fish Biology, 79, 155–177.

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.

Ryan, S.G., Miller, A.D., Austin, C.M. (2004) Allozyme variation and taxonomy of the river blackfish, Gadopsis marmoratus Richardson, in western Victoria. Proceedings of the Royal Society of Victoria, 16, 191–199.

Schmidt, D.J., Crook, D.A., O’Connor, J.P. & Hughes, J.M. (2011) Genetic analysis of threatened Australian grayling Prototroctes maraena suggests recruitment to coastal rivers from an unstructured marine larval source population. Journal of Fish Biology, 78, 98–111.

Schmidt, D.J., Bond, N.R., Adams, M. & Hughes, J.M. (2011) Cytonuclear evidence for hybridogenetic reproduction in natural populations of the Australian carp gudgeon (Hypseleotris: Eleotridae). Molecular Ecology, 20, 3367–3380.

Schmidt, D,J., Huey, J,A., Bond, N,R. & Hughes, J.M. (2013) Population structure of sexually reproducing carp gudgeons: does a metapopulation offer refuge from sexual parasitism? Marine and Freshwater Research 64, 223–232.

Schmidt, D.J., Real, K.M., Crook, D.A. & Hughes, J.M. (2013) Microsatellite markers for Australian temperate diadromous fishes Pseudaphritis urvillii (Bovichtidae) and Lovettia sealii (Galaxiidae). Conservation Genetics Resources, 5, 347–349.

Schmidt, D.J., Crook, D.A., Macdonald, J.I., Huey, J.A., Zampatti, B.P., Chilcott, S, Raadik, T.A. & Hughes, J.M. (2014) Migration history and stock structure of two putatively diadromous teleost fishes, as determined by genetic and otolith chemistry analyses. Freshwater Science, 33, 193–206.

Schwartz, T.S., Jenkins, F. & Beheregaray, L.B. (2005) Microsatellite DNA markers developed for the Australian bass (Macquaria novemaculeata) and their cross amplification in estuary perch (Macquaria colonorum). Molecular Ecology Notes, 5, 519–520.

Schwartz, T.S. & Beheregaray, L.B. (2008) Using genotype simulations and Bayesian analyses to identify individuals of hybrid origin in Australian bass: lessons for fisheries management. Journal of Fish Biology, 72, 435–450.

Shaddick, K., Gilligan, D.M., Burridge, C.P., Jerry, D.R., Truong, K. & Beheregaray, L.B. (2011) Historic divergence with contemporary connectivity in a catadromous fish, the estuary perch (Macquaria colonorum). Canadian Journal of Fisheries and Aquatic Sciences, 68, 304–318.

Shaddick, K., Burridge, C.P., Jerry, D.R., Schwartz, T.S., Truong, K., Gilligan, D.M. & Beheregaray, L.B. (2011) A hybrid zone and bidirectional introgression between two catadromous species: Australian bass Macquaria novemaculeata and estuary perch Macquaria colonorum. Journal of Fish Biology, 79, 1214–1235.

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.

Sharma, S. & Hughes, J.M. (2011) Genetic structure and phylogeography of two freshwater fishes, Rhadinocentrus ornatus and Hypseleotris compressa, in southern Queensland, Australia, inferred from allozymes and mitochondrial DNA. Journal of Fish Biology, 78, 57–77.

Shipham, A., Schmidt, D.J. & Hughes, J.H. (2013) Indirect estimates of natal dispersal distance from genetic data in a stream-dwelling fish (Mogurnda adspersa). Journal of Heredity, 104, 779–790.

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), with redescription of H. cyprinoides. 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. (2008) Phylogeography of Philypnodon species (Teleostei: Eleotridae) across eastern Australia: comparative evolution of a sister pair. Journal of the Linnean Society, 95, 175–192.

Thuesen, P.A., Pusey, B.J., Peck, D.R., Pearson, R. & Congdon, B.C. (2008) Genetic differentiation over small spatial scales in the absence of physical barriers in an Australian rainforest stream fish. Journal of Fish Biology, 72, 1174–1187.

Unmack, P.J. & Dowling, T.E. (2010) Biogeography of the genus Craterocephalus (Teleostei: Atherinidae) in Australia. Molecular Phylogenetics and Evolution, 55, 968–984.

Unmack, P.J., Hammer, M.P., Adams, M. & Dowling, T.E. (2011) A phylogenetic analysis of pygmy perches (Teleostei: Percichthyidae) with an assessment of the major historical influences on aquatic biogeography in southern Australia. Systematic Biology, 60, 797–812.

