Integration of ecology, demography and genetics to reveal population structure and persistence: A mini review and case study of stream-dwelling Dolly Varden

Ecology of Freshwater Fish

Volumn 20, Issue 3, 2011, Pages 352-363

  Koizumi, Itsuro ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Conservation; Dam; Female biased migration; Gene flow; Isolation by distance; Metapopulation; Partial migration; Rescue effect; Salvelinus malma

Indexed keywords

PISCES; SALVELINUS FONTINALIS; SALVELINUS MALMA;

EID: 79961011050     PISSN: 09066691     EISSN: 16000633     Source Type: Journal    
DOI: 10.1111/j.1600-0633.2010.00480.x     Document Type: Article

References (85)

1. Berger, A.M. & Gresswell, R.E. 2009. Factors influencing coastal cutthroat trout (Oncorhynchus clarkii clarkii) seasonal survival rates: a spatially continuous approach within stream networks. Canadian Journal of Fisheries and Aquatic Sciences 66: 613-632.
2. Burton, T.A. 2005. Fish and stream habitat risks from uncharacteristic wildfire: observations from 17years of fire-related disturbances on the Boise National Forest, Idaho. Forest Ecology and Management 211: 140-149.
3. Clinchy, M., Haydon, D.T. & Smith, A.T. 2002. Pattern does not equal process: what does patch occupancy really tell us about metapopulation dynamics? American Naturalist 159: 351-362.
4. Duncan, J.R. & Lockwood, J.L. 2001. Extinction in a field of bullets: a search for causes in the decline of the world's freshwater fishes. Biological Conservation 102: 97-105.
5. Dunham, J.B. & Rieman, B.E. 1999. Metapopulation structure of bull trout: influences of physical, biotic, and geometrical landscape characteristics. Ecological Applications 9: 642-655.
6. Elliott, J.M. 1987. Population regulation in contrasting populations of trout Salmo trutta in two Lake District streams. Journal of Animal Ecology 56: 83-98.
7. Elliott, J.M. 1994. Quantitative ecology and the brown trout. Oxford: Oxford University Press.
8. Fagan, W.F. 2002. Connectivity, fragmentation, and extinction risk in dendritic metapopulations. Ecology 83: 3243-3249.
9. Falke, J.A. & Fausch, K.D. 2010. From metapopulations to metacommunities: linking theory with empirical observations of the spatial population dynamics of stream fishes. In: Gido, K.B. & Jackson, D.A. ed. Community ecology of stream fishes. Bethesda: American Fisheries Society Symposium, 73, pp. 457-471.
10. Fausch, K.D. & Bramblett, R.G. 1991. Disturbance and fish communities in intermittent tributaries of a western Great Plains river. Copeia 1991: 659-674.
11. Frankham, R., Ballou, J.D. & Briscoe, D.A. 2002. Introduction to conservation genetics. Cambridge: Cambridge University Press.
12. Gagen, C.J., Standage, R.W. & Stoeckel, J.N. 1998. Ouachita madtom (Noturus lachneri) metapopulation dynamics in intermittent Ouachita Mountain streams. Copeia 1998: 874-882.
13. Gaggiotti, O.E., Jones, F., Amos, W., Harwood, J. & Nichols, R.A. 2002. Patterns of colonisation in a grey seal metapopulation. Nature 416: 424-427.
14. Garant, D., Dodson, J.J. & Bernatchez, L. 2000. Ecological determinants and temporal stability of within-river population structure in Atlantic salmon (Salmo salar L.). Molecular Ecology 9: 615-628.
15. Gerking, S.D. 1959. The restricted movement of fish populations. Biological Reviews 34: 221-242.
16. Gotelli, N.J. & Taylor, C.M. 1999. Testing metapopulation models with stream-fish assemblages. Evolutionary Ecology Research 1: 835-845.
17. Gowan, C. & Fausch, K.D. 1996. Mobile brook trout in two high-elevation Colorado streams: re-evaluating the concept of restricted movement. Canadian Journal of Fisheries and Aquatic Sciences 53: 1370-1381.
18. Gowan, C., Young, M.K., Fausch, K.D. & Riley, S.C. 1994. Restricted movement in resident stream salmonids: a paradigm lost? Canadian Journal of Fisheries and Aquatic Sciences 51: 2626-2637.
19. Grenouillet, G., Hugueny, B., Carrel, G.A., Olivier, J.M. & Pont, D. 2001. Large-scale synchrony and inter-annual variability in roach recruitment in the Rhone River: the relative role of climatic factors and density-dependent processes. Freshwater Biology 46: 11-26.
