Applications of species accumulation curves in large-scale biological data analysis

Abstract

The species accumulation curve, or collector’s curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional sampling. Traditional applications have focused on ecological populations but emerging large-scale applications, for example in DNA sequencing, are orders of magnitude larger and present new challenges. We developed a method to estimate accumulation curves for predicting the complexity of DNA sequencing libraries. This method uses rational function approximations to a classical non-parametric empirical Bayes estimator due to Good and Toulmin [Biometrika, 1956, 43, 45–63]. Here we demonstrate how the same approach can be highly effective in other large-scale applications involving biological data sets. These include estimating microbial species richness, immune repertoire size, and k-mer diversity for genome assembly applications. We show how the method can be modified to address populations containing an effectively infinite number of species where saturation cannot practically be attained. We also introduce a flexible suite of tools implemented as an R package that make these methods broadly accessible.

Graphical abstract

Keywords

species accumulation curve / accumulation region / rational function approximation / immune repertoire / microbiome diversity / species richness

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ACKNOWLEDGEMENTS

This work was funded by NIH grant R01 HG 007650. We would like to thank the Smith’s lab members, Micharl Waterman, Simon Tavaré, and Peter Calabrese for their helpful comments.

COMPLIANCE WITH ETHICS GUIDELINES

Chao Deng, Timothy Daley and Andrew Smith declare they have no conflict of interest.ƒThis article does not contain any studies with human or animal subjects performed by any of the authors.

RIGHTS & PERMISSIONS

2015 Higher Education Press and Springer-Verlag Berlin Heidelberg