Journal of Plant Ecology ›› 2012, Vol. 5 ›› Issue (1): 3-21.

• •

### Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages

Robert K. Colwell1,*, Anne Chao2, Nicholas J. Gotelli3, Shang-Yi Lin2, Chang Xuan Mao4, Robin L. Chazdon1 and John T. Longino5

1. 1 Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; 2 Institute of Statistics, National Tsing Hua University, Hsin-Chu 30043, Taiwan; 3 Department of Biology, University of Vermont, Burlington, VT 05405, USA; 4 School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai 200433, China; 5 Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
• 收稿日期:2011-07-20 接受日期:2011-10-17 出版日期:2012-01-12 发布日期:2012-03-01

### Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages

Robert K. Colwell1,*, Anne Chao2, Nicholas J. Gotelli3, Shang-Yi Lin2, Chang Xuan Mao4, Robin L. Chazdon1 and John T. Longino5

1. 1 Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; 2 Institute of Statistics, National Tsing Hua University, Hsin-Chu 30043, Taiwan; 3 Department of Biology, University of Vermont, Burlington, VT 05405, USA; 4 School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai 200433, China; 5 Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
• Received:2011-07-20 Accepted:2011-10-17 Online:2012-01-12 Published:2012-03-01
• Contact: Colwell, Robert

Methods The first objective is a problem in interpolation that we address with classical rarefaction (multinomial model) and Coleman rarefaction (Poisson model) for individual-based data and with sample-based rarefaction (Bernoulli product model) for incidence frequencies. The second is a problem in extrapolation that we address with sampling-theoretic predictors for the number of species in a larger sample (multinomial model), a larger area (Poisson model) or a larger number of sampling units (Bernoulli product model), based on an estimate of asymptotic species richness. Although published methods exist for many of these objectives, we bring them together here with some new estimators under a unified statistical and notational framework. This novel integration of mathematically distinct approaches allowed us to link interpolated (rarefaction) curves and extrapolated curves to plot a unified species accumulation curve for empirical examples. We provide new, unconditional variance estimators for classical, individual-based rarefaction and for Coleman rarefaction, long missing from the toolkit of biodiversity measurement. We illustrate these methods with datasets for tropical beetles, tropical trees and tropical ants.
Important findings Surprisingly, for all datasets we examined, the interpolation (rarefaction) curve and the extrapolation curve meet smoothly at the reference sample, yielding a single curve. Moreover, curves representing 95% confidence intervals for interpolated and extrapolated richness estimates also meet smoothly, allowing rigorous statistical comparison of samples not only for rarefaction but also for extrapolated richness values. The confidence intervals widen as the extrapolation moves further beyond the reference sample, but the method gives reasonable results for extrapolations up to about double or triple the original abundance or area of the reference sample. We found that the multinomial and Poisson models produced indistinguishable results, in units of estimated species, for all estimators and datasets. For sample-based abundance data, which allows the comparison of all three models, the Bernoulli product model generally yields lower richness estimates for rarefied data than either the multinomial or the Poisson models because of the ubiquity of non-random spatial distributions in nature.

Abstract: Aims In ecology and conservation biology, the number of species counted in a biodiversity study is a key metric but is usually a biased underestimate of total species richness because many rare species are not detected. Moreover, comparing species richness among sites or samples is a statistical challenge because the observed number of species is sensitive to the number of individuals counted or the area sampled. For individual-based data, we treat a single, empirical sample of species abundances from an investigator-defined species assemblage or community as a reference point for two estimation objectives under two sampling models: estimating the expected number of species (and its unconditional variance) in a random sample of (i) a smaller number of individuals (multinomial model) or a smaller area sampled (Poisson model) and (ii) a larger number of individuals or a larger area sampled. For sample-based incidence (presence–absence) data, under a Bernoulli product model, we treat a single set of species incidence frequencies as the reference point to estimate richness for smaller and larger numbers of sampling units.
Methods The first objective is a problem in interpolation that we address with classical rarefaction (multinomial model) and Coleman rarefaction (Poisson model) for individual-based data and with sample-based rarefaction (Bernoulli product model) for incidence frequencies. The second is a problem in extrapolation that we address with sampling-theoretic predictors for the number of species in a larger sample (multinomial model), a larger area (Poisson model) or a larger number of sampling units (Bernoulli product model), based on an estimate of asymptotic species richness. Although published methods exist for many of these objectives, we bring them together here with some new estimators under a unified statistical and notational framework. This novel integration of mathematically distinct approaches allowed us to link interpolated (rarefaction) curves and extrapolated curves to plot a unified species accumulation curve for empirical examples. We provide new, unconditional variance estimators for classical, individual-based rarefaction and for Coleman rarefaction, long missing from the toolkit of biodiversity measurement. We illustrate these methods with datasets for tropical beetles, tropical trees and tropical ants.
Important findings Surprisingly, for all datasets we examined, the interpolation (rarefaction) curve and the extrapolation curve meet smoothly at the reference sample, yielding a single curve. Moreover, curves representing 95% confidence intervals for interpolated and extrapolated richness estimates also meet smoothly, allowing rigorous statistical comparison of samples not only for rarefaction but also for extrapolated richness values. The confidence intervals widen as the extrapolation moves further beyond the reference sample, but the method gives reasonable results for extrapolations up to about double or triple the original abundance or area of the reference sample. We found that the multinomial and Poisson models produced indistinguishable results, in units of estimated species, for all estimators and datasets. For sample-based abundance data, which allows the comparison of all three models, the Bernoulli product model generally yields lower richness estimates for rarefied data than either the multinomial or the Poisson models because of the ubiquity of non-random spatial distributions in nature.