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

Volumn 56, Issue 5, 2011, Pages 812-827

  Cook, Benjamin D ^a   Kennard, Mark J ^a   Real, Kathryn ^a   Pusey, Bradley J ^a   Hughes, Jane M ^a  

^a GRIFFITH UNIVERSITY   (Australia)

Author keywords

Cryptic species; Isolation by distance; Stream gradient; Stream hierarchy model

Indexed keywords

ELEOTRIDAE; MOGURNDA MOGURNDA;

EID: 79953301138     PISSN: 00465070     EISSN: 13652427     Source Type: Journal    
DOI: 10.1111/j.1365-2427.2010.02527.x     Document Type: Article

References (69)

1. Allen G.R. & Jenkin A.P. (1999) A review of the Australian freshwater gudgeons, genus Mogurnda (Eleotridae) with descriptions of three new species. Aqua, Journal of Ichthyology and Aquatic Biology, 3, 141-156.
2. Avise J.C. (2000) Phylogeography: The History and Formation of Species. Harvard University Press, MA.
3. Balkenhol N., Waits L.P. & Dezzani R.J. (2009) Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data. Ecography, 32, 818-830.
4. Burridge C.P., Craw D. & Waters J.M. (2006) River capture, range expansion, and cladogenesis: the genetic signature of freshwater vicariance. Evolution, 60, 1038-1049.
5. Burridge C.P., Craw D. & Waters J.M. (2007) An empirical test of freshwater vicariance by river capture. Molecular Ecology, 16, 1883-1895.
6. Castric V., Bonney F. & Bernatchetz L. (2001) Landscape structure and hierarchical genetic diversity in the brook charr, Salvelinus fontinalus. Evolution, 55, 1016-1028.
7. Chan T., Hart B., Kennard M.J., Pusey B.J., Shenton W., Douglas M., Valentine E. & Patel S. (2010) Bayesian network models for environmental flow decision-making in the Daly River, Northern Territory, Australia. River Research & Applications,
8. Chaput-Bardy A., Fleurant C., Lemaire C. & Secondi J. (2009) Modelling the effect of in-stream and overland dispersal on gene flow in river networks. Ecological Modelling, 220, 3589-3598.
9. Clarke K.R. & Gorley R.N. (2001) PRIMER Version 5.2.8. PRIMER-E, Plymouth.
10. Cook B.D., Bunn S.E. & Hughes J.M. (2007a) A comparative analysis of population structuring and genetic diversity in sympatric lineages of freshwater shrimp (Atyidae: Paratya): concerted or independent responses to hydrographic factors? Freshwater Biology, 52, 2156-2171.
11. Cook B.D., Bunn S.E. & Hughes J.M. (2007b) 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.
12. Cook B.D., Pringle C.M. & Hughes J.M. (2008a) Phylogeography of an island endemic, the Puerto Rican freshwater crab (Epilobocera sinuatifrons). Journal of Heredity, 99, 157-164.
13. Cook B.D., Page T.J. & Hughes J.M. (2008b) Importance of cryptic species for identifying 'representative' units of biodiversity for freshwater conservation. Biological Conservation, 141, 2821-2831.
14. Cook B.D., Bernays S., Pringle C.M. & Hughes J.M. (2009) Marine dispersal determines the genetic population structure of migratory stream fauna of Puerto Rico: evidence for island scale population recovery processes. Journal of the North American Benthological Society, 28, 709-718.
15. Cushman S.A. & Landguth E.L. (2010) Spurious correlations and inference in landscape genetics. Molecular Ecology, 19, 3592-3602.
16. Dionne M., Caron F., Dodson J.J. & Bernatchez L. (2008) Landscape genetics and hierarchical genetic structure in Atlantic salmon: the interaction of gene flow and local adaptation. Molecular Ecology, 17, 2382-2396.
17. Evanno G., Regnaut S. & Goudet J. (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611-2620.
18. Excoffier L., Smouse P.E. & Quattro J.M. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.
19. Fagan W.F. (2002) Connectivity, fragmentation and extinction risk in dendritic metapopulations. Ecology, 83, 3243-3249.