Unmack, P.J., Bagley, J.C., Adams, M., Hammer, M.P. & Johnson, J.B. (2012) Molecular phylogeny and phylogeography of the Australian freshwater fish genus Galaxiella, with an emphasis on dwarf galaxias (G. pusilla). PLoS ONE, 7(6), e38433.

Unmack, P.J., Allen, G.R. & Johnson, J.B. (2013) Phylogeny and biogeogeography of rainbowfishes (Teleostei: Melanotaeniidae). Molecular Phylogenetics and Evolution, 67, 15–27.

Unmack, P.J., Hammer, M.P., Adams, M., Johnson, J.B. & Dowling, T.E. (2013) The role of continental shelf width in determining freshwater phylogeographic patterns in southeastern Australian pygmy perches (Teleostei: Percichthyidae). Molecular Ecology, 22, 1683–1699.

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. & White, R.W.G. (1997) Molecular phylogeny and biogeography of the Tasmanian and New Zealand mudfishes (Salmoniformes: Galaxiidae). Australian Journal of Zoology, 45, 39–48.

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., Lσpez, 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.

Waters, J.M., Saruwatari, T., Kobaysahi, T., Oohara, I., McDowall, R.M. & Wallis, G.P. (2002) Phylogenetic placement of retropinnid fishes: data set incongruence can be reduced by using asymmetric character state transformation costs. Systematic Biology, 51, 432–449.

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.

White, R.W.G., Bick, Y.A.E. & Wenqing, F. (1987) Karyology of the genus Paragalaxias (Pisces, Salmoniformes, Galaxiidae). Journal of Fish Biology, 31, 583–585.

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.

Woods, R.J., Macdonald, J.I., Crook, D.A., Schmidt, D.J. & Hughes, J.M. (2010) Contemporary and historical patterns of connectivity among populations of an inland river fish species inferred from genetics and otolith chemistry. Canadian Journal of Fisheries and Aquatic Sciences, 67, 1098–1115.

Wynen, L., Larson, H., Thorburn, D., Peverell, S., Morgan, D., Field, I. and Gibb, K. (2009) Mitochondrial DNA supports the identification of two endangered river sharks (Glyphis glyphis and Glyphis garricki) across northern Australia. Marine and Freshwater Research, 60, 554–562.

Young, M.J., Simmons, L.W. & Evans J.P. (2009) Isolation and characterization of 12 novel DNA microsatellites in the western rainbowfish, Melanotaenia australis. Molecular Ecology Resources, 9, 1252–1254.

Young, M.J., Evans J.P. & Simmons, L.W. (2011) Population genetic structure and a possible role for selection in driving phenotypic divergence in a rainbowfish (Melanotaeniidae). Biological Journal of the Linnean Society, 102, 144–160.

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

Alacs, E.A., Hillyer, M.J., Georges, A., FitzSimmons, N.N. & Hughes, J.M. (2009) Development of microsatellite markers in the Australasian snake-necked turtle Chelodina rugosa, and cross-species amplification. Molecular Ecology Resources, 9, 350–353.

Baggiano, O., Schmidt, D.J. & Hughes, J.M. (2011) Nine microsatellite markers for the Australian side-necked turtle Chelodina expansa (Chelidae) and cross species amplifications, Marine Genomics, 4, 297–300.

Fielder, D., Vernes, K., Alacs, E. and Georges, A. (2012) Mitochondrial variation among Australian freshwater turtles (genus Myuchelys), with special reference to the Endangered M. bellii. Endangered Species Research, 17, 63–71.

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.

Georges, A., Spencer, R-J., Welsh, M., Shaffer, H.B., Walsh, R. & Zhang, X. (2011) Application of the precautionary principle to taxa of uncertain status – the case of the Bellinger River Turtle. Endangered Species Research, 14, 127–134.

Georges, A., Zhang, X., Unmack, P.J., Reid, B.N., Le, M. & Mccord, W.P. (2014) Phylogeography of an endemic New Guinea freshwater turtle reflects geological events during the Miocene. Biological Journal of the Linnean Society, 111, 192–208.

Hodges, K., Donnellan, S. & Georges, A. (2014) Phylogeography of the Australian freshwater turtle Chelodina expansa reveals complex relationships among inland and coastal bioregions. Biological Journal of the Linnean Society, 111, 789–805.

Le, M., Reid, B.N., McCord, W. P., Naro-Maciel, E., Raxworthy, C.J., Amato, G., Georges, A. (2013) Resolving the phylogenetic history of the short-necked turtles, genera Elseya and Myuchelys (Testudines: Chelidae) from Australia and New Guinea. Molecular Phylogenetics and Evolution, 68, 251–258.

