Use of constrained additive and quadratic ordination in fish habitat studies: An application to introduced pumpkinseed (Lepomis gibbosus) and native brown trout (Salmo trutta) in an English stream

Fundamental and Applied Limnology

Volumn 180, Issue 1, 2012, Pages 69-75

  Vilizzi, Lorenzo ^a   Stakenas, Saulius ^b   Copp, Gordon H ^c,d,e  

^a MURRAY DARLING FRESHWATER RESEARCH CENTRE   (Australia)

^b Nature Research Centre   (Lithuania)

^c CENTRE FOR ENVIRONMENT   (United Kingdom)

^d TRENT UNIVERSITY   (Canada)

^e BOURNEMOUTH UNIVERSITY   (United Kingdom)

Author keywords

GAM GLM; Microhabitat preferences; Overlap; Repartition; VGAM VGLM

Indexed keywords

FRESHWATER ECOSYSTEM; HABITAT SELECTION; INTRODUCED SPECIES; MICROHABITAT; ORDINATION; PERCIFORM; RADIOTELEMETRY; SALMONID;

LEPOMIS GIBBOSUS; SALMO TRUTTA;

EID: 84875050782     PISSN: 18639135     EISSN: None     Source Type: Journal    
DOI: 10.1127/1863-9135/2012/0277     Document Type: Article

References (58)

