Molecular genetic and stable isotope signatures reveal complementary patterns of population connectivity in the regionally vulnerable southern pygmy perch (Nannoperca australis)

Biological Conservation

Volumn 138, Issue 1-2, 2007, Pages 60-72

  Cook, Benjamin D ^a   Bunn, Stuart E ^a   Hughes, Jane M ^a  

^a GRIFFITH UNIVERSITY   (Australia)

Author keywords

Drought; Genetic diversity; Microsatellites; Mitochondrial DNA; Nannoperca australis; Natural abundance stable isotopes; Stream restoration

Indexed keywords

CARBON ISOTOPE; CONNECTIVITY; ENDANGERED SPECIES; GENETIC ANALYSIS; GENETIC MARKER; GENETIC VARIATION; HABITAT CORRIDOR; HABITAT FRAGMENTATION; HABITAT RESTORATION; ISOLATED POPULATION; LOTIC ENVIRONMENT; MITOCHONDRIAL DNA; NITROGEN ISOTOPE; PERCID; POPULATION DECLINE; REFUGIUM; STABLE ISOTOPE; STREAM;

AUSTRALASIA; AUSTRALIA;

NANNOPERCA AUSTRALIS;

EID: 34249986634     PISSN: 00063207     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biocon.2007.04.002     Document Type: Article

References (98)