Reid, B., Le, M., McCord, W., Iverson, J., Georges, A., Bergmann, T., Amato, G., DeSalle, R. & Naro-Maciel, E. (2011) Comparing and combining distance-based and character-based approaches for barcoding turtles. Molecular Ecology Resources, 11, 956–967.

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.

Seddon, J.M., Baverstock P.R. & Georges, A. (1998) The rate of mitochondrial 12S rRNA gene evolution is similar in freshwater turtles and marsupials. Journal of Molecular Evolution, 46, 460–464.

Thomson, S. & Georges, A. (2009) A new genus for Elseya latisternum and related forms of Australian freshwater turtle (Testudines: Pleurodira: Chelidae). Zootaxa, 2053, 32–42.

Todd, E., Blair, D., Hamann, M. & Jerry, D. (2011) Twenty-nine microsatellite markers for two Australian freshwater turtles, Elseya albagula and Emydura macquarii krefftii: development from 454-sequence data and utility in related taxa. Conservation Genetics Resources, 3, 449–456.

Todd, E.V., Blair, D., Limpus, C.J., Limpus, D.J. & Jerry, D.R. (2013) High incidence of multiple paternity in an Australian snapping turtle (Elseya albagula). Australian Journal of Zoology, 60, 412–418.

Todd, E.V., Blair, D., Farley, S., Farrington, L., FitzSimmons, N.N., Georges, A., Limpus, C.J. & Jerry, D.R. (2013) Contemporary genetic structure reflects historical drainage isolation in an Australian snapping turtle, Elseya albagula. Zoological Journal of the Linnean Society, 169, 200–214.

Todd, E.V., Blair, D. & Jerry, D.R. (2014) Influence of drainage divides versus arid corridors on genetic structure and demography of a widespread freshwater turtle, Emydura macquarii krefftii, from Australia. Ecology and Evolution, 4, 606–622.

Todd, E.V., Blair, D., Georges, A., Lukoschek, V. & Jerry, D.R. (2014) A biogeographical history and timeline for the evolution of Australian snapping turtles (Elseya: Chelidae) in Australia and New Guinea. Journal of Biogeography, 41, 905–918.

Zhang, X. & Georges, A. (2014) A complete mitochondrial genome sequence for the Australian turtle, Chelodina longicollis, obtained using 454-pyrosequencing. Conservation Genetics Resources, DOI: 10.1007/s12686-014-0202-z

 

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.

Austin, C.M., Tan, M.H., Croft, L.J. & Gan, H.M. (2014) The complete mitogenome of the crayfish Cherax glaber (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA, 0(0), 1-2. doi: doi:10.3109/19401736.2014.880897

Austin, C.M., Tan, M.H., Croft, L.J. & Gan, H.M. (2014) The complete mitogenome of the freshwater crayfish Cherax cainii (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA, 0(0), 1-2. doi: doi:10.3109/19401736.2013.878907

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, 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, 53, 1592–1605.

Bentley, A.I, Schmidt, D.J. & Hughes J.M. (2010) Extensive intraspecific genetic diversity of a freshwater crayfish in a biodiversity hotspot. Freshwater Biology, 55, 1861–1873.

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.

Dawkins, K., Furse, J., Wild, C. & Hughes, J. (2010) Distribution and population genetics of the freshwater crayfish genus Tenuibranchiurus (Decapoda: Parastacidae). Marine and Freshwater Research, 61, 1048–1055.

Gan, H.M., Schultz, M.B. & Austin, C.M. (2014) Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evolutionary Biology, 14, 19

Gan, H.M., Tan, M.H. & Austin, C.M. (2014) The complete mitogenome of the red claw crayfish Cherax quadricarinatus (Von Martens, 1868) (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA, 0(0), 1–2. doi: doi:10.3109/19401736.2014.895997

Gan, H.M., Tan, M.H., Eprilurahman, R. & Austin, C.M. (2014) The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea. Mitochondrial DNA, 0(0), 1‑2. doi: doi:10.3109/19401736.2014.892105

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.

Gouws, G., Stewart, B.A. & Daniels, S.R. (2010) Phylogeographic structure in the gilgie (Decapoda: Parastacidae: Cherax quinquecarinatus): a south-western Australian freshwater crayfish. Biological Journal of the Linnean Society, 101, 385–402.