1. Ahmadi-Nedushan, B., St-Hilaire, A., Bérubé, M., Robichaud, É., Thiémonge, N. & Bobée, B., 2006: A review of statistical methods for the evaluation of aquatic habitat suitability for instream flow assessment. - Riv. Res. Appl. 22: 503-523.
2. Almeida, D., Gomes-Lopes, A., Muñoz-López, M., Merino- Aquirre, R. & Miranda, R., 2009: Ecología de la agresión interespecífica en el pez sol Lepomis gibbosus y efectos sobre la fauna autóctona. - Abstracts of Posters from the Symposium on non-native freshwater species introduction in the Iberian Peninsula, Pamplona, Spain. (http://www.unav.es/centro/especiesinvasoras/)
3. Baglinière, J.-L. & Maisse, G., 1999: Biology and Ecology of the Brown and Sea Trout. Series in Aquaculture and Fisheries. VII. - Springer-Praxis, Chichester.
4. Bain, M. B., Finn, J. T. & Booke H. E., 1985: Quantifying stream substrate for habitat analysis studies. - N. Am. J. Fish. Manage. 5: 499-500.
5. Beyer, K., Copp, G. H. & Gozlan, R. E., 2007: Microbabitat use and interspecific associations of introduced topmouth gudgeon Pseudorasbora parva and native fishes in a small stream. - J. Fish Biol. 71: 224-238.
6. Bollen, K. A., 2002: Latent variables in psychology and the social sciences. - Ann. Rev. Psychol. 53: 605-634.
7. Bovee, K. D., Lamb, B. L., Bartholow, J. M., Stalnaker, C. B., Taylor, J. & Henriksen, J., 1998: Stream Habitat Analysis Using the Instream Flow Incremental Methodology. - U.S. Geological Survey, Biological Resources Discipline Information and Technology Report USGS/BRD-1998-0004.
8. Chessel, D., 2000: Méthodes d'analyse des données et écologie des communautés. - Actes 32ème Jourrnées de Statistique, 15-19 mai 2000, Fès (Moroco). Société Française de Statistique.
9. Copp, G. H., 1992: An empirical model for predicting the microhabitat of 0+ juveniles in lowland streams. - Oecologia 91: 338-345.
10. Copp, G. H., 2010: Patterns of diel activity and species richness in young and small fishes of European streams: a review of 20 years of point abundance sampling by electrofishing. - Fish Fish. 11: 439-460.
11. Copp, G. H. & Fox, M. G., 2007: Growth and life history traits of introduced pumpkinseed (Lepomis gibbosus) in Europe, and the relevance to invasiveness potential. - In: Gherardi, F. (ed.): Freshwater Bioinvaders: Profiles, Distribution, and Threats. - Springer, Berlin, pp. 289-306.
12. Copp, G. H., Olivier, J.-M., Peňáz, M. & Roux, A.-L., 1991: Juvenile fishes as functional describers of fluvial ecosystem dynamics: Applications on the River Rhône, France. - Regul. Riv: Res. Manage. 6: 135-145.
13. Copp, G. H., Stakenas, S. & Cucherousset, J., 2010: Aliens versus the natives: interactions between introduced pumpkinseed and indigenous brown trout in small streams of southern England. - Am. Fish. Soc. Symp. 73: 347-370.
14. Copp, G. H. & Vilizzi, L., 2004: Spatial and ontogenetic variability in the microhabitat use of stream-dwelling spined loach Cobitis taenia and stone loach Barbatula barbatula. - J. Appl. Ichthyol. 20: 440-451.
15. Cucherousset, J., Copp, G. H., Fox, M. G., Sterud, E., van Kleef, H. H., Verreycken, H. & Záhorská, E., 2009: Growth, life-history traits and potential invasive-ness of introduced pumpkinseed Lepomis gibbosus populations in Northern Europe. - Biol. Inv. 11: 2171-2180.
16. Dare, M. R. & Hubert, W. A., 2003: Use of similar habitat by cutthroat trout and brown trout in a regulated river during winter. - Northwest Sci. 77: 36-45.
17. Durance, I. & Ormerod, S. J., 2007: Climage change effects on upland stream macroinvertebrates over a 25-year period. - Glob. Change Biol. 13: 942-957.
18. Elliott, J. M., 1994: Quantitative Ecology and the Brown Trout. - Oxford University Press, Oxford.
19. Fausch, K. D., Taniguchi, Y., Nakano, S., Grossman, G. D. & Townsend, C. R., 2001: Flood disturbance regimes influence rainbow trout invasion success among five Holarctic regions. - Ecol. Appl. 11: 1438-1455.
20. Gauch, H. G. Jr., 1982: Multivariate Analysis in Community Ecology. - Cambridge University Press, Cambridge.
21. Gibbins, C. N. & Acornley, R. M., 2000: Salmonid habitat modelling studies and their contribution to the development of an ecologically acceptable release policy for Kielder Reservoir, north-east England. - Reg. Riv.: Res. Manage. 16: 203-224.
22. Godinho, F. N., Ferreira, M. T. & Cortes, R. V., 1997: Composition and spatial organization of fish assemblages in the lower Guadiana basin, southern Iberia. - Ecol. Freshwat. Fish 6: 134-143.
23. Gozlan, R. E., Britton, J. R., Cowx, I. G. & Copp, G. H., 2010: Current knowledge on nonnative freshwater fish introductions. - J. Fish Biol. 76: 751-786.
24. Gutiérrez-Estrada, J. C., Pulido-Calvo, I. & Fernández-Delgado, C. G., 2000: Age-structure, growth and reproduction of the introduced pumpkinseed (Lepomis gibbosus, L. 1758) in a tributary of the Guadalquivir River (Southern Spain). - Limnetica 19: 21-29.
25. Harvey, B. C., 1991: Interactions among stream fishes: predator- induced habitat shifts and larval survival. - Oecologia 87: 29-36.
26. Harvey, B. C. & Stewart, A. J., 1991: Fish size and habitat depth relationships in headwater streams. - Oecologia 87: 336-342.
27. Hastie, T., Tibshirani, R. & Friedman, J., 2008: The Elements of Statistical Learning. 2nd ed. - Springer, New York.
28. Heggenes. J., 1989: Physical habitat selection by brown trout (Salmo trutta) in riverine systems. - Nord. J. Freshwat. Res. 64: 74-90.