20. Gresswell, R.E., Torgersen, C.E., Bateman, D.S., Guy, T., Hendricks, S.R. & Wofford, J.E. 2006. A spatially explicit approach for evaluating relationships among coastal cutthroat trout, habitat, and disturbance in small Oregon streams. In: Hughes, R., Wang, L. & Seelbach, P., ed Influences of landscapes on stream habitats and biological assemblages. Bethesda: American Fisheries Society Symposium 48, pp. 457-471.
21. Griffiths, A.M., Koizumi, I., Bright, D. & Stevens, J.R. 2009. A case of isolation by distance and short-term temporal stability of population structure in brown trout (Salmo trutta) within the River Dart, southwest England. Evolutionary Applications 2: 537-554.
22. Hanski, I. 1999. Metapopulation ecology. Oxford: Oxford University Press.
23. Harrison, S. & Taylor, A.D. 1997. Empirical evidence for metapopulation dynamics. In: Hanski, I. & Gilpin, M.E., ed Metapopulation biology. London: Academic Press, pp. 27-42.
24. Heino, M. 1998. Noise colour, synchrony and extinctions in spatially structured populations. Oikos 83: 368-375.
25. Hilderbrand, R.H. 2003. The roles of carrying capacity, immigration, and population synchrony on persistence of stream-dwelling cutthroat trout. Biological Conservation 110: 257-266.
26. Hill, M.F., Hastings, A. & Botsford, L.W. 2002. The effects of small dispersal rates on extinction times in structured metapopulation models. American Naturalist 160: 389-402.
27. Isaak, D.J., Thurow, R.F., Rieman, B.E. & Dunham, J.B. 2007. Chinook salmon use of spawning patches: relative roles of habitat quality, size, and connectivity. Ecological Applications 17: 352-364.
28. Jager, H.I., Chander, J.A., Lepka, K.B. & Winkle, W.V. 2001. A theoretical study of river fragmentation by dams and its effects on white sturgeon populations. Environmental Biology of Fishes 60: 347-361.
29. Jonsson, B. & Jonsson, N. 1993. Partial migration: niche shift versus sexual maturation in fishes. Reviews in Fish Biology and Fisheries 3: 348-365.
30. Kitano, S. 1997. Intrapopulation variation in growth and reproduction of fluvial dolly varden. Doctoral thesis, Hokkaido University (in Japanese).
31. Kitano, S. & Shimazaki, K. 1995. Spawning habitat and nest depth of female Dolly Varden Salvelinus malma of different body size. Fisheries Science 61: 776-779.
32. Koenig, W.D., van Vuren, D. & Hooge, P.N. 1996. Detectability, philopatry and the distribution of dispersal distances in vertebrates. Trends in Ecology and Evolution 11: 514-517.
33. Koizumi, I. 2006. A "tributary-mainstream" system function like a "river-ocean" system: seasonal migration of stream-dwelling salmonid in a unique river system in central Hokkaido, Japan. In: Kovar, K., Hrkal, Z. & Bruthans, J., ed Proceedings of HydroEco'2006 (International conference on hydrology and ecology: the groundwater/ecology connection). Karlovy Vary: Czech Republic, pp. 351-354.
34. Koizumi, I. & Maekawa, K. 2003. Spawning migration of stream-dwelling Dolly Varden in spring-fed tributaries of the Shiisorapuchi River, Japan. Journal of Freshwater Ecology 18: 321-331.
35. Koizumi, I. & Maekawa, K. 2004. Metapopulation structure of stream-dwelling Dolly Varden charr inferred from patterns of occurrence in the Sorachi River basin, Hokkaido, Japan. Freshwater Biology 49: 973-981.
36. Koizumi, I., Yamamoto, S. & Maekawa, K. 2006a. Female biased migration in stream-dwelling Dolly Varden in the Shiisorapuchi River, Hokkaido, Japan. Journal of Fish Biology 68: 1513-1529.
37. Koizumi, I., Yamamoto, S. & Maekawa, K. 2006b. Decomposed pairwise regression analysis of genetic and geographic distances reveals a metapopulation structure of stream-dwelling Dolly Varden charr. Molecular Ecology 15: 3175-3189.
38. Koizumi, I., Yamamoto, S., Nomoto, K. & Maekawa, K. 2008. Synchrony in local population dynamics of stream-dwelling Dolly Varden: do genetically similar groups show similar demography? Population Ecology 50: 367-377.