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. & Smolenski, A.J. (2002) A preliminary examination of the molecular relationships of some crayfish species from the genus Parastacoides (Decapoda: Parastacidae). In: Whisson, G.J. & Knott, B. (Eds.), Freshwater Crayfish 13: Proceedings of the 13th symposium of the International Association of Astacology, pp. 547-554.

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.

Hughes, J.M., Schmidt, D.J. & Finn, D.S. (2009) Genes in streams: a molecular approach to understanding movement of freshwater fauna and their riverine habitat. Bioscience, 59, 573–583.

Hughes, J.M., Huey, J.A. And Schmidt, D.J. (2013) Is realised connectivity among populations of aquatic fauna predictable from potential connectivity? Freshwater Biology, doi: 10.1111/fwb.12099

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.

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.

Miller, A.D., Sweeney, O.F., Whiterod, N.S., Van Rooyen, A.R., Hammer, M. & Weeks, A.R. (2014) Critically low levels of genetic diversity in fragmented populations of the endangered Glenelg spiny freshwater crayfish Euastacus bispinosus. Endangered Species Research, 25, 43–55.

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.

Page, T.J., Marshall, J.C. & Hughes, J.M. (2012) The world in a grain of sand: evolutionarily relevant, small-scale freshwater bioregions on subtropical dune islands. Freshwater Biology, 57, 612–627.

Page, T.J. & Hughes, J.M. (2014) Contrasting insights provided by single and multispecies data in a regional comparative phylogeographic study. Biological Journal of the Linnean Society, 111, 554–569.

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.

Pavasovic, A., Hair, C., Amin, S., Hurwood, D. A. & Prentis, P. J. (2013) Characterisation of candidate nuclear genes for species delineation in the genus Cherax. Conservation Genetics Resources, 5, 331–333.

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.

Schultz, M.B., Smith, S.A., Richardson, A.M.M., Horwitz, P., Crandall, K.A. & Austin, C.M. (2007) Cryptic diversity in Engaeus Erichson, Geocharax Clark and Gramastacus Riek (Decapoda: Parastacidae) revealed by mitochondrial 16S rDNA sequences. Invertebrate Systematics, 21, 569–587.

Schultz, M.B., Ierodiaconou, D.A., Smith, S.A., Horwitz, P., Richardson, A.M.M., Crandall, K.A. & Austin, C.M. (2008) Sea-level changes and palaeo-ranges: reconstruction of ancient shorelines and river drainages and the phylogeography of the Australian land crayfish Engaeus sericatus Clark (Decapoda: Parastacidae). Molecular Ecology, 17, 5291–5314.

Schultz, M.B., Smith, S.A., Horwitz, P., Richardson, A.M.M., Crandall, K.A. & Austin, C.M. (2009) Evolution underground: a molecular phylogenetic investigation of Australian burrowing freshwater crayfish (Decapoda: Parastacidae) with particular focus on Engaeus Erichson. Molecular Phylogenetics and Evolution, 50, 580–598.

Sherman, C. H., Ierodiaconou, D., Stanley, A., Weston, K., Gardner, M. & Schultz, M. 2012. Development of twenty-four novel microsatellite markers for the freshwater crayfish, Geocharax gracilis, using next generation sequencing. Conservation Genetics Resources, 4, 555–558.

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 Phylogenetics and Evolution, 37, 249–263.

Sinclair, E.A., Madsen, A., Walsh, T., Nelson, J. & Crandall, K.A. (2005) Cryptic genetic divergence in the giant Tasmanian freshwater crayfish Astacopsis gouldi (Decapoda: Parastacidae): implications for conservation. Animal Conservation, 14, 87–97.

Street, D., Edney, G., Rowe, D. & Lawler, S. (2010) A putative hybrid of the Murray Crayfish, Euastacus armatus (Crustacea: Decapoda: Parastacidae). Queensland Museum Memoirs, 55, 213–224.

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 crustaceans minus crayfishes

Abrams, K.M., Guzik, M.T., Cooper, S.J.B., Humphreys, W.F., King, R.A., Cho, J.-L. & Austin, A.D. (2012) What lies beneath: molecular phylogenetics and ancestral state reconstruction of the ancient subterranean Australian Parabathynellidae (Syncarida, Crustacea). Molecular Phylogenetics and Evolution, 64, 130–144.

Abrams, K.M., King, R.A., Guzik, M.T., Cooper, S.J.B. & Austin, A.D. (2013) Molecular phylogenetic, morphological and biogeographic evidence for a new genus of parabathynellid crustaceans (Syncarida : Bathynellacea) from groundwater in an ancient southern Australian landscape. Invertebrate Systematics, 27, 146–172.

