Conservation Genetics

, Volume 15, Issue 3, pp 707–716 | Cite as

Characterising genetic diversity and effective population size in one reservoir and two riverine populations of the threatened Macquarie perch

  • Lachlan W. FarringtonEmail author
  • Mark Lintermans
  • Brendan C. Ebner
Research Article


Nine polymorphic microsatellite loci have been used to infer population genetic diversity and structure of the threatened Australian freshwater fish, Macquarie perch, across three tributaries of the Murrumbidgee River in south-eastern Australia. This investigation has revealed a high level of divergence among all three populations, along with contrasting patterns of genetic diversity. The Cotter Reservoir, which is a stronghold population for the species, has typically higher diversity and effective population size than nearby riverine populations. This suggests that the reservoir population is unlikely to have undergone a genetic bottleneck during and following dam construction. Genetic diversity estimates were comparable with one riverine site but were significantly higher than a population sampled from the Queanbeyan River. This comparison revealed significantly less heterozygotes in the Queanbeyan River and lower estimates of effective population size. Options and considerations for stock replenishment of this population are discussed.


Macquaria australasica Endangered Translocation 



This work was carried out under funding supplied to Mark Lintermans by the Australian Government’s National Action Plan for Salinity and Water Quality, and the Natural Heritage Trust. The research was carried out under a contract with Adelaide Research and Innovation Pty Ltd. Brendan Ebner and Mark Lintermans collected Cotter Reservoir fish samples. Fish samples for Kissops Flat were collected by Mark Lintermans under licence F88/1416 from NSW Department of Primary Industries (Fisheries) and approval from the NSW Agriculture Director-General’s Animal Care and Ethics Committee. Laboratory work was undertaken at the South Australian Regional Facility for Molecular Evolution & Ecology at The University of Adelaide. Dr Michael Gardner, Kathy Saint and Leanne Wheaton provided technical support throughout the laboratory phase of this project. Administrative support was provided by the University of Adelaide and ACT Parks, Conservation and Lands, and Lachlan Farrington was kindly hosted by Professor Andy Austin and his research group.