1. Bank M.S., Crocker J.B., Davis S., Brotherton D.K., Cook R., Behler J., and Connery B. Population declines of northern dusky salamanders at Acadia National Park, Maine, USA. Biological Conservation 130 (2006) 230-238
2. Bekkevold D., Hansen M.M., and Mensberg K.L.D. Genetic detection of sex-specific dispersal in historical and contemporary populations of anadromous brown trout Salmo trutta. Molecular Ecology 13 (2004) 1707-1712
3. Bernatchez L., and Osinov A. Genetic diversity of trout (Genus Salmo) from its most eastern natural range based upon mitochondrial DNA and nuclear gene variation. Molecular Ecology 4 (1995) 285-297
4. Berry O., Tocher M.D., and Sare S.D. Can assignment tests measure dispersal?. Molecular Ecology 13 (2004) 551-561
5. Birky C.W.J., Fuerst P., and Maruyama T. Organelle gene diversity under migration, mutation, and drift: equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes. Genetics 121 (1989) 613-627
6. Bond N.R., and Lake P.S. Local habitat restoration in streams: constraints on the effectiveness of restoration for stream biota. Ecological Management and Restoration 4 (2003) 193-198
7. Bond N.R., and Lake P.S. Characterizing fish-habitat associations in streams as the first step in ecological restoration. Austral Ecology 28 (2003) 611-621
8. Bond N.R., and Lake P.S. Ecological restoration and large-scale ecological disturbance: the effects of drought on the response by fish to a habitat restoration experiment. Restoration Ecology 13 (2005) 39-48
9. Brown J.H., and Kodric-Brown A. Turnover rates in insular biogeography: effect of immigration on extinction. Ecology 58 (1977) 445-449
10. Campana S.E., and Thorrold S.R. Otoliths, increments, and elements: keys to a comprehensive understanding of fish populations?. Canadian Journal of Fisheries and Aquatic Sciences 58 (2001) 30-38
11. Castric V., Bonney F., and Bernatchez L. Landscape structure and hierarchical genetic diversity in the brook charr, Salvelinus fontinalus. Evolution 55 (2001) 1016-1028
12. Charles K., Roussel J.M., Lebel J.M., Baglinière J.L., and Ombredane D. Genetic differentiation between anadromous and freshwater brown trout (Salmo trutta L.): insights obtained from stable isotope analysis. Ecology of Freshwater Fish 15 (2006) 255-263
13. Clark K.R., and Gorley R.N. PRIMER version 5.2.8: user manual/tutorial (2001), PRIMER-E Ltd, Plymouth, UK
14. Clegg S.M., Kelly J.F., Kimura M., and Smith T.B. Combining genetic markers and stable isotopes to reveal population connectivity and migration patterns in a neotropical migrant, Wilson's warbler (Wilsonia pusilla). Molecular Ecology 12 (2003) 819-830
15. Clement M., Posada D., and Crandall K. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9 (2000) 1657-1660
16. Cook B.D., Ma J., Hillyer M.J., Song S.D., and Hughes J.M. Polymorphic microsatellite markers in an Australian freshwater fish, southern pygmy perch Nannoperca australis. Molecular Ecology Notes 6 (2006) 907-908
17. Cornuet J.M., and Luikart G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144 (1996) 2001-2014
18. Cournet J.M., Piry S., Luikart G., Estoupe A., and Solignac M. New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153 (1999) 1898-2000
19. Covich A.P., Crowl T.A., and Scatena F.N. Effects of extreme low flows on freshwater shrimps in a perennial stream. Freshwater Biology 48 (2003) 1199-1206
20. Cunjak R.A., Roussel J.-M., Gray M.A., Dietrich J.P., Cartwright D.F., Munkittrick K.R., and Jardine T.D. Using stable isotope analysis with telemetry or mark-recapture data to identify fish movement and foraging. Oecologia 144 (2005) 636-646
21. Davis, J.A., Finlayson, B., 2000. Sand Slugs and Stream Degradation: the Case of the Granite Creeks, North-East Victoria. Technical Report 7/2000. Cooperative Research Centre for Freshwater Ecology, Canberra.
22. Downes B.J., Lake P.S., Glaister A., and Bond N.R. Effects of sand sedimentation on the macroinvertebrate fauna of lowland streams: are the effects consistent?. Freshwater Biology 51 (2006) 144-160
23. Edwards T., Schwalbe C.R., Swann D.E., and Goldberg C.S. Implications of anthropogenic landscape change on inter-population movements of the dessert tortoise (Gopherus agassizii). Conservation Genetics 5 (2004) 485-499
24. Excoffier L., Smouse P.E., and Quattro J.M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131 (1992) 479-491
25. Fagan W.F. Connectivity, fragmentation and extinction risk in dendritic metapopulations. Ecology 83 (2002) 3243-3249