39. 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.
40. Lande, R. 1993. Risks of population extinction from demographic and environmental stochasticity and random catastrophes. American Naturalist 142: 911-927.
41. Larned, S.T., Datry, T., Arscott, D.B. & Tockner, T. 2010. Emerging concepts in temporary-river ecology. Freshwater Biology 55: 717-738.
42. Letcher, B.H., Nislow, K.H., Coombs, J.A., O'Donnell, M.J. & Dubreuil, T.L. 2007. Population response to habitat fragmentation in a stream-dwelling brook trout population. PLoS ONE 2: e1139.
43. Lobón-Cerviá, J. 2004. Discharge-dependent covariation patterns in the population dynamics of brown trout (Salmo trutta) within a Cantabrian river drainage. Canadian Journal of Fisheries and Aquatic Science 61: 1929-1939.
44. Lowe, W.H. & Allendorf, F.W. 2010. What can genetics tell us about population connectivity? Molecular Ecology 19: 3038-3051.
45. Lytle, D.H. & Poff, N.L. 2004. Adaptation to natural flow regimes. Trends in Ecology and Evolution 19: 94-100.
46. Magoulick, D.D. & Kobza, R.M. 2003. The role of refugia for fishes during drought: a review and synthesis. Freshwater Biology 48: 1186-1198.
47. McElhany, P., Ruckelshaus, M.H., Ford, M.J., Wainwright, T.C. & Bjorkstedt, E.P. 2000. Viable salmonid populations and the recovery of evolutionarily significant units. U.S. Department of Commerce, NOAA Technical Memorandum NMFS-NWFSC-42. Seattle: Northwest Fisheries Center.
48. McElroy, T.C., Kandl, K.L., Garcia, J. & Trexler, J.C. 2003. Extinction-colonization dynamics structure genetic variation of spotted sunfish (Lepomis punctatus) in the Florida Everglades. Molecular Ecology 12: 355-368.
49. Morita, K. & Yamamoto, S. 2002. Effects of habitat fragmentation by damming on the persistence of stream-dwelling charr populations. Conservation Biology 16: 1318-1323.
50. Morita, K. & Yokota, A. 2002. Population viability of stream-resident salmonids after habitat fragmentation: a case study with white-spotted charr (Salvelinus leucomaenis) by an individual based model. Ecological Modelling 155: 85-94.
51. Morita, K., Yamamoto, S. & Hoshino, N. 2000. Extreme life history change of white-spotted charr (Salvelinus leucomaenis) after damming. Canadian Journal of Fisheries and Aquatic Science 57: 1300-1306.
52. Morita, K., Morita, S.H. & Yamamoto, S. 2009. Effects of habitat fragmentation by damming on salmonid fishes: lessons from white-spotted charr in Japan. Ecological Research 24: 711-722.
53. Neville, H., Dunham, J., Rosenberger, A., Umek, J. & Nelson, B. 2009. Influences of Wildfire, habitat size, and connectivity on trout in headwater streams revealed by Patterns of genetic diversity. Transactions of the American Fisheries Society 138: 1314-1327.
54. Northcote, T.G. 1997. Potamodromy in Salmonidae: living and moving in the fast lane. North American Journal of Fisheries Management 17: 1029-1045.
55. Northcote, T.G. & Hartman, G.F. 1988. The biology and significance of stream trout populations (Salmo spp.) living above and below waterfalls. Polskie Archiwum Hydrobiologii 35: 409-442.
56. Palmqvist, E. & Lundberg, P. 1998. Population extinctions in correlated environments. Oikos 83: 359-367.
57. Pearsons, T.N., Li, H.W. & Lamberti, G.A. 1992. Influence of habitat complexity on resistance to flooding and resilience of stream fish assemblages. Transactions of the American Fisheries Society 121: 427-436.
58. Pringle, C.M., Freeman, M. & Freeman, B. 2000. Regional effects of hydrologic alterations on riverine macrobiota in the New World: tropical-temperate comparisons. BioScience 50: 807-823.
59. Real, L.A. 1994. Ecological genetics. Princeton: Princeton University Press.
60. Reynolds, J.D., Webb, T.J. & Hawkins, L.A. 2005. Life history and ecological correlates of extinction risk in European freshwater fishes. Canadian Journal of Fisheries and Aquatic Sciences 62: 854-862.
61. Riccardi, A. & Rasmussen, J.B. 1999. Extinction rates of North American freshwater fauna. Conservation Biology 13: 1220-1222.