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.

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, 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.

Bernays, S., Schmidt, D., Hurwood, D. & Hughes, J. (2014) Phylogeography of two freshwater prawn species from Far North Queensland. Marine and Freshwater Research.

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.

Bradford, T., Adams, M., Humphreys, W.F., Austin, A.D. & Cooper, S.J.B. (2010) DNA barcoding of stygofauna uncovers cryptic amphipod diversity in a calcrete aquifer in Western Australia’s arid zone. Molecular Ecology Resources, 10, 41–50.

Bradford, T., Humphreys, W.F., Austin, A.D. & Cooper, S.J.B. (2014) Identification of trophic niches of subterranean diving beetles in a calcrete aquifer by DNA and stable isotope analyses. Marine and Freshwater Research, 65, 95–104.

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.

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.

Cook, B.D., Page, T.J. & Hughes, J.M. (2008) Importance of cryptic species for identifying ‘representative’ units of biodiversity for freshwater conservation. Biological Conservation, 141, 2821–2831.

Cook, B.D., Page, T.J. & Hughes, J.M. (2011) Molecular and conservation biogeography of freshwater caridean shrimps in north-western Australia. In: Held, C., Koenemann, S. & Schubart, C.D. (Eds.), Phylogeography and Population Genetics in Crustacea, pp. 273–289. CRC Press.

Cook, B.D., Page, T.J. & Hughes, J.M. (2012) Phylogeography of related diadromous species in continental and island settings, and a comparison of their potential and realized dispersal patterns. Journal of Biogeography, 39, 421–430.

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.

Fawcett, J.H., Hurwood, D.A. & Hughes, J.M. (2010) Consequences of a translocation between two divergent lineages of the Paratya australiensis (Decapoda:Atyidae) complex: reproductive success and relative fitness. Journal of the North American Benthological Society, 29, 1170–1180.

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.

Finston, T. L., Francis, C.J. & Johnson, M.S. (2009) Biogeography of the stygobitic isopod Pygolabis (Malacostraca: Tainisopidae) in the Pilbara, Western Australia: evidence for multiple colonisations of the groundwater. Molecular Phylogenetics and Evolution, 52, 448–460.

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.

Gouws, G. & Stewart, B.A. (2013) Molecular species boundaries in the phreatoicidean genus Amphisopus (Isopoda : Amphisopidae) and evidence for a new freshwater isopod species from Western Australia. Invertebrate Systematics, 27, 173–185.

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.

Guzik, M.T., Adams, M.A., Murphy, N.P., Cooper, S.J.B. & Austin, A.D. (2012) Desert springs: deep phylogeographic structure in an ancient endemic crustacean (Phreatomerus latipes). PLoS ONE, 7(7), e37642.

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.

Huey, J.A., Schmidt, D.J., Balcombe, S.R., Marshall, J.C. & Hughes, J.M. (2011) High gene flow and metapopulation dynamics detected for three species in a dryland river system. Freshwater Biology, 56, 2378–2390.

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.

Hughes, J., Bentley, A., Carini, G., Cook, B., Masci, K., Page, T. & Sharma, S. (2009) Application of molecular tools for managing wild genetic resources in Australian freshwater crustaceans. In International Seminar on the Giant Malaysian Prawn. Malaysian Fisheries Society. pp. 43–54.

Hughes, J.M., Schmidt, D.J. & Finn, D.S. (2009) Genes in streams: a molecular approach to understanding movement of freshwater fauna and their riverine habitat. Bioscience, 59, 573–583.

Hughes, J.M., Huey, J.A. And Schmidt, D.J. (2013) Is realised connectivity among populations of aquatic fauna predictable from potential connectivity? Freshwater Biology, doi: 10.1111/fwb.12099

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.

Jarman, S.N. & Elliott, G. (2000) DNA evidence for morphological and cryptic Cenozoic speciations in the Anaspididae, 'living fossils' from the Triassic. Journal of Evolutionary Biology, 13, 624–633.

Jarman, S.N., Redd, K.S. & Gales N.J. (2006) Group-specific primers for amplifying DNA sequences that identify Amphipoda, Cephalopoda, Echinodermata, Gastropoda, Isopoda, Ostracoda and Thoracica. Molecular Ecology Notes, 6, 268–271.

Kilpert, F. & Podsiadlowski, L. (2010) The Australian fresh water isopod (Phreatoicidea: Isopoda) allows insights into the early mitogenomic evolution of isopods. Comparative Biochemistry and Physiology Part D, 5, 36–44.

