DNA barcoding to support conservation: Species identification, genetic structure and biogeography of fishes in the Murray-Darling River Basin, Australia

Marine and Freshwater Research

Volumn 62, Issue 8, 2011, Pages 887-901

  Hardy, Christopher M ^a   Adams, Mark ^b   Jerry, Dean R ^c   Court, Leon N ^a   Morgan, Matthew J ^a   Hartley, Diana M ^a  

^a CSIRO   (Australia)

^b SOUTH AUSTRALIAN MUSEUM   (Australia)

^c JAMES COOK UNIVERSITY   (Australia)

Author keywords

12S rRNA; 18S rRNA; mtDNA control region

Indexed keywords

BIOGEOGRAPHY; CAPTIVE BREEDING; CONSERVATION GENETICS; DNA FINGERPRINTING; ENDANGERED SPECIES; GENETIC DIFFERENTIATION; GENETIC STRUCTURE; INVASIVE SPECIES; LIFE HISTORY TRAIT; LOCAL EXTINCTION; MITOCHONDRIAL DNA; MORPHOLOGY; NATIVE SPECIES; OVERFISHING; POPULATION SIZE; RIVER SYSTEM; SPECIES CONSERVATION; STOCK ASSESSMENT; STOMACH CONTENT;

AUSTRALIA; MURRAY-DARLING BASIN;

PISCES;

EID: 80052073301     PISSN: 13231650     EISSN: None     Source Type: Journal    
DOI: 10.1071/MF11027     Document Type: Article

