Species diversity and community similarity in fluctuating environments: Parametric approaches using species abundance distributions

Journal of Animal Ecology

Volumn 82, Issue 4, 2013, Pages 721-738

  Sæther, Bernt Erik ^a   Engen, Steinar ^a   Grøtan, Vidar ^a  

^a NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

Author keywords

Community dynamics; Community similarity; Environmental stochasticity; Lognormal species abundance model; Poisson lognormal distribution; Preston canonical hypothesis; Species diversity; Species area curves

Indexed keywords

ABUNDANCE; COMMUNITY DYNAMICS; COMMUNITY STRUCTURE; DIVERSITY INDEX; ECOLOGICAL THEORY; ENVIRONMENTAL CHANGE; HYPOTHESIS TESTING; INVERSE ANALYSIS; PARAMETERIZATION; POPULATION DISTRIBUTION; POPULATION DYNAMICS; SAMPLING; SPATIOTEMPORAL ANALYSIS; SPECIES DIVERSITY; SPECIES-AREA RELATIONSHIP; STATISTICAL DISTRIBUTION; STOCHASTICITY;

ANIMAL; BIODIVERSITY; BIOLOGICAL MODEL; DEMOGRAPHY; ENVIRONMENT; STATISTICS;

ANIMALS; BIODIVERSITY; DEMOGRAPHY; ENVIRONMENT; MODELS, BIOLOGICAL; STOCHASTIC PROCESSES;

EID: 84879163856     PISSN: 00218790     EISSN: 13652656     Source Type: Journal    
DOI: 10.1111/1365-2656.12068     Document Type: Article

References (109)