King R.A. & Leys R. (2011) The Australian freshwater amphipods Austrochiltonia australis and Austrochiltonia subtenuis (Amphipoda: Talitroidea: Chiltoniidae) confirmed and two new cryptic Tasmanian species revealed using a combined molecular and morphological approach. Invertebrate Systematics, 25, 171–196.

King R.A., Bradford, T., Austin, A.D., Humphreys, W.F. & Cooper, S.J.B. (2012) Divergent molecular lineages and not-so-cryptic species: the first descriptions of stygobitic chiltoniid amphipods (Talitroidea: Chiltoniidae) from Western Australia. Journal of Crustacean Biology, 32, 465–488.

King, R.A. & Leys, R. (2014) Molecular evidence for mid-Pleistocene divergence of populations of three freshwater amphipod species (Talitroidea: Chiltoniidae) on Kangaroo Island, South Australia, with a new spring-associated genus and species. Australian Journal of Zoology, 62, 137–156.

Leijs, R., Bloechl, A. & Koenemann, S. (2011) Bogidiella veneris, a new species of subterranean amphipoda (Bogidiellidae) from Australia, with remarks on the systematics and biogeography. Journal of Crustacean Biology, 31, 566–575.

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

Masci, K.D., Ponniah, M. & Hughes, J.M. (2008) Patterns of connectivity between the Lake Eyre and Gulf drainages, Australia: a phylogeographic approach. Marine and Freshwater Research, 59, 761–760.

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.

Murphy, N.P., Guzic, M.T. & Wilmer, J.W. (2010) The influence of landscape on population structure of four invertebrates in groundwater springs. Freshwater Biology, 55, 2499–2509.

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. (2008) Molecular systematics of the Kakaducarididae (Crustacea: Decapoda: Caridea). Molecular Phylogenetics and Evolution, 46, 1003–1014.

Page, T.J., Humphreys, W.F. & Hughes, J.M. (2008) Shrimps Down Under: evolutionary relationships of subterranean crustaceans from Western Australia (Decapoda: Atyidae: Stygiocaris) PLoS ONE, 3(2), e1618.

Page T.J. & Hughes, J.M. (2011) Neither molecular nor morphological data have all the answers; with an example from Macrobrachium (Decapoda: Palaemonidae) from Australia. Zootaxa, 2874, 65–68.

Page, T.J., Marshall, J.C. & Hughes, J.M. (2012) The world in a grain of sand: evolutionarily relevant, small-scale freshwater bioregions on subtropical dune islands. Freshwater Biology, 57, 612–627.

Page, T.J. & Hughes, J.M. (2014) Contrasting insights provided by single and multispecies data in a regional comparative phylogeographic study. Biological Journal of the Linnean Society, 111, 554–569.

Pinceel, T., Vanschoenwinkel, B., Waterkeyn, A., Vanhove, M.P.M., Pinder, A., Timms, B.V. & Brendonck, L. (2012) Fairy shrimps in distress: a molecular taxonomic review of the diverse fairy shrimp genus Branchinella (Anostraca: Thamnocephalidae) in Australia in the light of ongoing environmental change. Hydrobiologia, 700, 313–327.

von Rintelen, K., Page, T.J., Cai, Y., Roe, K., Stelbrink, B., Kuhajda, B.R., Iliffe, T.M., Hughes, J. & von Rintelen, T. (2012) Drawn to the dark side: A molecular phylogeny of freshwater shrimps (Crustacea: Decapoda: Caridea: Atyidae) reveals frequent cave invasions and challenges current taxonomic hypotheses. Molecular Phylogenetics and Evolution, 63, 82–96.

Robertson, H.L. & Murphy, N.P. (2013) 16 microsatellite loci for the Australian Great Artesian Basin spring amphipod, Wangiannachiltonia guzikae. Australian Journal of Zoology, 61, 109–111.

Robertson, H.L., Guzik, M.T. & Murphy, N P. (2014, Persistence in the desert: ephemeral waterways and small-scale gene flow in the desert spring amphipod, Wangiannachiltonia guzikae. Freshwater Biology, 59, 653–665.

Sharma, S. & Hughes, J.M. (2009) Genetic structure and phylogeography of freshwater shrimps (Macrobrachium australiense and Macrobrachium tolmerum): the role of contemporary and historical events. Marine and Freshwater Research, 60, 541–553.

von Rintelen, K., Page, T.J., Cai, Y., Roe, K., Stelbrink, B., Kuhajda, B.R., Iliffe, T., Hughes, J.M. & von Rintelen, T. (2012) Drawn to the dark side: a molecular phylogeny of freshwater shrimps (Crustacea: Decapoda: Caridea: Atyidae) reveals frequent cave invasions and challenges current taxonomic hypotheses. Molecular Phylogenetics and Evolution, 63, 82–96.

