Modelling dendritic ecological networks in space: An integrated network perspective

Ecology Letters

Volumn 16, Issue 5, 2013, Pages 707-719

  Peterson, Erin E ^a   Ver Hoef, Jay M ^b   Isaak, Dan J ^c   Falke, Jeffrey A ^d   Fortin, Marie Josée ^e   Jordan, Chris E ^f   McNyset, Kristina ^d   Monestiez, Pascal ^g   Ruesch, Aaron S ^h,i   Sengupta, Aritra ^j   Som, Nicholas ^d,k   Steel, E Ashley ^l   Theobald, David M ^m   Torgersen, Christian E ^h   Wenger, Seth J ⁿ  

^a CSIRO   (Australia)

^b NOAA National Marine Mammal Laboratory   (United States)

^c ROCKY MOUNTAIN RESEARCH STATION   (United States)

^d OREGON STATE UNIVERSITY   (United States)

^e UNIVERSITY OF TORONTO   (Canada)

^f NOAA EARTH SYSTEM RESEARCH LABORATORY   (United States)

^g INRA   (France)

^h UNIVERSITY OF WASHINGTON   (United States)

ⁱ WISCONSIN DEPARTMENT OF NATURAL RESOURCES   (United States)

^j OHIO STATE UNIVERSITY   (United States)

^k U S FISH AND WILDLIFE SERVICE   (United States)

^l PACIFIC NORTHWEST RESEARCH STATION   (United States)

^m Department of Environmental and Radiological Health Sciences   (United States)

ⁿ Trout Unlimited   (United States)

more..

Author keywords

Connectivity; Dendritic ecological network; Directionality; Network analysis; Scales; Spatial statistics; Stream network; Taxonomy of network analyses

Indexed keywords

CONNECTIVITY; ECOLOGICAL MODELING; INTEGRATED APPROACH; MORPHOLOGY; NETWORK ANALYSIS; PLANT ARCHITECTURE; SPATIAL ANALYSIS; TAXONOMY; TOPOLOGY;

ARTICLE; BIOLOGICAL MODEL; ECOLOGY; ECOSYSTEM; METHODOLOGY; RIVER; STATISTICAL MODEL;

ECOLOGY; ECOSYSTEM; LINEAR MODELS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; RIVERS;

EID: 84876712129     PISSN: 1461023X     EISSN: 14610248     Source Type: Journal    
DOI: 10.1111/ele.12084     Document Type: Article

References (100)