20. Finn D.S., Theobald D.M., Black W.C. & Poff N.L. (2006) Spatial population genetic structure and limited dispersal in a Rocky Mountain alpine stream insect. Molecular Ecology, 15, 3553-3566.
21. Foll M. & Gaggiotti O. (2006) Identifying the environmental factors that determine the genetic structure of populations. Genetics, 174, 875-891.
22. Fu Y.X. (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915-925.
23. Gene Codes (2000) Sequencher Version 4.1.2. Gene Codes Corporation, Ann Arbor, MI, U.S.A.
24. Guillot G., Leblois R., Coulon A. & Frantz A.C. (2009) Statistical methods in spatial genetics. Molecular Ecology, 18, 4734-4756.
25. 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, 1397-1408.
26. 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 southeast Queensland, Australia. Journal of the North American Benthological Society, 14, 158-173.
27. 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.
28. Hughes J.M., Schmidt D.J. & Finn D.S. (2009) Genes in streams: using DNA to understand the movement of freshwater fauna and their riverine habitat. BioScience, 59, 573-583.
29. 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.
30. Kalinowski S.T. (2004) Counting alleles with rarefaction: private alleles and hierarchical sampling designs. Conservation Genetics, 5, 539-543.
31. Kalinowski S.T., Meeuwig M.H., Narum S.R. & Taper M.L. (2008) Stream trees: a statistical method for mapping genetic differences between populations of freshwater organisms to the sections of stream that connect them. Canadian Journal of Fisheries and Aquatic Sciences, 65, 2752-2760.
32. Kennard M.J., Pusey B.J., Olden J.D., Mackay S.J., Stein J.L. & Marsh N. (2010) Classification of natural flow regimes in Australia to support environmental flow management. Freshwater Biology, 55, 171-193.
33. Kimura M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111-120.
34. Kittlein M.J. & Gaggiotti O.E. (2008) Interactions between environmental factors can hide isolation by distance patterns: a case study of Ctenomys rionegrensis in Uruguay. Proceedings of the Royal Society of London B, 275, 2633-2638.
35. Körner C. (2007) The use of 'altitude' in ecological research. Trends in Ecology and Evolution, 22, 569-574.
36. Lara A., Ponce de León J.L., Rodríguez R., Casane D., Côté G., Bernatchez L. & García-Machado E. (2009) DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic conflicts. Molecular Ecology Resources, 10, 421-430.
37. Leclerc E., Mailhot Y., Mingelbier M. & Bernatchez L. (2008) The landscape genetics of yellow perch (Perca flavescens) in a large fluvial ecosystem. Molecular Ecology, 17, 1702-1717.
38. Legendre P. & Legendre L. (1998) Numerical Ecology, 2nd English edn. Elsevier Science BV, Amsterdam.
39. Lowe W.H., Likens G.E., McPeek M.A. & Buso D.C. (2006) Linking direct and indirect data on dispersal: isolation by slope in a headwater stream salamander. Ecology, 87, 334-339.
40. Manel S., Schwartz M.K., Luikart G. & Taberlet P. (2003) Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology and Evolution, 18, 189-197.
41. Mantel N.A. (1967) The detection of disease clustering and a generalised regression approach. Cancer Research, 27, 209-220.
42. 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.
43. McGlashan D.J. & Hughes J.M. (2002) Extensive genetic divergence among populations of the Australian freshwater fish, Pseudomugil signifier (Pseudomugilidae), at different hierarchical scales. Marine and Freshwater Research, 53, 897-907.
44. Meeuwig M.H., Guy C.S., Kalinowski S.T. & Fredenberg W.A. (2010) Landscape influences on genetic differentiation among bull trout populations in a stream-lake network. Molecular Ecology, 19, 3620-3633.