29. Heggenes, J., Saltveit, S. J., Bird, D. & Grew, R., 2002: Static habitat partitioning and dynamic selection by sympatric young Atlantic salmon and brown trout in south-west England streams. - J. Fish Biol. 60: 72-86.
30. Jowett, I. G. & Davey, A. J. H., 2007: A comparison of composite habitat suitability indices and generalized additive models of invertebrate abundance and fish presence-habitat availability. - Trans. Am. Fish. Soc. 136: 428-444.
31. Karr, J. R., 1981: Assessment of biotic integrity using fish communities. - Fisheries 6 (6): 21-27.
32. Klaar, M., Copp, G. H. & Horsfield, R., 2004: Autumnal habitat use of non-native pumpkinseed Lepomis gibbosus and associations with native fish species in small English streams. - Folia Zool. 53: 189-202.
33. Labonne, J., Allouche, S. & Gaudin, P., 2003: Use of a generalised linear model to test habitat preferences: the example of Zingel asper, an endemic endangered percid of the River Rhône. - Freshwat. Biol. 48: 687-697.
34. Leathwick, J. R., Elith, J. & Hastie, T., 2006: Comparative performance of generalized additive models and multivariate adaptive regression splines for statistical modelling of species distributions. - Ecol. Modell. 199: 188-196.
35. Legendre, P. & Legendre, L., 1998: Numerical Ecology. 2nd English ed. - Elsevier Science, Amsterdam, The Netherlands.
36. Lopes, L. F. G., Do Carmo, J. S. A., Cortes, R. M. V. & Oliveira, D., 2004: Hydrodynamics and water quality modelling in a regulated river segment: application on the instream flow definition. - Ecol. Modell. 173: 197-218.
37. Mäki-Petäys, A., Muotka, T., Huusko, A., Tikkanen, P. & Kreivi, P., 1997: Seasonal changes in habitat use and preferences by juvenile brown trout, Salmo trutta, in a northern boreal river. - Can. J. Fish. Aquat. Sci., 54: 520-530.
38. Mallet, J. P., Lamouroux, N., Sagnes, P. & Persat, H., 2000: Habitat preferences of European grayling in a medium size stream, the Ain river, France. - J. Fish Biol. 56, 1312-1326.
39. Mastrorillo, S. & Dauba, F., 1999: Short-term impact of reservoir cleaning on the microhabitat use of three non-salmonid fishes in a piedmont river in south west France. - Aquat. Sci. 61: 323-336.
40. Moisen, G. G., Freeman, E. A., Blackard, J. A., Frescino, T. S., Zimmermann, N. E. & Edwards, T. C. Jr., 2006: Predicting tree species presence and basal area in Utah: A comparison of stochastic gradient boosting, generalized additive models, and tree-based methods. - Ecol. Modell. 199: 176-187.
41. Moore, A., Russell, I. C. & Potter, E. C. E., 1990: Effects of intraperitoneally implanted dummy acoustic transmitters on the behaviour and physiology of juvenile Atlantic salmon, Salmo salar L. - J. Fish Biol. 37: 713-721.
42. Nilsson, C., Reidy, C. A., Dynesius, M. & Revenga, C., 2005: Fragmentation and flow regulation of the world's large river systems. - Science 308: 405-408.
43. Oberdorff, T. & Hughes, R. M., 1992: Modification of an index of biotic integrity based on fish assemblages to characterize rivers of the Seine basin, France. - Hydrobiologia 228: 117-130.
44. R Development Core Team, 2007: R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. - ISBN 3-900051-070, http://www.R-project.org.
45. Roussel, J.-M. & Bardonnet, A., 1997: Diel and seasonal patterns of habitat use by fish in a natural salmonid brook: an approach to the functional role of the riffle-pool sequence. - Bull. franç. Pêche Piscic. 346: 573-588.
46. Schmutz, S., Cowx, I. G., Haidvogl, G. & Pont, D., 2007: Fishbased methods for assessing European running waters: a synthesis. - Fish. Manage. Ecol. 14: 369-380.
47. Shiemer, F., 2000: Fish as indicators for the assessment of the ecological integrity of large rivers. - Hydrobiologia 422/423: 271-278.
48. ter Braak, C. J. F. & Verdonschot, D. F. M., 1995: Canonical correspondence analysis and related multivariate methods in aquatic ecology. - Aquat. Sci. 57: 255-289.
49. Vilizzi, L., Copp, G. H. & Roussel, J.-M., 2004: Assessing variation in suitability curves and electivity profiles in temporal studies of fish habitat use. - Riv. Res. Appl., 20: 605-618.
50. Vilizzi, L., Copp, G. H. & Roussel, J.-M., 2005: Assessing temporal variation and autocorrelation in fish habitat use. - Folia Zool. 54: 432-442.
51. Yamazaki, Y., Haramoto, S. & Takeshi, F., 2006: Habitat uses of freshwater fishes on the scale of reach system provided in small streams. - Env. Biol. Fish. 75: 333-341.
52. Yee, T. W., 2004: A new technique for maximum-likelihood canonical Gaussian ordination. - Ecol. Monogr. 74: 685-701.
53. Yee, T. W., 2006 a: Constrained additive ordination. - Ecology 87: 203-213.
54. Yee, T. W., 2006 b: VGAM Family Functions for Reduced-Rank Regression and Constrained Ordination. Beta version 0.6-5. - http://www.stat.auckland.ac.nz/ ~yee/VGAM/doc/rrvglm.pdf.
55. Yee, T. W. & Hastie, T. J., 2003: Reduced-rank vector generalized linear models. - Stat. Modell. 3: 15-41.
56. Yee, T. W. & MacKenzie, M., 2002: Vector generalized additive models in plant ecology. - Ecol. Modell. 157: 141-156.
57. Zhu, M., Hastie, T. J. & Walther, G., 2005: Constrained ordination analysis with flexible response functions. - Ecol. Modell. 187: 524-536.
58. Zuur, A. F., Ieno, E. N. & Smith, G. M., 2007: Analysing Ecological Data. - Springer, The Netherlands.