Quantitative Biology

, Volume 3, Issue 3, pp 135–144

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

Research Article

DOI: 10.1007/s40484-015-0049-7

Cite this article as:
Deng, C., Daley, T. & Smith, A. Quant Biol (2015) 3: 135. doi:10.1007/s40484-015-0049-7

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 nonparametric 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.

Keywords

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

40484_2015_49_MOESM1_ESM.pdf (445 kb)
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Copyright information

© Higher Education Press and Springer-Verlag GmbH 2015

Authors and Affiliations

  1. 1.Molecular and Computational BiologyUniversity of Southern CaliforniaLos AngelesUSA

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