26. Fausch K.D., and Young M.K. Evolutionary significant units and movement of resident stream fishes: a cautionary tale. American Fisheries Society Symposium 17 (1995) 360-370
27. Ferguson M.M., Danzmann R.G., and Hutchings J.A. Incongruent estimates of population differentiation among brook charr, Salvelinus fontinalis from Capen Race, Newfoundland, Canada based upon allozyme and mitochondrial DNA variation. Journal of Fisheries Biology 39 Suppl. A (1991) 79-85
28. Frankham R., Ballou J.D., and Briscoe D.A. An Introduction to Conservation Genetics (2002), Cambridge University Press, Sydney
29. Frankham R. Genetics and extinction. Biological Conservation 126 (2005) 131-140
30. Frankel O.H., and Soulé M.E. Conservation and Evolution (1981), Cambridge University Press, New York
31. Fraser D.F., Gilliam J.F., MacGowan M.P., Arcaro C.M., and Guillozet P.H. Habitat quality in a hostile river corridor. Ecology 80 (1999) 597-607
32. Fraser D.F., Gilliam J.F., Daley M.J., Le A.N., and Skalski G.T. Explaining leptokurtic movement distributions: intrapopulation variation in boldness and exploration. American Naturalist 158 (2001) 124-135
33. Frazer T.K., Ross R.M., Quetin L.B., and Montour J.P. Turnover of carbon and nitrogen during growth of larval krill, Euphausia superba Dana: a stable isotope approach. Journal of Experimental Marine Biology and Ecology 212 (1997) 259-275
34. Gaggiotti O.E., Brooks S.P., Amos W., and Harwod J. Combining demographic, environmental and genetic data to test hypotheses about colonisation processes in metapopulations. Molecular Ecology 13 (2004) 811-825
35. Gerking S.D. The restricted movement of fish populations. Biological Review 34 (1959) 221-242
36. Gowan C., Young M.K., Fausch K.D., and Riley S.C. Restricted movement in resident stream salmonids: a paradigm lost?. Canadian Journal of Fisheries and Aquatic Sciences 51 (1994) 2626-2637
37. Gowan C., and Fausch K.D. Long-term demographic responses of trout populations to habitat manipulation in six Colorado streams. Ecological Applications 6 (1996) 931-946
38. Gowan C., and Fausch K.D. Mobile brook trout in two high-elevation Colorado streams: re-evaluating the concept of restricted movement. Canadian Journal of Fisheries and Aquatic Sciences 53 (1996) 1370-1381
39. Grant E.H.C., Lowe W.H., and Fagan W.F. Living in the branches: population dynamics and ecological processes in dendritic networks. Ecology Letters 10 (2007) 165-175
40. Habicht C., Olsen J.B., Fair L., and Seeb J.E. Smaller effective population sizes evidenced by loss of microsatellite alleles in tributary-spawning populations of sockeye salmon from the Kvichak River, Alaska drainage. Environmental Biology of Fishes 69 (2004) 51-62
41. Hanfling B., and Weetman D. Concordant genetic estimators of migration reveal anthropogenically enhanced source-sink population structure in the river sculpin, Cottus gobio. Genetics 173 (2006) 1487-1501
42. Hanski I., and Gaggiotti O.E. Ecology, Genetics, and Evolution of Metapopulations (2004), Elsevier Academic Press, New York
43. Hedrick P.W., and Kalinowski S.T. Inbreeding depression in conservation biology. Annual Review of Ecology and Systematics 31 (2000) 139-162
44. Hughes J.M., Bunn S.E., Kingston D.M., and Hurwood D.A. Genetic differentiation and dispersal among populations of Paratya australiensis (Atyidae) in rainforest streams in southeastern Queensland, Australia. Journal of the North American Benthological Society 14 (1995) 127-158
45. Hughes J., Ponniah M., Hurwood D., Chenoweth S., and Arthington A. Strong genetic structuring in a habitat specialist, the oxleyan pygmy perch Nannoperca oxleyana. Heredity 83 (1999) 5-14
46. Humphries P. Life history, food and habitat of southern pygmy perch, Nannoperca australis, in the Macquarie River, Tasmania. Marine and Freshwater Research 46 (1995) 1159-1169
47. Hutchison D.W., and Templeton A.R. Correlation of pairwise genetic and geographic distance measures: inferring the relative influence of gene flow and drift on the distribution of genetic variability. Evolution 53 (1999) 1898-1914
48. Johnston C.E. Movement patterns of imperilled blue shiners (Pisces: Cyprinidae) among habitat patches. Ecology of Freshwater Fish 9 (2000) 170-176
49. Kalinowski S.T. HP-RARE: a computer program for performing rarefaction on measures of allelic diversity. Molecular Ecology Notes 5 (2005) 187-189
50. Knaepkens G., Bervoets L., Verheyen E., and Eens M. Relationship between population size and genetic diversity in endangered populations of the European bullhead (Cottus gobio): implications for conservation. Biological Conservation 115 (2004) 403-410