1. Adler, P.B., White, E.P., Lauenroth, W.E., Kaufman, D.M., Rassweiler, A. & Rusak, J.A. (2005) Evidence for a general species-time-area relationship. Ecology, 86, 2032-2039.
2. Bell, G. (2001) Neutral macroecology. Science, 293, 2413-2418.
3. Brook, B.W. & Bradshaw, C.J.A. (2006) Strength of evidence for density dependence in abundance time series of 1198 species. Ecology, 87, 1445-1451.
4. Brown, J.H. (1995) Macroecology. University of Chicago Press, Chicago, IL.
5. Bulmer, M.G. (1974) On fitting the Poisson lognormal distribution to species - abundance data. Biometrics, 30, 101-110.
6. Caswell, H. & Cohen, J.E. (1993) Local and regional regulation of species-area relations: a patch-occuppancy model. Species Diversity in Ecological Communities (eds R.E. Ricklefs & D. Schluter ), pp. 99-107. University of Chicago Press, Chicago, IL.
7. Chao, A. & Bunge, J. (2002) Estimating the number of species in a stochastic abundance model. Biometrics, 58, 531-539.
8. Chao, A., Chazdon, R.L., Colwell, R.K. & Shen, T.J. (2005) A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecology Letters, 8, 148-159.
9. Chao, A., Chazdon, R.L., Colwell, R.K. & Shen, T.J. (2006) Abundance-based similarity indices and their estimation when there are unseen species in samples. Biometrics, 62, 361-371.
10. Chesson, P. (2000) Mechanisms of maintenance of species diversity. Annual Review of Ecology and Systematics, 31, 343-366.
11. Cohen, J.E. (1968) Alternate derivations of a species-abundance relation. American Naturalist, 102, 165-172.
12. Condit, R., Pitman, N., Leigh, E.G., Chave, J., Terborgh, J., Foster, R.B., Nunez, P., Aguilar, S., Valencia, R., Villa, G., Muller-Landau, H.C., Losos, E. & Hubbell, S.P. (2002) Beta-diversity in tropical forest trees. Science, 295, 666-669.
13. Connolly, S.R. & Dornelas, M. (2011) Fitting and empirical evaluation of models for species abundance distributions. Biological Diversity (eds A.E. Magurran & B.J. McGill ), pp. 123-140. Oxford University Press, Oxford.
14. Crist, T.O. & Veech, J.A. (2006) Additive partitioning of rarefaction curves and species-area relationships: unifying alpha-, beta- and gamma-diversity with sample size and habitat area. Ecology Letters, 9, 923-932.
15. DeVries, P.J., Murray, D. & Lande, R. (1997) Species diversity in vertical, horizontal, and temporal dimensions of a fruit-feeding butterfly community in an Ecuadorian rainforest. Biological Journal of the Linnean Society, 62, 343-364.
16. Diserud, O. & Engen, S. (2000) A general and dynamic species abundance model, embracing the lognormal and the gamma models. American Naturalist, 155, 497-511.
17. Dorazio, R.M. & Royle, J.A. (2005) Estimating size and composition of biological communities by modeling the occurrence of species. Journal of the American Statistical Association, 100, 389-398.
18. Dorazio, R.M., Royle, J.A., Söderström, B. & Glimskär, A. (2006) Estimating species richness and accumulation by modelling species occurrence and detectability. Ecology, 87, 842-854.
19. Dornelas, M., Magurran, A.E., Buckland, S.T., Chao, A., Chazdon, R.L., Colwell, R.K., Curtis, T., Gaston, K.J., Gotelli, N.J., Kosnik, M.A., McGill, B., McCune, J.R., Morlon, H., Mumby, P.J., Øvreås, L., Studeny, A. & Vellend, M. (2012) Quantifying temporal change in biodiversity: challenges and opportunities. Proceedings of the Royal Society of London. Series B, Biological Sciences, 280, 20121931.
20. Engen, S. (1977) Comments on 2 different approaches to analysis of species frequency data. Biometrics, 33, 205-213.
21. Engen, S. (1978) Stochastic Abundance Models. Chapman & Hall, New York, NY.
22. Engen, S. (2007a) Heterogeneity in dynamic species abundance models: the selective effect of extinction processes. Mathematical Biosciences, 210, 490-507.
23. Engen, S. (2007b) Heterogeneous communities with lognormal species abundance distribution: species-area curves and sustainability. Journal of Theoretical Biology, 249, 791-803.
24. Engen, S., Aagaard, K. & Bongaard, T. (2011a) Disentangling the effects of heterogeneity, stochastic dynamics and sampling in a community of aquatic insects. Ecological Modelling, 222, 1387-1393.
25. Engen, S., Grøtan, V. & Sæther, B.-E. (2011b) Estimating similarity of communities: a parametric approach to spatio-temporal analysis of species diversity. Ecography, 34, 220-231.