References (69)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology 215, 403-410
2. Barrett, J., and Mallen-Cooper, M. (2006). The Murray Rivers Sea to Hume Dam fish passage program: progress to date and lessons learned. Ecological Management & Restoration 7, 173-183. doi:10.1111/J.1442-8903.2006.00307.X (Pubitemid 44704357)
3. Bertozzi, T., Adams, M., and Walker, K. F. (2000). Species boundaries in carp gudgeons (Eleotrididae: Hypseleotris) from the River Murray, South Australia: evidence for multiple species and extensive hybridization. Marine and Freshwater Research 51, 805-815. doi:10.1071/MF00039
4. Brown, J. M., Hedtke, S. M., Lemmon, A. R., and Lemmon, E. M. (2010). When trees grow too long: investigating the causes of highly inaccurate Bayesian branch-length estimates. Systematic Biology 59, 145-161. doi:10.1093/SYSBIO/ SYP081
5. Cook, B. D., Bunn, S. E., and 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. doi:10.1016/J.BIOCON.2007.04.002 (Pubitemid 46890831)
6. Davies, P. E., Harris, J. H., Hillman, T. J., and Walker, K. F. (2010). The Sustainable Rivers Audit: assessing river ecosystem health in the Murray-Darling Basin, Australia. Marine and Freshwater Research 61, 764-777. doi:10.1071/MF09043
7. Douglas, J. W., Gooley, G. J., Ingram, B. A., Murray, N. D., and Brown, L. D. (1995). Natural hybridization between Murray cod, Maccullochella peelii peelii (Mitchell), and trout cod, Maccullochella macquariensis (Cuvier) (Percichthyidae), in the Murray River, Australia. Marine and Freshwater Research 46, 729-734. doi:10.1071/MF9950729 (Pubitemid 26453231)
8. Faulks, L. K., Gilligan, D. M., and Beheregaray, L. B. (2008). Phylogeography of a threatened freshwater fish (Mogurnda adspersa) in eastern Australia: conservation implications. Marine and Freshwater Research 59, 89-96. doi:10.1071/MF07167 (Pubitemid 351170400)
9. Faulks, L. K., Gilligan, D. M., and Beheregaray, L. B. (2010a). Evolution and maintenance of divergent lineages in an endangered freshwater fish, Macquaria australasica. Conservation Genetics 11, 921-934. doi:10.1007/S10592- 009-9936-7
10. Faulks, L. K., Gilligan, D. M., and Beheregaray, L. B. (2010b). Clarifying an ambiguous evolutionary history: range-wide phylogeography of an Australian freshwater fish, the golden perch (Macquaria ambigua). Journal of Biogeography 37, 1329-1340. doi:10.1111/J.1365-2699.2010.02304.X
11. Fuller, S., Baverstock, P., and King, D. (1998). Biogeographic origins of goannas (Varanidae): a molecular perspective. Molecular Phylogenetics and Evolution 9, 294-307. doi:10.1006/MPEV.1997.0476 (Pubitemid 128349939)
12. Gillespie, J. J. (2004). Characterizing regions of ambiguous alignment caused by the expansion and contraction of hairpin-stem loops in ribosomal RNA molecules. Molecular Phylogenetics and Evolution 33, 936-943. doi:10.1016/J.YMPEV.2004.08.004 (Pubitemid 39444525)
13. Gleeson, D. J., McCallum, H. I., and Owens, I. P. F. (2000). Differences in initial and acquired resistance to Ichthyohthirius multifiliis between populations of rainbowfish. Journal of Fish Biology 57, 466-475.
14. Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41, 95-98.
15. Hammer, M. P., and Walker, K. F. (2004). A catalogue of South Australian freshwater fishes, including new records, range extensions and translocations. Transactions of the Royal Society of South Australia 128, 85-97. (Pubitemid 39606333)
16. Hammer, M. P., Adams, M., Unmack, P. J., and 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. doi:10.1071/MF05258 (Pubitemid 46639915)
17. Hardy, C. M., Krull, E. S., Hartley, D. M., and Oliver, R. L. (2010). Carbon source accounting for fish using combined DNA and stable isotope analyses in a regulated lowland river weir pool. Molecular Ecology 19, 197-212. doi:10.1111/J.1365-294X.2009.04411.X
18. Harper, G. L., King, R. A., Dodd, C. S., Harwood, J. D., Glen, D. M., Bruford, M. W., and Symondson, W. O. C. (2005). Rapid screening of invertebrate predators for multiple prey DNA targets. Molecular Ecology 14, 819-827. doi:10.1111/J.1365-294X.2005.02442.X (Pubitemid 40346473)
19. Higham, J., Hammer, M., and Geddes, M. (2002). Fish and invertebrates. In The Murray Mouth. Exploring the Implications of Closure or Restricted Flow. (Eds N. Goodwin and S. Bennett.) pp. 53-64. (Murray-Darling Basin Commission and Department of Land and Biodiversity Conservation: Canberra.)
20. Higham, J., Ye, Q., and Ferguson, G. (2005). Murray-Darling Basin drought monitoring. Monitoring small-bodied fish in the lower Murray during and after drought conditions in 2003-2004. RD04/0154. South Australian Research Development Institute (Aquatic Sciences), Adelaide.
21. Huey, J. A., Hughes, J. M., and Baker, A. M. (2006). Patterns of gene flow in two species of eel-tailed catfish, Neosilurus hyrtlii and Porochilus argenteus (Siluriformes: Plotosidae), in western Queenslands dryland rivers. Biological Journal of the Linnean Society. Linnean Society of London 87, 457-467. doi:10.1111/J.1095-8312.2006.00590.X (Pubitemid 43341297)