  1. Allendorf FW (1991) Ecological and genetic effects of fish introductions: synthesis and recommendations. Can J Fish Aquat Sci 48(S1):178–181CrossRefGoogle Scholar
  2. Appleford P, Anderson TA, Gooley GJ (1998) Reproductive cycle and gonadal development of Macquarie Perch, Cuvier (Percichthyidae), in L. Dartmouth and tributaries of the Murray-Darling Basin, Victoria, Australia. Mar Freshw Res 49:163–169CrossRefGoogle Scholar
  3. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) GENETIX 4.05, logiciel sous WindowsTM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier (France)Google Scholar
  4. Cadwallader PL, Gooley GJ (1985) Propagation and rearing of Murray cod Maccullochella peelii at the Warmwater Fisheries Station Pilot Project Lake Charlegrark. Government Printer, MelbourneGoogle Scholar
  5. Cadwallader PL, Rogan PL (1977) The Macquarie Perch, Macquaria australasica (Pisces: Percichthyidae) of Lake Eildon, Victoria. Aus J Ecol 2:409–418CrossRefGoogle Scholar
  6. Cook BD, Bunn SE, Hughes JM (2007) Molecular genetic and stable isotope signatures reveal complementary patterns of population connectivity in the regionally vulnerable southern pygmy perch (Nannoperca australis). Biol Cons 138(1):60–72Google Scholar
  7. Dudgeon D, Arthington AH, Gessner MO et al (2006) Freshwater biodiversity: importance, threats, status and conservation challenges. Biol Rev 81:163–182PubMedCrossRefGoogle Scholar
  8. Ebner B, Lintermans M (2007). Fish passage, movement requirements and habitat use for Macquarie perch. Final report to the Department of Agriculture, Fisheries and Forestry Australia. Canberra, Parks, Conservation and LandsGoogle Scholar
  9. Ebner B, Lintermans M, Dunford M (2011) A reservoir serves as refuge for adults of the endangered Macquarie perch. Lakes Reservoirs Res Manag 16:23–33CrossRefGoogle Scholar
  10. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620PubMedCrossRefGoogle Scholar
  11. Farrington LW (2011) Microsatellite markers for the threatened Australian freshwater fish, Macquarie Perch (Macquaria australasica). Conserv Genet Res 4(2):235–237Google Scholar
  12. Faulks LK, Gilligan DM, Beheregaray LB (2009) Evolution and maintenance of divergent lineages in an endangered freshwater fish, Macquaria australasica. Conserv Genet 11(3):921–934Google Scholar
  13. Faulks LK, Gilligan DM, Beheregaray LB (2011) The role of natural vs. anthropogenic in-stream structures in determining the genetic diversity of an endangered freshwater fish, Macquarie perch (Macquaria australasica). Evol App 19:4723–4737Google Scholar
  14. Frankham R, Ballou JD, Briscoe DA (2002) Introduction to Conservation Genetics. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  15. Gervasi V, Ciucci P, Boulanger J, Randi E, Boitani L (2012) A multiple data source approach to improve abundance estimates of small populations: the brown bear in the Apennines, Italy. Biol Conserv 152:10–20CrossRefGoogle Scholar
  16. Goudet J (1995) fstat version 1.2: a computer programme to calculate F-statistics. J Hered 86:485–486Google Scholar
  17. Gray SC, De Silva SS, Ingram BA, Gooley GJ (2000) Effects of river impoundment on body condition and reproductive performance of the Australian native fish, Macquarie perch (Macquaria australasica). Lakes Reservoirs Res Manag 5(4):281–291CrossRefGoogle Scholar
  18. Hansen MM, Nielsen EE, Mensberg KLD (1997) The problem of sampling families rather than populations: relatedness among individuals in samples of juvenile brown trout Salmo trutta L. Mol Ecol 6(5):469–474CrossRefGoogle Scholar
  19. Hunt TL, Douglas JW, Allen MS, Gwinn DC, Tonkin Z, Lyon J, Pickworth A (2011) Evaluation of population decline and fishing sustainability of the endangered Australian freshwater fish Macquaria australasica. Fisheries Manag Ecol 18:513–520CrossRefGoogle Scholar
  20. Ingram B, Douglas JW, Lintermans M (2000) Threatened fishes of the world: Macquaria australasica Cuvier, 1830 (Percichthyidae). Environ Biol Fishes 59:68CrossRefGoogle Scholar
  21. Ingram BA, Hayes B, Rourke ML (2011) Impacts of stock enhancement strategies on the effective population size of Murray cod, Maccullochella peelii, a threatened Australian fish. Fisheries Manag Ecol 18(6):467–481CrossRefGoogle Scholar
  22. Iorgu EI, Popa OP, Petrescu AM, Popa LO (2011) Cross-amplification of microsatellite loci in the endangered stone-crayfish Austropotamobius torrentium (Crustacea: Decapoda). Knowl Manag Aquat Ecosyst 401:8CrossRefGoogle Scholar
  23. Koehn JD, Lintermans M, Lyon JP, Ingram BA, Gilligan DM, Todd CR, Douglas JW (2013) Recovery of the endangered trout cod Maccullochella macquariensis: what have we achieved in more than 25 years? Mar Freshw Res 64:822–837CrossRefGoogle Scholar