1. Angermeier, P.L. & Krueger, K.L. & Dolloff, C.A. (2002). Discontinuity in stream-fish distributions: Implications for assessing and predicting species occurrence. In: Predicting Species Occurrences: Issues of Accuracy and Scale (eds Scott, J.M., Heglund, P., and Morrison, M.L.). Island Press, Covelo, CA, U.S.A., pp. 519-527.
2. Audergon, J.-M., Monestiez, P. & Habib, R. (1993). Spatial dependences and sampling in a fruit tree: A new concept for spatial prediction in fruit studies. J. Hortic. Sci., 68, 99-112.
3. Auerbach, D.A. & Poff, N.L. (2011). Spatio-temporal controls of simulated metacommunity dynamics in dendritic networks. J. N. Am. Benthol. Soc., 30, 235-251.
4. Barr, T.C. Jr & Holsinger, J.R. (1985). Speciation in cave faunas. Ann. Rev. Ecol. Syst., 16, 313-337.
5. Bascompte, J., Melián, C.J. & Sala, E. (2005). Interaction strength combinations and the overfishing of a marine food web. Proc. Natl. Acad. Sci. USA, 102, 5443-5447.
6. Benda, L., Poff, N.L., Miller, D., Reeves, G., Pess, G. & Pollock, M. (2004). The Network Dynamics Hypothesis: How channel networks structure riverine habitats. Bioscience, 54, 413-427.
7. Blonder, B., Wey, T.W., Dornhaus, A. & James, R. & Sih, A. (2012). Temporal dynamics and network analysis. Method. Ecol. Evol., 3, 958-972.
8. Brock, R.E. & Kelt, D.A. (2004). Influence of roads on the endangered Stephens' kangaroo rat (Dipodomys stephensi): are dirt and gravel roads different? Biol. Conserv., 118, 633-640.
9. Burnett, K.M. (2001). Relationships among juvenile anadromous salmonids, their freshwater habitat, and landscape characteristics over multiple years and spatial scales in Elk River, Oregon. Ph.D. Dissertation. Oregon State University, Corvallis, Oregon, USA.
10. Cadotte, M.W. (2006). Competition-colonization trade-offs and disturbance effects at multiple scales. Ecology, 88, 823-829.
11. Carranza, M.L., D'Alessandro, E., Saura, S. & Loy, A. (2012). Connectivity providers for semi-aquatic vertebrates: The case of the endangered otter in Italy. Landscape Ecol., 27, 281-290.
12. Carrara, F., Altermatt, F., Rodríguez-Iturbe, I. & Rinaldo, A. (2012). Dendritic connectivity controls biodiversity patterns in experimental metacommunities. Proc. Natl. Acad. Sci. USA, 109, 5761-5766.
13. Castellón, T.D. & Sieving, K.E. (2006). An experimental test of matrix permeability and corridor use by an endemic understory bird. Conserv. Biol., 20, 135-145.
14. Clement, L. & Thas, O. (2009). Testing for trends in the violatin frequency of an environmental threshold in rivers. Environmetrics, 20, 53-67.
15. Cote, D., Kehler, D.G., Bourne, C. & Wiersma, Y.F. (2009). A new measure of longitudinal connectivity for stream networks. Landscape Ecol., 24, 101-113.
16. Cressie, N. (1993). Statistics for Spatial Data. Revised edn. John Wiley & Sons, New York.
17. Cressie, N. & Johannesson, G. (2008). Fixed rank kriging for very large spatial data sets. J. R. Stat. Soc. B, 70, 209-226.
18. Cressie, N. & Wikle, C.K. (2011). Statistics for Spatio-temporal Data. John Wiley & Sons, Hoboken.
19. Cressie, N., Frey, J., Harch, B. & Smith, M. (2006). Spatial prediction on a river network. J. Agric. Biol. Environ. Stat., 11, 127-150.
20. Cressie, N., Calder, K.A., Clark, J.S., Ver Hoef, J.M. & Wikle, C.K. (2009). Accounting for uncertainty in ecological analysis: The strengths and limitations of hierarchical statistical modeling. Ecol. Appl., 19, 553-570.
21. Dale, M.R.T. & Fortin, M.-J. (2010). From graphs to spatial graphs. Annu. Rev. Ecol. Evol. Syst., 41, 21-38.
22. Diggle, P.J., Tawn, J.A. & Moyeed, R.A. (1998). Model-based geostatistics. J. R. Stat. Soc. C-App., 47, 299-350.
23. Dunham, J.B. & Rieman, B.E. (1999). Metapopulation structure of bull trout: influences of physical, biotic, and geometrical landscape characteristics. Ecol. Appl., 807(9), 642-655.
24. Erös, T., Schmera, D. & Schick, R.S. (2011). Network thinking in riverscape conservation - a graph-based approach. Biol. Conserv., 144, 184-192.
25. Fagan, W.F. (2002). Connectivity, fragmentation, and extinction risk in dendritic metapopulations. Ecology, 83, 3243-3249.
26. Falke, J.A. & Fausch, K.D. (2010). From metapopulations to metacommunities: linking theory with empirical observations of the spatial population dynamics of stream fishes. (eds Gido, K.B. and Jackson, D.A.). American Fisheries Society Special Publication, 73, 207-233.
