title: A general species delimitation method with applications to phylogenetic placements.
abstract: BACKGROUND
  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.
  
  
  METHODS
  The code is freely available at www.exelixis-lab.org/software.html. .
authors.affiliation: The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, D-68159 Heidelberg, Germany, Graduate School for Computing in Medicine and Life Sciences, University of Lübeck, Institut für Neuro- und Bioinformatik, University of Lübeck, 23538 Lübeck, Germany, Natural History Museum of Crete, University of Crete, GR-71409 Irakleio, Crete, Greece and Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas-FORTH, GR-70013 Heraklion, Crete, Greece.
authors.forename: Jiajie
authors.initials: J
authors.lastname: Zhang
authors.forename: Paschalia
authors.initials: P
authors.lastname: Kapli
authors.forename: Pavlos
authors.initials: P
authors.lastname: Pavlidis
authors.forename: Alexandros
authors.initials: A
authors.lastname: Stamatakis
mesh_terms: D000465:Algorithms; D000818:Animals; D010802:Phylogeny; D016012:Poisson Distribution; D017422:Sequence Analysis, DNA; D012984:Software