26. Engen, S. & Lande, R. (1996a) Population dynamic models generating species abundance distributions of the gamma type. Journal of Theoretical Biology, 178, 325-331.
27. Engen, S. & Lande, R. (1996b) Population dynamic models generating the lognormal species abundance distribution. Mathematical Biosciences, 132, 169-183.
28. Engen, S., Lande, R., Walla, T. & De Vries, P.J. (2002) Analyzing spatial structure of communities using the two - dimensional Poisson lognormal species abundance model. American Naturalist, 160, 60-73.
29. Engen, S., Sæther, B.-E., Sverdrup-Thygeson, A., Grøtan, V. & Ødegaard, F. (2008) Assessment of species diversity from species abundance distributions at different localities. Oikos, 117, 738-748.
30. Ernest, S.K.M., Brown, J.H., Thibault, K.M., White, E.P. & Goheen, J.R. (2008) Zero sum, the niche and metacommunities: long-term dynamics of community assembly. American Naturalist, 172, E257-E269.
31. Etienne, R.S. & Olff, H. (2004) A novel genealogical approach to neutral biodiversity theory. Ecology Letters, 7, 170-175.
32. Etienne, R.S. & Olff, H. (2005) Confronting different models of community structure to species-abundance data: a Bayesian model comparison. Ecology Letters, 8, 493-504.
33. Ewens, W.J. (1972) The sampling theory of selectively neutral alleles. Theoretical Population Biology, 3, 87-112.
34. Fisher, R.A., Corbet, A.S. & Williams, C.B. (1943) The relation between the number of species and the number of individuals in a random sample of an animal population. Journal of Animal Ecology, 12, 42-58.
35. Fournier, E. & Loreau, M. (2001) Respective roles of recent hedges and forest patch remnants in the maintenance of ground - beetle (Coleoptera: Carabidae) diversity in an agricultural landscape. Landscape Ecology, 16, 17-32.
36. Gaston, K.J. & Blackburn, T.M. (2000) Pattern and Process in Macroecology. Blackwell Science, Oxford.
37. Golicher, D.J., O'Hara, R.B., Ruíz-Montoya, L. & Cayuela, L. (2006) Lifting a veil on diversity: a bayesian approach to fitting relative-abundance models. Ecological Applications, 16, 202-212.
38. Gotelli, N.J. & Colwell, R.K. (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters, 4, 379-391.
39. Gotelli, N.J. & Colwell, R.K. (2011) Estimating species richness. Biological Diveristy (eds A.E. Magurran & B.J. McGill ), pp. 39-54. Oxford University Press, Oxford.
40. Gray, J.S. (1981) Detecting pollution induced changes in communities using the log-normal distribution of individuals among species. Marine Pollution Bulletin, 12, 173-176.
41. Gray, J.S. & Mirza, F.B. (1979) Possible method for the detection of pollution-induced disturbance on marine benthic communities. Marine Pollution Bulletin, 10, 142-146.
42. Gray, J.S. & Pearson, T.H. (1982) Objective selection of sensitive species indicative of pollution-induced change in benthic communities.1. Comparative methodology. Marine Ecology-Progress Series, 9, 111-119.
43. Grøtan, V., Lande, R., Engen, S., Sæther, B.-E. & DeVries, P.J. (2012) Seasonal cycles of species diversity and similarity in a tropical butterfly community. Journal of Animal Ecology, 81, 714-723.
44. Grundy, R.M. (1951) The expected frequencies in a sample of an animal population in which the abundances are lognormally distributed. Biometrika, 38, 427-434.
45. Hogstad, O. (1975) Structure of small passerine communities in subalpine birch forests in Fennoscandia. Ecological Studies. Analysis and Synrhesis, vol. 17. Fennoscandian Tundra Ecosystems, Part 2 (ed. F.E. Wielgolaski ), pp. 94-104. Springer-Verlag, Berlin.
46. Hubalek, Z. (1982) Coefficients of association and similarity, based on binary (presence-absence) data: an evaluation. Biological Reviews, 57, 669-689.
47. Hubbell, S.P. (2001) The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press, Princeton, NJ.
48. Jaccard, P. (1912) The distribution of the flora in the alpine zone. New Phytologist, 11, 37-50.
49. Järvinen, O. (1979) Geographical gradients of stability in european land bird communities. Oecologia, 38, 51-69.
50. Jost, L., Chao, A. & Chazdon, R.L. (2011) Compositional similarity and β (beta) diversity. Biological Diversity (eds A.E. Magurran & B.J. McGill ), pp. 66-84. Oxford University Press, Oxford.
51. Kempton, R.A. (1975) Generalized form of Fisher's logarithmic series. Biometrika, 62, 29-38.