  24. Laikre L, Schwartz MK, Waples RS, Ryman N (2010) Compromising genetic diversity in the wild: unmonitored large-scale release of plants and animals. Trends Ecol Evol 25:520–529PubMedCrossRefGoogle Scholar
  25. Lintermans M (2007) Fishes of the Murray-Darling Basin: an introductory guide. Murray-Darling Basin Commission, Canberra, p 166Google Scholar
  26. Lintermans M (2012) Managing potential impacts of reservoir enlargement on threatened Macquaria australasica and Gadopsis bispinosus in southeastern Australia. End Sp Res 16:1–16CrossRefGoogle Scholar
  27. Lintermans M (2013a) A review of on-ground recovery actions for threatened freshwater fish in Australia. Mar Freshw Res 64:775–791CrossRefGoogle Scholar
  28. Lintermans M (2013b) The rise and fall of a translocated population of the endangered Macquarie perch Macquaria australasica in southeastern Australia. Mar Freshw Res 64:838–850CrossRefGoogle Scholar
  29. Luikart G, Sherwin WB, Steel BM, Allendorf FW (1998) Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change. Mol Ecol 7:963–974PubMedCrossRefGoogle Scholar
  30. Markert JA, Champlin DM, Gutjahr-Gobell R, Grear JS, Kuhn A, McGreevy TJ Jr, Roth A, Bagley MJ, Nacci DE (2010) Population genetic diversity and fitness in multiple environments. BMC Evol Biol 10:205PubMedCentralPubMedCrossRefGoogle Scholar
  31. McCusker MR, Bentzen P (2010) Positive relationships between genetic diversity and abundance in fishes. Mol Ecol 19(22):4852–4862PubMedCrossRefGoogle Scholar
  32. Narum SR (2006) Beyond Bonferroni: less conservative analyses for conservation genetics. Conserv Genet 7:783–787CrossRefGoogle Scholar
  33. Nock CJ, Ovenden JR, Butler GL, Wooden I, Moore A, Baverstock PR (2011) Population structure, effective population size and adverse effects of stocking in the endangered Australian eastern freshwater cod Maccullochella ikei. J Fish Biol 74(1):303–321Google Scholar
  34. Olden JD et al (2007) Small fish, big fish, red fish, blue fish: size biased extinction risk of the world’s freshwater and marine fishes. Glob Ecol Biogeogr 16:694–701CrossRefGoogle Scholar
  35. Olden JD, Kennard MJ, Lawler JJ, Poff NL (2011) Challenges and opportunities in implementing managed relocation for conservation of freshwater species. Conserv Biol 25:40–47PubMedCrossRefGoogle Scholar
  36. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295CrossRefGoogle Scholar
  37. Philippart JC (1995) Is captive breeding an effective solution for the preservation of endemic species? Biol Conserv 72(2):281–295CrossRefGoogle Scholar
  38. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedCentralPubMedGoogle Scholar
  39. Raymond M, Rousset F (1995) Genepop: population genetics software for exact tests and ecumenicism. J Hered 86:249–284Google Scholar
  40. Rowland SJ (1983) Spawning of the Australian freshwater fish Murray cod, Maccullochella peeli (Mitchell), in earthen ponds. J Fish Biol 23:525–534CrossRefGoogle Scholar
  41. Saura M, Faria R (2011) Genetic tools for restoration of fish populations. Appl Ichthyol 27:5–15CrossRefGoogle Scholar
  42. Tallmon DA, Koyuk A, Luikart G, Beaumont MA (2008) ONeSAMP: a program to estimate effective populations size using approximate Bayesian computation. Mol Ecol Res 8:299–301CrossRefGoogle Scholar
  43. Tonkin Z, Lyon J, Pickworth A (2010) Spawning behaviour of the endangered Macquarie Perch Macquaria australasica in an upland Australian river. Ecol Manag Restor 11:223–226CrossRefGoogle Scholar
  44. van Oosterhout C, Hutchinson WF, Wills DPM, Shipley PF (2004) micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538CrossRefGoogle Scholar
  45. Vörösmarty CJ, McIntyre PB, Gessner MO, Dudgeon D, Prusevich A, Green P et al (2010) Global threats to human water security and river biodiversity. Nature 467:555–561PubMedCrossRefGoogle Scholar
  46. Waples RS, Do C (2008) LDNE: a program for estimating effective population size from data on linkage disequilibrium. Mol Ecol Res 8(4):753–756CrossRefGoogle Scholar
  47. Waples RS, Do C (2010) Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evol Appl 3:244–262PubMedCentralCrossRefGoogle Scholar
  48. Weeks AR, Sgro CM, Young AG, Frankham R, Mitchell NJ, Miller KA et al (2011) Assessing the benefits and risks of translocations in changing environments: a genetic perspective. Evol Apps 4:709–725CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Lachlan W. Farrington
    • 1
    • 2
    Email author
  • Mark Lintermans
    • 3
    • 4
  • Brendan C. Ebner
    • 4
    • 5
    • 6
  1. 1.Nature Glenelg TrustWarrnamboolAustralia
  2. 2.The University of AdelaideAdelaideAustralia
  3. 3.Institute for Applied EcologyUniversity of CanberraCanberraAustralia
  4. 4.Conservation Research UnitACT GovernmentCanberraAustralia
  5. 5.CSIRO Ecosystem SciencesAthertonAustralia
  6. 6.TropWATERJames Cook UniversityTownsvilleAustralia

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