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

Volumn 52, Issue 11, 2007, Pages 2156-2171

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

^a GRIFFITH UNIVERSITY   (Australia)

Author keywords

Cryptic species; Population genetics; Stable isotopes; Stream restoration; Temporal stability

Indexed keywords

ATYIDAE (CRUSTACEANS); DECAPODA (CRUSTACEA); PARATYA; PARATYA AUSTRALIENSIS;

EID: 35248891471     PISSN: 00465070     EISSN: 13652427     Source Type: Journal    
DOI: 10.1111/j.1365-2427.2007.01842.x     Document Type: Article

References (78)

1. Østergaard S., Hansen M.M., Loeschcke V. Nielsen E.E. (2003) Long-term temporal changes of genetic composition in brown trout (Salmo trutta L.) populations inhabiting an unstable environment. Molecular Ecology, 12, 3123 3135.
2. Avise J.C. (2000) Phylogeography: the History and Formation of Species. Harvard University Press, Cambridge.
3. 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.
4. Bohonak A.J. Jenkins D.G. (2003) Ecological and evolutionary significance of dispersal by freshwater invertebrates. Ecology Letters, 6, 783 796.
5. Bond N.R. Lake P.S. (2005) Ecological restoration and large-scale ecological disturbance: the effects of drought on the response by fish to a habitat restoration experiment. Restoration Ecology, 13, 39 48.
6. 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.
7. Charbonnel N., Quesnoit M., Razatavonjizay R., Brémond P. Jarne P. (2002) A spatial and temporal approach to microevolutionary forces affecting population biology in the freshwater snail Biomphalaria pfeifferi. The American Naturalist, 160, 741 755.
8. Charles K., Roussel J.-M., Lebel J.-M., Baglinière J.-L. Ombredane D. (2006) Genetic differentiation between anadromous and freshwater resident brown trout (Salmo trutta L.): insights obtained from stable isotope analysis. Ecology of Freshwater Fish, 15, 255 263.
9. Clarke K.R. Gorley R.N. (2001) PRIMER Version 5.2.8: User Manual/Tutorial. PRIMER-E Ltd, Plymouth.
10. Clegg S.M., Kelly J.F., Kimura M. Smith T.B. (2003) Combining genetics and stable isotopes to reveal population connectivity and migration patterns in a Neotropical migrant, Wilson's warbler (Wilsonia pusilla). Molecular Ecology, 12, 819 830.
11. Clement M., Posada D. Crandall K. (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657 1660.
12. 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.
13. 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.
14. Covich A.P., Crowl T.A., Johnson S.L., Varza D. Certain D.L. (1991) Post-hurricane Hugo increases in atyid shrimp abundances in a Puerto Rican montane stream. Biotropica, 23, 448 454.
15. Cunjak R.A., Roussel J.-M., Gray M.A., Dietrich J.P., Cartwright D.F., Munkittrick K.R. Jardine T.D. (2005) Using stable isotope analysis with telemetry or mark-recapture data to identify fish movement and foraging. Oecologia, 144, 636 646.
16. Daniels S.R., Gouws G., Stewart B.A. Coke M. (2003) Molecular and morphometric data demonstrate the presence of cryptic lineages among freshwater crabs (Decapoda: Potamonautidae: Potamonautes) from the Drakensberg Mountains, South Africa. Biological Journal of the Linnean Society, 78, 129 147.
17. 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.
18. Downes B.J., Lake P.S., Glaister A. Bond N.R. (2006) Effects of sand sedimentation on the macroinvertebrate fauna of lowland streams: are the effects consistent? Freshwater Biology, 51, 144 160.
19. 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.
20. Fagan W.F. (2002) Connectivity, fragmentation and extinction risk in dendritic metapopulations. Ecology, 83, 3243 3249.
21. Frankham R. (1996) Relationship of genetic variation to population size in wildlife. Conservation Biology, 10, 1500 1508.
22. Fraser D.F., Gilliam J.F., Daley M.J., Le A.N. Skalski G.T. (2001) Explaining leptokurtic movement distributions: intrapopulation variation in boldness and exploration. American Naturalist, 158, 124 135.
23. Fraser D.F., Gilliam J.F., MacGowan M.P., Arcaro C.M. Guillozet P.H. (1999) Habitat quality in a hostile river. Ecology, 80, 597 607.
24. Garant D., Dodson J.J. Bernatchez L. (2000) Ecological determinants and temporal stability of the within-river population structure in Atlantic salmon (Salmo salar L.). Molecular Ecology, 9, 615 628.
25. Gene Codes 2000) SEQUENCHER Version 4.1.2. Gene Code Corporation, Ann Arbor, MI.