51. Kuiter R.H., Humphries P., and Arthington A.H. Family Nannopercidae - Pygmy perches. In: McDowall R.M. (Ed). Freshwater Fishes of South-eastern Australia (1996), Reed Books, Sydney 168-175
52. Labbe T.R., and Fausch K.D. Dynamics of intermittent stream habitat regulate persistence of a threatened fish at multiple scales. Ecological Applications 10 (2000) 1774-1791
53. Lake P.S. Ecological effects of perturbation by drought in flowing waters. Freshwater Biology 48 (2003) 1161-1172
54. Llewellyn L.C. Spawning, development and distribution of the southern pigmy perch Nannoperca australis australis Günther from inland waters in eastern Australia. Australian Journal of Marine and Freshwater Research 25 (1974) 121-149
55. Lloyd L., and Walker K.F. Distribution and conservation status of small freshwater fish in the River Murray, South Australia. Transactions of the Royal Society of South Australia 100 (1986) 49-57
56. Lowe W.H. Linking dispersal to local population dynamics: a case study using a headwater salamander system. Ecology 84 (2003) 2145-2154
57. Lowe W.H., Likens G.E., and Power M.E. Linking scales in stream ecology. BioScience 56 (2006) 591-597
58. Magoulick D.D., and Kobza R.M. The role of refugia for fishes during drought: a review and synthesis. Freshwater Biology 48 (2003) 1186-1198
59. Mamuris Z., Stoumboudi M.T., Stamatis C., Barbier R., and Moutouk A. Genetic variation in populations of the endangered fish Ladigesocypris ghigii and its implications for conservation. Freshwater Biology 50 (2005) 1441-1453
60. Manel S., Gaggiotti O.E., and Waples R.S. Assignment methods: matching biological questions with appropriate techniques. Trends in Ecology and Evolution 20 (2005) 136-142
61. Maruyama A., Yamada Y., Rusuwa B., and Yuma M. Change in stable nitrogen isotope ratio in the muscle of a migratory goby, Rhinogobius sp., in a natural setting. Canadian Journal of Fisheries and Aquatic Sciences 58 (2001) 2125-2128
62. McGlashan DJ., and Hughes J.M. Reconciling patterns of genetic variation with stream structure, earth history and biology in the Australian freshwater fish Craterocephalus stercusmuscarum (Atherinidae). Molecular Ecology 9 (2000) 1737-1751
63. Meffe G.K., and Vrijenhoek R.C. Conservation genetics and the management of desert fishes. Conservation Biology 2 (1988) 157-169
64. Miller J.A., Banks M.A., Gomez-Uchida D., and Shanks A.L. A comparison of population structure in black rockfish (Sebastes melanops) as determined with otolith microchemistry and microsatellite DNA. Canadian Journal of Fisheries and Aquatic Sciences 62 (2005) 2189-2199
65. Morris, S.A., Pollard, D.A., Gehrke, P.C., Pogonoski, J.J., 2001. Threatened and potentially threatened freshwater fishes of coastal New South Wales and the Murray-Darling Basin. Report to Fisheries Action Program and World Wide Fund for Nature Project No. AA0959.98. New South Wales Fisheries Final Report Series No. 33. Sydney.
66. Na-Nakorn U., Sukmanomon S., Nakajima M., Taniguchi N., Kamonrat W., Poompuang S., and Nguyen T.T.T. MtDNA diversity in the critically endangered Mekong giant catfish (Pangasianodon gigas Chevey (1913)) and closely related species: implications for conservation. Animal Conservation 9 (2006) 483-494
67. Neville H.M., Dunham J.B., and Peacock M.M. Landscape attributes and life history variability shape genetic structure of trout populations in a stream network. Landscape Ecology 21 (2006) 901-916
68. Neville H., Isaak D., Thurow R., Dunham J., and Riean B. Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (Oncorhynchus tshawytscha) within a Snake River watershed. Conservation Genetics 8 (2007) 133-147
69. O'Grady J.J., Brook B.W., Reed D.H., Balloa J.D., Tonkyn D.W., and Frankham R. Realistic levels of inbreeding depression strongly affect extinction risk in wild populations. Biological Conservation 133 (2006) 42-51
70. Olsen J.B., Merkouris S.E., and Seeb J.E. An examination of spatial and temporal genetic variation in walleye pollok (Theragra chalcogramma) using allozyme, mitochondrial DNA, and microsatellite data. Fishery Bulletin US 100 (2002) 752-764
71. ST and microsatellite polymorphism in the marine fish, walleye pollock (Theragra chalcogramma): implications for resolving weak population structure. Molecular Ecology 13 (2004) 1799-1814
72. Paetkau D., Calvert W., Stirling I., and Strobeck C. Microsatellite analysis of population structure of Canadian polar bears. Molecular Ecology 4 (1995) 347-354
73. Peakall R., and Lindenmayer D. Genetic insights into population recovery following experimental perturbation in a fragmented landscape. Biological Conservation 132 (2006) 520-532