27. Fall, A., Fortin, M.-J., Manseau, M. & O'Brien, D. (2007). Spatial graphs: Principles and applications for habitat connectivity. Ecosystems, 10, 448-461.
28. Fausch, K.D. (2008). A paradox of trout invasions in North America. Biol. Invasions, 10, 685-701.
29. Fausch, K.D., Torgersen, C.E., Baxter, C.V. & Li, H.W. (2002). Landscapes to riverscapes: bridging the gap between research and conservation of stream reaches. Bioscience, 52, 483-498.
30. Finlay, J., Hood, J.M., Limm, M.P., Power, M.E., Schade, J.D. & Welter, J.R. (2011). Light-mediated thresholds in stream-water nutrient composition in a river network. Ecology, 92, 140-150.
31. Fisher, S.G. (1997). Creativity, idea generation, and the functional morphology of streams. J. N. Am. Benthol. Soc., 16, 305-318.
32. Fisher, S.G., Sponseller, R.A. & Heffernan, J.B. (2004). Horizons in stream biogeochemistry: Flowpaths to progress. Ecology, 85, 2369-2379.
33. Flitcroft, R.L., Burnett, K.M., Reeves, G.H. & Ganio, L.M. (2012). Do network relationships matter? Comparing network and instream habitat variables to explain densities of juvenile coho salmon (Oncorhynchus kisutch) in mid-coastal Oregon, USA. Aquat. Conserv., 22, 288-302.
34. Fortuna, M.A., Albaladejo, R.G., Fernandez, L., Aparicio, A. & Bascompte, J. (2009). Networks of spatial genetic variation across species. Proc. Natl. Acad. Sci. USA, 106, 19044-19049.
35. Fullerton, A.H., Lindley, S.T., Pess, G.R., Feist, B.E., Steel, E.A. & McElhany, P. (2011). Human influence on the spatial structure of threatened pacific salmon metapopulations. Conserv. Biol., 25, 932-944.
36. Ganio, L.M., Torgersen, C.E. & Gresswell, R.E. (2005). A geostatistical approach for describing spatial pattern in stream networks. Front. Ecol. Environ., 3, 138-144.
37. Gardner, K.K. & McGlynn, B.L. (2009). Seasonality in spatial variability and influence of land use/land cover and watershed characteristics on stream water nitrate concentrations in a developing watershed in the Rocky Mountain West. Water Resour. Res., 45, W08411.
38. Garreta, V., Monestiez, P. & Ver Hoef, J.M. (2009). Spatial modeling and prediction on river networks: up model, down model, or hybrid. Environmetrics, 21, 439-456.
39. Gassman, P.W., Reyes, M.R., Green, C.H. & Arnold, J.G. (2007). The Soil and Water Assessment Tool: Historical development, applications, and future research directions. Trans. ASABE, 50, 1211-1250.
40. Gilarranz, L.J. & Bascompte, J. (2012). Spatial network structure and metapopulation persistence. J. Theor. Biol., 297, 11-16.
41. Goldberg, E.E., Lynch, H.J., Neubert, M.G. & Fagan, W.F. (2010). Effects of branching spatial structure and life history on the asymptotic growth rate of a population. Theor. Ecol., 3, 137-152.
42. Grant, E.H.C., Lowe, W.H. & Fagan, W.F. (2007). Living in the branches: population dynamics and ecological processes in dendritic networks. Ecol. Lett., 10, 165-175.
43. Grant, E.H.C., Lynch, H.J., Muneepeerakul, R., Arunachalam, M. & Rodríguez-Iturbe, I. & Fagan, W.F. (2012). Interbasin water transfer, riverine connectivity, and spatial controls on fish biodiversity. PLoS ONE, 7, e34170.
44. Haak, A.L., Williams, J.E., Neville, H.M., Dauwalter, D.C. & Colyer, W.T. (2010). Conserving peripheral trout populations: The values and risks of life on the edge. Fisheries, 35, 530-549.
45. Habib, R., Tisne-Agostini, D., Vanniere, M.-P. & Monestiez, P. (1991). Geostatistical method for independent in kiwifruit vine to estimate yield components. New Zeal. J. Crop Hort., 19, 329-335.
46. Hankin, D.G. & Reeves, G.H. (1988). Estimating total fish abundance and total habitat area in small streams based on visual estimation methods. Can. J. Fish. Manage., 45, 834-844.
47. Hanski, I. (1998). Metapopulation dynamics. Nature, 396, 41-49.
48. Hari, R.E., Livingstone, D.M., Siber, R., Burkhardt-Holm, P. & Güttinger, H. (2006). Consequences of climiatic change for water temperature and brown trout populations in Alpine rivers and streams. Glob. Change Biol., 12, 10-26.
49. Harig, A.L., Fausch, K.D., and Young, M.K. (2000). Factors influencing Success of Greenback Cutthroat Trout Translocations. N. Am. J. Fish. Manage., 20, 994-1004.
50. Hermoso, V., Linke, S., Prenda, J. & Possingham, H.P. (2011). Addressing longitudinal connectivity in the conservation planning of fresh waters. Freshwater Biol., 56, 57-70.