52. Kempton, R.A. & Taylor, L.R. (1974) Log-series and log-normal parameters as diversity discriminants for the Lepidoptera. Journal of Animal Ecology, 43, 381-399.
53. Kendall, D.G. (1948) On some modes of population growth leading to R.A. Fisher's logarithmic series distribution. Biometrika, 35, 6-15.
54. Koleff, P., Gaston, K.J. & Lennon, J.J. (2003) Measuring beta diversity for presence-absence data. Journal of Animal Ecology, 72, 367-382.
55. Lande, R. (1996) Statistics and partitioning of species diversity, and similarity among multiple communities. Oikos, 76, 5-13.
56. Lande, R., Engen, S. & Sæther, B.-E. (2003) Stochastic Population Dynamics in Ecology and Conservation. Oxford University Press, Oxford.
57. Leigh, E.G. (2007) Neutral theory: a historical perspective. Journal of Evolutionary Biology, 20, 2075-2091.
58. Longuet-Higgins, M.S. (1971) On the Shannon-Weaver index of diversity, in relation to the distribution of species in bird censuses. Theoretical Population Biology, 2, 271-289.
59. MacArthur, R.H. (1957) On the relative abundance of bird species. Proceedings of the National Academy of Sciences of the United States of America, 43, 293-295.
60. MacArthur, R.H. (1960) On the relative abundance of species. American Naturalist, 94, 25-36.
61. MacArthur, R.H. & Wilson, E.O. (1967) The Theory of Island Biogeography. Princeton University Press, Princeton, NJ.
62. Magurran, A.E. (2004) Measuring Biological Diversity. Blackwell Publishing, Oxford.
63. Magurran, A.E. (2005) Species abundance distributions: pattern or process? Functional Ecology, 19, 177-181.
64. Magurran, A.E. (2007) Species abundance distributions over time. Ecology Letters, 10, 347-354.
65. Mao, C.X. & Colwell, R.K. (2005) Estimation of species richness: mixture models, the role of rare species, and inferential challenges. Ecology, 86, 1143-1153.
66. Maurer, B.A. (1999) Untangling Ecological Complexity. The Macroscopic Perspective. The University of Chicago Press, Chicago, IL.
67. Maurer, B.A. & McGill, B.J. (2011) Measurement of species diversity. Biological Diversity (eds A.E. Magurran & B.J. McGill ), pp. 55-65. Oxford University Press, Oxford.
68. May, R.M. (1975) Patterns of species abundance and diversity. Ecology and Evolution of Communities (eds M.L. Cody & J.M. Diamond ), pp. 81-120. Harvard University Press, Cambridge.
69. May, R.M. (1981) Models for single populations. Theoretical Ecology, 2nd edn (ed. R.M. May ), pp. 5-29. Blackwell Scientific Publications, Oxford.
70. May, R.M. (2011) Foreword. Biological Diversity (eds A.E. Magurran & B.J. McGill ), pp. 5-7. Oxford University Press, Oxford.
71. May, R.M., Crawley, M.J. & Sugihara, G. (2007) Communities: patterns. Theoretical Ecology, 3rd edn (eds R.M. May & A. McLean ), pp. 111-131. Oxford University Press, Oxford.
72. McGill, B.J. (2003a) Does Mother Nature really prefer rare species or are log-left-skewed SADs a sampling artefact? Ecology Letters, 6, 766-773.
73. McGill, B.J. (2003b) A test of the unified neutral theory of biodiversity. Nature, 422, 881-885.
74. McGill, B.J. (2011) Species abundance distributions. Biological Diversity. Frontiers in Measurement and Assessment. (eds A.E. Magurran & B.J. McGill ), pp. 105-122. Oxford University Press, Oxford.
75. McGill, B.J., Etienne, R.S., Gray, J.S., Alonso, D., Anderson, M.J., Benecha, H.K., Dornelas, M., Enquist, B.J., Green, J.L., He, F.L., Hurlbert, A.H., Magurran, A.E., Marquet, P.A., Maurer, B.A., Ostling, A., Soykan, C.U., Ugland, K.I. & White, E.P. (2007) Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecology Letters, 10, 995-1015.
76. McGuinness, K.A. (1984) Equations and explanations in the study of species-area relationships. Biological Reviews, 59, 423-440.
77. Mutshinda, C.M., O'Hara, R.B. & Woiwod, I.P. (2008) Species abundance dynamics under neutral assumptions: a Bayesian approach to the controversy. Functional Ecology, 22, 340-347.
78. Mutshinda, C.M., O'Hara, R.B. & Woiwod, I.P. (2009) What drives community dynamics? Proceedings of the Royal Society of London. Series B, Biological Sciences, 276, 2923-2929.
79. Mutshinda, C.M., O'Hara, R.B. & Woiwod, I.P. (2011) A multispecies perspective on ecological impacts of climatic forcing. Journal of Animal Ecology, 80, 101-107.
