Introduction

MOTIVATION: Sequence-based methods to delimit species are central to DNA taxonomy, microbial community surveys and DNA metabarcoding studies. Current approaches either rely on simple sequence similarity thresholds (OTU-picking) or on complex and compute-intensive evolutionary models. The OTU-picking methods scale well on large datasets, but the results are highly sensitive to the similarity threshold. Coalescent-based species delimitation approaches often rely on Bayesian statistics and Markov Chain Monte Carlo sampling, and can therefore only be applied to small datasets. RESULTS: We introduce the Poisson tree processes (PTP) model to infer putative species boundaries on a given phylogenetic input tree. We also integrate PTP with our evolutionary placement algorithm (EPA-PTP) to count the number of species in phylogenetic placements. We compare our approaches with popular OTU-picking methods and the General Mixed Yule Coalescent (GMYC) model. For de novo species delimitation, the stand-alone PTP model generally outperforms GYMC as well as OTU-picking methods when evolutionary distances between species are small. PTP neither requires an ultrametric input tree nor a sequence similarity threshold as input. In the open reference species delimitation approach, EPA-PTP yields more accurate results than de novo species delimitation methods. Finally, EPA-PTP scales on large datasets because it relies on the parallel implementations of the EPA and RAxML, thereby allowing to delimit species in high-throughput sequencing data. AVAILABILITY AND IMPLEMENTATION: The code is freely available at www.exelixis-lab.org/software.html. .

Publications

  1. A general species delimitation method with applications to phylogenetic placements.
    Cite this
    Zhang J, Kapli P, Pavlidis P, Stamatakis A, 2013-11-01 - Bioinformatics (Oxford, England)

Credits

  1. Jiajie Zhang
    Developer

    The Exelixis Lab, Scientific Computing Group, Greece

  2. Paschalia Kapli
    Developer

  3. Pavlos Pavlidis
    Developer

  4. Alexandros Stamatakis
    Investigator

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Summary
AccessionBT006380
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByAlexandros Stamatakis