22. Hughes, J. M., and 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, 270-291. doi:10.1111/J.0022-1112.2006. 01073.X (Pubitemid 43876141)
23. Jansen, G., Devaere, S., Weekers, P. H. H., and Adriaens, D. (2006). Phylogenetic relationships and divergence time estimate of African anguilliform catfish (Siluriformes: Clariidae) inferred from ribosomal gene and spacer sequences. Molecular Phylogenetics and Evolution 38, 65-78. doi:10.1016/J.YMPEV. 2005.09.011 (Pubitemid 41773274)
24. Jerry, D. R. (2005). Electrophoretic evidence for the presence of Tandanus tandanus (Pisces: Plotosidae) immediately north and south of the Hunter River, New South Wales. Proceedings of the Linnean Society of New South Wales 126, 121-124. (Pubitemid 44420664)
25. 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. doi:10.1071/MF07187 (Pubitemid 351693061)
26. Jerry, D. R., Raadik, T. A., Cairns, S. C., and Baverstock, P. R. (1999). Evidence for natural interspecific hybridization between the Australian bass (Macquaria novemaculeata) and estuary perch (M. colonorum). Marine and Freshwater Research 50, 661-666. doi:10.1071/MF98120 (Pubitemid 29461782)
27. Jerry, D. R., Elphinstone, M. S., and 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. doi:10.1006/MPEV.2000.0871 (Pubitemid 34299586)
28. Katoh, T., and Toh, H. (2008). Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9, 286-298. doi:10.1093/BIB/BBN013 (Pubitemid 351890825)
29. Kjer, K. M. (1995). Use of ribosomal RNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. Molecular Phylogenetics and Evolution 4, 314-330. doi:10.1006/MPEV.1995.1028
30. Krieger, J., Hett, A. K., Fuerst, P. A., Birstein, V. J., and Ludwig, A. (2006). Unusual intraindividual variation of the nuclear 18S rRNA gene is widespread within the Acipenseridae. The Journal of Heredity 97, 218-225. doi:10.1093/JHERED/ESJ035 (Pubitemid 43966689)
31. Kuiter, R. H. (2008). The southern pygmy perch. Fishes of Sahul 22, 414-417.
32. Li, J., Xia, R., McDowall, R. M., Lopez, J. A., Lei, G., and Fu, C. (2010). Phylogenetic position of the enigmatic Lepidogalaxias salamandroides with comment on the orders of lower euteleosean fishes. Molecular Phylogenetics and Evolution 57, 932-936. doi:10.1016/J.YMPEV.2010.07.016
33. Lintermans, M. (2000). Recolonization by the mountain galaxias Galaxias olidus of a montane stream after the eradication of rainbow trout Oncorhynchus mykiss. Marine and Freshwater Research 51, 799-804. doi:10.1071/MF00019
34. Lintermans, M. (2007). Fishes of the Murray-Darling Basin: An Introductory Guide. (Murray-Darling Basin Commission: Canberra.)
35. McDonald, D. B., Parchman, T. L., Bower, M. R., Hubert, W. A., and Rahel, F. J. (2008). An introduced and a native vertebrate hybridize to form a genetic bridge to a second native species. Proceedings of the National Academy of Sciences, USA 105, 10 837-10 842. doi:10.1073/PNAS.0712002105
36. McDowall, R. M. (2006). Crying wolf, crying foul, or crying shame: alien salmonids and a biodiversity crisis in the southern cool-temperate galaxioid fishes? Reviews in Fish Biology and Fisheries 16, 233-422. doi:10.1007/S11160- 006-9017-7 (Pubitemid 44882609)
37. McGlashan, D. J., and 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, 55-67. doi:10.1111/J.1095-8649.2001. TB01378.X (Pubitemid 34140223)
38. McNeil, D. G., Wilson, P. J., Hartwell, D., and Pellizzari, M. (2008). Olive perchlet (Ambassis agassizii) in the Lachlan River: population status and sustainability in theLakeBrewster region.Areport submitted to theLachlan Catchment Management Authority. South Australian Research and Development Institute (Aquatic Sciences), No. F2008/000846-1, Adelaide.
39. Miller, A. D., Waggy, G., Ryan, S. G., and Austin, C. M. (2004). Mitochondrial 12S rRNA sequences support the existence of a third species of freshwater blackfish (Percicthyidae: Gadopsis) from south-eastern Australia. Memoirs of the Museum Victoria 61, 121-127.
40. Miller, M. A., Holder, M. T., Vos, R., Midford, P. E., Liebowitz, T., et al. (2009). The CIPRES Portals (CIPRES 2009-08-04). Available at http://www.phylo.org/sub-sections/portal [Verified 4 March 2011].
41. Moore, A., Ingram, B. A., Friend, S., King Ho, H., Robinson, N., et al. (2010). Management of Genetic Resources for Fish and Crustaceans in the Murray-Darling Basin. (Bureau of Rural Sciences: Canberra.)
42. Moritz, C. (1994). Defining evolutionarily-significant-units for conservation. Trends in Ecology & Evolution 9, 373-375. doi:10.1016/0169- 5347(94)90057-4 (Pubitemid 2130029)
43. Moritz, C., and Cicero, C. (2004). DNA barcoding: promise and pitfalls. PLoS Biology 2, 1529-1531. doi:10.1371/JOURNAL.PBIO.0020354 (Pubitemid 39532912)
44. Nock, C. J., Elphinstone, M. S., Rowland, S. J., and Baverstock, P.R. (2010). Phylogenetics and revised taxonomy of the Australian freshwater cod genus, Maccullochella (Percichthyidae). Marine and Freshwater Research 61, 980-991. doi:10.1071/MF09145
45. Osinov, A. G., and Lebedev, V. S. (2000). Genetic divergence and phylogeny of the Salmoninae based on allozyme data. Journal of Fish Biology 57, 354-381