Wilson, G.D.F., Humphrey, C.L., Colgan, D.J., Gray, K-A. & Johnson, R.N. (2010) Monsoon-influenced speciation patterns in a species flock of Eophreatoicus Nicholls (Isopoda; Crustacea). Molecular Phylogenetics and Evolution, 51, 349–364.

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.

Hughes, J.M., Schmidt, D.J. & Finn, D.S. (2009) Genes in streams: a molecular approach to understanding movement of freshwater fauna and their riverine habitat. Bioscience, 59, 573–583.

Hughes, J.M., Huey, J.A. And Schmidt, D.J. (2013) Is realised connectivity among populations of aquatic fauna predictable from potential connectivity? Freshwater Biology, doi: 10.1111/fwb.12099

Murphy, N.P., Guzic, M.T. & Wilmer, J.W. (2010) The influence of landscape on population structure of four invertebrates in groundwater springs. Freshwater Biology, 55, 2499–2509.

Murphy, N.P., Breed, M.F., Guzik, M.T., Cooper, S.J.B. & Austin, A.D. (2012) Trapped in desert springs: phylogeography of Australian desert spring snails. Journal of Biogeography, 39, 1573–1582.

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.

Ponder, W.F. & Colgan, D.J. (2002) What makes a narrow-range taxon? Insights from Australian freshwater snails. Invertebrate Systematics, 16, 571–582.

Worthington Wilmer, J., 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.

Worthington Wilmer, J. & 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

Worthington Wilmer, J., Elkin, C., Wilcox, C., Murray, L., Niejalke, D. & Possingham, H. (2008) The influence of multiple dispersal mechanisms and landscape structure on population clustering and connectivity in fragmented artesian spring snail populations. Molecular Ecology, 17, 3733–3751.

Worthington Wilmer, J., Murray, L., Elkin, C., Wilcox, C., Niejalke, D. & Possingham, H. (2011) Catastrophic floods may pave the way for increased genetic diversity in endemic artesian spring snail populations. PLoS ONE, 6(12), e28645.

 

Genetic references for arthropods

Baggiano, O., Schmidt, D.J., Sheldon, F. & Hughes, J.M. (2012) The role of altitude and associated habitat stability in determining patterns of population genetic structure in two species of Atalophlebia (Ephemeroptera: Leptophlebiidae). Freshwater Biology, 56, 230–249.

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.

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.

Balke, M., Pons, J., Ribera, I., Sagata, K. & Vogler, A.P. (2007) Infrequent and unidirectional colonization of hyperdiverse Papuadytes diving beetles in New Caledonia and New Guinea. Molecular Phylogenetics and Evolution, 42, 505–516.

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.

Guzik, M.T., Cooper, S.J.B., Humphreys, W.F., Ong, S., Kawakami, T. & Austin, A.D. (2011) Evidence for population fragmentation within a subterranean aquatic habitat in the Western Australian desert. Heredity, 107, 215–230.

Hawlitschek, O., Hendrich, L., Espeland, M., Toussaint, E.F., Genner, M.J. & Balke, M. (2012) Pleistocene climate change promoted rapid diversification of aquatic invertebrates in southeast Australia. BMC Evolutionary Biology, 12, 142

Hendrich, L., Toussaint, E.F.A. & Balke, M. (2014) A new genus of Hydroporini from south-western Australia. Spixiana, 37, 103–109.

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.

Hughes, J.M., Schmidt, D.J. & Finn, D.S. (2009) Genes in streams: a molecular approach to understanding movement of freshwater fauna and their riverine habitat. Bioscience, 59, 573–583.

Hughes, J.M., Schmidt, D.J., McLean, A. & Wheatley, A. (2009) Population genetic structure in stream insects: what have we learned? In: Lancaster, J. & Briers, R.A. (Eds.), Aquatic Insects: Challenges and Populations, pp. 268–288.

Hughes, J.M., Huey, J.A., McLean, A. & Baggiano, O. (2011) Aquatic insects in eastern Australia: a window on ecology and evolution of dispersal in streams. Insects, 2, 447–461.

Hughes, J.M., Huey, J.A. And Schmidt, D.J. (2013) Is realised connectivity among populations of aquatic fauna predictable from potential connectivity? Freshwater Biology, doi: 10.1111/fwb.12099

Lada, H. & Taylor, A.C. (2009) Polymorphic nuclear markers for aquatic macroinvertebrates Anisops hackeri, Micronecta gracilis and Necterosoma wollastoni. Conservation Genetics, 10, 1625–1627.

