ABGD, Automatic Barcode Gap Discovery for primary species delimitation

By N. Puillandre, Amaury Lambert, S. Brouillet, Guillaume Achaz. Molecular Ecology, 2012

2,861 citations recorded by the source corpus.

Subfields: Ecological Modeling, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a46320f5516f855ad6b56e3bca584a70f5a954d4

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Citations in the corpus

Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics (2021, methodology): “The barcoding gap has also been used as an approach to delimit species, including lichen-forming fungi (Del Prado et al. 2011; Puillandre et al. 2012; Xu et al. 2017).”
Factors affecting species delimitations with the GMYC model: insights from a butterfly survey (2013, background): “Software directly producing ultrametric trees (e.g. BEAST) avoids intermediate steps, but it is computationally demanding for large data sets, thus limiting applicability (Puillandre et al. 2012).”
Environmental DNA (2012, methodology): “With the Automatic Barcode Gap Discovery method, Puillandre et al. (2012) propose a new approach for delimiting species from a set of DNA barcode sequences.”
New insights into the phylogeny, systematics and DNA barcoding of Nemertea (2014, methodology): “Complementary to this, automatic barcode gap discovery (ABGD; Puillandre et al. 2012) was employed to verify the Phylogeny and COI variation in Nemertea Invertebrate Systematics 293”
Tree of Life Reveals Clock-Like Speciation and Diversification (2014, background): “This resetting, which results in failed isolates, may explain “barcode gaps” (Puillandre et al. 2011), which we interpret as prespeciation loss of potential lineages.”
Applied aspects of methods to infer phylogenetic relationships amongst fungi (2020, methodology): “The Automatic Barcode Gap Discovery (ABGD) method (Puillandre et al. 2012) can be used as additional evidence for species delineation.”
Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity (2015, background): “Progress are being made to standardize and improve the clustering and taxonomic identification of sequences from metabarcoding studies (Jones et al., 2011; Puillandre et al., 2012; Zhang et al., 2013).”
DNA-based species delimitation in algae (2014, methodology): “ABGD, Automatic Barcode Gap Discovery for primary species delimitation.”
Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy (2017, background): “These groups were considered to be equivalent to species (Puillandre et al., 2012).”
A general species delimitation method with applications to phylogenetic placements (2013, neutral): “De novo OTU-picking usually relies on unsupervised machine learning methods (Cai and Sun, 2011; Edgar, 2010; Fu et al. , 2012) that cluster sequences based on, mostly arbitrary, sequence similarity thresholds (Puillandre et al. , 2012; Schloss and Westcott, 2011).”
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo (2016, methodology): “The correlation is also positive for the other three methods ( r ABGD ¼ 0.63/ P value ¼ 0.0009327, r Usearch ¼ 0.5/ P value ¼ 0.01294, r Crop ¼ 0.63/ P value ¼ 0.0009421) and comparable with PTP but smaller than for mPTP. Similarly, the slope of the regression line was greater for mPTP than for the ”