A general species delimitation method with applications to phylogenetic placements

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ID: 290287
2013
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Abstract
Abstract 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. Contact: Alexandros.Stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
Reference Key
openalex_W2125948619 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Jiajie Zhang, Paschalia Kapli, Pavlos Pavlidis, Alexandros Stamatakis
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Journal BMC Bioinformatics
Year 2013
DOI
10.1093/bioinformatics/btt499
URL
https://academic.oup.com/bioinformatics/article-pdf/29/22/2869/17100395/btt499.pdf
Keywords Keywords not found

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