Lada, H., Neville, C., Lacey, B., Taylor, A., MacNally, R. & Lake, S.P. (2010) Historic and current genetic population structure in two pond-dwelling macroinvertebrates in massively altered Australian woodland landscapes. Marine and Freshwater Research, 61, 1318–1326.

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.

McLean, A.J., Schmidt, D.J. & Hughes, J.M. (2008) Do lowland habitats represent barriers to dispersal for a rainforest mayfly, Bungona narilla, in South-East Queensland? Marine and Freshwater Research, 59, 761–771.

Murria, C. & Hughes, J.M. (2008) Cyclic habitat displacements during Pleistocene glaciations have induced independent evolution of Tasimia palpata populations (Trichoptera : Tasimiidae) in isolated subtropical rain forest patches. Journal of Biogeography, 35, 1727–1737.

Mynott, J.H., Webb, J.M. & 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.

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.

Schultheis, A.S., Marchant, R. & 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.

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.

Toussaint, E.F.A., Hall, R., Monaghan, M.T., Sagata, K., Ibalim, S., Shaverdo, H.V., Vogler, A.P., Pon, J. & Balke, M. (2014) The towering orogeny of New Guinea as a trigger for arthropod megadiversity. Nature Communications, 5. doi: 10.1038/ncomms5001

Toussaint, E.F., Condamine, F.L., Hawlitschek, O., Watts, C.H., Porch, N., Hendrich, L. & Balke, M. (2014) Unveiling the diversification dynamics of Australasian predaceous diving beetles in the Cenozoic. Systematic Biology, in press.

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

Young, B.A., Schmidt, D.J. & Sheldon, F. (2013) Small-scale patterns of genetic variation in a headwater specialist mayfly: no influence of selective forest harvesting on diversity. Austral Ecology, 38, 504–515.

 

Miscellaneous

Furlan, E., Umina, P. A., Mitrovski, P. J., Gust, N., Griffiths, J., & Weeks, A. R. (2010) High levels of genetic divergence between Tasmanian and Victorian platypuses, Ornithorhynchus anatinus, as revealed by microsatellite loci. Conservation Genetics, 11, 319–323.

Furlan, E.M., Griffiths, J., Gust, N., Handasyde, K.A., Grant, T.R., Gruber, B. & Weeks, A.R. (2013) Dispersal patterns and population structuring among platypuses, Ornithorhynchus anatinus, throughout south-eastern Australia. Conservation Genetics, 14, 837–853.

Gongora, J., Swan, A.B., Chong, A.Y., Ho, S.Y. W., Damayanti, C.S., Kolomyjec, S., Grant, T., Miller, E., Blair, D., Furlan, E. and Gust, N. (2012) Genetic structure and phylogeography of platypuses revealed by mitochondrial DNA. Journal of Zoology, 286, 110–119.

Kimura, H., Sugihara, M., Yamamoto, H., Patel, B., Kato, K. & Hanada, S. (2005) Microbial community in a geothermal aquifer associated with the subsurface of the Great Artesian Basin, Australia. Extremophiles, 9, 407–414.

Kolomyjec, S.H., Grant, T.R. and Blair, D. (2008) Ten polymorphic microsatellite DNA markers for the platypus, Ornithorhynchus anatinus. Molecular Ecology Resources, 8, 1133–1135.

Kolomyjec, S.H., Chong, J.Y.T., Blair, D., Gongora, J., Grant, T.R., Johnson, C.N. & Moran, C. (2009) Population genetics of the platypus (Ornithorhynchus anatinus): a fine-scale look at adjacent river systems. Australian Journal of Zoology, 57, 225–234.

Kolomyjec, S.H., Grant, T.R., Johnson, C.N. & Blair, D. (2014) Regional population structuring and conservation units in the platypus (Ornithorhynchus anatinus). Australian Journal of Zoology, 61, 378–385.

Lillie, M., Woodward, R.E., Sanderson, C.E., Eldridge, M.D.B. & Belov, K. (2012) Diversity at the major histocompatibility complex class II in the platypus, Ornithorhynchus anatinus. Journal of Heredity, 103, 467–478.

Luck, N.A., et al. (2012) Mitochondrial DNA analyses of the saltwater crocodile (Crocodylus porosus) from the Northern Territory of Australia. Australian Journal of Zoology, 60, 18–25.