26. Greathouse E.A., March J.G. Pringle C.M. (2005) Recovery of a tropical stream after a harvest-related chlorine poisoning event. Freshwater Biology, 26, 691 699.
27. Hancock M.A Bunn S.E. (1999) Swimming response to water current in Paratya australiensis Kemp, 1917 (Decapoda: Atyidae) under laboratory conditions. Crustaceana, 72, 313 323.
28. Hancock M.A., Hughes J.M. Bunn S.E. (1998) Influence of genetic and environmental factors on egg and clutch sizes among populations of Paratya australiensis Kemp (Decapoda: Atyidae) in upland rainforest streams, south-east Queensland. Oecologia, 115, 483 491.
29. Hansson S., Hobbie J.E., Elmgren R., Larsson U., Fry B. Johansson S. (1997) The stable nitrogen isotope ratio as a marker of food-web interactions and fish migration. Ecology, 78, 2249 2257.
30. Harrod C., Grey J., McCarthy T.K. Morrissey M. (2005) Stable isotope analyses provide new insights into ecological plasticity in a mixohaline population of European eel. Oecologia, 144, 673 683.
31. Hart R.C., Campbell L.M. Hecky R.E. (2003) Stable isotope analyses and demographic responses counter prospects of planktivory by Caridina (Decapoda: Atyidae) in Lake Victoria. Oecologia, 136, 270 278.
32. Hershey A.E, Pastor J., Peterson B.J. Kling G.W. (1993) Stable isotopes resolve the drift paradox for Baetis mayflies in an artic river. Ecology, 74, 2315 2325.
33. Hobson K.A. (1999) Tracing origins and migration of wildlife using stable isotopes: a review. Oecologia, 120, 314 326.
34. Hogg I.D., Stevens M.I., Schnabel K.E. Chapman M.A. (2006) Deeply divergent lineages of the widespread New Zealand amphipod Paracalliope fluviatilis revealed using allozyme and mitochondrial DNA analyses. Freshwater Biology, 51, 236 248.
35. 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.
36. 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.
37. Hughes J.M., Bunn S.E., Hurwood D.A., Choy S.C. Pearson R.G. (1996) Genetic differentiation among populations of Caridina zebra (Decapoda: Atyidae) in tropical rainforest streams, northern Australia. Freshwater Biology, 36, 289 296.
38. Hughes J., Goudkamp K., Hurwood D., Hancock M. Bunn S. (2003) Translocation causes extinction of a local population of the freshwater shrimp Paratya australiensis. Conservation Biology, 17, 1007 1012.
39. 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.
40. Hutchison D.W. Templeton A.R. (1999) 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, 1898 1914.
41. Kalinowski S.T. (2005) HP-RARE: a computer program for performing rarefraction on measures of allelic diversity. Molecular Ecology Notes, 5, 187 189.
42. Kyle C.J. Boulding E.G. (2000) Comparative population genetic structure of marine gastropods (Littorina spp.) with and without pelagic larval dispersal. Marine Biology, 137, 835 845.
43. Labbe T.R. Fausch K.D. (2000) Dynamics of intermittent stream habitat regulate persistence of a threatened fish at multiple scales. Ecological Applications, 10, 1774 1791.
44. Lake, P.S. (2003) Ecological effects of perturbation by drought in flowing waters. Freshwater Biology, 48, 1161 1172.
45. Lapointe F.-J. Rissler L.J. (2005) Congruence, consensus, and the comparative phylogeography of codistributed species in California. American Naturalist, 66, 290 299.
46. Larsen P.F., Hansen M.M., Nielsen E.E., Jensen L.F. Loeschchke V. (2005) Stocking impact and temporal stability of genetic composition in a brackish northern pike (Esox lucius L.), assessed using microsatellite DNA analysis of historical and contemporary samples. Heredity, 95, 136 143
47. Liu H.-P., Hershler R. Clift K. (2003) Mitochondrial DNA sequences reveal extensive cryptic diversity within a western American springsnail. Molecular Ecology, 12, 2771 2782.
48. MacNeale K.H., Peckarsky B.L. Likens G.E. (2004) Contradictory results from different methods for measuring direction of insect flight. Freshwater Biology, 49, 1260 1268.
49. Magalhães M.F., Beja P., Canas C. Collares-Pereira M.J. (2002) Functional heterogeneity of dry-season fish refugia across a Mediterranean catchment: the role of habitat and predation. Freshwater Biology, 47, 1919 1934.
50. Magoulick D.D. Kobza R.M. (2003) The role of refugia for fishes during drought: a review and synthesis. Freshwater Biology, 48, 1186 1198.
51. Manier M.K. Arnold S.J. (2005) Population genetic analysis identifies source- sink dynamics for two sympatric garter snake species (Thamnophis elegans and Thamnophis sirtalis). Molecular Ecology, 14, 3965 3976.
