Unveiling the species-rank abundance distribution by generalizing the Good-Turing sample coverage theory

Ecology

Volumn 96, Issue 5, 2015, Pages 1189-1201

  Chao, Anne ^a   Hsieh, T C ^a   Chazdon, Robin L ^b,c   Colwell, Robert K ^b,d   Gotelli, Nicholas J ^e   Inouye, B D ^f  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^b UNIVERSITY OF CONNECTICUT   (United States)

^c UNIVERSITY OF COLORADO   (United States)

^d UNIVERSITY OF COLORADO   (United States)

^e UNIVERSITY OF VERMONT   (United States)

^f NONE

Author keywords

Good Turing theory; Relative abundance; Sample coverage; Species abundance distribution (SAD); Species rank abundance distribution (RAD)

Indexed keywords

CILIATE; COMMUNITY STRUCTURE; ESTIMATION METHOD; FOREST ECOSYSTEM; POPULATION DISTRIBUTION; RELATIVE ABUNDANCE; SOIL BIOTA; SPIDER; STATISTICAL ANALYSIS;

ARANEAE; CILIOPHORA;

ANIMAL; BIOLOGICAL MODEL; COMPUTER SIMULATION; POPULATION DENSITY; SELECTION BIAS; STATISTICAL MODEL;

ANIMALS; COMPUTER SIMULATION; MODELS, BIOLOGICAL; MODELS, STATISTICAL; POPULATION DENSITY; SELECTION BIAS;

EID: 84929118882     PISSN: 00129658     EISSN: None     Source Type: Journal    
DOI: 10.1890/14-0550.1     Document Type: Article

References (34)

1. Caswell, H. 1976. Community structure: a neutral model analysis. Ecological Monographs 46:327-354.
2. Chao, A. 1984. Nonparametric estimation of the number of classes in a population. Scandinavian Journal of Statistics 11: 265-270.
3. Chao, A. 1987. Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43:783-791.
4. Chao, A., and C. H. Chiu. 2012. Estimation of species richness and shared species richness. Pages 76-111 in N. Balakrishnan, editor. Methods and applications of statistics in the atmospheric and earth sciences. Wiley, New York, New York, USA.
5. Chao, A., N. G. Gotelli, T. C. Hsieh, E. L. Sander, K. H. Ma, R. K. Colwell, and A. M. Ellison. 2014. Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species biodiversity studies. Ecological Monographs 84:45-67.
6. Chao, A., and L. Jost. 2012. Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size. Ecology 93:2533-2547.
7. Chao, A., Y. T. Wang, and L. Jost. 2013. Entropy and the species accumulation curve: a novel estimator of entropy via discovery rates of new species. Methods in Ecology and Evolution 4:1091-1110.
8. Chazdon, R. L., A. Chao, R. K. Colwell, S. Y. Lin, N. Norden, S. G. Letcher, D. B. Clark, B. Finegan, and J. P. Arroyo. 2011. A novel statistical method for classifying habitat generalists and specialists. Ecology 92:1332-1343.
9. Colwell, R. K., A. Chao, N. J. Gotelli, S. Y. Lin, C. X. Mao, R. L. Chazdon, and J. T. Longino. 2012. Models and estimators linking individual-based and sample-based rarefaction, extrapolation, and comparison of assemblages. Journal of Plant Ecology 5:3-21.
10. Dewdney, A. K. 2000. A dynamical model of communities and a new species-abundance distribution. Biological Bulletin 198:152-165.
11. Ellison, A. M., A. A. Barker-Plotkin, D. R. Foster, and D. A. Orwig. 2010. Experimentally testing the role of foundation species in forests: the Harvard Forest Hemlock Removal Experiment. Methods in Ecology and Evolution 1:168-179.
12. Fisher, R. A., A. S. Corbet, and C. B. Williams. 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.
13. Foissner, W., S. Agatha, and H. Berger. 2002. Soil ciliates (Protozoa, Ciliophora) from Namibia (Southwest Africa), with emphasis on two contrasting environments, the Etosha region and the Namib Desert. Denisia 5:1-1459.
14. Good, I. J. 1953. The population frequencies of species and the estimation of population parameters. Biometrika 40:237-264.
15. Good, I. J. 2000. Turing's anticipation of empirical Bayes in connection with the cryptanalysis of the naval enigma. Journal of Statistical Computation and Simulation 66:101-111.
16. Gotelli, N. J., R. M. Dorazio, A. M. Ellison, and G. D. Grossman. 2010. Detecting temporal trends in species assemblages with bootstrapping procedures and hierarchical models. Philosophical Transactions of the Royal Society B 365:3621-3631.
17. Green, J., and J. B. Plotkin. 2007. A statistical theory for sampling species abundances. Ecology Letters 10:1037-1045.
18. Hill, M. 1973. Diversity and evenness: a unifying notation and its consequences. Ecology 54:427-432.
19. Hubbell, S. P. 2001. A unified theory of biodiversity and biogeography. Princeton University Press, Princeton, New Jersey, USA.
20. Lande, R., P. J. DeVries, and T. R. Walla. 2000. When species accumulation curves intersect: implications for ranking diversity using small samples. Oikos 89:601-605.
21. Lehmann, E. L., and G. Casella. 1998. Theory of point estimation. Second edition. Springer-Verlag, New York, New York, USA.
22. MacArthur, R. H. 1957. On the relative abundance of bird species. Proceedings of the National Academy of Sciences USA 43:293-295.
23. MacArthur, R. H. 1960. On the relative abundance of species. American Naturalist 94:25-36.
24. MacKenzie, D. I., J. D. Nichols, J. A. Royle, K. H. Pollock, L. L. Bailey, and J. E. Hines. 2006. Occupancy estimation and modeling: inferring patterns and dynamics of species occurrence. Elsevier, Amsterdam, Netherlands.
25. Magurran, A. E. 2004. Measuring biological diversity. Blackwell, Oxford, UK.
26. Magurran, A. E., and B. J. McGill, editors. 2011. Biological diversity: frontiers in measurement and assessment. Oxford University Press, Oxford, UK.
27. McGill, B. J., R. S. Etienne, J. S. Gray, D. Alonso, M. J. Anderson, H. K. Benecha, M. Dornelas, B. J. Enquist, J. L. Green, and F. He. 2007. Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecology Letters 10:995-1015.
28. Preston, F. 1948. The commonness and rarity of species. Ecology 29:254-283.
29. Sackett, T. E., S. Record, S. Bewick, B. Baiser, N. J. Sanders, and A. M. Ellison. 2011. Response of macroarthropod assemblages to the loss of hemlock (Tsuga canadensis), a foundation species. Ecosphere 2: art 74.
30. Sugihara, G. 1980. Minimal community structure: an explanation of species abundance patterns. American Naturalist 116: 770-787.
31. Tokeshi, M. 1990. Niche apportionment or random assortment: species abundance patterns revisited. Journal of Animal Ecology 59:1129-1146.
32. Whittaker, R. H. 1965. Dominance and diversity in land plant communities. Nature 147:250-260.
33. Whittaker, R. H. 1970. Communities and ecosystems. MacMillan, New York, New York, USA.
34. Whittaker, R. H. 1972. Evolution and measurement of species diversity. Taxon 12:213-251.