51. Hidalgo, T., Gusdal, M.Y., Dingsør, G.E., Hjermann, D., Ottersen, G., Stige, L.C. et al. (2011). A combination of hydrodynamical and statistical modelling reveals non-stationary climate effects on fish larvae distributions. Proc. R. Soc. Biol. Sci., 279, 275-283.
52. Hitt, N.P. & Angermeier, P.L. (2008). River-stream connectivity affects fish bioassessment performance. Environ. Manage., 42, 132-150.
53. Horton, R.E. (1945). Erosional development of streams and their drainage basins; hydrophysical approach to quantitative morphology. Geol. Soc. Am. Bull., 56, 275-370.
54. Isaak, D.J., Thurow, R.F., Rieman, B.E. & Dunham, J.B. (2007). Relative roles of habitat quality, size, and connectivity in Chinook salmon use of spawning patches. Ecol. Appl., 17, 352-364.
55. Isaak, D.J., Luce, C.H., Rieman, B.E., Nagel, D.E., Peterson, E.E., Horan, D.L. et al. (2010). Effects of climate change and wildfire on stream temperatures and salmonid thermal habitat in a mountain river network. Ecol. Appl., 20, 1350-1371.
56. Jabot, F. & Bascompte, J. (2012). Bitrophic interactions shape biodiversity in space. Proc. Natl. Acad. Sci. USA, 109, 4521-4526.
57. Kolaczyk, E.D. (2009). Statistical Analysis of Network Data. Springer Series in Statistics, New York.
58. Le Pichon, C., Gorges, G., Boët, P., Baudry, J., Goreaud, F. & Thierry, F. (2006). A spatially explicit resource-based approach for managing stream fishes in riverscapes. Environ. Manage., 37, 322-335.
59. Legendre, P. & Fortin, M.-J. (2010). Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data. Mol. Ecol. Resour., 10, 831-844.
60. Legrand, A. & Barbosa, P. (2003). Plant morphological complexity impacts foraging efficiency of adult Coccinella septempunctata L. (Coleoptera: Coccinellidae). Environ. Entomol., 32, 1219-1226.
61. MacKenzie, D.I., Nichols, J.D., Lachman, G.B., Droege, S., Royle, J.A. & Langtimm, C.A. (2002). Estimating site occupancy rates when detection probabilities are less than one. Ecology, 83, 2248-2255.
62. Mantel, N. (1967). The detection of disease clustering and a generalized regression approach. Cancer Res., 27, 209-220.
63. Massol, F., Gravel, D., Mouquet, N., Cadotte, M.W., Fukami, T. & Leibold, M.A. (2011). Linking community and ecosystem dynamics through spatial ecology. Ecol. Lett., 14, 313-323.
64. Money, E., Carter, G. & Serre, M.L. (2009a). Modern space/time geostatistics using river distances: data integration of turbidity and E. coli measurements to assess fecal contamination along the Raritan River in New Jersey. Environ. Sci. Technol., 43, 3736-3742.
65. Money, E., Carter, G. & Serre, M.L. (2009b). Using river distance in the space/time estimation of dissolved oxygen along two impaired river networks in New Jersey. Water Res., 43, 1948-1958.
66. Muneepeerakul, R., Bertuzzo, E., Rinaldo, A. & Rodríguez-Iturbe, I. (2008). Patterns of vegetation biodiversity: The roles of dispersal directionality and river network structure. J. Theor. Biol., 252, 221-229.
67. Naiman, R.J. & Décamps, H. (1997). The ecology of interfaces: riparian zones. Annu. Rev. Ecol. Syst., 28, 621-658.
68. Pandey, P.K., Soupir, M.L., Haddad, M. & Rothwell, J.J. (2012). Assessing the impacts of watershed indexes and precipitation on spatial in-stream E. coli concentrations. Ecol. Indic., 23, 641-652.
69. Paola, C., Foufoula-Georgiou, E., Dietrich, W.E., Hondzo, M., Mohrig, D., Parker, G. et al. (2006). Toward a unified science of the Earth's surface: Opportunities for synthesis among hydrology, geomorphology, geochemistry, and ecology. Water Resour. Res., 42, W03S10.
70. Peterson, E.E. & Ver Hoef, J.M. (2010). A mixed-model moving-average approach to geostatistical modeling in stream networks. Ecology, 91, 644-651.
71. Peterson, E.E., Merton, A.A., Theobald, D.M. & Urquhart, N.S. (2006). Patterns of spatial autocorrelation in stream water chemistry. Environ. Monit. Assess., 121, 569-594.
72. Poos, M., Lawrie, D., Tu, C., Jackson, D.A. & Mandrak, N.E. (2012). Estimating local and regional population sizes for an endangered minnow, redside dace (Clinostomus elongates), in Canada. Aquat. Conserv., 22, 47-57.
73. Porter, H.J., Hanson, P.C. & Lin, C.C. (2012). Staying afloat in the sensor data deluge. Trends Ecol. Evol., 27, 121-129.
74. Power, M.E. & Dietrich, W.E. (2002). Food webs in river networks. Ecol. Res., 17, 451-471.