74. Peterson B.J., and Fry B. Stable isotopes in ecosystem studies. Annual Review of Ecology and Systematics 18 (1987) 293-320
75. Piry S., Alapetite A., Cornuet J.M., Paetkau D., Baudouin L., and Estoup A. GENECLASS version 2.0: a software for genetic assignment and first generation migrant detection. Journal of Heredity 95 (2004) 536-539
76. Primmer C.R., Veslov A.J., Zubchenko A., Poututkin A., Bakhmet I., and Koskinen M.T. Isolation by distance within a river system: genetic population structuring of Atlantic salmon, Salmo salar, in tributaries of the Varzuga River in northwest Russia. Molecular Ecology 15 (2005) 653-666
77. Pringle C.M. Hydrological connectivity and the management of biological reserves: a global perspective. Ecological Applications 11 (2001) 981-998
78. Pritchard J.K., Stephens M., and Donnelly P. Inference of population structure using multilocus genotype data. Genetics 155 (2000) 945-959
79. Rannala B., and Mountain J.L. Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences USA 94 (1997) 9197-9201
80. Raymond M., and Rousset F. GENEPOP version 1.2: population genetics software for exact tests and ecumenicism. Journal of Heredity 86 (1995) 248-249
81. Rubenstein D.R., and Hobson K.A. From birds to butterflies: animal movement patterns and stable isotopes. Trends in Ecology and Evolution 19 (2004) 256-263
82. Salgueiro P., Carvalho G., Collares-Pereira M.J., and Coelho M.M. Microsatellite analysis of genetic population structure of the endangered cyprinid Anaecypris hispanica in Portugal: implications for conservation. Biological Conservation 109 (2003) 47-56
83. Schlosser I.J., and Angermeier P.L. Spatial variation in demographic processes of lotic fishes: conceptual models, empirical evidence, and implications for conservation. American Fisheries Society Symposium 17 (1995) 392-401
84. Schneider S., Kuffer J., Rossli D., and Excoffier L. ARLEQUIN Version 2.0: A Software for Population Genetic Data Analysis (2000), Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva, Switzerland
85. Scott M.C. Winners and losers among stream fishes in relation to land use legacies and urban development in the southeastern US. Biological Conservation 127 (2006) 301-309
86. Sirkwan S., and Woodruff D.S. Genetic erosion in isolated small mammal populations following rainforest fragmentation. In: Young A.C., and Clarke G.M. (Eds). Genetics, Demography and Viability of Fragmented Populations (2000), Cambridge University Press, New York 149-172
87. Skalski G.T., and Gilliam J.F. Modeling diffusive spread in a heterogeneous population: a movement study with stream fish. Ecology 81 (2000) 1685-1700
88. Slatkin M. Gene flow in natural populations. Annual Review of Ecology and Systematics 16 (1985) 393-430
89. Smallwood K.S. Linking habitat restoration to meaningful units of animal demography. Restoration Ecology 9 (2001) 253-261
90. Sumner J., Jessop T., Paetkau D., and Moritz C. Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rain forest skink, Gnyptescincus queenslandiae. Molecular Ecology 13 (2004) 259-269
91. Taylor M.I., Morley J.I., Rico C., and Balshine S. Evidence for genetic monogamy and female-biased dispersal in the biparental mouthbrooding cichlid Eretmodus cyanostictus from Lake Tanganyika. Molecular Ecology 12 (2003) 3173-3177
92. Tibbets C.A., and Dowling T.E. Effects of intrinsic and extrinsic factors on population fragmentation in three species of North American minnows (Teleostei: Cyprinidae). Evolution 50 (1996) 1280-1292
93. Turner T.F., and Robison H.W. Genetic diversity of the caddo madtom, Noturus taylori, with comments on factors that promote genetic divergence in fishes endemic to the ouachita highlands. Southwestern Naturalist 51 (2006) 338-345
94. van Oosterhout C., Hutchinson W.F., Wills D.P.M., and Shipley P.F. Micro-Checker (2003), Department of Biological Sciences and Department of Computer Sciences, the University of Hull, UK
95. Vrijenhoek R.C. Genetic diversity and fitness in small populations. In: Loeschcke V., Tomiuk J., and Jain S.K. (Eds). Conservation Genetics (1994), Birkhauser-Verlag, Switzerland 37-53
96. Weir B.S., and Cockerham C.C. Estimating F-statistics for the analysis of population structure. Evolution 38 (1984) 1358-1370
97. Wilson A.J., Hutchings J.A., and Ferguson M.M. Dispersal in a stream dwelling salmonid: inferences from tagging and microsatellite studies. Conservation Genetics 5 (2004) 25-37
98. Wright S. Evolution in Mendelian populations. Genetics 16 (1931) 97-159