Accelerated species inventory on Madagascar using coalescent-based models of species delineation.

By M. Monaghan, R. Wild, M. Elliot, T. Fujisawa, M. Balke, D. Inward, D. Lees, R. Ranaivosolo, P. Eggleton, T. Barraclough and 1 more. Systematic Biology, 2009

710 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/44f05dedfb1e4b26586587759c28ecedc0d0d560

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Citations in the corpus

Small but mighty: headwaters are vital to stream network biodiversity at two levels of organization (2011, background): “For COI, evidence for stream insects suggests that 7 to 10 individuals are sufficient to capture most of the genetic diversity present in a local population (Monaghan et al. 2009).”
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo (2016, background): “This and previous studies (Monaghan et al., 2009; Esselstyn et al., 2012; Tang et al., 2014; Ratnasingham and Hebert, 2013) suggest that single-locus barcoding methods provide meaningful clusters, close to taxonomically acknowledged species.”
Unveiling cryptic species of the bumblebee subgenus Bombus s. str. worldwide with COI barcodes (Hymenoptera: Apidae) (2012, methodology): “Fortunately, recent pinned specimens can be used to recover the short ‘barcode’ sequence of the mitochondrial COI (cox-1) gene that has been found to enable discovery of species identical to those recognised by more traditional methods (Monaghan et al., 2009).”
A general species delimitation method with applications to phylogenetic placements (2013, methodology): “The General Mixed Yule Coalescent (GMYC) model (Fujisawa and Barraclough, 2013; Pons et al. , 2006) for delimiting species on single genes is frequently used in empirical studies (Carstens and Dewey, 2010; Fontaneto et al. , 2007; Monaghan et al. , 2009; Powell, 2012; Vuataz et al. , 2011).”
The impact of global climate change on genetic diversity within populations and species (2013, background): “Several different analytical tools and approaches facilitate assessments of cryptic diversity within a given sample (e.g. Ratnasingham & Hebert 2007; Monaghan et al. 2009).”
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).”
A response to recent proposals for integrative taxonomy (2010, methodology): “This trend has already begun to affect taxonomy, and now an increasing number of taxonomic studies exemplify how methods grounded in population genetics can be used to infer the existence and the degree of cohesion of species (e.g. Bond & Stockman, 2008; Monaghan et al., 2009; Leaché et al., 2009; D”
Building the Coleoptera tree‐of‐life for >8000 species: composition of public DNA data and fit with Linnaean classification (2014, background): “…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 (Ahrens et al.,…”
DNA Barcoding, species delineation and taxonomy: a historical perspective (2015, positive): “Actually, iterative procedures including DNA barcoding, taxonomy and natural history have been successfully applied for the delineation and description of new species in megadiverse, yet poorly described, biotas [12,40,48].”
ABGD, Automatic Barcode Gap Discovery for primary species delimitation (2012, methodology): “A General Mixed Yule Coalescent (GMYC) model has been proposed to delimit species from single locus genetic data (Pons et al. 2006; Monaghan et al. 2009).”
DNA-based species delimitation in algae (2014, methodology): “The GMYC model approach has been refined to allow for a variable transition from coalescence to speciation among lineages (Monaghan et al., 2009), and to account for uncertainty in phylogenetic relationships and parameters of the GMYC model (Powell, 2012; Reid & Carstens, 2012; Fujisawa &…”
ASAP: assemble species by automatic partitioning (2020, methodology): “Both were later expanded to infer “multiple thresholds”, allowing several transitions to occur in different subtrees (Kapli et al., 2017; Monaghan et al., 2009).”
The integrative future of taxonomy (2010, background): “A recent largescale study on insects of Madagascar [75] shows that single-locus coalescent models perform well for both testing and discovering species from large sample sets even without prior hypotheses of population coherence, providing thus a potential empirical substitute for traditional treeba”
A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System (2013, background): “Although GMYC has gained popularity due to its statistical robustness and accuracy [32–34], the high computational cost of phylogeny reconstruction and GMYC computation is a barrier to the analysis of large datasets.”
Factors affecting species delimitations with the GMYC model: insights from a butterfly survey (2013, methodology): “Given that the GMYC uses coalescence as a null model, the coalescent tree prior is considered a more adequate option and appears to fit better the majority of the data sets in model comparisons (Monaghan et al. 2009).”