75. Proulx, S.R., Promislow, D.E.L. & Phillips, P.C. (2005). Network thinking in ecology and evolution. Trends Ecol. Evol., 20, 345-353.
76. R Development Core Team (2010). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. Available at: http://www.R-project.org/.
77. Rathbun, S.L. (1998). Spatial modeling in irregularly shaped regions: Kriging estuaries. Environmetrics, 9, 109-129.
78. Rayfield, B., Fortin, M.-J. & Fall, A. (2011). Connectivity for conservation: A framework to classify network measures. Ecology, 92, 847-858.
79. Rodríguez-Iturbe, I., Muneepeerakul, R., Bertuzzo, E., Levin, S.A. & Rinaldo, A. (2009). River networks as ecological corridors: A complex systems perspective for integrating hydrologic, geomorphologic, and ecological dynamics. Water Resour. Res., 45, W01413.
80. Ruesch, A.S., Torgersen, C.E., Lawler, J.J., Olden, J.D., Peterson, E.E., Volk, C.J. et al. (2012). Projected climate-induced habitat loss for salmonids based on a network model of stream temperature. Conserv. Biol., 26, 873-882.
81. Sanderson, B.L., Barnas, K.A. & Wargo-Rub, A.M. (2009). Nonindigenous species of the Pacific Northwest: An overlooked risk to endangered salmon? Bioscience, 59, 245-256.
82. Schick, R.S. & Lindley, S.T. (2007). Directed connectivity among fish populations in a riverine network. J. Appl. Ecol., 44, 1116-1126.
83. Schlosser, I.J. & Angermeier, P.L. (1995). Spatial variation in demographic processes in lotic fishes: Conceptual models, empirical evidence, and implications for conservation. American Fisheries Society Symposium, 17, 360-370.
84. Smouse, P.E., Long, J.C. & Sokal, R.R. (1986). Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Syst. Zool., 35, 627-632.
85. Spooner, P.G., Lunt, I.D., Okabe, A. & Shiode, S. (2004). Spatial analysis of roadside Acacia populations on a road network using the network K-function. Landscape Ecol., 19, 491-499.
86. Stevens, D.L. Jr & Jensen, S.F. (2007). Sample design, execution, and analysis for wetland assessment. Wetlands, 27, 515-523.
87. Sylvaine, S., Morel, K., Durand, E., Brevalle, G., Girard, T. & Lauri, P. (2012). Aphids at crossroads: when branch architecture alters aphid infestation patterns in the apple tree. Trees, 26, 273-282.
88. Towler, E., Rajagopalan, B., Gilleland, E., Summers, R.S., Yates, D. & Katz, R.W. (2010). Modeling hydrologic and water quality extremes in a changing climate: a statistical approach based on extreme value theory. Water Resour. Res., 46, W11504.
89. Urban, D. & Keitt, T. (2001). Landscape connectivity: A graph-theoretic perspective. Ecology, 82, 1205-1218.
90. Urban, D.L., Minor, E.S., Treml, E.A. & Schick, R.S. (2009). Graph models of habitat mosaics. Ecol. Lett., 12, 260-273.
91. Ver Hoef, J.M. & Peterson, E.E. (2010). A moving average approach for spatial statistical models of stream networks. J. Am. Stat. Assoc., 105, 6-18. Rejoinder: 22-24.
92. Ver Hoef, J.M., Peterson, E.E. & Theobald, D. (2006). Spatial statistical models that use flow and stream distance. Environ. Ecol. Stat., 13, 449-464.
93. Ver Hoef, J.M., Peterson, E.E. & Clifford, D. & Shah, R. (in review). SSN: an R package for spatial statistical modeling on stream networks. Submitted to J. Stat. Softw. Available at: http://www.fs.fed.us/rm/boise/AWAE/projects/SpatialStreamNetworks.shtml.
94. Vörösmarty, C.J., McIntyre, P.B., Gessner, M.O., Dudgeon, D., Prusevich, A., Green, P. et al. (2010). Global threats to human water security and river biodiversity. Nature, 467, 555-561.
95. Ward, J.V. (1998). Riverine landscapes: biodiversity patterns, disturbance regimes, and aquatic conservation. Biol. Conserv., 83, 269-278.
96. Wiens, J.A. (2002). Riverine landscape: taking landscape ecology into the water. Freshwater Biol., 47, 501-515.
97. Wood, P.J., Gunn, J. & Rundle, S.D. (2008). Response of benthic cave invertebrates to organic pollution events. Aquat. Conserv., 18, 909-922.
98. Young, M.K. (1995). Conservation Assessment for Inland Cutthroat Trout. General Technical Report RM-256. U.S. Department of Agriculture, Forest Service, Rocky Mountain Forest and Range Experiment Station Fort Collins, CO, U.S.A.
99. Yuan, L.L. (2004). Using spatial interpolation to estimate stressor levels in unsampled streams. Environ. Monit. Assess., 94, 23-38.
100. Zimmerman, D. (2006). Optimal network design for spatial prediction, covariance parameter estimation, and empirical prediction. Environmetrics, 17, 635-652.