45. Meffe G.K. & Vrijenhoek R.C. (1988) Conservation genetics and the management of dessert fishes. Conservation Biology, 2, 157-169.
46. Moritz C. (2002) Strategies to protect biological diversity and the evolutionary processes that sustain it. Systematic Biology, 51, 238-254.
47. van Oosterhout C., Hutchinson W.F., Wills D.P.M. & Shipley P.F. (2003) Micro-Checker. Department of Biological Sciences and Department of Computer Sciences, The University of Hull, Hull, U.K.
48. Pritchard J.K., Wen X. & Falush D. (2009) Documentation for STRUCTURE software: version 2.3. Available at:
49. Pusey B., Kennard M. & Arthington A. (2004) Freshwater Fishes of North-Eastern Australia. CSIRO Publishing, Victoria, Australia.
50. Raymond M. & Rousset F. (1995) GENEPOP version 1.2: population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248-249.
51. Real K.M., Schmidt D.J. & Hughes J.M. (2008) Mogurnda adspersa microsatellite markers: multiplexing and multi-tailed primer tagging. Conservation Genetics Resources, 1, 411-414.
52. Rosenberg M.S. (2001) PASSAGE. Pattern Analysis, Spatial Statistics, and Geographic Exegesis. Version 1.0. Department of Biology, Arizona State University, Tempe, AZ.
53. Ryman N., Palm S., André C., Carvalho G.R., Dahlgren T.G., Jorde P.E., Laikre L., Larsson L.C., Palmé A. & Ruzzante D.E. (2006) Power for detecting genetic divergence: differences between statistical methods and marker loci. Molecular Ecology, 15, 2031-2045.
54. Saitou N. & Nei M. (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.
55. Schneider S., Kuffer J., Rossli D. & Excoffier L. (2000) ARLEQUIN Version 2.0: A Software for Population Genetic Data Analysis. Genetics and Biometry Laboratory, University of Geneva, Geneva.
56. Stein J.L., Hutchinson M.F. & Stein J.A. (2010) The National Catchment and Stream Environment Database, version 1.1, Fenner School of Environment and Society, Australian National University. Available at:
57. Storfer A., Murphy M.A., Evans J.S., Goldberg C.S., Robinson S., Spear S.F., Dezzani R., Delmelle E., Vierling L. & Waits L.P. (2007) Putting the 'landscape' in landscape genetics. Heredity, 98, 128-142.
58. Stork V.L. & Waits L. (2010) Contributions of landscape genetics -approaches, insights, and future potential. Molecular Ecology, 19, 3489-3495.
59. Tajima F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
60. Tamura K., Dudley J., Nei M. & Kumar S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596-1599.
61. Thuesen P.A., Pusey B.J., Peck D.R., Pearson R.G. & 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.
62. Voris H.K. (2000) Maps of Pleistocene sea levels in South East Asia: shorelines, river systems, time durations. Journal of Biogeography, 27, 1153-1167.
63. Wang I.J. (2010) Recognizing the temporal distinctions between landscape genetics and phylogeography. Molecular Ecology, 19, 2605-2608.
64. Waters J.M. & Wallis G.P. (2000) Across the Southern Alps by river capture? Freshwater fish phylogeography in South Island, New Zealand Molecular Ecology, 9, 1577-1582.
65. Wellborn G.A. & Cothran R.D. (2004) Phenotypic similarity and differentiation among sympatric cryptic species in a freshwater amphipod species complex. Freshwater Biology, 49, 1-13.
66. Wilcock H.R., Bruford M.W., Nichols R.A. & Hildrew A.G. (2007) Landscape, habitat characteristics and the genetic population structure of two caddiflies. Freshwater Biology, 52, 3553-3566.
67. Wishart M.J. & Hughes J.M. (2003) Genetic population structure of the net-winged midge, Elporia barnardi (Diptera: Blephariceridae), in streams of the south-western Cape, South Africa: implications for dispersal. Freshwater Biology, 48, 28-38.
68. 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.
69. Wright S. (1931) Evolution in Mendelian populations. Genetics, 16, 97-159.