52. March J.G., Benstead J.P., Pringle C.M. Scatena F.N. (1998) Migratory drift of larval freshwater shrimps in two tropical streams, Puerto Rico. Freshwater Biology, 40, 261 273.
53. 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.
54. McMillen-Jackson A.L. Bert T.M. (2003) Disparate patterns of population genetic structure and population history in two sympatric penaeid shrimp species (Farfantepenaeus aztecus and Litopenaeus setiferus) in the eastern United States. Molecular Ecology, 12, 2895 2905.
55. Meffe G.K. Vrijenhoek R.C. (1988) Conservation genetics and the management of desert fishes. Conservation Biology, 2, 157 169.
56. Müller K. (1982) The colonisation cycle of freshwater insects. Oecologia, 52, 202 207.
57. Neville H.M., Dunham J.B. Peacock M.M. (2006) Landscape attributes and life history variability shape genetic structure of trout populations in a stream network. Landscape Ecology, 21, 901 916.
58. 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 1066.
59. Peterson B.J. Fry B. (1987) Stable isotopes in ecosystem studies. Annual Review of Ecology and Systematics, 18, 293 320.
60. Piry S., Alapetite A., Cornuet J.-M., Paetkau D., Baudouin L. Estoup A. (2004) GENECLASS version 2.0: a software for genetic assignment and first generation migrant detection. Journal of Heredity, 95, 536 539.
61. Rannala B. Mountain J.L. (1997) Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences U.S.A., 94, 9197 9201.
62. Raymond M. Rousset F. (1995) GENEPOP version 1.2: population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248 249.
63. Rice W.R. (1989) Analysis tables of statistical tests. Evolution, 43, 223 225.
64. Richardson B.J., Baverstock P.R. Adams M. (1986) Allozyme Electrophoresis: a Handbook for Animal Systematics and Population Studies. Academic Press, Sydney, NSW.
65. Roy D., Kelly D.W., Fransen C.H.J.M., Heath D.D. Haffner G.D. (2006) Evidence of small-scale vicariance in Caridina lanceolata (Decapoda: Atyidae) from the Malili Lakes, Sulawesi. Evolutionary Ecology Research, 8, 1087 1099.
66. Rubenstein D.R Hobson K.A. (2004) From birds to butterflies: animal movement patterns and stable isotopes. Trends Ecology and Evolution, 19, 256 263.
67. Salgueiro P., Carvalho G., Collares-Pereira M.J. Coelho M.M. (2003) Microsatellite analysis of genetic population structure of the endangered cyprinid Anaecypris hispanica in Portugal: implication for conservation. Biological Conservation, 109, 47 56.
68. Schmidt 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.
69. Schneider S., Kuffer J., Rossli D. Excoffier L. (2000) ARLEQUIN Version 2.0: a Software for Population Genetic Data Analysis. Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva, Geneva, Switzerland.
70. Skalski G.T. Gilliam J.F. (2000) Modelling diffusive spread in a heterogeneous population: a movement study using stream fish. Ecology, 81, 1685 1700.
71. Sullivan J., Arellano E. Rogers D.S. (2000) Comparative phylogeography of Mesoamerican highland rodents: concerted versus independent response to past climatic fluctuations. American Naturalist, 155, 755 768.
72. Sweeney B.W. Funk D.H. (1991) Population genetics of the burrowing mayfly Dolania americana: geographic variation and the presence of cryptic species. Aquatic Insects, 13, 17 27.
73. Tibbets C.A. Dowling T.E. (1996) Effects of intrinsic and extrinsic factors on population fragmentation in three species of North American minnows (Teleostei: Cyprinidae). Evolution, 50, 1280 1292.
74. Turner T.F. Robison H.W. (2006) Genetic diversity of the caddo madtom, Noturus taylori, with comments on factors that promote genetic divergences in fishes endemic to the ouachita highlands. Southwestern Naturalist, 51, 338 345.
75. Weir B.S. Cockerham C.C. (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358 1370.
76. Whiteley A.R., Spruell P. Allendorf F.W. (2004) Ecological and life history characteristics predict population genetic divergence of two salmonids in the same landscape. Molecular Ecology, 13, 3675 3688.
77. Yam S.W. Dudgeon D. (2005) Stable isotope investigation of food use by Caridina spp. (Decapoda: Atyidae) in Hong Kong streams. Journal of the North American Benthological Society, 24, 68 81.
78. Zeller M., Reusch T.B.H. Lampert W. (2006) A comparative population genetic study of isolation-by-distance in two Eudiaptomus species with different potential for dispersal. Limnology and Oceanography, 51, 117 124.