62. Richter, B.D., Braun, D.P., Mendelson, M.A. & Master, L.L. 1997. Threats to imperiled freshwater fauna. Conservation Biology 11: 1081-1093.
63. Rieman, B.E. & Dunham, J.B. 2000. Metapopulation and salmonids: A synthesis of life history patterns and empirical observations. Ecology of Freshwater Fish 9: 51-64.
64. Rieman, B.E. & McIntyre, J.D. 1993. Demographic and habitat requirements for the conservation of bull trout Salvelinus confluentus. USDA Forest Service Intermountain Research Station, General Technical Report INT-302. Ogden: Utah.
65. Rieman, B.E. & McIntyre, J.D. 1995. Occurrence of bull trout in naturally fragmented habitat patches of varied size. Transactions of the American Fisheries Society 124: 285-296.
66. Rieman, B.E. & McIntyre, J.D. 1996. Spatial and temporal variability in bull trout redd counts. North American Journal of Fisheries Management 16: 132-141.
67. Rieman, B.E., Lee, D.C., Chandler, G. & Myers, D. 1997. Does wildfire threaten extinction for salmonids: responses of redband trout and bull trout following recent large fires on the Boise National Forest. In: Greenlee, J., ed Proceedings of the conference on wildfire and threatened and endangered species and habitats. International Association of Wildland Fire: Fairfield, Washington, pp. 47-57.
68. Rodríguez, M.A. 2002. Restricted movement in stream fish: the paradigm is incomplete, not lost. Ecology 83: 1-13.
69. Rosenfeld, J. & Hatfield, T. 2006. Information needs for assessing critical habitat of freshwater fish. Canadian Journal of Fisheries and Aquatic Sciences 63: 683-698.
70. Saccheri, I., Kuussaari, M., Kankare, M., Vikman, P., Fortelius, W. & Hanski, I. 1998. Inbreeding and extinction in a butterfly metapopulation. Nature 392: 491-494.
71. Scheurer, J.A., Fausch, K.D. & Bestgen, K.R. 2003. Multi-scale processes regulate brassy minnow persistence in a Great Plains river. Transactions of the American Fisheries Society 132: 840-855.
72. Schtickzelle, N. & Quinn, T.P. 2007. A metapopulation perspective for salmon and other anadromous fish. Fish and Fisheries 8: 297-314.
73. Schwartz, M.K., Luikart, G. & Waples, R.S. 2007. Genetic monitoring as a promising tool for conservation and management. Trends in Ecology and Evolution 22: 25-33.
74. Schwarz, C.J. & Seber, G.A.F. 1999. Estimating animal abundance: review III. Statistical Science 14: 427-456.
75. Skalski, G.T. & Gilliam, J.F. 2000. Modeling diffusive spread in a heterogeneous population: a movement study with stream fish. Ecology 81: 1685-1700.
76. Slatkin, M. 1987. Gene flow and the geographic structure of natural populations. Science 236: 787-792.
77. Slatkin, M. 1993. Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47: 264-279.
78. Spruell, P., Rieman, B.E., Knudsen, K.L., Utter, F.M. & Allendorf, F.W. 1999. Genetic population structure within streams: microsatellite analysis of bull trout populations. Ecology of Freshwater Fish 8: 114-121.
79. Swanberg, T.R. 1997. Movements of and habitat use by fluvial bull trout in the Blackfoot River, Montana. Transactions of the American Fisheries Society 126: 735-746.
80. Tilman, D. & Kareiva, P.M. 1997. Spatial ecology: the role of space in population dynamic and interspecific interactions. Princeton: Princeton University Press.
81. Turchin, P. 2003. Complex population dynamics: a theoretical/empirical synthesis. Princeton: Princeton University Press.
82. Whitlock, M.C. 1992. Nonequilibrium population structure in forked fungus beetles: extinction, colonization, and the genetic variance among populations. American Naturalist 139: 952-970.
83. Wright, S. 1943. Isolation by distance. Genetics 28: 139-156.
84. Xu, C.L., Letcher, B.H. & Nislow, K.H. 2010. Size-dependent survival of brook trout Salvelinus fontinalis in summer: effects of water temperature and stream flow. Journal of Fish Biology 76: 2342-2369.
85. Yamamoto, S., Morita, K., Koizumi, I. & Maekawa, K. 2004. Genetic differentiation of white-spotted charr (Salvelinus leucomaenis) populations after habitat fragmentation: spatio-temporal changes of gene frequencies. Conservation Genetics 5: 529-538.