80. Nee, S., Harvey, P.H. & Cotgreave, P. (1993) Species abundances. Mutualism and Community Organization. Behavioural, Theoretical and Food-Web Approaches (eds H. Kawanabe, J.E. Cohen & K. Iwasaki ), pp. 350-364. Oxford University Press, Oxford.
81. Nee, S., Harvey, P.H. & May, R.M. (1991) Lifting the veil on abundance patterns. Proceedings of the Royal Society of London. Series B, Biological Sciences, 243, 161-163.
82. O'Hara, R.B. (2005) Species richness estimators: how many species can dance on the head of a pin? Journal of Animal Ecology, 74, 375-386.
83. Palmer, M.W. (1990) The estimation of species richness by extrapolation. Ecology, 71, 1195-1198.
84. Patil, G.P. & Taillie, C. (1982) Diversity as a concept and its measurement. Journal of the American Statistical Association, 77, 548-561.
85. Patrick, R. (1968) Structure of diatom communities in similar ecological conditions. American Naturalist, 102, 173-183.
86. Pearson, T.H. (1975) The benthic ecology of Loch Linnhe and Loch Eil, a sea-loch system on the west coast of Scotland. 4. Changes in benthic fauna attributable to organic enrichment. Journal of Experimental Marine Biology and Ecology, 20, 1-41.
87. Pielou, E.C. (1975) Ecological Diversity. Wiley, New York, NY.
88. Preston, F.W. (1948) The commonness, and rarity, of species. Ecology, 29, 254-283.
89. Preston, F.W. (1962) The canonical distribution of commonness and rarity. Ecology, 43, 185-215, 410-432.
90. Preston, F.W. (1980) Noncanonical distributions of commonness and rarity. Ecology, 61, 88-97.
91. Rosenzweig, M.L. (1995) Species Diversity in Space and Time. Cambridge University Press, Cambridge.
92. Royama, T. (1992) Analytical Population Dynamics. Chapman & Hall, London.
93. Sæther, B.-E. & Engen, S. (2002) Pattern of variation in avian population growth rates. Philosophical Transactions of the Royal Society of London. Series B, Biological Science, 357, 1185-1195.
94. Sæther, B.-E., Engen, S., Grøtan, V., Fiedler, W., Matthysen, E., Visser, M.E., Wright, J., Møller, A.P., Adriaensen, F., van Balen, H., Balmer, D., Mainwaring, M.C., McCleery, R.H., Pampus, M. & Winkel, W. (2007) The extended Moran effect and large-scale synchronous fluctuations in the size of Great tit and Blue tit populations. Journal of Animal Ecology, 76, 315-325.
95. Simpson, E.H. (1949) Measurement of diversity. Nature, 163, 688.
96. Sørensen, T.A. (1948) A method of establishing groups of equal amplitude in plant sociology based on similarity of species content, and its application to analyses of the vegetation on Danish commons. Kongelige Danske Videnskabernes Selskabs Biologiske Skrifter, 5, 1-34.
97. Stacy, E.W. (1962) A generalization of the gamma distribution. Annals of Mathematical Statistics, 33, 1187-1192.
98. Sugihara, G. (1980) Minimal community structure : an explanation of species abundance patterns. American Naturalist, 116, 770-787.
99. z, z = 1/4: a reply to Connor and McCoy. American Naturalist, 117, 790-793.
100. Tomialojc, L., Wesolowski, T. & Walankiewicz, W. (1984) Breeding bird community of primaeval temperate forest (Bialowieza National Park, Poland). Acta Ornithologica, 20, 243-310.
101. Ugland, K.I. & Gray, J.S. (1982) Lognormal distributions and the concept of community equilibrium. Oikos, 39, 171-178.
102. Ulrich, W., Ollik, M. & Ugland, K.I. (2010) A meta-analysis of species-abundance distributions. Oikos, 119, 1149-1155.
103. Veech, J.A. & Crist, T.O. (2010) Toward a unified view of diversity partitioning. Ecology, 91, 1988-1992.
104. Wagner, H.H., Wildi, O. & Ewald, K.C. (2000) Additive partitioning of plant species diversity in an agricultural mosaic landscape. Landscape Ecology, 15, 219-227.
105. Walther, B.A. & Moore, J.L. (2005) The concepts of bias, precision and accuracy, and their use in testing the performance of species richness estimators, with a literature review of estimator performance. Ecography, 28, 815-829.
106. Whittaker, R.H. (1970) Communities and Ecosystems. Macmillan, New York, NY.
107. Whittaker, R.H. (1972) Evolution and measurement of species diversity. Taxon, 21, 213-251.
108. Williams, C.B. (1964) Patterns in the Balance of Nature and Related Problems in Quantitative Ecology. Academic Press, London.
109. Williamson, M. & Gaston, K.J. (2005) The lognormal distribution is not an appropriate null hypothesis for the species-abundance distribution. Journal of Animal Ecology, 74, 409-422.