46. Ovenden, J. R., Lloyd, J., Newman, S. J., Keenan, C. P., and Slater, L. S. (2002). Spatial genetic subdivision between northern Australian and southeast Asian populations of Pristipomoides multidens: a tropical marine reef fish species. Fisheries Research 59, 57-69. doi:10.1016/S0165-7836(01)00415-5 (Pubitemid 36035683)
47. Page, T. J., and 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. doi:10.1111/J.1095-8649.2010.02821.X
48. Raadik, T. (2001). When is a mountain galaxias not a mountain galaxias? Fishes of Sahul 15, 785-789.
49. Raadik, T. A., Saddlier, S. R., and Koehn, J. D. (1996). Threatened fishes of the world: Galaxias fuscus Mack, 1936 (Galaxiidae). Environmental Biology of Fishes 47, 108. doi:10.1007/BF00002385 (Pubitemid 26344176)
50. Ronquist, F., and Huelsenbeck, J. P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics (Oxford, England) 19, 1572-1574. doi:10.1093/BIOINFORMATICS/BTG180 (Pubitemid 37038874)
51. Rourke, M., Teske, P., Attard, C., Gilligan, D., and Beheregaray, L. (2010). Isolation and characterisation of microsatellite loci in the Australian freshwater catfish (Tandanus tandanus).ConservationGeneticsResources 2, 245-248. doi:10.1007/S12686-009-9161-1
52. Rowland, S. J. (1984). Hybridization between the estuarine fishes yellowfin bream, Acanthopagrus australis (Gunther), and black bream, Acanthopagrus butcheri (Munro) (Pisces, Sparidae). Australian Journal of Marine and Freshwater Research 35, 427-440. doi:10.1071/MF9840427
53. Rowland, S. J. (1993). Maccullochella ikei, an endangered species of freshwater cod (Pisces: Percichthyidae) from the Clarence River system, NSW and M. peelii mariensis, a new subspecies from the Mary River system, Qld. Records of the Australian Museum 45, 121-145. doi:10.3853/J.0067-1975.45.1993.132
54. Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, England) 22, 2688-2690. doi:10.1093/BIOINFORMATICS/BTL446 (Pubitemid 44642609)
55. Stamatakis, A., Hoover, P., and Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology 57, 758-771. doi:10.1080/10635150802429642
56. Swartz, E. R., Mwale, M., and Hanner, R. (2008).A role for barcoding in the study of African fish diversity and conservation. South African Journal of Science 104, 293-298.
57. Tavare, S. (1986). Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on Mathematics in the Life Sciences 17, 57-86.
58. Thacker, C. E., Unmack, P. J., Matsui, L., Duong, P., and Huang, E. (2008). Phylogeography of Philypnodon species (Teleostei: Eleotridae) across south-eastern Australia: testing patterns of connectivity across drainage divides and among coastal rivers. Biological Journal of the Linnean Society. Linnean Society of London 95, 175-192. doi:10.1111/J.1095-8312.2008.01000.X
59. Unmack, P. J. (2001). Biogeography of Australian freshwater fishes. Journal ofBiogeography 28, 1053-1089. doi:10.1046/J.1365-2699.2001.00615.X (Pubitemid 34018094)
60. Walker, K. F. (1985).Areview of the ecological effects of river regulation in Australia. Hydrobiologia 125, 111-129. doi:10.1007/BF00045929 (Pubitemid 17248709)
61. Wang, H. Y., Tsai, M. P., Dean, J., and Lee, S. C. (2001). Molecular phylogeny of gobioid fishes (Perciformes: Gobioidei) based on mitochondrial 12S rRNA sequences. Molecular Phylogenetics and Evolution 20, 390-408. doi:10.1006/MPEV.2001.0957 (Pubitemid 32835886)
62. Waples, R. S. (1991). Genetic interactions between hatchery and wild salmonids -Lessons from the Pacific-Northwest. Canadian Journal of Fisheries and Aquatic Sciences 48, 124-133.
63. Ward, R. D., Hanner, R., and Hebert, P. D. N. (2009). The campaign toDNA barcode all fishes, FISH-BOL. Journal of Fish Biology 74, 329-356. doi:10.1111/J.1095-8649.2008.02080.X
64. Waters, J. M., Esa, Y. B., and Wallis, G. P. (2001). Genetic and morphological evidence for reproductive isolation between sympatric populations of Galaxias (Teleostei: Galaxiidae) in South Island, New Zealand. Biological Journal of the Linnean Society. Linnean Society of London 73, 287-298. doi:10.1111/J.1095-8312.2001.TB01364.X (Pubitemid 32704220)
65. Wilson, W. D., and Turner, T. F. (2009). Phylogenetic analysis of the Pacific cutthroat trout (Oncorhynchus clarki ssp.: Salmonidae) based on partial mtDNA ND4 sequences: a closer look at the highly fragmented inland species. Molecular Phylogenetics and Evolution 52, 406-415. doi:10.1016/J.YMPEV.2009.03. 018
66. Winchell, C. J., Sullivan, J., Cameron, C. B., Swalla, B. J., and Mallatt, J. (2002). Evaluating hypotheses of deuterostome phylogeny and chordate evolution with new LSU and SSU ribosomal DNA data. Molecular Biology and Evolution 19, 762-776. (Pubitemid 34521307)
67. Wong, C. M., Williams, C. E., Pittock, J., Collier, U., and Schelle, P. (2007). Worlds Top 10 Rivers at Risk. (WWF International: Gland, Switzerland.)
68. Wuyts, J., Perriere, G., and Van de Peer, Y. (2004). The European ribosomal RNA database. Nucleic Acids Research 32, D101-D103. doi:10.1093/NAR/GKH065 (Pubitemid 38081613)
69. Yang, Z. (1996). Among-site rate variation and its impact on phylogenetic analyses. Trends in Ecology & Evolution 11, 367-372. doi:10.1016/0169- 5347(96)10041-0 (Pubitemid 126381530)