A general species delimitation method with applications to phylogenetic placements

By Jiajie Zhang, Paschalia Kapli, Pavlos Pavlidis, Alexandros Stamatakis. Bioinform., 2013

2,766 citations recorded by the source corpus.

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.

Subfields: Ecological Modeling, Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/77a4e83d6fb4b6a9d78ff0b8d156f59d3f8c5feb

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecological Modeling

In Ecology

In Molecular Biology

Citations in the corpus

Mammals of Italy: an annotated checklist (2019, background): “…of differential evolutionary, population genetics, and phylogenetic processes within and between species (Fujisawa and Barraclough, 2013; Zhang et al., 2013); (3) use of Bayesian models to understand genealogical processes to identify species (Yang and Rannala, 2014); 4) presence of…”
ASAP: assemble species by automatic partitioning (2020, methodology): “The most popular are general mixed Yule-Coalescent model (GMYC) (Pons et al., 2006), Poisson tree process (PTP) (Zhang et al., 2013), both first developed in a maximum likelihood framework, and later extended to a Bayesian framework (Reid & Carstens, 2012), and automatic barcode gap discovery…”
Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics (2021, background): “However, variational discontinuities in phylogenies can be assessed by employing quantitative species recognition methods, which assess branch length patterns within and between clades, such as the Generalized Mixed Yule Coalescent (GMYC) or the Poisson Tree Processes (PTP) approach (Fujisawa and Ba”
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data (2016, background): “…et al. 2010; Wang et al. 2014), extracting information from large sets of phylogenetic trees (Derelle and Lang 2012; Chiapello et al. 2015; Marcet-Houben and Gabald (cid:2) on 2015) and developing third party tools and databases (Zhang et al. 2013; Huerta-Cepas et al. 2014; Szitenberg et al. 2015).”
Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy (2017, methodology): “ITS) to search for evidence of independently evolving entities akin to species, optimising differences in branching patterns within and between species (Zhang et al., 2013).”
Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale (2020, background): “Environmental DNA includes both intracellular DNA (Zhang et al., 2013), which is the component of eDNA found within the cells and organelles of living or recently dead organisms, and extracellular DNA, which is the component of eDNA found outside of cells, including both adsorbed DNA and free DNA.”
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo (2016, background): “Additionally, sampling bias may also be responsible for observing different levels of intraspecific genetic diversity and it is already known to decrease the accuracy of PTP (Zhang et al., 2013).”