Sequence-based species delimitation for the DNA taxonomy of undescribed insects.

By J. Pons, T. Barraclough, J. Gómez‐Zurita, Anabela Cardoso, D. P. Duran, Steaphan P. Hazell, Sophien Kamoun, W. D. Sumlin, A. Vogler. Systematic Biology, 2006

2,386 citations recorded by the source corpus.

Subfields: Ecological Modeling, Ecology, Ecology, Evolution, Behavior and Systematics

View Paper: https://www.semanticscholar.org/paper/64b496e955dc937c8949d02e809f641605cf987e

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Citations in the corpus

Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci (2014, methodology): “Some methods are applicable to data of only a single locus (Pons et al. 2006).”
Building the Coleoptera tree‐of‐life for >8000 species: composition of public DNA data and fit with Linnaean classification (2014, background): “…e.g. molecular systematics of particular beetle families (e.g. Robertson et al., 2008; Marvaldi et al., 2009), composition of local faunas (Pons et al., 2006; Monaghan et al., 2009), phylogeography (Ribera & Balke, 2007; Papadopoulou et al., 2011), DNA identification of immature stages…”
Species Delimitation: A Decade After the Renaissance (2013, positive): “[56] described a four-step ap‐ proach to “generating robust speciation hypotheses” in mollusk family Turridae (genus Gemmula) based on: (a) collection of the COI DNA barcode gene for GMYC [14] and ABGD (Automatic Barcode Gap Discovery; [57]) analyses; coupled with (b) nuclear gene (rRNA 28S), morpho”
Accelerated species inventory on Madagascar using coalescent-based models of species delineation. (2009, methodology): “This is in agreement with other studies of widespread geographic samples (Hebert and Gregory 2005; Pons et al., 2006) where mtDNA patterns were retained under broad geographical sampling.”
Factors affecting species delimitations with the GMYC model: insights from a butterfly survey (2013, methodology): “The GMYC species delimitation tool (Pons et al. 2006; Fontaneto et al. 2007; Monaghan et al. 2009) was tested using the SPLITS package (Ezard, Fujisawa & Barraclough 2009) implemented in R statistical software for the single- and multiple-threshold options.”
Field and Laboratory Methods for DNA Studies on Deep-sea Isopod Crustaceans (2014, background): “Despite the apparent useful− ness of genetic data to address systematic questions in biological studies (Hebert et al. 2003; Pons et al. 2006), these data have rarely been applied for deep−sea Isopoda so far.”
Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi (2011, methodology): “Another method, the general mixed Yule coalescent method, aims at identifying the transition of tokogenetic (intraspecific) and phylogenetic relationships on a chronogram (Pons et al. 2006; Monaghan et al. 2009).”
Identifying Canadian Freshwater Fishes through DNA Barcodes (2008, background): “Although barcode analyses primarily seek to delineate species boundaries at the COI locus for the assignment of unknown individuals to known species, unsuspected diversity and overlooked species are often detected through barcodes analyses, sometimes spectacularly [10,18,47].”
Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota (2008, background): “© 2008 The Authors Journal compilation © 2008 Blackwell Publishing Ltd salt lake adapted tiger beetles remained constant over the past 4 Myr (Pons et al. 2006).”
How to fail at species delimitation (2013, methodology): “The general mixed Yule coalescent model (GMYC; Pons et al. 2006) takes an ultrametric genealogy estimated from a single genetic locus as input.”
Delimiting species without monophyletic gene trees. (2007, methodology): “5), but sampling will also be critical to accurately estimating the parameters used in the model for delimiting species (see also Pons et al., 2006).”
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo (2016, background): “The General Mixed Yule Coalescent (GMYC; Fujisawa and Barraclough, 2013; Pons et al. , 2006) and the recently introduced Poisson Tree Processes (PTP; Zhang et al. , 2013) are two similar models that bridge the gap between “species-tree” and distance-based methods.”
The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). (2010, background): “…(GMYC), based on coalescence within independently evolving populations, have been successfully used to delineate insect and bacterial molecular taxa (Pons et al., 2006; Barraclough et al., 2009) and have the potential to improve the sequence similarity-based VT taxonomy of MaarjAM in the future.”
Alleviating the taxonomic impediment of DNA barcoding and setting a bad precedent: names for ten species of ‘Astraptes fulgerator’ (Lepidoptera: Hesperiidae: Eudaminae) with DNA-based diagnoses (2010, background): “A number of authors criticized the announcement of these ‘species’ as premature and based on simplistic analysis of limited evidence (e.g. DeSalle et al., 2005; Brower, 2006; Pons et al., 2006; Rubinoff et al., 2006; Elias et al., 2007).”
Species Delimitation using Genome-Wide SNP Data (2013, methodology): “Methods including the GMYC (Pons et al. 2006), SpeDeSTEM (Ence and Carstens 2011), and BROWNIE (O’Meara 2010) are more appropriate heuristic tools for producing species assignments when the researcher has no preconceived species delimitation models to test.”
Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets (2013, methodology): “(Note that the description in Pons et al. 2006 of interpreting the effects of selection on coalescent p was incorrect.)”